Citrus Sinensis ID: 042210

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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
Protein Sequence
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIPQR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHcccccccHHHHHHHHHHcccccHHHHHHHHccccccccccHHHHHHHHHcccccHHHHHHHHHHHHcccccccEEcHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHcccHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHccccccEEEccccccccccccccccccccccHHHHHHHHccHHHcccccccEEccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHccccccHHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHHHHHHHcccccccEEEEEEEccHHHHHHHHHHHHHcHHHHHHHHHHHHHHcccccccEEccccccc
Coil and Loop (DISEMBL)
MHQLKQIHSQTIKlglltkphcpkqtRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIkgysridshkNGVLMYLDLLksdvrrdnytfpflfkgfTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYmscedddgLHELIRIKAVDDDLHELFPEYLVQMLalpdtfmgeglevipksqapreetprvgnleegtpqegrphehsqddmslisnsipqr
Flexible Loop (DISEMBL)
MHQLKQIHSQtiklglltkphcpKQTRYLLLYEKGDLKYECKVFrkitqpsvflWNTMIKGYsridshknGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIpksqapreetprvgnleegtpqegrphehsqddmslisnsipqr
Low Complexity Region (SEG)
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIPQR
Disordered region (IsUnstruct)
*********QTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEV*********************************************
Disordered Region (DISOPRED)
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIPQ*
Disordered Region (DISEMBL)
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGN*****************************
Disordered Region (DISPRO)
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMS*IS******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIPQR
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	230	2.2.26 [Sep-21-2011]
Q9LSB8	687	Putative pentatricopeptid	yes	no	0.617	0.206	0.407	2e-25
O82380	738	Pentatricopeptide repeat-	no	no	0.626	0.195	0.318	4e-14
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.569	0.188	0.315	4e-13
Q9C6T2	606	Pentatricopeptide repeat-	no	no	0.452	0.171	0.330	3e-12
Q9SJZ3	681	Pentatricopeptide repeat-	no	no	0.586	0.198	0.306	6e-12
A8MQA3	595	Pentatricopeptide repeat-	no	no	0.586	0.226	0.324	1e-11
Q9SJG6	559	Pentatricopeptide repeat-	no	no	0.595	0.245	0.285	1e-11
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.621	0.230	0.313	1e-10
Q9MA95	565	Putative pentatricopeptid	no	no	0.456	0.185	0.318	3e-10
Q0WQW5	638	Pentatricopeptide repeat-	no	no	0.569	0.205	0.316	3e-10

>sp|Q9LSB8|PP235_ARATH Putative pentatricopeptide repeat-containing protein At3g15930 OS=Arabidopsis thaliana GN=PCMP-E51 PE=3 SV=2

 Score =  115 bits (289), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 62/152 (40%), Positives = 89/152 (58%), Gaps = 10/152 (6%)

Query: 3   QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYE-KGDLKYECKVFRKITQPSVFLWNTMIKG 61
           Q KQ+HSQ+I  G+   P   K+          G + Y  K+F KI +P V +WN MIKG
Sbjct: 49  QFKQLHSQSITRGVAPNPTFQKKLFVFWCSRLGGHVSYAYKLFVKIPEPDVVVWNNMIKG 108

Query: 62  YSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRD---IAGSLEKSCIVMR----- 113
           +S++D    GV +YL++LK  V  D++TFPFL  G  RD   +A   +  C V++     
Sbjct: 109 WSKVDCDGEGVRLYLNMLKEGVTPDSHTFPFLLNGLKRDGGALACGKKLHCHVVKFGLGS 168

Query: 114 -VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
            ++VQNAL+  Y LCG +DMARG+F   C++D
Sbjct: 169 NLYVQNALVKMYSLCGLMDMARGVFDRRCKED 200

Arabidopsis thaliana (taxid: 3702)

>sp|O82380|PP175_ARATH Pentatricopeptide repeat-containing protein At2g29760, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H33 PE=2 SV=1

 Score = 78.6 bits (192), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 49/154 (31%), Positives = 75/154 (48%), Gaps = 10/154 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQTRYLL-LYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           + QLKQ H   I+ G  + P+   +   +  L     L+Y  KVF +I +P+ F WNT+I
Sbjct: 43  LRQLKQTHGHMIRTGTFSDPYSASKLFAMAALSSFASLEYARKVFDEIPKPNSFAWNTLI 102

Query: 60  KGYSRIDSHKNGVLMYLDLL-KSDVRRDNYTFPFLFKG--------FTRDIAGSLEKSCI 110
           + Y+        +  +LD++ +S    + YTFPFL K           + + G   KS +
Sbjct: 103 RAYASGPDPVLSIWAFLDMVSESQCYPNKYTFPFLIKAAAEVSSLSLGQSLHGMAVKSAV 162

Query: 111 VMRVFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
              VFV N+LI  Y  CG++D A  +F    E D
Sbjct: 163 GSDVFVANSLIHCYFSCGDLDSACKVFTTIKEKD 196

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTV8|PP224_ARATH Pentatricopeptide repeat-containing protein At3g12770 OS=Arabidopsis thaliana GN=PCMP-H43 PE=2 SV=1

 Score = 74.7 bits (182), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 46/146 (31%), Positives = 76/146 (52%), Gaps = 15/146 (10%)

Query: 3   QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEK---GDLKYECKVFRKITQPSVFLWNTMI 59
           QLKQIH++ + LGL        +    L++     GD+ +  +VF  + +P +F WN +I
Sbjct: 36  QLKQIHARLLVLGLQFSGFLITK----LIHASSSFGDITFARQVFDDLPRPQIFPWNAII 91

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFT--------RDIAGSLEKSCIV 111
           +GYSR +  ++ +LMY ++  + V  D++TFP L K  +        R +   + +    
Sbjct: 92  RGYSRNNHFQDALLMYSNMQLARVSPDSFTFPHLLKACSGLSHLQMGRFVHAQVFRLGFD 151

Query: 112 MRVFVQNALISTYCLCGEVDMARGIF 137
             VFVQN LI+ Y  C  +  AR +F
Sbjct: 152 ADVFVQNGLIALYAKCRRLGSARTVF 177

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C6T2|PPR68_ARATH Pentatricopeptide repeat-containing protein At1g31920 OS=Arabidopsis thaliana GN=PCMP-H11 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 60/112 (53%), Gaps = 8/112 (7%)

Query: 34  KGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFL 93
           +  + Y   +FR I  P  F +NTMI+GY  + S +  +  Y ++++     DN+T+P L
Sbjct: 79  ENSMNYAASIFRGIDDPCTFDFNTMIRGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCL 138

Query: 94  FKGFTR--------DIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIF 137
            K  TR         I G + K  +   VFVQN+LI+ Y  CGE++++  +F
Sbjct: 139 LKACTRLKSIREGKQIHGQVFKLGLEADVFVQNSLINMYGRCGEMELSSAVF 190

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJZ3|PP169_ARATH Pentatricopeptide repeat-containing protein At2g22410, mitochondrial OS=Arabidopsis thaliana GN=PCMP-E28 PE=2 SV=1

 Score = 71.2 bits (173), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 45/147 (30%), Positives = 72/147 (48%), Gaps = 12/147 (8%)

Query: 3   QLKQIHSQTIKLGLLTKPHCPKQ-TRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKG 61
            LKQI +Q I  GL+  P    +   +  L E   L Y  K+ + I  P++F WN  I+G
Sbjct: 68  HLKQIQAQMIINGLILDPFASSRLIAFCALSESRYLDYSVKILKGIENPNIFSWNVTIRG 127

Query: 62  YSRIDSHKNGVLMYLDLLK---SDVRRDNYTFPFLFK--------GFTRDIAGSLEKSCI 110
           +S  ++ K   L+Y  +L+    + R D++T+P LFK             I G + K  +
Sbjct: 128 FSESENPKESFLLYKQMLRHGCCESRPDHFTYPVLFKVCADLRLSSLGHMILGHVLKLRL 187

Query: 111 VMRVFVQNALISTYCLCGEVDMARGIF 137
            +   V NA I  +  CG+++ AR +F
Sbjct: 188 ELVSHVHNASIHMFASCGDMENARKVF 214

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 48/148 (32%), Positives = 80/148 (54%), Gaps = 13/148 (8%)

Query: 3   QLKQIHSQTIKLGL-LTKPHCPKQTRYLL--LYEKGDLKYECKVFRKITQP-SVFLWNTM 58
           +L+QIH+ +I+ G+ ++     K   + L  L     + Y  KVF KI +P +VF+WNT+
Sbjct: 32  KLRQIHAFSIRHGVSISDAELGKHLIFYLVSLPSPPPMSYAHKVFSKIEKPINVFIWNTL 91

Query: 59  IKGYSRIDSHKNGVLMYLDLLKSD-VRRDNYTFPFLFKGFT--RDIAGSLEKSCIVMR-- 113
           I+GY+ I +  +   +Y ++  S  V  D +T+PFL K  T   D+        +V+R  
Sbjct: 92  IRGYAEIGNSISAFSLYREMRVSGLVEPDTHTYPFLIKAVTTMADVRLGETIHSVVIRSG 151

Query: 114 ----VFVQNALISTYCLCGEVDMARGIF 137
               ++VQN+L+  Y  CG+V  A  +F
Sbjct: 152 FGSLIYVQNSLLHLYANCGDVASAYKVF 179

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJG6|PP200_ARATH Pentatricopeptide repeat-containing protein At2g42920, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E75 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 72/147 (48%), Gaps = 10/147 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIK 60
           M +LKQIH+  IK GL++      +          D+ Y   VF +I   + F+WNT+I+
Sbjct: 38  MRELKQIHASLIKTGLISDTVTASRVLAFCCASPSDMNYAYLVFTRINHKNPFVWNTIIR 97

Query: 61  GYSRIDSHKNGVLMYLDLLKS--DVRRDNYTFPFLFKGF--------TRDIAGSLEKSCI 110
           G+SR    +  + +++D+L S   V+    T+P +FK +         R + G + K  +
Sbjct: 98  GFSRSSFPEMAISIFIDMLCSSPSVKPQRLTYPSVFKAYGRLGQARDGRQLHGMVIKEGL 157

Query: 111 VMRVFVQNALISTYCLCGEVDMARGIF 137
               F++N ++  Y  CG +  A  IF
Sbjct: 158 EDDSFIRNTMLHMYVTCGCLIEAWRIF 184

Arabidopsis thaliana (taxid: 3702)

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

 Score = 66.6 bits (161), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/153 (31%), Positives = 72/153 (47%), Gaps = 10/153 (6%)

Query: 3   QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGD-LKYECKVFRKITQPSVFLWNTMIK 60
           +LKQIH++ +K GL+   +   K   + +     D L Y   VF    +P  FLWN MI+
Sbjct: 29  ELKQIHARMLKTGLMQDSYAITKFLSFCISSTSSDFLPYAQIVFDGFDRPDTFLWNLMIR 88

Query: 61  GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGF--------TRDIAGSLEKSCIVM 112
           G+S  D  +  +L+Y  +L S    + YTFP L K          T  I   + K     
Sbjct: 89  GFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETTQIHAQITKLGYEN 148

Query: 113 RVFVQNALISTYCLCGEVDMARGIFYMSCEDDD 145
            V+  N+LI++Y + G   +A  +F    E DD
Sbjct: 149 DVYAVNSLINSYAVTGNFKLAHLLFDRIPEPDD 181

Arabidopsis thaliana (taxid: 3702)

>sp|Q9MA95|PP214_ARATH Putative pentatricopeptide repeat-containing protein At3g05240 OS=Arabidopsis thaliana GN=PCMP-E82 PE=3 SV=2

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 59/113 (52%), Gaps = 8/113 (7%)

Query: 33  EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPF 92
           E  +L Y   VF  I  PSV++WN+MI+GYS   +    ++ Y ++L+     D +TFP+
Sbjct: 53  ETMNLSYARSVFESIDCPSVYIWNSMIRGYSNSPNPDKALIFYQEMLRKGYSPDYFTFPY 112

Query: 93  LFKGFT--RDIA------GSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIF 137
           + K  +  RDI       G + K+   + ++V   L+  Y  CGEV+    +F
Sbjct: 113 VLKACSGLRDIQFGSCVHGFVVKTGFEVNMYVSTCLLHMYMCCGEVNYGLRVF 165

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WQW5|PPR85_ARATH Pentatricopeptide repeat-containing protein At1g59720, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H51 PE=2 SV=2

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/155 (31%), Positives = 74/155 (47%), Gaps = 24/155 (15%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEK--------GDLKYECKVFRKITQPSV 52
           M QLKQ+H+ T++         P++   L LY K         D+ Y  +VF  I   S 
Sbjct: 61  MSQLKQLHAFTLRTTY------PEEPATLFLYGKILQLSSSFSDVNYAFRVFDSIENHSS 114

Query: 53  FLWNTMIKGYSRIDSHKNGVLM-YLDLL-KSDVRRDNYTFPFLFK------GFT--RDIA 102
           F+WNT+I+  +   S K    M Y  +L + +   D +TFPF+ K      GF+  + + 
Sbjct: 115 FMWNTLIRACAHDVSRKEEAFMLYRKMLERGESSPDKHTFPFVLKACAYIFGFSEGKQVH 174

Query: 103 GSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIF 137
             + K      V+V N LI  Y  CG +D+AR +F
Sbjct: 175 CQIVKHGFGGDVYVNNGLIHLYGSCGCLDLARKVF 209

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	230
255553251	512	pentatricopeptide repeat-containing prot	0.626	0.281	0.549	1e-33
224134923	635	predicted protein [Populus trichocarpa]	0.626	0.226	0.496	6e-31
449491161	744	PREDICTED: LOW QUALITY PROTEIN: putative	0.595	0.184	0.458	7e-29
449436619	723	PREDICTED: putative pentatricopeptide re	0.595	0.189	0.458	7e-29
356528966	712	PREDICTED: putative pentatricopeptide re	0.608	0.196	0.469	6e-28
356522333	650	PREDICTED: putative pentatricopeptide re	0.617	0.218	0.457	5e-27
297743485	605	unnamed protein product [Vitis vinifera]	0.626	0.238	0.457	4e-26
225442904	724	PREDICTED: putative pentatricopeptide re	0.626	0.198	0.457	5e-26
357468161	874	Pentatricopeptide repeat-containing prot	0.604	0.159	0.449	2e-24
15233234	687	pentatricopeptide repeat-containing prot	0.617	0.206	0.407	1e-23

>gi|255553251|ref|XP_002517668.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223543300|gb|EEF44832.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  149 bits (375), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 84/153 (54%), Positives = 101/153 (66%), Gaps = 9/153 (5%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M QLKQIHSQTIK G + KP    +   +    E GD+ Y  ++F  I +P+VF WNTM+
Sbjct: 1   MDQLKQIHSQTIKTGTICKPIIQNKIFSFCCTQEFGDMNYARQLFDTIPEPTVFHWNTML 60

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKS--CIVMR---- 113
           KGYSRIDS K GV MYLD+LK+DV  D YT+PFL KGF +DIA    K   C V++    
Sbjct: 61  KGYSRIDSPKLGVSMYLDMLKNDVLPDCYTYPFLIKGFKKDIAFEYGKELHCHVVKYGLG 120

Query: 114 --VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
             VFVQNALI+ Y LCG  DMARGIF MS + D
Sbjct: 121 SNVFVQNALINMYSLCGLTDMARGIFDMSYKTD 153

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134923|ref|XP_002327523.1| predicted protein [Populus trichocarpa] gi|222836077|gb|EEE74498.1| predicted protein [Populus trichocarpa]

 Score =  140 bits (352), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 76/153 (49%), Positives = 99/153 (64%), Gaps = 9/153 (5%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M+ LKQIHS+TIK G++  P    +   +    E GD+ Y  ++F  I +PSVF WN M 
Sbjct: 27  MYHLKQIHSRTIKTGIICNPIIQNKILSFCCSREFGDMCYARQLFDTIPEPSVFSWNIMF 86

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSL--EKSCIVMR---- 113
           KGYSRI   K GV +YL++L+ +V+ D YT+PFLFKGFTR +A  L  E  C V++    
Sbjct: 87  KGYSRIACPKLGVSLYLEMLERNVKPDCYTYPFLFKGFTRSVALQLGRELHCHVVKYGLD 146

Query: 114 --VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
             VF  NALI+ Y LCG +DMARGIF MSC+ D
Sbjct: 147 SNVFAHNALINMYSLCGLIDMARGIFDMSCKSD 179

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491161|ref|XP_004158817.1| PREDICTED: LOW QUALITY PROTEIN: putative pentatricopeptide repeat-containing protein At3g15930-like [Cucumis sativus]

 Score =  133 bits (334), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 67/146 (45%), Positives = 94/146 (64%), Gaps = 9/146 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M QL+Q+H Q IK GL   P    +   +   +E GD +Y  ++F +I +P++F+WNTMI
Sbjct: 52  MDQLQQVHCQAIKKGLNANPVLQNRVMTFCCTHEYGDFQYARRLFDEIPEPNLFIWNTMI 111

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA--------GSLEKSCIV 111
           +GYSR+D  + GV +YL++L+  V+ D YTFPFLFKGFTRDIA        G + K  + 
Sbjct: 112 RGYSRLDFPQLGVSLYLEMLRRGVKPDRYTFPFLFKGFTRDIALEYGRQLHGHVLKHGLQ 171

Query: 112 MRVFVQNALISTYCLCGEVDMARGIF 137
             VFV  AL+  Y LCG++D ARG+F
Sbjct: 172 YNVFVHTALVQMYLLCGQLDTARGVF 197

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436619|ref|XP_004136090.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g15930-like [Cucumis sativus]

 Score =  133 bits (334), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 67/146 (45%), Positives = 94/146 (64%), Gaps = 9/146 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M QL+Q+H Q IK GL   P    +   +   +E GD +Y  ++F +I +P++F+WNTMI
Sbjct: 31  MDQLQQVHCQAIKKGLNANPVLQNRVMTFCCTHEYGDFQYARRLFDEIPEPNLFIWNTMI 90

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA--------GSLEKSCIV 111
           +GYSR+D  + GV +YL++L+  V+ D YTFPFLFKGFTRDIA        G + K  + 
Sbjct: 91  RGYSRLDFPQLGVSLYLEMLRRGVKPDRYTFPFLFKGFTRDIALEYGRQLHGHVLKHGLQ 150

Query: 112 MRVFVQNALISTYCLCGEVDMARGIF 137
             VFV  AL+  Y LCG++D ARG+F
Sbjct: 151 YNVFVHTALVQMYLLCGQLDTARGVF 176

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528966|ref|XP_003533068.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g15930-like [Glycine max]

 Score =  130 bits (326), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 70/149 (46%), Positives = 94/149 (63%), Gaps = 9/149 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M+QLKQIHS TIK+GL + P   K+   +   +E G + Y  +VF  I QP++F+WNTMI
Sbjct: 20  MYQLKQIHSHTIKMGLSSDPLFQKRVIAFCCAHESGKMIYARQVFDAIPQPTLFIWNTMI 79

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRV----- 114
           KGYSRI+  +NGV MYL +L S+++ D +TFPFL KGFTR++A    K  +   V     
Sbjct: 80  KGYSRINHPQNGVSMYLLMLASNIKPDRFTFPFLLKGFTRNMALQYGKVLLNHAVKHGFD 139

Query: 115 ---FVQNALISTYCLCGEVDMARGIFYMS 140
              FVQ A I  + LC  VD+AR +F M 
Sbjct: 140 SNLFVQKAFIHMFSLCRLVDLARKVFDMG 168

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522333|ref|XP_003529801.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g15930-like [Glycine max]

 Score =  127 bits (318), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 70/153 (45%), Positives = 94/153 (61%), Gaps = 11/153 (7%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M+QLKQIHS TIK+GL + P    +   +   +E G++ Y  +VF  I  PS+F+WNTMI
Sbjct: 20  MYQLKQIHSHTIKMGLSSDPLFRNRVIAFCCAHESGNMNYAHQVFDTIPHPSMFIWNTMI 79

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRV----- 114
           KGYS+I   +NGV MYL +L S+++ D +TFPF  KGFTRD+A    K  +   V     
Sbjct: 80  KGYSKISHPENGVSMYLLMLTSNIKPDRFTFPFSLKGFTRDMALQHGKELLNHAVKHGFD 139

Query: 115 ---FVQNALISTYCLCGEVDMARGIFYM--SCE 142
              FVQ A I  + LCG VD+A  +F M  +CE
Sbjct: 140 SNLFVQKAFIHMFSLCGIVDLAHKVFDMGDACE 172

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743485|emb|CBI36352.3| unnamed protein product [Vitis vinifera]

 Score =  124 bits (310), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 70/153 (45%), Positives = 89/153 (58%), Gaps = 9/153 (5%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M QLKQIHSQTI  GL++ P  P Q   +   +E GD++Y   VF  +  P+ F+WN MI
Sbjct: 32  MAQLKQIHSQTICTGLISNPIVPAQIIAFCCKHELGDMEYARMVFDTMPGPNHFVWNNMI 91

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA--------GSLEKSCIV 111
           KGYSR+    + V MY ++L+  V  D YT+PFL K FTRD A          + K    
Sbjct: 92  KGYSRVGCPNSAVSMYCEMLERGVMPDEYTYPFLLKRFTRDTAVKCGRELHDHIVKLGFS 151

Query: 112 MRVFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
             VFVQNALI  Y L GEV +ARG+F  S + D
Sbjct: 152 SNVFVQNALIHLYSLSGEVSVARGVFDRSSKGD 184

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225442904|ref|XP_002264123.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g15930 [Vitis vinifera]

 Score =  123 bits (309), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 70/153 (45%), Positives = 89/153 (58%), Gaps = 9/153 (5%)

Query: 1   MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M QLKQIHSQTI  GL++ P  P Q   +   +E GD++Y   VF  +  P+ F+WN MI
Sbjct: 32  MAQLKQIHSQTICTGLISNPIVPAQIIAFCCKHELGDMEYARMVFDTMPGPNHFVWNNMI 91

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA--------GSLEKSCIV 111
           KGYSR+    + V MY ++L+  V  D YT+PFL K FTRD A          + K    
Sbjct: 92  KGYSRVGCPNSAVSMYCEMLERGVMPDEYTYPFLLKRFTRDTAVKCGRELHDHIVKLGFS 151

Query: 112 MRVFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
             VFVQNALI  Y L GEV +ARG+F  S + D
Sbjct: 152 SNVFVQNALIHLYSLSGEVSVARGVFDRSSKGD 184

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357468161|ref|XP_003604365.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355505420|gb|AES86562.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  118 bits (296), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 67/149 (44%), Positives = 89/149 (59%), Gaps = 10/149 (6%)

Query: 1   MHQLKQIHSQTIKLGLLTKP-HCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
           M+++ QIHSQTIK GL +      K   +    E GD+ Y  KVF +I QPSVF+WNTMI
Sbjct: 48  MYEINQIHSQTIKTGLSSNHLFLTKVIIFCCTKESGDVYYARKVFDEIPQPSVFIWNTMI 107

Query: 60  KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRV----- 114
           KGYSRI+  ++GV +Y  +L  +++ D +TFPFL KGFT+D+A    K  +   V     
Sbjct: 108 KGYSRINCSESGVSLYKLMLVHNIKPDGFTFPFLLKGFTKDMALKYGKVLLNHAVIHGFL 167

Query: 115 ----FVQNALISTYCLCGEVDMARGIFYM 139
               FVQ   I  + LCG V+ AR IF M
Sbjct: 168 DSNLFVQKGFIHLFSLCGLVNYARKIFDM 196

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15233234|ref|NP_188214.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|218546758|sp|Q9LSB8.2|PP235_ARATH RecName: Full=Putative pentatricopeptide repeat-containing protein At3g15930 gi|332642227|gb|AEE75748.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 62/152 (40%), Positives = 89/152 (58%), Gaps = 10/152 (6%)

Query: 3   QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYE-KGDLKYECKVFRKITQPSVFLWNTMIKG 61
           Q KQ+HSQ+I  G+   P   K+          G + Y  K+F KI +P V +WN MIKG
Sbjct: 49  QFKQLHSQSITRGVAPNPTFQKKLFVFWCSRLGGHVSYAYKLFVKIPEPDVVVWNNMIKG 108

Query: 62  YSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRD---IAGSLEKSCIVMR----- 113
           +S++D    GV +YL++LK  V  D++TFPFL  G  RD   +A   +  C V++     
Sbjct: 109 WSKVDCDGEGVRLYLNMLKEGVTPDSHTFPFLLNGLKRDGGALACGKKLHCHVVKFGLGS 168

Query: 114 -VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
            ++VQNAL+  Y LCG +DMARG+F   C++D
Sbjct: 169 NLYVQNALVKMYSLCGLMDMARGVFDRRCKED 200

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
TAIR|locus:2093920	687	AT3G15930 "AT3G15930" [Arabido	0.613	0.205	0.405	3.3e-24
TAIR|locus:2060640	738	OTP81 "ORGANELLE TRANSCRIPT PR	0.626	0.195	0.324	1.3e-13
TAIR|locus:2034456	606	AT1G31920 [Arabidopsis thalian	0.586	0.222	0.308	2.5e-13
TAIR|locus:4010713895	595	AT4G21065 "AT4G21065" [Arabido	0.617	0.238	0.322	1.1e-12
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.591	0.199	0.308	4.6e-12
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	0.621	0.230	0.320	8.3e-12
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.595	0.245	0.292	4.4e-11
TAIR|locus:2095289	1028	AT3G09040 "AT3G09040" [Arabido	0.591	0.132	0.302	8.6e-10
TAIR|locus:2090857	455	AT3G26630 "AT3G26630" [Arabido	0.582	0.294	0.298	5.5e-09
TAIR|locus:2049562	584	AT2G01510 "AT2G01510" [Arabido	0.939	0.369	0.261	8.4e-09

TAIR|locus:2093920 AT3G15930 "AT3G15930" [Arabidopsis thaliana (taxid:3702)]

 Score = 286 (105.7 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 62/153 (40%), Positives = 92/153 (60%)

Query:     3 QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEK--GDLKYECKVFRKITQPSVFLWNTMIK 60
             Q KQ+HSQ+I  G+   P   K+  ++    +  G + Y  K+F KI +P V +WN MIK
Sbjct:    49 QFKQLHSQSITRGVAPNPTFQKKL-FVFWCSRLGGHVSYAYKLFVKIPEPDVVVWNNMIK 107

Query:    61 GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRD---IAGSLEKSCIVMR---- 113
             G+S++D    GV +YL++LK  V  D++TFPFL  G  RD   +A   +  C V++    
Sbjct:   108 GWSKVDCDGEGVRLYLNMLKEGVTPDSHTFPFLLNGLKRDGGALACGKKLHCHVVKFGLG 167

Query:   114 --VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
               ++VQNAL+  Y LCG +DMARG+F   C++D
Sbjct:   168 SNLYVQNALVKMYSLCGLMDMARGVFDRRCKED 200

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2060640 OTP81 "ORGANELLE TRANSCRIPT PROCESSING 81" [Arabidopsis thaliana (taxid:3702)]

 Score = 188 (71.2 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 50/154 (32%), Positives = 74/154 (48%)

Query:     1 MHQLKQIHSQTIKLGLLTKPH-CPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
             + QLKQ H   I+ G  + P+   K      L     L+Y  KVF +I +P+ F WNT+I
Sbjct:    43 LRQLKQTHGHMIRTGTFSDPYSASKLFAMAALSSFASLEYARKVFDEIPKPNSFAWNTLI 102

Query:    60 KGYSRIDSHKNGVLMYLDLL-KSDVRRDNYTFPFLFKGFT--------RDIAGSLEKSCI 110
             + Y+        +  +LD++ +S    + YTFPFL K           + + G   KS +
Sbjct:   103 RAYASGPDPVLSIWAFLDMVSESQCYPNKYTFPFLIKAAAEVSSLSLGQSLHGMAVKSAV 162

Query:   111 VMRVFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
                VFV N+LI  Y  CG++D A  +F    E D
Sbjct:   163 GSDVFVANSLIHCYFSCGDLDSACKVFTTIKEKD 196

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2034456 AT1G31920 [Arabidopsis thaliana (taxid:3702)]

 Score = 184 (69.8 bits), Expect = 2.5e-13, P = 2.5e-13
 Identities = 45/146 (30%), Positives = 72/146 (49%)

Query:     3 QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKG---DLKYECKVFRKITQPSVFLWNTMI 59
             + KQ+H++ IKL L         +        G    + Y   +FR I  P  F +NTMI
Sbjct:    45 EFKQVHARFIKLSLFYSSSFSASSVLAKCAHSGWENSMNYAASIFRGIDDPCTFDFNTMI 104

Query:    60 KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR--------DIAGSLEKSCIV 111
             +GY  + S +  +  Y ++++     DN+T+P L K  TR         I G + K  + 
Sbjct:   105 RGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCLLKACTRLKSIREGKQIHGQVFKLGLE 164

Query:   112 MRVFVQNALISTYCLCGEVDMARGIF 137
               VFVQN+LI+ Y  CGE++++  +F
Sbjct:   165 ADVFVQNSLINMYGRCGEMELSSAVF 190

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0010075 "regulation of meristem growth" evidence=RCA

GO:0016556 "mRNA modification" evidence=RCA

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

 Score = 178 (67.7 bits), Expect = 1.1e-12, P = 1.1e-12
 Identities = 50/155 (32%), Positives = 82/155 (52%)

Query:     3 QLKQIHSQTIKLGL-LTKPHCPKQTRYLL--LYEKGDLKYECKVFRKITQP-SVFLWNTM 58
             +L+QIH+ +I+ G+ ++     K   + L  L     + Y  KVF KI +P +VF+WNT+
Sbjct:    32 KLRQIHAFSIRHGVSISDAELGKHLIFYLVSLPSPPPMSYAHKVFSKIEKPINVFIWNTL 91

Query:    59 IKGYSRIDSHKNGVLMYLDLLKSD-VRRDNYTFPFLFKGFTR--DIA-GSLEKSCIVMR- 113
             I+GY+ I +  +   +Y ++  S  V  D +T+PFL K  T   D+  G    S ++   
Sbjct:    92 IRGYAEIGNSISAFSLYREMRVSGLVEPDTHTYPFLIKAVTTMADVRLGETIHSVVIRSG 151

Query:   114 ----VFVQNALISTYCLCGEVDMARGIFYMSCEDD 144
                 ++VQN+L+  Y  CG+V  A  +F    E D
Sbjct:   152 FGSLIYVQNSLLHLYANCGDVASAYKVFDKMPEKD 186

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2041198 SLO1 "SLOW GROWTH 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 4.6e-12, P = 4.6e-12
 Identities = 46/149 (30%), Positives = 74/149 (49%)

Query:     1 MHQLKQIHSQTIKLGLLTKPHCPKQT-RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMI 59
             +H LKQI +Q I  GL+  P    +   +  L E   L Y  K+ + I  P++F WN  I
Sbjct:    67 LH-LKQIQAQMIINGLILDPFASSRLIAFCALSESRYLDYSVKILKGIENPNIFSWNVTI 125

Query:    60 KGYSRIDSHKNGVLMYLDLLKS---DVRRDNYTFPFLFK--------GFTRDIAGSLEKS 108
             +G+S  ++ K   L+Y  +L+    + R D++T+P LFK             I G + K 
Sbjct:   126 RGFSESENPKESFLLYKQMLRHGCCESRPDHFTYPVLFKVCADLRLSSLGHMILGHVLKL 185

Query:   109 CIVMRVFVQNALISTYCLCGEVDMARGIF 137
              + +   V NA I  +  CG+++ AR +F
Sbjct:   186 RLELVSHVHNASIHMFASCGDMENARKVF 214

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2154855 AT5G66520 "AT5G66520" [Arabidopsis thaliana (taxid:3702)]

 Score = 170 (64.9 bits), Expect = 8.3e-12, P = 8.3e-12
 Identities = 49/153 (32%), Positives = 73/153 (47%)

Query:     3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGD-LKYECKVFRKITQPSVFLWNTMIK 60
             +LKQIH++ +K GL+   +   K   + +     D L Y   VF    +P  FLWN MI+
Sbjct:    29 ELKQIHARMLKTGLMQDSYAITKFLSFCISSTSSDFLPYAQIVFDGFDRPDTFLWNLMIR 88

Query:    61 GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG------F--TRDIAGSLEKSCIVM 112
             G+S  D  +  +L+Y  +L S    + YTFP L K       F  T  I   + K     
Sbjct:    89 GFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETTQIHAQITKLGYEN 148

Query:   113 RVFVQNALISTYCLCGEVDMARGIFYMSCEDDD 145
              V+  N+LI++Y + G   +A  +F    E DD
Sbjct:   149 DVYAVNSLINSYAVTGNFKLAHLLFDRIPEPDD 181

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2045580 AT2G42920 [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 4.4e-11, P = 4.4e-11
 Identities = 43/147 (29%), Positives = 73/147 (49%)

Query:     1 MHQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIK 60
             M +LKQIH+  IK GL++      +          D+ Y   VF +I   + F+WNT+I+
Sbjct:    38 MRELKQIHASLIKTGLISDTVTASRVLAFCCASPSDMNYAYLVFTRINHKNPFVWNTIIR 97

Query:    61 GYSRIDSHKNGVLMYLDLLKSD--VRRDNYTFPFLFKGF-----TRD---IAGSLEKSCI 110
             G+SR    +  + +++D+L S   V+    T+P +FK +      RD   + G + K  +
Sbjct:    98 GFSRSSFPEMAISIFIDMLCSSPSVKPQRLTYPSVFKAYGRLGQARDGRQLHGMVIKEGL 157

Query:   111 VMRVFVQNALISTYCLCGEVDMARGIF 137
                 F++N ++  Y  CG +  A  IF
Sbjct:   158 EDDSFIRNTMLHMYVTCGCLIEAWRIF 184

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2095289 AT3G09040 "AT3G09040" [Arabidopsis thaliana (taxid:3702)]

 Score = 163 (62.4 bits), Expect = 8.6e-10, P = 8.6e-10
 Identities = 45/149 (30%), Positives = 78/149 (52%)

Query:     7 IHSQTIKLGLLTKPHCPKQTRYLLLYEKGD-LKYECKVFRKITQPSVFLWNTMIKGYSRI 65
             +H++ IKLGL +  +       + +Y K + ++   KVF  + + +   WN MI+GY+  
Sbjct:   349 VHAEAIKLGLASNIYVGSSL--VSMYSKCEKMEAAAKVFEALEEKNDVFWNAMIRGYAHN 406

Query:    66 -DSHKNGVLMYLDLLKSDVRRDNYTFPFLFK--GFTRDIA-GSLEKSCIVMR-----VFV 116
              +SHK  + +++D+  S    D++TF  L      + D+  GS   S I+ +     +FV
Sbjct:   407 GESHKV-MELFMDMKSSGYNIDDFTFTSLLSTCAASHDLEMGSQFHSIIIKKKLAKNLFV 465

Query:   117 QNALISTYCLCGEVDMARGIFYMSCEDDD 145
              NAL+  Y  CG ++ AR IF   C+ D+
Sbjct:   466 GNALVDMYAKCGALEDARQIFERMCDRDN 494

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2090857 AT3G26630 "AT3G26630" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 5.5e-09, P = 5.5e-09
 Identities = 43/144 (29%), Positives = 67/144 (46%)

Query:     3 QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGY 62
             QLKQIH++ IK  L       +Q    +    G+ +Y   VF ++  PS F WN MI+  
Sbjct:    35 QLKQIHTKIIKHNLTNDQLLVRQL-ISVSSSFGETQYASLVFNQLQSPSTFTWNLMIRSL 93

Query:    63 SRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKG--------FTRDIAGSLEKSCIVMR 113
             S     +  +L+++ ++ S   + D +TFPF+ K             + G   K+     
Sbjct:    94 SVNHKPREALLLFILMMISHQSQFDKFTFPFVIKACLASSSIRLGTQVHGLAIKAGFFND 153

Query:   114 VFVQNALISTYCLCGEVDMARGIF 137
             VF QN L+  Y  CG+ D  R +F
Sbjct:   154 VFFQNTLMDLYFKCGKPDSGRKVF 177

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2049562 AT2G01510 "AT2G01510" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 8.4e-09, P = 8.4e-09
 Identities = 61/233 (26%), Positives = 102/233 (43%)

Query:     3 QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGY 62
             QLK+IH+  ++ G   K     Q    L+   GD+ Y  +VF ++ +P +FLWNT+ KGY
Sbjct:    26 QLKKIHAIVLRTGFSEKNSLLTQLLENLVVI-GDMCYARQVFDEMHKPRIFLWNTLFKGY 84

Query:    63 SRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR--DIA-GSLEKSCIVMRVF---- 115
              R       +L+Y  +    VR D +T+PF+ K  ++  D + G    + +V   F    
Sbjct:    85 VRNQLPFESLLLYKKMRDLGVRPDEFTYPFVVKAISQLGDFSCGFALHAHVVKYGFGCLG 144

Query:   116 -VQNALISTYCLCGEVDMARGIFY-MSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLA 173
              V   L+  Y   GE+  A  +F  M  +D    +  + +  V      +  EY  +M A
Sbjct:   145 IVATELVMMYMKFGELSSAEFLFESMQVKDLVAWNAFLAV-CVQTGNSAIALEYFNKMCA 203

Query:   174 LPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNS 226
               D    +   V+    A      ++G+LE G     R  +   D   ++ N+
Sbjct:   204 --DAVQFDSFTVVSMLSA----CGQLGSLEIGEEIYDRARKEEIDCNIIVENA 250

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	230
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-10
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-05
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-04

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

 Score = 59.1 bits (143), Expect = 3e-10
 Identities = 38/111 (34%), Positives = 58/111 (52%), Gaps = 8/111 (7%)

Query: 35  GDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLF 94
           G+L +   VF K+ +  +F WN ++ GY++       + +Y  +L + VR D YTFP + 
Sbjct: 135 GELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVL 194

Query: 95  K--GFTRDIAGSLEKSCIVMR------VFVQNALISTYCLCGEVDMARGIF 137
           +  G   D+A   E    V+R      V V NALI+ Y  CG+V  AR +F
Sbjct: 195 RTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF 245

Length = 857

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

 Score = 52.6 bits (126), Expect = 5e-08
 Identities = 32/151 (21%), Positives = 64/151 (42%), Gaps = 25/151 (16%)

Query: 5   KQIHSQTIKLGLLTKPHCPKQTRYLL-----LYEK-GDLKYECKVFRKITQPSVFLWNTM 58
           +Q+H   +K G++          ++      +Y K GD++    VF  + + +   WN+M
Sbjct: 244 QQLHCCVLKTGVV-------GDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSM 296

Query: 59  IKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQN 118
           + GY+     +  + +Y ++  S V  D +TF  + + F+R     LE +       ++ 
Sbjct: 297 LAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSR--LALLEHAKQAHAGLIRT 354

Query: 119 ----------ALISTYCLCGEVDMARGIFYM 139
                     AL+  Y   G ++ AR +F  
Sbjct: 355 GFPLDIVANTALVDLYSKWGRMEDARNVFDR 385

Length = 697

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

 Score = 38.9 bits (92), Expect = 8e-05
 Identities = 12/48 (25%), Positives = 25/48 (52%)

Query: 50 PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGF 97
          P V  +NT+I GY +    +  + ++ ++ K  ++ + YT+  L  G 
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 42.1 bits (99), Expect = 1e-04
 Identities = 30/123 (24%), Positives = 50/123 (40%), Gaps = 10/123 (8%)

Query: 31  LYEK-GDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYT 89
           +Y K GD+     VF ++ +     WN MI GY        G+ ++  + +  V  D  T
Sbjct: 231 MYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMT 290

Query: 90  FPFLF--------KGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFY-MS 140
              +         +   R++ G + K+   + V V N+LI  Y   G    A  +F  M 
Sbjct: 291 ITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME 350

Query: 141 CED 143
            +D
Sbjct: 351 TKD 353

Length = 857

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
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
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PF13041	50	PPR_2: PPR repeat family	99.64
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.3
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.28
PF13041	50	PPR_2: PPR repeat family	99.28
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.97
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.93
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.9
PF12854	34	PPR_1: PPR repeat	98.87
PF12854	34	PPR_1: PPR repeat	98.84
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.79
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.79
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.73
KOG4422	625	consensus Uncharacterized conserved protein [Funct	98.66
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.49
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.48
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.33
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.3
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.29
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.14
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.08
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.04
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.04
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.04
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.0
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	97.99
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	97.97
PF13812	34	PPR_3: Pentatricopeptide repeat domain	97.95
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	97.93
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.91
PRK12370	553	invasion protein regulator; Provisional	97.78
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.74
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.72
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.66
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.66
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.65
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.63
PRK12370	553	invasion protein regulator; Provisional	97.63
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.6
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.53
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	97.48
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.42
KOG1126	638	consensus DNA-binding cell division cycle control	97.41
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.41
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.4
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.38
PRK14574	822	hmsH outer membrane protein; Provisional	97.37
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.31
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.24
PRK14574	822	hmsH outer membrane protein; Provisional	97.07
KOG1126	638	consensus DNA-binding cell division cycle control	97.04
PRK11189	296	lipoprotein NlpI; Provisional	96.96
PRK15359	144	type III secretion system chaperone protein SscB;	96.86
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	96.83
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.77
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.69
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.67
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.66
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	96.63
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.59
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	96.59
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.46
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	96.44
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	96.43
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.24
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.19
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	96.18
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.14
PRK11189	296	lipoprotein NlpI; Provisional	96.09
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.02
KOG2003	840	consensus TPR repeat-containing protein [General f	95.96
KOG3785	557	consensus Uncharacterized conserved protein [Funct	95.83
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.83
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	95.79
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.78
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.77
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	95.77
KOG1915	677	consensus Cell cycle control protein (crooked neck	95.76
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	95.72
TIGR02552	135	LcrH_SycD type III secretion low calcium response	95.7
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	95.64
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	95.64
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	95.64
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	95.6
PRK15359	144	type III secretion system chaperone protein SscB;	95.59
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	95.53
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.52
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	95.49
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	95.47
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	95.44
KOG1128	777	consensus Uncharacterized conserved protein, conta	95.37
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	95.36
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	95.31
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	95.25
KOG3941	406	consensus Intermediate in Toll signal transduction	95.17
PF13762	145	MNE1: Mitochondrial splicing apparatus component	95.17
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	95.11
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.07
KOG1129	478	consensus TPR repeat-containing protein [General f	95.03
KOG1129	478	consensus TPR repeat-containing protein [General f	94.98
KOG3060	289	consensus Uncharacterized conserved protein [Funct	94.92
KOG1915	677	consensus Cell cycle control protein (crooked neck	94.56
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	94.56
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	94.41
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	94.39
KOG2003	840	consensus TPR repeat-containing protein [General f	94.19
KOG2047	835	consensus mRNA splicing factor [RNA processing and	94.12
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	94.11
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	94.1
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	94.09
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	94.08
COG4783	484	Putative Zn-dependent protease, contains TPR repea	94.04
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	93.93
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	93.81
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	93.7
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	93.49
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	93.37
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	93.25
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	93.22
KOG0547	606	consensus Translocase of outer mitochondrial membr	93.1
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	93.09
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	93.02
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	92.98
KOG3941	406	consensus Intermediate in Toll signal transduction	92.82
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	92.6
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.59
KOG2076	895	consensus RNA polymerase III transcription factor	92.5
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	92.46
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.17
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	92.05
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	91.99
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.9
KOG2796	366	consensus Uncharacterized conserved protein [Funct	91.87
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	91.84
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	91.58
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	91.52
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	91.33
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	91.25
PRK14720	906	transcript cleavage factor/unknown domain fusion p	91.0
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	90.97
KOG2047	835	consensus mRNA splicing factor [RNA processing and	90.91
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	90.86
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	90.74
PF13371	73	TPR_9: Tetratricopeptide repeat	90.61
KOG2376	652	consensus Signal recognition particle, subunit Srp	90.12
PF13428	44	TPR_14: Tetratricopeptide repeat	89.95
KOG2076	895	consensus RNA polymerase III transcription factor	89.86
PF03704	146	BTAD: Bacterial transcriptional activator domain;	89.64
smart00299	140	CLH Clathrin heavy chain repeat homology.	89.61
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	89.58
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	89.36
PRK14720	906	transcript cleavage factor/unknown domain fusion p	89.34
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.22
KOG3616	1636	consensus Selective LIM binding factor [Transcript	89.0
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	88.94
PRK10803	263	tol-pal system protein YbgF; Provisional	88.9
KOG3785	557	consensus Uncharacterized conserved protein [Funct	88.74
KOG4340	459	consensus Uncharacterized conserved protein [Funct	88.52
KOG0547	606	consensus Translocase of outer mitochondrial membr	88.48
PF12688	120	TPR_5: Tetratrico peptide repeat	88.32
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	88.12
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	88.04
PF12688	120	TPR_5: Tetratrico peptide repeat	88.01
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	87.92
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	87.9
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	87.75
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	87.63
KOG1125	579	consensus TPR repeat-containing protein [General f	87.27
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	87.26
PRK10370	198	formate-dependent nitrite reductase complex subuni	87.13
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	87.0
KOG1128	777	consensus Uncharacterized conserved protein, conta	86.96
PLN02789	320	farnesyltranstransferase	86.59
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	86.51
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	86.47
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	86.4
KOG2376	652	consensus Signal recognition particle, subunit Srp	86.07
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	85.62
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	84.8
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	83.8
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	83.3
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	83.01
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	82.14
PF13371	73	TPR_9: Tetratricopeptide repeat	81.96
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	81.83
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	81.82
PF09477	116	Type_III_YscG: Bacterial type II secretion system	81.71
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	81.6
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	81.33
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	81.23
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	80.58

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

Probab=100.00  E-value=4e-41  Score=304.73  Aligned_cols=215  Identities=17%  Similarity=0.241  Sum_probs=204.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +.++++|..+.+.|+.||..+ ++||++|+  ++|++++|.++|++|+++|+++||++|.+|++.|++++|+++|++|.+
T Consensus       241 ~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~--k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~  318 (697)
T PLN03081        241 RAGQQLHCCVLKTGVVGDTFVSCALIDMYS--KCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRD  318 (697)
T ss_pred             HHHHHHHHHHHHhCCCccceeHHHHHHHHH--HCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456777888888888899999 99999999  999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHH
Q 042210           81 SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIR  152 (230)
Q Consensus        81 ~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li  152 (230)
                      .|+.||..||++++++|++.|++  |.++|..|.      |..+||+||++|+|+|++++|.++|++|.+||++|||+||
T Consensus       319 ~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI  398 (697)
T PLN03081        319 SGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALI  398 (697)
T ss_pred             cCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHH
Confidence            99999999999999999999999  999999998      8999999999999999999999999999999999999999


Q ss_pred             HHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccc-cCCCccccccccC
Q 042210          153 IKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE-HSQDDMSLISNSI  227 (230)
Q Consensus       153 ~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~-~~~~~~~~~~n~l  227 (230)
                      .+|+.    ++|+++|++|.+.| +.||..||++  +++       +|++.|.+++|.++|..|.+ .|+.|+..+|++|
T Consensus       399 ~~y~~~G~~~~A~~lf~~M~~~g-~~Pd~~T~~~--ll~-------a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~l  468 (697)
T PLN03081        399 AGYGNHGRGTKAVEMFERMIAEG-VAPNHVTFLA--VLS-------ACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACM  468 (697)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCCHHHHHH--HHH-------HHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhH
Confidence            99985    58999999999999 8999999999  766       99999999999999999986 6999999999987


Q ss_pred             C
Q 042210          228 P  228 (230)
Q Consensus       228 ~  228 (230)
                      .
T Consensus       469 i  469 (697)
T PLN03081        469 I  469 (697)
T ss_pred             H
Confidence            5

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

Probab=100.00  E-value=1.1e-39  Score=295.43  Aligned_cols=215  Identities=15%  Similarity=0.172  Sum_probs=206.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +.|.++|..|++.|+.||..+ +.++.+|+  +.|++++|.++|++|+.||.++||++|.+|++.|++++|+++|++|.+
T Consensus       140 ~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~--k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~  217 (697)
T PLN03081        140 RCVKAVYWHVESSGFEPDQYMMNRVLLMHV--KCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWE  217 (697)
T ss_pred             HHHHHHHHHHHHhCCCcchHHHHHHHHHHh--cCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            468999999999999999999 99999999  999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHH
Q 042210           81 SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIR  152 (230)
Q Consensus        81 ~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li  152 (230)
                      .|+.||..||+.++++|++.|+.  +.++|..+.      |..+||+||++|+++|++++|.++|++|.+||+++||+||
T Consensus       218 ~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li  297 (697)
T PLN03081        218 DGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSML  297 (697)
T ss_pred             hCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHH
Confidence            99999999999999999999998  999999887      8999999999999999999999999999999999999999


Q ss_pred             HHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCCccccccccCC
Q 042210          153 IKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIP  228 (230)
Q Consensus       153 ~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~~~n~l~  228 (230)
                      .+|+.    ++|+++|++|.+.| +.||.+||++  ++.       +|++.|++++|+++|+.|.+.|+.||..+||+|+
T Consensus       298 ~~y~~~g~~~eA~~lf~~M~~~g-~~pd~~t~~~--ll~-------a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li  367 (697)
T PLN03081        298 AGYALHGYSEEALCLYYEMRDSG-VSIDQFTFSI--MIR-------IFSRLALLEHAKQAHAGLIRTGFPLDIVANTALV  367 (697)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHcC-CCCCHHHHHH--HHH-------HHHhccchHHHHHHHHHHHHhCCCCCeeehHHHH
Confidence            99986    57999999999998 8999999999  666       9999999999999999999999999999999875

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=3.2e-39  Score=298.20  Aligned_cols=215  Identities=17%  Similarity=0.215  Sum_probs=205.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +.++++|..|.+.|+.||+.+ +++|.+|+  +.|++++|.++|++|+.||.++||++|.+|++.|++++|+++|++|.+
T Consensus       204 ~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~--k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~  281 (857)
T PLN03077        204 ARGREVHAHVVRFGFELDVDVVNALITMYV--KCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRE  281 (857)
T ss_pred             hhHHHHHHHHHHcCCCcccchHhHHHHHHh--cCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456788888888888889999 99999999  999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHH
Q 042210           81 SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIR  152 (230)
Q Consensus        81 ~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li  152 (230)
                      .|+.||..||+++|.+|++.|++  +.++|..+.      |..+||+||++|+++|++++|+++|++|..||.++||+||
T Consensus       282 ~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li  361 (857)
T PLN03077        282 LSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMI  361 (857)
T ss_pred             cCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHH
Confidence            99999999999999999999999  999999998      9999999999999999999999999999999999999999


Q ss_pred             HHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCCccccccccCC
Q 042210          153 IKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIP  228 (230)
Q Consensus       153 ~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~~~n~l~  228 (230)
                      .+|.+    ++|+++|++|.+.+ +.||.+|+++  ++.       +|++.|++++|.++|+.+.+.|+.|+..+||+|+
T Consensus       362 ~~~~~~g~~~~A~~lf~~M~~~g-~~Pd~~t~~~--ll~-------a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li  431 (857)
T PLN03077        362 SGYEKNGLPDKALETYALMEQDN-VSPDEITIAS--VLS-------ACACLGDLDVGVKLHELAERKGLISYVVVANALI  431 (857)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CCCCceeHHH--HHH-------HHhccchHHHHHHHHHHHHHhCCCcchHHHHHHH
Confidence            99986    57999999999998 8999999999  666       9999999999999999999999999999999875

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.2e-38  Score=292.68  Aligned_cols=215  Identities=13%  Similarity=0.159  Sum_probs=190.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      +.|.++|++|++.|+.||..+ +++|.+|+  +.|++++|.++|++|.    .||..+||++|.+|++.|++++|.++|+
T Consensus       454 e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~--k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~  531 (1060)
T PLN03218        454 DGALRVLRLVQEAGLKADCKLYTTLISTCA--KSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYG  531 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--hCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            578899999999999999999 99999999  9999999999999998    7899999999999999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh--------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC----
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM--------RVFVQNALISTYCLCGEVDMARGIFYMSCE----  142 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~--------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----  142 (230)
                      +|++.|+.||..||+.||++|++.|++  |.++|+.|.        |.++||+||++|+++|++++|.++|++|.+    
T Consensus       532 ~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~  611 (1060)
T PLN03218        532 IMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIK  611 (1060)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence            999999999999999999999999999  999999884        788999999999999999999999999986    


Q ss_pred             CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCC
Q 042210          143 DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQD  218 (230)
Q Consensus       143 ~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~  218 (230)
                      |+..+||++|.+|+.    ++|.++|++|.+.| +.||.+||+.  ++.       +|++.|++++|.++|..|.+.|+.
T Consensus       612 p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~G-v~PD~~Tyns--LI~-------a~~k~G~~eeA~~l~~eM~k~G~~  681 (1060)
T PLN03218        612 GTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKG-VKPDEVFFSA--LVD-------VAGHAGDLDKAFEILQDARKQGIK  681 (1060)
T ss_pred             CChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC-CCCCHHHHHH--HHH-------HHHhCCCHHHHHHHHHHHHHcCCC
Confidence            677899999988875    47888888888888 7888888888  555       888888888888888888888888


Q ss_pred             ccccccccCC
Q 042210          219 DMSLISNSIP  228 (230)
Q Consensus       219 ~~~~~~n~l~  228 (230)
                      ||..+||+|+
T Consensus       682 pd~~tynsLI  691 (1060)
T PLN03218        682 LGTVSYSSLM  691 (1060)
T ss_pred             CCHHHHHHHH
Confidence            8888887764

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.5e-38  Score=290.58  Aligned_cols=214  Identities=18%  Similarity=0.201  Sum_probs=204.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +.|+++|..|.+.|+.||..+ +++|.+|+  +.|++++|.++|++|..||.++||++|.+|++.|++++|+++|++|++
T Consensus       305 ~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~--k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~  382 (857)
T PLN03077        305 RLGREMHGYVVKTGFAVDVSVCNSLIQMYL--SLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQ  382 (857)
T ss_pred             HHHHHHHHHHHHhCCccchHHHHHHHHHHH--hcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            568899999999999999999 99999999  999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHH
Q 042210           81 SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIR  152 (230)
Q Consensus        81 ~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li  152 (230)
                      .|+.||..||+++|.+|++.|++  |.++|+.+.      +..+||+||++|+++|++++|.++|++|.+||+++||+||
T Consensus       383 ~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi  462 (857)
T PLN03077        383 DNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSII  462 (857)
T ss_pred             hCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHH
Confidence            99999999999999999999999  999999998      8999999999999999999999999999999999999999


Q ss_pred             HHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCCccccccccCC
Q 042210          153 IKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLISNSIP  228 (230)
Q Consensus       153 ~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~~~n~l~  228 (230)
                      .+|..    ++|+++|++|.. + +.||.+|+.+  ++.       +|++.|+++.|+++|..+.+.|+.+|..++|+|+
T Consensus       463 ~~~~~~g~~~eA~~lf~~m~~-~-~~pd~~t~~~--lL~-------a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi  531 (857)
T PLN03077        463 AGLRLNNRCFEALIFFRQMLL-T-LKPNSVTLIA--ALS-------ACARIGALMCGKEIHAHVLRTGIGFDGFLPNALL  531 (857)
T ss_pred             HHHHHCCCHHHHHHHHHHHHh-C-CCCCHhHHHH--HHH-------HHhhhchHHHhHHHHHHHHHhCCCccceechHHH
Confidence            99985    479999999975 4 7999999999  766       9999999999999999999999999999998874

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=4.2e-38  Score=290.85  Aligned_cols=215  Identities=10%  Similarity=0.048  Sum_probs=184.7

Q ss_pred             hhHHHHHHHHHH--hcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHH
Q 042210            2 HQLKQIHSQTIK--LGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLM   74 (230)
Q Consensus         2 ~~a~~~~~~m~~--~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~   74 (230)
                      ++|.++|++|.+  .|+.||..+ +++|.+|+  +.|++++|.++|++|.    .|+..+||++|.+|++.|++++|.++
T Consensus       559 deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~--k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~l  636 (1060)
T PLN03218        559 DRAFDVLAEMKAETHPIDPDHITVGALMKACA--NAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSI  636 (1060)
T ss_pred             HHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHH
Confidence            457777777765  467777777 77777777  7777777777777776    56667888888888888888888888


Q ss_pred             HHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc----C
Q 042210           75 YLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSC----E  142 (230)
Q Consensus        75 ~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~----~  142 (230)
                      |++|.+.|+.||..||+++|++|++.|++  |.++|+.|.      |..+||+||++|+++|++++|.++|++|.    .
T Consensus       637 f~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~  716 (1060)
T PLN03218        637 YDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLR  716 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence            88888888888888888888888888888  888888887      88999999999999999999999999996    4


Q ss_pred             CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCC
Q 042210          143 DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQD  218 (230)
Q Consensus       143 ~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~  218 (230)
                      ||.++||+||.+|+.    ++|+++|++|.+.| +.||.+||+.  ++.       +|++.|++++|.++|.+|.+.|+.
T Consensus       717 PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~G-i~Pd~~Ty~s--LL~-------a~~k~G~le~A~~l~~~M~k~Gi~  786 (1060)
T PLN03218        717 PTVSTMNALITALCEGNQLPKALEVLSEMKRLG-LCPNTITYSI--LLV-------ASERKDDADVGLDLLSQAKEDGIK  786 (1060)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCCHHHHHH--HHH-------HHHHCCCHHHHHHHHHHHHHcCCC
Confidence            999999999999975    58999999999988 8999999999  655       999999999999999999999999


Q ss_pred             ccccccccCC
Q 042210          219 DMSLISNSIP  228 (230)
Q Consensus       219 ~~~~~~n~l~  228 (230)
                      ||..+||+|.
T Consensus       787 pd~~tynsLI  796 (1060)
T PLN03218        787 PNLVMCRCIT  796 (1060)
T ss_pred             CCHHHHHHHH
Confidence            9999999874

>PF13041 PPR_2: PPR repeat family

Probab=99.64  E-value=3.4e-16  Score=93.73  Aligned_cols=50  Identities=26%  Similarity=0.676  Sum_probs=49.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           50 PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        50 ~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ||+++||++|++|++.|++++|+++|++|++.|++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            89999999999999999999999999999999999999999999999985

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.30  E-value=2.5e-10  Score=96.87  Aligned_cols=174  Identities=11%  Similarity=-0.036  Sum_probs=127.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCc----H-HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH----C-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVL   73 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~----~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~   73 (230)
                      ++|.+.++.+.+.+-.++..    . ..+...+.  +.|++++|...|+++.  .| +...+..+...|.+.|++++|..
T Consensus       158 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~  235 (389)
T PRK11788        158 QKAIDVAERLEKLGGDSLRVEIAHFYCELAQQAL--ARGDLDAARALLKKALAADPQCVRASILLGDLALAQGDYAAAIE  235 (389)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            45677777777665333221    2 33455666  8888888888888865  33 34567777788888999999999


Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD  145 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~  145 (230)
                      +|+++...+-.....+++.+..+|.+.|++  |...+..+.    +...+..+...|.+.|++++|.++|+++.+  |+.
T Consensus       236 ~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~  315 (389)
T PRK11788        236 ALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSL  315 (389)
T ss_pred             HHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCH
Confidence            999887653222235677888889888888  777777766    445568888999999999999999987765  888


Q ss_pred             hhhHHHHHHhh-------hcchhhhHHHHHHHhhhcCchh
Q 042210          146 GLHELIRIKAV-------DDDLHELFPEYLVQMLALPDTF  178 (230)
Q Consensus       146 ~t~n~li~~~~-------~~~~~~~~~~m~~~~~~~p~~~  178 (230)
                      .+++.++....       ..+++++|++|.+.+ +.||..
T Consensus       316 ~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~-~~~~p~  354 (389)
T PRK11788        316 RGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQ-LKRKPR  354 (389)
T ss_pred             HHHHHHHHHhhhccCCccchhHHHHHHHHHHHH-HhCCCC
Confidence            88888776543       247889999999888 666644

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.28  E-value=1.1e-10  Score=99.13  Aligned_cols=206  Identities=10%  Similarity=-0.009  Sum_probs=115.9

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCC--CC------hhhHHHHHHHHHhcCChhHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQ--PS------VFLWNTMIKGYSRIDSHKNGVL   73 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~--~~------~~~yn~li~~~~~~~~~~~a~~   73 (230)
                      +|..+|+.+.+.. .++..+ ..+...+.  +.|++++|.+.++.+.+  |+      ...|..+...+.+.|++++|..
T Consensus       125 ~A~~~~~~~l~~~-~~~~~~~~~la~~~~--~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  201 (389)
T PRK11788        125 RAEELFLQLVDEG-DFAEGALQQLLEIYQ--QEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARA  201 (389)
T ss_pred             HHHHHHHHHHcCC-cchHHHHHHHHHHHH--HhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence            4455555554431 112333 55556666  66666666666665541  11      1123444455556666666666


Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCE--D  143 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~  143 (230)
                      .|+++.+.. +.+...+..+...+.+.|++  |.+.++.+.      ...+++.+...|.+.|++++|...|+++.+  |
T Consensus       202 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p  280 (389)
T PRK11788        202 LLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYP  280 (389)
T ss_pred             HHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            666665432 11233455555666666666  666666655      134567777778888888888887777664  6


Q ss_pred             ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCCCc
Q 042210          144 DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDD  219 (230)
Q Consensus       144 ~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~  219 (230)
                      +...++.+...+..    ++|.+.++++.+.   .||..++..  ++...    -.....|+.+++..+++.+.+.++.|
T Consensus       281 ~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~---~P~~~~~~~--l~~~~----~~~~~~g~~~~a~~~~~~~~~~~~~~  351 (389)
T PRK11788        281 GADLLLALAQLLEEQEGPEAAQALLREQLRR---HPSLRGFHR--LLDYH----LAEAEEGRAKESLLLLRDLVGEQLKR  351 (389)
T ss_pred             CchHHHHHHHHHHHhCCHHHHHHHHHHHHHh---CcCHHHHHH--HHHHh----hhccCCccchhHHHHHHHHHHHHHhC
Confidence            66555555555443    3455555554443   477666554  22200    01222567888888888888877766


Q ss_pred             cc
Q 042210          220 MS  221 (230)
Q Consensus       220 ~~  221 (230)
                      +.
T Consensus       352 ~p  353 (389)
T PRK11788        352 KP  353 (389)
T ss_pred             CC
Confidence            63

>PF13041 PPR_2: PPR repeat family

Probab=99.28  E-value=5.9e-12  Score=75.17  Aligned_cols=45  Identities=24%  Similarity=0.295  Sum_probs=42.0

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC----CChhhhHHHHHHhhh
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE----DDDGLHELIRIKAVD  157 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----~~~~t~n~li~~~~~  157 (230)
                      |+++||++|++|++.|++++|.++|++|.+    ||..|||+||+++++
T Consensus         2 ~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    2 DVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             chHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            678999999999999999999999999986    999999999999863

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

Probab=98.97  E-value=2.3e-08  Score=92.54  Aligned_cols=185  Identities=12%  Similarity=0.071  Sum_probs=112.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  ..|++++|..+++.+.   ..+...|..+...+.+.|++++|...|+++...+  |+..++..+..++.+
T Consensus       673 ~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~  748 (899)
T TIGR02917       673 IGLAQLLL--AAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLA  748 (899)
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHH
Confidence            44455555  5555555555555554   2334455556666666666666666666665543  444566666777777


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHHHHHhhh---cchhhhHHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELIRIKAVD---DDLHELFPE  166 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~li~~~~~---~~~~~~~~~  166 (230)
                      .|+.  |...+..+.     +...++.+...|.+.|+.++|...|+++.+   ++...++.+...+..   .++++.+++
T Consensus       749 ~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~A~~~~~~  828 (899)
T TIGR02917       749 SGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKDPRALEYAEK  828 (899)
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            7776  655555554     677777788888888888888888887764   345566666544432   345555555


Q ss_pred             HHHHhhhcCch-hhhhhhhhcccccCCcccccccCCccCCccccccccccCCCcccccc
Q 042210          167 YLVQMLALPDT-FMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSLIS  224 (230)
Q Consensus       167 m~~~~~~~p~~-~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~~~  224 (230)
                      .....   |+. .++..+..         .+.+.|++++|..+++.+.+.+.. +..++
T Consensus       829 ~~~~~---~~~~~~~~~~~~---------~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~  874 (899)
T TIGR02917       829 ALKLA---PNIPAILDTLGW---------LLVEKGEADRALPLLRKAVNIAPE-AAAIR  874 (899)
T ss_pred             HHhhC---CCCcHHHHHHHH---------HHHHcCCHHHHHHHHHHHHhhCCC-ChHHH
Confidence            54433   332 22222112         566789999999999888887654 44444

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=98.93  E-value=5.1e-08  Score=90.23  Aligned_cols=117  Identities=14%  Similarity=0.102  Sum_probs=68.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...|.  +.|++++|..+++.+.   +.+...|..+...|.+.|++++|...|+++.+.. +.+...+..+..++.+
T Consensus       571 ~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  647 (899)
T TIGR02917       571 LALAQYYL--GKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAV  647 (899)
T ss_pred             HHHHHHHH--HCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHH
Confidence            44555555  6666666666666554   3344556666666666666666666666665432 1233445556666666


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .|++  |...+..+.     +...+..+...+.+.|++++|.++++.+.+
T Consensus       648 ~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  697 (899)
T TIGR02917       648 MKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQK  697 (899)
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            6666  555555554     455666666666666666666666666654

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.

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.90  E-value=7.9e-08  Score=80.13  Aligned_cols=135  Identities=8%  Similarity=0.100  Sum_probs=94.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhH----HH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKN----GV   72 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~----a~   72 (230)
                      +.|+.++++-.....+.+..+ |.+|.+-.+ ..|     .++..+|.    .||..|+|+++++.++.|+++.    |+
T Consensus       224 ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~-~~~-----K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aal  297 (625)
T KOG4422|consen  224 ERARELYKEHRAAKGKVYREAFNGLIGASSY-SVG-----KKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAAL  297 (625)
T ss_pred             HHHHHHHHHHHHhhheeeHHhhhhhhhHHHh-hcc-----HHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHH
Confidence            344444444444444555555 555544432 111     23333443    7999999999999999997764    67


Q ss_pred             HHHHHHHhCCCCCCcccHHHHHHHhhhcCch---hhHHHhhhh--------------hHhHHHHHHHHHHhcCCHHHHHH
Q 042210           73 LMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG---SLEKSCIVM--------------RVFVQNALISTYCLCGEVDMARG  135 (230)
Q Consensus        73 ~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~---a~~~~~~~~--------------~~~~~~~li~~y~~~g~~~~A~~  135 (230)
                      +++.+|++-|+.|...+|..+|.-+++.++.   +..+..++.              |..-+...++.+.+..+.+-|.+
T Consensus       298 qil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~  377 (625)
T KOG4422|consen  298 QILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQ  377 (625)
T ss_pred             HHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHH
Confidence            7888999999999999999999999998887   444444443              66667788888889999999988


Q ss_pred             HHhhccC
Q 042210          136 IFYMSCE  142 (230)
Q Consensus       136 vf~~m~~  142 (230)
                      |-.-.+.
T Consensus       378 v~~ll~t  384 (625)
T KOG4422|consen  378 VHGLLKT  384 (625)
T ss_pred             HHHHHHc
Confidence            8766553

>PF12854 PPR_1: PPR repeat

Probab=98.87  E-value=3.1e-09  Score=57.72  Aligned_cols=29  Identities=38%  Similarity=0.499  Sum_probs=24.4

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      |.++||+||++||+.|++++|.++|++|+
T Consensus         6 d~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    6 DVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             cHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            67788888888888888888888888884

>PF12854 PPR_1: PPR repeat

Probab=98.84  E-value=4e-09  Score=57.31  Aligned_cols=30  Identities=23%  Similarity=0.585  Sum_probs=19.9

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210           49 QPSVFLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        49 ~~~~~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      .||.++||+||++|++.|++++|.++|++|
T Consensus         4 ~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    4 EPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            466666666666666666666666666666

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.79  E-value=1.1e-08  Score=55.70  Aligned_cols=35  Identities=17%  Similarity=0.440  Sum_probs=33.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc
Q 042210           53 FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        53 ~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   87 (230)
                      ++||++|.+|++.|++++|.++|++|++.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999984

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.

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

Probab=98.79  E-value=3.1e-08  Score=88.66  Aligned_cols=188  Identities=13%  Similarity=0.065  Sum_probs=116.9

Q ss_pred             HHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC----------------------------CCChhhHH
Q 042210            6 QIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT----------------------------QPSVFLWN   56 (230)
Q Consensus         6 ~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~----------------------------~~~~~~yn   56 (230)
                      .++..+...|+.|+.++ .++|.-||  ..|+++.|- +|..|+                            .|-.-+|.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc--~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt   87 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYC--TKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYT   87 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHc--ccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHH
Confidence            56788999999999999 99999999  999999998 887775                            23445788


Q ss_pred             HHHHHHHhcCChhHHHHHHHH-HHh-------CCCCCCcccHHHHHHHhhhc--------------Cch--hhHH-----
Q 042210           57 TMIKGYSRIDSHKNGVLMYLD-LLK-------SDVRRDNYTFPFLFKGFTRD--------------IAG--SLEK-----  107 (230)
Q Consensus        57 ~li~~~~~~~~~~~a~~~~~~-M~~-------~g~~p~~~t~~~ll~~~~~~--------------~~~--a~~~-----  107 (230)
                      .|+.+|.+.||+.. ++.-++ |..       .|+.--..-|-..|.+|...              |-+  +.++     
T Consensus        88 ~Ll~ayr~hGDli~-fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~P  166 (1088)
T KOG4318|consen   88 NLLKAYRIHGDLIL-FEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVP  166 (1088)
T ss_pred             HHHHHHHhccchHH-HHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            88888888888765 333333 321       12211111111111111111              101  1111     


Q ss_pred             -----------Hhhhh--------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChh-----hhHHH
Q 042210          108 -----------SCIVM--------------------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDG-----LHELI  151 (230)
Q Consensus       108 -----------~~~~~--------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~-----t~n~l  151 (230)
                                 +.++.                    ++.+|.++++.-.-.|+++.|..++.+|++.+..     -|-.+
T Consensus       167 vsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl  246 (1088)
T KOG4318|consen  167 VSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLL  246 (1088)
T ss_pred             cccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhh
Confidence                       11111                    7788888888888999999999999999985432     24444


Q ss_pred             HHHhhhcchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcc
Q 042210          152 RIKAVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTP  207 (230)
Q Consensus       152 i~~~~~~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~  207 (230)
                      ++.....+.....+.|...| +.||..|+.-  .+.       .+.+.|....++.
T Consensus       247 ~g~~~~q~~e~vlrgmqe~g-v~p~seT~ad--yvi-------p~l~N~~t~~~~e  292 (1088)
T KOG4318|consen  247 LGINAAQVFEFVLRGMQEKG-VQPGSETQAD--YVI-------PQLSNGQTKYGEE  292 (1088)
T ss_pred             hcCccchHHHHHHHHHHHhc-CCCCcchhHH--HHH-------hhhcchhhhhccc
Confidence            44333334555555666666 8999888877  322       5666555544443

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.73  E-value=2.2e-08  Score=54.30  Aligned_cols=34  Identities=9%  Similarity=0.356  Sum_probs=32.5

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR   85 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p   85 (230)
                      +.+||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999999999999999998

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.66  E-value=1e-06  Score=73.63  Aligned_cols=167  Identities=11%  Similarity=0.099  Sum_probs=133.8

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHH----HHHhcC----CCChhhHHHHHHHHHhcCChhH-HH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECK----VFRKIT----QPSVFLWNTMIKGYSRIDSHKN-GV   72 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~----~~~~m~----~~~~~~yn~li~~~~~~~~~~~-a~   72 (230)
                      ..+++..+|....+.||..| |+++.+..  +.|+++.|+.    ++.+|+    .|...+|.-+|.-+++.+++.+ +.
T Consensus       256 ~~K~Lv~EMisqkm~Pnl~TfNalL~c~a--kfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as  333 (625)
T KOG4422|consen  256 VGKKLVAEMISQKMTPNLFTFNALLSCAA--KFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVAS  333 (625)
T ss_pred             ccHHHHHHHHHhhcCCchHhHHHHHHHHH--HhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhH
Confidence            45789999999999999999 99999999  9998887654    556676    8999999999999999888865 55


Q ss_pred             HHHHHHHh----CCCC---C-CcccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHHHHHHHHhcCC
Q 042210           73 LMYLDLLK----SDVR---R-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNALISTYCLCGE  129 (230)
Q Consensus        73 ~~~~~M~~----~g~~---p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~li~~y~~~g~  129 (230)
                      .+..++..    .-++   | |..-|...+..|.+..+.  |.++++...             ..+-|..+....|....
T Consensus       334 ~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es  413 (625)
T KOG4422|consen  334 SWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMES  413 (625)
T ss_pred             HHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHH
Confidence            55566543    2233   3 455678889999988887  999998887             45566778888999999


Q ss_pred             HHHHHHHHhhccC----CChhhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          130 VDMARGIFYMSCE----DDDGLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       130 ~~~A~~vf~~m~~----~~~~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                      ++.-.+.++.|.-    |+..+-..++.+.-.++++++..++..+|
T Consensus       414 ~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~  459 (625)
T KOG4422|consen  414 IDVTLKWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDS  459 (625)
T ss_pred             HHHHHHHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHH
Confidence            9999999998874    66666666777777788888888877777

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

Probab=98.49  E-value=7.8e-07  Score=72.38  Aligned_cols=197  Identities=14%  Similarity=0.078  Sum_probs=90.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +.|.+.++.+.+.+-. ++.. ..++.. .  ..+++++|.+++...-  .++...+...+..+.+.++++++.++++..
T Consensus        61 ~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~--~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~  136 (280)
T PF13429_consen   61 DEAIEAYEKLLASDKA-NPQDYERLIQL-L--QDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKL  136 (280)
T ss_dssp             -------------------------------------------------------------H-HHHTT-HHHHHHHHHHH
T ss_pred             cccccccccccccccc-ccccccccccc-c--ccccccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHH
Confidence            4567777777766533 2333 555555 6  8899999998887653  556677888999999999999999999997


Q ss_pred             HhCC-CCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhh
Q 042210           79 LKSD-VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGL  147 (230)
Q Consensus        79 ~~~g-~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t  147 (230)
                      .... .+++...|..+-..+.+.|+.  |...++...     |....+.++..+...|+.++++.+++....   .|...
T Consensus       137 ~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~  216 (280)
T PF13429_consen  137 EELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDL  216 (280)
T ss_dssp             HH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCH
T ss_pred             HhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHH
Confidence            6543 556777888888899999999  888888877     788899999999999999998888887754   45556


Q ss_pred             hHHHHHHhh----hcchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          148 HELIRIKAV----DDDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       148 ~n~li~~~~----~~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      |..+-.++.    .++|++.+++..+..   |+ ..+...  .-.       ++...|+.++|.++...+-+
T Consensus       217 ~~~la~~~~~lg~~~~Al~~~~~~~~~~---p~d~~~~~~--~a~-------~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  217 WDALAAAYLQLGRYEEALEYLEKALKLN---PDDPLWLLA--YAD-------ALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             CHHHHHHHHHHT-HHHHHHHHHHHHHHS---TT-HHHHHH--HHH-------HHT-----------------
T ss_pred             HHHHHHHhcccccccccccccccccccc---ccccccccc--ccc-------cccccccccccccccccccc
Confidence            666655543    468888888866654   43 333333  111       67789999999988776543

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

Probab=98.48  E-value=1.9e-07  Score=49.36  Aligned_cols=31  Identities=13%  Similarity=0.504  Sum_probs=29.2

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 042210           53 FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDV   83 (230)
Q Consensus        53 ~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~   83 (230)
                      ++||++|++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            5899999999999999999999999999885

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.

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

Probab=98.33  E-value=4.5e-07  Score=47.86  Aligned_cols=30  Identities=33%  Similarity=0.471  Sum_probs=27.6

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhccCCC
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSCEDD  144 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~~~~  144 (230)
                      ++||+||++|++.|++++|.++|++|.+.+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            589999999999999999999999998654

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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.30  E-value=0.00017  Score=55.73  Aligned_cols=135  Identities=10%  Similarity=-0.023  Sum_probs=70.7

Q ss_pred             hHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      +|.+.++...+.  .|+. .. ..+...+.  ..|+.++|.+.+++..   +.+...+..+-..+...|++++|...|++
T Consensus        49 ~A~~~~~~~l~~--~p~~~~~~~~la~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~  124 (234)
T TIGR02521        49 VAKENLDKALEH--DPDDYLAYLALALYYQ--QLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQ  124 (234)
T ss_pred             HHHHHHHHHHHh--CcccHHHHHHHHHHHH--HcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            344445444433  2332 22 44445555  6666666666665543   22334455555566666666666666666


Q ss_pred             HHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           78 LLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        78 M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .......| ....+..+-..+...|+.  |...+....     +...+..+...|.+.|++++|.+.+++..
T Consensus       125 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  196 (234)
T TIGR02521       125 AIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQ  196 (234)
T ss_pred             HHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            55432211 223344445555555665  555555444     34455556666666666666666666543

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

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.29  E-value=4.5e-05  Score=69.43  Aligned_cols=117  Identities=9%  Similarity=-0.035  Sum_probs=60.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  ..|+.++|...++.+.  .|+ ...+..+ ..+.+.|++++|...++.+.+..-.++...+..+...+.+
T Consensus       148 ~~la~~l~--~~g~~~eA~~~~~~~~~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~  224 (656)
T PRK15174        148 ALHLRTLV--LMDKELQAISLARTQAQEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCA  224 (656)
T ss_pred             HHHHHHHH--HCCChHHHHHHHHHHHHhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHH
Confidence            44555555  6666666666665542  222 2222222 2355556666666666665443222233333344455556


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHH----HHHHHhhccC
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDM----ARGIFYMSCE  142 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~----A~~vf~~m~~  142 (230)
                      .|+.  |...+....     +...+..+-..|.+.|++++    |...|++..+
T Consensus       225 ~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~  278 (656)
T PRK15174        225 VGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQ  278 (656)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHh
Confidence            6665  555555444     45555556666666666654    5555555543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.14  E-value=2.3e-06  Score=46.25  Aligned_cols=28  Identities=32%  Similarity=0.442  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ++||++|++|++.|++++|.++|++|.+
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~   28 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLE   28 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4799999999999999999999999986

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.

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.08  E-value=4.3e-05  Score=65.45  Aligned_cols=197  Identities=14%  Similarity=0.085  Sum_probs=122.5

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-H--HHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-P--KQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~--~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      +.|.+.+.++.+  ..|+... .  .....+.  ..|+.+.|...++.+.   +.+......+...|.+.|++++|.+++
T Consensus       135 ~~A~~~l~~A~~--~~~~~~~~~~l~~a~l~l--~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l  210 (398)
T PRK10747        135 ARANQHLERAAE--LADNDQLPVEITRVRIQL--ARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDIL  210 (398)
T ss_pred             HHHHHHHHHHHh--cCCcchHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            345566666644  3466543 3  3356777  8999999999999876   345667888999999999999999999


Q ss_pred             HHHHhCCCCCCc-------ccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           76 LDLLKSDVRRDN-------YTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        76 ~~M~~~g~~p~~-------~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..+.+.+..++.       .+|..++.--.+..+.  ..++|+.+.     ++.....+...+.+.|+.++|.+++++..
T Consensus       211 ~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l  290 (398)
T PRK10747        211 PSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGL  290 (398)
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            999988755322       1333333333333333  556666654     77788888999999999999999888665


Q ss_pred             C--CChhhhHHHHHHh----hhcchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          142 E--DDDGLHELIRIKA----VDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       142 ~--~~~~t~n~li~~~----~~~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      +  ||....  ++.+.    ..+++++..++..+..   ||......  .+.      ..|.+.|++++|+..++.+.+.
T Consensus       291 ~~~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~---P~~~~l~l--~lg------rl~~~~~~~~~A~~~le~al~~  357 (398)
T PRK10747        291 KRQYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQH---GDTPLLWS--TLG------QLLMKHGEWQEASLAFRAALKQ  357 (398)
T ss_pred             hcCCCHHHH--HHHhhccCCChHHHHHHHHHHHhhC---CCCHHHHH--HHH------HHHHHCCCHHHHHHHHHHHHhc
Confidence            4  232111  11111    1234555555555443   33222111  111      0455667777777777766654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.04  E-value=0.00019  Score=55.47  Aligned_cols=176  Identities=9%  Similarity=-0.033  Sum_probs=122.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|+.++|.+.+++..   +.+...+..+-..|...|++++|...|++..+.. +.+...+..+-..+..
T Consensus        35 ~~la~~~~--~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~  111 (234)
T TIGR02521        35 VQLALGYL--EQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQ  111 (234)
T ss_pred             HHHHHHHH--HCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHH
Confidence            45567777  9999999999999865   3345678888889999999999999999876643 2234567777788888


Q ss_pred             cCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHHHHHHhhh----cchhhh
Q 042210          100 DIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGLHELIRIKAVD----DDLHEL  163 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~li~~~~~----~~~~~~  163 (230)
                      .|++  |...+....       ....+..+-..|.+.|++++|.+.|++..+  |+ ...|..+...+..    +++.+.
T Consensus       112 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  191 (234)
T TIGR02521       112 QGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAY  191 (234)
T ss_pred             cccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHH
Confidence            8988  888887775       345677778889999999999999998765  43 4455555444433    456666


Q ss_pred             HHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCcccccccc
Q 042210          164 FPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPH  213 (230)
Q Consensus       164 ~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~  213 (230)
                      +++..+..   |+ ...+..  ...       .+...|+.+++..+.+.+.
T Consensus       192 ~~~~~~~~---~~~~~~~~~--~~~-------~~~~~~~~~~a~~~~~~~~  230 (234)
T TIGR02521       192 LERYQQTY---NQTAESLWL--GIR-------IARALGDVAAAQRYGAQLQ  230 (234)
T ss_pred             HHHHHHhC---CCCHHHHHH--HHH-------HHHHHhhHHHHHHHHHHHH
Confidence            66655542   32 222222  111       4456788888777655443

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.

>TIGR00540 hemY_coli hemY protein

Probab=98.04  E-value=0.00016  Score=62.12  Aligned_cols=207  Identities=14%  Similarity=0.057  Sum_probs=131.2

Q ss_pred             hHHHHHHHHHHhcCCCCCc--H-HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPH--C-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~--~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      .|.+.+....+.  .|+..  + -.....+.  ..|+.+.|...++.+.  .| +...+..+...+.+.|++++|.+.+.
T Consensus       136 ~A~~~l~~a~~~--~p~~~l~~~~~~a~l~l--~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~  211 (409)
T TIGR00540       136 RANQHLEEAAEL--AGNDNILVEIARTRILL--AQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIID  211 (409)
T ss_pred             HHHHHHHHHHHh--CCcCchHHHHHHHHHHH--HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            455555555433  35543  3 44567777  8999999999999987  34 55678889999999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHh---h----hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRRDNYTFPFLFKGF---T----RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~---~----~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ...+.++.+....-..-..+.   .    .....  ..+.+....     +...+-.+...+...|+.++|.+++++..+
T Consensus       212 ~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~  291 (409)
T TIGR00540       212 NMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLK  291 (409)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHh
Confidence            999987653332211111111   1    11111  444555554     788899999999999999999999998865


Q ss_pred             --CChhhhH-HHHHHhh---hc---chhhhHHHHHHHhhhcCchh--h-hhhhhhcccccCCcccccccCCccCCccccc
Q 042210          143 --DDDGLHE-LIRIKAV---DD---DLHELFPEYLVQMLALPDTF--M-GEGLEVIPKSQAPREETPRVGNLEEGTPQEG  210 (230)
Q Consensus       143 --~~~~t~n-~li~~~~---~~---~~~~~~~~m~~~~~~~p~~~--t-~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~  210 (230)
                        ||...-. .++..+.   .+   ++.+.+++-.+   ..||..  . ..++..         .+.+.|++++|++.++
T Consensus       292 ~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk---~~p~~~~~~ll~sLg~---------l~~~~~~~~~A~~~le  359 (409)
T TIGR00540       292 KLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAK---NVDDKPKCCINRALGQ---------LLMKHGEFIEAADAFK  359 (409)
T ss_pred             hCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHH---hCCCChhHHHHHHHHH---------HHHHcccHHHHHHHHH
Confidence              6554210 1222111   12   34444443333   345544  2 223222         4678899999999998


Q ss_pred             cccccCCCccccccc
Q 042210          211 RPHEHSQDDMSLISN  225 (230)
Q Consensus       211 ~~~~~~~~~~~~~~n  225 (230)
                      ........||..++.
T Consensus       360 ~a~a~~~~p~~~~~~  374 (409)
T TIGR00540       360 NVAACKEQLDANDLA  374 (409)
T ss_pred             HhHHhhcCCCHHHHH
Confidence            655555567766543

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.

>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=98.04  E-value=0.00029  Score=63.82  Aligned_cols=107  Identities=12%  Similarity=-0.120  Sum_probs=55.5

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      ..|++++|...|++..   +.+...|..+-..+...|++++|...|++-...  .| +...+..+-..+.+.|+.  |..
T Consensus       377 ~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~  454 (615)
T TIGR00990       377 ELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQYKEGSIASSMA  454 (615)
T ss_pred             HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHHHHHHCCCHHHHHH
Confidence            4555555555554432   223344555555555555555555555554332  22 223344444455555555  555


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .++...     +...|+.+-..|...|++++|.+.|+.-.
T Consensus       455 ~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al  494 (615)
T TIGR00990       455 TFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAI  494 (615)
T ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            555443     45566666666666666666666666543

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

Probab=98.00  E-value=4.3e-05  Score=62.15  Aligned_cols=147  Identities=16%  Similarity=0.109  Sum_probs=94.9

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTF   90 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~   90 (230)
                      +++.. ...+..+.  +.++.+++..+++...     +++...|..+-..+.+.|++++|.+.|++-.+.  .| |....
T Consensus       108 ~~~~~l~~~l~~~~--~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~  183 (280)
T PF13429_consen  108 GDPRYLLSALQLYY--RLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDAR  183 (280)
T ss_dssp             ----------H-HH--HTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHH
T ss_pred             cccchhhHHHHHHH--HHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHH
Confidence            45566 77888888  9999999999998854     456778888889999999999999999996553  35 35568


Q ss_pred             HHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH-H----Hhh
Q 042210           91 PFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR-I----KAV  156 (230)
Q Consensus        91 ~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li-~----~~~  156 (230)
                      ..++..+...|+.  +.+++....     |...|..+-.+|...|+.++|...|++...  |+..+|-... .    .+.
T Consensus       184 ~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~  263 (280)
T PF13429_consen  184 NALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGR  263 (280)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT----
T ss_pred             HHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccccccccccccccccccccccc
Confidence            8899999999988  666666665     788899999999999999999999998765  6655554432 2    333


Q ss_pred             hcchhhhHHHHH
Q 042210          157 DDDLHELFPEYL  168 (230)
Q Consensus       157 ~~~~~~~~~~m~  168 (230)
                      .++|.++..+..
T Consensus       264 ~~~A~~~~~~~~  275 (280)
T PF13429_consen  264 KDEALRLRRQAL  275 (280)
T ss_dssp             ------------
T ss_pred             cccccccccccc
Confidence            456666655543

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=97.99  E-value=0.00047  Score=65.26  Aligned_cols=196  Identities=9%  Similarity=-0.060  Sum_probs=129.0

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLL   79 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~   79 (230)
                      +|...+......  .|+... ..+...+.  ..|++++|...|+++.  .|+...+..+-..+.+.|++++|...|++..
T Consensus       494 eAi~a~~~Al~~--~Pd~~~~L~lA~al~--~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL  569 (987)
T PRK09782        494 VALYAWLQAEQR--QPDAWQHRAVAYQAY--QVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAE  569 (987)
T ss_pred             HHHHHHHHHHHh--CCchHHHHHHHHHHH--HCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344444444333  366444 34445556  8999999999998765  3444556666677888999999999999887


Q ss_pred             hCCCCCCcc-cHHHHHHHhhhcCch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh-hhH
Q 042210           80 KSDVRRDNY-TFPFLFKGFTRDIAG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG-LHE  149 (230)
Q Consensus        80 ~~g~~p~~~-t~~~ll~~~~~~~~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~-t~n  149 (230)
                      +.+  |+.. .+..+.....+.|+.  |...+....    +...|..+-..+.+.|+.++|...|++..+  |+.. .++
T Consensus       570 ~l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~  647 (987)
T PRK09782        570 QRG--LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQA  647 (987)
T ss_pred             hcC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            654  4332 222223334445888  777777776    667788888999999999999999998876  6544 444


Q ss_pred             HHHHHhh----hcchhhhHHHHHHHhhhcCchh-hhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          150 LIRIKAV----DDDLHELFPEYLVQMLALPDTF-MGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       150 ~li~~~~----~~~~~~~~~~m~~~~~~~p~~~-t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      .+-..+.    .+++++.+++..+.   .|+.. .+..+..         ++...|++++|+..++...+..
T Consensus       648 nLG~aL~~~G~~eeAi~~l~~AL~l---~P~~~~a~~nLA~---------al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        648 ALGYALWDSGDIAQSREMLERAHKG---LPDDPALIRQLAY---------VNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHH---------HHHHCCCHHHHHHHHHHHHhcC
Confidence            4433333    34566666655544   35422 2233222         6778899999998888776653

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=97.97  E-value=0.00047  Score=62.91  Aligned_cols=142  Identities=8%  Similarity=0.050  Sum_probs=87.1

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhH----HHHHHHHHHhCCCCC-CcccHHHHHHH
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKN----GVLMYLDLLKSDVRR-DNYTFPFLFKG   96 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~----a~~~~~~M~~~g~~p-~~~t~~~ll~~   96 (230)
                      +...+.  +.|+.++|...++...   ..+...+..+-..|.+.|++++    |...|++..+.  .| +...+..+-..
T Consensus       218 l~~~l~--~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a~~~lg~~  293 (656)
T PRK15174        218 AVDTLC--AVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRIVTLYADA  293 (656)
T ss_pred             HHHHHH--HCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHHHHHHHHH
Confidence            344555  6666666666666544   2234455556666666677664    56666665542  34 34466666777


Q ss_pred             hhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH-----HHhhhcchhh
Q 042210           97 FTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR-----IKAVDDDLHE  162 (230)
Q Consensus        97 ~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li-----~~~~~~~~~~  162 (230)
                      +.+.|++  |...++...     +...+..+-..|.+.|++++|.+.|+.+..  |+...+....     .....++|.+
T Consensus       294 l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~  373 (656)
T PRK15174        294 LIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAES  373 (656)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHH
Confidence            7777777  666666655     566677777888888888888888887764  5544433221     1222356666


Q ss_pred             hHHHHHHH
Q 042210          163 LFPEYLVQ  170 (230)
Q Consensus       163 ~~~~m~~~  170 (230)
                      .+++..+.
T Consensus       374 ~l~~al~~  381 (656)
T PRK15174        374 VFEHYIQA  381 (656)
T ss_pred             HHHHHHHh
Confidence            66665544

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=97.95  E-value=7.6e-06  Score=44.00  Aligned_cols=30  Identities=27%  Similarity=0.292  Sum_probs=27.4

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhccCCC
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSCEDD  144 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~~~~  144 (230)
                      ++||++|.+|++.|+++.|.++|++|++.+
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~g   31 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQG   31 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            689999999999999999999999998644

>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=97.93  E-value=0.0011  Score=60.18  Aligned_cols=165  Identities=12%  Similarity=0.019  Sum_probs=121.5

Q ss_pred             hhHHHHHHHHHHhc-CCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLG-LLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g-~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|.+.|+...+.+ ..|+...  ..+-..+.  ..|++++|...|++..  .|+ ...|..+-..+...|++++|...|
T Consensus       311 ~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~--~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~  388 (615)
T TIGR00990       311 EEAARAFEKALDLGKLGEKEAIALNLRGTFKC--LKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDF  388 (615)
T ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            35667777777665 3454433  44556666  8999999999999875  444 457888888889999999999999


Q ss_pred             HHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-h
Q 042210           76 LDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-D  145 (230)
Q Consensus        76 ~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~  145 (230)
                      ++..+.. +-+...|..+-..+...|++  |...+....     +...+..+-..|.+.|++++|...|++..+  |+ .
T Consensus       389 ~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~  467 (615)
T TIGR00990       389 DKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAP  467 (615)
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCh
Confidence            9976642 22456788888889999999  888888776     677788888999999999999999998765  44 4


Q ss_pred             hhhHHHHHHhhh----cchhhhHHHHHH
Q 042210          146 GLHELIRIKAVD----DDLHELFPEYLV  169 (230)
Q Consensus       146 ~t~n~li~~~~~----~~~~~~~~~m~~  169 (230)
                      ..|+.+-..+..    ++|.+.|++-..
T Consensus       468 ~~~~~lg~~~~~~g~~~~A~~~~~~Al~  495 (615)
T TIGR00990       468 DVYNYYGELLLDQNKFDEAIEKFDTAIE  495 (615)
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            566665444443    455555555443

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

Probab=97.91  E-value=1.4e-05  Score=72.22  Aligned_cols=89  Identities=10%  Similarity=-0.090  Sum_probs=49.9

Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch-hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChh
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDG  146 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~  146 (230)
                      ++..|+..|+.||.+||.++|.-||..|++ |-.+|..|.      ...++++++.+....++.+.+.       +|..-
T Consensus        12 fla~~e~~gi~PnRvtyqsLiarYc~~gdieaatif~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------ep~aD   84 (1088)
T KOG4318|consen   12 FLALHEISGILPNRVTYQSLIARYCTKGDIEAATIFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------EPLAD   84 (1088)
T ss_pred             HHHHHHHhcCCCchhhHHHHHHHHcccCCCccccchhhhhcccccccchhHHHHHhcccccccccCCC-------CCchh
Confidence            445555566666666666666666666666 333555555      4555555555555555555544       45555


Q ss_pred             hhHHHHHHhhhcchhhhHHHHHH
Q 042210          147 LHELIRIKAVDDDLHELFPEYLV  169 (230)
Q Consensus       147 t~n~li~~~~~~~~~~~~~~m~~  169 (230)
                      ||+.++.+|+..+.+..|++..+
T Consensus        85 tyt~Ll~ayr~hGDli~fe~veq  107 (1088)
T KOG4318|consen   85 TYTNLLKAYRIHGDLILFEVVEQ  107 (1088)
T ss_pred             HHHHHHHHHHhccchHHHHHHHH
Confidence            56666666655555555554444

>PRK12370 invasion protein regulator; Provisional

Probab=97.78  E-value=0.0014  Score=58.59  Aligned_cols=168  Identities=8%  Similarity=-0.066  Sum_probs=110.9

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      +|...++...+.  .|+..-  ..+-..+.  ..|++++|...|++..  .|+ ...|..+-..+...|++++|...+++
T Consensus       322 ~A~~~~~~Al~l--dP~~~~a~~~lg~~~~--~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~  397 (553)
T PRK12370        322 KAKEHAIKATEL--DHNNPQALGLLGLINT--IHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINE  397 (553)
T ss_pred             HHHHHHHHHHhc--CCCCHHHHHHHHHHHH--HccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            344445444433  465443  44555667  8999999999999865  444 55677788889999999999999999


Q ss_pred             HHhCCCCCCcc-cHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh
Q 042210           78 LLKSDVRRDNY-TFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG  146 (230)
Q Consensus        78 M~~~g~~p~~~-t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~  146 (230)
                      ..+..  |+.. .+..+...+...|+.  |...+....      +...+..+-..|...|+.++|+..+.+...  |+..
T Consensus       398 Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~  475 (553)
T PRK12370        398 CLKLD--PTRAAAGITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGL  475 (553)
T ss_pred             HHhcC--CCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhH
Confidence            76642  3322 223334445567777  766666553      455677778889999999999999998765  4433


Q ss_pred             -hhHHHHHHhh--hcchhhhHHHHHHHhhhcCc
Q 042210          147 -LHELIRIKAV--DDDLHELFPEYLVQMLALPD  176 (230)
Q Consensus       147 -t~n~li~~~~--~~~~~~~~~~m~~~~~~~p~  176 (230)
                       .++.+-..+.  .+++...++++.+.....|+
T Consensus       476 ~~~~~l~~~~~~~g~~a~~~l~~ll~~~~~~~~  508 (553)
T PRK12370        476 IAVNLLYAEYCQNSERALPTIREFLESEQRIDN  508 (553)
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHHhhHhhc
Confidence             3333333333  24677777777665544443

>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=97.74  E-value=0.0001  Score=56.86  Aligned_cols=86  Identities=9%  Similarity=0.184  Sum_probs=63.4

Q ss_pred             CCCcH-HHHHHHHhh---hccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhc----------------CChhHHHH
Q 042210           18 TKPHC-PKQTRYLLL---YEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRI----------------DSHKNGVL   73 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~---~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~----------------~~~~~a~~   73 (230)
                      .+..+ ..+++.|..   .+.|+++-...-+..|.    ..|+.+|+.||+.+-+.                .+-+-|++
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            34445 666666661   14567777777777776    78888899888888663                24456888


Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG  103 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~  103 (230)
                      ++++|+..|+-||..|+..|++.+++.+..
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhccccHH
Confidence            888888888888888888888888887765

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

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.72  E-value=0.0022  Score=59.63  Aligned_cols=167  Identities=5%  Similarity=-0.115  Sum_probs=117.2

Q ss_pred             hhHHHHHHHHHHhcCC-CCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-----hhhHHHHHHHHHhcCChhHHH
Q 042210            2 HQLKQIHSQTIKLGLL-TKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-----VFLWNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~-~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-----~~~yn~li~~~~~~~~~~~a~   72 (230)
                      ++|++.|+.+.+.+-. |+ .. ..+-..|.  ..|++++|...|+++.  .|.     ...+..+..++...|++++|.
T Consensus       254 ~eA~~~~~~ll~~~~~~P~-~a~~~la~~yl--~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~  330 (765)
T PRK10049        254 KDVISEYQRLKAEGQIIPP-WAQRWVASAYL--KLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGAL  330 (765)
T ss_pred             HHHHHHHHHhhccCCCCCH-HHHHHHHHHHH--hcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHH
Confidence            4678888888777532 22 23 44566788  9999999999999875  222     234555666788999999999


Q ss_pred             HHHHHHHhCC-----------CCCCc---ccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHH
Q 042210           73 LMYLDLLKSD-----------VRRDN---YTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        73 ~~~~~M~~~g-----------~~p~~---~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~  131 (230)
                      .+++.+....           -.|+.   ..+..+...+...|+.  |.++++.+.     +...+..+...+.+.|+++
T Consensus       331 ~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~  410 (765)
T PRK10049        331 TVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPR  410 (765)
T ss_pred             HHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHH
Confidence            9999987642           12332   1344566788888998  888888877     8889999999999999999


Q ss_pred             HHHHHHhhccC--CChhh-hHHHHHHh----hhcchhhhHHHHHHHh
Q 042210          132 MARGIFYMSCE--DDDGL-HELIRIKA----VDDDLHELFPEYLVQM  171 (230)
Q Consensus       132 ~A~~vf~~m~~--~~~~t-~n~li~~~----~~~~~~~~~~~m~~~~  171 (230)
                      +|++.+++...  ||... +-......    ..++|..+++++.+..
T Consensus       411 ~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~  457 (765)
T PRK10049        411 AAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVARE  457 (765)
T ss_pred             HHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            99999998876  66432 22222222    2345666666665543

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=97.66  E-value=0.0012  Score=56.15  Aligned_cols=117  Identities=11%  Similarity=0.044  Sum_probs=91.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      ..|+..+.  ..++++.|.++|+++.+.+...+-.+...+...++-.+|.+++.+..+. .+-|......-.+.|.+.++
T Consensus       173 ~~Ll~~l~--~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~~  249 (395)
T PF09295_consen  173 DTLLKYLS--LTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKKK  249 (395)
T ss_pred             HHHHHHHh--hcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcCC
Confidence            44555666  7789999999999998666666667888888888889999999887643 22233344444556778887


Q ss_pred             h--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          103 G--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       103 ~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .  |..+.+...     +-.+|..|...|.+.|++++|...++.++-
T Consensus       250 ~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  250 YELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             HHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            7  888888887     788999999999999999999999999874

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

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

Probab=97.66  E-value=0.00027  Score=48.81  Aligned_cols=76  Identities=17%  Similarity=0.358  Sum_probs=62.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCChhhHHHHHHHHHhcC--------ChhHHHHHHHHHHhCCCCCCccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSVFLWNTMIKGYSRID--------SHKNGVLMYLDLLKSDVRRDNYT   89 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~~~yn~li~~~~~~~--------~~~~a~~~~~~M~~~g~~p~~~t   89 (230)
                      ..-|.-+.  ..+++.....+|+.++     .|++.+||.++.+.+++.        +..+.+.+|++|...+++|+..|
T Consensus        29 i~~I~~~~--~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   29 IDNINSCF--ENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHH--hhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            34455566  6799999999998876     688999999999998853        35578899999999999999999


Q ss_pred             HHHHHHHhhhc
Q 042210           90 FPFLFKGFTRD  100 (230)
Q Consensus        90 ~~~ll~~~~~~  100 (230)
                      |+.++..+.+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            99999887653

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 [, , ].

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.65  E-value=0.00091  Score=58.58  Aligned_cols=203  Identities=11%  Similarity=0.048  Sum_probs=133.0

Q ss_pred             ChhHHHHHHHHHHh-----c-CCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC-------CCC----hhhHHHHHHH
Q 042210            1 MHQLKQIHSQTIKL-----G-LLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT-------QPS----VFLWNTMIKG   61 (230)
Q Consensus         1 l~~a~~~~~~m~~~-----g-~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~~----~~~yn~li~~   61 (230)
                      +++|..++++..+.     | -.|.+.+  +.+-..|.  ..+++++|..+|+++-       -++    ..+++.|-..
T Consensus       215 ~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~--~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~l  292 (508)
T KOG1840|consen  215 LEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYR--SLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVL  292 (508)
T ss_pred             HHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHH--HhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            46777777776555     3 2344444  55667788  9999999999998874       122    2467777778


Q ss_pred             HHhcCChhHHHHHHHHHHh-----CCCC-CCcc-cHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHH
Q 042210           62 YSRIDSHKNGVLMYLDLLK-----SDVR-RDNY-TFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNA  119 (230)
Q Consensus        62 ~~~~~~~~~a~~~~~~M~~-----~g~~-p~~~-t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~  119 (230)
                      |.+.|++++|...+++-.+     .|.. |... -++.+...|+..+.+  +..++....             -.-+++.
T Consensus       293 y~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~n  372 (508)
T KOG1840|consen  293 YYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYAN  372 (508)
T ss_pred             HhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHH
Confidence            9999999999988877321     2322 2222 344555666666666  444444333             4577899


Q ss_pred             HHHHHHhcCCHHHHHHHHhhccC-------CCh----hhhHHHHHHhh----hcchhhhHHHHHHHhh-hcCc----hhh
Q 042210          120 LISTYCLCGEVDMARGIFYMSCE-------DDD----GLHELIRIKAV----DDDLHELFPEYLVQML-ALPD----TFM  179 (230)
Q Consensus       120 li~~y~~~g~~~~A~~vf~~m~~-------~~~----~t~n~li~~~~----~~~~~~~~~~m~~~~~-~~p~----~~t  179 (230)
                      |=..|-+.|++++|+++|.+...       ...    ...|-|-..|-    ..++.++|.+-..-+. +-||    .++
T Consensus       373 l~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~  452 (508)
T KOG1840|consen  373 LAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYT  452 (508)
T ss_pred             HHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHH
Confidence            99999999999999999997764       111    12333322332    3467777777655442 3344    344


Q ss_pred             hhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          180 GEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       180 ~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      +..  +..       .|.+.|++|.|.++.+.+.+
T Consensus       453 ~~n--L~~-------~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  453 YLN--LAA-------LYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHH--HHH-------HHHHcccHHHHHHHHHHHHH
Confidence            444  322       89999999999999888764

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.63  E-value=0.0014  Score=63.58  Aligned_cols=136  Identities=13%  Similarity=-0.006  Sum_probs=71.5

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.+++..+.  .|+.. . ..+-..|.  +.|++++|...+++..  .| +...+-.+-..+...++.++|...++
T Consensus       478 ~eA~~~~~~Al~~--~P~~~~~~~~LA~~~~--~~G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~  553 (1157)
T PRK11447        478 AQAAELQRQRLAL--DPGSVWLTYRLAQDLR--QAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLN  553 (1157)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            3455666665544  35433 3 56667777  8888888888888763  23 22222222223444555555555555


Q ss_pred             HHHhCC---------------------------------------CCCCcccHHHHHHHhhhcCch--hhHHHhhhh---
Q 042210           77 DLLKSD---------------------------------------VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM---  112 (230)
Q Consensus        77 ~M~~~g---------------------------------------~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~---  112 (230)
                      .+....                                       .+++...+..+-..+.+.|+.  |...++...   
T Consensus       554 ~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~  633 (1157)
T PRK11447        554 TLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE  633 (1157)
T ss_pred             hCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            432211                                       112223334444445555555  555554444   


Q ss_pred             --hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          113 --RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       113 --~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                        +...+..+...|...|+.++|.+.++...
T Consensus       634 P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll  664 (1157)
T PRK11447        634 PGNADARLGLIEVDIAQGDLAAARAQLAKLP  664 (1157)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence              45555555666666666666666666544

>PRK12370 invasion protein regulator; Provisional

Probab=97.63  E-value=0.0029  Score=56.64  Aligned_cols=163  Identities=11%  Similarity=-0.009  Sum_probs=112.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCChh-hHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVF-LWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~-~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...+++..+..  |+...  ..+-..+.  ..|++++|...++...  .|+.. .+..+...+...|++++|...++
T Consensus       355 ~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~--~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~  430 (553)
T PRK12370        355 IVGSLLFKQANLLS--PISADIKYYYGWNLF--MAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGD  430 (553)
T ss_pred             HHHHHHHHHHHHhC--CCCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHH
Confidence            46777787776664  66544  55667777  9999999999999976  45432 33344445666899999999999


Q ss_pred             HHHhCCCCCCcc-cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----C
Q 042210           77 DLLKSDVRRDNY-TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE-----D  143 (230)
Q Consensus        77 ~M~~~g~~p~~~-t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----~  143 (230)
                      +..+.. .|+.. .+..+-.++...|+.  |.+.+..+.     +....+.+-..|.+.|  ++|...++.+.+     +
T Consensus       431 ~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~  507 (553)
T PRK12370        431 ELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRID  507 (553)
T ss_pred             HHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhh
Confidence            976543 34333 355666777889998  888887766     4555666777778777  588887777654     4


Q ss_pred             ChhhhHHHHHHhh-hcchhhhHHHHHHHh
Q 042210          144 DDGLHELIRIKAV-DDDLHELFPEYLVQM  171 (230)
Q Consensus       144 ~~~t~n~li~~~~-~~~~~~~~~~m~~~~  171 (230)
                      +...+-.++.+.. ..+...+++++.+++
T Consensus       508 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  536 (553)
T PRK12370        508 NNPGLLPLVLVAHGEAIAEKMWNKFKNED  536 (553)
T ss_pred             cCchHHHHHHHHHhhhHHHHHHHHhhccc
Confidence            4455566665554 456666677777666

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.60  E-value=0.0036  Score=58.25  Aligned_cols=135  Identities=7%  Similarity=-0.043  Sum_probs=99.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+++.....  ..|... . ..+-..+.  +.|++++|..+|++..   +.+...+..+...+...|++++|...++
T Consensus        32 ~~A~~~~~~~~~--~~~~~a~~~~~lA~~~~--~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~  107 (765)
T PRK10049         32 AEVITVYNRYRV--HMQLPARGYAAVAVAYR--NLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAK  107 (765)
T ss_pred             HHHHHHHHHHHh--hCCCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            456666766655  234443 3 66667777  8999999999999853   4445667788888888999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +..+.  .|+...+..+-..+...|+.  |...++...     +...+..+...+.+.|..++|.+.++....
T Consensus       108 ~~l~~--~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~  178 (765)
T PRK10049        108 QLVSG--APDKANLLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANL  178 (765)
T ss_pred             HHHHh--CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCC
Confidence            87665  33322277777788888888  777777776     666667778888888999999988887665

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

Probab=97.53  E-value=0.00096  Score=57.17  Aligned_cols=108  Identities=13%  Similarity=0.125  Sum_probs=87.7

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcC-CCC-----hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT-QPS-----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTF   90 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-~~~-----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~   90 (230)
                      .+... ..+++.+.  ..-+++.+..++...+ .|+     ..|.+++|..|...|..+.++.+++.=...|+=||..||
T Consensus        64 vS~~dld~fvn~~~--~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   64 VSSLDLDIFVNNVE--SKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CcHHHHHHHHhhcC--CHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            34444 77778777  7778888999888876 332     235679999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhc
Q 042210           91 PFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLC  127 (230)
Q Consensus        91 ~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~  127 (230)
                      +.||+.+.+.|++  |.++...|.      +..|+..-+.++.+.
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            9999999999999  777777777      666666666666555

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 [].

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=97.48  E-value=0.008  Score=57.18  Aligned_cols=134  Identities=7%  Similarity=-0.096  Sum_probs=82.2

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCC--CCh-hhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQ--PSV-FLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~--~~~-~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +|...++.+...  .|+... ..+...+.  +.|++++|...++....  |+. ..+..+.....+.|++++|...|++-
T Consensus       527 eAi~~~rka~~~--~p~~~a~~~la~all--~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~A  602 (987)
T PRK09782        527 TALAAWQKISLH--DMSNEDLLAAANTAQ--AAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRS  602 (987)
T ss_pred             HHHHHHHHHhcc--CCCcHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            455555554322  333333 44555666  77888888888777652  221 12222222333347888888887775


Q ss_pred             HhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           79 LKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        79 ~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .+.  .|+...|..+-..+.+.|+.  |...+....     +...++.+-..+...|+.++|...|++..+
T Consensus       603 L~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~  671 (987)
T PRK09782        603 LNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHK  671 (987)
T ss_pred             HHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            542  35556677777777777777  666666665     666677777777777788887777776654

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

Probab=97.42  E-value=0.0012  Score=56.53  Aligned_cols=79  Identities=13%  Similarity=0.154  Sum_probs=72.1

Q ss_pred             CcH-HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHH
Q 042210           20 PHC-PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLF   94 (230)
Q Consensus        20 ~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll   94 (230)
                      ..+ .++++.|.  +.|..+.+..+++.=.    -||..+||.||+.+.+.|++..|.++..+|...+...+..|+...+
T Consensus       103 ~~t~ha~vR~~l--~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l  180 (429)
T PF10037_consen  103 PSTHHALVRQCL--ELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALAL  180 (429)
T ss_pred             CccHHHHHHHHH--hcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHH
Confidence            446 99999999  9999999999997754    6999999999999999999999999999998888888889999999


Q ss_pred             HHhhhc
Q 042210           95 KGFTRD  100 (230)
Q Consensus        95 ~~~~~~  100 (230)
                      .+|.+.
T Consensus       181 ~~~~~~  186 (429)
T PF10037_consen  181 YSCYKY  186 (429)
T ss_pred             HHHHHh
Confidence            999887

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 [].

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

Probab=97.41  E-value=0.0024  Score=56.41  Aligned_cols=199  Identities=9%  Similarity=0.008  Sum_probs=118.2

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--C------------------------------
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--Q------------------------------   49 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~------------------------------   49 (230)
                      +|..+|+.. .....-+..+ ..+=.+|.  ..++.++|+++|+..+  .                              
T Consensus       337 ~A~~~~~kl-p~h~~nt~wvl~q~GrayF--El~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~L  413 (638)
T KOG1126|consen  337 EALNLFEKL-PSHHYNTGWVLSQLGRAYF--ELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDL  413 (638)
T ss_pred             HHHHHHHhh-HHhcCCchHHHHHHHHHHH--HHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHH
Confidence            455566552 2222223345 77778888  8889999999997764  1                              


Q ss_pred             ----C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhC------------------------------CCCCCcccHHHHH
Q 042210           50 ----P-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS------------------------------DVRRDNYTFPFLF   94 (230)
Q Consensus        50 ----~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~------------------------------g~~p~~~t~~~ll   94 (230)
                          | ...+|.++=++|+--++.+.|++.|++-.+-                              .+..|...|+++.
T Consensus       414 i~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwY  493 (638)
T KOG1126|consen  414 IDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWY  493 (638)
T ss_pred             HhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHH
Confidence                1 3457888888888889999999998875532                              2223333333321


Q ss_pred             H---HhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhh-h---HHHHHHhhh
Q 042210           95 K---GFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGL-H---ELIRIKAVD  157 (230)
Q Consensus        95 ~---~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t-~---n~li~~~~~  157 (230)
                      -   .|.+.++.  |+--|....     +.+.-..+-..|-++|+.|+|.+++++-..   .|+.+ |   ..+......
T Consensus       494 GlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~  573 (638)
T KOG1126|consen  494 GLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRY  573 (638)
T ss_pred             hhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcch
Confidence            1   23333333  333333333     555555555666677777777777776543   23322 2   223444556


Q ss_pred             cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          158 DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       158 ~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      ++|+..+++++.   +.|+..+...|..-        .|-+.|+.+.|..=|..+...
T Consensus       574 ~eal~~LEeLk~---~vP~es~v~~llgk--------i~k~~~~~~~Al~~f~~A~~l  620 (638)
T KOG1126|consen  574 VEALQELEELKE---LVPQESSVFALLGK--------IYKRLGNTDLALLHFSWALDL  620 (638)
T ss_pred             HHHHHHHHHHHH---hCcchHHHHHHHHH--------HHHHHccchHHHHhhHHHhcC
Confidence            778888887655   45776665553222        566778887777666655554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.41  E-value=0.0054  Score=59.70  Aligned_cols=114  Identities=9%  Similarity=-0.006  Sum_probs=83.7

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCC-CCCcccHHHH---------
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDV-RRDNYTFPFL---------   93 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~-~p~~~t~~~l---------   93 (230)
                      ..+.  ..|++++|...|++..  .| |...+..+-..|.+.|++++|...|++..+..= .++...|..+         
T Consensus       277 ~~~~--~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        277 LAAV--DSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHH--HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            4455  8899999999998865  34 667788888899999999999999998765321 1121122222         


Q ss_pred             ---HHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           94 ---FKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        94 ---l~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         -..+.+.|++  |...+....     +...+..+-..|...|++++|.+.|++..+
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~  413 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALR  413 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence               2345677787  888888776     666777788899999999999999988765

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.40  E-value=0.028  Score=48.19  Aligned_cols=164  Identities=13%  Similarity=-0.030  Sum_probs=116.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCcHH--------HHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHCP--------KQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKN   70 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~~--------~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~   70 (230)
                      ++|..++..+.+.+..++....        .++..-.  +..+.+...++|+..+   +.+....-.+...+...|+.++
T Consensus       204 ~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~--~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~  281 (398)
T PRK10747        204 SSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAM--ADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDT  281 (398)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH--HhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHH
Confidence            4577788888888765433212        2233333  4556778888888886   4567788889999999999999


Q ss_pred             HHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-
Q 042210           71 GVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE-  142 (230)
Q Consensus        71 a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-  142 (230)
                      |..++++-.+.  .||.  --.++.+....++.  +.+..+...     |...+.++=..+.+.|++++|++.|+...+ 
T Consensus       282 A~~~L~~~l~~--~~~~--~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~  357 (398)
T PRK10747        282 AQQIILDGLKR--QYDE--RLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ  357 (398)
T ss_pred             HHHHHHHHHhc--CCCH--HHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            99999887663  4443  22345555555776  444444443     888889999999999999999999998875 


Q ss_pred             -CChhhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          143 -DDDGLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       143 -~~~~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                       |+..+|-.+-..+...+..+...++.+++
T Consensus       358 ~P~~~~~~~La~~~~~~g~~~~A~~~~~~~  387 (398)
T PRK10747        358 RPDAYDYAWLADALDRLHKPEEAAAMRRDG  387 (398)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence             88888887777766655555556666665

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

Probab=97.38  E-value=0.00041  Score=56.79  Aligned_cols=181  Identities=13%  Similarity=0.044  Sum_probs=106.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccH-HHHHHHhhhcC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTF-PFLFKGFTRDI  101 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~-~~ll~~~~~~~  101 (230)
                      .-+.+++.  ..|+.+.+..-...-..|.......+-..+...++-+.+..-+++....+..++..++ ...-..+...|
T Consensus        39 ~~~~Rs~i--Alg~~~~vl~ei~~~~~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~  116 (290)
T PF04733_consen   39 FYQYRSYI--ALGQYDSVLSEIKKSSSPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEG  116 (290)
T ss_dssp             HHHHHHHH--HTT-HHHHHHHS-TTSSCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHH--HcCChhHHHHHhccCCChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcC
Confidence            34557777  8888776555544444666655544443333334444455544444333333222222 22223455567


Q ss_pred             ch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhH------HHHHHh-hhcchhhhHHHHHHH
Q 042210          102 AG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHE------LIRIKA-VDDDLHELFPEYLVQ  170 (230)
Q Consensus       102 ~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n------~li~~~-~~~~~~~~~~~m~~~  170 (230)
                      ++  |.++...-.+.......|..|.+.+++|.|.+.++.|++  .|....+      .+..|. ...+|+-.|+++.+.
T Consensus       117 ~~~~AL~~l~~~~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~  196 (290)
T PF04733_consen  117 DYEEALKLLHKGGSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK  196 (290)
T ss_dssp             HHHHHHCCCTTTTCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHccCcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc
Confidence            77  666666656777888889999999999999999999987  4544322      222222 246899999997655


Q ss_pred             hhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          171 MLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       171 ~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      -  .++..+.+++.+         ++...|++++|+.++....+..
T Consensus       197 ~--~~t~~~lng~A~---------~~l~~~~~~eAe~~L~~al~~~  231 (290)
T PF04733_consen  197 F--GSTPKLLNGLAV---------CHLQLGHYEEAEELLEEALEKD  231 (290)
T ss_dssp             S----SHHHHHHHHH---------HHHHCT-HHHHHHHHHHHCCC-
T ss_pred             c--CCCHHHHHHHHH---------HHHHhCCHHHHHHHHHHHHHhc
Confidence            3  355556666444         6778899999999887766543

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.37  E-value=0.023  Score=53.08  Aligned_cols=142  Identities=7%  Similarity=-0.057  Sum_probs=112.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCC---------CChhhHHHHHHHHHhcCChhHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQ---------PSVFLWNTMIKGYSRIDSHKNG   71 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~---------~~~~~yn~li~~~~~~~~~~~a   71 (230)
                      ..+.+.++.+...|.+....+ -.+-++|.  ..+++++|..++...-.         ++......|.-+|...+++++|
T Consensus       309 ~~vi~~y~~l~~~~~~~P~y~~~a~adayl--~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A  386 (822)
T PRK14574        309 ADLIKEYEAMEAEGYKMPDYARRWAASAYI--DRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKA  386 (822)
T ss_pred             HHHHHHHHHhhhcCCCCCHHHHHHHHHHHH--hcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHH
Confidence            467788888888887766668 99999999  99999999999998742         1233357889999999999999


Q ss_pred             HHHHHHHHhCCC-----------CC--Cccc-HHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCH
Q 042210           72 VLMYLDLLKSDV-----------RR--DNYT-FPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEV  130 (230)
Q Consensus        72 ~~~~~~M~~~g~-----------~p--~~~t-~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~  130 (230)
                      ..+++.+.+..-           .|  |... +..+...+.-.|+.  |++.++.+.     |..+...+-+.+..-|.+
T Consensus       387 ~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p  466 (822)
T PRK14574        387 YQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLP  466 (822)
T ss_pred             HHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCH
Confidence            999999987210           12  2222 23456777888998  999999888     999999999999999999


Q ss_pred             HHHHHHHhhccC--CCh
Q 042210          131 DMARGIFYMSCE--DDD  145 (230)
Q Consensus       131 ~~A~~vf~~m~~--~~~  145 (230)
                      ..|+..++....  |+.
T Consensus       467 ~~A~~~~k~a~~l~P~~  483 (822)
T PRK14574        467 RKAEQELKAVESLAPRS  483 (822)
T ss_pred             HHHHHHHHHHhhhCCcc
Confidence            999999976553  554

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

Probab=97.31  E-value=0.0038  Score=51.16  Aligned_cols=105  Identities=13%  Similarity=0.053  Sum_probs=82.0

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch--hhH
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~  106 (230)
                      ..|++++|.++++.-  .+.......+..|.+.++++.|.+.++.|++.+  .| .+..-+..++..    ...+  |..
T Consensus       114 ~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD-~~l~qLa~awv~l~~g~e~~~~A~y  188 (290)
T PF04733_consen  114 HEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQID--ED-SILTQLAEAWVNLATGGEKYQDAFY  188 (290)
T ss_dssp             CCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CC-HHHHHHHHHHHHHHHTTTCCCHHHH
T ss_pred             HcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--Cc-HHHHHHHHHHHHHHhCchhHHHHHH
Confidence            889999999998876  455666778899999999999999999998753  33 355555555443    2245  999


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +|+++.     ++.+.|.+..++...|++++|.+++.+.-+
T Consensus       189 ~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~  229 (290)
T PF04733_consen  189 IFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALE  229 (290)
T ss_dssp             HHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCC
T ss_pred             HHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            999987     778888888899999999999999998765

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.

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

Probab=97.24  E-value=0.0066  Score=49.65  Aligned_cols=203  Identities=12%  Similarity=0.136  Sum_probs=128.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC-CCChhh------HHHHHHHHHhcCChhHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT-QPSVFL------WNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~-~~~~~~------yn~li~~~~~~~~~~~a~   72 (230)
                      ++|..+|-+|.+.  .|.++-  -+|=+.|-  +.|.+|+|..+...+. .||...      ---|-.-|-..|-++.|.
T Consensus        52 dKAvdlF~e~l~~--d~~t~e~~ltLGnLfR--sRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE  127 (389)
T COG2956          52 DKAVDLFLEMLQE--DPETFEAHLTLGNLFR--SRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAE  127 (389)
T ss_pred             chHHHHHHHHHhc--CchhhHHHHHHHHHHH--hcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            4678888888773  344433  34446666  8889999999988866 666432      223444556678899999


Q ss_pred             HHHHHHHhCC-CCCCcccHHHHHHHhhhcCch--hhHHHhhhh--hHhHHHH--------HHHHHHhcCCHHHHHHHHhh
Q 042210           73 LMYLDLLKSD-VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM--RVFVQNA--------LISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        73 ~~~~~M~~~g-~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~--~~~~~~~--------li~~y~~~g~~~~A~~vf~~  139 (230)
                      .+|..+...| +.++  ..--|+..|-...+|  |..+-..+.  +.-.|+.        |-..+.-..+++.|+.++.+
T Consensus       128 ~~f~~L~de~efa~~--AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~k  205 (389)
T COG2956         128 DIFNQLVDEGEFAEG--ALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKK  205 (389)
T ss_pred             HHHHHHhcchhhhHH--HHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            9999887754 4444  356688888888888  655555444  2333333        33334456678888888887


Q ss_pred             ccC--CChhhhHHHHHH-----hhhcchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          140 SCE--DDDGLHELIRIK-----AVDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       140 m~~--~~~~t~n~li~~-----~~~~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                      --+  |..+--++++.-     +...+|.+.++...++.   |+ +....+..+      .++|.+.|..+++...+.++
T Consensus       206 Alqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn---~~-yl~evl~~L------~~~Y~~lg~~~~~~~fL~~~  275 (389)
T COG2956         206 ALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQN---PE-YLSEVLEML------YECYAQLGKPAEGLNFLRRA  275 (389)
T ss_pred             HHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhC---hH-HHHHHHHHH------HHHHHHhCCHHHHHHHHHHH
Confidence            654  555555555432     22346777777776655   32 222222222      23899999999998888877


Q ss_pred             cccCCCcc
Q 042210          213 HEHSQDDM  220 (230)
Q Consensus       213 ~~~~~~~~  220 (230)
                      .+....++
T Consensus       276 ~~~~~g~~  283 (389)
T COG2956         276 METNTGAD  283 (389)
T ss_pred             HHccCCcc
Confidence            77654444

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.07  E-value=0.025  Score=52.92  Aligned_cols=132  Identities=10%  Similarity=-0.037  Sum_probs=99.1

Q ss_pred             ccCChHHHHHHHHhcC--CCCh--hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHH---HHHhhhcCch--
Q 042210           33 EKGDLKYECKVFRKIT--QPSV--FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFL---FKGFTRDIAG--  103 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~~--~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~l---l~~~~~~~~~--  103 (230)
                      +.|+++.|...|++..  .|+.  ..+ .++..+...|+.++|...+++-.    .|+...+..+   ...+...|++  
T Consensus        46 r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~----~p~n~~~~~llalA~ly~~~gdyd~  120 (822)
T PRK14574         46 RAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQ----SSMNISSRGLASAARAYRNEKRWDQ  120 (822)
T ss_pred             hCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhc----cCCCCCHHHHHHHHHHHHHcCCHHH
Confidence            9999999999999887  4553  244 88888889999999999998876    4544434333   3467777888  


Q ss_pred             hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHHHhhh------cchhhhHHHHHHH
Q 042210          104 SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRIKAVD------DDLHELFPEYLVQ  170 (230)
Q Consensus       104 a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~~~~~------~~~~~~~~~m~~~  170 (230)
                      |.++++.+.     +...+..++..|...++.++|.+.+++...  |+...+  +..++..      .++++.++++.+.
T Consensus       121 Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~--l~layL~~~~~~~~~AL~~~ekll~~  198 (822)
T PRK14574        121 ALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNY--MTLSYLNRATDRNYDALQASSEAVRL  198 (822)
T ss_pred             HHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHH--HHHHHHHHhcchHHHHHHHHHHHHHh
Confidence            999999888     677788889999999999999999999876  554444  3223322      2577777777776


Q ss_pred             h
Q 042210          171 M  171 (230)
Q Consensus       171 ~  171 (230)
                      .
T Consensus       199 ~  199 (822)
T PRK14574        199 A  199 (822)
T ss_pred             C
Confidence            5

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

Probab=97.04  E-value=0.0038  Score=55.18  Aligned_cols=174  Identities=9%  Similarity=-0.037  Sum_probs=120.6

Q ss_pred             ChHHHHHHHHhcC--CCChh-hHHHHHHHHHhcCChhHHHHHHHHHHhCC-C-CCCcccHHHHHHHhhhcCch---hhHH
Q 042210           36 DLKYECKVFRKIT--QPSVF-LWNTMIKGYSRIDSHKNGVLMYLDLLKSD-V-RRDNYTFPFLFKGFTRDIAG---SLEK  107 (230)
Q Consensus        36 ~~~~a~~~~~~m~--~~~~~-~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~-~p~~~t~~~ll~~~~~~~~~---a~~~  107 (230)
                      +..+|...|...+  .+|+. +-.-+=.+|-..+++++|.++|+..++.. . .-+...|++.+--+-+.-.+   +..+
T Consensus       334 ~~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~L  413 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDL  413 (638)
T ss_pred             HHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHH
Confidence            4667888888765  45554 12233456777899999999999987742 2 24677899999888776555   7777


Q ss_pred             Hhhhh-hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhhcchhhhHHHHHHHhhhcCchhhhhhh
Q 042210          108 SCIVM-RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVDDDLHELFPEYLVQMLALPDTFMGEGL  183 (230)
Q Consensus       108 ~~~~~-~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~~~~~~~~~~m~~~~~~~p~~~t~~~l  183 (230)
                      .+..+ .+.+|.++=+.|+--++.+.|.+-|++-.+  | ...+|+.+-.=+...+.++....-++.. +..|...|++ 
T Consensus       414 i~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~A-l~~~~rhYnA-  491 (638)
T KOG1126|consen  414 IDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKA-LGVDPRHYNA-  491 (638)
T ss_pred             HhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhh-hcCCchhhHH-
Confidence            77777 899999999999999999999999998877  3 4566665533333344445555555555 5555555665 


Q ss_pred             hhcccccCCcccccccCCccCCccccccccccC
Q 042210          184 EVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       184 ~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                       ++..-    ..|-+.+.+|.|+--|+.+.+-+
T Consensus       492 -wYGlG----~vy~Kqek~e~Ae~~fqkA~~IN  519 (638)
T KOG1126|consen  492 -WYGLG----TVYLKQEKLEFAEFHFQKAVEIN  519 (638)
T ss_pred             -HHhhh----hheeccchhhHHHHHHHhhhcCC
Confidence             22211    15668888888887777666654

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.96  E-value=0.043  Score=45.12  Aligned_cols=175  Identities=8%  Similarity=-0.085  Sum_probs=109.8

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhcCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRDIA  102 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~~~  102 (230)
                      ..|.  +.|+.++|...|++..   +.+...|+.+=..+...|++++|...|+...+  +.|+ ..+|..+-.++...|+
T Consensus        72 ~~~~--~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~--l~P~~~~a~~~lg~~l~~~g~  147 (296)
T PRK11189         72 VLYD--SLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLE--LDPTYNYAYLNRGIALYYGGR  147 (296)
T ss_pred             HHHH--HCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCC
Confidence            4556  8899999999998865   44567899998999999999999999998765  3453 4466666677778888


Q ss_pred             h--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHHHHHhhhc-chhhhHHHHHHHh
Q 042210          103 G--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELIRIKAVDD-DLHELFPEYLVQM  171 (230)
Q Consensus       103 ~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~li~~~~~~-~~~~~~~~m~~~~  171 (230)
                      .  |.+.++...     +.. .......+...++.++|...|++...   |+...|. +...+..+ ...+.+..+.+..
T Consensus       148 ~~eA~~~~~~al~~~P~~~~-~~~~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~~-~~~~~lg~~~~~~~~~~~~~~~  225 (296)
T PRK11189        148 YELAQDDLLAFYQDDPNDPY-RALWLYLAESKLDPKQAKENLKQRYEKLDKEQWGWN-IVEFYLGKISEETLMERLKAGA  225 (296)
T ss_pred             HHHHHHHHHHHHHhCCCCHH-HHHHHHHHHccCCHHHHHHHHHHHHhhCCccccHHH-HHHHHccCCCHHHHHHHHHhcC
Confidence            8  777777665     321 12222234456789999999965433   3333332 22211111 1123444444322


Q ss_pred             h----hcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          172 L----ALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       172 ~----~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      .    ..|+ ...|..+..         .+.+.|+.++|...+....+.+
T Consensus       226 ~~~~~l~~~~~ea~~~Lg~---------~~~~~g~~~~A~~~~~~Al~~~  266 (296)
T PRK11189        226 TDNTELAERLCETYFYLAK---------YYLSLGDLDEAAALFKLALANN  266 (296)
T ss_pred             CCcHHHHHHHHHHHHHHHH---------HHHHCCCHHHHHHHHHHHHHhC
Confidence            1    1111 112333223         6778999999999999888765

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.86  E-value=0.028  Score=41.02  Aligned_cols=93  Identities=10%  Similarity=-0.099  Sum_probs=59.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCC
Q 042210           57 TMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGE  129 (230)
Q Consensus        57 ~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~  129 (230)
                      ..-..+.+.|++++|...|+...... +.+...|..+-.++.+.|++  |...++...     +...+..+-..|.+.|+
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~g~  107 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMGE  107 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCC
Confidence            34445555666666666666654332 11444555555566666666  555555555     67778888888889999


Q ss_pred             HHHHHHHHhhccC--CChhhhHH
Q 042210          130 VDMARGIFYMSCE--DDDGLHEL  150 (230)
Q Consensus       130 ~~~A~~vf~~m~~--~~~~t~n~  150 (230)
                      .++|...|+.-.+  |+..-|..
T Consensus       108 ~~eAi~~~~~Al~~~p~~~~~~~  130 (144)
T PRK15359        108 PGLAREAFQTAIKMSYADASWSE  130 (144)
T ss_pred             HHHHHHHHHHHHHhCCCChHHHH
Confidence            9999999988754  65554443

>TIGR00540 hemY_coli hemY protein

Probab=96.83  E-value=0.25  Score=42.53  Aligned_cols=163  Identities=14%  Similarity=0.072  Sum_probs=101.5

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHH---hh--hccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYL---LL--YEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~---~~--~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~   72 (230)
                      +.|.+++..+.+.+..++... ..-...+   ..  ......+...+.++..+   +.+...+-.+...+...|+.++|.
T Consensus       204 ~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~  283 (409)
T TIGR00540       204 QALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQ  283 (409)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHH
Confidence            456788888888875544322 2222222   10  02223445556666665   247788889999999999999999


Q ss_pred             HHHHHHHhCCCCCCcccH-HHHHHHhhh--cCch--hhHHHhhhh-----hH--hHHHHHHHHHHhcCCHHHHHHHHh--
Q 042210           73 LMYLDLLKSDVRRDNYTF-PFLFKGFTR--DIAG--SLEKSCIVM-----RV--FVQNALISTYCLCGEVDMARGIFY--  138 (230)
Q Consensus        73 ~~~~~M~~~g~~p~~~t~-~~ll~~~~~--~~~~--a~~~~~~~~-----~~--~~~~~li~~y~~~g~~~~A~~vf~--  138 (230)
                      .++++..+..  ||.... -.++..+..  .++.  +.+.++...     |.  ....++=..+.+.|++++|++.|+  
T Consensus       284 ~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a  361 (409)
T TIGR00540       284 EIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNV  361 (409)
T ss_pred             HHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHh
Confidence            9999976642  333211 013333333  3444  444443333     66  677788889999999999999999  


Q ss_pred             hcc--CCChhhhHHHHHHhhh----cchhhhHHH
Q 042210          139 MSC--EDDDGLHELIRIKAVD----DDLHELFPE  166 (230)
Q Consensus       139 ~m~--~~~~~t~n~li~~~~~----~~~~~~~~~  166 (230)
                      ...  .||...+..+...+..    +++.+.+++
T Consensus       362 ~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~  395 (409)
T TIGR00540       362 AACKEQLDANDLAMAADAFDQAGDKAEAAAMRQD  395 (409)
T ss_pred             HHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            342  4888887777655554    345455544

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.

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=96.77  E-value=0.024  Score=46.24  Aligned_cols=39  Identities=8%  Similarity=-0.058  Sum_probs=19.1

Q ss_pred             hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          104 SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       104 a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      |..||+...     +...|...|+.+.+.++.+.|+.||++...
T Consensus        55 A~~Ife~glk~f~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~   98 (280)
T PF05843_consen   55 ARKIFERGLKKFPSDPDFWLEYLDFLIKLNDINNARALFERAIS   98 (280)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence            444444443     445555555555555555555555555443

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.

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

Probab=96.69  E-value=0.02  Score=54.96  Aligned_cols=120  Identities=8%  Similarity=0.032  Sum_probs=76.8

Q ss_pred             CCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--------CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC
Q 042210           17 LTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD   86 (230)
Q Consensus        17 ~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   86 (230)
                      .|+..+  -..|....  ..+++++|++++++..        +--.-.|-++++.-..-|.-+...++|++..+.- .| 
T Consensus      1454 sPNSSi~WI~YMaf~L--elsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc-d~- 1529 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHL--ELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC-DA- 1529 (1710)
T ss_pred             CCCcchHHHHHHHHHh--hhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc-ch-
Confidence            365554  66677777  8888888888888754        1123356666666666666666777777765531 11 


Q ss_pred             cccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210           87 NYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus        87 ~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      ...|..|...|.+.+..  |.++++.|.     ...+|....+.+.+..+-+.|+.++.+-
T Consensus      1530 ~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rA 1590 (1710)
T KOG1070|consen 1530 YTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRA 1590 (1710)
T ss_pred             HHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            23566677777777666  777777776     5666666666666666666666666544

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

Probab=96.67  E-value=0.12  Score=44.55  Aligned_cols=131  Identities=12%  Similarity=0.058  Sum_probs=69.4

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      .|++.++.+++.  .|+...  ......+.  +.++.++|.+.++.+.  .|+ ...+-.+-.+|.+.|++.+|...+++
T Consensus       324 ~A~~~l~~L~~~--~P~N~~~~~~~~~i~~--~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~  399 (484)
T COG4783         324 EALKLLQPLIAA--QPDNPYYLELAGDILL--EANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNR  399 (484)
T ss_pred             hHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHH
Confidence            344444444333  344333  44556666  6666666666666654  344 33444455556666666666666666


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhh
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLH  148 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~  148 (230)
                      -... .+-|...|..|-.+|...|+.          ...--+.-.+|...|+++.|......-.+   ++..+|
T Consensus       400 ~~~~-~p~dp~~w~~LAqay~~~g~~----------~~a~~A~AE~~~~~G~~~~A~~~l~~A~~~~~~~~~~~  462 (484)
T COG4783         400 YLFN-DPEDPNGWDLLAQAYAELGNR----------AEALLARAEGYALAGRLEQAIIFLMRASQQVKLGFPDW  462 (484)
T ss_pred             Hhhc-CCCCchHHHHHHHHHHHhCch----------HHHHHHHHHHHHhCCCHHHHHHHHHHHHHhccCCcHHH
Confidence            4332 233445566666666666664          12222223455666666666666555443   444444

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

Probab=96.66  E-value=0.072  Score=51.41  Aligned_cols=167  Identities=12%  Similarity=0.093  Sum_probs=120.8

Q ss_pred             ChhHHHHHHHHHHh-cCCC---CCcH-HHHHHHHhhhccCChHHHHHHHHhcCC-CC-hhhHHHHHHHHHhcCChhHHHH
Q 042210            1 MHQLKQIHSQTIKL-GLLT---KPHC-PKQTRYLLLYEKGDLKYECKVFRKITQ-PS-VFLWNTMIKGYSRIDSHKNGVL   73 (230)
Q Consensus         1 l~~a~~~~~~m~~~-g~~~---~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~-~~-~~~yn~li~~~~~~~~~~~a~~   73 (230)
                      +++|++++++..+. ++.-   -... .++++.-.  -.|.-+...++|+...+ .| ...|-.|..-|.+....++|-+
T Consensus      1474 iekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn--~yG~eesl~kVFeRAcqycd~~~V~~~L~~iy~k~ek~~~A~e 1551 (1710)
T KOG1070|consen 1474 IEKARKIAERALKTINFREEEEKLNIWIAYLNLEN--AYGTEESLKKVFERACQYCDAYTVHLKLLGIYEKSEKNDEADE 1551 (1710)
T ss_pred             hHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHH--hhCcHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhcchhHHH
Confidence            46788888877554 2221   1223 56666666  66777888899988763 23 4578999999999999999999


Q ss_pred             HHHHHHhC-CCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-
Q 042210           74 MYLDLLKS-DVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYMSCE-  142 (230)
Q Consensus        74 ~~~~M~~~-g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-  142 (230)
                      +|+.|.+. |  -....|......+.+.++-  |+.++....       .+.........-.++|+.+.++.+|+..-. 
T Consensus      1552 ll~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~a 1629 (1710)
T KOG1070|consen 1552 LLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSA 1629 (1710)
T ss_pred             HHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhh
Confidence            99999764 4  4456788889988888875  666666655       566667777777899999999999998875 


Q ss_pred             --CChhhhHHHHHHhhhcc----hhhhHHHHHHHh
Q 042210          143 --DDDGLHELIRIKAVDDD----LHELFPEYLVQM  171 (230)
Q Consensus       143 --~~~~t~n~li~~~~~~~----~~~~~~~m~~~~  171 (230)
                        +-.-.|+..|..-...+    .-++|++...-.
T Consensus      1630 yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~ 1664 (1710)
T KOG1070|consen 1630 YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELK 1664 (1710)
T ss_pred             CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcC
Confidence              34567999988776644    444555544443

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

Probab=96.63  E-value=0.19  Score=42.23  Aligned_cols=183  Identities=15%  Similarity=0.070  Sum_probs=123.3

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-------cccHHHHH
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-------NYTFPFLF   94 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-------~~t~~~ll   94 (230)
                      .-....  ..|+.+.|..-.++..   ..+...-.....+|.+.|++.....+...|.+.|+--|       ..+|..++
T Consensus       159 rarlll--~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL  236 (400)
T COG3071         159 RARLLL--NRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLL  236 (400)
T ss_pred             HHHHHH--hCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHH
Confidence            334555  6777777777766644   56777889999999999999999999999999886433       34677777


Q ss_pred             HHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC----CC-------------------
Q 042210           95 KGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE----DD-------------------  144 (230)
Q Consensus        95 ~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----~~-------------------  144 (230)
                      +=+...+..  -...|+...     ++..-.+++.-+.++|+.++|.++..+--+    |+                   
T Consensus       237 ~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~  316 (400)
T COG3071         237 QQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKA  316 (400)
T ss_pred             HHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHH
Confidence            776666655  456677776     788999999999999999999987664432    11                   


Q ss_pred             ----------hh-hhHHHHHHhhhcchhhhHHHHHHHh-hhcCchhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          145 ----------DG-LHELIRIKAVDDDLHELFPEYLVQM-LALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       145 ----------~~-t~n~li~~~~~~~~~~~~~~m~~~~-~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                                .. .+.++-.-|..++-+.-.++.++.. ...|+..++..+.-         ++.+.|+.++|.++.++.
T Consensus       317 ~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~---------~~~~~g~~~~A~~~r~e~  387 (400)
T COG3071         317 AEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELAD---------ALDQLGEPEEAEQVRREA  387 (400)
T ss_pred             HHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHH---------HHHHcCChHHHHHHHHHH
Confidence                      11 1222222223333333333333322 14677888877433         788999999998887766


Q ss_pred             cccCCC
Q 042210          213 HEHSQD  218 (230)
Q Consensus       213 ~~~~~~  218 (230)
                      ...-.+
T Consensus       388 L~~~~~  393 (400)
T COG3071         388 LLLTRQ  393 (400)
T ss_pred             HHHhcC
Confidence            543333

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=96.59  E-value=0.018  Score=47.02  Aligned_cols=127  Identities=13%  Similarity=0.062  Sum_probs=88.9

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhh-----HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFL-----WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGF   97 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~-----yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~   97 (230)
                      ..++...-  +.+.++.|+.+|....+.+..+     ..++|. |...++.+.|..+|+...+. +.-+..-|..-++-+
T Consensus         5 i~~m~~~~--r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E-~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    5 IQYMRFMR--RTEGIEAARKVFKRARKDKRCTYHVYVAYALME-YYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHH--HHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHH-HHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHH--HhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            56677777  8888999999999887433333     334432 22246777799999996543 444555677778888


Q ss_pred             hhcCch--hhHHHhhhh--------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHH
Q 042210           98 TRDIAG--SLEKSCIVM--------RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRI  153 (230)
Q Consensus        98 ~~~~~~--a~~~~~~~~--------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~  153 (230)
                      .+.++.  ++.+|+...        ...+|...|+.=.+.|+++.+.+|..++.+  |+..+...++.
T Consensus        81 ~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~~~~~~f~~  148 (280)
T PF05843_consen   81 IKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPEDNSLELFSD  148 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS-HHHHHHC
T ss_pred             HHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            888988  999999887        246899999999999999999999998876  55444444443

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.

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

Probab=96.59  E-value=0.018  Score=39.92  Aligned_cols=45  Identities=9%  Similarity=0.048  Sum_probs=39.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCC-CCCcccHHHHHHHhhhc
Q 042210           56 NTMIKGYSRIDSHKNGVLMYLDLLKSDV-RRDNYTFPFLFKGFTRD  100 (230)
Q Consensus        56 n~li~~~~~~~~~~~a~~~~~~M~~~g~-~p~~~t~~~ll~~~~~~  100 (230)
                      -..|..+...+++.....+|+.+++.|+ .|+..+|+.++++-++.
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R   74 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKR   74 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHc
Confidence            4566677777999999999999999999 89999999999988775

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 [, , ].

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

Probab=96.46  E-value=0.097  Score=40.38  Aligned_cols=92  Identities=13%  Similarity=0.064  Sum_probs=64.7

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHh-hhcCc--h--hhHHHhhhh-----hHhHH
Q 042210           49 QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGF-TRDIA--G--SLEKSCIVM-----RVFVQ  117 (230)
Q Consensus        49 ~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~-~~~~~--~--a~~~~~~~~-----~~~~~  117 (230)
                      ..|...|..+-..|...|++++|...|++-.+..  | +...+..+-.++ ...|+  .  +.++++...     +...+
T Consensus        70 P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~--P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al  147 (198)
T PRK10370         70 PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR--GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTAL  147 (198)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHH
Confidence            3456678888888888888888888888765532  4 333444444443 45555  2  777777776     77778


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          118 NALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       118 ~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ..+-..+.+.|++++|...|+++.+
T Consensus       148 ~~LA~~~~~~g~~~~Ai~~~~~aL~  172 (198)
T PRK10370        148 MLLASDAFMQADYAQAIELWQKVLD  172 (198)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            8888888888888888888888765

>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=96.44  E-value=0.033  Score=43.26  Aligned_cols=108  Identities=8%  Similarity=-0.026  Sum_probs=73.3

Q ss_pred             hHHHHHHHHhc--CCCChhhHHHHHHHHHhc-----CChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch-hhHHH
Q 042210           37 LKYECKVFRKI--TQPSVFLWNTMIKGYSRI-----DSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-SLEKS  108 (230)
Q Consensus        37 ~~~a~~~~~~m--~~~~~~~yn~li~~~~~~-----~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-a~~~~  108 (230)
                      +..-...|+..  ...|-.+|..+|..|.+.     |..+=....+..|.+-|+.-|..+|+.||+.+-+ |.+ -..++
T Consensus        30 l~~~~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fvp~n~f  108 (228)
T PF06239_consen   30 LAPHEELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFVPRNFF  108 (228)
T ss_pred             ccchHHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcccccHH
Confidence            44455667776  478888999999999764     6666677778899999999999999999999987 544 33333


Q ss_pred             hhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC----CChhhhHHHHHHhh
Q 042210          109 CIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE----DDDGLHELIRIKAV  156 (230)
Q Consensus       109 ~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----~~~~t~n~li~~~~  156 (230)
                      ..+..         -|  -.+-+-|.+|+++|..    ||..|+..++..+.
T Consensus       109 Q~~F~---------hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG  149 (228)
T PF06239_consen  109 QAEFM---------HY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFG  149 (228)
T ss_pred             HHHhc---------cC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc
Confidence            33320         00  1223445566666664    66666666666554

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

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=96.43  E-value=0.06  Score=47.46  Aligned_cols=135  Identities=10%  Similarity=0.050  Sum_probs=93.9

Q ss_pred             hHHHHHHHHHHhc-CCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC-------CCC----hhhHHHHHHHHHhcCCh
Q 042210            3 QLKQIHSQTIKLG-LLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT-------QPS----VFLWNTMIKGYSRIDSH   68 (230)
Q Consensus         3 ~a~~~~~~m~~~g-~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~~----~~~yn~li~~~~~~~~~   68 (230)
                      .|..|.+.  ..| ..|.+..  +.+...++  ..++++.|..++....       .++    ..+|+-|=..|-..|++
T Consensus       308 ~Al~I~~~--~~~~~~~~v~~~l~~~~~~~~--~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~  383 (508)
T KOG1840|consen  308 RALEIYEK--LLGASHPEVAAQLSELAAILQ--SMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKY  383 (508)
T ss_pred             HHHHHHHH--hhccChHHHHHHHHHHHHHHH--HhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcch
Confidence            44555554  223 2344444  66777788  8889999888887542       222    24688898999999999


Q ss_pred             hHHHHHHHHHHhC-----C-CCC-CcccHHHHHHHhhhcCch--hhHHHhhhh------------hHhHHHHHHHHHHhc
Q 042210           69 KNGVLMYLDLLKS-----D-VRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM------------RVFVQNALISTYCLC  127 (230)
Q Consensus        69 ~~a~~~~~~M~~~-----g-~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~------------~~~~~~~li~~y~~~  127 (230)
                      .+|.++|+.-...     | ..+ ....++-|-..|.+.++.  +.++|....            ...+|..|...|.+.
T Consensus       384 ~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~  463 (508)
T KOG1840|consen  384 KEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQ  463 (508)
T ss_pred             hHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHc
Confidence            9999999885431     1 223 244566677777777776  666666655            577888899999999


Q ss_pred             CCHHHHHHHHhhcc
Q 042210          128 GEVDMARGIFYMSC  141 (230)
Q Consensus       128 g~~~~A~~vf~~m~  141 (230)
                      |++++|.++-+...
T Consensus       464 g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  464 GNYEAAEELEEKVL  477 (508)
T ss_pred             ccHHHHHHHHHHHH
Confidence            99999988877554

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

Probab=96.24  E-value=0.32  Score=38.69  Aligned_cols=107  Identities=14%  Similarity=0.043  Sum_probs=51.4

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEK  107 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~  107 (230)
                      -.|+-+....+.....   ..|...-+.......+.|++..|...|.+-.. .-+||..+|+.+=-+|.+.|+.  |+.-
T Consensus        78 ~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~-l~p~d~~~~~~lgaaldq~Gr~~~Ar~a  156 (257)
T COG5010          78 LRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAAR-LAPTDWEAWNLLGAALDQLGRFDEARRA  156 (257)
T ss_pred             hcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhc-cCCCChhhhhHHHHHHHHccChhHHHHH
Confidence            3344444444433322   23333444455555555555555555554322 2334555555555555555555  4444


Q ss_pred             Hhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210          108 SCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus       108 ~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      |.+..     +....|.|--.|.-.|+.+.|+.++.+-
T Consensus       157 y~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a  194 (257)
T COG5010         157 YRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPA  194 (257)
T ss_pred             HHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHH
Confidence            44443     4444555544455555555555555543

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

Probab=96.19  E-value=0.059  Score=34.37  Aligned_cols=26  Identities=15%  Similarity=0.043  Sum_probs=14.8

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      .++..+...+...|+.++|...|...
T Consensus        69 ~~~~~~~~~~~~~~~~~~a~~~~~~~   94 (100)
T cd00189          69 KAYYNLGLAYYKLGKYEEALEAYEKA   94 (100)
T ss_pred             hHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            34445555566666666666666544

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

Probab=96.18  E-value=0.094  Score=46.82  Aligned_cols=188  Identities=13%  Similarity=0.047  Sum_probs=109.8

Q ss_pred             cCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCCcc
Q 042210           15 GLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD-VRRDNY   88 (230)
Q Consensus        15 g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~~p~~~   88 (230)
                      ...|+..+  ..+-..|-  ..|++|.|...++...  +|+ ...||-|-.++-..|++.+|...|+.-.... -.||  
T Consensus       280 ~lrpn~A~a~gNla~iYy--eqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~had--  355 (966)
T KOG4626|consen  280 NLRPNHAVAHGNLACIYY--EQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHAD--  355 (966)
T ss_pred             hcCCcchhhccceEEEEe--ccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHH--
Confidence            34455433  44444455  7777777777777654  444 3467777777777788888887777654432 2223  


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh-hhhHHHHHHhhh-
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD-GLHELIRIKAVD-  157 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~-~t~n~li~~~~~-  157 (230)
                      +.+.|-+.+...|.+  |..++....     -....|.|-..|-..|++++|..-+.+-.+  |+. -+|+.|-..|.. 
T Consensus       356 am~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~  435 (966)
T KOG4626|consen  356 AMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEM  435 (966)
T ss_pred             HHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHh
Confidence            456677777777777  666666555     345567777778788888888777776654  443 244444443433 


Q ss_pred             ---cchhhhHHHHHHHhhhcCchh-hhhhhhhcccccCCcccccccCCccCCccccccccccCCCcc
Q 042210          158 ---DDLHELFPEYLVQMLALPDTF-MGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDM  220 (230)
Q Consensus       158 ---~~~~~~~~~m~~~~~~~p~~~-t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~  220 (230)
                         .+|+..+.+-.   .+.|.-. ..+-|..         .|-++|++.+|.+-++...+.  +||
T Consensus       436 g~v~~A~q~y~rAI---~~nPt~AeAhsNLas---------i~kDsGni~~AI~sY~~aLkl--kPD  488 (966)
T KOG4626|consen  436 GDVSAAIQCYTRAI---QINPTFAEAHSNLAS---------IYKDSGNIPEAIQSYRTALKL--KPD  488 (966)
T ss_pred             hhHHHHHHHHHHHH---hcCcHHHHHHhhHHH---------HhhccCCcHHHHHHHHHHHcc--CCC
Confidence               23333333222   1334311 1222212         566888888888877765543  454

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

Probab=96.14  E-value=0.081  Score=37.57  Aligned_cols=88  Identities=14%  Similarity=0.095  Sum_probs=48.4

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcC
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDI  101 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~  101 (230)
                      +...+.  +.|+.++|.+.|+...   +.+...|..+-..+.+.|++++|...|+.....+  |+               
T Consensus        23 ~a~~~~--~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--p~---------------   83 (135)
T TIGR02552        23 LAYNLY--QQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD--PD---------------   83 (135)
T ss_pred             HHHHHH--HcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CC---------------
Confidence            334444  5566666666655543   2234455555555555556666665555543321  21               


Q ss_pred             chhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          102 AGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       102 ~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                                 +...+..+-..|...|+.++|.+.|+...+
T Consensus        84 -----------~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        84 -----------DPRPYFHAAECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             -----------ChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                       344444455567777888888877776654

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

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.09  E-value=0.63  Score=38.21  Aligned_cols=160  Identities=9%  Similarity=-0.047  Sum_probs=92.7

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      +|...|++..+.  .|+...  +.+-..+.  ..|++++|.+.|+...  .| +...|..+-..+...|++++|.+.|+.
T Consensus        82 ~A~~~~~~Al~l--~P~~~~a~~~lg~~~~--~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~  157 (296)
T PRK11189         82 LARNDFSQALAL--RPDMADAYNYLGIYLT--QAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLA  157 (296)
T ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            455556555543  565444  66777888  9999999999999875  44 356777777788889999999999998


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh---hHhHHHHHHHHHHhcCCHHHHHHHHhhccC----------
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM---RVFVQNALISTYCLCGEVDMARGIFYMSCE----------  142 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~---~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----------  142 (230)
                      -.+.  .|+..........+...++.  |...+....   +...|.. --.+...|+.+++ +.|..+.+          
T Consensus       158 al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~-~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~  233 (296)
T PRK11189        158 FYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYEKLDKEQWGW-NIVEFYLGKISEE-TLMERLKAGATDNTELAE  233 (296)
T ss_pred             HHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhCCccccHH-HHHHHHccCCCHH-HHHHHHHhcCCCcHHHHH
Confidence            6653  34432222222233344555  666664433   2233321 2222335665544 24443331          


Q ss_pred             CChhhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          143 DDDGLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       143 ~~~~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      +...+|..+-..+..    ++|...|++....
T Consensus       234 ~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        234 RLCETYFYLAKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            122345555444443    4666666665543

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.02  E-value=0.45  Score=39.60  Aligned_cols=117  Identities=15%  Similarity=0.100  Sum_probs=90.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      +..|..+.  ..|+...|.++-.+.+-||-..|-.-|.+++..++|++-..+-.. +   -  .+.-|-..+.+|.+.|+
T Consensus       181 ~~Ti~~li--~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s-k---K--sPIGyepFv~~~~~~~~  252 (319)
T PF04840_consen  181 NDTIRKLI--EMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS-K---K--SPIGYEPFVEACLKYGN  252 (319)
T ss_pred             HHHHHHHH--HCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC-C---C--CCCChHHHHHHHHHCCC
Confidence            66678888  999999999999999999999999999999999999977665432 1   1  23668889999999998


Q ss_pred             h--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHHH
Q 042210          103 G--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRI  153 (230)
Q Consensus       103 ~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li~  153 (230)
                      .  |......    ..+.--+..|.++|++.+|.+.--+.+  |.....-+..
T Consensus       253 ~~eA~~yI~k----~~~~~rv~~y~~~~~~~~A~~~A~~~k--d~~~L~~i~~  299 (319)
T PF04840_consen  253 KKEASKYIPK----IPDEERVEMYLKCGDYKEAAQEAFKEK--DIDLLKQILK  299 (319)
T ss_pred             HHHHHHHHHh----CChHHHHHHHHHCCCHHHHHHHHHHcC--CHHHHHHHHH
Confidence            7  6655554    444667899999999999988755543  4444444433

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

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

Probab=95.96  E-value=0.19  Score=43.25  Aligned_cols=137  Identities=9%  Similarity=0.098  Sum_probs=82.4

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      +.|++++|.+.|-++.   .-+..+.--+-+-|-...++..|.+++  |+...+.| |....+-|-..|-+.|+-  |.+
T Consensus       536 ~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~--~q~~slip~dp~ilskl~dlydqegdksqafq  613 (840)
T KOG2003|consen  536 ALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELL--MQANSLIPNDPAILSKLADLYDQEGDKSQAFQ  613 (840)
T ss_pred             HhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHH--HHhcccCCCCHHHHHHHHHHhhcccchhhhhh
Confidence            5566666666665543   222222222333444445555666555  33334444 566677777777777776  655


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhc--cCCChhhhHHHHHHhhh-----cchhhhHHHHHHHh
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMS--CEDDDGLHELIRIKAVD-----DDLHELFPEYLVQM  171 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m--~~~~~~t~n~li~~~~~-----~~~~~~~~~m~~~~  171 (230)
                      .|-+--     ++.+.-=|-.-|....-+++|...|++-  .+|+..-|-.||..|.+     .+++++++...+.-
T Consensus       614 ~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkf  690 (840)
T KOG2003|consen  614 CHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKF  690 (840)
T ss_pred             hhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhC
Confidence            554433     5666555666677777778888888854  35888888888876653     36777777665543

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.83  E-value=0.082  Score=44.08  Aligned_cols=143  Identities=10%  Similarity=0.044  Sum_probs=101.1

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      -|++.|+..=.++.+-|+..  .++-+.+.  -.-+++++.-.++.++    .-|.+.|| +-.+++..|+..+|.++|-
T Consensus       341 iAqqffqlVG~Sa~ecDTIpGRQsmAs~fF--L~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~  417 (557)
T KOG3785|consen  341 IAQQFFQLVGESALECDTIPGRQSMASYFF--LSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFI  417 (557)
T ss_pred             HHHHHHHHhcccccccccccchHHHHHHHH--HHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHh
Confidence            46677776666777777776  56666666  5567777777777766    45666666 4568888899999999997


Q ss_pred             HHHhCCCCCCcccHHHH-HHHhhhcCch--hhHHHhhhh---hHhHHHHHH-HHHHhcCCHHHHHHHHhhccC--CChhh
Q 042210           77 DLLKSDVRRDNYTFPFL-FKGFTRDIAG--SLEKSCIVM---RVFVQNALI-STYCLCGEVDMARGIFYMSCE--DDDGL  147 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~l-l~~~~~~~~~--a~~~~~~~~---~~~~~~~li-~~y~~~g~~~~A~~vf~~m~~--~~~~t  147 (230)
                      +.....++ |..+|.++ -++|.+++..  |+.++-.+.   +.++.-.+| +-+-+++++--|.+.|+++..  |+..-
T Consensus       418 ~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEn  496 (557)
T KOG3785|consen  418 RISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPEN  496 (557)
T ss_pred             hhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCccc
Confidence            76655555 45566655 5677888887  888877776   444433344 567789999999999998875  66665


Q ss_pred             hH
Q 042210          148 HE  149 (230)
Q Consensus       148 ~n  149 (230)
                      |.
T Consensus       497 We  498 (557)
T KOG3785|consen  497 WE  498 (557)
T ss_pred             cC
Confidence            65

>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=95.83  E-value=0.042  Score=34.07  Aligned_cols=40  Identities=15%  Similarity=0.060  Sum_probs=30.3

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR  152 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li  152 (230)
                      +...+-.+...|.+.|++++|.+++++...  |+...|..++
T Consensus        24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~   65 (68)
T PF14559_consen   24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLL   65 (68)
T ss_dssp             SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            566667788899999999999999998876  7755665554

...

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

Probab=95.79  E-value=0.26  Score=35.73  Aligned_cols=107  Identities=13%  Similarity=0.052  Sum_probs=67.1

Q ss_pred             ccCChHHHHHHHHhcC--CCCh-hh---HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcc--cHHHHHHHhhhcCch-
Q 042210           33 EKGDLKYECKVFRKIT--QPSV-FL---WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNY--TFPFLFKGFTRDIAG-  103 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~~-~~---yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~--t~~~ll~~~~~~~~~-  103 (230)
                      ..++...+...++.+.  -|+. ..   .=.+-..+...|++++|...|+......-.|+..  ..-.|-..+...|++ 
T Consensus        23 ~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d  102 (145)
T PF09976_consen   23 QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYD  102 (145)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHH
Confidence            4667777777777765  2332 11   1123355666788888888888887766223211  222345566666777 


Q ss_pred             -hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          104 -SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       104 -a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                       |...+....    ....+...=+.|.+.|+.++|+..|+.
T Consensus       103 ~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  103 EALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence             666666554    455556666788888888888888764

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=95.78  E-value=0.027  Score=40.91  Aligned_cols=65  Identities=11%  Similarity=0.185  Sum_probs=48.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh-----CCCCCCccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-----SDVRRDNYT   89 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-----~g~~p~~~t   89 (230)
                      ..+...+.  ..|+++.|......+.   +-|-..|-.+|.+|...|+...|.++|+++.+     .|+.|+..+
T Consensus        66 ~~l~~~~~--~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   66 ERLAEALL--EAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHH--HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHH--hccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            45666677  8999999999999876   55677999999999999999999999998754     499998754

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>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=95.77  E-value=0.11  Score=36.92  Aligned_cols=80  Identities=9%  Similarity=-0.057  Sum_probs=62.7

Q ss_pred             cH-HHHHHHHhhhccCChHHHHHHHHhcC-------------------CCChhhHHHHHHHHHhcCChhHHHHHHHHH-H
Q 042210           21 HC-PKQTRYLLLYEKGDLKYECKVFRKIT-------------------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDL-L   79 (230)
Q Consensus        21 ~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-------------------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M-~   79 (230)
                      .+ .++|.+++  +.|+++....+.+..=                   -|+..+-.+++.+|+.++++..|+++.+.. .
T Consensus         3 ~~~~~ii~al~--r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    3 ELLCNIIYALG--RSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             HHHHHHHHHHh--hcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            45 77888899  9999999888886531                   366777889999999999999999998885 4


Q ss_pred             hCCCCCCcccHHHHHHHhhhcCc
Q 042210           80 KSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        80 ~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      ..+++-+..+|..|++=+....+
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhcC
Confidence            56888778888888886655443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=95.77  E-value=0.56  Score=36.78  Aligned_cols=146  Identities=12%  Similarity=0.063  Sum_probs=89.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCCc-ccHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKSD-VRRDN-YTFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~~p~~-~t~~~ll   94 (230)
                      -.....+.  +.|+++.|...|++..  .|+.    ..|..+-.++.+.|++++|...|++..+.. -.|.. .++..+-
T Consensus        37 ~~~g~~~~--~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g  114 (235)
T TIGR03302        37 YEEAKEAL--DSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRG  114 (235)
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHH
Confidence            44556677  8899999999998765  3332    355667778888899999999999986532 11211 1232232


Q ss_pred             HHhhhc--------Cch--hhHHHhhhh-----hHhHH-----------------HHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           95 KGFTRD--------IAG--SLEKSCIVM-----RVFVQ-----------------NALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        95 ~~~~~~--------~~~--a~~~~~~~~-----~~~~~-----------------~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .++.+.        |+.  |.+.+....     +...+                 -.+-..|.+.|++++|...|++..+
T Consensus       115 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~  194 (235)
T TIGR03302       115 LSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINRFETVVE  194 (235)
T ss_pred             HHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            333322        444  666666554     11111                 1334567888999999999998764


Q ss_pred             --CCh----hhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          143 --DDD----GLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       143 --~~~----~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                        |+.    ..|..+...+..    +++.+.++.+..+
T Consensus       195 ~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       195 NYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence              432    456666555543    4566666655443

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).

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

Probab=95.76  E-value=0.19  Score=43.50  Aligned_cols=104  Identities=13%  Similarity=0.043  Sum_probs=67.1

Q ss_pred             ccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHH
Q 042210           33 EKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKS  108 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~  108 (230)
                      ..|++..|+++|...-  +|+...|++.|+-=.+-+.++.|-.+|++..-  +.|+..+|.--.+-=-+.|++  ++.++
T Consensus       153 ~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  153 MLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             HhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            4455566666665533  67777777777777777777777777777543  347777776666666666766  66666


Q ss_pred             hhhh--------hHhHHHHHHHHHHhcCCHHHHHHHHh
Q 042210          109 CIVM--------RVFVQNALISTYCLCGEVDMARGIFY  138 (230)
Q Consensus       109 ~~~~--------~~~~~~~li~~y~~~g~~~~A~~vf~  138 (230)
                      ....        +...+++.-..=.++..++.|+-+|.
T Consensus       231 erAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iyk  268 (677)
T KOG1915|consen  231 ERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYK  268 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6655        44455555555556666777766655

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

Probab=95.72  E-value=0.62  Score=40.29  Aligned_cols=57  Identities=11%  Similarity=0.007  Sum_probs=41.2

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-CCh--hhhHHHHHHhh----hcchhhhHHHHHH
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE-DDD--GLHELIRIKAV----DDDLHELFPEYLV  169 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-~~~--~t~n~li~~~~----~~~~~~~~~~m~~  169 (230)
                      |...|.+|=+.|.+.+++++|.+-|.+-.. -|+  ..+..+-..|.    .++|...|++..+
T Consensus       431 DsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  431 DSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             chHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            999999999999999999999999987665 222  44555544443    2456666665554

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

Probab=95.70  E-value=0.13  Score=36.57  Aligned_cols=89  Identities=2%  Similarity=-0.096  Sum_probs=64.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|.+.++.....+ ..+... ..+-..+.  +.|++++|...|+...   +.+...|..+-..|...|++++|...|++
T Consensus        34 ~~A~~~~~~~~~~~-p~~~~~~~~la~~~~--~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~  110 (135)
T TIGR02552        34 DEALKLFQLLAAYD-PYNSRYWLGLAACCQ--MLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPESALKALDL  110 (135)
T ss_pred             HHHHHHHHHHHHhC-CCcHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            45677777776654 223444 66777888  9999999999998864   44556677777788999999999999988


Q ss_pred             HHhCCCCCCcccHHHHHH
Q 042210           78 LLKSDVRRDNYTFPFLFK   95 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~   95 (230)
                      ..+.  .|+...+..+..
T Consensus       111 al~~--~p~~~~~~~~~~  126 (135)
T TIGR02552       111 AIEI--CGENPEYSELKE  126 (135)
T ss_pred             HHHh--ccccchHHHHHH
Confidence            7664  366655544433

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

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

Probab=95.64  E-value=0.68  Score=38.62  Aligned_cols=108  Identities=12%  Similarity=0.020  Sum_probs=69.6

Q ss_pred             cCChHHHHHHHHhcC--CCCh-hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHH
Q 042210           34 KGDLKYECKVFRKIT--QPSV-FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKS  108 (230)
Q Consensus        34 ~~~~~~a~~~~~~m~--~~~~-~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~  108 (230)
                      .+..+.+.+.++...  .|+. .....+-..+...|++++|...+++..+.. +.+...+..+-..+...|++  +...+
T Consensus        93 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l  171 (355)
T cd05804          93 SGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFM  171 (355)
T ss_pred             ccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHH
Confidence            445555555555422  1221 222334446677888899999888876643 22445666777778888888  77766


Q ss_pred             hhhh---------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          109 CIVM---------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       109 ~~~~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ....         ....|..+-..|...|+.++|.+++++...
T Consensus       172 ~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         172 ESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             HhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            6655         123455677788888999999999988753

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=95.64  E-value=0.39  Score=44.27  Aligned_cols=126  Identities=12%  Similarity=-0.042  Sum_probs=100.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCCh-hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcc-cHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPSV-FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNY-TFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~-~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~-t~~~ll~~~~   98 (230)
                      -.|-..-.  +.|+.++|..+++..-  .||. ...-.+...+.+.+++++|+..+++....  .|+.. ....+-.++.
T Consensus        90 ~~La~i~~--~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a~~l~  165 (694)
T PRK15179         90 VLVARALE--AAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEAKSWD  165 (694)
T ss_pred             HHHHHHHH--HcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHH
Confidence            44556666  8899999999999876  5654 45677888899999999999999987653  45444 4455566777


Q ss_pred             hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHHH
Q 042210           99 RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELIR  152 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~li  152 (230)
                      +.|+.  |..+|+...     +...+.++=..+-+.|+.++|...|+.-.+   +.+.-||-.+
T Consensus       166 ~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~  229 (694)
T PRK15179        166 EIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRRL  229 (694)
T ss_pred             HhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHHH
Confidence            88888  999999988     578888899999999999999999997754   7777777654

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

Probab=95.64  E-value=0.044  Score=35.76  Aligned_cols=74  Identities=14%  Similarity=0.039  Sum_probs=35.3

Q ss_pred             CChhHHHHHHHHHHhCCC-CCCcccHHHHHHHhhhcCch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHh
Q 042210           66 DSHKNGVLMYLDLLKSDV-RRDNYTFPFLFKGFTRDIAG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFY  138 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~~g~-~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~  138 (230)
                      |+++.|..+|+++....- .|+...+-.+-.++.+.|+.  |..+++...    +....-.+-.+|.+.|++++|.++|+
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            445555555555444321 11222233344555555555  444444422    22222233556777888888888776


Q ss_pred             h
Q 042210          139 M  139 (230)
Q Consensus       139 ~  139 (230)
                      +
T Consensus        83 ~   83 (84)
T PF12895_consen   83 K   83 (84)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

Probab=95.60  E-value=0.75  Score=40.57  Aligned_cols=102  Identities=7%  Similarity=0.041  Sum_probs=77.0

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch-hhHHHhhhh-----hHhHHHHHHHHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG-SLEKSCIVM-----RVFVQNALISTY  124 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~-a~~~~~~~~-----~~~~~~~li~~y  124 (230)
                      ..+|-..|+.--+..-+..|-.+|.+..+.+..+ +...+++++.-+|..... |.++|+.=.     ++.--...++.+
T Consensus       366 tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  366 TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            3467777777777788888888888888887777 777888888888877666 888887654     566667788888


Q ss_pred             HhcCCHHHHHHHHhhccCC------ChhhhHHHHH
Q 042210          125 CLCGEVDMARGIFYMSCED------DDGLHELIRI  153 (230)
Q Consensus       125 ~~~g~~~~A~~vf~~m~~~------~~~t~n~li~  153 (230)
                      ...++-..|+.+|++....      ....|..||.
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~  480 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWDRMLE  480 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHH
Confidence            8888888888888877643      2245777765

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=95.59  E-value=0.3  Score=35.53  Aligned_cols=87  Identities=9%  Similarity=-0.102  Sum_probs=69.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ...-..+.  ..|++++|...|+...   +.+...|..+-..+.+.|++++|...|+.....+ +.+...+..+-.++.+
T Consensus        28 ~~~g~~~~--~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~  104 (144)
T PRK15359         28 YASGYASW--QEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKM  104 (144)
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHH
Confidence            33445556  9999999999999865   4567788889999999999999999999987642 3366678888888999


Q ss_pred             cCch--hhHHHhhhh
Q 042210          100 DIAG--SLEKSCIVM  112 (230)
Q Consensus       100 ~~~~--a~~~~~~~~  112 (230)
                      .|+.  |...+....
T Consensus       105 ~g~~~eAi~~~~~Al  119 (144)
T PRK15359        105 MGEPGLAREAFQTAI  119 (144)
T ss_pred             cCCHHHHHHHHHHHH
Confidence            9998  777777765

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

Probab=95.53  E-value=0.086  Score=48.99  Aligned_cols=138  Identities=14%  Similarity=0.110  Sum_probs=91.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|.++|++..+.. ..+.+. |-+=-.++  ..|++.+|..+|.+..   ..+..+|=-+-++|...|++..|.++|+.
T Consensus       629 ~KAlq~y~kvL~~d-pkN~yAANGIgiVLA--~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~  705 (1018)
T KOG2002|consen  629 EKALQLYGKVLRND-PKNMYAANGIGIVLA--EKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYEN  705 (1018)
T ss_pred             HHHHHHHHHHHhcC-cchhhhccchhhhhh--hccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHH
Confidence            45667776655542 123444 55656666  8889999999998887   23445777788888888999999999988


Q ss_pred             -HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHH------------------HhcCCH
Q 042210           78 -LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTY------------------CLCGEV  130 (230)
Q Consensus        78 -M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y------------------~~~g~~  130 (230)
                       |+...-.-+......|-+++-+.|.+  +.+..-...      ..+.+|..+-..                  ..-+.+
T Consensus       706 ~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~a~v~kkla~s~lr~~k~t~eev~~a~~~l  785 (1018)
T KOG2002|consen  706 CLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNLALVLKKLAESILRLEKRTLEEVLEAVKEL  785 (1018)
T ss_pred             HHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence             55555445666777788888888877  333222222      455555544222                  234557


Q ss_pred             HHHHHHHhhccC
Q 042210          131 DMARGIFYMSCE  142 (230)
Q Consensus       131 ~~A~~vf~~m~~  142 (230)
                      +.|.++|.+|..
T Consensus       786 e~a~r~F~~ls~  797 (1018)
T KOG2002|consen  786 EEARRLFTELSK  797 (1018)
T ss_pred             HHHHHHHHHHHh
Confidence            888888888865

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.52  E-value=0.099  Score=47.60  Aligned_cols=104  Identities=9%  Similarity=0.068  Sum_probs=71.4

Q ss_pred             ccCChHHHHHHHHhcCCCChh--hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHH
Q 042210           33 EKGDLKYECKVFRKITQPSVF--LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKS  108 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~--~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~  108 (230)
                      +.+.+.+|..+++.++..++.  -|..+-+.|+..|+++.|.++|.+         ..-|+-.|..|.+.|+|  |..+-
T Consensus       744 ~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e---------~~~~~dai~my~k~~kw~da~kla  814 (1636)
T KOG3616|consen  744 GAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTE---------ADLFKDAIDMYGKAGKWEDAFKLA  814 (1636)
T ss_pred             hhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHh---------cchhHHHHHHHhccccHHHHHHHH
Confidence            666777888888877744443  477778888888888888888865         22366678888888888  66555


Q ss_pred             hhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCCh
Q 042210          109 CIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCEDDD  145 (230)
Q Consensus       109 ~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~  145 (230)
                      ....    .+..|-+=-.-.-+.|++.+|++++-.+..|+.
T Consensus       815 ~e~~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~  855 (1636)
T KOG3616|consen  815 EECHGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDK  855 (1636)
T ss_pred             HHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchH
Confidence            5544    444444444455667777777777777766664

>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=95.49  E-value=0.31  Score=41.77  Aligned_cols=112  Identities=11%  Similarity=-0.053  Sum_probs=82.7

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcC
Q 042210           56 NTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCG  128 (230)
Q Consensus        56 n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g  128 (230)
                      .+++..+...++++.|..+|+++.+..  |+.  ...+.+.+...++-  |.++..+..     +....+.-...+.+.+
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRERD--PEV--AVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhcC--CcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence            456666667899999999999998875  553  45577777776665  555555444     6666777778889999


Q ss_pred             CHHHHHHHHhhccC--CCh-hhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          129 EVDMARGIFYMSCE--DDD-GLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       129 ~~~~A~~vf~~m~~--~~~-~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                      +.+.|.++..+..+  |+. .+|..|..+|...+..+-+---.+..
T Consensus       249 ~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  249 KYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             CHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence            99999999999987  654 59999999998765555544333433

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

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

Probab=95.47  E-value=1.3  Score=37.37  Aligned_cols=162  Identities=10%  Similarity=-0.104  Sum_probs=111.1

Q ss_pred             HHHHHHHHHHhcCCCCCcH--------HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHH
Q 042210            4 LKQIHSQTIKLGLLTKPHC--------PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         4 a~~~~~~m~~~g~~~~~~~--------~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~   72 (230)
                      +..+...|.+.|.-.|...        ..++.=..  ..+..+.-...|+..+   +.++..--+++.-+.++|+.++|.
T Consensus       206 ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~--~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~  283 (400)
T COG3071         206 LLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQAR--DDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQ  283 (400)
T ss_pred             HHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHh--ccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHH
Confidence            4556677777777666442        23333333  3334444444666666   334555667888899999999999


Q ss_pred             HHHHHHHhCCCCCCcccHHHHHHHhhhcCch------hhHHHhhhh-hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C
Q 042210           73 LMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG------SLEKSCIVM-RVFVQNALISTYCLCGEVDMARGIFYMSCE--D  143 (230)
Q Consensus        73 ~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~------a~~~~~~~~-~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~  143 (230)
                      ++.++-.+.+..|+    -..+-.+.+-++.      ++.-...-. ++-.+.+|=..|.|.+.+.+|...|+.-..  |
T Consensus       284 ~~i~~~Lk~~~D~~----L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~  359 (400)
T COG3071         284 EIIEDALKRQWDPR----LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRP  359 (400)
T ss_pred             HHHHHHHHhccChh----HHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCC
Confidence            99999888888887    2233345555554      333333333 888888888999999999999999996554  8


Q ss_pred             ChhhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          144 DDGLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       144 ~~~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                      +..+|+-+-.++..-+-.+...++.+++
T Consensus       360 s~~~~~~la~~~~~~g~~~~A~~~r~e~  387 (400)
T COG3071         360 SASDYAELADALDQLGEPEEAEQVRREA  387 (400)
T ss_pred             ChhhHHHHHHHHHHcCChHHHHHHHHHH
Confidence            9999999888887666556666666655

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

Probab=95.44  E-value=0.64  Score=40.98  Aligned_cols=120  Identities=10%  Similarity=0.049  Sum_probs=91.8

Q ss_pred             CCCCcHHHHHHHHhhhccCChHHHHHHHHhcC----CC-ChhhHHHHHHHHHhcCChhHHHHHHHH-HHhCCCCCCcccH
Q 042210           17 LTKPHCPKQTRYLLLYEKGDLKYECKVFRKIT----QP-SVFLWNTMIKGYSRIDSHKNGVLMYLD-LLKSDVRRDNYTF   90 (230)
Q Consensus        17 ~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~----~~-~~~~yn~li~~~~~~~~~~~a~~~~~~-M~~~g~~p~~~t~   90 (230)
                      .|+..-...++.--  |..-++.|+.+|.+..    .+ ++..++++|.-||. ++..-|.++|+- |+..|=.|   .|
T Consensus       364 ~~tLv~~~~mn~ir--R~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d~p---~y  437 (656)
T KOG1914|consen  364 DLTLVYCQYMNFIR--RAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGDSP---EY  437 (656)
T ss_pred             CCceehhHHHHHHH--HhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCCCh---HH
Confidence            34432277777777  8888999999999987    34 77889999988876 688899999987 66665444   33


Q ss_pred             H-HHHHHhhhcCch--hhHHHhhhh--------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           91 P-FLFKGFTRDIAG--SLEKSCIVM--------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        91 ~-~ll~~~~~~~~~--a~~~~~~~~--------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      . .-++-+...++-  ++.+|+...        ...+|..+|+-=+.-|++..+.+|=+++..
T Consensus       438 v~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  438 VLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            2 335555666665  888888887        468999999999999999999988776654

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

Probab=95.37  E-value=0.19  Score=45.46  Aligned_cols=177  Identities=14%  Similarity=0.019  Sum_probs=108.4

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG   96 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~   96 (230)
                      |-... ..+-..+.  +.|-...|..+|+..     ..|.-+|.+|...|+..+|..+..+-.+  -+||..-|..+-+.
T Consensus       396 p~Wq~q~~laell~--slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv  466 (777)
T KOG1128|consen  396 PIWQLQRLLAELLL--SLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDV  466 (777)
T ss_pred             CcchHHHHHHHHHH--HcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhh
Confidence            44444 66777888  889999999998875     3577788899999988888888766555  45777777777665


Q ss_pred             hhhcCch--hhHHHhhhh---------------------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           97 FTRDIAG--SLEKSCIVM---------------------------------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        97 ~~~~~~~--a~~~~~~~~---------------------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .....-+  |.++.++..                                 -.-+|=.+=.++-+++++..|.+-|..-.
T Consensus       467 ~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcv  546 (777)
T KOG1128|consen  467 LHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCV  546 (777)
T ss_pred             ccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHh
Confidence            4433222  444444433                                 11122222223347778888888888776


Q ss_pred             C--CC-hhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          142 E--DD-DGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       142 ~--~~-~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      .  || ...||.+-.+|..    .++...++|-.+.-     ...+..  ..+.|.    ...+.|.+++|.+.+.++..
T Consensus       547 tL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-----~~~w~i--WENyml----vsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  547 TLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-----YQHWQI--WENYML----VSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             hcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-----CCCCee--eechhh----hhhhcccHHHHHHHHHHHHH
Confidence            5  54 5679988776654    45555555443332     111221  111111    44588888888776666544

>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=95.36  E-value=0.16  Score=32.22  Aligned_cols=84  Identities=12%  Similarity=0.086  Sum_probs=58.9

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhc
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRD  100 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~  100 (230)
                      .+...+.  ..|++++|...|+...   +.+...+..+-..+...+++++|...|++..+.. +.+..++..+...+...
T Consensus         5 ~~a~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   81 (100)
T cd00189           5 NLGNLYY--KLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHH--HHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHHHH
Confidence            3445666  8889999999998865   3334567777888888899999999998876643 22334666677777777


Q ss_pred             Cch--hhHHHhh
Q 042210          101 IAG--SLEKSCI  110 (230)
Q Consensus       101 ~~~--a~~~~~~  110 (230)
                      |+.  +...+..
T Consensus        82 ~~~~~a~~~~~~   93 (100)
T cd00189          82 GKYEEALEAYEK   93 (100)
T ss_pred             HhHHHHHHHHHH
Confidence            776  5555443

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

Probab=95.31  E-value=1.1  Score=35.77  Aligned_cols=105  Identities=14%  Similarity=0.053  Sum_probs=44.0

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC-CCCCCcccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS-DVRRDNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~-g~~p~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      +.|++..|...|.+..   ++|-..||.+=-+|-+.|+.++|-.-|.+-.+- +=  +...++.|--.+.=.|+.  |..
T Consensus       112 ~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~--~p~~~nNlgms~~L~gd~~~A~~  189 (257)
T COG5010         112 RNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPN--EPSIANNLGMSLLLRGDLEDAET  189 (257)
T ss_pred             HhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccC--CchhhhhHHHHHHHcCCHHHHHH
Confidence            4444444444444433   334444444444444444444444444443221 11  111233333333333444  333


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ++....     |..+-..|.-..+.-|++++|+++-..
T Consensus       190 lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~  227 (257)
T COG5010         190 LLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQ  227 (257)
T ss_pred             HHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhccc
Confidence            333333     444444444444444445444444443

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

Probab=95.25  E-value=1.5  Score=36.42  Aligned_cols=30  Identities=17%  Similarity=0.100  Sum_probs=22.0

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      -..+...|..+|...|++++....+.++.+
T Consensus       248 l~evl~~L~~~Y~~lg~~~~~~~fL~~~~~  277 (389)
T COG2956         248 LSEVLEMLYECYAQLGKPAEGLNFLRRAME  277 (389)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            455667777888888888888777777665

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.17  E-value=0.068  Score=43.23  Aligned_cols=78  Identities=6%  Similarity=0.059  Sum_probs=59.4

Q ss_pred             CChHHHHHHHHhcC----CCChhhHHHHHHHHHhcC----------------ChhHHHHHHHHHHhCCCCCCcccHHHHH
Q 042210           35 GDLKYECKVFRKIT----QPSVFLWNTMIKGYSRID----------------SHKNGVLMYLDLLKSDVRRDNYTFPFLF   94 (230)
Q Consensus        35 ~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~----------------~~~~a~~~~~~M~~~g~~p~~~t~~~ll   94 (230)
                      ++++-...-++.|+    .+|..+|+.||+.+-+..                .-+-+..++++|+..|+.||..+--.|+
T Consensus        86 ~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lv  165 (406)
T KOG3941|consen   86 THVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILV  165 (406)
T ss_pred             chHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHH
Confidence            45666666666665    788888988888876632                3456889999999999999999999999


Q ss_pred             HHhhhcCch---hhHHHhhhh
Q 042210           95 KGFTRDIAG---SLEKSCIVM  112 (230)
Q Consensus        95 ~~~~~~~~~---a~~~~~~~~  112 (230)
                      +++++.+..   ..++.-.|.
T Consensus       166 n~FGr~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  166 NAFGRWNFPTKKVKRMLYWMP  186 (406)
T ss_pred             HHhccccccHHHHHHHHHhhh
Confidence            999998876   444444444

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=95.17  E-value=0.21  Score=36.35  Aligned_cols=91  Identities=11%  Similarity=0.060  Sum_probs=71.1

Q ss_pred             HHHHHhcCCCCCcH---HHHHHHHhhhccCChHHHHHHHHhcC---------CCChhhHHHHHHHHHhcCC-hhHHHHHH
Q 042210            9 SQTIKLGLLTKPHC---PKQTRYLLLYEKGDLKYECKVFRKIT---------QPSVFLWNTMIKGYSRIDS-HKNGVLMY   75 (230)
Q Consensus         9 ~~m~~~g~~~~~~~---~~ll~~~~~~~~~~~~~a~~~~~~m~---------~~~~~~yn~li~~~~~~~~-~~~a~~~~   75 (230)
                      ..|.+.+..+++.+   |.+|.-..  .-+++.....+++.+.         ..+-.+|++++.+.++..- --.+..+|
T Consensus        26 ~y~~~~~~~~~~k~~fiN~iL~hl~--~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf  103 (145)
T PF13762_consen   26 PYMQEENASQSTKTIFINCILNHLA--SYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLF  103 (145)
T ss_pred             HHhhhcccChhHHHHHHHHHHHHHH--HccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHH
Confidence            34455667776544   77887777  7788888888887775         3455679999999987766 45688899


Q ss_pred             HHHHhCCCCCCcccHHHHHHHhhhcC
Q 042210           76 LDLLKSDVRRDNYTFPFLFKGFTRDI  101 (230)
Q Consensus        76 ~~M~~~g~~p~~~t~~~ll~~~~~~~  101 (230)
                      +-|++.+.+++..-|..+|++|.+..
T Consensus       104 ~~Lk~~~~~~t~~dy~~li~~~l~g~  129 (145)
T PF13762_consen  104 NFLKKNDIEFTPSDYSCLIKAALRGY  129 (145)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCC
Confidence            99999889999999999999998763

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

Probab=95.11  E-value=0.54  Score=37.78  Aligned_cols=38  Identities=8%  Similarity=-0.054  Sum_probs=17.3

Q ss_pred             hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          104 SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       104 a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      |.-+|+++-     ++-+.|....+....|++++|..++++.-
T Consensus       192 AfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL  234 (299)
T KOG3081|consen  192 AFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEAL  234 (299)
T ss_pred             HHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHH
Confidence            444444443     33334444444444455555555544443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.07  E-value=0.53  Score=32.15  Aligned_cols=27  Identities=11%  Similarity=0.006  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          116 VQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .+..+-..|.+.|+.++|.+.+++..+
T Consensus        78 ~~~~~~~~~~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        78 ALLKLGMSLQELGDKEKAKATLQQVIK  104 (119)
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHH
Confidence            344445556667777777777776654

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.

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

Probab=95.03  E-value=0.28  Score=40.64  Aligned_cols=123  Identities=15%  Similarity=0.040  Sum_probs=81.8

Q ss_pred             CCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHH-
Q 042210           16 LLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFP-   91 (230)
Q Consensus        16 ~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~-   91 (230)
                      ...|..- +.+=.+|.  +.|-+.+|++.|+.-.  .|-+.||--|-+.|.+..++..|+.+|.+=..  ..|..+||- 
T Consensus       219 ~~~dwwWk~Q~gkCyl--rLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld--~fP~~VT~l~  294 (478)
T KOG1129|consen  219 CTLDWWWKQQMGKCYL--RLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLD--SFPFDVTYLL  294 (478)
T ss_pred             chHhHHHHHHHHHHHH--HhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhh--cCCchhhhhh
Confidence            3445555 77777888  8888888888887643  56666777788888888888888888766322  335444542 


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      -+-+.+-..++.  +.++++...     ++....++-.+|--.+++|.|.+.+.++-+
T Consensus       295 g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLq  352 (478)
T KOG1129|consen  295 GQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQ  352 (478)
T ss_pred             hhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHH
Confidence            233444445555  667776665     566666666777777777777777776554

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

Probab=94.98  E-value=0.18  Score=41.68  Aligned_cols=186  Identities=10%  Similarity=0.051  Sum_probs=120.7

Q ss_pred             CCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHH-HHHHHHHhcCChhHHHHHHHHHHh-CCCCCCcccHH
Q 042210           17 LTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWN-TMIKGYSRIDSHKNGVLMYLDLLK-SDVRRDNYTFP   91 (230)
Q Consensus        17 ~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn-~li~~~~~~~~~~~a~~~~~~M~~-~g~~p~~~t~~   91 (230)
                      .|-+.+ --|-..|-  +..+++.|..+|.+-.  -|.-+||- -+-.-+-..++.++|.++|++-.+ ..+  +.....
T Consensus       253 ~~~~dTfllLskvY~--ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~~~--nvEaiA  328 (478)
T KOG1129|consen  253 FPHPDTFLLLSKVYQ--RIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLHPI--NVEAIA  328 (478)
T ss_pred             CCchhHHHHHHHHHH--HhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcCCc--cceeee
Confidence            355556 77778898  9999999999998865  45555543 333444456888999999988543 322  333344


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhc----cCCChh--hhHHHHHHhhhc
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMS----CEDDDG--LHELIRIKAVDD  158 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m----~~~~~~--t~n~li~~~~~~  158 (230)
                      ++-.+|.-.++.  |...++.+.     ++..|+.+=-.+.-.+++|.+.--|.+-    .+|+..  .|-.+-.....-
T Consensus       329 cia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~i  408 (478)
T KOG1129|consen  329 CIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTI  408 (478)
T ss_pred             eeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEec
Confidence            444555555666  888888776     8888888766666778888887666643    345543  244343333445


Q ss_pred             chhhhHHHHHHHhhhcCch---hhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          159 DLHELFPEYLVQMLALPDT---FMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       159 ~~~~~~~~m~~~~~~~p~~---~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      +.+.+..+.++-- ...|.   ..++-|.++         -.+.|++++|+.++.......
T Consensus       409 GD~nlA~rcfrla-L~~d~~h~ealnNLavL---------~~r~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  409 GDFNLAKRCFRLA-LTSDAQHGEALNNLAVL---------AARSGDILGARSLLNAAKSVM  459 (478)
T ss_pred             cchHHHHHHHHHH-hccCcchHHHHHhHHHH---------HhhcCchHHHHHHHHHhhhhC
Confidence            7777777777666 33443   344444443         358899999999988666543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.92  E-value=1.3  Score=35.47  Aligned_cols=135  Identities=16%  Similarity=0.049  Sum_probs=90.9

Q ss_pred             hHHHHHHHHH---Hhc-CCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCChhHH
Q 042210            3 QLKQIHSQTI---KLG-LLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSVFLWNTMIKGYSRIDSHKNG   71 (230)
Q Consensus         3 ~a~~~~~~m~---~~g-~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~~~yn~li~~~~~~~~~~~a   71 (230)
                      +..+++.+++   ++| ..++..+  -.+.-+-.  -.|+.+.|...++.+.     ++.+.-.-++  -+-..|.+++|
T Consensus        30 evv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAl--d~~~~~lAq~C~~~L~~~fp~S~RV~~lkam--~lEa~~~~~~A  105 (289)
T KOG3060|consen   30 EVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAAL--DTGRDDLAQKCINQLRDRFPGSKRVGKLKAM--LLEATGNYKEA  105 (289)
T ss_pred             HHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHH--HhcchHHHHHHHHHHHHhCCCChhHHHHHHH--HHHHhhchhhH
Confidence            4455666653   334 6677766  44555555  7889999999998876     2233332222  12336789999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhhcCch---hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG---SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~---a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .++|+.+.+.+ +-|.+++.-=+-..-..|+-   .+.+-+.+.    |...|.-|-+.|...|++++|.--++++.-
T Consensus       106 ~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  106 IEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             HHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            99999998877 44666665444444344443   333333333    999999999999999999999999998863

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

Probab=94.56  E-value=1.2  Score=38.80  Aligned_cols=136  Identities=12%  Similarity=0.112  Sum_probs=102.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCCh-hhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSV-FLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~-~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      +.|+++|+....-. ..+... -..+.+=+  ++.++..|+.+|+...  -|.+ ..|---+..=-..|++..|-.+|++
T Consensus        90 ~RARSv~ERALdvd-~r~itLWlkYae~Em--knk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqifer  166 (677)
T KOG1915|consen   90 QRARSVFERALDVD-YRNITLWLKYAEFEM--KNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFER  166 (677)
T ss_pred             HHHHHHHHHHHhcc-cccchHHHHHHHHHH--hhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHHH
Confidence            46788888765554 222223 66777778  9999999999999865  3443 2343344444456889999999988


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      =.  ...|+...|.+-|+-=.+-..+  |+.+++...    ++..|--....=.++|.+..|+.||+.-.+
T Consensus       167 W~--~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerAie  235 (677)
T KOG1915|consen  167 WM--EWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERAIE  235 (677)
T ss_pred             HH--cCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            43  3679999999999999998888  999999887    677777777777889999999999886654

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

Probab=94.56  E-value=2.3  Score=35.38  Aligned_cols=117  Identities=10%  Similarity=0.049  Sum_probs=74.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCCcc-cHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSR----IDSHKNGVLMYLDLLKSDVRRDNY-TFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~----~~~~~~a~~~~~~M~~~g~~p~~~-t~~~ll   94 (230)
                      ...+.+..+...|++++|.+.+++..  .| |...++. ...+..    .+....+.+.+..  ..+..|+.. ....+-
T Consensus        45 ~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a  121 (355)
T cd05804          45 RAHVEALSAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLA  121 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHH
Confidence            44444444338899999999998754  33 4444442 223333    3444444444433  222334332 223344


Q ss_pred             HHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           95 KGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        95 ~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ..+...|++  |...++...     +...+..+-..|...|++++|...+++..+
T Consensus       122 ~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~  176 (355)
T cd05804         122 FGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRD  176 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhh
Confidence            567788888  877777776     677888899999999999999999997664

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.

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

Probab=94.41  E-value=0.8  Score=41.21  Aligned_cols=120  Identities=12%  Similarity=0.131  Sum_probs=83.9

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc-ccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN-YTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~-~t~~~ll~~~~   98 (230)
                      +.|-..|.  ..|.++.|..+|...-  -|. ....|-|-.-|-+.|++++|..-|++-.+  ++|+- ..|+.+=+.|.
T Consensus       358 ~NLgni~~--E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmGnt~k  433 (966)
T KOG4626|consen  358 NNLGNIYR--EQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMGNTYK  433 (966)
T ss_pred             HHHHHHHH--HhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcchHHH
Confidence            66666777  7777777777766544  233 33577788888888999999998888554  56642 24555555666


Q ss_pred             hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh
Q 042210           99 RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG  146 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~  146 (230)
                      ..|+.  |.+.+....     -....+.|-+.|-..|++.+|..-+++--.  ||..
T Consensus       434 e~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPDfp  490 (966)
T KOG4626|consen  434 EMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPDFP  490 (966)
T ss_pred             HhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCCCc
Confidence            66666  555555554     355678899999999999999999987654  6653

>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=94.39  E-value=0.28  Score=34.93  Aligned_cols=91  Identities=7%  Similarity=-0.067  Sum_probs=58.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhh-hHhHHHHHHHHHHhcCC
Q 042210           51 SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVM-RVFVQNALISTYCLCGE  129 (230)
Q Consensus        51 ~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~-~~~~~~~li~~y~~~g~  129 (230)
                      |..++.++|.++++.|+++....+.+.  -.|+.++...=..-   +.. +.       -+. +..+..+++++|+..|+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~--~WgI~~~~~~~~~~---~~~-~s-------pl~Pt~~lL~AIv~sf~~n~~   67 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKS--VWGIDVNGKKKEGD---YPP-SS-------PLYPTSRLLIAIVHSFGYNGD   67 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHH--hcCCCCCCccccCc---cCC-CC-------CCCCCHHHHHHHHHHHHhccc
Confidence            345788899999999999988888753  33444332100000   000 00       011 78888889999999999


Q ss_pred             HHHHHHHHhhccC--C---ChhhhHHHHHH
Q 042210          130 VDMARGIFYMSCE--D---DDGLHELIRIK  154 (230)
Q Consensus       130 ~~~A~~vf~~m~~--~---~~~t~n~li~~  154 (230)
                      +..|.++.+...+  |   +-.+|..|+.-
T Consensus        68 i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   68 IFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            9999999887765  1   24567777653

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

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

Probab=94.19  E-value=0.38  Score=41.48  Aligned_cols=114  Identities=8%  Similarity=0.022  Sum_probs=78.2

Q ss_pred             HHhcCCC-CCcH-HHHHHHHhhhccCChHHHHHHHHhc-C--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC
Q 042210           12 IKLGLLT-KPHC-PKQTRYLLLYEKGDLKYECKVFRKI-T--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD   86 (230)
Q Consensus        12 ~~~g~~~-~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m-~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   86 (230)
                      ....+.| |+.+ +.|-+.|-  +.|+-..|++.+-+- +  +.|+.+-.=|-..|....-++++...|+.  ..-+.|+
T Consensus       583 q~~slip~dp~ilskl~dlyd--qegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ek--aaliqp~  658 (840)
T KOG2003|consen  583 QANSLIPNDPAILSKLADLYD--QEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEK--AALIQPN  658 (840)
T ss_pred             HhcccCCCCHHHHHHHHHHhh--cccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHH--HHhcCcc
Confidence            3344555 5666 88999999  999988888765432 2  55665555566667777778888888765  2346788


Q ss_pred             cccHHHHHHHhhh-cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCC
Q 042210           87 NYTFPFLFKGFTR-DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGE  129 (230)
Q Consensus        87 ~~t~~~ll~~~~~-~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~  129 (230)
                      .+-|..+|..|.+ .|+.  |..++++.-     |+...--|+...+..|.
T Consensus       659 ~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  659 QSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            8888888776654 4666  666666654     77777777777666654

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

Probab=94.12  E-value=3.2  Score=37.65  Aligned_cols=110  Identities=13%  Similarity=0.093  Sum_probs=75.7

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCC------CCCCcccHHHHHHHhhhcCch---
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD------VRRDNYTFPFLFKGFTRDIAG---  103 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g------~~p~~~t~~~ll~~~~~~~~~---  103 (230)
                      ..+-++-+..++..-.+-+...-+--|..++..+++++|-+.+.......      -+-+..-|.-+.+..++.-+.   
T Consensus       150 ~~~lPets~rvyrRYLk~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~s  229 (835)
T KOG2047|consen  150 SHGLPETSIRVYRRYLKVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQS  229 (835)
T ss_pred             hCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcc
Confidence            44455555555555443333445667777888888888888887765421      233455666666666665544   


Q ss_pred             --hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          104 --SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       104 --a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                        ..++.+.+.      -...|++|-+-|.+.|++|+|+++|++-.+
T Consensus       230 lnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  230 LNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             cCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence              666666666      478999999999999999999999997543

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

Probab=94.11  E-value=0.88  Score=42.31  Aligned_cols=108  Identities=14%  Similarity=0.111  Sum_probs=87.4

Q ss_pred             CCCCcHHHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHH
Q 042210           17 LTKPHCPKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFL   93 (230)
Q Consensus        17 ~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~l   93 (230)
                      .|+.....++.++...|.|+.++|..+++...   .-|..|..++-.+|-..+..++|..+|++-.+  .-|+..-...+
T Consensus        39 ~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~--~~P~eell~~l  116 (932)
T KOG2053|consen   39 HPNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQ--KYPSEELLYHL  116 (932)
T ss_pred             CCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHh--hCCcHHHHHHH
Confidence            36654477788887669999999999998876   44778999999999999999999999998654  45777778889


Q ss_pred             HHHhhhcCch------hhHHHhhhh-hHhHHHHHHHHHHh
Q 042210           94 FKGFTRDIAG------SLEKSCIVM-RVFVQNALISTYCL  126 (230)
Q Consensus        94 l~~~~~~~~~------a~~~~~~~~-~~~~~~~li~~y~~  126 (230)
                      +.+|.|.+++      |.++++..+ ..+.+-+.++.+..
T Consensus       117 FmayvR~~~yk~qQkaa~~LyK~~pk~~yyfWsV~Slilq  156 (932)
T KOG2053|consen  117 FMAYVREKSYKKQQKAALQLYKNFPKRAYYFWSVISLILQ  156 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHH
Confidence            9999999887      788888777 77777777776653

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

Probab=94.10  E-value=2.3  Score=33.52  Aligned_cols=45  Identities=13%  Similarity=0.109  Sum_probs=21.9

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ..|+...|..-+++..   +.+..+|.++-..|-+.|..+.|.+-|+.
T Consensus        47 ~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~Yrk   94 (250)
T COG3063          47 QQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRK   94 (250)
T ss_pred             HCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHH
Confidence            5555555555555443   12223445555555555555555555544

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=94.09  E-value=1.5  Score=32.66  Aligned_cols=27  Identities=11%  Similarity=-0.010  Sum_probs=16.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      .|..+-..+...|++++|...|++...
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~   63 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALK   63 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345555555566666666666666544

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

Probab=94.08  E-value=0.66  Score=37.30  Aligned_cols=111  Identities=14%  Similarity=0.070  Sum_probs=61.2

Q ss_pred             HHHhhhcCch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC-CChhhhHHHHH-------Hh-hhcchhh
Q 042210           94 FKGFTRDIAG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE-DDDGLHELIRI-------KA-VDDDLHE  162 (230)
Q Consensus        94 l~~~~~~~~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-~~~~t~n~li~-------~~-~~~~~~~  162 (230)
                      ...|+..++.  |........+......=+..+.|..++|.|++.+..|.+ .+..|-|-|-.       +. ...+|+-
T Consensus       115 a~i~~~~~~~deAl~~~~~~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfy  194 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLGENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFY  194 (299)
T ss_pred             hHHhhcCCChHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHH
Confidence            3445566666  555555433444444444455666777777777777776 33334333322       11 2346677


Q ss_pred             hHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          163 LFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       163 ~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      +|++|-+.-  .|+.-+.+++.+         +|...|++++|+.++..+...
T Consensus       195 ifeE~s~k~--~~T~~llnG~Av---------~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  195 IFEELSEKT--PPTPLLLNGQAV---------CHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             HHHHHhccc--CCChHHHccHHH---------HHHHhcCHHHHHHHHHHHHhc
Confidence            777765543  344455555334         555667777777776665544

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

Probab=94.04  E-value=1.1  Score=38.89  Aligned_cols=105  Identities=10%  Similarity=-0.018  Sum_probs=53.2

Q ss_pred             ccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      ..|+.++|+..++.+.  .| |+..+.....-+...++..+|.+.++.+...  .|+ ....-.+-+++.+.|+.  +..
T Consensus       318 ~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~  395 (484)
T COG4783         318 LAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIR  395 (484)
T ss_pred             HhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHH
Confidence            4455555555555543  33 3334444455555566666666666655442  233 22233334455555555  333


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ++....     |+..|..|-.+|.+.|+..+|..-.-+
T Consensus       396 ~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE  433 (484)
T COG4783         396 ILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAE  433 (484)
T ss_pred             HHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHH
Confidence            333332     566666666666666666555544443

>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=93.93  E-value=0.096  Score=32.37  Aligned_cols=49  Identities=16%  Similarity=0.192  Sum_probs=36.1

Q ss_pred             ccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           33 EKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      +.|++++|.+.|+.+.  .| |...+-.+..+|.+.|++++|..+++.....
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6778888888888765  33 5566677888888888888888888776553

...

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=93.81  E-value=1.2  Score=38.52  Aligned_cols=90  Identities=11%  Similarity=0.156  Sum_probs=75.6

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCCcccHHHHHHHhhhcCch-hhHHHhhhh-----hHhHHHHHHHHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD-VRRDNYTFPFLFKGFTRDIAG-SLEKSCIVM-----RVFVQNALISTY  124 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~~p~~~t~~~ll~~~~~~~~~-a~~~~~~~~-----~~~~~~~li~~y  124 (230)
                      ...|.+.|++--+...++.|-.+|.+..+.| +.|+...+++.|.-++..... |..+|+.-.     +..--+-.++.+
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~fL  476 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYNIFELGLLKFPDSTLYKEKYLLFL  476 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHHHHHHHHHhCCCchHHHHHHHHHH
Confidence            3468889999889899999999999999999 679999999999999887666 888887655     455557788888


Q ss_pred             HhcCCHHHHHHHHhhcc
Q 042210          125 CLCGEVDMARGIFYMSC  141 (230)
Q Consensus       125 ~~~g~~~~A~~vf~~m~  141 (230)
                      .+.++-+.|+.+|+.-.
T Consensus       477 i~inde~naraLFetsv  493 (660)
T COG5107         477 IRINDEENARALFETSV  493 (660)
T ss_pred             HHhCcHHHHHHHHHHhH
Confidence            99999999999999443

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

Probab=93.70  E-value=0.19  Score=32.67  Aligned_cols=44  Identities=5%  Similarity=0.143  Sum_probs=17.9

Q ss_pred             ccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210           33 EKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      +.|+.++|..+++..+  ..+....-.+-.+|.+.|++++|..+|+
T Consensus        37 ~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen   37 QQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             HTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            5555555555554422  1111111122334444555555555544

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=93.49  E-value=2.9  Score=32.64  Aligned_cols=24  Identities=8%  Similarity=-0.029  Sum_probs=11.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHH
Q 042210           55 WNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        55 yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +-.+...+.+.|+++.|...|++.
T Consensus        36 ~~~~g~~~~~~~~~~~A~~~~~~~   59 (235)
T TIGR03302        36 LYEEAKEALDSGDYTEAIKYFEAL   59 (235)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            333444444555555555555554

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).

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=93.37  E-value=0.28  Score=30.00  Aligned_cols=52  Identities=17%  Similarity=0.265  Sum_probs=41.5

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      ..+.  +.|++++|...|+...  .| +...|..+-..+.+.|++++|...|++..+
T Consensus         5 ~~~~--~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALY--QQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHH--HCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3455  8999999999999976  33 456777888888899999999999998754

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=93.25  E-value=1.8  Score=29.43  Aligned_cols=86  Identities=12%  Similarity=0.049  Sum_probs=49.7

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhCC--CCCCcccHHHHHHH
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD--VRRDNYTFPFLFKG   96 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g--~~p~~~t~~~ll~~   96 (230)
                      +...+.  +.|+.++|.+.|..+.  .|+    ...+..+-..+.+.|+++.|...|+......  -+.....+..+-.+
T Consensus         8 ~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~   85 (119)
T TIGR02795         8 AALLVL--KAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMS   85 (119)
T ss_pred             HHHHHH--HcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHH
Confidence            344455  7777777777777764  232    1234456666777777777777777765432  11112345555556


Q ss_pred             hhhcCch--hhHHHhhhh
Q 042210           97 FTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        97 ~~~~~~~--a~~~~~~~~  112 (230)
                      +.+.|+.  +...+..+.
T Consensus        86 ~~~~~~~~~A~~~~~~~~  103 (119)
T TIGR02795        86 LQELGDKEKAKATLQQVI  103 (119)
T ss_pred             HHHhCChHHHHHHHHHHH
Confidence            6666666  555555544

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.

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

Probab=93.22  E-value=1.1  Score=39.62  Aligned_cols=123  Identities=12%  Similarity=0.095  Sum_probs=89.1

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh--CCCCCCccc----HHHHHHHhhhcCch
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK--SDVRRDNYT----FPFLFKGFTRDIAG  103 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~--~g~~p~~~t----~~~ll~~~~~~~~~  103 (230)
                      +.++++.|.++|.+..   +.|+...|-+=...-..+.+.+|...|+.-..  ..+-+...+    ++.|=.+|.+.+..
T Consensus       392 ~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~  471 (611)
T KOG1173|consen  392 RTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKY  471 (611)
T ss_pred             HhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhH
Confidence            7889999999998865   66777777775555667889999999987542  223333323    44444466666666


Q ss_pred             --hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc--CCChhhhHHHHHHh
Q 042210          104 --SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC--EDDDGLHELIRIKA  155 (230)
Q Consensus       104 --a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~--~~~~~t~n~li~~~  155 (230)
                        |...++...     +..+++++-=.|...|+++.|.+-|++--  .||-.+-+.|++.+
T Consensus       472 ~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  472 EEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHH
Confidence              555555554     89999999889999999999999999764  48887777776643

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

Probab=93.10  E-value=1.8  Score=37.89  Aligned_cols=45  Identities=11%  Similarity=0.128  Sum_probs=20.7

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      |.++++++...|++.+   +.....||-.-..+...++++.|.+.|+.
T Consensus       440 r~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~  487 (606)
T KOG0547|consen  440 RQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDK  487 (606)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHH
Confidence            4445555555554443   12233444444444444555555555444

>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=93.09  E-value=6.2  Score=35.25  Aligned_cols=134  Identities=7%  Similarity=0.059  Sum_probs=91.2

Q ss_pred             HHHHHHHHhcCCCCCcHHHHHHHHhhhccCChHHHHHHHHhcC------------------CCChhhH--HHHHHHHHhc
Q 042210            6 QIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKIT------------------QPSVFLW--NTMIKGYSRI   65 (230)
Q Consensus         6 ~~~~~m~~~g~~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~------------------~~~~~~y--n~li~~~~~~   65 (230)
                      .....+.+.|+ |+.+ +.|-..|.  .....+-..+++....                  .|....|  .-+-..|-+.
T Consensus       132 ~yl~~~l~Kgv-PslF-~~lk~Ly~--d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~  207 (517)
T PF12569_consen  132 EYLRPQLRKGV-PSLF-SNLKPLYK--DPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYL  207 (517)
T ss_pred             HHHHHHHhcCC-chHH-HHHHHHHc--ChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHh
Confidence            33444444553 2222 56666666  5555554555554431                  2333334  5556677889


Q ss_pred             CChhHHHHHHHHHHhCCCCCCc-ccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHH
Q 042210           66 DSHKNGVLMYLDLLKSDVRRDN-YTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIF  137 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~~g~~p~~-~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf  137 (230)
                      |++++|++..++-+..  .|+. .-|..--+.+-+.|++  |.+..+...     |.++=+-...-+-|+|++++|.+++
T Consensus       208 g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~  285 (517)
T PF12569_consen  208 GDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTA  285 (517)
T ss_pred             CCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            9999999999975553  3542 3566667888899999  777777766     8998899999999999999999999


Q ss_pred             hhccCCCh
Q 042210          138 YMSCEDDD  145 (230)
Q Consensus       138 ~~m~~~~~  145 (230)
                      ..-.+++.
T Consensus       286 ~~Ftr~~~  293 (517)
T PF12569_consen  286 SLFTREDV  293 (517)
T ss_pred             HhhcCCCC
Confidence            88877653

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 [], [].

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=93.02  E-value=1.4  Score=37.32  Aligned_cols=92  Identities=7%  Similarity=0.006  Sum_probs=52.6

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      ..|++++|.+.|++..   ..+...|..+-.+|.+.|++++|+..+++..+.  .|+                       
T Consensus        14 ~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l--~P~-----------------------   68 (356)
T PLN03088         14 VDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIEL--DPS-----------------------   68 (356)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcC-----------------------
Confidence            4556666666665543   223344555555555566666666665554432  121                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR  152 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li  152 (230)
                         +...|..+-.+|...|++++|...|++..+  |+.......+
T Consensus        69 ---~~~a~~~lg~~~~~lg~~~eA~~~~~~al~l~P~~~~~~~~l  110 (356)
T PLN03088         69 ---LAKAYLRKGTACMKLEEYQTAKAALEKGASLAPGDSRFTKLI  110 (356)
T ss_pred             ---CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence               344566666677788888888888887664  5544433333

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=92.98  E-value=4.2  Score=37.70  Aligned_cols=106  Identities=8%  Similarity=-0.088  Sum_probs=80.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+++...+  +.|+...  ..+...+.  +.+++++|....+...  .|+ ....+.+-.++.+.|++++|..+|+
T Consensus       103 ~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~--~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~  178 (694)
T PRK15179        103 DEGLAVWRGIHQ--RFPDSSEAFILMLRGVK--RQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEIGQSEQADACFE  178 (694)
T ss_pred             HHHHHHHHHHHh--hCCCcHHHHHHHHHHHH--HhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHHHHHHH
Confidence            455556655444  4687665  67788888  9999999999999876  444 4456667778888999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~  112 (230)
                      +....+ +-+..++..+=.++-..|+.  |...|....
T Consensus       179 ~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~  215 (694)
T PRK15179        179 RLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGL  215 (694)
T ss_pred             HHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            988732 22355777888888888988  878787776

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=92.82  E-value=1.2  Score=36.35  Aligned_cols=105  Identities=9%  Similarity=0.010  Sum_probs=76.7

Q ss_pred             HHHHHHHHhcC--CCChhhHHHHHHHHHhc-----CChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch-------
Q 042210           38 KYECKVFRKIT--QPSVFLWNTMIKGYSRI-----DSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-------  103 (230)
Q Consensus        38 ~~a~~~~~~m~--~~~~~~yn~li~~~~~~-----~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-------  103 (230)
                      --.++.|...+  ++|-.+|-+.+..+...     +.++=....++.|++.|+.-|..+|+.||+.+-+..-+       
T Consensus        51 v~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~  130 (406)
T KOG3941|consen   51 VHVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQK  130 (406)
T ss_pred             cchhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHH
Confidence            34456676666  77778888888888653     55555666678899999999999999999988765322       


Q ss_pred             -----------hhHHHhhhh------hHhHHHHHHHHHHhcCC-HHHHHHHHhhccC
Q 042210          104 -----------SLEKSCIVM------RVFVQNALISTYCLCGE-VDMARGIFYMSCE  142 (230)
Q Consensus       104 -----------a~~~~~~~~------~~~~~~~li~~y~~~g~-~~~A~~vf~~m~~  142 (230)
                                 +..++++|.      |..+-..||+++++.+- ..+..++.-.|++
T Consensus       131 ~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmPk  187 (406)
T KOG3941|consen  131 VFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMPK  187 (406)
T ss_pred             HHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhhhh
Confidence                       455566665      77888888888888765 4556666666664

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

Probab=92.60  E-value=4.8  Score=35.10  Aligned_cols=134  Identities=10%  Similarity=0.077  Sum_probs=99.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...|+...+.  -|....  +.+=+-|.  ...+...|.+-++...   +.|...|=.+=.+|.-.+.+.=|+-.|+
T Consensus       347 EKAv~YFkRALkL--Np~~~~aWTLmGHEyv--EmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfq  422 (559)
T KOG1155|consen  347 EKAVMYFKRALKL--NPKYLSAWTLMGHEYV--EMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQ  422 (559)
T ss_pred             HHHHHHHHHHHhc--CcchhHHHHHhhHHHH--HhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHH
Confidence            3555566554444  344444  33446677  7777777777776644   6677778888888888888877888877


Q ss_pred             HHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           77 DLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        77 ~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +-.  .++| |...|.+|=++|.+.+++  |...+....     +...+..|-+.|-+.++.++|...|+.-.
T Consensus       423 kA~--~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v  493 (559)
T KOG1155|consen  423 KAL--ELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYV  493 (559)
T ss_pred             HHH--hcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            643  3666 788999999999999998  888888777     44888999999999999999999888644

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.59  E-value=1.7  Score=35.86  Aligned_cols=132  Identities=11%  Similarity=0.049  Sum_probs=82.1

Q ss_pred             hhhHHHHHHHHHh--cCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh--cCch------hhHHHhhhh---------
Q 042210           52 VFLWNTMIKGYSR--IDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR--DIAG------SLEKSCIVM---------  112 (230)
Q Consensus        52 ~~~yn~li~~~~~--~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~--~~~~------a~~~~~~~~---------  112 (230)
                      ..++.+++.....  ...++....+++.|++.|++-+..+|-+..-....  ..+.      +..+++.|.         
T Consensus        60 ~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~  139 (297)
T PF13170_consen   60 RFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSP  139 (297)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCc
Confidence            4455555544443  12344677888999999999998888774444433  2232      899999998         


Q ss_pred             hHhHHHHHHHHHHhcCCH----HHHHHHHhhccC-----CChhhhHHHHHHhh-------hcchhhhHHHHHHHhhhcCc
Q 042210          113 RVFVQNALISTYCLCGEV----DMARGIFYMSCE-----DDDGLHELIRIKAV-------DDDLHELFPEYLVQMLALPD  176 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~----~~A~~vf~~m~~-----~~~~t~n~li~~~~-------~~~~~~~~~~m~~~~~~~p~  176 (230)
                      +-.++.+|+..  ...++    +.++..++.+.+     -|..-+-+-|-+..       ..++.++++.+.+.+ +++.
T Consensus       140 ~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~-~kik  216 (297)
T PF13170_consen  140 EDYPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNG-VKIK  216 (297)
T ss_pred             cchhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcC-Cccc
Confidence            56677777766  33333    555666666654     23333333222221       246778888888887 6666


Q ss_pred             hhhhhhhhhc
Q 042210          177 TFMGEGLEVI  186 (230)
Q Consensus       177 ~~t~~~l~~~  186 (230)
                      ...|..+.++
T Consensus       217 ~~~yp~lGlL  226 (297)
T PF13170_consen  217 YMHYPTLGLL  226 (297)
T ss_pred             cccccHHHHH
Confidence            6667766666

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

Probab=92.50  E-value=2.7  Score=39.20  Aligned_cols=94  Identities=14%  Similarity=0.103  Sum_probs=79.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHH
Q 042210           51 SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALIST  123 (230)
Q Consensus        51 ~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~  123 (230)
                      +.-.|--+-.+|-+.|.+.+|+++|..+.....--+...|--+-.++-..|..  |.+.+....     +.-.--+|-+.
T Consensus       413 ~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl  492 (895)
T KOG2076|consen  413 DVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASL  492 (895)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHH
Confidence            45578889999999999999999999998877666788898888999888888  888888887     44444556678


Q ss_pred             HHhcCCHHHHHHHHhhccCCC
Q 042210          124 YCLCGEVDMARGIFYMSCEDD  144 (230)
Q Consensus       124 y~~~g~~~~A~~vf~~m~~~~  144 (230)
                      |-+.|+.|+|.++++.|..||
T Consensus       493 ~~~~g~~EkalEtL~~~~~~D  513 (895)
T KOG2076|consen  493 YQQLGNHEKALETLEQIINPD  513 (895)
T ss_pred             HHhcCCHHHHHHHHhcccCCC
Confidence            899999999999999998877

>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=92.46  E-value=2.8  Score=37.34  Aligned_cols=113  Identities=10%  Similarity=-0.069  Sum_probs=51.9

Q ss_pred             HHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCC-------ChhhhHHHHHHhhhcc
Q 042210           94 FKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCED-------DDGLHELIRIKAVDDD  159 (230)
Q Consensus        94 l~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~-------~~~t~n~li~~~~~~~  159 (230)
                      -..|-..|+.  |.+..+...     .+..|..--..|-+.|++++|.+..+.-+.-       |..+--.++.+...++
T Consensus       201 Aqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~  280 (517)
T PF12569_consen  201 AQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEE  280 (517)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHH
Confidence            3344444444  444444433     3444444445555555555555555554431       1112222334444445


Q ss_pred             hhhhHHHHHHHhhhcCchhhhhhhhhcccccC------CcccccccCCccCCccccccccc
Q 042210          160 LHELFPEYLVQMLALPDTFMGEGLEVIPKSQA------PREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       160 ~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~------~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      |.+.+....+.+ ..|-.       -+..||+      .-.+|.+.|++..|.+-+..+.+
T Consensus       281 A~~~~~~Ftr~~-~~~~~-------~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  281 AEKTASLFTRED-VDPLS-------NLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHHHHHhhcCCC-CCccc-------CHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            555544443333 11211       1222222      23377788888887765554443

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 [], [].

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.17  E-value=3.2  Score=29.67  Aligned_cols=120  Identities=12%  Similarity=0.024  Sum_probs=77.9

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..++..+.  +.+.++....+++.+.   ..+....|.+|..|++.. .....+.++.      .++......+++.|.+
T Consensus        11 ~~vv~~~~--~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~   81 (140)
T smart00299       11 SEVVELFE--KRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHH--hCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHH
Confidence            67888888  8888888888888865   234567899999998763 4445555542      2355666778888888


Q ss_pred             cCch--hhHHHhhhhhHhHHHHHHHHHHhc-CCHHHHHHHHhhccCCChhhhHHHHHHhh
Q 042210          100 DIAG--SLEKSCIVMRVFVQNALISTYCLC-GEVDMARGIFYMSCEDDDGLHELIRIKAV  156 (230)
Q Consensus       100 ~~~~--a~~~~~~~~~~~~~~~li~~y~~~-g~~~~A~~vf~~m~~~~~~t~n~li~~~~  156 (230)
                      .+.+  +..++..+.   -|.-.++.+.+. ++++.|.+.+.+-.  +...|..++..+.
T Consensus        82 ~~l~~~~~~l~~k~~---~~~~Al~~~l~~~~d~~~a~~~~~~~~--~~~lw~~~~~~~l  136 (140)
T smart00299       82 AKLYEEAVELYKKDG---NFKDAIVTLIEHLGNYEKAIEYFVKQN--NPELWAEVLKALL  136 (140)
T ss_pred             cCcHHHHHHHHHhhc---CHHHHHHHHHHcccCHHHHHHHHHhCC--CHHHHHHHHHHHH
Confidence            7776  556665554   122233334333 77788887777632  4446666665443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=92.05  E-value=3  Score=30.89  Aligned_cols=27  Identities=4%  Similarity=-0.001  Sum_probs=17.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      .|..+...+...|++++|...|++-..
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~   63 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMR   63 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            455555566666777777777766544

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=91.99  E-value=1.9  Score=36.44  Aligned_cols=90  Identities=9%  Similarity=0.014  Sum_probs=67.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      +.|.+++++.++.  .|+...  ..+-.+|.  +.|++++|...++...   ..+...|..+-.+|.+.|++++|...|+
T Consensus        19 ~~Ai~~~~~Al~~--~P~~~~a~~~~a~~~~--~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~eA~~~~~   94 (356)
T PLN03088         19 ALAVDLYTQAIDL--DPNNAELYADRAQANI--KLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQTAKAALE   94 (356)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            4677788877765  454433  55667777  9999999999999875   3456678888889999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHh
Q 042210           77 DLLKSDVRRDNYTFPFLFKGF   97 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~   97 (230)
                      +..+  +.|+...+..++.-|
T Consensus        95 ~al~--l~P~~~~~~~~l~~~  113 (356)
T PLN03088         95 KGAS--LAPGDSRFTKLIKEC  113 (356)
T ss_pred             HHHH--hCCCCHHHHHHHHHH
Confidence            9776  446655555555544

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.90  E-value=1  Score=37.12  Aligned_cols=86  Identities=13%  Similarity=0.175  Sum_probs=62.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-CC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-QP------SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFK   95 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-~~------~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~   95 (230)
                      ..++..-.  ...+++++...+-+++ +|      +...| +.+.-+- .-++++++.+...=++.|+-||..|++.+|+
T Consensus        68 d~~V~v~~--~~~~idd~~~~LyKlRhs~~a~~~~~~~~~-~~irlll-ky~pq~~i~~l~npIqYGiF~dqf~~c~l~D  143 (418)
T KOG4570|consen   68 DRLVDVIS--SREEIDDAEYYLYKLRHSPNAWYLRNWTIH-TWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQFTFCLLMD  143 (418)
T ss_pred             hhhhhccc--cccchhHHHHHHHHHhcCcchhhhccccHH-HHHHHHH-ccChHHHHHHHhCcchhccccchhhHHHHHH
Confidence            55555444  6778999999888776 33      22222 2233333 3467899999998899999999999999999


Q ss_pred             HhhhcCch--hhHHHhhhh
Q 042210           96 GFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        96 ~~~~~~~~--a~~~~~~~~  112 (230)
                      .+.+.+++  |.++...|.
T Consensus       144 ~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  144 SFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             HHHhcccHHHHHHHHHHHH
Confidence            99999999  666666665

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.87  E-value=5.9  Score=32.11  Aligned_cols=126  Identities=13%  Similarity=0.060  Sum_probs=79.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHH---
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFK---   95 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~---   95 (230)
                      +.++..+.  ..+.+.-....+++..    +.+...-..|.+.--+.||.+.|...|++-++..-+.|..+++.++-   
T Consensus       181 y~~~~~ll--G~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  181 YSMANCLL--GMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHh--cchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            55555555  6666655555555554    33445555666666668999999999998777665666666666543   


Q ss_pred             --HhhhcCch--hhHHHhhhh-----hHhHHHH--HHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH
Q 042210           96 --GFTRDIAG--SLEKSCIVM-----RVFVQNA--LISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR  152 (230)
Q Consensus        96 --~~~~~~~~--a~~~~~~~~-----~~~~~~~--li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li  152 (230)
                        .+.-.++.  +...++++.     ++..-|.  |+-.|  .|+..+|.++.+.|.+  |...+-++++
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllY--lg~l~DAiK~~e~~~~~~P~~~l~es~~  326 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLY--LGKLKDALKQLEAMVQQDPRHYLHESVL  326 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHH--HHHHHHHHHHHHHHhccCCccchhhhHH
Confidence              23333444  566666565     4443333  44444  5889999999999987  6666656553

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=91.84  E-value=5  Score=34.98  Aligned_cols=114  Identities=16%  Similarity=0.145  Sum_probs=86.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCChhHHHHHHHH-HHhCCCCCCcccHH-HHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSVFLWNTMIKGYSRIDSHKNGVLMYLD-LLKSDVRRDNYTFP-FLFK   95 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~~~yn~li~~~~~~~~~~~a~~~~~~-M~~~g~~p~~~t~~-~ll~   95 (230)
                      ...|..-.  |..-++.|+.+|-+..     .+++..|+++|.-++. |+..-|.++|+- |+.-   ||...|. --+.
T Consensus       401 C~~~N~v~--r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~f---~d~~~y~~kyl~  474 (660)
T COG5107         401 CVHLNYVL--RKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLKF---PDSTLYKEKYLL  474 (660)
T ss_pred             HHHHHHHH--HHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHhC---CCchHHHHHHHH
Confidence            55666666  8888999999998876     6788899999987775 688889999976 4443   4554443 2355


Q ss_pred             HhhhcCch--hhHHHhhhh-----h--HhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           96 GFTRDIAG--SLEKSCIVM-----R--VFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        96 ~~~~~~~~--a~~~~~~~~-----~--~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      -+.+.++-  |+.+|+...     +  ...|..+|+-=++.|++..|..+=+.|.+
T Consensus       475 fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         475 FLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            56677776  999998554     3  68899999999999999888777666654

>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=91.58  E-value=0.13  Score=32.75  Aligned_cols=54  Identities=17%  Similarity=0.219  Sum_probs=37.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---------CCC-hhhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---------QPS-VFLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---------~~~-~~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +.+-..|.  +.|++++|...|++..         .|+ ..+++.+=..|...|++++|+..+++-
T Consensus         9 ~~la~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    9 NNLARVYR--ELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHH--HTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            55666777  8888888888887653         122 346777777788888888888888763

...

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

Probab=91.52  E-value=0.57  Score=43.86  Aligned_cols=116  Identities=8%  Similarity=0.033  Sum_probs=91.2

Q ss_pred             ChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhh
Q 042210           36 DLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCI  110 (230)
Q Consensus        36 ~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~  110 (230)
                      ..++|.++|.+..   +.|...=|-+=-.++..|++..|..+|.+-+..... +..+|-.+-.+|...|++  |.++|+.
T Consensus       627 ~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~-~~dv~lNlah~~~e~~qy~~AIqmYe~  705 (1018)
T KOG2002|consen  627 HQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSD-FEDVWLNLAHCYVEQGQYRLAIQMYEN  705 (1018)
T ss_pred             HHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhh-CCceeeeHHHHHHHHHHHHHHHHHHHH
Confidence            5678888888764   556666677777888999999999999998876552 334688899999999999  9999988


Q ss_pred             hh-------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C--ChhhhHHHH
Q 042210          111 VM-------RVFVQNALISTYCLCGEVDMARGIFYMSCE--D--DDGLHELIR  152 (230)
Q Consensus       111 ~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~--~~~t~n~li  152 (230)
                      ..       ++.+.+.|-.++-+.|.+.+|.+..-.-..  |  .++-+|..+
T Consensus       706 ~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~a~  758 (1018)
T KOG2002|consen  706 CLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNLAL  758 (1018)
T ss_pred             HHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHHHH
Confidence            77       788889999999999999999887664433  3  345567543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=91.33  E-value=2  Score=40.72  Aligned_cols=128  Identities=13%  Similarity=0.003  Sum_probs=82.7

Q ss_pred             HHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            6 QIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         6 ~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      .++...+...+.|+...  +.|=..|.  ..-+...|.+-|++..   ..|...+-...+.|++..+++.|+.+.-.  .
T Consensus       477 al~ali~alrld~~~apaf~~LG~iYr--d~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~--~  552 (1238)
T KOG1127|consen  477 ALHALIRALRLDVSLAPAFAFLGQIYR--DSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLR--A  552 (1238)
T ss_pred             HHHHHHHHHhcccchhHHHHHHHHHHH--HHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHH--H
Confidence            44444455555555444  44445555  4456778888888766   45667889999999999999999998322  2


Q ss_pred             CCCCC-CcccHHHHHHHhhhcCch---hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           81 SDVRR-DNYTFPFLFKGFTRDIAG---SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        81 ~g~~p-~~~t~~~ll~~~~~~~~~---a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ....| -...++-.-     .|-.   +.+.++.+.           |...|..|.++|.++|++..|.++|++...
T Consensus       553 ~qka~a~~~k~nW~~-----rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~  624 (1238)
T KOG1127|consen  553 AQKAPAFACKENWVQ-----RGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASL  624 (1238)
T ss_pred             hhhchHHHHHhhhhh-----ccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHh
Confidence            11111 111111111     2222   444444333           889999999999999999999999987665

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=91.25  E-value=4.5  Score=29.96  Aligned_cols=79  Identities=15%  Similarity=0.146  Sum_probs=42.7

Q ss_pred             ccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      ..|++++|..+|...-  .| +..-|-.|=.++-..|++++|...|......+  ||                       
T Consensus        47 ~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~--~d-----------------------  101 (157)
T PRK15363         47 EVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK--ID-----------------------  101 (157)
T ss_pred             HCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CC-----------------------
Confidence            5566666666666544  22 22233344444444566666666665543332  21                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                         |+..+-.+=..|-+.|+.+.|++-|+.
T Consensus       102 ---dp~~~~~ag~c~L~lG~~~~A~~aF~~  128 (157)
T PRK15363        102 ---APQAPWAAAECYLACDNVCYAIKALKA  128 (157)
T ss_pred             ---CchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence               455555555666667777777766664

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

Probab=91.00  E-value=4.9  Score=38.25  Aligned_cols=119  Identities=7%  Similarity=-0.050  Sum_probs=72.9

Q ss_pred             hcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCCh---hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC
Q 042210           14 LGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPSV---FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD   86 (230)
Q Consensus        14 ~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~---~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   86 (230)
                      ..+.|+..-  ..|+..+.  ..+++++|.++.+.-.  .|+.   ..|..+  -+.+.++.+.+..+  .+.  +..+.
T Consensus        24 ~~~~p~n~~a~~~Li~~~~--~~~~~deai~i~~~~l~~~P~~i~~yy~~G~--l~~q~~~~~~~~lv--~~l--~~~~~   95 (906)
T PRK14720         24 NNYSLSKFKELDDLIDAYK--SENLTDEAKDICEEHLKEHKKSISALYISGI--LSLSRRPLNDSNLL--NLI--DSFSQ   95 (906)
T ss_pred             ccCCcchHHHHHHHHHHHH--hcCCHHHHHHHHHHHHHhCCcceehHHHHHH--HHHhhcchhhhhhh--hhh--hhccc
Confidence            346666555  88999999  9999999999988654  4443   233333  45555666665555  211  11111


Q ss_pred             c--------------------ccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           87 N--------------------YTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        87 ~--------------------~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      .                    ..+-.+-.+|-+.|+.  +..+++.+.     |..+.|.+--.|+.. ++++|..++..
T Consensus        96 ~~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~K  174 (906)
T PRK14720         96 NLKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKK  174 (906)
T ss_pred             ccchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHH
Confidence            1                    2344455555555666  666666665     666777777777777 77777766665


Q ss_pred             cc
Q 042210          140 SC  141 (230)
Q Consensus       140 m~  141 (230)
                      -.
T Consensus       175 AV  176 (906)
T PRK14720        175 AI  176 (906)
T ss_pred             HH
Confidence            43

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

Probab=90.97  E-value=6.2  Score=31.21  Aligned_cols=144  Identities=10%  Similarity=-0.080  Sum_probs=90.9

Q ss_pred             HHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210            4 LKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus         4 a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      |+.-++...+.  .|+..-  ..+-..|.  +.|+.+.|.+-|.+..   +.+..+.|-.=.-+|..|++++|...|++-
T Consensus        54 A~~nlekAL~~--DPs~~~a~~~~A~~Yq--~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~A  129 (250)
T COG3063          54 AKKNLEKALEH--DPSYYLAHLVRAHYYQ--KLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERA  129 (250)
T ss_pred             HHHHHHHHHHh--CcccHHHHHHHHHHHH--HcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHHHHHHHHH
Confidence            44444444443  355544  44556666  8888888888887754   333334333333346667888888888885


Q ss_pred             HhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHH
Q 042210           79 LKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHEL  150 (230)
Q Consensus        79 ~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~  150 (230)
                      ....--| -..||..+--+..+.|+.  ++..++.-.     .....-.+-....+.|+.-.|+..++....+...+-.+
T Consensus       130 l~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~~~A~s  209 (250)
T COG3063         130 LADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQRGGAQAES  209 (250)
T ss_pred             HhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhcccccHHH
Confidence            5543222 334677776677777877  777777766     45566667777778888888888888776644444344


Q ss_pred             H
Q 042210          151 I  151 (230)
Q Consensus       151 l  151 (230)
                      |
T Consensus       210 L  210 (250)
T COG3063         210 L  210 (250)
T ss_pred             H
Confidence            3

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

Probab=90.91  E-value=12  Score=34.06  Aligned_cols=162  Identities=15%  Similarity=0.176  Sum_probs=88.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-H--HHHHHHhhhccCChHHHHHHHHhcC----CCChh-hHHHHHHHHHh---cCChhH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-P--KQTRYLLLYEKGDLKYECKVFRKIT----QPSVF-LWNTMIKGYSR---IDSHKN   70 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~--~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~-~yn~li~~~~~---~~~~~~   70 (230)
                      +..+.+++.+....+.....+ |  -+|.     .+..++++.++++.-.    .|++. .||.-+.-+.+   ...++.
T Consensus       494 estk~vYdriidLriaTPqii~NyAmfLE-----eh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEr  568 (835)
T KOG2047|consen  494 ESTKAVYDRIIDLRIATPQIIINYAMFLE-----EHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLER  568 (835)
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHH-----hhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHH
Confidence            445677777777765433322 2  1222     4456788888887643    56653 57766666655   356788


Q ss_pred             HHHHHHHHHhCCCCCCcccHHHHHHHhhh--cCch--hhHHHhhhh-------hHhHHHHHHH-----------------
Q 042210           71 GVLMYLDLLKSDVRRDNYTFPFLFKGFTR--DIAG--SLEKSCIVM-------RVFVQNALIS-----------------  122 (230)
Q Consensus        71 a~~~~~~M~~~g~~p~~~t~~~ll~~~~~--~~~~--a~~~~~~~~-------~~~~~~~li~-----------------  122 (230)
                      |-.+|++-.. |++|...-+--|+.+=..  .|-.  +..+++...       -...||..|+                 
T Consensus       569 aRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~a~~l~myni~I~kaae~yGv~~TR~iYek  647 (835)
T KOG2047|consen  569 ARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATSAVKEAQRLDMYNIYIKKAAEIYGVPRTREIYEK  647 (835)
T ss_pred             HHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhCCcccHHHHHH
Confidence            8888888766 787765444333332211  1222  555555544       2334444442                 


Q ss_pred             -------------------HHHhcCCHHHHHHHHhhccC---CCh--hhhHHHHHHhhhcchhhhHHHHHH
Q 042210          123 -------------------TYCLCGEVDMARGIFYMSCE---DDD--GLHELIRIKAVDDDLHELFPEYLV  169 (230)
Q Consensus       123 -------------------~y~~~g~~~~A~~vf~~m~~---~~~--~t~n~li~~~~~~~~~~~~~~m~~  169 (230)
                                         .=++.|++|.|+.++.--.+   |.+  .-|.+-=.=-.+.+..+-.++|++
T Consensus       648 aIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FEvrHGnedT~keMLR  718 (835)
T KOG2047|consen  648 AIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFEVRHGNEDTYKEMLR  718 (835)
T ss_pred             HHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHHHhcCCHHHHHHHHH
Confidence                               22478999999998875443   433  335443222222333444555544

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=90.86  E-value=0.98  Score=27.46  Aligned_cols=27  Identities=15%  Similarity=-0.075  Sum_probs=12.0

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210          114 VFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus       114 ~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      ...+..+-..+...|++++|...|++.
T Consensus        31 ~~a~~~lg~~~~~~g~~~~A~~~~~~a   57 (65)
T PF13432_consen   31 PEAWYLLGRILYQQGRYDEALAYYERA   57 (65)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            333444444444455555555555444

>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=90.74  E-value=0.067  Score=38.69  Aligned_cols=112  Identities=14%  Similarity=0.127  Sum_probs=61.9

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~   98 (230)
                      ..+++.+.  +.+.++....+++.+.    ..+....|.++..|++.++.+...++++.       .+......+++.|.
T Consensus        11 ~~vi~~~~--~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~   81 (143)
T PF00637_consen   11 SEVISAFE--ERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCE   81 (143)
T ss_dssp             CCCHHHCT--TTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHH
T ss_pred             HHHHHHHH--hCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHH
Confidence            34556666  6666666666666554    23455677777777777666666666551       11122234555555


Q ss_pred             hcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----------CChhhhHHHHHHhhh
Q 042210           99 RDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE-----------DDDGLHELIRIKAVD  157 (230)
Q Consensus        99 ~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----------~~~~t~n~li~~~~~  157 (230)
                      +.|.              |...+-.|.+.|+.++|.++...+..           +|...|..+++.+..
T Consensus        82 ~~~l--------------~~~a~~Ly~~~~~~~~al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l~  137 (143)
T PF00637_consen   82 KHGL--------------YEEAVYLYSKLGNHDEALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCLD  137 (143)
T ss_dssp             TTTS--------------HHHHHHHHHCCTTHTTCSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHCT
T ss_pred             hcch--------------HHHHHHHHHHcccHHHHHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHHh
Confidence            4433              33334467777777777665444332           445566666665543

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.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=90.61  E-value=0.97  Score=28.12  Aligned_cols=52  Identities=12%  Similarity=0.146  Sum_probs=42.8

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      ..|.  +.+++++|.++++.+.   +.+...|...=..+.+.|++.+|...|+...+
T Consensus         3 ~~~~--~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYL--QQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHH--hCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            4567  8999999999999876   44556677777788899999999999998764

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

Probab=90.12  E-value=1.6  Score=38.97  Aligned_cols=175  Identities=10%  Similarity=-0.026  Sum_probs=100.4

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhh--h
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFT--R   99 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~--~   99 (230)
                      =++.+.  +.+++++|....+++.   +-|...+.+=+.+..+.+.+++|+.+.+.   .+..-....|. .=++||  +
T Consensus        18 ~ln~~~--~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk---~~~~~~~~~~~-fEKAYc~Yr   91 (652)
T KOG2376|consen   18 DLNRHG--KNGEYEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKK---NGALLVINSFF-FEKAYCEYR   91 (652)
T ss_pred             HHHHhc--cchHHHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHh---cchhhhcchhh-HHHHHHHHH
Confidence            356677  8899999999998876   23445566666788999999999966443   22111111111 344454  3


Q ss_pred             cCch--hhHHHhhhh--hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHHHHhhhcchhhhHHHHHHHhhhcC
Q 042210          100 DIAG--SLEKSCIVM--RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLALP  175 (230)
Q Consensus       100 ~~~~--a~~~~~~~~--~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li~~~~~~~~~~~~~~m~~~~~~~p  175 (230)
                      .+..  +...+.-..  +..+-..=-..+-|.|++++|.+++..+.+.+...+-.-+......-+-.+--...+.-...|
T Consensus        92 lnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~  171 (652)
T KOG2376|consen   92 LNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVP  171 (652)
T ss_pred             cccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCC
Confidence            4444  444444222  333333334566789999999999999977666666665554332211111111222222334


Q ss_pred             chhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          176 DTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       176 ~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                       ..||..  +++...    .+...|.+.+|++++...
T Consensus       172 -e~syel--~yN~Ac----~~i~~gky~qA~elL~kA  201 (652)
T KOG2376|consen  172 -EDSYEL--LYNTAC----ILIENGKYNQAIELLEKA  201 (652)
T ss_pred             -cchHHH--HHHHHH----HHHhcccHHHHHHHHHHH
Confidence             334444  333111    344678888998887766

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=89.95  E-value=0.77  Score=25.77  Aligned_cols=36  Identities=19%  Similarity=0.110  Sum_probs=28.3

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHH
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGLHEL  150 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~  150 (230)
                      .+|..+-..|.+.|++++|+++|++..+  || ...|..
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~   40 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRA   40 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHH
Confidence            4577888999999999999999999876  54 334443

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

Probab=89.86  E-value=4.4  Score=37.91  Aligned_cols=171  Identities=10%  Similarity=0.098  Sum_probs=107.5

Q ss_pred             HHHHhhhccCChHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccH----------
Q 042210           26 TRYLLLYEKGDLKYECKVFRKIT-----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTF----------   90 (230)
Q Consensus        26 l~~~~~~~~~~~~~a~~~~~~m~-----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~----------   90 (230)
                      ++.|-  ..++-+.|.+.++...     .-+...+|.+...|.+...++.|.....++......+|..-|          
T Consensus       287 ~~~~~--~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~  364 (895)
T KOG2076|consen  287 AHYFI--THNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEP  364 (895)
T ss_pred             HHHHH--HhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccc
Confidence            44555  6666677777776654     223445788888888888899999888888762222222222          


Q ss_pred             ------------HHHH-H---HhhhcCch--hhHHHhhhh--------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--
Q 042210           91 ------------PFLF-K---GFTRDIAG--SLEKSCIVM--------RVFVQNALISTYCLCGEVDMARGIFYMSCE--  142 (230)
Q Consensus        91 ------------~~ll-~---~~~~~~~~--a~~~~~~~~--------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--  142 (230)
                                  ..=+ +   +..+....  ...+.....        ++..|.-+.++|...|.+.+|.++|..+..  
T Consensus       365 ~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~  444 (895)
T KOG2076|consen  365 NALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNRE  444 (895)
T ss_pred             cccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCc
Confidence                        1111 1   11111111  222222222        678888899999999999999999999986  


Q ss_pred             --CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc----hhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          143 --DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD----TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       143 --~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~----~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                        .+...|--+-.++..    ++|.+.++......   ||    .+|..+            -+.+.|+.|+|.+.+..+
T Consensus       445 ~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~---p~~~D~Ri~Las------------l~~~~g~~EkalEtL~~~  509 (895)
T KOG2076|consen  445 GYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILA---PDNLDARITLAS------------LYQQLGNHEKALETLEQI  509 (895)
T ss_pred             cccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcC---CCchhhhhhHHH------------HHHhcCCHHHHHHHHhcc
Confidence              344566666666653    56777777665543   55    334444            345889999988877765


Q ss_pred             c
Q 042210          213 H  213 (230)
Q Consensus       213 ~  213 (230)
                      .
T Consensus       510 ~  510 (895)
T KOG2076|consen  510 I  510 (895)
T ss_pred             c
Confidence            4

>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=89.64  E-value=1.3  Score=31.95  Aligned_cols=41  Identities=12%  Similarity=0.101  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhh
Q 042210          116 VQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAV  156 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~  156 (230)
                      ....++..+...|++++|.++......  | |-..|-.+|.++.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~  107 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALA  107 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            344445555555555555555555543  2 2334555555443

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=89.61  E-value=4.1  Score=29.08  Aligned_cols=89  Identities=6%  Similarity=-0.056  Sum_probs=59.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch-hhHHHhhhhhHhHHHHHHHHHHhcCCHH
Q 042210           53 FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-SLEKSCIVMRVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        53 ~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-a~~~~~~~~~~~~~~~li~~y~~~g~~~  131 (230)
                      .....+|..+...+.+.....+++.+...+- .+...++.++..|++...- ....+..-.+.+....++..+-+.+.++
T Consensus         8 ~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~~~~ll~~l~~~~~~yd~~~~~~~c~~~~l~~   86 (140)
T smart00299        8 IDVSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYDPQKEIERLDNKSNHYDIEKVGKLCEKAKLYE   86 (140)
T ss_pred             CCHHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHCHHHHHHHHHhccccCCHHHHHHHHHHcCcHH
Confidence            3455688888888899999999999888773 5777899999999987665 4444442112233333555555556666


Q ss_pred             HHHHHHhhccC
Q 042210          132 MARGIFYMSCE  142 (230)
Q Consensus       132 ~A~~vf~~m~~  142 (230)
                      ++.-++..+..
T Consensus        87 ~~~~l~~k~~~   97 (140)
T smart00299       87 EAVELYKKDGN   97 (140)
T ss_pred             HHHHHHHhhcC
Confidence            66666665543

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

Probab=89.58  E-value=2.2  Score=30.77  Aligned_cols=102  Identities=8%  Similarity=-0.057  Sum_probs=69.8

Q ss_pred             hHHHHHHHHHHhcCCCCC-cH--HHH--HHHHhhhccCChHHHHHHHHhcC--CCChh----hHHHHHHHHHhcCChhHH
Q 042210            3 QLKQIHSQTIKLGLLTKP-HC--PKQ--TRYLLLYEKGDLKYECKVFRKIT--QPSVF----LWNTMIKGYSRIDSHKNG   71 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~-~~--~~l--l~~~~~~~~~~~~~a~~~~~~m~--~~~~~----~yn~li~~~~~~~~~~~a   71 (230)
                      .+...++.+.+..  |+. ..  ..|  -..+.  ..|++++|...|+...  .||..    ..-.+-..+...|++++|
T Consensus        29 ~~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~--~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~A  104 (145)
T PF09976_consen   29 KAEAAAEQLAKDY--PSSPYAALAALQLAKAAY--EQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEA  104 (145)
T ss_pred             HHHHHHHHHHHHC--CCChHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            4566677777764  333 33  333  36677  9999999999999876  34432    333456677789999999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhh
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCI  110 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~  110 (230)
                      +..++......+.|.  .+...=+.+.+.|+.  |...|..
T Consensus       105 l~~L~~~~~~~~~~~--~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  105 LATLQQIPDEAFKAL--AAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHhccCcchHHH--HHHHHHHHHHHCCCHHHHHHHHHH
Confidence            999977544444433  455566788889998  8877764

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

Probab=89.36  E-value=14  Score=35.69  Aligned_cols=101  Identities=15%  Similarity=-0.086  Sum_probs=67.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--h----------------hHHHhhh
Q 042210           50 PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--S----------------LEKSCIV  111 (230)
Q Consensus        50 ~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a----------------~~~~~~~  111 (230)
                      -|...|--+|+...+.|.+++-.+.+..-++..-.|...  +.||-+|++.+++  .                .+.|+.-
T Consensus      1131 dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~ 1208 (1666)
T KOG0985|consen 1131 DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEK 1208 (1666)
T ss_pred             CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhh
Confidence            355678889999999999998888777666666667654  4788899988776  1                2222211


Q ss_pred             h---------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHHHH
Q 042210          112 M---------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIK  154 (230)
Q Consensus       112 ~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li~~  154 (230)
                      .         ++.-|.-|-..+...|++..|.+--++-  .+..||--.--+
T Consensus      1209 ~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKA--ns~ktWK~Vcfa 1258 (1666)
T KOG0985|consen 1209 MYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKA--NSTKTWKEVCFA 1258 (1666)
T ss_pred             hhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhc--cchhHHHHHHHH
Confidence            1         5666777777888888877776544432  355566654333

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

Probab=89.34  E-value=9.8  Score=36.31  Aligned_cols=130  Identities=12%  Similarity=0.073  Sum_probs=80.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      -.+-.+|-  +.|+.++|..+|++..   ..|...-|-+-..|+.. ++++|..++..-...               +..
T Consensus       120 ~~LA~~Yd--k~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~---------------~i~  181 (906)
T PRK14720        120 RTLAEAYA--KLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR---------------FIK  181 (906)
T ss_pred             HHHHHHHH--HcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH---------------HHh
Confidence            44556666  7788888888887765   44566667776677777 777777777664332               221


Q ss_pred             cCch--hhHHHhhhh-------------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhH
Q 042210          100 DIAG--SLEKSCIVM-------------------------RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHE  149 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-------------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n  149 (230)
                      ..+.  +..+|..+.                         -+.++--|-.-|-+..+++++..+|...-+   .|...-.
T Consensus       182 ~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~  261 (906)
T PRK14720        182 KKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKARE  261 (906)
T ss_pred             hhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHH
Confidence            2222  223333332                         234444455778888899999999998765   5666666


Q ss_pred             HHHHHhhhc-chhhhHHHHHHH
Q 042210          150 LIRIKAVDD-DLHELFPEYLVQ  170 (230)
Q Consensus       150 ~li~~~~~~-~~~~~~~~m~~~  170 (230)
                      -++.+|... +....|++..+-
T Consensus       262 ~l~~~y~~kY~~~~~~ee~l~~  283 (906)
T PRK14720        262 ELIRFYKEKYKDHSLLEDYLKM  283 (906)
T ss_pred             HHHHHHHHHccCcchHHHHHHH
Confidence            677777632 335555555443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=89.22  E-value=2.7  Score=34.24  Aligned_cols=72  Identities=10%  Similarity=0.050  Sum_probs=60.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh-----CCCCCCcccHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-----SDVRRDNYTFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-----~g~~p~~~t~~~ll   94 (230)
                      ..++..+.  ..|+.+.+.+.++++-   +-|-..|-.+|.+|.+.|+...|.+.|+.+.+     .|+.|...+.....
T Consensus       157 ~~lae~~~--~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~  234 (280)
T COG3629         157 TKLAEALI--ACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYE  234 (280)
T ss_pred             HHHHHHHH--hcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHH
Confidence            66777788  8899999999998876   45667899999999999999999999998866     58999887777766


Q ss_pred             HH
Q 042210           95 KG   96 (230)
Q Consensus        95 ~~   96 (230)
                      ..
T Consensus       235 ~~  236 (280)
T COG3629         235 EI  236 (280)
T ss_pred             HH
Confidence            66

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=89.00  E-value=2.5  Score=39.05  Aligned_cols=78  Identities=8%  Similarity=-0.044  Sum_probs=62.2

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           64 RIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        64 ~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ....|.+|+.+++.++.....-  .-|..+-+.|+..|++  |+++|..   .-.++-.|.+|++.|+++.|.++-++..
T Consensus       744 ~akew~kai~ildniqdqk~~s--~yy~~iadhyan~~dfe~ae~lf~e---~~~~~dai~my~k~~kw~da~kla~e~~  818 (1636)
T KOG3616|consen  744 GAKEWKKAISILDNIQDQKTAS--GYYGEIADHYANKGDFEIAEELFTE---ADLFKDAIDMYGKAGKWEDAFKLAEECH  818 (1636)
T ss_pred             hhhhhhhhHhHHHHhhhhcccc--ccchHHHHHhccchhHHHHHHHHHh---cchhHHHHHHHhccccHHHHHHHHHHhc
Confidence            3567888888888777765543  3478888999999999  8888874   4556777999999999999999999988


Q ss_pred             CCChh
Q 042210          142 EDDDG  146 (230)
Q Consensus       142 ~~~~~  146 (230)
                      .|...
T Consensus       819 ~~e~t  823 (1636)
T KOG3616|consen  819 GPEAT  823 (1636)
T ss_pred             CchhH
Confidence            77543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=88.94  E-value=3.6  Score=30.48  Aligned_cols=57  Identities=5%  Similarity=-0.304  Sum_probs=32.4

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh-h-hhHH---HHHHhhhcchhhhHHHHHH
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD-G-LHEL---IRIKAVDDDLHELFPEYLV  169 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~-~-t~n~---li~~~~~~~~~~~~~~m~~  169 (230)
                      +..-|-.|=-.+-..|++++|...|...-.  ||. . .+|.   .+.....+++.+-|+....
T Consensus        68 ~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363         68 SFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344455555666677888888888886654  433 2 2332   2333334556666665443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=88.90  E-value=6  Score=31.99  Aligned_cols=87  Identities=8%  Similarity=-0.016  Sum_probs=50.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCC----CCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----h---HhHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSD----VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----R---VFVQNA  119 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g----~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~---~~~~~~  119 (230)
                      .|+..+..+.+.|++++|...|+...+.-    ..|+  .+--+-..+...|+.  |...|..+.     +   ...+-.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~--A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~k  222 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPN--ANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFK  222 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHH
Confidence            46666655566688888888888876531    1222  233345555566666  555555554     1   222222


Q ss_pred             HHHHHHhcCCHHHHHHHHhhccC
Q 042210          120 LISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       120 li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +...|.+.|+.++|.++|++..+
T Consensus       223 lg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        223 VGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            34456667777777777776654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.74  E-value=1.9  Score=36.26  Aligned_cols=180  Identities=10%  Similarity=0.040  Sum_probs=91.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHH-----HHh----cCChhHHHHHHHHHHhCCCC----CCccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKG-----YSR----IDSHKNGVLMYLDLLKSDVR----RDNYT   89 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~-----~~~----~~~~~~a~~~~~~M~~~g~~----p~~~t   89 (230)
                      -.++--|.  +.+++.+|..+.+++.+-...  .-++.+     +++    .....-|...|+---.++..    |...+
T Consensus       289 lNL~iYyL--~q~dVqeA~~L~Kdl~PttP~--EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQs  364 (557)
T KOG3785|consen  289 LNLIIYYL--NQNDVQEAISLCKDLDPTTPY--EYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQS  364 (557)
T ss_pred             hhheeeec--ccccHHHHHHHHhhcCCCChH--HHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHH
Confidence            33455566  899999999998888633322  222222     222    22333455555544344433    33333


Q ss_pred             HHHHHHHhhhcCch---hhHHHhhhh--hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHHHH-Hhhhcch
Q 042210           90 FPFLFKGFTRDIAG---SLEKSCIVM--RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELIRI-KAVDDDL  160 (230)
Q Consensus        90 ~~~ll~~~~~~~~~---a~~~~~~~~--~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~li~-~~~~~~~  160 (230)
                      ..+-+-.+.+-.++   ...+-....  |.+.+| +-.+++-.|+..+|+++|-.+..   +|-.+|-+++. +|...+-
T Consensus       365 mAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkk  443 (557)
T KOG3785|consen  365 MASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKK  443 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCC
Confidence            22222222221111   111111111  455444 45677888999999999988876   46678888765 5555554


Q ss_pred             hhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          161 HELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       161 ~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      -++.=+|.-......+.++.-.  ++      .+-|-+.+.+=-|-+.|+.+...
T Consensus       444 P~lAW~~~lk~~t~~e~fsLLq--lI------An~CYk~~eFyyaaKAFd~lE~l  490 (557)
T KOG3785|consen  444 PQLAWDMMLKTNTPSERFSLLQ--LI------ANDCYKANEFYYAAKAFDELEIL  490 (557)
T ss_pred             chHHHHHHHhcCCchhHHHHHH--HH------HHHHHHHHHHHHHHHhhhHHHcc
Confidence            4444444333322223333222  32      22555666655555555555543

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.52  E-value=5.6  Score=32.82  Aligned_cols=113  Identities=14%  Similarity=0.132  Sum_probs=73.4

Q ss_pred             HHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-------------CCccc-
Q 042210           28 YLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVR-------------RDNYT-   89 (230)
Q Consensus        28 ~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~-------------p~~~t-   89 (230)
                      +|...+.|+.+.|.+-|+...    -...+.||.-+..| +.++...|++...++.++|++             ||..+ 
T Consensus       151 gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsv  229 (459)
T KOG4340|consen  151 GCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSV  229 (459)
T ss_pred             hheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcc
Confidence            343348888999988888765    23456788777544 457888899988888877654             22111 


Q ss_pred             -------HHHHHH-------HhhhcCch--hhHHHhhhh----------------------------------------h
Q 042210           90 -------FPFLFK-------GFTRDIAG--SLEKSCIVM----------------------------------------R  113 (230)
Q Consensus        90 -------~~~ll~-------~~~~~~~~--a~~~~~~~~----------------------------------------~  113 (230)
                             -+.++.       .+-+.++.  |++-+.+|+                                        .
T Consensus       230 gNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqFLL~~nPfP  309 (459)
T KOG4340|consen  230 GNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQFLLQQNPFP  309 (459)
T ss_pred             cchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcccCCccccHHHHHHHHhcCCCC
Confidence                   112222       22344555  555555555                                        5


Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          114 VFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       114 ~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..|+..++-.|||..-++-|.+|+-+=.
T Consensus       310 ~ETFANlLllyCKNeyf~lAADvLAEn~  337 (459)
T KOG4340|consen  310 PETFANLLLLYCKNEYFDLAADVLAENA  337 (459)
T ss_pred             hHHHHHHHHHHhhhHHHhHHHHHHhhCc
Confidence            6777888888888888888888877644

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

Probab=88.48  E-value=5.7  Score=34.90  Aligned_cols=111  Identities=10%  Similarity=-0.008  Sum_probs=54.1

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~  102 (230)
                      .+|.  ...+.++-...|++..   +-|.-+|.--=..+.-.+++++|..=|++-++  +.| +...|.-+-.+.-|.+.
T Consensus       368 ~~y~--d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~--L~pe~~~~~iQl~~a~Yr~~k  443 (606)
T KOG0547|consen  368 AAYA--DENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAIS--LDPENAYAYIQLCCALYRQHK  443 (606)
T ss_pred             HHHh--hhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhh--cChhhhHHHHHHHHHHHHHHH
Confidence            4455  6666777777776654   22222333222223333455555555554333  223 22233333333334444


Q ss_pred             h--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          103 G--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       103 ~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +  ++..|++..     -+.+||-.-..+...+++++|.+-|+.-.
T Consensus       444 ~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai  489 (606)
T KOG0547|consen  444 IAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAI  489 (606)
T ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHH
Confidence            4  555555554     45556655566666666666666555443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=88.32  E-value=7  Score=27.50  Aligned_cols=21  Identities=0%  Similarity=0.091  Sum_probs=10.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHH
Q 042210           58 MIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        58 li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +-+.+-..|++++|..+|++-
T Consensus        44 lastlr~LG~~deA~~~L~~~   64 (120)
T PF12688_consen   44 LASTLRNLGRYDEALALLEEA   64 (120)
T ss_pred             HHHHHHHcCCHHHHHHHHHHH
Confidence            333444455555555555553

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=88.12  E-value=14  Score=30.79  Aligned_cols=85  Identities=7%  Similarity=-0.046  Sum_probs=65.3

Q ss_pred             CCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHH
Q 042210           17 LTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFK   95 (230)
Q Consensus        17 ~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~   95 (230)
                      -|+.-. -.-+.+++  +.+++++-.++...  +..+.-|-.++.+|.+.|+..+|..+...          .++.--+.
T Consensus       205 v~dkrfw~lki~aLa--~~~~w~eL~~fa~s--kKsPIGyepFv~~~~~~~~~~eA~~yI~k----------~~~~~rv~  270 (319)
T PF04840_consen  205 VPDKRFWWLKIKALA--ENKDWDELEKFAKS--KKSPIGYEPFVEACLKYGNKKEASKYIPK----------IPDEERVE  270 (319)
T ss_pred             CcHHHHHHHHHHHHH--hcCCHHHHHHHHhC--CCCCCChHHHHHHHHHCCCHHHHHHHHHh----------CChHHHHH
Confidence            367777 88899999  99999999887665  44568899999999999999999988766          34467888


Q ss_pred             HhhhcCch--hhHHHhhhhhHh
Q 042210           96 GFTRDIAG--SLEKSCIVMRVF  115 (230)
Q Consensus        96 ~~~~~~~~--a~~~~~~~~~~~  115 (230)
                      .|.++|++  |-+.-....|..
T Consensus       271 ~y~~~~~~~~A~~~A~~~kd~~  292 (319)
T PF04840_consen  271 MYLKCGDYKEAAQEAFKEKDID  292 (319)
T ss_pred             HHHHCCCHHHHHHHHHHcCCHH
Confidence            89999987  444333333433

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

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=88.04  E-value=4.4  Score=29.69  Aligned_cols=71  Identities=8%  Similarity=0.095  Sum_probs=49.1

Q ss_pred             HHHHHHHhhh-ccCChHHHHHHHHhcC--CCC---hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHH
Q 042210           23 PKQTRYLLLY-EKGDLKYECKVFRKIT--QPS---VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG   96 (230)
Q Consensus        23 ~~ll~~~~~~-~~~~~~~a~~~~~~m~--~~~---~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~   96 (230)
                      +.||+....+ ...+++++..+++.|.  .|+   ..++...|  +.++|++.+|.++|++....+..+   .|..-+.+
T Consensus        11 ~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~~~~---p~~kAL~A   85 (153)
T TIGR02561        11 GGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSAGAP---PYGKALLA   85 (153)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccCCCc---hHHHHHHH
Confidence            5555554422 7789999999999987  444   45666664  567899999999999998875332   34444444


Q ss_pred             hh
Q 042210           97 FT   98 (230)
Q Consensus        97 ~~   98 (230)
                      +|
T Consensus        86 ~C   87 (153)
T TIGR02561        86 LC   87 (153)
T ss_pred             HH
Confidence            44

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=88.01  E-value=7.1  Score=27.48  Aligned_cols=92  Identities=10%  Similarity=0.066  Sum_probs=61.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH---HHHHHHHhhhccCChHHHHHHHHhcC--CCC---h-hhHHHHHHHHHhcCChhHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC---PKQTRYLLLYEKGDLKYECKVFRKIT--QPS---V-FLWNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~---~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~---~-~~yn~li~~~~~~~~~~~a~   72 (230)
                      ++|..+++.....|...+...   -.+-+.+.  ..|++++|..+|++..  .|+   . ...-.+--++...|+.++|+
T Consensus        18 ~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr--~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~gr~~eAl   95 (120)
T PF12688_consen   18 EEAIPLYRRALAAGLSGADRRRALIQLASTLR--NLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNLGRPKEAL   95 (120)
T ss_pred             HHHHHHHHHHHHcCCCchHHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHCCCHHHHH
Confidence            478889999999887765333   33446677  8999999999999865  354   1 11112223667789999999


Q ss_pred             HHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           73 LMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        73 ~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      +.+-.-...    +...|.--|..|++
T Consensus        96 ~~~l~~la~----~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   96 EWLLEALAE----TLPRYRRAIRFYAD  118 (120)
T ss_pred             HHHHHHHHH----HHHHHHHHHHHHHh
Confidence            988664432    33356665655543

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=87.92  E-value=1.1  Score=23.88  Aligned_cols=24  Identities=21%  Similarity=0.164  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          116 VQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      +|+.|=..|.+.|++++|..+|++
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~   24 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQ   24 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHH
Confidence            477888999999999999999987

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=87.90  E-value=0.18  Score=36.40  Aligned_cols=111  Identities=8%  Similarity=0.007  Sum_probs=71.3

Q ss_pred             HHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 042210            5 KQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDV   83 (230)
Q Consensus         5 ~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~   83 (230)
                      .+..+.+.+.+-..+... +.++..|+  +.++.++..++++....   .-...++..|-+.|.++++.-++.++....-
T Consensus        27 ~~yLe~~~~~~~~~~~~~~~~L~~ly~--~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~a~~Ly~~~~~~~~  101 (143)
T PF00637_consen   27 IEYLEALVKENKENNPDLHTLLLELYI--KYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEEAVYLYSKLGNHDE  101 (143)
T ss_dssp             TCCHHHHHHTSTC-SHHHHHHHHHHHH--CTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHHHHHHHHCCTTHTT
T ss_pred             HHHHHHHHhcccccCHHHHHHHHHHHH--hcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHHHHHHHHHcccHHH
Confidence            345566666665566777 99999999  99888888888874433   3345577788888888888888877543211


Q ss_pred             CCCcccHHHHHHHhhhcCch--hhHHHhhhhhHhHHHHHHHHHHhcCC
Q 042210           84 RRDNYTFPFLFKGFTRDIAG--SLEKSCIVMRVFVQNALISTYCLCGE  129 (230)
Q Consensus        84 ~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~~~~~~~~li~~y~~~g~  129 (230)
                               .+..+...+++  |.+......+..+|..+++.+...+.
T Consensus       102 ---------al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l~~~~  140 (143)
T PF00637_consen  102 ---------ALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCLDSKP  140 (143)
T ss_dssp             ---------CSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHCTSTC
T ss_pred             ---------HHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHHhcCc
Confidence                     11113333444  55445545577778777777765543

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.

>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=87.75  E-value=2.5  Score=26.66  Aligned_cols=65  Identities=14%  Similarity=0.087  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A  133 (230)
                      +|+.+=..|...|++++|+..|++-.+.               +...|+-      ......+++.+-..|.+.|++++|
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~---------------~~~~~~~------~~~~a~~~~~lg~~~~~~g~~~~A   65 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDI---------------EEQLGDD------HPDTANTLNNLGECYYRLGDYEEA   65 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH---------------HHHTTTH------HHHHHHHHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH---------------HHHHCCC------CHHHHHHHHHHHHHHHHcCCHHHH
Confidence            5677777788888888888888774332               0000100      000255666777788888888888


Q ss_pred             HHHHhh
Q 042210          134 RGIFYM  139 (230)
Q Consensus       134 ~~vf~~  139 (230)
                      .+.|++
T Consensus        66 ~~~~~~   71 (78)
T PF13424_consen   66 LEYYQK   71 (78)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887775

...

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

Probab=87.63  E-value=4.3  Score=36.09  Aligned_cols=97  Identities=11%  Similarity=0.007  Sum_probs=48.2

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC------CChhhhHHHHH----Hhh----hcchhhhHHHHHHHhhhcCchh
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE------DDDGLHELIRI----KAV----DDDLHELFPEYLVQMLALPDTF  178 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~------~~~~t~n~li~----~~~----~~~~~~~~~~m~~~~~~~p~~~  178 (230)
                      |+.+.+=+=-.+-..+.+.+|...|..-..      +...+|-.+..    .+.    .++|+..++.-..--...+  .
T Consensus       413 Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~--~  490 (611)
T KOG1173|consen  413 DPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDA--S  490 (611)
T ss_pred             cchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCch--h
Confidence            444444433333445666666666664432      22224544432    222    2466666665544332233  3


Q ss_pred             hhhhhhhcccccCCcccccccCCccCCccccccccccCCCcccc
Q 042210          179 MGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSL  222 (230)
Q Consensus       179 t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~  222 (230)
                      |+.++..         .+...|+++.|...+..  ...+.||..
T Consensus       491 ~~asig~---------iy~llgnld~Aid~fhK--aL~l~p~n~  523 (611)
T KOG1173|consen  491 THASIGY---------IYHLLGNLDKAIDHFHK--ALALKPDNI  523 (611)
T ss_pred             HHHHHHH---------HHHHhcChHHHHHHHHH--HHhcCCccH
Confidence            3444223         46677888888766553  234455543

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=87.27  E-value=13  Score=33.12  Aligned_cols=94  Identities=11%  Similarity=0.134  Sum_probs=65.0

Q ss_pred             HHHHHHH-HHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 042210            5 KQIHSQT-IKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLL   79 (230)
Q Consensus         5 ~~~~~~m-~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~   79 (230)
                      .++|-.+ ...+-++|+.+ ..|=-.|-  -.|.+++|..-|+...   +-|...||-|=..++...+..+|..-|++-.
T Consensus       414 ~~~fLeaa~~~~~~~DpdvQ~~LGVLy~--ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rAL  491 (579)
T KOG1125|consen  414 QELFLEAARQLPTKIDPDVQSGLGVLYN--LSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRAL  491 (579)
T ss_pred             HHHHHHHHHhCCCCCChhHHhhhHHHHh--cchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHH
Confidence            3444444 45555567777 55555555  7889999999999865   4467899999999999999999999998865


Q ss_pred             hCCCCCCcc--cHHHHHHHhhhcCch
Q 042210           80 KSDVRRDNY--TFPFLFKGFTRDIAG  103 (230)
Q Consensus        80 ~~g~~p~~~--t~~~ll~~~~~~~~~  103 (230)
                      +  ++|+-+  -||.-|. |...|.+
T Consensus       492 q--LqP~yVR~RyNlgIS-~mNlG~y  514 (579)
T KOG1125|consen  492 Q--LQPGYVRVRYNLGIS-CMNLGAY  514 (579)
T ss_pred             h--cCCCeeeeehhhhhh-hhhhhhH
Confidence            5  455432  3444333 5555555

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

Probab=87.26  E-value=22  Score=34.44  Aligned_cols=98  Identities=14%  Similarity=0.234  Sum_probs=72.9

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch-hhHHHhhh
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-SLEKSCIV  111 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-a~~~~~~~  111 (230)
                      ..+++++|.++-+...+|.  .|+-+-.+-.+.|...+|.+-|-+  .    -|...|.-+++.+.+.|.+ -.--+-.|
T Consensus      1087 ~i~~ldRA~efAe~~n~p~--vWsqlakAQL~~~~v~dAieSyik--a----dDps~y~eVi~~a~~~~~~edLv~yL~M 1158 (1666)
T KOG0985|consen 1087 NIGSLDRAYEFAERCNEPA--VWSQLAKAQLQGGLVKDAIESYIK--A----DDPSNYLEVIDVASRTGKYEDLVKYLLM 1158 (1666)
T ss_pred             HhhhHHHHHHHHHhhCChH--HHHHHHHHHHhcCchHHHHHHHHh--c----CCcHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            4557777777777776666  788998898899999988887632  1    2677899999999999998 22112222


Q ss_pred             h-----hHhHHHHHHHHHHhcCCHHHHHHHHh
Q 042210          112 M-----RVFVQNALISTYCLCGEVDMARGIFY  138 (230)
Q Consensus       112 ~-----~~~~~~~li~~y~~~g~~~~A~~vf~  138 (230)
                      .     .+.+=+.||-+|+|.+++.+-+..+.
T Consensus      1159 aRkk~~E~~id~eLi~AyAkt~rl~elE~fi~ 1190 (1666)
T KOG0985|consen 1159 ARKKVREPYIDSELIFAYAKTNRLTELEEFIA 1190 (1666)
T ss_pred             HHHhhcCccchHHHHHHHHHhchHHHHHHHhc
Confidence            2     66677889999999999988776654

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

Probab=87.13  E-value=12  Score=28.77  Aligned_cols=94  Identities=13%  Similarity=0.054  Sum_probs=70.2

Q ss_pred             CCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHH-HHhcCC--hhHHHHHHHHHHhCCCCCCc
Q 042210           16 LLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKG-YSRIDS--HKNGVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        16 ~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~-~~~~~~--~~~a~~~~~~M~~~g~~p~~   87 (230)
                      ..|+...  ..+-..|.  ..|+.++|...|+...   ..|...|..+-.+ +.+.|+  .++|..++++-.+.+-. +.
T Consensus        68 ~~P~~~~~w~~Lg~~~~--~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~  144 (198)
T PRK10370         68 ANPQNSEQWALLGEYYL--WRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EV  144 (198)
T ss_pred             HCCCCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-Ch
Confidence            3465554  66667888  9999999999999865   4456667666665 356676  58999999997765432 45


Q ss_pred             ccHHHHHHHhhhcCch--hhHHHhhhh
Q 042210           88 YTFPFLFKGFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        88 ~t~~~ll~~~~~~~~~--a~~~~~~~~  112 (230)
                      ..+..+-..+.+.|++  |...|+.+.
T Consensus       145 ~al~~LA~~~~~~g~~~~Ai~~~~~aL  171 (198)
T PRK10370        145 TALMLLASDAFMQADYAQAIELWQKVL  171 (198)
T ss_pred             hHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            5777788888899999  888888876

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=87.00  E-value=10  Score=27.95  Aligned_cols=57  Identities=7%  Similarity=0.091  Sum_probs=43.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ..+...+.  ..|++++|...|+...  .|+    ..+|..+=..|...|++++|...++.-.+.
T Consensus        39 ~~~g~~~~--~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         39 YRDGMSAQ--SEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            33445555  8899999999998874  333    246778888899999999999999886653

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

Probab=86.96  E-value=3.8  Score=37.56  Aligned_cols=125  Identities=10%  Similarity=-0.087  Sum_probs=82.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHH-Hh--C--CCCC-CcccHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDL-LK--S--DVRR-DNYTFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M-~~--~--g~~p-~~~t~~~ll   94 (230)
                      ..+|.+|.  ..|+..+|.++..+-.  +||...|..+-+....-.-+++|+++++.- .+  .  |-.+ +...|....
T Consensus       428 ~~vi~CY~--~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~  505 (777)
T KOG1128|consen  428 DPVILCYL--LLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRSLALLILSNKDFSEAD  505 (777)
T ss_pred             HHHHHHHH--HhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHhhccccccchhHHHHH
Confidence            67888888  8998888888876543  677777877777776666677777777663 22  1  1111 223344443


Q ss_pred             HHh---------------------hhcCch---hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChh
Q 042210           95 KGF---------------------TRDIAG---SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDG  146 (230)
Q Consensus        95 ~~~---------------------~~~~~~---a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~  146 (230)
                      +.+                     .+.+++   ++..+....    +-..||.+-.+|.+.|.-.+|.+.+.+--+-|-.
T Consensus       506 ~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~  585 (777)
T KOG1128|consen  506 KHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ  585 (777)
T ss_pred             HHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence            322                     233343   333333333    7889999999999999999999999987764444


Q ss_pred             hhH
Q 042210          147 LHE  149 (230)
Q Consensus       147 t~n  149 (230)
                      .|+
T Consensus       586 ~w~  588 (777)
T KOG1128|consen  586 HWQ  588 (777)
T ss_pred             CCe
Confidence            443

>PLN02789 farnesyltranstransferase

Probab=86.59  E-value=18  Score=30.24  Aligned_cols=125  Identities=6%  Similarity=-0.054  Sum_probs=83.1

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcC-ChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRID-SHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~-~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      -+-..+.  ..++.++|..+.++..  .| +...|+.-=..+...| ++++++..++++.+.+-+ +...|+.---.+.+
T Consensus        42 ~~ra~l~--~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~l~~  118 (320)
T PLN02789         42 YFRAVYA--SDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWLAEK  118 (320)
T ss_pred             HHHHHHH--cCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHHHHH
Confidence            3444555  7788999999998876  33 3445654444455556 678999999998775433 22345433333334


Q ss_pred             cCch----hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHH
Q 042210          100 DIAG----SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELI  151 (230)
Q Consensus       100 ~~~~----a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~l  151 (230)
                      .|..    ...+.+.+.     +...|+..--.+.+.|+++++.+.++++.+   .|...|+.-
T Consensus       119 l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R  182 (320)
T PLN02789        119 LGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQR  182 (320)
T ss_pred             cCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHH
Confidence            4432    344444444     788888888888999999999999999876   466677754

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=86.51  E-value=5.6  Score=27.13  Aligned_cols=75  Identities=15%  Similarity=0.076  Sum_probs=51.1

Q ss_pred             hHHHHHHHHHHhcCCCCCcHHHHH--HHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            3 QLKQIHSQTIKLGLLTKPHCPKQT--RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~~~ll--~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +|..+-+++...+-.  ..+..+|  ..++  ..|++++|..+.+....||...|-+|  +-.+.|-.++...-+.+|..
T Consensus        23 EA~tIAdwL~~~~~~--~E~v~lIRlsSLm--NrG~Yq~Al~l~~~~~~pdlepw~AL--ce~rlGl~s~l~~rl~rla~   96 (115)
T TIGR02508        23 EANTIADWLHLKGES--EEAVQLIRLSSLM--NRGDYQSALQLGNKLCYPDLEPWLAL--CEWRLGLGSALESRLNRLAA   96 (115)
T ss_pred             HHHHHHHHHhcCCch--HHHHHHHHHHHHH--ccchHHHHHHhcCCCCCchHHHHHHH--HHHhhccHHHHHHHHHHHHh
Confidence            455556665555321  1114444  4455  88999999999999889999988877  55667777777777777777


Q ss_pred             CCC
Q 042210           81 SDV   83 (230)
Q Consensus        81 ~g~   83 (230)
                      +|-
T Consensus        97 sg~   99 (115)
T TIGR02508        97 SGD   99 (115)
T ss_pred             CCC
Confidence            664

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.

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=86.47  E-value=11  Score=30.92  Aligned_cols=104  Identities=11%  Similarity=0.081  Sum_probs=78.3

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHh-CCCCCCcccHHHHHHHhhhc--Cch---hhHHHhhhh-----hHhHHH
Q 042210           50 PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-SDVRRDNYTFPFLFKGFTRD--IAG---SLEKSCIVM-----RVFVQN  118 (230)
Q Consensus        50 ~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-~g~~p~~~t~~~ll~~~~~~--~~~---a~~~~~~~~-----~~~~~~  118 (230)
                      -|...|-.|=..|.+.|+...|..-|..-.+ .|=.|+.  +..+-.++...  +..   +.+++++..     |+..-.
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~--~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEI--LLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHH--HHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHH
Confidence            4677899999999999999999999988544 4554543  44444433333  333   888998888     777777


Q ss_pred             HHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHHHh
Q 042210          119 ALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRIKA  155 (230)
Q Consensus       119 ~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~~~  155 (230)
                      -|--.+...|++.+|...|+.|-+  |....|..+|...
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie~~  270 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIERS  270 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHHHH
Confidence            777889999999999999999987  6667777777643

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=86.40  E-value=0.98  Score=32.36  Aligned_cols=31  Identities=16%  Similarity=0.281  Sum_probs=26.1

Q ss_pred             CChhHHHHHHHHHHhCCCCCCcccHHHHHHHhh
Q 042210           66 DSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFT   98 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~   98 (230)
                      |.-..|..+|+.|..+|-+||.  |+.|+..+.
T Consensus       109 gsk~DaY~VF~kML~~G~pPdd--W~~Ll~~a~  139 (140)
T PF11663_consen  109 GSKTDAYAVFRKMLERGNPPDD--WDALLKEAK  139 (140)
T ss_pred             ccCCcHHHHHHHHHhCCCCCcc--HHHHHHHhc
Confidence            4456789999999999999995  889988763

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

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

Probab=86.07  E-value=22  Score=32.07  Aligned_cols=138  Identities=5%  Similarity=-0.059  Sum_probs=87.9

Q ss_pred             CCCCCcH-HHHHHHHhhhccC-ChHHHHHHHHhcC--CCC--hhhHHHHHHHHHhcCChhHHHHHHH--------HHHhC
Q 042210           16 LLTKPHC-PKQTRYLLLYEKG-DLKYECKVFRKIT--QPS--VFLWNTMIKGYSRIDSHKNGVLMYL--------DLLKS   81 (230)
Q Consensus        16 ~~~~~~~-~~ll~~~~~~~~~-~~~~a~~~~~~m~--~~~--~~~yn~li~~~~~~~~~~~a~~~~~--------~M~~~   81 (230)
                      ..|...+ +.+...+-  ... ...++.+++....  .|+  .++--.++.-....|+++.|.+++.        .+..-
T Consensus       336 ~~p~~~~~~ll~~~t~--~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~  413 (652)
T KOG2376|consen  336 MSPESLFPILLQEATK--VREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEA  413 (652)
T ss_pred             cCchHHHHHHHHHHHH--HHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhh
Confidence            3455555 44554444  222 3566666666654  222  3344556666777899999999999        66666


Q ss_pred             CCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CC
Q 042210           82 DVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------------RVFVQNALISTYCLCGEVDMARGIFYMSCE---DD  144 (230)
Q Consensus        82 g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~  144 (230)
                      +-.|..+.+  +...+.+.++.  +.++++...            -..++.-+.+.--+.|+.++|..+++++.+   +|
T Consensus       414 ~~~P~~V~a--iv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d  491 (652)
T KOG2376|consen  414 KHLPGTVGA--IVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPND  491 (652)
T ss_pred             ccChhHHHH--HHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCch
Confidence            777766554  55555555544  666655555            233444445555678999999999999986   56


Q ss_pred             hhhhHHHHHHhhh
Q 042210          145 DGLHELIRIKAVD  157 (230)
Q Consensus       145 ~~t~n~li~~~~~  157 (230)
                      .-+--.++.+|+.
T Consensus       492 ~~~l~~lV~a~~~  504 (652)
T KOG2376|consen  492 TDLLVQLVTAYAR  504 (652)
T ss_pred             HHHHHHHHHHHHh
Confidence            6666677777764

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=85.62  E-value=15  Score=29.86  Aligned_cols=19  Identities=21%  Similarity=0.202  Sum_probs=10.9

Q ss_pred             HHhcCCHHHHHHHHhhccC
Q 042210          124 YCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       124 y~~~g~~~~A~~vf~~m~~  142 (230)
                      +...|++..|.+.|++..+
T Consensus       206 ~L~~~D~v~A~~~~~~~~~  224 (282)
T PF14938_consen  206 HLAMGDYVAARKALERYCS  224 (282)
T ss_dssp             HHHTT-HHHHHHHHHHHGT
T ss_pred             HHHcCCHHHHHHHHHHHHh
Confidence            3335667777777776554

>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=84.80  E-value=2.4  Score=25.93  Aligned_cols=53  Identities=11%  Similarity=0.202  Sum_probs=37.8

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcC-ChhHHHHHHHHHH
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRID-SHKNGVLMYLDLL   79 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~-~~~~a~~~~~~M~   79 (230)
                      +=..+.  +.|++++|...|++..   +.+...|..+=.+|.+.| ++++|...|+.-.
T Consensus         9 ~g~~~~--~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    9 LGQIYF--QQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHH--HTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHH--HcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            334555  7888888888888765   334556777777777788 6888888887643

...

>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=83.80  E-value=14  Score=32.37  Aligned_cols=98  Identities=12%  Similarity=0.028  Sum_probs=47.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      +.+++.+-  +.|..+.|.++-..-   +     .=.....+.|+++.|.++-++.      ++...|..|-+...+.|+
T Consensus       299 ~~i~~fL~--~~G~~e~AL~~~~D~---~-----~rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~  362 (443)
T PF04053_consen  299 QSIARFLE--KKGYPELALQFVTDP---D-----HRFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEALRQGN  362 (443)
T ss_dssp             HHHHHHHH--HTT-HHHHHHHSS-H---H-----HHHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHHHHTTB
T ss_pred             HHHHHHHH--HCCCHHHHHhhcCCh---H-----HHhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHHHHcCC
Confidence            66677776  777777777764321   1     1122233455555555553222      133355555555555555


Q ss_pred             h--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          103 G--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       103 ~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      +  |+..+....   -|..|+=.|.-.|+.++-.++-+.
T Consensus       363 ~~lAe~c~~k~~---d~~~L~lLy~~~g~~~~L~kl~~~  398 (443)
T PF04053_consen  363 IELAEECYQKAK---DFSGLLLLYSSTGDREKLSKLAKI  398 (443)
T ss_dssp             HHHHHHHHHHCT----HHHHHHHHHHCT-HHHHHHHHHH
T ss_pred             HHHHHHHHHhhc---CccccHHHHHHhCCHHHHHHHHHH
Confidence            5  555555333   233444445555555555544443

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.

>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=83.30  E-value=4.5  Score=24.66  Aligned_cols=26  Identities=19%  Similarity=0.106  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          116 VQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +|..+=..|.+.|++++|...|++..
T Consensus         5 ~~~~~g~~~~~~~~~~~A~~~~~~ai   30 (69)
T PF13414_consen    5 AWYNLGQIYFQQGDYEEAIEYFEKAI   30 (69)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444444444455555555554443

...

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=83.01  E-value=17  Score=26.97  Aligned_cols=72  Identities=8%  Similarity=0.080  Sum_probs=50.3

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhh
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTR   99 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~   99 (230)
                      ..+.  +.|++++|...|++..  .|+    ...|..+-..+.+.|++++|...+++..+.  .|+ ...+..+-..+..
T Consensus        43 ~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~  118 (172)
T PRK02603         43 MSAQ--ADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAVIYHK  118 (172)
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHH
Confidence            4455  8899999999999875  232    357888888999999999999999987663  332 3334444444444


Q ss_pred             cCc
Q 042210          100 DIA  102 (230)
Q Consensus       100 ~~~  102 (230)
                      .|+
T Consensus       119 ~g~  121 (172)
T PRK02603        119 RGE  121 (172)
T ss_pred             cCC
Confidence            444

>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=82.14  E-value=2.9  Score=20.45  Aligned_cols=24  Identities=21%  Similarity=0.180  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          116 VQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ....+-..+...|++++|++++++
T Consensus         3 a~~~la~~~~~~G~~~eA~~~l~~   26 (26)
T PF07721_consen    3 ARLALARALLAQGDPDEAERLLRR   26 (26)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHhC
Confidence            345567788999999999998864

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

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=81.96  E-value=3.9  Score=25.27  Aligned_cols=20  Identities=15%  Similarity=0.111  Sum_probs=10.2

Q ss_pred             HHHhcCCHHHHHHHHhhccC
Q 042210          123 TYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       123 ~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .|.+.+++++|.++++.+..
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~   23 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALE   23 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHH
Confidence            44455555555555555443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.83  E-value=28  Score=32.32  Aligned_cols=105  Identities=11%  Similarity=0.024  Sum_probs=75.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh-CCCCCCcccHHHHHHHhhhcC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-SDVRRDNYTFPFLFKGFTRDI  101 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-~g~~p~~~t~~~ll~~~~~~~  101 (230)
                      +.-+..+.  .-|+-.+|.++-.+.+-||-..|--=+.+++..+++++-+.+=+.++. -|.       -....+|.+.|
T Consensus       688 ~dTv~~li--~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskksPIGy-------~PFVe~c~~~~  758 (829)
T KOG2280|consen  688 HDTVTTLI--LIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKKSPIGY-------LPFVEACLKQG  758 (829)
T ss_pred             HHHHHHHH--HccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccCCCCCc-------hhHHHHHHhcc
Confidence            66667777  888899999999999988888888888889988888877666555543 233       33677788888


Q ss_pred             ch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          102 AG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       102 ~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      +.  |...+....+..   -.+.+|.++|++.+|.++--+
T Consensus       759 n~~EA~KYiprv~~l~---ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  759 NKDEAKKYIPRVGGLQ---EKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             cHHHHhhhhhccCChH---HHHHHHHHhccHHHHHHHHHH
Confidence            77  555555444221   467888888888888776443

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=81.82  E-value=3  Score=22.14  Aligned_cols=25  Identities=12%  Similarity=0.159  Sum_probs=20.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +|+.|=..|.+.|++++|.++|++.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4677788899999999999999884

>PF09477 Type_III_YscG: Bacterial type II secretion system chaperone protein (type_III_yscG); InterPro: IPR013348 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)

Probab=81.71  E-value=10  Score=26.19  Aligned_cols=74  Identities=12%  Similarity=0.044  Sum_probs=48.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHH--HHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQT--RYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll--~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      ++|..+.+++...+-   ..- ..+|  ..++  +.|+++.|...=.....||...|-+|  +-.+.|-.+++...+.++
T Consensus        23 ~EA~tIa~wL~~~~~---~~E~v~lIr~~sLm--NrG~Yq~ALl~~~~~~~pdL~p~~AL--~a~klGL~~~~e~~l~rl   95 (116)
T PF09477_consen   23 QEANTIADWLEQEGE---MEEVVALIRLSSLM--NRGDYQEALLLPQCHCYPDLEPWAAL--CAWKLGLASALESRLTRL   95 (116)
T ss_dssp             HHHHHHHHHHHHTTT---THHHHHHHHHHHHH--HTT-HHHHHHHHTTS--GGGHHHHHH--HHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCc---HHHHHHHHHHHHHH--hhHHHHHHHHhcccCCCccHHHHHHH--HHHhhccHHHHHHHHHHH
Confidence            467778888877754   222 4444  4455  88999999555555668999998777  667788888888888877


Q ss_pred             HhCC
Q 042210           79 LKSD   82 (230)
Q Consensus        79 ~~~g   82 (230)
                      ..+|
T Consensus        96 a~~g   99 (116)
T PF09477_consen   96 ASSG   99 (116)
T ss_dssp             CT-S
T ss_pred             HhCC
Confidence            6654

The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia, and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.; GO: 0009405 pathogenesis; PDB: 3PH0_D 2UWJ_G 2P58_C.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=81.60  E-value=3  Score=22.38  Aligned_cols=27  Identities=19%  Similarity=0.145  Sum_probs=22.7

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .+++.|-..|...|++++|..++++..
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            578889999999999999999998754

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

Probab=81.33  E-value=33  Score=29.80  Aligned_cols=151  Identities=8%  Similarity=-0.062  Sum_probs=97.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH-HHhCCCCCCcccHHHH-HHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD-LLKSDVRRDNYTFPFL-FKGF   97 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~-M~~~g~~p~~~t~~~l-l~~~   97 (230)
                      .-++.+-.+-..++++.|.=-|...+   +.+...|.-|+.+|...|.+.+|.-.-++ |+.-+  .+..+.+.+ -..|
T Consensus       336 alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~--~sA~~LtL~g~~V~  413 (564)
T KOG1174|consen  336 ALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQ--NSARSLTLFGTLVL  413 (564)
T ss_pred             HHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhh--cchhhhhhhcceee
Confidence            34444333227789999988888765   56788999999999999999998876554 33222  233344333 1233


Q ss_pred             h--hcCch-hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHH-------------H
Q 042210           98 T--RDIAG-SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRI-------------K  154 (230)
Q Consensus        98 ~--~~~~~-a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~-------------~  154 (230)
                      .  ..++- |+.+++.-.     -.-.-+.+-..+...|..+++..+++.--.  ||....+.+-.             .
T Consensus       414 ~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~  493 (564)
T KOG1174|consen  414 FPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEY  493 (564)
T ss_pred             ccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHH
Confidence            3  33333 777777665     333445666778888999999999987653  78777666522             1


Q ss_pred             hh--------hcchhhhHHHHHHHhhhcCc
Q 042210          155 AV--------DDDLHELFPEYLVQMLALPD  176 (230)
Q Consensus       155 ~~--------~~~~~~~~~~m~~~~~~~p~  176 (230)
                      |.        .+.+++-.+.|.+++ -.||
T Consensus       494 y~~ALr~dP~~~~sl~Gl~~lEK~~-~~~D  522 (564)
T KOG1174|consen  494 YYKALRQDPKSKRTLRGLRLLEKSD-DESD  522 (564)
T ss_pred             HHHHHhcCccchHHHHHHHHHHhcc-CCCC
Confidence            11        235667777777777 3454

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=81.23  E-value=6.4  Score=26.61  Aligned_cols=31  Identities=10%  Similarity=0.175  Sum_probs=19.3

Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 042210           49 QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLL   79 (230)
Q Consensus        49 ~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~   79 (230)
                      .|+...-++.+.+|-+.+|+..|.++|+-.+
T Consensus        39 VP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          39 VPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            4555556666666666666666666666554

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.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=80.58  E-value=32  Score=31.68  Aligned_cols=65  Identities=11%  Similarity=-0.016  Sum_probs=46.7

Q ss_pred             hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh---------------hhHHHHHHhhhcchhhhHHH
Q 042210          104 SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG---------------LHELIRIKAVDDDLHELFPE  166 (230)
Q Consensus       104 a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~---------------t~n~li~~~~~~~~~~~~~~  166 (230)
                      |.++|..|.|.   .+++......+++++|.++-++.++  ||+.               .--+.++++...+|.++.+.
T Consensus       766 AaeIF~k~gD~---ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQ  842 (1081)
T KOG1538|consen  766 AAEIFLKMGDL---KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQ  842 (1081)
T ss_pred             HHHHHHHhccH---HHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHH
Confidence            77777777644   3567888899999999999998887  5543               12234556666788888887


Q ss_pred             HHHHh
Q 042210          167 YLVQM  171 (230)
Q Consensus       167 m~~~~  171 (230)
                      +....
T Consensus       843 Ltnna  847 (1081)
T KOG1538|consen  843 LTNNA  847 (1081)
T ss_pred             hhhhh
Confidence            77665

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	230
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.81
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.67
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.65
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.12
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.09
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.05
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.03
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.98
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	98.95
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.93
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.9
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.89
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.84
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.84
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.83
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.8
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	98.78
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.77
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.72
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.72
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.65
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.64
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.63
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.62
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.61
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	98.61
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.6
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.59
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.53
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.53
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.51
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.5
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.5
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.48
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.46
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.44
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.43
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.42
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.4
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.39
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.38
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.31
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.28
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.28
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.23
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.21
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.2
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.19
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.15
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	97.99
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	97.99
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.98
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	97.96
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.94
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	97.92
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	97.87
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	97.86
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.83
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	97.8
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.77
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.75
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.72
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	97.71
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	97.71
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.69
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.68
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.68
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.64
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.62
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.6
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	97.52
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.49
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.49
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.49
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.48
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.47
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.45
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.4
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	97.37
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.31
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.31
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.3
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.29
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.28
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.28
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.27
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.24
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.19
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.19
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.19
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.18
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.18
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.16
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.14
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.14
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.11
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.08
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.07
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.06
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.05
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.04
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.97
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	96.94
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	96.93
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	96.93
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.92
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	96.91
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.89
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	96.87
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.85
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	96.8
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	96.78
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.77
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	96.76
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.75
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	96.75
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	96.71
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	96.7
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	96.67
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.66
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	96.63
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	96.6
4g1t_A	472	Interferon-induced protein with tetratricopeptide	96.6
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	96.59
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.57
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.57
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	96.56
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	96.49
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.42
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.41
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	96.39
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.36
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	96.34
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.34
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.32
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.32
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.28
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	96.26
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	96.24
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.23
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	96.2
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	96.2
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.16
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.16
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.15
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.09
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.03
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	96.03
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.02
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	96.0
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	95.99
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.97
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	95.94
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	95.94
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	95.91
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	95.91
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	95.89
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	95.85
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	95.74
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	95.64
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	95.64
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	95.53
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	95.49
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	95.41
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	95.4
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	95.23
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.12
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	95.11
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	95.07
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	94.94
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	94.94
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	94.73
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.61
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	94.33
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	94.29
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	94.07
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	94.07
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	94.06
2l6j_A	111	TPR repeat-containing protein associated with HSP;	93.91
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	93.78
2l6j_A	111	TPR repeat-containing protein associated with HSP;	93.7
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	93.68
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	93.61
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	93.55
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	93.5
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	93.44
2kat_A	115	Uncharacterized protein; NESG, structure, structur	93.43
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	93.35
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	93.33
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.04
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	92.96
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	92.93
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	92.23
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	91.99
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	91.94
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	91.62
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	90.76
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	90.5
2p58_C	116	Putative type III secretion protein YSCG; type III	90.31
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	89.65
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	89.2
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	88.97
1klx_A	138	Cysteine rich protein B; structural genomics, heli	88.86
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	88.12
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	86.63
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	85.29
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	85.21
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	83.35
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	80.65
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	80.09
1klx_A	138	Cysteine rich protein B; structural genomics, heli	80.02

>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=99.98  E-value=2.1e-32  Score=237.94  Aligned_cols=178  Identities=12%  Similarity=0.119  Sum_probs=151.6

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC----CCChhhHHHHHHHHHhcCC---------
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT----QPSVFLWNTMIKGYSRIDS---------   67 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~---------   67 (230)
                      .+..+...+++.+..+++..  +.+|++|+  |.|++++|.++|++|.    +||.++||+||.+|++.+.         
T Consensus         8 ~~e~L~~~~~~k~~~~spe~~l~~~id~c~--k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~   85 (501)
T 4g26_A            8 PSENLSRKAKKKAIQQSPEALLKQKLDMCS--KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPG   85 (501)
T ss_dssp             ----------------CHHHHHHHHHHHTT--TSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHH
T ss_pred             hHHHHHHHHHHhcccCCCHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcch
Confidence            45677888888888776554  88999999  9999999999999998    8999999999999998765         


Q ss_pred             hhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           68 HKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        68 ~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ++.|.++|++|+..|+.||..||++||++|++.|++  |.++|+.|.      |..+||+||.+|++.|++++|.++|++
T Consensus        86 l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~  165 (501)
T 4g26_A           86 LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAH  165 (501)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHH
Confidence            678999999999999999999999999999999999  999999998      999999999999999999999999999


Q ss_pred             ccC----CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhh
Q 042210          140 SCE----DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGL  183 (230)
Q Consensus       140 m~~----~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l  183 (230)
                      |.+    ||..|||+||.+|+.    ++|.+++++|.+.+ ..|+..|++.+
T Consensus       166 M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g-~~ps~~T~~~l  216 (501)
T 4g26_A          166 MVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLV-RQVSKSTFDMI  216 (501)
T ss_dssp             HHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SSBCHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhC-CCcCHHHHHHH
Confidence            985    999999999999885    57999999999998 89999999983

>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=99.97  E-value=4.8e-30  Score=223.03  Aligned_cols=155  Identities=9%  Similarity=0.005  Sum_probs=148.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCC---------hHHHHHHHHhcC----CCChhhHHHHHHHHHhcCC
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGD---------LKYECKVFRKIT----QPSVFLWNTMIKGYSRIDS   67 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~---------~~~a~~~~~~m~----~~~~~~yn~li~~~~~~~~   67 (230)
                      ++|.++|++|++.|++||..+ |+||.+|+  +.+.         +++|.++|++|.    .||.++||+||.+|++.|+
T Consensus        43 ~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~--~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~  120 (501)
T 4g26_A           43 LEALRLYDEARRNGVQLSQYHYNVLLYVCS--LAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDD  120 (501)
T ss_dssp             HHHHHHHHHHHHHTCCCCHHHHHHHHHHHT--TCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCCHhHHHHHHHHHH--hCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC
Confidence            679999999999999999999 99999999  7664         688999999997    8999999999999999999


Q ss_pred             hhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           68 HKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        68 ~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      +++|.++|++|++.|+.||..||++||.+|++.|++  |.++|+.|.      |..+|++||++|++.|++++|.++|++
T Consensus       121 ~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~  200 (501)
T 4g26_A          121 PEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQR  200 (501)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999  999999998      999999999999999999999999999


Q ss_pred             ccC----CChhhhHHHHHHhhhc
Q 042210          140 SCE----DDDGLHELIRIKAVDD  158 (230)
Q Consensus       140 m~~----~~~~t~n~li~~~~~~  158 (230)
                      |++    |+..||++++..++..
T Consensus       201 Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          201 LRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HHHhCCCcCHHHHHHHHHHHhcC
Confidence            985    9999999999988753

>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=1.2e-20  Score=171.24  Aligned_cols=121  Identities=9%  Similarity=0.038  Sum_probs=110.6

Q ss_pred             CcH-HHHHHHHhhhccCChHHHHHHHHhcC-------CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHH
Q 042210           20 PHC-PKQTRYLLLYEKGDLKYECKVFRKIT-------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFP   91 (230)
Q Consensus        20 ~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~   91 (230)
                      ..+ |++|++|+  +.|++++|.++|++|.       .||++|||+||++||+.|++++|.++|++|++.|+.||.+||+
T Consensus       127 ~~TynaLIdglc--K~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYn  204 (1134)
T 3spa_A          127 QQRLLAFFKCCL--LTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYA  204 (1134)
T ss_dssp             HHHHHHHHHHHH--HHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHHHHHHHH--hCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence            346 99999999  9999999999998764       7999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcCch---hhHHHhhhh------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           92 FLFKGFTRDIAG---SLEKSCIVM------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        92 ~ll~~~~~~~~~---a~~~~~~~~------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +||+++|+.|+.   |.+++++|.      |.++||++++++.+.+-++.+++++.++.-
T Consensus       205 tLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p  264 (1134)
T 3spa_A          205 AALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSL  264 (1134)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCC
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCC
Confidence            999999999974   789999998      999999999999998888888888776654

>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=2.2e-20  Score=169.63  Aligned_cols=120  Identities=6%  Similarity=-0.110  Sum_probs=110.8

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHh---CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh------hHhHHHHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLK---SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM------RVFVQNAL  120 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~---~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~------~~~~~~~l  120 (230)
                      ..|||++|++|++.|++++|.++|++|.+   .|+.||.+|||+||++||+.|++  |.++|++|.      |++|||+|
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            35899999999999999999999988764   58999999999999999999999  999999998      99999999


Q ss_pred             HHHHHhcCCH-HHHHHHHhhccC----CChhhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          121 ISTYCLCGEV-DMARGIFYMSCE----DDDGLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       121 i~~y~~~g~~-~~A~~vf~~m~~----~~~~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                      |+++||.|+. ++|.++|++|.+    ||.+|||+++.++.++..++..+++....
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f  262 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTF  262 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCC
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCccc
Confidence            9999999985 789999999986    99999999999999999999888884443

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.67  E-value=1.2e-16  Score=140.34  Aligned_cols=209  Identities=8%  Similarity=-0.046  Sum_probs=171.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|.++|+.+.+.  .++..+ +.+..+|.  +.|++++|.++|+++.   +.+..+|+.++.+|.+.|++++|..+|++
T Consensus       289 ~~A~~~~~~~~~~--~~~~~~~~~l~~~~~--~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  364 (597)
T 2xpi_A          289 RRAEDYLSSINGL--EKSSDLLLCKADTLF--VRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISND  364 (597)
T ss_dssp             HHHHHHHHTSTTG--GGCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcC--CchHHHHHHHHHHHH--HhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            4677888877665  467777 99999999  9999999999999986   45788999999999999999999999999


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhh
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGL  147 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t  147 (230)
                      +.+. .+.+..+|..+..+|.+.|++  |.++|+.+.     +..+|+.++.+|.+.|++++|.++|+++.+   ++..+
T Consensus       365 ~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  443 (597)
T 2xpi_A          365 LVDR-HPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLP  443 (597)
T ss_dssp             HHHH-CTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHH
T ss_pred             HHhh-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHH
Confidence            9853 344678999999999999999  999999886     688999999999999999999999998865   47789


Q ss_pred             hHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc----CCCc
Q 042210          148 HELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH----SQDD  219 (230)
Q Consensus       148 ~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~----~~~~  219 (230)
                      |+.+...+..    ++|.+.|+++.+..  ..+..++..+  ..       .+.+.|++++|.+++..+.+.    +..|
T Consensus       444 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l--~~-------~~~~~g~~~~A~~~~~~~~~~~~~~~~~p  512 (597)
T 2xpi_A          444 YLFLGMQHMQLGNILLANEYLQSSYALF--QYDPLLLNEL--GV-------VAFNKSDMQTAINHFQNALLLVKKTQSNE  512 (597)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCCHHHHHHH--HH-------HHHHTTCHHHHHHHHHHHHHHHHHSCCCS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHH--HH-------HHHHhCCHHHHHHHHHHHHHhhhccccch
Confidence            9998887764    56777777776554  2345556653  22       788999999999999998876    6677


Q ss_pred             c--cccccc
Q 042210          220 M--SLISNS  226 (230)
Q Consensus       220 ~--~~~~n~  226 (230)
                      +  ..+++.
T Consensus       513 ~~~~~~~~~  521 (597)
T 2xpi_A          513 KPWAATWAN  521 (597)
T ss_dssp             GGGHHHHHH
T ss_pred             hhHHHHHHH
Confidence            7  445543

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.65  E-value=7.5e-16  Score=135.18  Aligned_cols=201  Identities=9%  Similarity=0.001  Sum_probs=169.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|.++|+.+.+.+- .+..+ +.++.+|.  +.|+.++|.++|+++.   +.+..+|+.+...|.+.|++++|.++|++
T Consensus       322 ~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~--~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  398 (597)
T 2xpi_A          322 IDVLAITTKILEIDP-YNLDVYPLHLASLH--ESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSK  398 (597)
T ss_dssp             HHHHHHHHHHHHHCT-TCCTTHHHHHHHHH--HHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCc-ccHHHHHHHHHHHH--HhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            578999999988762 25566 99999999  9999999999999886   55688999999999999999999999999


Q ss_pred             HHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChh
Q 042210           78 LLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDG  146 (230)
Q Consensus        78 M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~  146 (230)
                      +.+.  .| +..+|+.+..++.+.|++  |.++++.+.     +..+|+.+...|.+.|++++|.++|+++.+   .+..
T Consensus       399 ~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  476 (597)
T 2xpi_A          399 SSTM--DPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPL  476 (597)
T ss_dssp             HHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHH
T ss_pred             HHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChH
Confidence            9773  34 566999999999999999  999998886     788999999999999999999999999875   5678


Q ss_pred             hhHHHHHHhhh----cchhhhHHHHHHHhh---hcCc--hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          147 LHELIRIKAVD----DDLHELFPEYLVQML---ALPD--TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       147 t~n~li~~~~~----~~~~~~~~~m~~~~~---~~p~--~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      +|+.+...+..    ++|.+.|+++.+...   ..|+  ..++..  +..       +|.+.|++++|..++..+.+.+
T Consensus       477 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~--l~~-------~~~~~g~~~~A~~~~~~~~~~~  546 (597)
T 2xpi_A          477 LLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWAN--LGH-------AYRKLKMYDAAIDALNQGLLLS  546 (597)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHH--HHH-------HHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHH--HHH-------HHHHhcCHHHHHHHHHHHHHhC
Confidence            89999887764    578888888877631   3676  445555  333       8889999999999999888765

>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=99.12  E-value=3.2e-09  Score=88.20  Aligned_cols=201  Identities=11%  Similarity=0.030  Sum_probs=115.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.++.+.+.  .|+...  ..+-..+.  +.|++++|.+.|+++.  .| +..+|+.+-..+.+.|++++|...|+
T Consensus       118 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  193 (388)
T 1w3b_A          118 EGAVQAYVSALQY--NPDLYCVRSDLGNLLK--ALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFE  193 (388)
T ss_dssp             SHHHHHHHHHHHH--CTTCTHHHHHHHHHHH--TTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHH--HccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            4566666666654  355444  44555566  6677777777776654  23 34566666666666777777776666


Q ss_pred             HHHhCC--------------------------------CCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhH
Q 042210           77 DLLKSD--------------------------------VRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFV  116 (230)
Q Consensus        77 ~M~~~g--------------------------------~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~  116 (230)
                      ++.+.+                                +.| +..++..+...+.+.|++  |...++.+.     +..+
T Consensus       194 ~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  273 (388)
T 1w3b_A          194 KAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDA  273 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHH
T ss_pred             HHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHH
Confidence            654421                                123 234555566666666666  555555554     4556


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhHHHHHHhhhcchhhhHHHHHHHhh-hcCc-hhhhhhhhhcccccC
Q 042210          117 QNALISTYCLCGEVDMARGIFYMSCE---DDDGLHELIRIKAVDDDLHELFPEYLVQML-ALPD-TFMGEGLEVIPKSQA  191 (230)
Q Consensus       117 ~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n~li~~~~~~~~~~~~~~m~~~~~-~~p~-~~t~~~l~~~~~~~~  191 (230)
                      |+.+...|.+.|++++|.+.|+++.+   ++..+|+.+...+...+..+...+.++... ..|+ ..++..+..      
T Consensus       274 ~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~------  347 (388)
T 1w3b_A          274 YCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLAS------  347 (388)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHH------
Confidence            66677777777777777777776653   345566666555554333332223222221 2243 223333211      


Q ss_pred             CcccccccCCccCCcccccccccc
Q 042210          192 PREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       192 ~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                         .+.+.|++++|...+..+.+.
T Consensus       348 ---~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          348 ---VLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             ---HHHTTTCCHHHHHHHHHHHTT
T ss_pred             ---HHHHcCCHHHHHHHHHHHHhh
Confidence               667788888888888777663

>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=99.09  E-value=4.4e-09  Score=87.34  Aligned_cols=197  Identities=12%  Similarity=0.069  Sum_probs=146.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...|+.+.+.  .|+.. . ..+...+.  +.|++++|.+.|+++.  .|+ ...+..+-..+...|++++|...|+
T Consensus        84 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  159 (388)
T 1w3b_A           84 QEAIEHYRHALRL--KPDFIDGYINLAAALV--AAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYL  159 (388)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc--CcchHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            5788899988775  47655 4 78889999  9999999999999876  555 4567777788888999999999999


Q ss_pred             HHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh---------------------------------------hH
Q 042210           77 DLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM---------------------------------------RV  114 (230)
Q Consensus        77 ~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~---------------------------------------~~  114 (230)
                      ++.+.  .| +..+|..+-..+.+.|++  |...++.+.                                       +.
T Consensus       160 ~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~  237 (388)
T 1w3b_A          160 KAIET--QPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHA  237 (388)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCH
T ss_pred             HHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCH
Confidence            98774  34 456788888888888887  666665543                                       45


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcc
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIP  187 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~  187 (230)
                      .++..+...|.+.|++++|.+.|+++.+  | +..+|+.+...+..    ++|.+.++++.+..  .++..++..+..  
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~--  313 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC--PTHADSLNNLAN--  313 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC--TTCHHHHHHHHH--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cccHHHHHHHHH--
Confidence            6777888888888899999888888764  4 34567766655543    46677777666543  223444444222  


Q ss_pred             cccCCcccccccCCccCCcccccccccc
Q 042210          188 KSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       188 ~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                             .+.+.|++++|...+..+.+.
T Consensus       314 -------~~~~~g~~~~A~~~~~~al~~  334 (388)
T 1w3b_A          314 -------IKREQGNIEEAVRLYRKALEV  334 (388)
T ss_dssp             -------HHHTTTCHHHHHHHHHHHTTS
T ss_pred             -------HHHHcCCHHHHHHHHHHHHhc
Confidence                   677889999999998887764

>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=99.05  E-value=2.4e-09  Score=90.34  Aligned_cols=205  Identities=11%  Similarity=-0.053  Sum_probs=149.5

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+|+.+.+.  .|+ ... ..+...|.  +.|++++|...|+++.   +.+...|..+...|.+.|++++|...|+
T Consensus        43 ~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  118 (450)
T 2y4t_A           43 ADALSQFHAAVDG--DPDNYIAYYRRATVFL--AMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFK  118 (450)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            5688888888766  343 444 77888888  9999999999999876   4457789999999999999999999999


Q ss_pred             HHHhCCCCCCc----ccHHHHHHH------------hhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHH
Q 042210           77 DLLKSDVRRDN----YTFPFLFKG------------FTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        77 ~M~~~g~~p~~----~t~~~ll~~------------~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A  133 (230)
                      ++.+.  .|+.    ..+..+...            +.+.|++  |...+..+.     +...+..+...|.+.|++++|
T Consensus       119 ~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  196 (450)
T 2y4t_A          119 KVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKA  196 (450)
T ss_dssp             HHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGG
T ss_pred             HHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHH
Confidence            98774  3433    455555433            7788888  888888876     788899999999999999999


Q ss_pred             HHHHhhccC---CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhh-hhhhcc---cccCCcccccccCCc
Q 042210          134 RGIFYMSCE---DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGE-GLEVIP---KSQAPREETPRVGNL  202 (230)
Q Consensus       134 ~~vf~~m~~---~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~-~l~~~~---~~~~~~~a~~~~g~~  202 (230)
                      .++|+++.+   .+..+|+.+...+..    ++|++.++++.+.   .|+..... .+..+.   ........+.+.|++
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  273 (450)
T 2y4t_A          197 ISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL---DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRY  273 (450)
T ss_dssp             HHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence            999998865   467788888776654    4677777777643   45533321 110000   000001267788999


Q ss_pred             cCCcccccccccc
Q 042210          203 EEGTPQEGRPHEH  215 (230)
Q Consensus       203 ~~a~~i~~~~~~~  215 (230)
                      ++|...+..+.+.
T Consensus       274 ~~A~~~~~~~l~~  286 (450)
T 2y4t_A          274 TDATSKYESVMKT  286 (450)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc
Confidence            9998888887764

>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=99.03  E-value=3e-09  Score=89.72  Aligned_cols=197  Identities=11%  Similarity=0.046  Sum_probs=134.4

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-h---hhHHHHHHH------------
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-V---FLWNTMIKG------------   61 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~---~~yn~li~~------------   61 (230)
                      ++|...++.+.+.+  |+. .. ..+...|.  +.|++++|...|+++.  .|+ .   ..|..+...            
T Consensus        77 ~~A~~~~~~al~~~--p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  152 (450)
T 2y4t_A           77 KAALPDLTKVIQLK--MDFTAARLQRGHLLL--KQGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALN  152 (450)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CCcHHHHHHHHHHHH--HcCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            46788888887764  443 34 77888888  9999999999999876  343 3   556655443            


Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHH
Q 042210           62 YSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMAR  134 (230)
Q Consensus        62 ~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~  134 (230)
                      +.+.|++++|...|+++.+.. +.+...+..+..++.+.|++  |...+..+.     +..+|..+...|.+.|++++|.
T Consensus       153 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  231 (450)
T 2y4t_A          153 AFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSL  231 (450)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            788899999999999887642 23566788888899999988  888888776     6788888999999999999999


Q ss_pred             HHHhhccC--CChh-hhHHH------------HHHhh----hcchhhhHHHHHHHhhhcCchh-----hhhhhhhccccc
Q 042210          135 GIFYMSCE--DDDG-LHELI------------RIKAV----DDDLHELFPEYLVQMLALPDTF-----MGEGLEVIPKSQ  190 (230)
Q Consensus       135 ~vf~~m~~--~~~~-t~n~l------------i~~~~----~~~~~~~~~~m~~~~~~~p~~~-----t~~~l~~~~~~~  190 (230)
                      ..|+++.+  |+.. .|..+            ...+.    .++|.+.++++.+..   |+..     .+..+  .    
T Consensus       232 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~---p~~~~~~~~~~~~l--~----  302 (450)
T 2y4t_A          232 SEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE---PSIAEYTVRSKERI--C----  302 (450)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC---CSSHHHHHHHHHHH--H----
T ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---CcchHHHHHHHHHH--H----
Confidence            99988764  5443 33332            22222    346666666665533   4311     22221  1    


Q ss_pred             CCcccccccCCccCCcccccccccc
Q 042210          191 APREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       191 ~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                         ..+.+.|++++|...+..+.+.
T Consensus       303 ---~~~~~~g~~~~A~~~~~~a~~~  324 (450)
T 2y4t_A          303 ---HCFSKDEKPVEAIRVCSEVLQM  324 (450)
T ss_dssp             ---HHHHTTTCHHHHHHHHHHHHHH
T ss_pred             ---HHHHHCCCHHHHHHHHHHHHHh
Confidence               1555667777776666665543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.98  E-value=2.4e-09  Score=86.43  Aligned_cols=181  Identities=13%  Similarity=0.019  Sum_probs=140.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccH-HHHHHHhhhcC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTF-PFLFKGFTRDI  101 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~-~~ll~~~~~~~  101 (230)
                      -.+...|.  ..|+++.|...++....|+..++..+...+...++.++|.+.++++...+..|+...+ ..+-..+.+.|
T Consensus        38 ~~l~r~yi--~~g~~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g  115 (291)
T 3mkr_A           38 VFLYRAYL--AQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQ  115 (291)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHH--HCCCHHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCC
Confidence            44668888  9999999999888766777888999999999999999999999999988877865544 44447888999


Q ss_pred             ch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHH---HHHH----hhhcchhhhHHHHHHH
Q 042210          102 AG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHEL---IRIK----AVDDDLHELFPEYLVQ  170 (230)
Q Consensus       102 ~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~---li~~----~~~~~~~~~~~~m~~~  170 (230)
                      ++  |...++.-.+...+..+...|.+.|++++|.+.|+++.+  |+....+.   .+..    ...++|.+.|+++.+.
T Consensus       116 ~~~~Al~~l~~~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~  195 (291)
T 3mkr_A          116 NPDAALRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK  195 (291)
T ss_dssp             CHHHHHHHHTTCCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh
Confidence            99  888888733888999999999999999999999999875  66532221   1121    3356888999988876


Q ss_pred             hhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          171 MLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       171 ~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      .  ..+...+..+..         ++.+.|++++|+..+..+.+..
T Consensus       196 ~--p~~~~~~~~la~---------~~~~~g~~~eA~~~l~~al~~~  230 (291)
T 3mkr_A          196 C--SPTLLLLNGQAA---------CHMAQGRWEAAEGVLQEALDKD  230 (291)
T ss_dssp             S--CCCHHHHHHHHH---------HHHHTTCHHHHHHHHHHHHHHC
T ss_pred             C--CCcHHHHHHHHH---------HHHHcCCHHHHHHHHHHHHHhC
Confidence            4  233444555333         6778999999999998877653

>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=98.95  E-value=1.6e-10  Score=97.86  Aligned_cols=169  Identities=12%  Similarity=-0.015  Sum_probs=68.1

Q ss_pred             CCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHH
Q 042210           19 KPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFK   95 (230)
Q Consensus        19 ~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~   95 (230)
                      |... ..++..+.  +.|++++|...++...  .++..+.+.++.+|.+.|++.++.++++       .|+..+|..+-.
T Consensus        60 D~~~y~~V~~~ae--~~g~~EeAi~yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd  130 (449)
T 1b89_A           60 DPSSYMEVVQAAN--TSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGD  130 (449)
T ss_dssp             ---------------------------------------------------CHHHHTTTTT-------CC----------
T ss_pred             CHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHH
Confidence            3334 44555555  5555555555444333  2334455555555555555555555543       255556666666


Q ss_pred             HhhhcCch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHHHHhhhcchhhhHHHHHHHhhh
Q 042210           96 GFTRDIAG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKAVDDDLHELFPEYLVQMLA  173 (230)
Q Consensus        96 ~~~~~~~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li~~~~~~~~~~~~~~m~~~~~~  173 (230)
                      .|...|.+  |...|..   ...|..|.+.+.+.|++++|.+.+.++.  ++.+|..++.+|...+-+++..........
T Consensus       131 ~~~~~g~yeeA~~~Y~~---a~n~~~LA~~L~~Lg~yq~AVea~~KA~--~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~  205 (449)
T 1b89_A          131 RCYDEKMYDAAKLLYNN---VSNFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFRLAQMCGLHIVV  205 (449)
T ss_dssp             ------CTTTHHHHHHH---TTCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTCHHHHHHTTTTTTT
T ss_pred             HHHHcCCHHHHHHHHHH---hhhHHHHHHHHHHhccHHHHHHHHHHcC--CchhHHHHHHHHHHcCcHHHHHHHHHHHHh
Confidence            66666666  5555553   3578888888888888888888888873  778888888888877666666443332223


Q ss_pred             cCchhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          174 LPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       174 ~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                      .||...  .  ++.       .|.+.|.++++..+++..
T Consensus       206 ~ad~l~--~--lv~-------~Yek~G~~eEai~lLe~a  233 (449)
T 1b89_A          206 HADELE--E--LIN-------YYQDRGYFEELITMLEAA  233 (449)
T ss_dssp             CHHHHH--H--HHH-------HHHHTTCHHHHHHHHHHH
T ss_pred             CHhhHH--H--HHH-------HHHHCCCHHHHHHHHHHH
Confidence            343311  1  222       667778887776665543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.93  E-value=1.1e-07  Score=76.51  Aligned_cols=148  Identities=6%  Similarity=-0.035  Sum_probs=117.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLL   79 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~   79 (230)
                      ++|.+.++.+...+..|+...  ..+-..+.  +.|++++|.+.++.  ..+...+..+...|.+.|++++|...|+++.
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~--~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYF--YDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHH--HTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHH--HCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467888888888887787665  44447788  99999999999998  5677889999999999999999999999998


Q ss_pred             hCCCCCCcccHHHH----HHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-Ch
Q 042210           80 KSDVRRDNYTFPFL----FKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DD  145 (230)
Q Consensus        80 ~~g~~p~~~t~~~l----l~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~  145 (230)
                      +..  |+.. ...+    +..+...|+.  |..+++.+.     +...|+.+-..|.+.|++++|...|++..+  | +.
T Consensus       158 ~~~--p~~~-~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~  234 (291)
T 3mkr_A          158 DQD--EDAT-LTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHP  234 (291)
T ss_dssp             HHC--TTCH-HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             hhC--cCcH-HHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCH
Confidence            764  6643 2233    3334444777  889998887     788999999999999999999999998764  4 55


Q ss_pred             hhhHHHHHHhh
Q 042210          146 GLHELIRIKAV  156 (230)
Q Consensus       146 ~t~n~li~~~~  156 (230)
                      .+|+.++..+.
T Consensus       235 ~~l~~l~~~~~  245 (291)
T 3mkr_A          235 ETLINLVVLSQ  245 (291)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            67777765554

>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=98.90  E-value=1.8e-07  Score=72.56  Aligned_cols=166  Identities=10%  Similarity=-0.083  Sum_probs=128.9

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.++...+..  |+ ... ..+...|.  +.|++++|.+.|++..   +.+...|..+...|...|++++|...|+
T Consensus        54 ~~A~~~~~~al~~~--~~~~~~~~~la~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  129 (252)
T 2ho1_A           54 EQAKVPLRKALEID--PSSADAHAALAVVFQ--TEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLL  129 (252)
T ss_dssp             GGGHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--CChHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            57888888887763  43 334 77778888  9999999999999865   4467788999999999999999999999


Q ss_pred             HHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-Ch
Q 042210           77 DLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DD  145 (230)
Q Consensus        77 ~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~  145 (230)
                      +....+..| +...+..+...+.+.|++  |...+....     +...+..+...|.+.|++++|...|++..+  | +.
T Consensus       130 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~  209 (252)
T 2ho1_A          130 EASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNA  209 (252)
T ss_dssp             HHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCH
T ss_pred             HHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcH
Confidence            987754555 455777888889999998  888888776     678899999999999999999999998865  3 44


Q ss_pred             hhhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          146 GLHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       146 ~t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      ..|..+...+..    +++.+.++++.+..
T Consensus       210 ~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          210 RSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            455555555543    45666666655443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.89  E-value=1.2e-08  Score=83.95  Aligned_cols=198  Identities=11%  Similarity=0.021  Sum_probs=141.9

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+++.+.+..  |+ ..+ ..+-..|.  +.|++++|...|++..   +.+...|..+...|.+.|++++|...|+
T Consensus        82 ~~A~~~~~~al~~~--p~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  157 (365)
T 4eqf_A           82 PVTILFMEAAILQD--PGDAEAWQFLGITQA--ENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALK  157 (365)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--cCCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHH
Confidence            56788888887764  44 344 77888888  9999999999999875   4457789999999999999999999999


Q ss_pred             HHHhCCCC-C--------CcccHHHHHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHh
Q 042210           77 DLLKSDVR-R--------DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFY  138 (230)
Q Consensus        77 ~M~~~g~~-p--------~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~  138 (230)
                      +..+..-. +        ....+..+...+.+.|++  |...+....       +..+|..+...|.+.|++++|.+.|+
T Consensus       158 ~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  237 (365)
T 4eqf_A          158 NWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFN  237 (365)
T ss_dssp             HHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            98663210 0        122334457788888888  888888877       47789999999999999999999999


Q ss_pred             hccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccc
Q 042210          139 MSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEG  210 (230)
Q Consensus       139 ~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~  210 (230)
                      +..+  | +..+|+.+...+..    ++|.+.+++..+.   .|+ ..++..+..         .+.+.|++++|...+.
T Consensus       238 ~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~---------~~~~~g~~~~A~~~~~  305 (365)
T 4eqf_A          238 AALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEI---QPGFIRSRYNLGI---------SCINLGAYREAVSNFL  305 (365)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHH---------HHHHHTCCHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCCchHHHHHHHH---------HHHHCCCHHHHHHHHH
Confidence            8765  4 56778888776654    4666666665554   354 333444222         6788999999999988


Q ss_pred             ccccc
Q 042210          211 RPHEH  215 (230)
Q Consensus       211 ~~~~~  215 (230)
                      .+.+.
T Consensus       306 ~al~~  310 (365)
T 4eqf_A          306 TALSL  310 (365)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            87764

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.84  E-value=5.7e-07  Score=68.02  Aligned_cols=174  Identities=11%  Similarity=-0.119  Sum_probs=125.2

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhc-CChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRI-DSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~-~~~~~a~~~~   75 (230)
                      ++|.+.++...+..  |+ ... ..+...|.  ..|+.++|.+.|++..   +.+...|..+...|... |++++|...|
T Consensus        25 ~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~  100 (225)
T 2vq2_A           25 RQATASIEDALKSD--PKNELAWLVRAEIYQ--YLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYF  100 (225)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--ccchHHHHHHHHHHH--HcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            46777787777653  43 334 77778888  9999999999998875   44667888899999999 9999999999


Q ss_pred             HHHHhCCCCCC-cccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C--
Q 042210           76 LDLLKSDVRRD-NYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D--  143 (230)
Q Consensus        76 ~~M~~~g~~p~-~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~--  143 (230)
                      ++..+.+..|+ ...+..+...+...|++  |...+....     +...+..+...|.+.|++++|.+.|++..+  |  
T Consensus       101 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~  180 (225)
T 2vq2_A          101 DKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVL  180 (225)
T ss_dssp             HHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSC
T ss_pred             HHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            99887444443 45777888889999998  888887776     678888999999999999999999998764  4  


Q ss_pred             ChhhhHHHHHHhhhcchhhhHHHHHHHhh-hcCchhh
Q 042210          144 DDGLHELIRIKAVDDDLHELFPEYLVQML-ALPDTFM  179 (230)
Q Consensus       144 ~~~t~n~li~~~~~~~~~~~~~~m~~~~~-~~p~~~t  179 (230)
                      +...|..+...+...+..+......+... ..|+...
T Consensus       181 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~~~~  217 (225)
T 2vq2_A          181 QADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYSEE  217 (225)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHH
Confidence            44455555444444333333333333321 3455433

>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=98.84  E-value=1.4e-07  Score=75.81  Aligned_cols=200  Identities=10%  Similarity=0.060  Sum_probs=146.5

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcC-ChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRID-SHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~-~~~~a~~~~   75 (230)
                      ++|.++++.+.+..  |+. .. ..+...+.  +.|+.++|...++++.   +.+...|..+-..+...| ++++|...|
T Consensus        39 ~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~  114 (330)
T 3hym_B           39 KMCYKLTSVVMEKD--PFHASCLPVHIGTLV--ELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYL  114 (330)
T ss_dssp             HHHHHHHHHHHHHC--TTCTTTHHHHHHHHH--HHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC--CCChhhHHHHHHHHH--HhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            56788888887664  333 33 56777888  9999999999998875   445678888888999999 999999999


Q ss_pred             HHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-Ch
Q 042210           76 LDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DD  145 (230)
Q Consensus        76 ~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~  145 (230)
                      ++..+.. +.+...|..+-..+...|++  |...+....     +...+..+...|.+.|++++|.+.|++..+  | +.
T Consensus       115 ~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~  193 (330)
T 3hym_B          115 SKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDP  193 (330)
T ss_dssp             HHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCH
T ss_pred             HHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCCh
Confidence            9987653 22456788889999999998  888888776     467777889999999999999999998875  3 45


Q ss_pred             hhhHHHHHHhhh----cchhhhHHHHHHHhhhc------Cc-hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          146 GLHELIRIKAVD----DDLHELFPEYLVQMLAL------PD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       146 ~t~n~li~~~~~----~~~~~~~~~m~~~~~~~------p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      ..|+.+...+..    ++|.+.+++..+...-.      |+ ..++..+..         .+.+.|++++|...+..+.+
T Consensus       194 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~---------~~~~~g~~~~A~~~~~~a~~  264 (330)
T 3hym_B          194 FVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGH---------VCRKLKKYAEALDYHRQALV  264 (330)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHH---------HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHH---------HHHHhcCHHHHHHHHHHHHh
Confidence            566666555543    46777777766653111      21 223333212         56678888888888877766


Q ss_pred             c
Q 042210          215 H  215 (230)
Q Consensus       215 ~  215 (230)
                      .
T Consensus       265 ~  265 (330)
T 3hym_B          265 L  265 (330)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=98.83  E-value=1.5e-07  Score=76.93  Aligned_cols=199  Identities=11%  Similarity=0.010  Sum_probs=139.6

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++.+.+.  .|+.. . ..+-..+.  +.|++++|...|++..   +.+...|..+...|...|++++|...|+
T Consensus        81 ~~A~~~~~~al~~--~p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  156 (368)
T 1fch_A           81 PNAVLLFEAAVQQ--DPKHMEAWQYLGTTQA--ENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILR  156 (368)
T ss_dssp             HHHHHHHHHHHHS--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            4567777777665  34433 3 66777777  8888888888888765   4466778888888888888888888888


Q ss_pred             HHHhCC-----------------------------------------------CCC---CcccHHHHHHHhhhcCch--h
Q 042210           77 DLLKSD-----------------------------------------------VRR---DNYTFPFLFKGFTRDIAG--S  104 (230)
Q Consensus        77 ~M~~~g-----------------------------------------------~~p---~~~t~~~ll~~~~~~~~~--a  104 (230)
                      +.....                                               ..|   +..++..+-..+.+.|++  |
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A  236 (368)
T 1fch_A          157 DWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKA  236 (368)
T ss_dssp             HHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHH
Confidence            765532                                               112   355677788888888888  8


Q ss_pred             hHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhh----hcchhhhHHHHHHHhh
Q 042210          105 LEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAV----DDDLHELFPEYLVQML  172 (230)
Q Consensus       105 ~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~----~~~~~~~~~~m~~~~~  172 (230)
                      ...+....     +...|..+...|.+.|++++|.+.|++..+  | +..+|..+...+.    .++|.+.+++..+...
T Consensus       237 ~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~  316 (368)
T 1fch_A          237 VDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQR  316 (368)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            88887776     677889999999999999999999998764  4 4556666655554    3577777777766542


Q ss_pred             hc--Cc-------hhhhhhhhhcccccCCcccccccCCccCCcccccccc
Q 042210          173 AL--PD-------TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPH  213 (230)
Q Consensus       173 ~~--p~-------~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~  213 (230)
                      -.  |+       ..++..+..         ++.+.|+.++|..++....
T Consensus       317 ~~~~~~~~~~~~~~~~~~~l~~---------~~~~~g~~~~A~~~~~~~l  357 (368)
T 1fch_A          317 KSRGPRGEGGAMSENIWSTLRL---------ALSMLGQSDAYGAADARDL  357 (368)
T ss_dssp             TC------CCCCCHHHHHHHHH---------HHHHHTCGGGHHHHHTTCH
T ss_pred             CCCCccccccchhhHHHHHHHH---------HHHHhCChHhHHHhHHHHH
Confidence            11  00       233444222         7788899999988776443

>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=98.80  E-value=2.2e-07  Score=74.49  Aligned_cols=199  Identities=6%  Similarity=-0.103  Sum_probs=128.4

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+++.+.+..  |+. .. ..+...+.  +.|++++|...|++..   +.+...|..+...|...|++++|...|+
T Consensus        38 ~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  113 (327)
T 3cv0_A           38 AEAALAFEAVCQAA--PEREEAWRSLGLTQA--ENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLR  113 (327)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--CCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            45777777776653  433 33 56667777  8888888888888765   4456677777778888888888888877


Q ss_pred             HHHhCCC------------------------------------------------CCCcccHHHHHHHhhhcCch--hhH
Q 042210           77 DLLKSDV------------------------------------------------RRDNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        77 ~M~~~g~------------------------------------------------~p~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      +..+..-                                                +.+...+..+...+.+.|++  |..
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  193 (327)
T 3cv0_A          114 AWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAA  193 (327)
T ss_dssp             HHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHH
Confidence            7654310                                                11334455555666666666  666


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhc
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLAL  174 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~  174 (230)
                      .+....     +...|..+...|.+.|++++|.+.|++..+  | +..+|..+...+..    ++|.+.+++..+.. ..
T Consensus       194 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-~~  272 (327)
T 3cv0_A          194 NLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQ-VG  272 (327)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-TT
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-Cc
Confidence            666554     566777778888888888888888877654  3 34556665555443    46667776666544 22


Q ss_pred             C-----------chhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          175 P-----------DTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       175 p-----------~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      +           +...+..+..         ++.+.|+.++|..++....+
T Consensus       273 ~~~~~~~~~~~~~~~~~~~l~~---------~~~~~g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          273 GTTPTGEASREATRSMWDFFRM---------LLNVMNRPDLVELTYAQNVE  314 (327)
T ss_dssp             SCC-----CCTHHHHHHHHHHH---------HHHHTTCHHHHHHHTTCCSH
T ss_pred             cccccccchhhcCHHHHHHHHH---------HHHhcCCHHHHHHHHHHHHH
Confidence            1           1223333212         67788999999888876554

>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=98.78  E-value=2.7e-08  Score=84.28  Aligned_cols=152  Identities=11%  Similarity=-0.056  Sum_probs=72.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      ++|++.++..++.  .+++.+ +.++.+|.  +.|+++++.++++   .|+..+|+.+-..|...|.+++|...|..+  
T Consensus        78 EeAi~yl~~ark~--~~~~~i~~~Li~~Y~--Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a--  148 (449)
T 1b89_A           78 EELVKYLQMARKK--ARESYVETELIFALA--KTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV--  148 (449)
T ss_dssp             -----------------------------------CHHHHTTTTT---CC----------------CTTTHHHHHHHT--
T ss_pred             HHHHHHHHHHHHh--CccchhHHHHHHHHH--HhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh--
Confidence            5667766655553  455778 99999999  9999999988875   477778888888888888888888888876  


Q ss_pred             CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC-CChhhhHHHHHHhhh
Q 042210           81 SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE-DDDGLHELIRIKAVD  157 (230)
Q Consensus        81 ~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-~~~~t~n~li~~~~~  157 (230)
                             ..|..+..++.+.|++  |.+.+....++.+|..++.+|...|+++.|......+.. |+.  .-.++..|..
T Consensus       149 -------~n~~~LA~~L~~Lg~yq~AVea~~KA~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~~ad~--l~~lv~~Yek  219 (449)
T 1b89_A          149 -------SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADE--LEELINYYQD  219 (449)
T ss_dssp             -------TCHHHHHHHHHTTTCHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHH--HHHHHHHHHH
T ss_pred             -------hhHHHHHHHHHHhccHHHHHHHHHHcCCchhHHHHHHHHHHcCcHHHHHHHHHHHHhCHhh--HHHHHHHHHH
Confidence                   4688888888888888  777777777888888888888888888887666555442 322  1235555554


Q ss_pred             cchhhhHHHHHHHh
Q 042210          158 DDLHELFPEYLVQM  171 (230)
Q Consensus       158 ~~~~~~~~~m~~~~  171 (230)
                      .+-.+..-.+++.+
T Consensus       220 ~G~~eEai~lLe~a  233 (449)
T 1b89_A          220 RGYFEELITMLEAA  233 (449)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            44333333333333

>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=98.77  E-value=3.7e-07  Score=73.23  Aligned_cols=198  Identities=13%  Similarity=0.096  Sum_probs=148.9

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccC-ChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKG-DLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~-~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|..+++.+.+.  .|+ ... ..+-..+.  ..| +.++|...|++..   +.+...|..+-..+...|++++|...|
T Consensus        73 ~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~--~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~  148 (330)
T 3hym_B           73 NELFYLSHKLVDL--YPSNPVSWFAVGCYYL--MVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAY  148 (330)
T ss_dssp             HHHHHHHHHHHHH--CTTSTHHHHHHHHHHH--HSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CcCCHHHHHHHHHHHH--HhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHH
Confidence            4677777777765  343 444 77778888  999 9999999999865   445678999999999999999999999


Q ss_pred             HHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC------
Q 042210           76 LDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE------  142 (230)
Q Consensus        76 ~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~------  142 (230)
                      ++..+.. +.+...+..+-..+...|++  |...+....     +...+..+...|.+.|++++|...|++..+      
T Consensus       149 ~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~  227 (330)
T 3hym_B          149 FTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIG  227 (330)
T ss_dssp             HHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhcc
Confidence            9987643 22455677788899999999  888888876     788899999999999999999999987753      


Q ss_pred             -----C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCcccccc
Q 042210          143 -----D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGR  211 (230)
Q Consensus       143 -----~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~  211 (230)
                           | +..+|..+...+..    ++|.+.+++..+..   |+ ...+..+..         .+.+.|+.++|...+..
T Consensus       228 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~---~~~~~~~~~la~---------~~~~~g~~~~A~~~~~~  295 (330)
T 3hym_B          228 NEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI---PQNASTYSAIGY---------IHSLMGNFENAVDYFHT  295 (330)
T ss_dssp             CSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS---TTCSHHHHHHHH---------HHHHHTCHHHHHHHHHT
T ss_pred             ccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC---ccchHHHHHHHH---------HHHHhccHHHHHHHHHH
Confidence                 2 23466666655543    46777777666544   33 233333222         67788999999999888


Q ss_pred             ccccC
Q 042210          212 PHEHS  216 (230)
Q Consensus       212 ~~~~~  216 (230)
                      +.+..
T Consensus       296 al~~~  300 (330)
T 3hym_B          296 ALGLR  300 (330)
T ss_dssp             TTTTC
T ss_pred             HHccC
Confidence            77653

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.72  E-value=6.3e-07  Score=68.77  Aligned_cols=165  Identities=10%  Similarity=-0.002  Sum_probs=125.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+  ..|+.. . ..+...+.  +.|++++|.+.|++..   +.+...|..+...|...|++++|...|+
T Consensus        40 ~~A~~~~~~~l~--~~~~~~~~~~~la~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  115 (243)
T 2q7f_A           40 EKAAEAFTKAIE--ENKEDAIPYINFANLLS--SVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFE  115 (243)
T ss_dssp             --CCTTHHHHHT--TCTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--hCcccHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHH
Confidence            345566666655  334433 3 66777888  9999999999999865   4467788889999999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-Chh
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDG  146 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~  146 (230)
                      +..+.. +.+...+..+...+.+.|++  |...+....     +...+..+...|.+.|++++|.+.|++..+  | +..
T Consensus       116 ~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~  194 (243)
T 2q7f_A          116 KALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHAD  194 (243)
T ss_dssp             HHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHH
Confidence            987643 23556788888899999999  888888776     678888999999999999999999998764  3 455


Q ss_pred             hhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          147 LHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       147 t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      +|..+...+..    ++|.+.+++..+..
T Consensus       195 ~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          195 AFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            66666555543    46777777665543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.72  E-value=3.9e-07  Score=77.77  Aligned_cols=198  Identities=9%  Similarity=-0.086  Sum_probs=133.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|...|+.+.+..  |+... ..+..+|.  +.|++++|...|+++.   +.+...|..+..+|.+.|++++|...|++
T Consensus        23 ~~A~~~~~~al~~~--p~~~~~~~la~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~   98 (514)
T 2gw1_A           23 DDAIKYYNWALELK--EDPVFYSNLSACYV--SVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKFADAMFDLSV   98 (514)
T ss_dssp             HHHHHHHHHHHHHC--CCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC--ccHHHHHhHHHHHH--HHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            57889999998886  78777 88899999  9999999999999875   44567899999999999999999999999


Q ss_pred             HHhCCCCCCccc--------------------------------------------------------------------
Q 042210           78 LLKSDVRRDNYT--------------------------------------------------------------------   89 (230)
Q Consensus        78 M~~~g~~p~~~t--------------------------------------------------------------------   89 (230)
                      +...+- ++...                                                                    
T Consensus        99 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (514)
T 2gw1_A           99 LSLNGD-FNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTF  177 (514)
T ss_dssp             HHHSSS-CCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCC
T ss_pred             HHhcCC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHH
Confidence            876541 11111                                                                    


Q ss_pred             -----------HHHHHHHhh---hcCch--hhHHHhhhh-------------------hHhHHHHHHHHHHhcCCHHHHH
Q 042210           90 -----------FPFLFKGFT---RDIAG--SLEKSCIVM-------------------RVFVQNALISTYCLCGEVDMAR  134 (230)
Q Consensus        90 -----------~~~ll~~~~---~~~~~--a~~~~~~~~-------------------~~~~~~~li~~y~~~g~~~~A~  134 (230)
                                 +...-..+.   +.|++  |...+..+.                   +...+..+...|.+.|++++|.
T Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~  257 (514)
T 2gw1_A          178 ANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAH  257 (514)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHH
T ss_pred             HHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHH
Confidence                       111111111   25666  655555433                   3567778888899999999999


Q ss_pred             HHHhhccC--CChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccc
Q 042210          135 GIFYMSCE--DDDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQ  208 (230)
Q Consensus       135 ~vf~~m~~--~~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i  208 (230)
                      ..|++..+  |+..+|..+...+..    +++.+.+++.......  +...+..+..         .+...|++++|...
T Consensus       258 ~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~l~~---------~~~~~~~~~~A~~~  326 (514)
T 2gw1_A          258 EDIKKAIELFPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSN--NSSVYYHRGQ---------MNFILQNYDQAGKD  326 (514)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTT--CTHHHHHHHH---------HHHHTTCTTHHHHH
T ss_pred             HHHHHHHhhCccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcC--CHHHHHHHHH---------HHHHhCCHHHHHHH
Confidence            99998764  555555555554443    4677777766554311  1222222111         45566777777766


Q ss_pred             ccccccc
Q 042210          209 EGRPHEH  215 (230)
Q Consensus       209 ~~~~~~~  215 (230)
                      +..+.+.
T Consensus       327 ~~~~~~~  333 (514)
T 2gw1_A          327 FDKAKEL  333 (514)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            6665543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.65  E-value=1.4e-06  Score=66.67  Aligned_cols=181  Identities=12%  Similarity=0.001  Sum_probs=122.5

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPF   92 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~   92 (230)
                      ++... ..+-..+.  +.|++++|...|++..   +.+...|..+-..+.+.|++++|...|++..+.  .| +...+..
T Consensus         3 ~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~   78 (217)
T 2pl2_A            3 TAEQNPLRLGVQLY--ALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVAR--TPRYLGGYMV   78 (217)
T ss_dssp             -CCHHHHHHHHHHH--HTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             CcHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHH
Confidence            44555 66667788  9999999999999864   445678888889999999999999999997664  34 4457778


Q ss_pred             HHHHhhhc-----------Cch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHH
Q 042210           93 LFKGFTRD-----------IAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIR  152 (230)
Q Consensus        93 ll~~~~~~-----------~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li  152 (230)
                      +-..+.+.           |++  |...++...     +...|..+-..|...|++++|...|++..+  .+...|..+-
T Consensus        79 lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la  158 (217)
T 2pl2_A           79 LSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALA  158 (217)
T ss_dssp             HHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHH
Confidence            88888888           888  888887776     678888899999999999999999997654  4555666554


Q ss_pred             HHhh----hcchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          153 IKAV----DDDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       153 ~~~~----~~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      ..+.    .++|.+.+++..+..   |+ ...+..+..         .+.+.|+.++|...+.....
T Consensus       159 ~~~~~~g~~~~A~~~~~~al~~~---P~~~~~~~~la~---------~~~~~g~~~~A~~~~~~~~~  213 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQYAKALEQA---PKDLDLRVRYAS---------ALLLKGKAEEAARAAALEHH  213 (217)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHS---TTCHHHHHHHHH---------HHTC----------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC---CCChHHHHHHHH---------HHHHccCHHHHHHHHHHHhh
Confidence            4443    457777777766544   44 223333222         67789999999988876553

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.64  E-value=2.5e-07  Score=78.93  Aligned_cols=198  Identities=9%  Similarity=-0.064  Sum_probs=149.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|...++...+..  |+... ..+...+.  +.|++++|...++...   +.+...|..+...|...|++++|...|++
T Consensus       254 ~~A~~~~~~~l~~~--~~~~~~~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  329 (514)
T 2gw1_A          254 LGAHEDIKKAIELF--PRVNSYIYMALIMA--DRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDK  329 (514)
T ss_dssp             HHHHHHHHHHHHHC--CCHHHHHHHHHHHH--TSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC--ccHHHHHHHHHHHH--HCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            46778888887765  44444 77888888  9999999999999865   44677899999999999999999999999


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC----
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD----  144 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~----  144 (230)
                      ..+..- .+...+..+...+.+.|++  |...+....     +...+..+...|.+.|++++|.+.|++..+  |+    
T Consensus       330 ~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  408 (514)
T 2gw1_A          330 AKELDP-ENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGI  408 (514)
T ss_dssp             HHHTCS-SCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSC
T ss_pred             HHHhCh-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchH
Confidence            877532 2556788889999999999  888888776     678899999999999999999999998764  22    


Q ss_pred             ---hhhhHHHHHHhhh---c----chhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCcccccccc
Q 042210          145 ---DGLHELIRIKAVD---D----DLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPH  213 (230)
Q Consensus       145 ---~~t~n~li~~~~~---~----~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~  213 (230)
                         ..+|..+...+..   .    +|.+.+++....   .|+ ..++..+..         .+.+.|+.++|...+..+.
T Consensus       409 ~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~---~~~~~~~~~~la~---------~~~~~g~~~~A~~~~~~a~  476 (514)
T 2gw1_A          409 YVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKL---DPRSEQAKIGLAQ---------MKLQQEDIDEAITLFEESA  476 (514)
T ss_dssp             SSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHH---CTTCHHHHHHHHH---------HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHh---CcccHHHHHHHHH---------HHHHhcCHHHHHHHHHHHH
Confidence               2267766655554   3    555666655543   343 223333212         6778899999999988877


Q ss_pred             ccC
Q 042210          214 EHS  216 (230)
Q Consensus       214 ~~~  216 (230)
                      +..
T Consensus       477 ~~~  479 (514)
T 2gw1_A          477 DLA  479 (514)
T ss_dssp             HHC
T ss_pred             Hhc
Confidence            654

>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=98.63  E-value=4.8e-07  Score=70.09  Aligned_cols=179  Identities=10%  Similarity=-0.097  Sum_probs=134.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  ..|++++|.+.|++..   +.+...|..+...|.+.|++++|...|++..+.. +.+...+..+...+..
T Consensus        41 ~~~a~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  117 (252)
T 2ho1_A           41 IQLGLGYL--QRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFLYE  117 (252)
T ss_dssp             HHHHHHHH--HTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHH
Confidence            44556677  9999999999999875   4467788999999999999999999999987653 2256678888899999


Q ss_pred             cCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhh
Q 042210          100 DIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHEL  163 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~  163 (230)
                      .|++  |...+....       +...+..+...|.+.|++++|.+.|++..+  | +...|..+...+..    ++|.+.
T Consensus       118 ~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  197 (252)
T 2ho1_A          118 QKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQY  197 (252)
T ss_dssp             TTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999  777777664       677888899999999999999999998765  4 45667666665554    456666


Q ss_pred             HHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          164 FPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       164 ~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      +++..+.   .|+ ...+..  ...       .+.+.|+.++|.+.+..+.+..
T Consensus       198 ~~~~~~~---~~~~~~~~~~--~~~-------~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          198 YDLFAQG---GGQNARSLLL--GIR-------LAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             HHHHHTT---SCCCHHHHHH--HHH-------HHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHh---CcCcHHHHHH--HHH-------HHHHccCHHHHHHHHHHHHHHC
Confidence            6665443   233 222223  111       5678899999999988887653

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.62  E-value=8.4e-08  Score=78.79  Aligned_cols=166  Identities=11%  Similarity=-0.020  Sum_probs=123.2

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-----------hhhHHHHHHHHHhcC
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-----------VFLWNTMIKGYSRID   66 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-----------~~~yn~li~~~~~~~   66 (230)
                      ++|...++...+..  |+ ... ..+...|.  +.|++++|...|+++.  .|+           ...++.+...+.+.|
T Consensus       116 ~~A~~~~~~al~~~--p~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g  191 (365)
T 4eqf_A          116 QAAIVALQRCLELQ--PNNLKALMALAVSYT--NTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSS  191 (365)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCH
T ss_pred             HHHHHHHHHHHhcC--CCCHHHHHHHHHHHH--ccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhh
Confidence            56788888887763  54 344 78888999  9999999999999875  222           223344578889999


Q ss_pred             ChhHHHHHHHHHHhCC-CCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHh
Q 042210           67 SHKNGVLMYLDLLKSD-VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFY  138 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~g-~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~  138 (230)
                      ++++|...|++..+.. -.++..++..+-..+.+.|++  |...+....     +..+|+.+...|.+.|++++|...|+
T Consensus       192 ~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  271 (365)
T 4eqf_A          192 VLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYT  271 (365)
T ss_dssp             HHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999987753 223577899999999999999  888888876     78899999999999999999999999


Q ss_pred             hccC--CC-hhhhHHHHHHhh----hcchhhhHHHHHHHh
Q 042210          139 MSCE--DD-DGLHELIRIKAV----DDDLHELFPEYLVQM  171 (230)
Q Consensus       139 ~m~~--~~-~~t~n~li~~~~----~~~~~~~~~~m~~~~  171 (230)
                      +..+  |+ ..+|..+...+.    .++|.+.+++..+..
T Consensus       272 ~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  311 (365)
T 4eqf_A          272 RALEIQPGFIRSRYNLGISCINLGAYREAVSNFLTALSLQ  311 (365)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            8765  54 566777655554    357788888777654

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.61  E-value=1.1e-06  Score=67.93  Aligned_cols=166  Identities=8%  Similarity=-0.026  Sum_probs=123.6

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--C----CC----hhhHHHHHHHHHhcCChhH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--Q----PS----VFLWNTMIKGYSRIDSHKN   70 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~----~~----~~~yn~li~~~~~~~~~~~   70 (230)
                      ++|...++...+..  .+... ..+-..+.  ..|++++|...|+...  .    ++    ...|..+-..|.+.|++++
T Consensus        22 ~~A~~~~~~a~~~~--~~~~~~~~~~~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   97 (258)
T 3uq3_A           22 DEAIEHYNKAWELH--KDITYLNNRAAAEY--EKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKK   97 (258)
T ss_dssp             HHHHHHHHHHHHHS--CCTHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhh--ccHHHHHHHHHHHH--HcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHH
Confidence            57889999998888  77777 88889999  9999999999999865  1    22    4788899999999999999


Q ss_pred             HHHHHHHHHhCC------------------------CCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHH
Q 042210           71 GVLMYLDLLKSD------------------------VRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQN  118 (230)
Q Consensus        71 a~~~~~~M~~~g------------------------~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~  118 (230)
                      |...|++..+..                        ..| +...+..+-..+...|++  |...+....     +...|.
T Consensus        98 A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~  177 (258)
T 3uq3_A           98 TIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYS  177 (258)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHH
Confidence            999999987632                        223 334566677777788887  777777765     677788


Q ss_pred             HHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          119 ALISTYCLCGEVDMARGIFYMSCE--DD-DGLHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       119 ~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      .+...|.+.|++++|.+.|++..+  |+ ..+|..+-..+..    ++|.+.+++..+..
T Consensus       178 ~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          178 NRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            888888888888888888887754  43 4555555444432    45666666555443

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=98.61  E-value=5.6e-07  Score=68.07  Aligned_cols=180  Identities=8%  Similarity=-0.061  Sum_probs=135.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  ..|++++|.+.|++..   +.+...|..+...|...|++++|...|++..+.. +.+..++..+...+..
T Consensus        12 ~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~   88 (225)
T 2vq2_A           12 TQLAMEYM--RGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWFLCG   88 (225)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHH--HHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHH
Confidence            55667788  9999999999999865   4557789999999999999999999999987643 2256678888999999


Q ss_pred             c-Cch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhh----hcchhh
Q 042210          100 D-IAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAV----DDDLHE  162 (230)
Q Consensus       100 ~-~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~----~~~~~~  162 (230)
                      . |++  |...+....       +...+..+...|.+.|++++|...|++..+  | +...|..+...+.    .++|.+
T Consensus        89 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  168 (225)
T 2vq2_A           89 RLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADY  168 (225)
T ss_dssp             TTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             hcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHH
Confidence            9 998  777777765       478889999999999999999999998765  4 3556666655544    357777


Q ss_pred             hHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          163 LFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       163 ~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      .+++..+.. ...+...+..+..         .+...|+.+++..++..+.+.
T Consensus       169 ~~~~~~~~~-~~~~~~~~~~~~~---------~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          169 YFKKYQSRV-EVLQADDLLLGWK---------IAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHHHHHH-CSCCHHHHHHHHH---------HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-CCCCHHHHHHHHH---------HHHhcCcHHHHHHHHHHHHHh
Confidence            777776654 1122333333111         556788899888888777654

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.60  E-value=1.1e-06  Score=60.42  Aligned_cols=116  Identities=15%  Similarity=0.137  Sum_probs=82.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  ..|++++|..+|+++.   +.+...|..+...+...|++++|...|++....+ +.+...+..+...+.+
T Consensus         5 ~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            5 YNLGNAYY--KQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHH--HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHH--HcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            34556667  8888888888888764   4456677778888888888888888888876643 2234456666777777


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .|++  |...+..+.     +...+..+...|.+.|++++|.+.|+++.
T Consensus        82 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            7777  666666655     56667777777777788877777777654

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.59  E-value=1.5e-07  Score=72.37  Aligned_cols=179  Identities=12%  Similarity=-0.005  Sum_probs=126.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|++++|...|++..   +.+...|..+...|.+.|++++|...|++..+.. +.+...+..+...+..
T Consensus        27 ~~~a~~~~--~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  103 (243)
T 2q7f_A           27 GQQMGRGS--EFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGNVYVV  103 (243)
T ss_dssp             -----------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHH
Confidence            44455666  8999999999999875   4467788889999999999999999999987653 2256678888899999


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhh----hcchhhhHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAV----DDDLHELFP  165 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~----~~~~~~~~~  165 (230)
                      .|++  |...+....     +...+..+...|.+.|++++|...|++..+  | +...|..+...+.    .++|.+.++
T Consensus       104 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  183 (243)
T 2q7f_A          104 KEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFA  183 (243)
T ss_dssp             TTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHH
T ss_pred             hccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999  888888776     778899999999999999999999998764  3 4556666555444    356777777


Q ss_pred             HHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          166 EYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       166 ~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      +..+..   |+ ..++..+..         .+.+.|+.++|...+..+.+..
T Consensus       184 ~~~~~~---~~~~~~~~~la~---------~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          184 AVTEQD---PGHADAFYNAGV---------TYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHC---TTCHHHHHHHHH---------HHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHhC---cccHHHHHHHHH---------HHHHccCHHHHHHHHHHHHccC
Confidence            766554   33 333333212         6778999999999998887753

>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=98.53  E-value=5e-07  Score=77.66  Aligned_cols=198  Identities=12%  Similarity=0.014  Sum_probs=147.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|...++...+.  .|+... ..+-..+.  +.|++++|...|++..   +.+...|..+-..+...|++++|...|++
T Consensus       260 ~~A~~~~~~~~~~--~~~~~~~~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  335 (537)
T 3fp2_A          260 LDAQVLLQESINL--HPTPNSYIFLALTLA--DKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQK  335 (537)
T ss_dssp             HHHHHHHHHHHHH--CCCHHHHHHHHHHTC--CSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCCchHHHHHHHHHH--HhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            4677778777776  466455 77778888  9999999999999875   45577899999999999999999999999


Q ss_pred             HHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhh
Q 042210           78 LLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGL  147 (230)
Q Consensus        78 M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t  147 (230)
                      ..+.. +-+...|..+-..+...|++  |...+....     +...+..+-..|.+.|++++|.+.|++..+  |+ ...
T Consensus       336 a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~  414 (537)
T 3fp2_A          336 AQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKI  414 (537)
T ss_dssp             HHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSC
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhh
Confidence            87643 22456788899999999999  888888876     677899999999999999999999998764  21 111


Q ss_pred             hH----------HHHHH----------hhhcchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCc
Q 042210          148 HE----------LIRIK----------AVDDDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGT  206 (230)
Q Consensus       148 ~n----------~li~~----------~~~~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~  206 (230)
                      |.          ++...          ...++|.+.+++..+..   |+ ...+..+..         .+.+.|+.++|.
T Consensus       415 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~---p~~~~~~~~l~~---------~~~~~g~~~~A~  482 (537)
T 3fp2_A          415 HVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD---PRSEQAKIGLAQ---------LKLQMEKIDEAI  482 (537)
T ss_dssp             SSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC---TTCHHHHHHHHH---------HHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC---CCCHHHHHHHHH---------HHHHhccHHHHH
Confidence            11          11222          44457777777766654   43 233333222         677899999999


Q ss_pred             cccccccccC
Q 042210          207 PQEGRPHEHS  216 (230)
Q Consensus       207 ~i~~~~~~~~  216 (230)
                      ..+..+.+..
T Consensus       483 ~~~~~al~~~  492 (537)
T 3fp2_A          483 ELFEDSAILA  492 (537)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHHhC
Confidence            9888877654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.53  E-value=1.1e-06  Score=68.78  Aligned_cols=202  Identities=9%  Similarity=-0.068  Sum_probs=138.9

Q ss_pred             hhHHHHHHHHHHhcCCCC---CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK---PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLM   74 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~---~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~   74 (230)
                      ++|.+.++.+.+.....+   ..+ ..+-..+.  ..|++++|...|++..   +.+...|..+-..|.+.|++++|...
T Consensus        22 ~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~   99 (275)
T 1xnf_A           22 EVILARMEQILASRALTDDERAQLLYERGVLYD--SLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEA   99 (275)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccCchhHHHHHHHHHHHH--HcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHH
Confidence            567888888877643222   233 56667777  9999999999999875   45678899999999999999999999


Q ss_pred             HHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CCh
Q 042210           75 YLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDD  145 (230)
Q Consensus        75 ~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~  145 (230)
                      |++..+.. +.+...+..+-..+.+.|++  |...++...    +.......+..+.+.|++++|...|++...   ++.
T Consensus       100 ~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~  178 (275)
T 1xnf_A          100 FDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQ  178 (275)
T ss_dssp             HHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCS
T ss_pred             HHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcch
Confidence            99987642 22566888899999999999  888888877    222344455556777999999999976653   444


Q ss_pred             hhhHHHHHHhhh----cchhhhHHHHHHHhh-hcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          146 GLHELIRIKAVD----DDLHELFPEYLVQML-ALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       146 ~t~n~li~~~~~----~~~~~~~~~m~~~~~-~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      ..|+ +...+..    +++++.+.+...... ..|+ ...+..+..         .+.+.|+.++|...+..+.+..
T Consensus       179 ~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~---------~~~~~g~~~~A~~~~~~al~~~  245 (275)
T 1xnf_A          179 WGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGK---------YYLSLGDLDSATALFKLAVANN  245 (275)
T ss_dssp             THHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHH---------HHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHH---------HHHHcCCHHHHHHHHHHHHhCC
Confidence            4444 3332222    345555555443321 1111 223333212         6778899999999998887754

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.51  E-value=7.4e-06  Score=59.63  Aligned_cols=146  Identities=11%  Similarity=0.001  Sum_probs=114.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  ..|++++|...|++..   +.+...|..+...+...|++++|...+++..+.. +.+...+..+...+..
T Consensus        12 ~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~   88 (186)
T 3as5_A           12 RDKGISHA--KAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYVQ   88 (186)
T ss_dssp             HHHHHHHH--HHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHH
Confidence            34556677  8999999999999976   3466788889999999999999999999987652 2355678888888999


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFP  165 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~  165 (230)
                      .|++  |...+....     +...+..+...|.+.|++++|.+.|++..+  | +...|..+...+..    ++|.+.++
T Consensus        89 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  168 (186)
T 3as5_A           89 VQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFK  168 (186)
T ss_dssp             HTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999  888888776     678888899999999999999999998765  3 44566666555543    46666666


Q ss_pred             HHHHHh
Q 042210          166 EYLVQM  171 (230)
Q Consensus       166 ~m~~~~  171 (230)
                      +..+..
T Consensus       169 ~~~~~~  174 (186)
T 3as5_A          169 KANELD  174 (186)
T ss_dssp             HHHHHH
T ss_pred             HHHHcC
Confidence            665543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.50  E-value=9.1e-06  Score=63.44  Aligned_cols=178  Identities=11%  Similarity=0.037  Sum_probs=127.8

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcc--cHHHHHHHhh
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNY--TFPFLFKGFT   98 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~--t~~~ll~~~~   98 (230)
                      ..-..+.  +.|++++|...|++..   +.+...|..+-..|.+.|++++|...|++..+.+-.|+..  .|..+-..+.
T Consensus         8 ~~a~~~~--~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~   85 (272)
T 3u4t_A            8 RYADFLF--KNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILM   85 (272)
T ss_dssp             HHHHHHH--TTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHH--HhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHH
Confidence            3445666  9999999999999875   3445588888899999999999999999988744222221  2788888999


Q ss_pred             hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHH-HHhh---hcchhhhH
Q 042210           99 RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIR-IKAV---DDDLHELF  164 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li-~~~~---~~~~~~~~  164 (230)
                      +.|++  |...+....     +...|..+-..|.+.|++++|...|++..+  | +...|..+- ..+.   .++|.+.+
T Consensus        86 ~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~  165 (272)
T 3u4t_A           86 KKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSSF  165 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999  888888776     678899999999999999999999998876  4 344555554 4443   35677777


Q ss_pred             HHHHHHhhhcCch-hhhhhhhhcccccCCcccccccCC---ccCCcccccccccc
Q 042210          165 PEYLVQMLALPDT-FMGEGLEVIPKSQAPREETPRVGN---LEEGTPQEGRPHEH  215 (230)
Q Consensus       165 ~~m~~~~~~~p~~-~t~~~l~~~~~~~~~~~a~~~~g~---~~~a~~i~~~~~~~  215 (230)
                      ++..+..   |+. ..+..+..         .+...|+   .++|...+..+.+.
T Consensus       166 ~~a~~~~---p~~~~~~~~~~~---------~~~~~~~~~~~~~A~~~~~~a~~~  208 (272)
T 3u4t_A          166 VKVLELK---PNIYIGYLWRAR---------ANAAQDPDTKQGLAKPYYEKLIEV  208 (272)
T ss_dssp             HHHHHHS---TTCHHHHHHHHH---------HHHHHSTTCSSCTTHHHHHHHHHH
T ss_pred             HHHHHhC---ccchHHHHHHHH---------HHHHcCcchhhHHHHHHHHHHHHH
Confidence            7666543   442 22222111         3444565   77787777666554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.50  E-value=1.1e-06  Score=71.18  Aligned_cols=81  Identities=6%  Similarity=-0.059  Sum_probs=38.0

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHH
Q 042210           60 KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~  132 (230)
                      ..+...|++++|...|++..+.. +.+...+..+-..+...|++  |...+....     +...+..+...|.+.|++++
T Consensus       128 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  206 (359)
T 3ieg_A          128 LDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHEL  206 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHH
Confidence            33444444444444444443321 11233444444555555555  444444443     44455555555555555555


Q ss_pred             HHHHHhhcc
Q 042210          133 ARGIFYMSC  141 (230)
Q Consensus       133 A~~vf~~m~  141 (230)
                      |...|++..
T Consensus       207 A~~~~~~a~  215 (359)
T 3ieg_A          207 SLSEVRECL  215 (359)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555443

>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=98.48  E-value=2.2e-06  Score=69.93  Aligned_cols=161  Identities=9%  Similarity=-0.014  Sum_probs=122.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HH---------------HHHHHhhhccCChHHHHHHHHhcC--CC---ChhhHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PK---------------QTRYLLLYEKGDLKYECKVFRKIT--QP---SVFLWNTMI   59 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~---------------ll~~~~~~~~~~~~~a~~~~~~m~--~~---~~~~yn~li   59 (230)
                      ++|...++.+.+..  |+...  ..               .+..+.  +.|++++|...|+++.  .|   +..+|..+-
T Consensus       149 ~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~  224 (368)
T 1fch_A          149 RQACEILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLL--SDSLFLEVKELFLAAVRLDPTSIDPDVQCGLG  224 (368)
T ss_dssp             HHHHHHHHHHHHTS--TTTGGGCC---------------CTTHHHH--HHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--cCcHHHHHHHHHHhhhhcccHHHHHHHHHh--hcccHHHHHHHHHHHHHhCcCcccHHHHHHHH
Confidence            45667777776654  33222  21               366666  8899999999999876  34   477899999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHH
Q 042210           60 KGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~  132 (230)
                      ..|.+.|++++|...|++..... +.+...|..+...+.+.|++  |...+....     +...+..+...|.+.|++++
T Consensus       225 ~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~  303 (368)
T 1fch_A          225 VLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHRE  303 (368)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHH
Confidence            99999999999999999977642 22456888999999999999  888888876     67889999999999999999


Q ss_pred             HHHHHhhccC--CC------------hhhhHHHHHHhhhcchhhhHHHH
Q 042210          133 ARGIFYMSCE--DD------------DGLHELIRIKAVDDDLHELFPEY  167 (230)
Q Consensus       133 A~~vf~~m~~--~~------------~~t~n~li~~~~~~~~~~~~~~m  167 (230)
                      |...|++..+  |+            ..+|..+...+...+..+.....
T Consensus       304 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  352 (368)
T 1fch_A          304 AVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAA  352 (368)
T ss_dssp             HHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHH
T ss_pred             HHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHh
Confidence            9999998765  32            46788877766654444444433

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.46  E-value=3.1e-06  Score=68.36  Aligned_cols=206  Identities=10%  Similarity=-0.060  Sum_probs=145.5

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+.  .|+. .. ..+-..+.  +.|++++|...|++..   +.+...|..+-..|.+.|++++|...|+
T Consensus        20 ~~A~~~~~~~l~~--~p~~~~~~~~~a~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~   95 (359)
T 3ieg_A           20 ADALSQFHAAVDG--DPDNYIAYYRRATVFL--AMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFK   95 (359)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhh--CcccHHHHHHHHHHHH--HccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHH
Confidence            5678888888775  3443 34 77778888  9999999999999875   3466789999999999999999999999


Q ss_pred             HHHhCCCCC----CcccHHHH------------HHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHH
Q 042210           77 DLLKSDVRR----DNYTFPFL------------FKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        77 ~M~~~g~~p----~~~t~~~l------------l~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A  133 (230)
                      +..+.  .|    +...+..+            ...+...|++  |...+....     +...+..+...|.+.|++++|
T Consensus        96 ~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A  173 (359)
T 3ieg_A           96 KVLKS--NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKA  173 (359)
T ss_dssp             HHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHH
Confidence            98764  34    22333333            4678888888  888888876     788899999999999999999


Q ss_pred             HHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhh-hhhhhhcc---cccCCcccccccCCc
Q 042210          134 RGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFM-GEGLEVIP---KSQAPREETPRVGNL  202 (230)
Q Consensus       134 ~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t-~~~l~~~~---~~~~~~~a~~~~g~~  202 (230)
                      ...|++..+  | +..+|..+...+..    +++.+.+++..+..   |+... +..+..+.   ........+.+.|++
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  250 (359)
T 3ieg_A          174 ISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD---QDHKRCFAHYKQVKKLNKLIESAEELIRDGRY  250 (359)
T ss_dssp             HHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC---TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC---ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCH
Confidence            999998875  3 45566666555443    46777777666543   43221 11100000   000001146678999


Q ss_pred             cCCccccccccccC
Q 042210          203 EEGTPQEGRPHEHS  216 (230)
Q Consensus       203 ~~a~~i~~~~~~~~  216 (230)
                      ++|...+..+.+..
T Consensus       251 ~~A~~~~~~~~~~~  264 (359)
T 3ieg_A          251 TDATSKYESVMKTE  264 (359)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhcC
Confidence            99998888777654

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.44  E-value=1e-05  Score=63.15  Aligned_cols=200  Identities=7%  Similarity=-0.123  Sum_probs=144.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcCC--CChh----hHHHHHHHHHhcCChhHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKITQ--PSVF----LWNTMIKGYSRIDSHKNGVL   73 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~~--~~~~----~yn~li~~~~~~~~~~~a~~   73 (230)
                      ++|...++...+..  |+.. . ..+-..|.  +.|++++|.+.|++...  ++..    .|..+-..|...|++++|..
T Consensus        20 ~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~   95 (272)
T 3u4t_A           20 AEAIEVFNKLEAKK--YNSPYIYNRRAVCYY--ELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQ   95 (272)
T ss_dssp             HHHHHHHHHHHHTT--CCCSTTHHHHHHHHH--HTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhC--CCcHHHHHHHHHHHH--HHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHH
Confidence            56788888877653  4433 5 77778888  99999999999998652  2322    38888899999999999999


Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHH-HHHHhcCCHHHHHHHHhhccC--C
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALI-STYCLCGEVDMARGIFYMSCE--D  143 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li-~~y~~~g~~~~A~~vf~~m~~--~  143 (230)
                      .|++..+.. +-+...|..+-..+...|++  |...+....     +...|..+- ..|. .+++++|.+.|++..+  |
T Consensus        96 ~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~a~~~~p  173 (272)
T 3u4t_A           96 QYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYY-NKEYVKADSSFVKVLELKP  173 (272)
T ss_dssp             HHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhCc
Confidence            999977642 12446888999999999999  888888887     677777777 5555 4599999999998875  5


Q ss_pred             C-hhhhHHHHHHhh-------hcchhhhHHHHHHHhhhcCch------hhhhhhhhcccccCCcccccccCCccCCcccc
Q 042210          144 D-DGLHELIRIKAV-------DDDLHELFPEYLVQMLALPDT------FMGEGLEVIPKSQAPREETPRVGNLEEGTPQE  209 (230)
Q Consensus       144 ~-~~t~n~li~~~~-------~~~~~~~~~~m~~~~~~~p~~------~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~  209 (230)
                      + ...|..+...+.       .++|.+.+++..+.....|+.      ..+..+..         .+.+.|+.++|...+
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~---------~~~~~~~~~~A~~~~  244 (272)
T 3u4t_A          174 NIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAY---------YYTINRDKVKADAAW  244 (272)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHH---------HHHHTTCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHH---------HHHHcCCHHHHHHHH
Confidence            4 344444433332       345788888877765444552      12222212         567889999999999


Q ss_pred             ccccccC
Q 042210          210 GRPHEHS  216 (230)
Q Consensus       210 ~~~~~~~  216 (230)
                      ..+.+..
T Consensus       245 ~~al~~~  251 (272)
T 3u4t_A          245 KNILALD  251 (272)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhcC
Confidence            8877653

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.43  E-value=1.6e-05  Score=63.94  Aligned_cols=165  Identities=10%  Similarity=0.021  Sum_probs=117.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-hh-hHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-VF-LWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~~-~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|+.+++...+. +.|+.. . ..+...+.  +.|++++|..+|++..  .|+ .. .|..+...+.+.|++++|..+|
T Consensus        81 ~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  157 (308)
T 2ond_A           81 DEAANIYERAIST-LLKKNMLLYFAYADYEE--SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIF  157 (308)
T ss_dssp             HHHHHHHHHHHTT-TTTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-hCcccHHHHHHHHHHHH--hcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHH
Confidence            4566777665552 356555 4 78888888  9999999999999875  443 33 7999999999999999999999


Q ss_pred             HHHHhCCCCCCcccHHHHHHHhh-hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----
Q 042210           76 LDLLKSDVRRDNYTFPFLFKGFT-RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE-----  142 (230)
Q Consensus        76 ~~M~~~g~~p~~~t~~~ll~~~~-~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----  142 (230)
                      ++..+.+ +++...|........ ..|+.  |..+|+...     +...|..++..+.+.|++++|+.+|++...     
T Consensus       158 ~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~  236 (308)
T 2ond_A          158 KKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             HHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCC
Confidence            9987643 223334433322222 25777  888888876     788999999999999999999999998765     


Q ss_pred             C--ChhhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          143 D--DDGLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       143 ~--~~~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      |  ....|..++.-...    +++..++++..+.
T Consensus       237 p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            2  23467776654443    3455555554433

>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=98.42  E-value=4.4e-06  Score=66.75  Aligned_cols=136  Identities=9%  Similarity=0.013  Sum_probs=108.4

Q ss_pred             HhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--
Q 042210           29 LLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--  103 (230)
Q Consensus        29 ~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--  103 (230)
                      +.  ..|++++|...+++..   +.+...|..+...|.+.|++++|...|++..+.. +.+..+|..+...+.+.|++  
T Consensus       148 ~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  224 (327)
T 3cv0_A          148 FA--APNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQE  224 (327)
T ss_dssp             TT--SHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HH--HcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHH
Confidence            66  8899999999999875   4567889999999999999999999999987643 22456788899999999999  


Q ss_pred             hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-------------hhhhHHHHHHhhhcchhhh
Q 042210          104 SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-------------DGLHELIRIKAVDDDLHEL  163 (230)
Q Consensus       104 a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-------------~~t~n~li~~~~~~~~~~~  163 (230)
                      |...+....     +...|..+...|.+.|++++|.+.|++..+  |+             ..+|..+...+...+..+.
T Consensus       225 A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  304 (327)
T 3cv0_A          225 ALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDL  304 (327)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHH
Confidence            888888776     678899999999999999999999998764  44             4567666666655443333


Q ss_pred             HHHH
Q 042210          164 FPEY  167 (230)
Q Consensus       164 ~~~m  167 (230)
                      ..+.
T Consensus       305 A~~~  308 (327)
T 3cv0_A          305 VELT  308 (327)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3333

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.40  E-value=7.9e-06  Score=63.72  Aligned_cols=187  Identities=9%  Similarity=0.001  Sum_probs=128.2

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+..  |+ ... ..+-..|.  +.|++++|...|++..   +.+...|..+-..|.+.|++++|...|+
T Consensus        60 ~~A~~~~~~al~~~--~~~~~~~~~la~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  135 (275)
T 1xnf_A           60 ALARNDFSQALAIR--PDMPEVFNYLGIYLT--QAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLL  135 (275)
T ss_dssp             HHHHHHHHHHHHHC--CCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC--CCcHHHHHHHHHHHH--HccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHH
Confidence            46778888877763  44 445 77888888  9999999999999876   4467889999999999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCC-----
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCEDD-----  144 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~-----  144 (230)
                      +..+.  .|+.......+..+...|+.  |...+....     +...+. +...+...++.++|.+.+++..+.+     
T Consensus       136 ~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  212 (275)
T 1xnf_A          136 AFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAE  212 (275)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHH
T ss_pred             HHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccc
Confidence            98763  46665566666666777777  777776555     334443 7777888888999999999877622     


Q ss_pred             --hhhhHHHHHHhhhc----chhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccc
Q 042210          145 --DGLHELIRIKAVDD----DLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQE  209 (230)
Q Consensus       145 --~~t~n~li~~~~~~----~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~  209 (230)
                        ..+|..+...+...    +|.+.+++...   ..|+......  .         ++...|++++|.+-+
T Consensus       213 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~--~---------~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          213 HLSETNFYLGKYYLSLGDLDSATALFKLAVA---NNVHNFVEHR--Y---------ALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TCCTTCHHHH--H---------HHHHHHHHHHC----
T ss_pred             cccHHHHHHHHHHHHcCCHHHHHHHHHHHHh---CCchhHHHHH--H---------HHHHHHHHHhhHHHH
Confidence              35566665555543    45555555443   3454322222  1         444666776665543

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=98.39  E-value=2.8e-05  Score=61.06  Aligned_cols=194  Identities=9%  Similarity=-0.084  Sum_probs=139.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhc----cCChHHHHHHHHhcC-CCChhhHHHHHHHHHh----cCChhHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYE----KGDLKYECKVFRKIT-QPSVFLWNTMIKGYSR----IDSHKNG   71 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~----~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~----~~~~~~a   71 (230)
                      ++|.+.++...+.   -+... ..+-..|.  .    .+++++|...|++.. ..+...+..+-..|.+    .+++++|
T Consensus        23 ~~A~~~~~~a~~~---~~~~a~~~lg~~~~--~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A   97 (273)
T 1ouv_A           23 TQAKKYFEKACDL---KENSGCFNLGVLYY--QGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKA   97 (273)
T ss_dssp             HHHHHHHHHHHHT---TCHHHHHHHHHHHH--HTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHHHC---CCHHHHHHHHHHHH--cCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCcccCHHHH
Confidence            4677788777762   23334 56666777  7    999999999998865 4467778888888888    9999999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch--hhHHHhhhh---hHhHHHHHHHHHHh----cCCHHHHHHHHh
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLEKSCIVM---RVFVQNALISTYCL----CGEVDMARGIFY  138 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~~~~~~~---~~~~~~~li~~y~~----~g~~~~A~~vf~  138 (230)
                      ...|++-.+.+   +...+..+-..+.+    .++.  |...+....   +...+..+-..|.+    .+++++|...|+
T Consensus        98 ~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~  174 (273)
T 1ouv_A           98 LQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYD  174 (273)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            99999987775   55677777778887    7887  888887776   67778888888888    899999999999


Q ss_pred             hccC-CChhhhHHHHHHhhh--------cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccc----cCCccCC
Q 042210          139 MSCE-DDDGLHELIRIKAVD--------DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPR----VGNLEEG  205 (230)
Q Consensus       139 ~m~~-~~~~t~n~li~~~~~--------~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~----~g~~~~a  205 (230)
                      +..+ .+...+..+-..+..        ++|++.+++..+.+.  |+  .+..+..         .+.+    .++.++|
T Consensus       175 ~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~--~~--a~~~l~~---------~~~~g~~~~~~~~~A  241 (273)
T 1ouv_A          175 KACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN--GG--GCFNLGA---------MQYNGEGVTRNEKQA  241 (273)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC--HH--HHHHHHH---------HHHTTSSSSCCSTTH
T ss_pred             HHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC--HH--HHHHHHH---------HHHcCCCcccCHHHH
Confidence            8765 344455555444433        356666666555441  22  2222112         3334    8899999


Q ss_pred             ccccccccccC
Q 042210          206 TPQEGRPHEHS  216 (230)
Q Consensus       206 ~~i~~~~~~~~  216 (230)
                      ...+....+.|
T Consensus       242 ~~~~~~a~~~~  252 (273)
T 1ouv_A          242 IENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHcC
Confidence            99998888776

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.38  E-value=4.9e-06  Score=60.61  Aligned_cols=117  Identities=11%  Similarity=0.029  Sum_probs=99.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  ..|++++|...+++..   +.+...|..+...+...|++++|...|++..+.. +.+...+..+...+..
T Consensus        46 ~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~  122 (186)
T 3as5_A           46 LHLGIAYV--KTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDN  122 (186)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHH
Confidence            66778888  9999999999999875   4567788889999999999999999999987652 2356678888889999


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .|++  |...+....     +...+..+...|.+.|++++|.+.|++..+
T Consensus       123 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  172 (186)
T 3as5_A          123 LGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANE  172 (186)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            9999  888888776     678899999999999999999999998754

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.31  E-value=3.4e-05  Score=56.74  Aligned_cols=144  Identities=14%  Similarity=0.028  Sum_probs=109.5

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+=..|.  +.|++++|.+.|++..   +-+...|..+-..|.+.|++++|...++......-. +...+..+-..+..
T Consensus         9 ~~lG~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~   85 (184)
T 3vtx_A            9 MDIGDKKR--TKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTT-SAEAYYILGSANFM   85 (184)
T ss_dssp             HHHHHHHH--HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCch-hHHHHHHHHHHHHH
Confidence            55667777  9999999999999865   456778999999999999999999999987664322 34456666677777


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFP  165 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~  165 (230)
                      .++.  +...+....     +...+..+-..|.+.|++++|.+.|++..+  | +..+|..+-..+..    ++|.+.|+
T Consensus        86 ~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~  165 (184)
T 3vtx_A           86 IDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFK  165 (184)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHH
Confidence            7887  777666665     788888999999999999999999998765  4 45567766555554    45666666


Q ss_pred             HHHH
Q 042210          166 EYLV  169 (230)
Q Consensus       166 ~m~~  169 (230)
                      +..+
T Consensus       166 ~al~  169 (184)
T 3vtx_A          166 KALE  169 (184)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5543

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.28  E-value=9.3e-06  Score=62.53  Aligned_cols=180  Identities=7%  Similarity=-0.045  Sum_probs=133.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCC--CCCC----cccHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD--VRRD----NYTFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g--~~p~----~~t~~~ll   94 (230)
                      ..+-..+.  +.|++++|...|++..  ..+...|..+-..|...|++++|...|++..+..  ..|+    ...|..+-
T Consensus         9 ~~~g~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~   86 (258)
T 3uq3_A            9 KAEGNKFY--KARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIG   86 (258)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHH
Confidence            44556677  9999999999998754  3677889999999999999999999999976532  2233    46788888


Q ss_pred             HHhhhcCch--hhHHHhhhh-------------------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           95 KGFTRDIAG--SLEKSCIVM-------------------------------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        95 ~~~~~~~~~--a~~~~~~~~-------------------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..+.+.|++  |...+....                               +...|..+-..|.+.|++++|.+.|++..
T Consensus        87 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~  166 (258)
T 3uq3_A           87 NAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMI  166 (258)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            899999998  666665543                               45677888899999999999999999876


Q ss_pred             C--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCcccccccc
Q 042210          142 E--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPH  213 (230)
Q Consensus       142 ~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~  213 (230)
                      +  | +..+|..+...+..    ++|.+.+++..+..   |+ ...+..+..         .+.+.|+.++|...+..+.
T Consensus       167 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~---~~~~~~~~~l~~---------~~~~~g~~~~A~~~~~~a~  234 (258)
T 3uq3_A          167 KRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD---PNFVRAYIRKAT---------AQIAVKEYASALETLDAAR  234 (258)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---TTCHHHHHHHHH---------HHHHTTCHHHHHHHHHHHH
T ss_pred             hcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC---HHHHHHHHHHHH---------HHHHHhhHHHHHHHHHHHH
Confidence            5  3 45667766655543    46777777665543   44 333333222         6778899999998888776


Q ss_pred             ccC
Q 042210          214 EHS  216 (230)
Q Consensus       214 ~~~  216 (230)
                      +..
T Consensus       235 ~~~  237 (258)
T 3uq3_A          235 TKD  237 (258)
T ss_dssp             HHH
T ss_pred             HhC
Confidence            643

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.28  E-value=1.5e-05  Score=64.24  Aligned_cols=201  Identities=13%  Similarity=0.027  Sum_probs=134.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhh-----hccCCh-------HHHHHHHHhcC---CC-ChhhHHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLL-----YEKGDL-------KYECKVFRKIT---QP-SVFLWNTMIKGYS   63 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~-----~~~~~~-------~~a~~~~~~m~---~~-~~~~yn~li~~~~   63 (230)
                      ++|..+|++..+..  |+.. . ..+...+..     .+.|++       ++|..+|++..   .| +...|..+...+.
T Consensus        33 ~~a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            35667787777653  4433 3 444444430     035786       89999998854   34 4558999999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCcc--cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHH-hcCCHHHH
Q 042210           64 RIDSHKNGVLMYLDLLKSDVRRDNY--TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYC-LCGEVDMA  133 (230)
Q Consensus        64 ~~~~~~~a~~~~~~M~~~g~~p~~~--t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~-~~g~~~~A  133 (230)
                      +.|++++|..+|++..+  +.|+..  .|..+...+.+.|++  |..+++...     +...|........ ..|+.++|
T Consensus       111 ~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A  188 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVA  188 (308)
T ss_dssp             HTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHH
T ss_pred             hcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999877  456543  788899999999998  889998877     3334433333322 36999999


Q ss_pred             HHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc--hhhhhhhhhcccccCCcccccccCCccC
Q 042210          134 RGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD--TFMGEGLEVIPKSQAPREETPRVGNLEE  204 (230)
Q Consensus       134 ~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~--~~t~~~l~~~~~~~~~~~a~~~~g~~~~  204 (230)
                      +++|++..+  | +...|..++..+..    +++..+|++........|+  ...+..  .+.       ...+.|+.+.
T Consensus       189 ~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~--~~~-------~~~~~g~~~~  259 (308)
T 2ond_A          189 FKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWAR--FLA-------FESNIGDLAS  259 (308)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHH--HHH-------HHHHHSCHHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHH--HHH-------HHHHcCCHHH
Confidence            999998765  4 45667777665544    4566666665554212343  223333  221       3346788888


Q ss_pred             Ccccccccccc
Q 042210          205 GTPQEGRPHEH  215 (230)
Q Consensus       205 a~~i~~~~~~~  215 (230)
                      +..++.++.+.
T Consensus       260 a~~~~~~a~~~  270 (308)
T 2ond_A          260 ILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            88888877665

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.23  E-value=3.4e-05  Score=52.72  Aligned_cols=115  Identities=15%  Similarity=0.124  Sum_probs=89.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCL  126 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~  126 (230)
                      .|..+...+...|++++|..+|+++.+.+ +.+...+..+...+...|++  |...+....     +...+..+...|.+
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH
Confidence            57778889999999999999999987653 23556778888889999998  888888776     67788889999999


Q ss_pred             cCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHH
Q 042210          127 CGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLV  169 (230)
Q Consensus       127 ~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~  169 (230)
                      .|++++|.+.|+++.+  | +..+|..+...+..    +++.+.++++.+
T Consensus        82 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            9999999999998765  3 45667766666654    355555555543

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.21  E-value=1.3e-05  Score=68.78  Aligned_cols=144  Identities=12%  Similarity=-0.003  Sum_probs=114.9

Q ss_pred             HHHHHHHhhhccCCh-HHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDL-KYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~-~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~   98 (230)
                      ..+-..+.  ..|++ ++|.+.|++..   +.+...|..+-..|.+.|++++|...|++..+..  |+...+..+-..+.
T Consensus       106 ~~lg~~~~--~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg~~~~  181 (474)
T 4abn_A          106 MLKGKALN--VTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLSMVLR  181 (474)
T ss_dssp             HHHHHHHT--SSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHHHHHT
T ss_pred             HHHHHHHH--hccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHHHHHH
Confidence            55556677  99999 99999999865   4457789999999999999999999999987654  77778888888898


Q ss_pred             hc---------Cch--hhHHHhhhh-----hHhHHHHHHHHHHhc--------CCHHHHHHHHhhccC--C----Chhhh
Q 042210           99 RD---------IAG--SLEKSCIVM-----RVFVQNALISTYCLC--------GEVDMARGIFYMSCE--D----DDGLH  148 (230)
Q Consensus        99 ~~---------~~~--a~~~~~~~~-----~~~~~~~li~~y~~~--------g~~~~A~~vf~~m~~--~----~~~t~  148 (230)
                      ..         |++  |...+....     +...|..+-..|.+.        |++++|.+.|++..+  |    +...|
T Consensus       182 ~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~  261 (474)
T 4abn_A          182 QLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLH  261 (474)
T ss_dssp             TCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHH
T ss_pred             HhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHH
Confidence            88         888  888888776     788899999999998        999999999998764  5    45567


Q ss_pred             HHHHHHhhh----cchhhhHHHHHHH
Q 042210          149 ELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       149 n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      ..+-..+..    ++|.+.|++..+.
T Consensus       262 ~~lg~~~~~~g~~~~A~~~~~~al~l  287 (474)
T 4abn_A          262 LNRATLHKYEESYGEALEGFSQAAAL  287 (474)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            666555543    4566666665543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.20  E-value=1.2e-05  Score=61.51  Aligned_cols=131  Identities=10%  Similarity=-0.028  Sum_probs=67.2

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhcc-----------CChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcC
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEK-----------GDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRID   66 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~-----------~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~   66 (230)
                      +|...++...+.  .|+...  ..+-..+.  +.           |++++|...|++..  .| +...|..+=..|...|
T Consensus        57 ~A~~~~~~al~~--~P~~~~a~~~lg~~~~--~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g  132 (217)
T 2pl2_A           57 PALENGKTLVAR--TPRYLGGYMVLSEAYV--ALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLG  132 (217)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHHHHHH--HhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcC
Confidence            444555554444  244332  44445555  66           66677766666654  23 3455666666666667


Q ss_pred             ChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           67 SHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ++++|...|++..+..  .+...+..+-.++...|++  |...++...     +...+..+-..|.+.|++++|...|++
T Consensus       133 ~~~~A~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          133 ERDKAEASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC-------------
T ss_pred             ChHHHHHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            7777777776665554  4555555566666666666  555555544     455555666666666666666666554

>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=98.19  E-value=3e-05  Score=66.46  Aligned_cols=203  Identities=8%  Similarity=-0.032  Sum_probs=143.3

Q ss_pred             hHHHHHHHHHHhcCCCCCc--------H-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHH
Q 042210            3 QLKQIHSQTIKLGLLTKPH--------C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNG   71 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~--------~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a   71 (230)
                      +|..+++.+.+.  .|+..        + ..+-..+.  ..|++++|...|+...  .|+...|..+-..|...|++++|
T Consensus       220 ~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  295 (537)
T 3fp2_A          220 KSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFHF--LKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEF  295 (537)
T ss_dssp             HHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHH
T ss_pred             HHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHHH--hcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHH
Confidence            455666655543  34421        2 33335666  8899999999999876  67778889999999999999999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--  142 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--  142 (230)
                      ...|++..+.. +.+..+|..+-..+...|++  |...+....     +...|..+...|.+.|++++|...|++..+  
T Consensus       296 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  374 (537)
T 3fp2_A          296 FKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF  374 (537)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999987643 22466788899999999999  888888876     678899999999999999999999998865  


Q ss_pred             C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCccccccc----------CCccCCcc
Q 042210          143 D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRV----------GNLEEGTP  207 (230)
Q Consensus       143 ~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~----------g~~~~a~~  207 (230)
                      | +...|..+...+..    ++|.+.+++..+.....++.....+. .+.    ....+.+.          |++++|..
T Consensus       375 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~-~~~----~a~~~~~~~~~~~~~~~~~~~~~A~~  449 (537)
T 3fp2_A          375 PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGP-LIG----KATILARQSSQDPTQLDEEKFNAAIK  449 (537)
T ss_dssp             TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHH-HHH----HHHHHHHHHTC----CCHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHH-HHH----HHHHHHHHhhccchhhhHhHHHHHHH
Confidence            4 44566666555443    56777787777665322222111100 000    00034444          89999999


Q ss_pred             cccccccc
Q 042210          208 QEGRPHEH  215 (230)
Q Consensus       208 i~~~~~~~  215 (230)
                      .+..+.+.
T Consensus       450 ~~~~a~~~  457 (537)
T 3fp2_A          450 LLTKACEL  457 (537)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            88887765

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.15  E-value=6.1e-05  Score=55.33  Aligned_cols=136  Identities=11%  Similarity=-0.031  Sum_probs=110.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.|+...+.  .|+...  ..+-..|.  +.|++++|...+....   ..+...+..+-..+...++++.+...+.
T Consensus        22 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~   97 (184)
T 3vtx_A           22 DGAIRAYKKVLKA--DPNNVETLLKLGKTYM--DIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAAIDALQ   97 (184)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            5788888888776  465444  67778888  9999999999998875   4455677777788888999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +..... +-+...+..+-..+.+.|++  |...++...     +...|..+-..|.+.|++++|.+.|++..+
T Consensus        98 ~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A           98 RAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            876532 12455777888889999999  888888776     788899999999999999999999998655

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=97.99  E-value=4.8e-05  Score=60.16  Aligned_cols=139  Identities=9%  Similarity=-0.061  Sum_probs=102.8

Q ss_pred             hhHHHHHHHHHHhc------CCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcCC-------C----ChhhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLG------LLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKITQ-------P----SVFLWNTMIKGY   62 (230)
Q Consensus         2 ~~a~~~~~~m~~~g------~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~-------~----~~~~yn~li~~~   62 (230)
                      ++|..+++...+.-      -.|. ... ..+-..|.  ..|++++|...+++...       +    ....|..+-..|
T Consensus        44 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~  121 (311)
T 3nf1_A           44 EVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYR--DQNKYKDAANLLNDALAIREKTLGKDHPAVAATLNNLAVLY  121 (311)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHH
Confidence            45666676665531      1222 233 56667788  99999999999987641       2    235688888999


Q ss_pred             HhcCChhHHHHHHHHHHhC------CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHHH
Q 042210           63 SRIDSHKNGVLMYLDLLKS------DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNAL  120 (230)
Q Consensus        63 ~~~~~~~~a~~~~~~M~~~------g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~l  120 (230)
                      ...|++++|...|++..+.      +-.| ....+..+-..+...|++  |...+....             ...++..+
T Consensus       122 ~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  201 (311)
T 3nf1_A          122 GKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNL  201 (311)
T ss_dssp             HTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHH
T ss_pred             HHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            9999999999999997653      2223 345677788889999998  776666654             45678888


Q ss_pred             HHHHHhcCCHHHHHHHHhhccC
Q 042210          121 ISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       121 i~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ...|.+.|++++|.+.|++..+
T Consensus       202 a~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          202 ASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999999999999987763

>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=97.99  E-value=0.00092  Score=52.20  Aligned_cols=162  Identities=9%  Similarity=-0.052  Sum_probs=122.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhc----cCChHHHHHHHHhcC-CCChhhHHHHHHHHHh----cCChhHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYE----KGDLKYECKVFRKIT-QPSVFLWNTMIKGYSR----IDSHKNG   71 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~----~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~----~~~~~~a   71 (230)
                      ++|...++...+.+   ++.. ..+-..|.  .    .++.++|...|++.. ..+...+..+-..|.+    .+++++|
T Consensus        59 ~~A~~~~~~a~~~~---~~~a~~~lg~~~~--~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A  133 (273)
T 1ouv_A           59 KKAASFYAKACDLN---YSNGCHLLGNLYY--SGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKA  133 (273)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHH--HTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHh--CCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHH
Confidence            46778888887776   4455 66667777  7    999999999999865 4466778888888888    9999999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch--hhHHHhhhh---hHhHHHHHHHHHHh----cCCHHHHHHHHh
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLEKSCIVM---RVFVQNALISTYCL----CGEVDMARGIFY  138 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~~~~~~~---~~~~~~~li~~y~~----~g~~~~A~~vf~  138 (230)
                      ...|++-.+.+   +...+..+-..+.+    .++.  |...+....   +...+..+-..|.+    .+++++|...|+
T Consensus       134 ~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~  210 (273)
T 1ouv_A          134 VEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYS  210 (273)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHH
Confidence            99999988766   44566667677776    6777  888887766   67788888889999    999999999999


Q ss_pred             hccCC-ChhhhHHHHHHhhh--------cchhhhHHHHHHHh
Q 042210          139 MSCED-DDGLHELIRIKAVD--------DDLHELFPEYLVQM  171 (230)
Q Consensus       139 ~m~~~-~~~t~n~li~~~~~--------~~~~~~~~~m~~~~  171 (230)
                      +..+. +...+..+-..+..        ++|.+.+++-.+.+
T Consensus       211 ~a~~~~~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          211 KACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            87653 34445544444432        46777777766665

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.98  E-value=0.00017  Score=62.33  Aligned_cols=149  Identities=11%  Similarity=0.039  Sum_probs=107.7

Q ss_pred             hHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CCC-h-hhHHHHHHHHHhcCChhHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-V-FLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~-~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      +|+.+++...+. +.|+.. . ..+...+.  +.|++++|..+|+...  .|+ . ..|......+.+.|++++|..+|+
T Consensus       304 ~A~~~~~~Al~~-~~p~~~~l~~~~~~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~  380 (530)
T 2ooe_A          304 EAANIYERAIST-LLKKNMLLYFAYADYEE--SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  380 (530)
T ss_dssp             HHHHHHHHHTTT-TCSSCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-hCcccHHHHHHHHHHHH--hcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            566666655431 346544 4 77888888  9999999999999875  444 2 479999988889999999999999


Q ss_pred             HHHhCCCCCC-cccHHHHHHH-hhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-
Q 042210           77 DLLKSDVRRD-NYTFPFLFKG-FTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-  144 (230)
Q Consensus        77 ~M~~~g~~p~-~~t~~~ll~~-~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-  144 (230)
                      +-.+.  .|+ ...|...... +...|+.  |..+|+...     +...|..++..+.+.|+.++|+.+|++...  |. 
T Consensus       381 ~Al~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~  458 (530)
T 2ooe_A          381 KARED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  458 (530)
T ss_dssp             HHHTC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSC
T ss_pred             HHHhc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCC
Confidence            97664  333 2222221112 2357777  888888776     788999999999999999999999998754  22 


Q ss_pred             ----hhhhHHHHHHhh
Q 042210          145 ----DGLHELIRIKAV  156 (230)
Q Consensus       145 ----~~t~n~li~~~~  156 (230)
                          ...|...+.-..
T Consensus       459 ~~~~~~lw~~~~~~e~  474 (530)
T 2ooe_A          459 PEKSGEIWARFLAFES  474 (530)
T ss_dssp             GGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHH
Confidence                226766655433

>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=97.96  E-value=0.00016  Score=65.46  Aligned_cols=143  Identities=10%  Similarity=0.056  Sum_probs=115.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~   98 (230)
                      +.+=..|.  +.|++++|.+.|++..  .| +...|+.+=..|.+.|++++|...|++-.+.  .|+ ...|..+-.++.
T Consensus        13 ~nLG~~~~--~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~~l~   88 (723)
T 4gyw_A           13 NNLANIKR--EQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTLK   88 (723)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            66777888  9999999999999865  44 5678999999999999999999999997653  453 557888889999


Q ss_pred             hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHHHHHHhh----hcchhhhH
Q 042210           99 RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGLHELIRIKAV----DDDLHELF  164 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~li~~~~----~~~~~~~~  164 (230)
                      +.|++  |.+.++...     +...|+.+-..|.+.|++++|.+.|++..+  |+ ...|..+...+.    .+++.+.+
T Consensus        89 ~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~  168 (723)
T 4gyw_A           89 EMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERM  168 (723)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHH
Confidence            99999  888888776     788999999999999999999999998765  54 456666655443    35666666


Q ss_pred             HHHHH
Q 042210          165 PEYLV  169 (230)
Q Consensus       165 ~~m~~  169 (230)
                      ++..+
T Consensus       169 ~kal~  173 (723)
T 4gyw_A          169 KKLVS  173 (723)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66554

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=97.94  E-value=0.00019  Score=53.77  Aligned_cols=114  Identities=10%  Similarity=0.016  Sum_probs=94.8

Q ss_pred             HHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--
Q 042210           26 TRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--  103 (230)
Q Consensus        26 l~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--  103 (230)
                      -..+.  +.|++++|...|++...|+...|..+-..|.+.|++++|...|++..+.. +.+...|..+-.++.+.|++  
T Consensus        13 g~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~   89 (213)
T 1hh8_A           13 GVLAA--DKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDL   89 (213)
T ss_dssp             HHHHH--HTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHH--HhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccHHH
Confidence            34566  88999999999999988888899999999999999999999999976643 23456778888888899998  


Q ss_pred             hhHHHhhhh-----hH----------------hHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          104 SLEKSCIVM-----RV----------------FVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       104 a~~~~~~~~-----~~----------------~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      |...+....     +.                ..+..+-..|.+.|++++|.+.|+...+
T Consensus        90 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  149 (213)
T 1hh8_A           90 AIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  149 (213)
T ss_dssp             HHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            777777665     22                7788888999999999999999998765

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=97.92  E-value=0.00015  Score=62.71  Aligned_cols=196  Identities=15%  Similarity=0.107  Sum_probs=129.3

Q ss_pred             HHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhc-------cCChH-------HHHHHHHhcC---CC-ChhhHHHHHHHHH
Q 042210            4 LKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYE-------KGDLK-------YECKVFRKIT---QP-SVFLWNTMIKGYS   63 (230)
Q Consensus         4 a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~-------~~~~~-------~a~~~~~~m~---~~-~~~~yn~li~~~~   63 (230)
                      +..++++..+.  .|+. .. ......+.  +       .|+++       +|..+|+...   .| +...|..+...+.
T Consensus       257 a~~~y~~al~~--~p~~~~~w~~~~~~~~--~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~  332 (530)
T 2ooe_A          257 VMFAYEQCLLV--LGHHPDIWYEAAQYLE--QSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  332 (530)
T ss_dssp             HHHHHHHHHHH--HTTCHHHHHHHHHHHH--HHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHH--HhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            44566666554  2432 33 44555555  4       68987       8999999865   24 4678999999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCCc--ccHHHHHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHH
Q 042210           64 RIDSHKNGVLMYLDLLKSDVRRDN--YTFPFLFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        64 ~~~~~~~a~~~~~~M~~~g~~p~~--~t~~~ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~  132 (230)
                      +.|++++|..+|++..+  +.|+.  ..|......+.+.|++  |..+++...       ......+++. |...|+.++
T Consensus       333 ~~g~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~-~~~~~~~~~  409 (530)
T 2ooe_A          333 SRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALME-YYCSKDKSV  409 (530)
T ss_dssp             HTTCHHHHHHHHHHHHH--SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHH-HHHTCCHHH
T ss_pred             hcCCHHHHHHHHHHHhC--ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHH-HHHcCChhH
Confidence            99999999999999887  45653  3688888888888888  888888877       1222222332 336899999


Q ss_pred             HHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc--hhhhhhhhhcccccCCcccccccCCcc
Q 042210          133 ARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQMLALPD--TFMGEGLEVIPKSQAPREETPRVGNLE  203 (230)
Q Consensus       133 A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~--~~t~~~l~~~~~~~~~~~a~~~~g~~~  203 (230)
                      |+++|+...+  | +...|..++.....    +++..+|++........|+  ...+..  .+.       -..+.|+.+
T Consensus       410 A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~--~~~-------~e~~~G~~~  480 (530)
T 2ooe_A          410 AFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWAR--FLA-------FESNIGDLA  480 (530)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHH--HHH-------HHHHSSCHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHH--HHH-------HHHHcCCHH
Confidence            9999997654  5 46778887766554    3556666655554312232  112322  121       223568888


Q ss_pred             CCcccccccccc
Q 042210          204 EGTPQEGRPHEH  215 (230)
Q Consensus       204 ~a~~i~~~~~~~  215 (230)
                      .+..+..++.+.
T Consensus       481 ~~~~~~~r~~~~  492 (530)
T 2ooe_A          481 SILKVEKRRFTA  492 (530)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            888877766554

>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=97.87  E-value=2.2e-05  Score=61.08  Aligned_cols=118  Identities=11%  Similarity=-0.004  Sum_probs=91.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC----------CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhC------CCCC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT----------QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS------DVRR   85 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~----------~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~------g~~p   85 (230)
                      ..+-..|.  ..|++++|...+++..          .| ....|+.+-..|...|++++|...|++....      .-.|
T Consensus        47 ~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  124 (283)
T 3edt_B           47 NILALVYR--DQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHP  124 (283)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHH--HcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCCh
Confidence            56667777  9999999999998764          11 2356888889999999999999999987653      1122


Q ss_pred             -CcccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           86 -DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        86 -~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                       ...++..+-..+...|++  |...+....             ...++..+-..|.+.|++++|...|++..+
T Consensus       125 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          125 DVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             355777888888899998  666666654             456788888999999999999999987753

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=97.86  E-value=3.9e-05  Score=60.70  Aligned_cols=146  Identities=11%  Similarity=0.005  Sum_probs=106.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCC--------CC---hhhHHHHHHHHHhcCChhHHHHHHHHHHhC------CCCC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQ--------PS---VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS------DVRR   85 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~--------~~---~~~yn~li~~~~~~~~~~~a~~~~~~M~~~------g~~p   85 (230)
                      ..+-..+.  ..|++++|...|++...        .+   ...|..+-..|...|++++|...|++....      +-.|
T Consensus        31 ~~l~~~~~--~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  108 (311)
T 3nf1_A           31 HNLVIQYA--SQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHP  108 (311)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCCh
Confidence            55667777  99999999999988652        12   346888888999999999999999997653      2222


Q ss_pred             -CcccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-------
Q 042210           86 -DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNALISTYCLCGEVDMARGIFYMSCE-------  142 (230)
Q Consensus        86 -~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-------  142 (230)
                       ...++..+-..+...|++  |...+....             ....+..+-..|.+.|++++|.+.|++..+       
T Consensus       109 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~  188 (311)
T 3nf1_A          109 AVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLG  188 (311)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhC
Confidence             455788888899999998  666666554             456678888999999999999999987753       


Q ss_pred             C-C---hhhhHHHHHHhh----hcchhhhHHHHHHH
Q 042210          143 D-D---DGLHELIRIKAV----DDDLHELFPEYLVQ  170 (230)
Q Consensus       143 ~-~---~~t~n~li~~~~----~~~~~~~~~~m~~~  170 (230)
                      + +   ..+|..+...+.    .++|.+.+++..+.
T Consensus       189 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  224 (311)
T 3nf1_A          189 PDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTR  224 (311)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            1 1   224444444443    35777777777653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.83  E-value=0.00015  Score=57.55  Aligned_cols=200  Identities=9%  Similarity=-0.050  Sum_probs=132.1

Q ss_pred             hhHHHHHHHHHHhcCCCCC-----cH-HHHHHHHhhhccCChHHHHHHHHhcC-----C----CChhhHHHHHHHHHhcC
Q 042210            2 HQLKQIHSQTIKLGLLTKP-----HC-PKQTRYLLLYEKGDLKYECKVFRKIT-----Q----PSVFLWNTMIKGYSRID   66 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~----~~~~~yn~li~~~~~~~   66 (230)
                      ++|...++...+..  |+.     .. ..+-..|.  ..|++++|.+.+++..     .    .....|..+-..|...|
T Consensus        22 ~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   97 (338)
T 3ro2_A           22 RAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYF--YLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLG   97 (338)
T ss_dssp             HHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhhC--cccHHHHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHcc
Confidence            56888888888873  443     33 56667788  9999999999998753     1    12456788888899999


Q ss_pred             ChhHHHHHHHHHHhCC-CCCC----cccHHHHHHHhhhcCc--------------------h--hhHHHhhhh-------
Q 042210           67 SHKNGVLMYLDLLKSD-VRRD----NYTFPFLFKGFTRDIA--------------------G--SLEKSCIVM-------  112 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~g-~~p~----~~t~~~ll~~~~~~~~--------------------~--a~~~~~~~~-------  112 (230)
                      ++++|...+++..+.. -.++    ..++..+-..+...|+                    +  |...+....       
T Consensus        98 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~  177 (338)
T 3ro2_A           98 NFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALG  177 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999998865421 1122    3367777778888888                    6  655555543       


Q ss_pred             ----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----CCh----hhhHHHHHHhh----hcchhhhHHHHHHHhhhcC
Q 042210          113 ----RVFVQNALISTYCLCGEVDMARGIFYMSCE-----DDD----GLHELIRIKAV----DDDLHELFPEYLVQMLALP  175 (230)
Q Consensus       113 ----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----~~~----~t~n~li~~~~----~~~~~~~~~~m~~~~~~~p  175 (230)
                          ....+..+-..|...|++++|.+.|++..+     ++.    .+|..+...+.    .+++.+.+++......-.+
T Consensus       178 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~  257 (338)
T 3ro2_A          178 DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLK  257 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhc
Confidence                345778888899999999999999987654     221    24444433333    3466677766655432222


Q ss_pred             c----hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          176 D----TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       176 ~----~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      +    ..++..+         -..+...|+.++|...+....+
T Consensus       258 ~~~~~~~~~~~l---------a~~~~~~g~~~~A~~~~~~a~~  291 (338)
T 3ro2_A          258 DRAVEAQSCYSL---------GNTYTLLQDYEKAIDYHLKHLA  291 (338)
T ss_dssp             CHHHHHHHHHHH---------HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHH---------HHHHHHhcCHHHHHHHHHHHHH
Confidence            2    1122221         1156678888888887776554

>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=97.80  E-value=0.00024  Score=59.31  Aligned_cols=174  Identities=7%  Similarity=-0.095  Sum_probs=125.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCC-hhHHHHHHHHHHhCCCCC-CcccHHHHHHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDS-HKNGVLMYLDLLKSDVRR-DNYTFPFLFKGF   97 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~-~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~   97 (230)
                      ..+-..+.  +.|+.++|.+.+++..   +.+...|+.+-..+.+.|+ +++|+..|++..+.  .| +...|..+-.++
T Consensus       101 ~~lg~~~~--~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l--~P~~~~a~~~~g~~~  176 (382)
T 2h6f_A          101 DYFRAVLQ--RDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE--QPKNYQVWHHRRVLV  176 (382)
T ss_dssp             HHHHHHHH--HTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHH--HCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHH
Confidence            44556666  8899999999999875   4456788999899999996 99999999998764  33 455788888888


Q ss_pred             hhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh-----cch--
Q 042210           98 TRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD-----DDL--  160 (230)
Q Consensus        98 ~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~-----~~~--  160 (230)
                      .+.|++  |...++...     +...|..+-..|.+.|++++|...|++..+  | +...|+.+-..+..     ++|  
T Consensus       177 ~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~  256 (382)
T 2h6f_A          177 EWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVL  256 (382)
T ss_dssp             HHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHH
T ss_pred             HHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHH
Confidence            899998  888888887     788899999999999999999999998875  4 56678876555443     344  


Q ss_pred             ---hhhHHHHHHHhhhcCch-hhhhhhhhcccccCCcccccccC--CccCCccccccc
Q 042210          161 ---HELFPEYLVQMLALPDT-FMGEGLEVIPKSQAPREETPRVG--NLEEGTPQEGRP  212 (230)
Q Consensus       161 ---~~~~~~m~~~~~~~p~~-~t~~~l~~~~~~~~~~~a~~~~g--~~~~a~~i~~~~  212 (230)
                         ++.+++...   ..|+. ..+..+..         .+.+.|  +.+++......+
T Consensus       257 ~~el~~~~~Al~---l~P~~~~a~~~l~~---------ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          257 EREVQYTLEMIK---LVPHNESAWNYLKG---------ILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             HHHHHHHHHHHH---HSTTCHHHHHHHHH---------HHTTTCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH---HCCCCHHHHHHHHH---------HHHccCccchHHHHHHHHHh
Confidence               344554443   44552 23333222         233445  566666655544

>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=97.77  E-value=0.002  Score=48.78  Aligned_cols=118  Identities=5%  Similarity=-0.053  Sum_probs=94.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---C-CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---Q-PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGF   97 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~-~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~   97 (230)
                      ...-..+.  +.|++++|...|++..   + ++...|..+-.++.+.|++++|...|++-.+.  .| +...|..+-..+
T Consensus        11 ~~~g~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~   86 (228)
T 4i17_A           11 KNEGNDAL--NAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKSAAY   86 (228)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHHHHH
Confidence            44455666  9999999999999865   3 67777777888899999999999999997754  34 445778888889


Q ss_pred             hhcCch--hhHHHhhhh-----hH-------hHHHHHHHHHHhcCCHHHHHHHHhhccC--CC
Q 042210           98 TRDIAG--SLEKSCIVM-----RV-------FVQNALISTYCLCGEVDMARGIFYMSCE--DD  144 (230)
Q Consensus        98 ~~~~~~--a~~~~~~~~-----~~-------~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~  144 (230)
                      ...|+.  |...++...     +.       ..|..+=..|.+.|++++|.+.|++..+  |+
T Consensus        87 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~  149 (228)
T 4i17_A           87 RDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSK  149 (228)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCH
T ss_pred             HHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCC
Confidence            999998  888887776     34       4577777788899999999999998876  55

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.75  E-value=0.0001  Score=60.96  Aligned_cols=200  Identities=11%  Similarity=0.012  Sum_probs=130.2

Q ss_pred             hhHHHHHHHHHHhcCCCCC-----cH-HHHHHHHhhhccCChHHHHHHHHhcC---------CCChhhHHHHHHHHHhcC
Q 042210            2 HQLKQIHSQTIKLGLLTKP-----HC-PKQTRYLLLYEKGDLKYECKVFRKIT---------QPSVFLWNTMIKGYSRID   66 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---------~~~~~~yn~li~~~~~~~   66 (230)
                      ++|...++...+.+  |+.     .. ..+-..|.  ..|++++|...|++..         ......|..+-..|...|
T Consensus        65 ~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g  140 (411)
T 4a1s_A           65 RAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYF--YLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMG  140 (411)
T ss_dssp             HHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCC
Confidence            46788888887763  442     23 55667777  8999999999988754         112356788888888999


Q ss_pred             ChhHHHHHHHHHHhC----CCC-CCcccHHHHHHHhhhcCc-----------------h--hhHHHhhhh----------
Q 042210           67 SHKNGVLMYLDLLKS----DVR-RDNYTFPFLFKGFTRDIA-----------------G--SLEKSCIVM----------  112 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~----g~~-p~~~t~~~ll~~~~~~~~-----------------~--a~~~~~~~~----------  112 (230)
                      ++++|...|++..+.    +-. ....++..+-..+...|+                 +  |...+....          
T Consensus       141 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~  220 (411)
T 4a1s_A          141 RFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRG  220 (411)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             CHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHH
Confidence            999999999886543    111 133467777778888888                 6  655555543          


Q ss_pred             -hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----CCh----hhhHHHHHHhhh----cchhhhHHHHHHHhhhcCc--
Q 042210          113 -RVFVQNALISTYCLCGEVDMARGIFYMSCE-----DDD----GLHELIRIKAVD----DDLHELFPEYLVQMLALPD--  176 (230)
Q Consensus       113 -~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----~~~----~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~--  176 (230)
                       ....+..+-..|...|++++|.+.|++..+     ++.    .+|..+...+..    ++|.+.+++..+...-..+  
T Consensus       221 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  300 (411)
T 4a1s_A          221 AQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGERE  300 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHH
Confidence             345778888899999999999999987654     221    144444444432    4666666665554421122  


Q ss_pred             --hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          177 --TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       177 --~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                        ..++..+         -..+.+.|++++|...+....+
T Consensus       301 ~~~~~~~~l---------a~~~~~~g~~~~A~~~~~~al~  331 (411)
T 4a1s_A          301 VEAQSCYSL---------GNTYTLLHEFNTAIEYHNRHLA  331 (411)
T ss_dssp             HHHHHHHHH---------HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---------HHHHHHcCCHHHHHHHHHHHHH
Confidence              1122221         1156678888888877766554

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.72  E-value=0.00045  Score=55.88  Aligned_cols=150  Identities=11%  Similarity=-0.036  Sum_probs=104.5

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--C---CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-----C
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--Q---PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-----D   86 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~---~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-----~   86 (230)
                      ++... ..+-..+.  ..|++++|.+++.+..  .   -+...+-..+..+.+.|+++.|.+.+++|.+.  .|     +
T Consensus        98 ~~~~~~~~la~i~~--~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~  173 (310)
T 3mv2_B           98 NSPYELYLLATAQA--ILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGD  173 (310)
T ss_dssp             CCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHH
T ss_pred             CCcHHHHHHHHHHH--HcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--Cccccccc
Confidence            44444 55556777  8999999999999863  2   24567888899999999999999999999774  55     3


Q ss_pred             cccHHHHHHHhhh--cC--ch--hhHHHhhhh----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC------------C-
Q 042210           87 NYTFPFLFKGFTR--DI--AG--SLEKSCIVM----RVFVQNALISTYCLCGEVDMARGIFYMSCE------------D-  143 (230)
Q Consensus        87 ~~t~~~ll~~~~~--~~--~~--a~~~~~~~~----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~------------~-  143 (230)
                      ..+..-|..++..  .|  +.  |..+|+++.    +..+...|++++.+.|++++|+++++.+.+            | 
T Consensus       174 d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~  253 (310)
T 3mv2_B          174 NEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLY  253 (310)
T ss_dssp             HHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSS
T ss_pred             hHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCC
Confidence            5566666666333  23  55  999999987    223456677789999999999999986543            3 


Q ss_pred             Chhhh-HHH-HHHhhhcchhhhHHHHHHHh
Q 042210          144 DDGLH-ELI-RIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       144 ~~~t~-n~l-i~~~~~~~~~~~~~~m~~~~  171 (230)
                      |.-+. |.+ +.....+++.+++.++.+..
T Consensus       254 ~~~~LaN~i~l~~~lgk~a~~l~~qL~~~~  283 (310)
T 3mv2_B          254 KPTFLANQITLALMQGLDTEDLTNQLVKLD  283 (310)
T ss_dssp             HHHHHHHHHHHHHHTTCTTHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHhChHHHHHHHHHHHhC
Confidence            33344 333 22223356777777776654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=97.71  E-value=0.00082  Score=57.53  Aligned_cols=145  Identities=10%  Similarity=-0.027  Sum_probs=114.8

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhc---------CCh
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRI---------DSH   68 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~---------~~~   68 (230)
                      ++|.+.++...+..  |+. .. ..+-..|.  +.|++++|.+.|++..  .|+...|..+-..|...         |++
T Consensus       120 ~~A~~~~~~al~~~--p~~~~a~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~  195 (474)
T 4abn_A          120 PEAEVLLSKAVKLE--PELVEAWNQLGEVYW--KKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHV  195 (474)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC--CCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhH
Confidence            67888888887763  553 34 77778888  9999999999999875  67778888888899998         999


Q ss_pred             hHHHHHHHHHHhCCCCCCcccHHHHHHHhhhc--------Cch--hhHHHhhhh--------hHhHHHHHHHHHHhcCCH
Q 042210           69 KNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRD--------IAG--SLEKSCIVM--------RVFVQNALISTYCLCGEV  130 (230)
Q Consensus        69 ~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~--------~~~--a~~~~~~~~--------~~~~~~~li~~y~~~g~~  130 (230)
                      ++|...|++..+.. +-+...|..+-.++...        |++  |...++...        +...|..+-..|.+.|++
T Consensus       196 ~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~  274 (474)
T 4abn_A          196 MDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESY  274 (474)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCH
Confidence            99999999976642 12456788888888887        777  777777765        457788899999999999


Q ss_pred             HHHHHHHhhccC--CCh-hhhHHH
Q 042210          131 DMARGIFYMSCE--DDD-GLHELI  151 (230)
Q Consensus       131 ~~A~~vf~~m~~--~~~-~t~n~l  151 (230)
                      ++|.+.|++..+  |+. ..|..+
T Consensus       275 ~~A~~~~~~al~l~p~~~~a~~~l  298 (474)
T 4abn_A          275 GEALEGFSQAAALDPAWPEPQQRE  298 (474)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHH
Confidence            999999998764  543 345544

>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=97.71  E-value=0.00054  Score=61.94  Aligned_cols=134  Identities=6%  Similarity=-0.006  Sum_probs=112.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.|++..+.  .|+...  ..+=..|.  +.|++++|.+.|++..  .| +...|+.+=..|.+.|++++|.+.|+
T Consensus        26 ~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~--~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l~~~g~~~~A~~~~~  101 (723)
T 4gyw_A           26 EEAVRLYRKALEV--FPEFAAAHSNLASVLQ--QQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYT  101 (723)
T ss_dssp             HHHHHHHHHHHHH--CSCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            5788888887766  466544  77778888  9999999999999865  44 56789999999999999999999999


Q ss_pred             HHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           77 DLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        77 ~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +-.+.  .| +...|..+-.++.+.|++  |.+.++...     +...|..|...|.+.|++++|.+.|++..
T Consensus       102 kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~kal  172 (723)
T 4gyw_A          102 RAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLV  172 (723)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHHHHH
T ss_pred             HHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHHHHH
Confidence            86653  34 455788899999999999  888888776     78899999999999999999998887664

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.69  E-value=0.00073  Score=45.30  Aligned_cols=87  Identities=15%  Similarity=0.157  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhc
Q 042210           55 WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLC  127 (230)
Q Consensus        55 yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~  127 (230)
                      |..+...+.+.|++++|...|++..+.. +.+...+..+...+.+.|++  |...+..+.     +..++..+...|.+.
T Consensus        12 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~   90 (125)
T 1na0_A           12 WYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQ   90 (125)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh
Confidence            3334444444444444444444433321 11222333344444444444  333333332     455667777888888


Q ss_pred             CCHHHHHHHHhhccC
Q 042210          128 GEVDMARGIFYMSCE  142 (230)
Q Consensus       128 g~~~~A~~vf~~m~~  142 (230)
                      |++++|...|++..+
T Consensus        91 ~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           91 GDYDEAIEYYQKALE  105 (125)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHH
Confidence            888888888887654

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=97.68  E-value=0.00072  Score=49.42  Aligned_cols=143  Identities=11%  Similarity=0.084  Sum_probs=99.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHh--
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGF--   97 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~--   97 (230)
                      ...-..+.  +.|++++|...|++..   +.+...|..+-..+.+.|++++|...|++....  .|+. .+..+...+  
T Consensus        10 ~~~a~~~~--~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~--~p~~-~~~~~~~~~~~   84 (176)
T 2r5s_A           10 LKQVSELL--QQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLE--YQDN-SYKSLIAKLEL   84 (176)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG--GCCH-HHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc--cCCh-HHHHHHHHHHH
Confidence            34455677  9999999999999976   445678888999999999999999999886443  2333 222222111  


Q ss_pred             hh-cCch-hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC---hhhhHHHHHHhh----hcchh
Q 042210           98 TR-DIAG-SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD---DGLHELIRIKAV----DDDLH  161 (230)
Q Consensus        98 ~~-~~~~-a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~---~~t~n~li~~~~----~~~~~  161 (230)
                      .+ .+.. +...++...     +...+..+-..|.+.|++++|...|++..+  |+   ...|..+...+.    .+++.
T Consensus        85 ~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~  164 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIA  164 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHH
T ss_pred             HhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHH
Confidence            11 1222 455555544     688899999999999999999999998865  44   346666655444    34677


Q ss_pred             hhHHHHHHH
Q 042210          162 ELFPEYLVQ  170 (230)
Q Consensus       162 ~~~~~m~~~  170 (230)
                      ..+++....
T Consensus       165 ~~y~~al~~  173 (176)
T 2r5s_A          165 SKYRRQLYS  173 (176)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777665543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.68  E-value=0.00026  Score=58.05  Aligned_cols=200  Identities=9%  Similarity=-0.052  Sum_probs=130.0

Q ss_pred             hhHHHHHHHHHHhcCCCCC-----cH-HHHHHHHhhhccCChHHHHHHHHhcC-----CC----ChhhHHHHHHHHHhcC
Q 042210            2 HQLKQIHSQTIKLGLLTKP-----HC-PKQTRYLLLYEKGDLKYECKVFRKIT-----QP----SVFLWNTMIKGYSRID   66 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~----~~~~yn~li~~~~~~~   66 (230)
                      ++|...++...+.+  |+.     .+ ..+-..|.  ..|++++|...|++..     ..    ....|..+-..|...|
T Consensus        26 ~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  101 (406)
T 3sf4_A           26 RAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYF--YLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLG  101 (406)
T ss_dssp             HHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhcC--cccHHHHHHHHHHHHHHHH--HhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHcC
Confidence            46788888887773  432     23 55667777  9999999999988753     11    1346778888888999


Q ss_pred             ChhHHHHHHHHHHhCC-CCCC----cccHHHHHHHhhhcCc--------------------h--hhHHHhhhh-------
Q 042210           67 SHKNGVLMYLDLLKSD-VRRD----NYTFPFLFKGFTRDIA--------------------G--SLEKSCIVM-------  112 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~g-~~p~----~~t~~~ll~~~~~~~~--------------------~--a~~~~~~~~-------  112 (230)
                      ++++|...|++..... -.++    ..++..+-..+...|+                    +  |...+....       
T Consensus       102 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~  181 (406)
T 3sf4_A          102 NFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALG  181 (406)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999998865421 1112    3367777778888888                    6  555555443       


Q ss_pred             ----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-----CCh----hhhHHHHHHhh----hcchhhhHHHHHHHhhhcC
Q 042210          113 ----RVFVQNALISTYCLCGEVDMARGIFYMSCE-----DDD----GLHELIRIKAV----DDDLHELFPEYLVQMLALP  175 (230)
Q Consensus       113 ----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-----~~~----~t~n~li~~~~----~~~~~~~~~~m~~~~~~~p  175 (230)
                          ...++..+-..|...|++++|.+.|++..+     ++.    .+|..+-..+.    .++|.+.+++..+...-.+
T Consensus       182 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  261 (406)
T 3sf4_A          182 DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLK  261 (406)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             CcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCc
Confidence                345778888899999999999999887654     221    24444444443    3466666666554432222


Q ss_pred             c----hhhhhhhhhcccccCCcccccccCCccCCccccccccc
Q 042210          176 D----TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       176 ~----~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~  214 (230)
                      +    ..++..+         -..+.+.|++++|...+....+
T Consensus       262 ~~~~~~~~~~~l---------a~~~~~~g~~~~A~~~~~~a~~  295 (406)
T 3sf4_A          262 DRAVEAQSCYSL---------GNTYTLLQDYEKAIDYHLKHLA  295 (406)
T ss_dssp             CHHHHHHHHHHH---------HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHH---------HHHHHHhCcHHHHHHHHHHHHH
Confidence            2    1122221         1156678888888887766554

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.64  E-value=0.0011  Score=44.45  Aligned_cols=100  Identities=11%  Similarity=0.107  Sum_probs=77.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+...+.  +.|++++|.+.|+++.   +.+...|..+...+.+.|++++|...|+++.+.. +.+..++..+...+..
T Consensus        13 ~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~   89 (125)
T 1na0_A           13 YNLGNAYY--KQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYK   89 (125)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHH
Confidence            55667788  9999999999999875   4456788889999999999999999999987643 2355678888889999


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYC  125 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~  125 (230)
                      .|++  |...+....     +...+..+-..+.
T Consensus        90 ~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  122 (125)
T 1na0_A           90 QGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            9998  888877765     4444444444443

>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=97.62  E-value=0.001  Score=63.56  Aligned_cols=171  Identities=16%  Similarity=0.069  Sum_probs=110.4

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      ..+=.++.  +.|++++|.+-|.+.  .|...|.-++.+|.+.|++++|.+.|..-++..  ++....+.+..+|++.++
T Consensus      1109 sqLAKAql--~~G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~r 1182 (1630)
T 1xi4_A         1109 SQLAKAQL--QKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNR 1182 (1630)
T ss_pred             HHHHHHHH--hCCCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcC
Confidence            66777777  888888888888665  555678889999999999999999997655443  333334457777777776


Q ss_pred             h-hhHHH-hhhh-------------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCChhhhHHHHHHh
Q 042210          103 G-SLEKS-CIVM-------------------------RVFVQNALISTYCLCGEVDMARGIFYMSCEDDDGLHELIRIKA  155 (230)
Q Consensus       103 ~-a~~~~-~~~~-------------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~~t~n~li~~~  155 (230)
                      + ..+-+ ....                         ....|..+...|.+.|++++|.+.+.+-  .+..+|..+-.+|
T Consensus      1183 leele~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA~ny~rLA~tLvkLge~q~AIEaarKA--~n~~aWkev~~ac 1260 (1630)
T 1xi4_A         1183 LAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFAC 1260 (1630)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHhhhHHHHHHHHHHHhCCHHHHHHHHHHh--CCHHHHHHHHHHH
Confidence            6 22111 1110                         3557788888888888888888888865  4567777666666


Q ss_pred             hhcchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccc
Q 042210          156 VDDDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRP  212 (230)
Q Consensus       156 ~~~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~  212 (230)
                      ...+-++++......-.+.||..  ..  +..       .|.+.|.+++|..+++..
T Consensus      1261 ve~~Ef~LA~~cgl~Iiv~~deL--ee--li~-------yYe~~G~feEAI~LlE~a 1306 (1630)
T 1xi4_A         1261 VDGKEFRLAQMCGLHIVVHADEL--EE--LIN-------YYQDRGYFEELITMLEAA 1306 (1630)
T ss_pred             hhhhHHHHHHHHHHhhhcCHHHH--HH--HHH-------HHHHcCCHHHHHHHHHHH
Confidence            55555555554433222233332  22  222       566777777777766433

>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=97.60  E-value=0.00085  Score=58.52  Aligned_cols=135  Identities=5%  Similarity=-0.087  Sum_probs=99.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.+++..+.  .|+.. . ..+-..+.  +.|++++|.+.|++..   +.+...|..+-..|.+.|++++|...|+
T Consensus         6 ~~A~~~~~~al~~--~p~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~   81 (568)
T 2vsy_A            6 PRELLQLRAAVRH--RPQDFVAWLMLADAEL--GMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQ   81 (568)
T ss_dssp             -----------------CCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            4566677665543  45543 3 66777888  9999999999999865   3456788889899999999999999999


Q ss_pred             HHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhc---CCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLC---GEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~---g~~~~A~~vf~~m~~  142 (230)
                      +..+.  .| +...+..+-.++.+.|+.  |.+.++...     +...+..+...|.+.   |+.++|.+.|++..+
T Consensus        82 ~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           82 QASDA--APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHhc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            97664  24 456788888899999999  888888776     678888999999999   999999999997754

>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=97.52  E-value=0.0053  Score=51.10  Aligned_cols=192  Identities=10%  Similarity=-0.024  Sum_probs=137.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCC-hHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGD-LKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~-~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|...++..++.  .|+...  +.+-..+.  +.|+ +++|...|++..   ..+...|+.+=..+.+.|++++|+..|
T Consensus       114 ~~Al~~~~~al~l--~P~~~~a~~~~g~~l~--~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~eAl~~~  189 (382)
T 2h6f_A          114 ERAFKLTRDAIEL--NAANYTVWHFRRVLLK--SLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFI  189 (382)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHH
T ss_pred             HHHHHHHHHHHHh--CccCHHHHHHHHHHHH--HcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHHHHHHH
Confidence            5677788877765  466554  66777777  9996 999999999876   456778999999999999999999999


Q ss_pred             HHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHh-cCCHHHH-----HHHHhhcc
Q 042210           76 LDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCL-CGEVDMA-----RGIFYMSC  141 (230)
Q Consensus        76 ~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~-~g~~~~A-----~~vf~~m~  141 (230)
                      ++..+.  .| +...|..+-.++.+.|++  |...++...     +...|+.+-..|.+ .|..++|     ...|++..
T Consensus       190 ~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al  267 (382)
T 2h6f_A          190 ADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMI  267 (382)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHH
T ss_pred             HHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHH
Confidence            998764  33 556788888888899998  888888887     78899999999999 6665777     36676654


Q ss_pred             C--C-ChhhhHHHHHHhhh------cchhhhHHHHHHHhhhcCch-hhhhhhhhcccccCCcccccccC--------C-c
Q 042210          142 E--D-DDGLHELIRIKAVD------DDLHELFPEYLVQMLALPDT-FMGEGLEVIPKSQAPREETPRVG--------N-L  202 (230)
Q Consensus       142 ~--~-~~~t~n~li~~~~~------~~~~~~~~~m~~~~~~~p~~-~t~~~l~~~~~~~~~~~a~~~~g--------~-~  202 (230)
                      .  | +...|+.+-..+..      +++++.+.++    ...|+. ..+..+.-         .+.+.|        + +
T Consensus       268 ~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~----~~~p~~~~al~~La~---------~~~~~~~~~~~~~~~~~  334 (382)
T 2h6f_A          268 KLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL----QPSHSSPYLIAFLVD---------IYEDMLENQCDNKEDIL  334 (382)
T ss_dssp             HHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH----TTTCCCHHHHHHHHH---------HHHHHHHTTCSSHHHHH
T ss_pred             HHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh----ccCCCCHHHHHHHHH---------HHHHHhcccccchHHHH
Confidence            3  4 45677776554443      3455655554    244553 33333211         344432        2 4


Q ss_pred             cCCccccccc
Q 042210          203 EEGTPQEGRP  212 (230)
Q Consensus       203 ~~a~~i~~~~  212 (230)
                      ++|..++..+
T Consensus       335 ~~A~~~~~~l  344 (382)
T 2h6f_A          335 NKALELCEIL  344 (382)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7787777776

>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=97.49  E-value=0.0018  Score=56.49  Aligned_cols=136  Identities=10%  Similarity=-0.062  Sum_probs=92.4

Q ss_pred             cCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHH
Q 042210           34 KGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEK  107 (230)
Q Consensus        34 ~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~  107 (230)
                      .|++++|.+.|++..   +.+...|..+-..|.+.|++++|...|++-.+.  .| +...|..+-..+...|++  |.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLAL--HPGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--STTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            468889999998865   345678888989999999999999999997664  34 456788888899999999  8888


Q ss_pred             Hhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh-------cchhhhHHHHHHHh
Q 042210          108 SCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD-------DDLHELFPEYLVQM  171 (230)
Q Consensus       108 ~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~-------~~~~~~~~~m~~~~  171 (230)
                      ++...     +...+..+-..|.+.|++++|.+.|++..+  | +...|..+...+..       ++|.+.+++..+..
T Consensus        80 ~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A           80 LQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            88776     778899999999999999999999998765  4 34555555444432       35666666655544

>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=97.49  E-value=0.0025  Score=48.23  Aligned_cols=160  Identities=9%  Similarity=-0.061  Sum_probs=106.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      ++|...|+...+..-.++... ..+-..+.  +.|++++|...|++..  .| +...|..+-..|...|++++|...|++
T Consensus        24 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~  101 (228)
T 4i17_A           24 AVAFEKYSEYLKLTNNQDSVTAYNCGVCAD--NIKKYKEAADYFDIAIKKNYNLANAYIGKSAAYRDMKNNQEYIATLTE  101 (228)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCcHHHHHHHHHHH--HhhcHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            568888888887764355555 55777777  9999999999999875  34 456788899999999999999999999


Q ss_pred             HHhCCCCCCc--------ccHHHHHHHhhhcCch--hhHHHhhhh----h---HhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210           78 LLKSDVRRDN--------YTFPFLFKGFTRDIAG--SLEKSCIVM----R---VFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus        78 M~~~g~~p~~--------~t~~~ll~~~~~~~~~--a~~~~~~~~----~---~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      ..+.  .|+.        ..|..+=..+.+.|++  |...+....    +   ...|..+-..|...|+.     +++++
T Consensus       102 al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~-----~~~~a  174 (228)
T 4i17_A          102 GIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYNNGAD-----VLRKA  174 (228)
T ss_dssp             HHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHH-----HHHHH
T ss_pred             HHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHH-----HHHHH
Confidence            7653  2432        2355566667777888  888888776    2   34556666666555443     33333


Q ss_pred             cC---CChhhhHHHHHH--hhhcchhhhHHHHHHH
Q 042210          141 CE---DDDGLHELIRIK--AVDDDLHELFPEYLVQ  170 (230)
Q Consensus       141 ~~---~~~~t~n~li~~--~~~~~~~~~~~~m~~~  170 (230)
                      ..   .+...|......  ...++|++.+++..+.
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l  209 (228)
T 4i17_A          175 TPLASSNKEKYASEKAKADAAFKKAVDYLGEAVTL  209 (228)
T ss_dssp             GGGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            32   233444443321  1135666666665544

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.49  E-value=0.0018  Score=45.93  Aligned_cols=82  Identities=9%  Similarity=0.047  Sum_probs=48.1

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      ..|++++|...|+...   +.+...|..+-..+...|++++|...|++..+..  |+                       
T Consensus        25 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~-----------------------   79 (166)
T 1a17_A           25 KAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KK-----------------------   79 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-----------------------
T ss_pred             HccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cc-----------------------
Confidence            5566666666665543   3344555555555666666666666665543321  11                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         +...|..+-..|.+.|++++|...|++..+
T Consensus        80 ---~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~  109 (166)
T 1a17_A           80 ---YIKGYYRRAASNMALGKFRAALRDYETVVK  109 (166)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---cHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence               344566666677777788888777776654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.48  E-value=0.00021  Score=58.59  Aligned_cols=181  Identities=12%  Similarity=-0.015  Sum_probs=122.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCC--------------------hhHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDS--------------------HKNGVL   73 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~--------------------~~~a~~   73 (230)
                      ..+-..|.  ..|++++|...+++..     .++    ...|..+-..|...|+                    +++|..
T Consensus        91 ~~la~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~  168 (406)
T 3sf4_A           91 GNLGNTLK--VLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVD  168 (406)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHH
Confidence            55566777  9999999999998764     122    3467888888888999                    999999


Q ss_pred             HHHHHHh----CCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHH
Q 042210           74 MYLDLLK----SDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARG  135 (230)
Q Consensus        74 ~~~~M~~----~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~  135 (230)
                      .+++...    .+-.| ...++..+-..+...|++  |...+....           ....+..+-..|.+.|++++|..
T Consensus       169 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  248 (406)
T 3sf4_A          169 FYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  248 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            9887543    22122 234677777888888988  777777665           23478888999999999999999


Q ss_pred             HHhhccC-----CC----hhhhHHHHHHhh----hcchhhhHHHHHHHhhhcCc----hhhhhhhhhcccccCCcccccc
Q 042210          136 IFYMSCE-----DD----DGLHELIRIKAV----DDDLHELFPEYLVQMLALPD----TFMGEGLEVIPKSQAPREETPR  198 (230)
Q Consensus       136 vf~~m~~-----~~----~~t~n~li~~~~----~~~~~~~~~~m~~~~~~~p~----~~t~~~l~~~~~~~~~~~a~~~  198 (230)
                      .|++..+     ++    ..+|..+-..+.    .++|.+.+++........++    ..++..+..         .+.+
T Consensus       249 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~---------~~~~  319 (406)
T 3sf4_A          249 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGN---------AYTA  319 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------HHHH
T ss_pred             HHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHH---------HHHH
Confidence            9987653     22    234444444443    35677777766554422222    112222111         6678


Q ss_pred             cCCccCCccccccccc
Q 042210          199 VGNLEEGTPQEGRPHE  214 (230)
Q Consensus       199 ~g~~~~a~~i~~~~~~  214 (230)
                      .|++++|...+....+
T Consensus       320 ~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          320 LGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            8999999887776544

>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=97.47  E-value=0.0053  Score=55.00  Aligned_cols=150  Identities=9%  Similarity=-0.129  Sum_probs=110.2

Q ss_pred             hhHHHHHHHHH------HhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhH
Q 042210            2 HQLKQIHSQTI------KLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKN   70 (230)
Q Consensus         2 ~~a~~~~~~m~------~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~   70 (230)
                      ++|.+.++...      .....|+.. . ..+-..+.  +.|++++|.+.|++..   ..+...|..+=..|.+.|++++
T Consensus       408 ~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~--~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~  485 (681)
T 2pzi_A          408 VQTLDSLRAARHGALDADGVDFSESVELPLMEVRALL--DLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDS  485 (681)
T ss_dssp             HHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHhhhhcccccccccccchhHHHHHHHHHH--hcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHH
Confidence            35666666665      113445543 3 66667788  9999999999999876   4566788888889999999999


Q ss_pred             HHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch-hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC-
Q 042210           71 GVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG-SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE-  142 (230)
Q Consensus        71 a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~-a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~-  142 (230)
                      |...|++..+.  .| +...|..+-.++.+.|++ ..+.++...     +...|..+-..|.+.|++++|.+.|++..+ 
T Consensus       486 A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  563 (681)
T 2pzi_A          486 ATKHFTEVLDT--FPGELAPKLALAATAELAGNTDEHKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPT  563 (681)
T ss_dssp             HHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCTTCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTT
T ss_pred             HHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHHHHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhccc
Confidence            99999997653  24 455677788888888887 433333333     778899999999999999999999999876 


Q ss_pred             -CC-hhhhHHHHHHh
Q 042210          143 -DD-DGLHELIRIKA  155 (230)
Q Consensus       143 -~~-~~t~n~li~~~  155 (230)
                       |+ ...|..+...+
T Consensus       564 ~P~~~~a~~~~~~~~  578 (681)
T 2pzi_A          564 SRHFTTARLTSAVTL  578 (681)
T ss_dssp             STTHHHHHHHHHHHT
T ss_pred             CcccHHHHHHHHHHH
Confidence             54 34555554444

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.45  E-value=0.00029  Score=55.82  Aligned_cols=182  Identities=12%  Similarity=-0.011  Sum_probs=122.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCC--------------------hhHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDS--------------------HKNGVL   73 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~--------------------~~~a~~   73 (230)
                      ..+-..|.  ..|++++|...+++..     .++    ..+|..+-..|...|+                    +++|..
T Consensus        87 ~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~  164 (338)
T 3ro2_A           87 GNLGNTLK--VLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVD  164 (338)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHH
Confidence            55667777  9999999999998864     233    3377888888888999                    999999


Q ss_pred             HHHHHHhC----CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHH
Q 042210           74 MYLDLLKS----DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARG  135 (230)
Q Consensus        74 ~~~~M~~~----g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~  135 (230)
                      .+++....    +-.| ....+..+-..+...|++  |...+....           ....+..+...|.+.|++++|.+
T Consensus       165 ~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  244 (338)
T 3ro2_A          165 LYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  244 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            99875432    2111 234677777888888988  777777665           23478888999999999999999


Q ss_pred             HHhhccC-----CC----hhhhHHHHHHhh----hcchhhhHHHHHHHhhhcCc----hhhhhhhhhcccccCCcccccc
Q 042210          136 IFYMSCE-----DD----DGLHELIRIKAV----DDDLHELFPEYLVQMLALPD----TFMGEGLEVIPKSQAPREETPR  198 (230)
Q Consensus       136 vf~~m~~-----~~----~~t~n~li~~~~----~~~~~~~~~~m~~~~~~~p~----~~t~~~l~~~~~~~~~~~a~~~  198 (230)
                      .|++..+     ++    ..++..+-..+.    .++|.+.+++..+.....++    ..++..+         -..+.+
T Consensus       245 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l---------a~~~~~  315 (338)
T 3ro2_A          245 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSL---------GNAYTA  315 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH---------HHHHHH
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHH---------HHHHHH
Confidence            9987653     22    234444433333    34677777766554322222    1122221         116778


Q ss_pred             cCCccCCcccccccccc
Q 042210          199 VGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       199 ~g~~~~a~~i~~~~~~~  215 (230)
                      .|+.++|...+....+.
T Consensus       316 ~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          316 LGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             HTCHHHHHHHHHHHHHC
T ss_pred             cCChHHHHHHHHHHHHH
Confidence            89999998888776553

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.40  E-value=0.0028  Score=50.34  Aligned_cols=141  Identities=6%  Similarity=0.035  Sum_probs=100.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHH-Hhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFK-GFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~-~~~   98 (230)
                      ..+-..+.  +.|++++|...|++..   +.+...+..+-..+.+.|++++|...|++....  .|+......... .+.
T Consensus       121 ~~~a~~~~--~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~l~  196 (287)
T 3qou_A          121 AQQAMQLM--QESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIELL  196 (287)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--hCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHHHH
Confidence            45556677  9999999999999875   445668888999999999999999999886543  354432222221 233


Q ss_pred             hcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC---hhhhHHHHHHhhh----cchhh
Q 042210           99 RDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD---DGLHELIRIKAVD----DDLHE  162 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~---~~t~n~li~~~~~----~~~~~  162 (230)
                      +.+..  +...+....     +...+..+-..|...|++++|...|.+..+  |+   ...+..+...+..    +++..
T Consensus       197 ~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~  276 (287)
T 3qou_A          197 XQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALAS  276 (287)
T ss_dssp             HHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHH
T ss_pred             hhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHH
Confidence            44444  555555554     788899999999999999999999998875  54   4467766665543    45555


Q ss_pred             hHHHH
Q 042210          163 LFPEY  167 (230)
Q Consensus       163 ~~~~m  167 (230)
                      .+++-
T Consensus       277 ~~r~a  281 (287)
T 3qou_A          277 XYRRQ  281 (287)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55543

>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=97.37  E-value=0.0028  Score=48.82  Aligned_cols=138  Identities=10%  Similarity=0.059  Sum_probs=90.6

Q ss_pred             hhHHHHHHHHHHhc------CCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC-------CC----ChhhHHHHHHHH
Q 042210            2 HQLKQIHSQTIKLG------LLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT-------QP----SVFLWNTMIKGY   62 (230)
Q Consensus         2 ~~a~~~~~~m~~~g------~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~----~~~~yn~li~~~   62 (230)
                      ++|.+.++...+..      -.|+ ... ..+-..|.  ..|++++|...|++..       .+    ....|..+-..|
T Consensus       102 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~  179 (283)
T 3edt_B          102 KEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQ--NQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCY  179 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--TTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence            35666666665441      1232 223 66677888  9999999999998764       12    235688888999


Q ss_pred             HhcCChhHHHHHHHHHHhC-------CCCCCcccHHHHHHHhhhcCch---------hhHHHhhhh-----hHhHHHHHH
Q 042210           63 SRIDSHKNGVLMYLDLLKS-------DVRRDNYTFPFLFKGFTRDIAG---------SLEKSCIVM-----RVFVQNALI  121 (230)
Q Consensus        63 ~~~~~~~~a~~~~~~M~~~-------g~~p~~~t~~~ll~~~~~~~~~---------a~~~~~~~~-----~~~~~~~li  121 (230)
                      .+.|++++|...|++..+.       ...|....+-..+..+...+..         +...+....     ...++..+-
T Consensus       180 ~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la  259 (283)
T 3edt_B          180 LKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLG  259 (283)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            9999999999999987652       2345444444444433333322         111222221     567788899


Q ss_pred             HHHHhcCCHHHHHHHHhhcc
Q 042210          122 STYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       122 ~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..|.+.|++++|.+.|++..
T Consensus       260 ~~~~~~g~~~~A~~~~~~al  279 (283)
T 3edt_B          260 ALYRRQGKLEAAHTLEDCAS  279 (283)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHH
Confidence            99999999999999998653

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.31  E-value=0.0074  Score=46.69  Aligned_cols=147  Identities=8%  Similarity=-0.009  Sum_probs=100.9

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCC-cccHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD-VRRD-NYTFPFLF   94 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~~p~-~~t~~~ll   94 (230)
                      -..-..+.  +.|++++|...|++..  .|+    ...|..+-.+|.+.|++++|...|++..+.. -.|+ ...+..+-
T Consensus        19 ~~~a~~~~--~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg   96 (261)
T 3qky_A           19 FERAMEFY--NQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERA   96 (261)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHH
T ss_pred             HHHHHHHH--HhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHH
Confidence            33445566  9999999999999976  343    4567777788999999999999999977642 1222 23455556


Q ss_pred             HHhhh--------cCch--hhHHHhhhh-----hHhHH-----------------HHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           95 KGFTR--------DIAG--SLEKSCIVM-----RVFVQ-----------------NALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        95 ~~~~~--------~~~~--a~~~~~~~~-----~~~~~-----------------~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .++..        .|++  |...+....     +...+                 -.+-..|.+.|++++|...|++..+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  176 (261)
T 3qky_A           97 MCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFD  176 (261)
T ss_dssp             HHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            66666        7887  888888776     33333                 3456788999999999999998865


Q ss_pred             --CChh----hhHHHHHHhh--------------hcchhhhHHHHHHHh
Q 042210          143 --DDDG----LHELIRIKAV--------------DDDLHELFPEYLVQM  171 (230)
Q Consensus       143 --~~~~----t~n~li~~~~--------------~~~~~~~~~~m~~~~  171 (230)
                        |+..    .+..+..++.              .++|.+.+++..+..
T Consensus       177 ~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~  225 (261)
T 3qky_A          177 AYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF  225 (261)
T ss_dssp             HCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC
T ss_pred             HCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC
Confidence              5532    2333333332              256777777766654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.31  E-value=0.0034  Score=42.22  Aligned_cols=82  Identities=7%  Similarity=0.003  Sum_probs=44.5

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      ..|++++|...|++..   +.+...|..+-..+...|++++|...+++....  .|+                       
T Consensus        24 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~-----------------------   78 (131)
T 2vyi_A           24 KVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICI--DPA-----------------------   78 (131)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc--Ccc-----------------------
Confidence            5555555555555432   223344444445555555555555555443332  111                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         +...+..+-..|.+.|++++|.+.|++..+
T Consensus        79 ---~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  108 (131)
T 2vyi_A           79 ---YSKAYGRMGLALSSLNKHVEAVAYYKKALE  108 (131)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---CHHHHHHHHHHHHHhCCHHHHHHHHHHHHh
Confidence               345566666677777788888777776543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.30  E-value=0.0063  Score=45.67  Aligned_cols=123  Identities=8%  Similarity=-0.028  Sum_probs=82.8

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhc
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRD  100 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~  100 (230)
                      +-..|.  +.|++++|...|++..   +.+...|..+-..|...|++++|...|++..+.  .|+ ...|..+-..+...
T Consensus        60 lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~  135 (208)
T 3urz_A           60 LALAYK--KNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLT  135 (208)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHH--HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHH
Confidence            556677  9999999999998865   446778888999999999999999999997663  353 44566665555544


Q ss_pred             Cch----hhHHHhhhh--hH--hHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHH
Q 042210          101 IAG----SLEKSCIVM--RV--FVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELI  151 (230)
Q Consensus       101 ~~~----a~~~~~~~~--~~--~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~l  151 (230)
                      |..    +...+....  +.  ..+..+-.++...|++++|...|++..+  |+......+
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          136 AEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            432    333344333  22  1222233345567899999999998776  775544443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.29  E-value=0.0029  Score=51.09  Aligned_cols=114  Identities=9%  Similarity=0.001  Sum_probs=82.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC-----hhhHHHHHHHHH----hcCChhHHHHHHHHHHhCCCCCCcccHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS-----VFLWNTMIKGYS----RIDSHKNGVLMYLDLLKSDVRRDNYTFP   91 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-----~~~yn~li~~~~----~~~~~~~a~~~~~~M~~~g~~p~~~t~~   91 (230)
                      ...+..+.  +.|+++.|.+.+++|.  .||     -.+..-+..++.    ..++..+|+.+|+++.+.  .|+..+-.
T Consensus       140 ~l~vqi~L--~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~  215 (310)
T 3mv2_B          140 LLAIEVAL--LNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQL  215 (310)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHH
T ss_pred             HHHHHHHH--HCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHH
Confidence            56778888  9999999999999998  552     333334444422    234899999999998654  35544556


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh---------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM---------------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~---------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .+++++.+.|++  |+..++.+.               +..+.-.+|..+...|+  +|.++++++.+
T Consensus       216 lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          216 GLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            777789999999  887776432               56666556666666787  88999998875

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.28  E-value=0.0033  Score=42.31  Aligned_cols=92  Identities=8%  Similarity=-0.055  Sum_probs=60.5

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~  131 (230)
                      ...|..+-..+...|++++|...|++....  .|+                          +...+..+...|...|+++
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~--------------------------~~~~~~~~a~~~~~~~~~~   63 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIEL--NPA--------------------------NAVYFCNRAAAYSKLGNYA   63 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT--------------------------CHHHHHHHHHHHHHTTCHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHc--CCC--------------------------CHHHHHHHHHHHHHhhchH
Confidence            345666666777778888888887775542  121                          3455667777888899999


Q ss_pred             HHHHHHhhccC--CC-hhhhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          132 MARGIFYMSCE--DD-DGLHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       132 ~A~~vf~~m~~--~~-~~t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      +|.+.+++..+  |+ ...|..+...+..    +++.+.+++..+..
T Consensus        64 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~  110 (131)
T 2vyi_A           64 GAVQDCERAICIDPAYSKAYGRMGLALSSLNKHVEAVAYYKKALELD  110 (131)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhcCccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            99999987764  43 4556555444443    46666776665543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.28  E-value=0.00033  Score=57.90  Aligned_cols=177  Identities=12%  Similarity=0.007  Sum_probs=121.0

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CCC-h----hhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-CcccHHHHH
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QPS-V----FLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR-DNYTFPFLF   94 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~~-~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p-~~~t~~~ll   94 (230)
                      ..+.  ..|++++|...|++..  .|+ .    ..|..+-..|...|++++|...|++..+.    +-.| ....+..+-
T Consensus        56 ~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~  133 (411)
T 4a1s_A           56 ERLC--NAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLG  133 (411)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHH--HhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHH
Confidence            4556  8999999999999875  343 2    46888888999999999999999986542    2122 345677788


Q ss_pred             HHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCC-----------------HHHHHHHHhhccC--
Q 042210           95 KGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGE-----------------VDMARGIFYMSCE--  142 (230)
Q Consensus        95 ~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~-----------------~~~A~~vf~~m~~--  142 (230)
                      ..+...|++  |...+....           ...++..+-..|...|+                 +++|.+.|++..+  
T Consensus       134 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~  213 (411)
T 4a1s_A          134 NTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLM  213 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            888899998  777766655           45578888899999999                 9999988876543  


Q ss_pred             ---CC----hhhhHHHHHHhh----hcchhhhHHHHHHHhhhcCchh----hhhhhhhcccccCCcccccccCCccCCcc
Q 042210          143 ---DD----DGLHELIRIKAV----DDDLHELFPEYLVQMLALPDTF----MGEGLEVIPKSQAPREETPRVGNLEEGTP  207 (230)
Q Consensus       143 ---~~----~~t~n~li~~~~----~~~~~~~~~~m~~~~~~~p~~~----t~~~l~~~~~~~~~~~a~~~~g~~~~a~~  207 (230)
                         ++    ..+|..+-..+.    .++|.+.+++..+...-.++..    .+..+..         .+...|++++|..
T Consensus       214 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~---------~~~~~g~~~~A~~  284 (411)
T 4a1s_A          214 RDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGN---------SHIFLGQFEDAAE  284 (411)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH---------HHHTTTCHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHH---------HHHHCcCHHHHHH
Confidence               22    123444433333    3567777777665442222211    2222111         6778899999988


Q ss_pred             ccccccc
Q 042210          208 QEGRPHE  214 (230)
Q Consensus       208 i~~~~~~  214 (230)
                      .+....+
T Consensus       285 ~~~~al~  291 (411)
T 4a1s_A          285 HYKRTLA  291 (411)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8876654

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=97.27  E-value=0.0093  Score=53.47  Aligned_cols=148  Identities=7%  Similarity=0.021  Sum_probs=105.1

Q ss_pred             hhHH-HHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcCC-------------CC------------hh
Q 042210            2 HQLK-QIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKITQ-------------PS------------VF   53 (230)
Q Consensus         2 ~~a~-~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~~-------------~~------------~~   53 (230)
                      +.|+ ++++...+  ..|....  -..+...-  +.|++++|+++|+....             |.            ..
T Consensus       360 ~~a~r~il~rAi~--~~P~s~~Lwl~~a~~ee--~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~  435 (679)
T 4e6h_A          360 STVITKYLKLGQQ--CIPNSAVLAFSLSEQYE--LNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTY  435 (679)
T ss_dssp             TTHHHHHHHHHHH--HCTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--hCCCCHHHHHHHHHHHH--HhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHH
Confidence            3564 78877764  3454443  56777778  99999999999988652             42            23


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhC-C-CCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKS-D-VRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTY  124 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~-g-~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y  124 (230)
                      .|-..+...-+.|+.+.|..+|.+-.+. + ..+......+.+.-.. .++.  |+.+|+...     +...|...++..
T Consensus       436 vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe  514 (679)
T 4e6h_A          436 VYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKYFATDGEYINKYLDFL  514 (679)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHCCCchHHHHHHHHHH
Confidence            6888888888889999999999998765 2 2233333333333222 2335  889988887     777888999999


Q ss_pred             HhcCCHHHHHHHHhhccC--CC----hhhhHHHHHH
Q 042210          125 CLCGEVDMARGIFYMSCE--DD----DGLHELIRIK  154 (230)
Q Consensus       125 ~~~g~~~~A~~vf~~m~~--~~----~~t~n~li~~  154 (230)
                      ...|+.+.|+.+|+....  |+    ...|...+.-
T Consensus       515 ~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~f  550 (679)
T 4e6h_A          515 IYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFF  550 (679)
T ss_dssp             HHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            999999999999998776  32    2457766653

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.24  E-value=0.0053  Score=41.31  Aligned_cols=100  Identities=10%  Similarity=0.017  Sum_probs=56.6

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCCcccHHHHHHHhhhcC
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDV--RRDNYTFPFLFKGFTRDI  101 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~--~p~~~t~~~ll~~~~~~~  101 (230)
                      ..+.  ..|++++|...|++..   +.+...|..+-..|...|++++|...|++.....-  .++   +..         
T Consensus        12 ~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---~~~---------   77 (131)
T 1elr_A           12 NDAY--KKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENRED---YRQ---------   77 (131)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTC---HHH---------
T ss_pred             HHHH--HhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchh---HHH---------
Confidence            4444  5556666666655543   23344455555555555666666555555433210  000   000         


Q ss_pred             chhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHH
Q 042210          102 AGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELI  151 (230)
Q Consensus       102 ~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~l  151 (230)
                                 ....|..+-..|.+.|++++|.+.|++..+  |+...+..+
T Consensus        78 -----------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l  118 (131)
T 1elr_A           78 -----------IAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKC  118 (131)
T ss_dssp             -----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             -----------HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHH
Confidence                       155677778889999999999999987764  554444433

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.19  E-value=0.0085  Score=47.48  Aligned_cols=133  Identities=8%  Similarity=-0.050  Sum_probs=99.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHH-HHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMI-KGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li-~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+.  .|+.. . ..+-..+.  +.|++++|...++...  .|+........ ..+.+.++.++|...|+
T Consensus       134 ~~A~~~~~~al~~--~P~~~~a~~~la~~~~--~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~  209 (287)
T 3qou_A          134 TDALPLLXDAWQL--SNQNGEIGLLLAETLI--ALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQAADTPEIQQLQ  209 (287)
T ss_dssp             HHHHHHHHHHHHH--TTSCHHHHHHHHHHHH--HTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCcchhHHHHHHHHHH--HCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhhcccCccHHHHH
Confidence            4567777776665  46544 3 67778888  9999999999999987  46544332222 23566778888988888


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      +..... +.+...+..+-..+...|+.  |...+....       +...+..|...|...|+.++|...|++
T Consensus       210 ~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~r~  280 (287)
T 3qou_A          210 QQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXYRR  280 (287)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            865532 22456788888899999999  888888777       377899999999999999999887764

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.19  E-value=0.0016  Score=48.04  Aligned_cols=109  Identities=9%  Similarity=-0.101  Sum_probs=57.6

Q ss_pred             ccCChHHHHH---HHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHh----CCCCC-CcccHHHHHHHhhhcCch-
Q 042210           33 EKGDLKYECK---VFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK----SDVRR-DNYTFPFLFKGFTRDIAG-  103 (230)
Q Consensus        33 ~~~~~~~a~~---~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~----~g~~p-~~~t~~~ll~~~~~~~~~-  103 (230)
                      ..|++++|.+   .+..-+......|+.+-..+...|++++|...|++...    .+..| ....+..+-..+...|++ 
T Consensus         4 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   83 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWD   83 (203)
T ss_dssp             ---CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            4566666666   33332222344556666666666666666666666433    12222 233455555566666666 


Q ss_pred             -hhHHHhhhh------------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          104 -SLEKSCIVM------------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       104 -a~~~~~~~~------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                       |...+....            ....+..+-..|...|++++|.+.|++..
T Consensus        84 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  134 (203)
T 3gw4_A           84 AARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSL  134 (203)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence             444444433            12345556667777777777777766544

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.19  E-value=0.0049  Score=41.74  Aligned_cols=82  Identities=9%  Similarity=0.078  Sum_probs=46.5

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...|++..   +.+...|..+-..|...|++++|...|++..+.  .|+                       
T Consensus        28 ~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~-----------------------   82 (133)
T 2lni_A           28 QKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQL--EPT-----------------------   82 (133)
T ss_dssp             HTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCC-----------------------
Confidence            5555555555555533   223444555555555555555555555554332  111                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         +...+..+-..|.+.|++++|.+.|++..+
T Consensus        83 ---~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  112 (133)
T 2lni_A           83 ---FIKGYTRKAAALEAMKDYTKAMDVYQKALD  112 (133)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---chHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence               345566666677777888888877776643

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.18  E-value=0.0056  Score=41.46  Aligned_cols=92  Identities=7%  Similarity=-0.094  Sum_probs=61.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~  131 (230)
                      ...|..+-..+.+.|++++|...|++..+.  .|+                          +...+..+-..|.+.|+++
T Consensus        16 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~~~--------------------------~~~~~~~la~~~~~~~~~~   67 (133)
T 2lni_A           16 ALMVKNKGNECFQKGDYPQAMKHYTEAIKR--NPK--------------------------DAKLYSNRAACYTKLLEFQ   67 (133)
T ss_dssp             HHHHHHHHHHHHHTTCSHHHHHHHHHHHTT--CTT--------------------------CHHHHHHHHHHHTTTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCC--------------------------cHHHHHHHHHHHHHhccHH
Confidence            445666777777788888888887776543  222                          3455667777888899999


Q ss_pred             HHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          132 MARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       132 ~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      +|.+.|++..+  | +...|..+-..+..    ++|.+.+++..+..
T Consensus        68 ~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  114 (133)
T 2lni_A           68 LALKDCEECIQLEPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLD  114 (133)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            99999987764  4 44556655555543    45666666655443

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.18  E-value=0.0014  Score=47.60  Aligned_cols=112  Identities=9%  Similarity=0.067  Sum_probs=76.9

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHH-hhhcCc---h-h
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG-FTRDIA---G-S  104 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~-~~~~~~---~-a  104 (230)
                      ..|++++|...++...   +.+...|..+-..|...|++++|...|++..+.. +.+...+..+-.+ +...|+   - |
T Consensus        22 ~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A  100 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQT  100 (177)
T ss_dssp             -----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             hccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHH
Confidence            5667777777777643   4456778888888888888888888888865532 1134455555555 556666   3 6


Q ss_pred             hHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh
Q 042210          105 LEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD  145 (230)
Q Consensus       105 ~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~  145 (230)
                      ...+....     +...+..+-..|.+.|++++|...|++..+  |+.
T Consensus       101 ~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~  148 (177)
T 2e2e_A          101 RAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPR  148 (177)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTT
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCC
Confidence            66666665     677788888899999999999999998764  544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.16  E-value=0.02  Score=48.68  Aligned_cols=106  Identities=18%  Similarity=0.063  Sum_probs=50.5

Q ss_pred             cCChHHHHHHHHhcC-CCChhhHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch-
Q 042210           34 KGDLKYECKVFRKIT-QPSVFLWNTMIKGYSR----IDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG-  103 (230)
Q Consensus        34 ~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~----~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~-  103 (230)
                      .++.++|...|+... .-+...+..+-..|..    .++.++|...|++-.+.|   +...+..|-..|.+    .++. 
T Consensus       128 ~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~  204 (490)
T 2xm6_A          128 KVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDA  204 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHH
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHH
Confidence            445555555555433 2233334444444443    445555555555544433   23334444444443    3344 


Q ss_pred             -hhHHHhhhh---hHhHHHHHHHHHHh----cCCHHHHHHHHhhccC
Q 042210          104 -SLEKSCIVM---RVFVQNALISTYCL----CGEVDMARGIFYMSCE  142 (230)
Q Consensus       104 -a~~~~~~~~---~~~~~~~li~~y~~----~g~~~~A~~vf~~m~~  142 (230)
                       |...+....   +...+..|-..|..    .++.++|.+.|++..+
T Consensus       205 ~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~  251 (490)
T 2xm6_A          205 ISAQWYRKSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAE  251 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence             444444443   44455555555554    5666666666665544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.14  E-value=0.019  Score=48.90  Aligned_cols=198  Identities=10%  Similarity=-0.061  Sum_probs=120.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhc----cCChHHHHHHHHhcC-CCChhhHHHHHHHHHh----cCChhHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYE----KGDLKYECKVFRKIT-QPSVFLWNTMIKGYSR----IDSHKNG   71 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~----~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~----~~~~~~a   71 (230)
                      ++|...++...+.|   ++.. ..+=..|.  .    .++.++|.+.|++.. ..+...+..|=..|..    .+++++|
T Consensus        60 ~~A~~~~~~a~~~~---~~~a~~~Lg~~y~--~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A  134 (490)
T 2xm6_A           60 TQAMDWFRRAAEQG---YTPAEYVLGLRYM--NGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAES  134 (490)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHH--HTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             HHHHHHHHHHHHCC---CHHHHHHHHHHHH--cCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            35666666666553   3334 44555555  6    788889988888765 4455566666666766    6788999


Q ss_pred             HHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch--hhHHHhhhh---hHhHHHHHHHHHHh----cCCHHHHHHHHh
Q 042210           72 VLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLEKSCIVM---RVFVQNALISTYCL----CGEVDMARGIFY  138 (230)
Q Consensus        72 ~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~~~~~~~---~~~~~~~li~~y~~----~g~~~~A~~vf~  138 (230)
                      ...|++-...|   +...+..|-..|..    .++.  |...+....   +...+..|-..|.+    .++.++|.+.|+
T Consensus       135 ~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~  211 (490)
T 2xm6_A          135 VKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYR  211 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHH
Confidence            99998877765   33445555555555    4555  777777665   77777788888887    889999999998


Q ss_pred             hccC-CChhhhHHHHHHhhh--------cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccc
Q 042210          139 MSCE-DDDGLHELIRIKAVD--------DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQE  209 (230)
Q Consensus       139 ~m~~-~~~~t~n~li~~~~~--------~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~  209 (230)
                      +..+ .+..++..+-..+..        +++.+.|++..+.+.  |+....-+  .+-     ..+....++.++|..++
T Consensus       212 ~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~--~~a~~~lg--~~y-----~~g~~~~~d~~~A~~~~  282 (490)
T 2xm6_A          212 KSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGN--SIAQFRLG--YIL-----EQGLAGAKEPLKALEWY  282 (490)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTC--HHHHHHHH--HHH-----HHTTTSSCCHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC--HHHHHHHH--HHH-----HCCCCCCCCHHHHHHHH
Confidence            7665 344455555444432        355555555544431  22111111  110     00222256677777776


Q ss_pred             ccccccC
Q 042210          210 GRPHEHS  216 (230)
Q Consensus       210 ~~~~~~~  216 (230)
                      ....+.|
T Consensus       283 ~~a~~~~  289 (490)
T 2xm6_A          283 RKSAEQG  289 (490)
T ss_dssp             HHHHTTT
T ss_pred             HHHHHcC
Confidence            6665543

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.14  E-value=0.0014  Score=46.76  Aligned_cols=106  Identities=10%  Similarity=-0.033  Sum_probs=70.4

Q ss_pred             ccCChHHHHHHHHhcCCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKITQP---SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~---~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      ..|++++|.+.+....+.   +...+-.+=..|.+.|++++|.+.|++..+.  .| +...|..+-.++.+.|++  |..
T Consensus         9 ~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~   86 (150)
T 4ga2_A            9 SKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEENTDKAVE   86 (150)
T ss_dssp             CHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCchHHHHH
Confidence            556788888888776522   2334555667788888888888888886553  34 344666666677777777  666


Q ss_pred             HHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHH-Hhhc
Q 042210          107 KSCIVM-----RVFVQNALISTYCLCGEVDMARGI-FYMS  140 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~v-f~~m  140 (230)
                      .+....     +...|..+-..|.+.|+.++|.+. +++.
T Consensus        87 ~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~a  126 (150)
T 4ga2_A           87 CYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERA  126 (150)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            666655     566677777777777777665544 3543

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.11  E-value=0.0098  Score=39.09  Aligned_cols=30  Identities=3%  Similarity=-0.119  Sum_probs=24.0

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +...+..+-..|.+.|++++|.+.|++..+
T Consensus        71 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           71 WGKGYSRKAAALEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            456677777888889999999999887765

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.08  E-value=0.025  Score=42.76  Aligned_cols=141  Identities=6%  Similarity=-0.041  Sum_probs=81.1

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcc----cHHHHHHH
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNY----TFPFLFKG   96 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~----t~~~ll~~   96 (230)
                      ..+.  +.|++++|...|+++.  .|+.    ..+..+-.+|.+.|++++|...|++..+.  .|+..    .+-.+-.+
T Consensus        12 ~~~~--~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~--~P~~~~~~~a~~~~g~~   87 (225)
T 2yhc_A           12 QQKL--QDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL--NPTHPNIDYVMYMRGLT   87 (225)
T ss_dssp             HHHH--HHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTTHHHHHHHHHHH
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCcHHHHHHHHHHH
Confidence            4455  7777777777777765  2332    34555666777777777777777776542  13221    12222222


Q ss_pred             hhh------------------cCch--hhHHHhhhh-----hHhHH-----------------HHHHHHHHhcCCHHHHH
Q 042210           97 FTR------------------DIAG--SLEKSCIVM-----RVFVQ-----------------NALISTYCLCGEVDMAR  134 (230)
Q Consensus        97 ~~~------------------~~~~--a~~~~~~~~-----~~~~~-----------------~~li~~y~~~g~~~~A~  134 (230)
                      +.+                  .|+.  |...++.+.     +...+                 -.+-..|.+.|++++|.
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~  167 (225)
T 2yhc_A           88 NMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVV  167 (225)
T ss_dssp             HHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHH
Confidence            221                  3444  666666555     22222                 23445788999999999


Q ss_pred             HHHhhccC--CChh----hhHHHHHHhhh----cchhhhHHHHHHHh
Q 042210          135 GIFYMSCE--DDDG----LHELIRIKAVD----DDLHELFPEYLVQM  171 (230)
Q Consensus       135 ~vf~~m~~--~~~~----t~n~li~~~~~----~~~~~~~~~m~~~~  171 (230)
                      ..|++..+  |+..    .+..+..++..    ++|.+.++.+....
T Consensus       168 ~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          168 NRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            99998875  6543    34444444443    46666666655544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.07  E-value=0.0019  Score=53.14  Aligned_cols=202  Identities=6%  Similarity=-0.042  Sum_probs=119.0

Q ss_pred             hhHHHHHHHHHHhcC-CCCC----cH-HHHHHHHhhhccCChHHHHHHHHhcC-----CCC-----hhhHHHHHHHHHhc
Q 042210            2 HQLKQIHSQTIKLGL-LTKP----HC-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS-----VFLWNTMIKGYSRI   65 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~-~~~~----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~-----~~~yn~li~~~~~~   65 (230)
                      ++|...++...+.-- .++.    .+ ..+-..|.  ..|+.++|...+++..     .++     ..+++.+-..|...
T Consensus       120 ~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~  197 (383)
T 3ulq_A          120 LSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYY--YMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDL  197 (383)
T ss_dssp             HHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHh
Confidence            355666666554311 1222    23 44556666  8899998888887754     222     24677777888888


Q ss_pred             CChhHHHHHHHHHHhC----CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhc
Q 042210           66 DSHKNGVLMYLDLLKS----DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLC  127 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~~----g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~  127 (230)
                      |++++|...|++..+.    +-.+ ...++..+-..|...|+.  |...+....           ...++..+-..|.+.
T Consensus       198 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~  277 (383)
T 3ulq_A          198 KQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKL  277 (383)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHC
Confidence            9999999998886542    1111 123677777788888888  666665554           345677788889999


Q ss_pred             CCHHHHHHHHhhccC-----CChh---hhHHHHHHhhhcch---hhhHHHHHHHhhhcCchh-hhhhhhhcccccCCccc
Q 042210          128 GEVDMARGIFYMSCE-----DDDG---LHELIRIKAVDDDL---HELFPEYLVQMLALPDTF-MGEGLEVIPKSQAPREE  195 (230)
Q Consensus       128 g~~~~A~~vf~~m~~-----~~~~---t~n~li~~~~~~~~---~~~~~~m~~~~~~~p~~~-t~~~l~~~~~~~~~~~a  195 (230)
                      |++++|...|++..+     .|..   .++.+-..+...+.   .+..-...+.....|+.. .+..   +      -..
T Consensus       278 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~---l------a~~  348 (383)
T 3ulq_A          278 GKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAID---V------AKY  348 (383)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHH---H------HHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHH---H------HHH
Confidence            999999988886553     2221   22333333333222   122222222221222221 2222   1      116


Q ss_pred             ccccCCccCCccccccccc
Q 042210          196 TPRVGNLEEGTPQEGRPHE  214 (230)
Q Consensus       196 ~~~~g~~~~a~~i~~~~~~  214 (230)
                      +.+.|+.++|...+....+
T Consensus       349 y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            7788999999888876655

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.06  E-value=0.0057  Score=49.78  Aligned_cols=88  Identities=9%  Similarity=0.034  Sum_probs=51.4

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC--CCC----------------hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT--QPS----------------VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR   85 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----------------~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p   85 (230)
                      .+-..|.  +.|++++|...|++..  .|+                ...|..+-.+|.+.|++++|...|++..+.  .|
T Consensus       152 ~~g~~~~--~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~p  227 (336)
T 1p5q_A          152 ERGTVYF--KEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL--DS  227 (336)
T ss_dssp             HHHHHHH--HHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT
T ss_pred             HHHHHHH--HCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CC
Confidence            3344555  6777777777776654  232                256666666666677777777776665442  12


Q ss_pred             CcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           86 DNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        86 ~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +                          +...|..+-.+|.+.|++++|...|++..
T Consensus       228 ~--------------------------~~~a~~~lg~~~~~~g~~~~A~~~~~~al  257 (336)
T 1p5q_A          228 N--------------------------NEKGLSRRGEAHLAVNDFELARADFQKVL  257 (336)
T ss_dssp             T--------------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             C--------------------------cHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            1                          34444555555666666666666666554

>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=97.05  E-value=0.018  Score=45.45  Aligned_cols=115  Identities=10%  Similarity=-0.036  Sum_probs=83.4

Q ss_pred             HHHHhhhccCChHHHHHHHHhcCC-----CCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-CCc----ccHH
Q 042210           26 TRYLLLYEKGDLKYECKVFRKITQ-----PSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVR-RDN----YTFP   91 (230)
Q Consensus        26 l~~~~~~~~~~~~~a~~~~~~m~~-----~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~-p~~----~t~~   91 (230)
                      +..+.  +.|++++|...+++...     |+.    ..|..+-..+...+++++|...|++....... ++.    ..|+
T Consensus        82 i~~~~--~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           82 VIMLC--KQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHH--HTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHH--HHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            56667  88999999999988652     221    12344656666678999999999998774333 232    2577


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM------------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      .+-..|...|++  |...+....            ...+|..+-..|.+.|++++|...+++..+
T Consensus       160 ~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~  224 (293)
T 3u3w_A          160 AIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIE  224 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence            888888888888  666666654            344778888899999999999998886553

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.04  E-value=0.0061  Score=51.19  Aligned_cols=94  Identities=13%  Similarity=-0.087  Sum_probs=54.5

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh-hhhHHHHHHhh-----------------------hcchhhhHHH
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD-GLHELIRIKAV-----------------------DDDLHELFPE  166 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~-~t~n~li~~~~-----------------------~~~~~~~~~~  166 (230)
                      +...+..+-..|.+.|++++|...|++..+  |+. .+|+.+-..|.                       .+++.+.+++
T Consensus       246 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  325 (472)
T 4g1t_A          246 VTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKK  325 (472)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            566677778888888888888888887654  543 34444322221                       1233333333


Q ss_pred             HHHHhhhcCc-hhhhhhhhhcccccCCcccccccCCccCCccccccccccCCC
Q 042210          167 YLVQMLALPD-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQD  218 (230)
Q Consensus       167 m~~~~~~~p~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~  218 (230)
                      ....   .|+ ..++..+..         .+.+.|++++|...+..+.+....
T Consensus       326 a~~~---~~~~~~~~~~lg~---------~~~~~~~~~~A~~~~~kaL~~~~~  366 (472)
T 4g1t_A          326 ADEA---NDNLFRVCSILAS---------LHALADQYEEAEYYFQKEFSKELT  366 (472)
T ss_dssp             HHHH---CTTTCCCHHHHHH---------HHHHTTCHHHHHHHHHHHHHSCCC
T ss_pred             Hhhc---CCchhhhhhhHHH---------HHHHhccHHHHHHHHHHHHhcCCC
Confidence            3322   233 222222112         567889999998888877665443

>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=96.97  E-value=0.0021  Score=47.78  Aligned_cols=147  Identities=8%  Similarity=0.000  Sum_probs=83.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCC------------
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSD-VRRD------------   86 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g-~~p~------------   86 (230)
                      +....+..  ..|+++++.+.|+.-.   ......|..+-..+.+.|++++|...|++..+.. -.|+            
T Consensus         8 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   85 (198)
T 2fbn_A            8 HHHSSGRE--NLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKN   85 (198)
T ss_dssp             ----------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHH
T ss_pred             cchhhhhh--hhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHH
Confidence            34444455  6667777777665433   1233456667777888999999999999876532 1221            


Q ss_pred             --cccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHHHHHH
Q 042210           87 --NYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGLHELIRIK  154 (230)
Q Consensus        87 --~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~li~~  154 (230)
                        ...|..+-.++.+.|++  |...+....     +...+..+-..|.+.|++++|.+.|++..+  |+ ...+..+-..
T Consensus        86 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~  165 (198)
T 2fbn_A           86 IEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELC  165 (198)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHH
Confidence              15677777788888888  777777766     677888888999999999999999998754  54 3445544333


Q ss_pred             hhh----cch-hhhHHHHHHHh
Q 042210          155 AVD----DDL-HELFPEYLVQM  171 (230)
Q Consensus       155 ~~~----~~~-~~~~~~m~~~~  171 (230)
                      +..    .++ ...+..|+..+
T Consensus       166 ~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          166 VNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHHHHC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHhccc
Confidence            321    222 24555555554

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=96.94  E-value=0.045  Score=43.23  Aligned_cols=56  Identities=13%  Similarity=0.003  Sum_probs=28.8

Q ss_pred             HHHHHHhhhcc-CChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           24 KQTRYLLLYEK-GDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        24 ~ll~~~~~~~~-~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      .+-..|.  +. |++++|...|++..     ..+    ..+|+.+-..|.+.|++++|...|++....
T Consensus       122 ~lg~~~~--~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  187 (292)
T 1qqe_A          122 ELGEILE--NDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKS  187 (292)
T ss_dssp             HHHHHHH--HTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHH--HhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            3444444  53 66666666655533     111    123555555556666666666666655443

>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=96.93  E-value=0.0083  Score=44.58  Aligned_cols=84  Identities=6%  Similarity=-0.228  Sum_probs=71.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhc
Q 042210           55 WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLC  127 (230)
Q Consensus        55 yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~  127 (230)
                      +..+-..+...|++++|...|++.    +.|+...|..+-..+.+.|++  |...+....     +...|..+-..|.+.
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~   84 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQT   84 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHc
Confidence            444556777899999999999876    467888899999999999999  888887776     678889999999999


Q ss_pred             CCHHHHHHHHhhccC
Q 042210          128 GEVDMARGIFYMSCE  142 (230)
Q Consensus       128 g~~~~A~~vf~~m~~  142 (230)
                      |++++|...|++..+
T Consensus        85 ~~~~~A~~~~~~al~   99 (213)
T 1hh8_A           85 EKYDLAIKDLKEALI   99 (213)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHH
Confidence            999999999998764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=96.93  E-value=0.019  Score=47.00  Aligned_cols=145  Identities=7%  Similarity=-0.092  Sum_probs=102.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhC----CC-CCCcc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DV-RRDNY   88 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~-~p~~~   88 (230)
                      +.+-..|.  ..|++++|...|++..     .++.    .+|+.+=..|...|++++|...|++-.+.    +- +....
T Consensus       188 ~~lg~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  265 (383)
T 3ulq_A          188 SLFATNFL--DLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQ  265 (383)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHH
T ss_pred             HHHHHHHH--HhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHH
Confidence            55557777  9999999999998764     2222    36788888899999999999999986651    33 33455


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh----------hHhHHHHHHHHHHhcCC---HHHHHHHHhhccCC-Ch-hhhHHH
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM----------RVFVQNALISTYCLCGE---VDMARGIFYMSCED-DD-GLHELI  151 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~----------~~~~~~~li~~y~~~g~---~~~A~~vf~~m~~~-~~-~t~n~l  151 (230)
                      ++..+-..+.+.|+.  |...+....          ....++.+-..|.+.|+   +++|..++++...+ +. ..+..+
T Consensus       266 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~l  345 (383)
T 3ulq_A          266 AYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDV  345 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            788888899999998  777777665          23335667788888999   89999999988542 22 233334


Q ss_pred             HHHhhh----cchhhhHHHHHH
Q 042210          152 RIKAVD----DDLHELFPEYLV  169 (230)
Q Consensus       152 i~~~~~----~~~~~~~~~m~~  169 (230)
                      -..+..    ++|.+.+++..+
T Consensus       346 a~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          346 AKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            344443    456666665544

>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=96.92  E-value=0.014  Score=40.00  Aligned_cols=88  Identities=7%  Similarity=-0.150  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCL  126 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~  126 (230)
                      .|..+-..+...|++++|...|++..... +.+...|..+-.++...|++  |...+....     +...|..+-..|.+
T Consensus        11 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~   89 (137)
T 3q49_B           11 ELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLE   89 (137)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHH
Confidence            33334444444444444444444433221 01222333333444444444  333333333     45667777788888


Q ss_pred             cCCHHHHHHHHhhccC
Q 042210          127 CGEVDMARGIFYMSCE  142 (230)
Q Consensus       127 ~g~~~~A~~vf~~m~~  142 (230)
                      .|++++|...|++..+
T Consensus        90 ~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           90 MESYDEAIANLQRAYS  105 (137)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHH
Confidence            8888888888887654

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=96.91  E-value=0.012  Score=45.45  Aligned_cols=138  Identities=6%  Similarity=-0.033  Sum_probs=99.0

Q ss_pred             hhHHHHHHHHHHhcCCCCC----cH-HHHHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHh------
Q 042210            2 HQLKQIHSQTIKLGLLTKP----HC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSR------   64 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~------   64 (230)
                      ++|...|+...+..  |+.    .. ..+-..|.  +.|++++|...|+...  .|+    ...|..+-.++.+      
T Consensus        32 ~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~--~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~  107 (261)
T 3qky_A           32 DRAIEYFKAVFTYG--RTHEWAADAQFYLARAYY--QNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYE  107 (261)
T ss_dssp             HHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTT
T ss_pred             HHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHH--HhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhccccc
Confidence            46778888776653  443    23 44556677  9999999999999875  332    2345566667777      


Q ss_pred             --cCChhHHHHHHHHHHhCCCCCCc-ccH-----------------HHHHHHhhhcCch--hhHHHhhhh--------hH
Q 042210           65 --IDSHKNGVLMYLDLLKSDVRRDN-YTF-----------------PFLFKGFTRDIAG--SLEKSCIVM--------RV  114 (230)
Q Consensus        65 --~~~~~~a~~~~~~M~~~g~~p~~-~t~-----------------~~ll~~~~~~~~~--a~~~~~~~~--------~~  114 (230)
                        .|++++|...|++..+..  |+. ...                 -.+-..+.+.|++  |...++...        ..
T Consensus       108 ~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~  185 (261)
T 3qky_A          108 LDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWAD  185 (261)
T ss_dssp             SCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHH
T ss_pred             ccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHH
Confidence              899999999999977642  432 233                 3346678888998  888888776        23


Q ss_pred             hHHHHHHHHHHhc----------CCHHHHHHHHhhccC--CCh
Q 042210          115 FVQNALISTYCLC----------GEVDMARGIFYMSCE--DDD  145 (230)
Q Consensus       115 ~~~~~li~~y~~~----------g~~~~A~~vf~~m~~--~~~  145 (230)
                      ..+..+-..|.+.          |++++|...|++..+  |+.
T Consensus       186 ~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~  228 (261)
T 3qky_A          186 DALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDS  228 (261)
T ss_dssp             HHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCC
Confidence            4666777788766          899999999998875  655

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.89  E-value=0.025  Score=38.97  Aligned_cols=89  Identities=8%  Similarity=-0.140  Sum_probs=52.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----cccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD----NYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNAL  120 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~----~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~l  120 (230)
                      ...|..+-..+.+.|++++|...|++..+.  .|+    ...|..+-.++...|++  |...+....     +...|..+
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~  105 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHH
Confidence            344555555555666666666666655442  233    33444444555555555  444444443     45566677


Q ss_pred             HHHHHhcCCHHHHHHHHhhccC
Q 042210          121 ISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       121 i~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      -..|.+.|++++|.+.|++..+
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            7788888888888888887654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=96.87  E-value=0.0035  Score=51.48  Aligned_cols=138  Identities=10%  Similarity=-0.017  Sum_probs=93.0

Q ss_pred             hhHHHHHHHHHHhcC-CCCC----cH-HHHHHHHhhhccCChHHHHHHHHhcC-----CCC-----hhhHHHHHHHHHhc
Q 042210            2 HQLKQIHSQTIKLGL-LTKP----HC-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS-----VFLWNTMIKGYSRI   65 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~-~~~~----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~-----~~~yn~li~~~~~~   65 (230)
                      ++|...++...+.-- .++.    .+ ..+-..|.  ..|+++.|...+++..     .++     ..+++.+=..|...
T Consensus       118 ~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~  195 (378)
T 3q15_A          118 VEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYY--HMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDF  195 (378)
T ss_dssp             HHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHH--HcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHh
Confidence            356666666554421 1221    12 44556677  8899999888887753     122     34677788888889


Q ss_pred             CChhHHHHHHHHHHhC----CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh----------hHhHHHHHHHHHHhcC
Q 042210           66 DSHKNGVLMYLDLLKS----DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM----------RVFVQNALISTYCLCG  128 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~~----g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~----------~~~~~~~li~~y~~~g  128 (230)
                      |++++|...|++-.+.    +-.+ ...++..+-..+...|+.  |...+....          ...++..+-..|.+.|
T Consensus       196 ~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g  275 (378)
T 3q15_A          196 KHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAG  275 (378)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCC
Confidence            9999999999885442    2111 223566677778888888  666666554          4556777888899999


Q ss_pred             CHHHHHHHHhhcc
Q 042210          129 EVDMARGIFYMSC  141 (230)
Q Consensus       129 ~~~~A~~vf~~m~  141 (230)
                      +.++|...|++..
T Consensus       276 ~~~~A~~~~~~al  288 (378)
T 3q15_A          276 QTQKAFQFIEEGL  288 (378)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH
Confidence            9999999988654

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.85  E-value=0.0078  Score=41.92  Aligned_cols=115  Identities=10%  Similarity=-0.017  Sum_probs=67.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-Ccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR-DNY   88 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p-~~~   88 (230)
                      ..+-..+.  ..|++++|...+++..     .++.    ..+..+-..+...|++++|...+++....    +-.+ ...
T Consensus        13 ~~l~~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           13 GNLGNTHY--LLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHH--HhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            34445566  8888888888887754     1221    36777777888888999998888875432    1111 122


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      .+..+-..+...|++  |...+....           ....+..+-..|...|++++|.+.+++
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~  154 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEK  154 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            344444555555555  444444333           233445555556666666666665554

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=96.80  E-value=0.016  Score=42.44  Aligned_cols=118  Identities=4%  Similarity=-0.217  Sum_probs=86.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCC---------CChhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC--Cc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQ---------PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR--DN   87 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~---------~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p--~~   87 (230)
                      ..+-..+.  ..|++++|...+++...         .....++.+-..|...|++++|...|++-.+.    +-.|  ..
T Consensus        30 ~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  107 (203)
T 3gw4_A           30 FMLGYVYA--FMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAAS  107 (203)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHH--HhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHH
Confidence            55667777  99999999999987641         12346777888889999999999999886442    2111  13


Q ss_pred             ccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           88 YTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        88 ~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ..+..+-..+...|++  |...+....           ...++..+-..|.+.|++++|.+.|++..+
T Consensus       108 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          108 ANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3466677788888888  766666654           233457778889999999999999987544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=96.78  E-value=0.0079  Score=39.21  Aligned_cols=92  Identities=13%  Similarity=0.001  Sum_probs=60.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|++++|...|++..   +.+...|..+-..+.+.|++++|...|++..+..  |+.            
T Consensus        10 ~~~~~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~------------   73 (112)
T 2kck_A           10 YLEGVLQY--DAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI--EDE------------   73 (112)
T ss_dssp             GGHHHHHH--SSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--CCT------------
T ss_pred             HHHHHHHH--HhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--ccc------------
Confidence            55556667  8888888888887754   4455667777777778888888888887766542  220            


Q ss_pred             cCchhhHHHhhhhhHhHHHHHHHHHHhc-CCHHHHHHHHhhccC
Q 042210          100 DIAGSLEKSCIVMRVFVQNALISTYCLC-GEVDMARGIFYMSCE  142 (230)
Q Consensus       100 ~~~~a~~~~~~~~~~~~~~~li~~y~~~-g~~~~A~~vf~~m~~  142 (230)
                         .         +...+..+-..|.+. |++++|.+.|++...
T Consensus        74 ---~---------~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           74 ---Y---------NKDVWAAKADALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             ---T---------CHHHHHHHHHHHTTCSSCSHHHHHHHHHHGG
T ss_pred             ---c---------hHHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Confidence               0         234455556666667 777777777766554

>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=96.77  E-value=0.014  Score=41.36  Aligned_cols=87  Identities=9%  Similarity=-0.051  Sum_probs=46.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCC
Q 042210           58 MIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGE  129 (230)
Q Consensus        58 li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~  129 (230)
                      +-..+.+.|++++|...|++....  .| +...|..+-.+|...|++  |...++...     +...|..+-..|...|+
T Consensus        27 ~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~  104 (148)
T 2vgx_A           27 LAFNQYQSGXYEDAHXVFQALCVL--DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLLQXGE  104 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHc--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCC
Confidence            333444444444444444443321  11 222333333444444444  444444333     45666777778888899


Q ss_pred             HHHHHHHHhhccC--CChh
Q 042210          130 VDMARGIFYMSCE--DDDG  146 (230)
Q Consensus       130 ~~~A~~vf~~m~~--~~~~  146 (230)
                      +++|.+.|+...+  |+..
T Consensus       105 ~~~A~~~~~~al~~~p~~~  123 (148)
T 2vgx_A          105 LAEAESGLFLAQELIANXP  123 (148)
T ss_dssp             HHHHHHHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHHHHHCcCCC
Confidence            9999988887654  5443

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=96.76  E-value=0.016  Score=39.85  Aligned_cols=82  Identities=7%  Similarity=0.039  Sum_probs=49.0

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|.+.|++..   +.+...|..+-.+|.+.|++++|...|++-.+.  .|+                       
T Consensus        25 ~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~-----------------------   79 (126)
T 4gco_A           25 KKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRL--DSK-----------------------   79 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHh--hhh-----------------------
Confidence            5555555555555532   334445555555555555555555555543321  111                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         +...|..+-..|.+.|++++|.+.|++..+
T Consensus        80 ---~~~a~~~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           80 ---FIKGYIRKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---hhHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence               456677777788888888888888887654

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.75  E-value=0.011  Score=41.24  Aligned_cols=80  Identities=13%  Similarity=-0.051  Sum_probs=42.8

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHH
Q 042210           61 GYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        61 ~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~  132 (230)
                      .+.+.|++++|...|++....  .| +...|..+-.++.+.|++  |...++...     +...+..+-..|...|++++
T Consensus        27 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~  104 (142)
T 2xcb_A           27 NQYQAGKWDDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQLGDLDG  104 (142)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHH
Confidence            334444444444444443321  11 222333333344444444  444443333     45566777778888899999


Q ss_pred             HHHHHhhccC
Q 042210          133 ARGIFYMSCE  142 (230)
Q Consensus       133 A~~vf~~m~~  142 (230)
                      |.+.|+...+
T Consensus       105 A~~~~~~al~  114 (142)
T 2xcb_A          105 AESGFYSARA  114 (142)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9988887654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=96.75  E-value=0.011  Score=42.46  Aligned_cols=90  Identities=6%  Similarity=-0.146  Sum_probs=53.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYC  125 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~  125 (230)
                      .|..+=..+.+.|++++|...|++....  .| +...|..+=.++.+.|++  |...++...     +...|..+-.+|.
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHH
Confidence            3444444555556666666666554432  12 233444455555555555  555554444     5667777778888


Q ss_pred             hcCCHHHHHHHHhhccC--CCh
Q 042210          126 LCGEVDMARGIFYMSCE--DDD  145 (230)
Q Consensus       126 ~~g~~~~A~~vf~~m~~--~~~  145 (230)
                      +.|++++|...|++..+  ||.
T Consensus       116 ~lg~~~eA~~~~~~al~l~~~~  137 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQHSNDE  137 (151)
T ss_dssp             HTTCHHHHHHHHHHHHHHCCCH
T ss_pred             HcCCHHHHHHHHHHHHHhCCCH
Confidence            88888888888887654  544

>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=96.71  E-value=0.045  Score=38.41  Aligned_cols=90  Identities=9%  Similarity=-0.071  Sum_probs=57.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A  133 (230)
                      .|..+-..+...|++++|...|++..+.  .|+                          +...+..+-..|.+.|++++|
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~--~~~--------------------------~~~~~~~~a~~~~~~~~~~~A   66 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIEL--NPS--------------------------NAIYYGNRSLAYLRTECYGYA   66 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--STT--------------------------CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHh--CCC--------------------------ChHHHHHHHHHHHHcCCHHHH
Confidence            3555566666777777777777765442  121                          355667777788889999999


Q ss_pred             HHHHhhccC--C-ChhhhHHHHHHhh----hcchhhhHHHHHHHh
Q 042210          134 RGIFYMSCE--D-DDGLHELIRIKAV----DDDLHELFPEYLVQM  171 (230)
Q Consensus       134 ~~vf~~m~~--~-~~~t~n~li~~~~----~~~~~~~~~~m~~~~  171 (230)
                      .+.|++..+  | +...|..+-..+.    .++|.+.+++..+..
T Consensus        67 ~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~  111 (166)
T 1a17_A           67 LGDATRAIELDKKYIKGYYRRAASNMALGKFRAALRDYETVVKVK  111 (166)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            999987664  4 4445555544443    346666666665543

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=96.70  E-value=0.014  Score=43.78  Aligned_cols=145  Identities=12%  Similarity=0.061  Sum_probs=97.6

Q ss_pred             ccCChHHHHHHHHhcC--CCC-hhhHHH----------------HHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHH
Q 042210           33 EKGDLKYECKVFRKIT--QPS-VFLWNT----------------MIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPF   92 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~-~~~yn~----------------li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~   92 (230)
                      +.|++++|...|++..  .|+ ...|..                +-..|.+.|++++|...|++..+.  .| +...|..
T Consensus        16 ~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~   93 (208)
T 3urz_A           16 EAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK--APNNVDCLEA   93 (208)
T ss_dssp             HTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHH
Confidence            8999999999999875  343 344555                777888999999999999997663  34 4567788


Q ss_pred             HHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCC--HHHHHHHHhhccCCChhhhHHHHH------Hhhh
Q 042210           93 LFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGE--VDMARGIFYMSCEDDDGLHELIRI------KAVD  157 (230)
Q Consensus        93 ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~--~~~A~~vf~~m~~~~~~t~n~li~------~~~~  157 (230)
                      +-..+...|++  |...++...     +...|..+-..|...|+  .+.+...+.....|+...|...-.      ....
T Consensus        94 lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~~~~~  173 (208)
T 3urz_A           94 CAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGLSKLFTTRY  173 (208)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHccCH
Confidence            88889999999  888888877     67788888888766654  455667777776666543322211      1223


Q ss_pred             cchhhhHHHHHHHhhhcCchhhhhh
Q 042210          158 DDLHELFPEYLVQMLALPDTFMGEG  182 (230)
Q Consensus       158 ~~~~~~~~~m~~~~~~~p~~~t~~~  182 (230)
                      ++|.+.|++..+   ..|+......
T Consensus       174 ~~A~~~~~~al~---l~P~~~~~~~  195 (208)
T 3urz_A          174 EKARNSLQKVIL---RFPSTEAQKT  195 (208)
T ss_dssp             HHHHHHHHHHTT---TSCCHHHHHH
T ss_pred             HHHHHHHHHHHH---hCCCHHHHHH
Confidence            456666665443   3466443333

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=96.67  E-value=0.025  Score=36.66  Aligned_cols=76  Identities=7%  Similarity=0.099  Sum_probs=60.8

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CC--ChhhHHHHHHHHHhc-CChhHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QP--SVFLWNTMIKGYSRI-DSHKNGVL   73 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~--~~~~yn~li~~~~~~-~~~~~a~~   73 (230)
                      ++|...++...+..  |+ ... ..+-..+.  +.|++++|...|++..   ..  +...|..+-..+.+. |++++|.+
T Consensus        23 ~~A~~~~~~a~~~~--~~~~~~~~~~a~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~   98 (112)
T 2kck_A           23 TESIDLFEKAIQLD--PEESKYWLMKGKALY--NLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALRYIEGKEVEAEI   98 (112)
T ss_dssp             HHHHHHHHHHHHHC--CCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTTCSSCSHHHHH
T ss_pred             HHHHHHHHHHHHhC--cCCHHHHHHHHHHHH--HccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHHhCCHHHHHH
Confidence            46778888877763  43 334 66777888  9999999999999865   33  577889999999999 99999999


Q ss_pred             HHHHHHhC
Q 042210           74 MYLDLLKS   81 (230)
Q Consensus        74 ~~~~M~~~   81 (230)
                      .|++....
T Consensus        99 ~~~~~~~~  106 (112)
T 2kck_A           99 AEARAKLE  106 (112)
T ss_dssp             HHHHHGGG
T ss_pred             HHHHHhhc
Confidence            99997664

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=96.66  E-value=0.015  Score=41.49  Aligned_cols=87  Identities=7%  Similarity=-0.054  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhc
Q 042210           55 WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLC  127 (230)
Q Consensus        55 yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~  127 (230)
                      |..+-..+.+.|++++|...|++..+.. +-+...|..+-.++.+.|++  |...+....     +...|..+-..|.+.
T Consensus        14 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~   92 (164)
T 3sz7_A           14 LKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLARFDM   92 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            3334444444455555555554433321 01233344444444444544  444444433     567778888899999


Q ss_pred             CCHHHHHHHHhhccC
Q 042210          128 GEVDMARGIFYMSCE  142 (230)
Q Consensus       128 g~~~~A~~vf~~m~~  142 (230)
                      |++++|.+.|++..+
T Consensus        93 g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           93 ADYKGAKEAYEKGIE  107 (164)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHH
Confidence            999999999998765

>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=96.63  E-value=0.016  Score=42.08  Aligned_cols=131  Identities=10%  Similarity=-0.000  Sum_probs=89.6

Q ss_pred             hHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHH-HHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKG-YSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~-~~~~~~~~~a~~~~~~   77 (230)
                      +|...++...+.  .|+.. . ..+-..+.  +.|++++|...|+...  .|+...+...-.. +...+...+|...|++
T Consensus        24 ~A~~~~~~al~~--~P~~~~a~~~la~~~~--~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~   99 (176)
T 2r5s_A           24 QALNVIQTLSDE--LQSRGDVKLAKADCLL--ETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQ   99 (176)
T ss_dssp             HHHHHHHTSCHH--HHTSHHHHHHHHHHHH--HTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHH--CCCcHHHHHHHHHHHH--HCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHhhcccchHHHHHHH
Confidence            445555544332  35443 3 66777888  9999999999999986  4444333222111 2222333456777877


Q ss_pred             HHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210           78 LLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus        78 M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                      ..+  ..| +...+..+-..+...|+.  |...+....       +...+..+...|...|+.++|...|++
T Consensus       100 al~--~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~  169 (176)
T 2r5s_A          100 ELA--ANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRR  169 (176)
T ss_dssp             HHH--HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHH
T ss_pred             HHH--hCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHH
Confidence            654  335 456778888899999999  888888776       245889999999999999999988875

>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=96.60  E-value=0.054  Score=42.65  Aligned_cols=114  Identities=16%  Similarity=0.048  Sum_probs=85.2

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC-----CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHh----C-CCCCC-ccc
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT-----QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLK----S-DVRRD-NYT   89 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~----~-g~~p~-~~t   89 (230)
                      +-..+.  ..++.++|...|++..     .++.    ..|+.+-..|...|++++|...|++..+    . +-.|. ..+
T Consensus       121 l~~~~~--~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  198 (293)
T 3u3w_A          121 VAAYVL--KKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKV  198 (293)
T ss_dssp             HHHHHT--TSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHH--cccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHH
Confidence            445555  7889999999998764     2332    2688898999999999999999999764    1 22222 236


Q ss_pred             HHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCC-HHHHHHHHhhc
Q 042210           90 FPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGE-VDMARGIFYMS  140 (230)
Q Consensus        90 ~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~-~~~A~~vf~~m  140 (230)
                      |..+-..|.+.|+.  |...+....           -..+|..+=..|.+.|+ .++|.+.|++.
T Consensus       199 ~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          199 RYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence            77888889999998  777776665           25678888888999994 68888777754

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=96.60  E-value=0.11  Score=43.39  Aligned_cols=202  Identities=13%  Similarity=-0.045  Sum_probs=104.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHh--hhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLL--LYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLM   74 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~--~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~   74 (230)
                      ++|.+.++...+.  .|+...  ..+-..+.  .-..++.++|.+.+++..   +.+...|+.+-..|.+.|++++|...
T Consensus       192 ~~al~~~~~al~l--~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~  269 (472)
T 4g1t_A          192 QNAIDPLRQAIRL--NPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIEL  269 (472)
T ss_dssp             CCTHHHHHHHHHH--CSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhhc--CCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHH
Confidence            3566667766655  355443  33333333  004467888999988754   45567788888899999999999999


Q ss_pred             HHHHHhCCCCCCc-ccHHHHHHHhhhc-------------------Cch--hhHHHhhhh-----hHhHHHHHHHHHHhc
Q 042210           75 YLDLLKSDVRRDN-YTFPFLFKGFTRD-------------------IAG--SLEKSCIVM-----RVFVQNALISTYCLC  127 (230)
Q Consensus        75 ~~~M~~~g~~p~~-~t~~~ll~~~~~~-------------------~~~--a~~~~~~~~-----~~~~~~~li~~y~~~  127 (230)
                      |++..+.  .|+. ..+..+-.+|...                   +..  +...+....     +...+..+-..|.+.
T Consensus       270 ~~~al~~--~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~  347 (472)
T 4g1t_A          270 LKKALEY--IPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALA  347 (472)
T ss_dssp             HHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHT
T ss_pred             HHHHHHh--CCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHh
Confidence            9886653  3443 3444443333211                   011  444444443     567788888999999


Q ss_pred             CCHHHHHHHHhhccC--CChhh----hHHHHH--Hhh---hcchhhhHHHHHHH--------------------h-hhcC
Q 042210          128 GEVDMARGIFYMSCE--DDDGL----HELIRI--KAV---DDDLHELFPEYLVQ--------------------M-LALP  175 (230)
Q Consensus       128 g~~~~A~~vf~~m~~--~~~~t----~n~li~--~~~---~~~~~~~~~~m~~~--------------------~-~~~p  175 (230)
                      |++++|...|++..+  |+...    +..+..  .+.   .++|++.+++..+-                    . ...|
T Consensus       348 ~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p  427 (472)
T 4g1t_A          348 DQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNG  427 (472)
T ss_dssp             TCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             ccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999987643  33221    111111  011   13455544443221                    1 1123


Q ss_pred             c-hhhhhhhhhcccccCCcccccccCCccCCccccccccccC
Q 042210          176 D-TFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHS  216 (230)
Q Consensus       176 ~-~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~  216 (230)
                      + ..++..|..         .+...|+.++|.+.++...+.|
T Consensus       428 ~~~~~~~~LG~---------~~~~~g~~~~A~~~y~kALe~~  460 (472)
T 4g1t_A          428 ADSEALHVLAF---------LQELNEKMQQADEDSERGLESG  460 (472)
T ss_dssp             -CTTHHHHHHH---------HHHHHHHCC-------------
T ss_pred             CCHHHHHHHHH---------HHHHcCCHHHHHHHHHHHHhcC
Confidence            3 334444333         5678899999999999888764

>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=96.59  E-value=0.14  Score=38.24  Aligned_cols=160  Identities=9%  Similarity=-0.093  Sum_probs=114.8

Q ss_pred             hHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC-CCChhhHHHHHHHHHhcC----ChhHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT-QPSVFLWNTMIKGYSRID----SHKNGVLMYL   76 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~~~----~~~~a~~~~~   76 (230)
                      +|.+.|....+.|   ++.. ..+=..|.  ..++.++|...|++.- .-+...+..+=..|.. +    ++++|...|+
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~--~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWV--SSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAE   77 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHh--cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHH
Confidence            5667777777664   5555 66777788  8999999999999876 4455666666666766 6    8999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhh----cCch--hhHHHhhhh---h----HhHHHHHHHHHHh----cCCHHHHHHHHhh
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLEKSCIVM---R----VFVQNALISTYCL----CGEVDMARGIFYM  139 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~~~~~~~---~----~~~~~~li~~y~~----~g~~~~A~~vf~~  139 (230)
                      +-.+.|   +...+..|=..|..    .++.  |...+....   +    ...+..|=..|..    .++.++|...|++
T Consensus        78 ~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~  154 (212)
T 3rjv_A           78 KAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKG  154 (212)
T ss_dssp             HHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            987765   33455556556655    5566  888887776   4    7888888888888    8899999999998


Q ss_pred             ccC--CChhhhHHHHHHhh----------hcchhhhHHHHHHHh
Q 042210          140 SCE--DDDGLHELIRIKAV----------DDDLHELFPEYLVQM  171 (230)
Q Consensus       140 m~~--~~~~t~n~li~~~~----------~~~~~~~~~~m~~~~  171 (230)
                      -.+  ++...+..|-..|.          .++|.+.+++-.+.|
T Consensus       155 A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          155 SSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            754  45555555544332          245666666666655

>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=96.57  E-value=0.029  Score=37.87  Aligned_cols=81  Identities=9%  Similarity=0.009  Sum_probs=46.0

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...|++..   +.+...|..+-.+|.+.|++++|...|++..+.  .|+                       
T Consensus        16 ~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~-----------------------   70 (126)
T 3upv_A           16 TKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK--DPN-----------------------   70 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCC-----------------------
Confidence            5555555555555433   233444555555555555555555555553332  121                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                         +...|..+-..|.+.|++++|...|++..
T Consensus        71 ---~~~~~~~lg~~~~~~~~~~~A~~~~~~al   99 (126)
T 3upv_A           71 ---FVRAYIRKATAQIAVKEYASALETLDAAR   99 (126)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ---cHHHHHHHHHHHHHHhCHHHHHHHHHHHH
Confidence               35556666777778888888888777654

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=96.57  E-value=0.099  Score=39.38  Aligned_cols=135  Identities=7%  Similarity=-0.078  Sum_probs=92.8

Q ss_pred             hhHHHHHHHHHHhcCCCCC----cH-HHHHHHHhhhccCChHHHHHHHHhcC--CCChh----hHHHHHHHHHh------
Q 042210            2 HQLKQIHSQTIKLGLLTKP----HC-PKQTRYLLLYEKGDLKYECKVFRKIT--QPSVF----LWNTMIKGYSR------   64 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~----~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~----~yn~li~~~~~------   64 (230)
                      ++|...|+.+.+..  |+.    .. ..+-.+|.  +.|++++|...|+...  .|+..    .|-.+-.++.+      
T Consensus        21 ~~A~~~~~~~~~~~--p~~~~~~~a~~~lg~~~~--~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~   96 (225)
T 2yhc_A           21 RQAITQLEALDNRY--PFGPYSQQVQLDLIYAYY--KNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSAL   96 (225)
T ss_dssp             HHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHH--hcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhh
Confidence            56888888888763  332    23 44556777  9999999999999875  34322    22223233332      


Q ss_pred             ------------cCChhHHHHHHHHHHhCCCCCCcc-cHH-----------------HHHHHhhhcCch--hhHHHhhhh
Q 042210           65 ------------IDSHKNGVLMYLDLLKSDVRRDNY-TFP-----------------FLFKGFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        65 ------------~~~~~~a~~~~~~M~~~g~~p~~~-t~~-----------------~ll~~~~~~~~~--a~~~~~~~~  112 (230)
                                  .|++++|...|++..+.  -|+.. .+.                 .+-..+.+.|++  |...++.+.
T Consensus        97 ~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l  174 (225)
T 2yhc_A           97 QGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGML  174 (225)
T ss_dssp             -----------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHH
Confidence                        47899999999998764  24433 221                 233456677887  777777776


Q ss_pred             -----h---HhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          113 -----R---VFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       113 -----~---~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                           +   ...+..+..+|.+.|+.++|.+.|+.+..
T Consensus       175 ~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~  212 (225)
T 2yhc_A          175 RDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA  212 (225)
T ss_dssp             HHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHh
Confidence                 2   35677889999999999999999997764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=96.56  E-value=0.03  Score=44.30  Aligned_cols=118  Identities=11%  Similarity=-0.061  Sum_probs=73.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-------CCC--hhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-Ccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-------QPS--VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR-DNY   88 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~~--~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p-~~~   88 (230)
                      ......|.  ..|++++|.+.|.+..       .|.  ..+|+.+-..|.+.|++++|...|++-...    |-.+ -..
T Consensus        41 ~~a~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  118 (292)
T 1qqe_A           41 VQAATIYR--LRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (292)
T ss_dssp             HHHHHHHH--HTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            33455667  7777777777776543       111  346777777777777888777777764331    1111 123


Q ss_pred             cHHHHHHHhhhc-Cch--hhHHHhhhh-----h------HhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           89 TFPFLFKGFTRD-IAG--SLEKSCIVM-----R------VFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        89 t~~~ll~~~~~~-~~~--a~~~~~~~~-----~------~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ++..+-..|... |++  |...+....     +      ..+++.+-..|.+.|++++|...|++..+
T Consensus       119 ~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  186 (292)
T 1qqe_A          119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIK  186 (292)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            566677777774 777  666665554     0      34566777777888888888887776553

>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=96.49  E-value=0.041  Score=38.88  Aligned_cols=103  Identities=8%  Similarity=-0.106  Sum_probs=78.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~   98 (230)
                      -.+-..|.  +.|++++|.+.|++..   +.+...|..+-..|.+.|++++|...|++..+.  .| +...|..+-..+.
T Consensus        35 ~~la~~y~--~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~  110 (150)
T 4ga2_A           35 FYFAKLYY--EAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAELLC  110 (150)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            34557788  9999999999999865   456778999999999999999999999997663  45 3457778888888


Q ss_pred             hcCch--hhH-HHhhhh-----hHhHHHHHHHHHHhcCC
Q 042210           99 RDIAG--SLE-KSCIVM-----RVFVQNALISTYCLCGE  129 (230)
Q Consensus        99 ~~~~~--a~~-~~~~~~-----~~~~~~~li~~y~~~g~  129 (230)
                      +.|+.  +.. .++...     ++.+|+..-..+.+.|+
T Consensus       111 ~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A          111 KNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             HcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            88887  443 345443     67777776666665553

>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=96.42  E-value=0.041  Score=35.91  Aligned_cols=87  Identities=5%  Similarity=-0.063  Sum_probs=64.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  ..|++++|...|+...   +.+...|..+-..+.+.|++++|...+++..+.. +.+...+..+-.++..
T Consensus         8 ~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~   84 (118)
T 1elw_A            8 KEKGNKAL--SVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEF   84 (118)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHH
Confidence            44556667  8899999999998864   4466778888888888899999999998876542 1245567777788888


Q ss_pred             cCch--hhHHHhhhh
Q 042210          100 DIAG--SLEKSCIVM  112 (230)
Q Consensus       100 ~~~~--a~~~~~~~~  112 (230)
                      .|++  |...+....
T Consensus        85 ~~~~~~A~~~~~~~~   99 (118)
T 1elw_A           85 LNRFEEAKRTYEEGL   99 (118)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHH
Confidence            8888  777776655

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.41  E-value=0.028  Score=44.69  Aligned_cols=117  Identities=5%  Similarity=-0.180  Sum_probs=77.0

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC--cccHHHHHHHhhhc
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD--NYTFPFLFKGFTRD  100 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~--~~t~~~ll~~~~~~  100 (230)
                      ....+.  ..|++++|.++|+.+.  .|+....-.+-..+.+.+++++|+..|+...... .|.  ...+..+=.++.+.
T Consensus       108 yA~~L~--~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~L  184 (282)
T 4f3v_A          108 FAACEA--AQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAANL  184 (282)
T ss_dssp             HHHHHH--HHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHH--HCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHHC
Confidence            445566  8999999999999987  4543344444457888999999999997443321 111  12344555667777


Q ss_pred             Cch--hhHHHhhhh--h------HhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC
Q 042210          101 IAG--SLEKSCIVM--R------VFVQNALISTYCLCGEVDMARGIFYMSCE--DD  144 (230)
Q Consensus       101 ~~~--a~~~~~~~~--~------~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~  144 (230)
                      |++  |...++...  +      .......-.++.+.|+.++|..+|+++..  |+
T Consensus       185 G~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          185 ALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             TCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             CCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            777  777777664  1      12334445566777888888888887764  55

>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=96.39  E-value=0.14  Score=49.46  Aligned_cols=142  Identities=10%  Similarity=0.002  Sum_probs=77.5

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG   96 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~   96 (230)
                      +++.. +.+.-+|+  +.+++++...+.   ..++...|..+=..|-..|++++|..+|...         ..|..+...
T Consensus      1165 ~e~~Idt~LafaYA--Kl~rleele~fI---~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~t 1230 (1630)
T 1xi4_A         1165 RESYVETELIFALA--KTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLAST 1230 (1630)
T ss_pred             ccccccHHHHHHHH--hhcCHHHHHHHH---hCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHH
Confidence            44444 55556666  666665444332   2334444444444555555555555555542         245555555


Q ss_pred             hhhcCch--hhHHHhhhh------------------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--
Q 042210           97 FTRDIAG--SLEKSCIVM------------------------------RVFVQNALISTYCLCGEVDMARGIFYMSCE--  142 (230)
Q Consensus        97 ~~~~~~~--a~~~~~~~~------------------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--  142 (230)
                      +.+.|++  |.+.++...                              +...+..++..|.+.|.+++|.++++.--.  
T Consensus      1231 LvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le 1310 (1630)
T 1xi4_A         1231 LVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE 1310 (1630)
T ss_pred             HHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC
Confidence            5555555  333333332                              444566788889999999999999976544  


Q ss_pred             -CChhhhHHHHHHhh---hcchhhhHHHHHHHhhh
Q 042210          143 -DDDGLHELIRIKAV---DDDLHELFPEYLVQMLA  173 (230)
Q Consensus       143 -~~~~t~n~li~~~~---~~~~~~~~~~m~~~~~~  173 (230)
                       .....|+-+-..+.   -++..+-.+-....+++
T Consensus      1311 raH~gmftELaiLyaKy~peklmEhlk~f~~rini 1345 (1630)
T 1xi4_A         1311 RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNI 1345 (1630)
T ss_pred             hhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhccc
Confidence             23345555544443   34444444444456643

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.36  E-value=0.077  Score=41.74  Aligned_cols=116  Identities=9%  Similarity=-0.073  Sum_probs=82.6

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC--CCC-h------hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-CC----ccc
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT--QPS-V------FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVR-RD----NYT   89 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~--~~~-~------~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~-p~----~~t   89 (230)
                      ..+..+.  ..|+.++|.+.+.+..  .+. .      ..+..+-..+...|++++|...|++....... .+    ..+
T Consensus        80 ~~~~~~~--~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           80 DQVIMLC--KQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHH--HTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHH--HhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            3455667  8899999999887643  121 1      12334445567778999999999987653221 12    336


Q ss_pred             HHHHHHHhhhcCch--hhHHHhhhh------------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           90 FPFLFKGFTRDIAG--SLEKSCIVM------------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        90 ~~~ll~~~~~~~~~--a~~~~~~~~------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      |+.+-..|...|++  |...+....            ...+++.+-..|.+.|++++|...|++..
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal  223 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAI  223 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHH
Confidence            77788888889988  777776654            22588888999999999999999998754

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=96.34  E-value=0.045  Score=36.83  Aligned_cols=85  Identities=11%  Similarity=-0.012  Sum_probs=48.7

Q ss_pred             ccCChHHHHHHHHhcC--CCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhH
Q 042210           33 EKGDLKYECKVFRKIT--QPSV----FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~~----~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~  106 (230)
                      +.|++++|...|+...  .|+.    ..+..+-.++.+.|++++|...|++..+..  |+...                 
T Consensus        14 ~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~-----------------   74 (129)
T 2xev_A           14 KNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDK-----------------   74 (129)
T ss_dssp             HTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTT-----------------
T ss_pred             HhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcc-----------------
Confidence            5566666666666543  2322    244444555555666666666665544321  22100                 


Q ss_pred             HHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          107 KSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       107 ~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                            ....+..+-..|.+.|++++|...|++...
T Consensus        75 ------~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           75 ------AAGGLLKLGLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             ------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                  134455566778888889999888887764

>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=96.34  E-value=0.02  Score=42.29  Aligned_cols=114  Identities=9%  Similarity=-0.077  Sum_probs=81.7

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCCh----------------hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSV----------------FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR   85 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~----------------~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p   85 (230)
                      +-..+.  +.|++++|...|++..   +.+.                ..|..+-.+|.+.|++++|...+++..+.. +.
T Consensus        44 ~g~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~  120 (198)
T 2fbn_A           44 EGNEFF--KKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KN  120 (198)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TT
T ss_pred             HHHHHH--HcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cc
Confidence            334566  8999999999998864   2222                678888888999999999999999976642 22


Q ss_pred             CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHH-HHHhhcc
Q 042210           86 DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMAR-GIFYMSC  141 (230)
Q Consensus        86 ~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~-~vf~~m~  141 (230)
                      +...|..+-.++...|++  |...+....     +...+..+-..+.+.++.+++. ..|..|-
T Consensus       121 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          121 NVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHC----------
T ss_pred             cHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            456777788889999998  888887776     6777888888888877777766 4444443

>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=96.32  E-value=0.028  Score=38.31  Aligned_cols=87  Identities=8%  Similarity=0.000  Sum_probs=69.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|++++|...|+...   +.+...|..+-.++...|++++|...|++..+.. +-+...|..+-.++..
T Consensus        13 ~~~g~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~   89 (137)
T 3q49_B           13 KEQGNRLF--VGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQLE   89 (137)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHH
Confidence            55556777  9999999999999864   4456788889899999999999999999976643 1245577888888889


Q ss_pred             cCch--hhHHHhhhh
Q 042210          100 DIAG--SLEKSCIVM  112 (230)
Q Consensus       100 ~~~~--a~~~~~~~~  112 (230)
                      .|++  |...+....
T Consensus        90 ~~~~~~A~~~~~~a~  104 (137)
T 3q49_B           90 MESYDEAIANLQRAY  104 (137)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHH
Confidence            9998  777777665

>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=96.32  E-value=0.017  Score=45.56  Aligned_cols=86  Identities=7%  Similarity=-0.025  Sum_probs=59.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~   98 (230)
                      ..+-..+.  +.|++++|...|++..   +.+...|..+-.+|.+.|++++|...+++..+.  .| +...+..+-.++.
T Consensus         8 ~~~g~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            8 KEQGNRLF--VGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            34445666  8888888888888764   335667788888888888888888888876543  34 3345556666666


Q ss_pred             hcCch--hhHHHhhhh
Q 042210           99 RDIAG--SLEKSCIVM  112 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~  112 (230)
                      ..|++  |...+....
T Consensus        84 ~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           84 EMESYDEAIANLQRAY   99 (281)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH
Confidence            67776  666665554

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.28  E-value=0.0034  Score=42.37  Aligned_cols=30  Identities=3%  Similarity=-0.062  Sum_probs=22.0

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +...+..+-..|.+.|++++|...|++...
T Consensus        60 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   89 (117)
T 3k9i_A           60 HQALRVFYAMVLYNLGRYEQGVELLLKIIA   89 (117)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455666677778888888888888876543

>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=96.26  E-value=0.062  Score=43.52  Aligned_cols=105  Identities=10%  Similarity=-0.015  Sum_probs=66.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~  131 (230)
                      ...|..+=..|.+.|++++|...|++-.+..  |+...+         ......++-.  .....|..+-..|.+.|+++
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~---------~~~~~~~~~~--~~~~~~~nla~~~~~~g~~~  213 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSF---------SNEEAQKAQA--LRLASHLNLAMCHLKLQAFS  213 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCC---------CSHHHHHHHH--HHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccC---------ChHHHHHHHH--HHHHHHHHHHHHHHHcCCHH
Confidence            4567778888889999999999999865532  221110         0000111000  04677888899999999999


Q ss_pred             HHHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHH
Q 042210          132 MARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLV  169 (230)
Q Consensus       132 ~A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~  169 (230)
                      +|...|++..+  | +...|..+-.++..    ++|.+.|++..+
T Consensus       214 ~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  258 (336)
T 1p5q_A          214 AAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  258 (336)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999998765  4 44555555444432    455555555444

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=96.24  E-value=0.042  Score=37.64  Aligned_cols=80  Identities=9%  Similarity=-0.000  Sum_probs=63.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.|+...+.  .|+.. . ..+-.+|.  +.|++++|...|++..   +.+...|..+-.+|...|++++|...|+
T Consensus        30 ~~A~~~~~~al~~--~p~~~~~~~~~~~~~~--~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~  105 (126)
T 4gco_A           30 PTAMRHYNEAVKR--DPENAILYSNRAACLT--KLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLVAMREWSKAQRAYE  105 (126)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHhhHHH--hhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            5678888887766  35544 3 66778888  9999999999999865   5567789999999999999999999999


Q ss_pred             HHHhCCCCCCc
Q 042210           77 DLLKSDVRRDN   87 (230)
Q Consensus        77 ~M~~~g~~p~~   87 (230)
                      +-.+  +.|+.
T Consensus       106 ~al~--l~P~~  114 (126)
T 4gco_A          106 DALQ--VDPSN  114 (126)
T ss_dssp             HHHH--HCTTC
T ss_pred             HHHH--HCcCC
Confidence            9765  34654

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.23  E-value=0.04  Score=38.31  Aligned_cols=85  Identities=6%  Similarity=-0.156  Sum_probs=67.6

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcC
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDI  101 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~  101 (230)
                      +-..+.  +.|++++|...|+...   +.+...|..+-.+|.+.|++++|...|++..... +-+...|..+-.++...|
T Consensus        24 ~a~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g  100 (142)
T 2xcb_A           24 LGFNQY--QAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLG  100 (142)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHH--HHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcC
Confidence            445566  9999999999999865   4466788888889999999999999999976643 224456777888899999


Q ss_pred             ch--hhHHHhhhh
Q 042210          102 AG--SLEKSCIVM  112 (230)
Q Consensus       102 ~~--a~~~~~~~~  112 (230)
                      ++  |...++...
T Consensus       101 ~~~~A~~~~~~al  113 (142)
T 2xcb_A          101 DLDGAESGFYSAR  113 (142)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH
Confidence            98  887777665

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=96.20  E-value=0.025  Score=40.47  Aligned_cols=86  Identities=14%  Similarity=-0.002  Sum_probs=70.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFT   98 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~   98 (230)
                      ..+-..+.  +.|++++|...|+...   +.+...|..+=.+|.+.|++++|...|++..+..  | +...|..+=.++.
T Consensus        40 ~~lg~~~~--~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           40 YSYAYDFY--NKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KNDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SSCCHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHH
Confidence            33445566  9999999999999876   4567789999999999999999999999976632  3 4567888888999


Q ss_pred             hcCch--hhHHHhhhh
Q 042210           99 RDIAG--SLEKSCIVM  112 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~  112 (230)
                      +.|+.  |...++...
T Consensus       116 ~lg~~~eA~~~~~~al  131 (151)
T 3gyz_A          116 RLKAPLKAKECFELVI  131 (151)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH
Confidence            99999  888887766

>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=96.20  E-value=0.033  Score=49.86  Aligned_cols=135  Identities=11%  Similarity=-0.097  Sum_probs=103.3

Q ss_pred             ccCChHHHHHHHHhcC-----------CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhc
Q 042210           33 EKGDLKYECKVFRKIT-----------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRD  100 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~-----------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~  100 (230)
                      ..|++++|.+.+++..           ..+...|..+-..|.+.|++++|...|++..+.  .| +...|..+=.++.+.
T Consensus       403 ~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          403 VLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--VGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--CcchHHHHHHHHHHHHHc
Confidence            8999999999998764           445667888888999999999999999997663  24 445677777888899


Q ss_pred             Cch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhhcchhhhHHHHHHH
Q 042210          101 IAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVDDDLHELFPEYLVQ  170 (230)
Q Consensus       101 ~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~~~~~~~~~~m~~~  170 (230)
                      |++  |...|+...     +...|..+-..|.+.|++++ .+.|++..+  | +...|..+-..+...+..+...+.++.
T Consensus       481 g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~  559 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDE  559 (681)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence            999  888888876     77888999999999999999 999988764  4 455676665555554434443333333

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.16  E-value=0.0095  Score=51.03  Aligned_cols=104  Identities=7%  Similarity=-0.119  Sum_probs=78.7

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhH
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLE  106 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~  106 (230)
                      +.|++++|.+.|++..   +.+...|..+-.+|.+.|++++|...|++-.+.  .| +...|..+-.++.+.|++  |.+
T Consensus        18 ~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~eA~~   95 (477)
T 1wao_1           18 KAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFRAALR   95 (477)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            7889999999998764   445778888989999999999999999987765  33 455777888888889998  888


Q ss_pred             HHhhhh-----hHhHHHHHHHH--HHhcCCHHHHHHHHh
Q 042210          107 KSCIVM-----RVFVQNALIST--YCLCGEVDMARGIFY  138 (230)
Q Consensus       107 ~~~~~~-----~~~~~~~li~~--y~~~g~~~~A~~vf~  138 (230)
                      .++...     +...+..+-.+  +.+.|++++|.+.++
T Consensus        96 ~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           96 DYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            887776     44555555555  888899999999998

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.16  E-value=0.15  Score=40.06  Aligned_cols=112  Identities=16%  Similarity=0.111  Sum_probs=84.8

Q ss_pred             HHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhC-CCCCC-----cccHH
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS-DVRRD-----NYTFP   91 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~-g~~p~-----~~t~~   91 (230)
                      ..+.  ..|+.++|...+++..     ..+    ..+|+.+-..|...|++++|...|++.... ...|+     ..+|.
T Consensus       123 ~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~  200 (293)
T 2qfc_A          123 AYVL--KKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRY  200 (293)
T ss_dssp             HHHH--TSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHh--cCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHH
Confidence            4455  8889999999988753     122    347888889999999999999999986531 11222     24788


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh----h-------HhHHHHHHHHHHhcCCHHHH-HHHHhhc
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM----R-------VFVQNALISTYCLCGEVDMA-RGIFYMS  140 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~----~-------~~~~~~li~~y~~~g~~~~A-~~vf~~m  140 (230)
                      .+-..|.+.|++  |...+....    +       ..+|..+-..|.+.|+.++| ...|++.
T Consensus       201 nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          201 NHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            888899999999  877777765    2       56788888899999999999 6666643

>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=96.15  E-value=0.044  Score=36.54  Aligned_cols=85  Identities=14%  Similarity=0.153  Sum_probs=63.6

Q ss_pred             hhHHHHHHHHHHhcCCCC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC------CCC----hhhHHHHHHHHHhcCChh
Q 042210            2 HQLKQIHSQTIKLGLLTK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT------QPS----VFLWNTMIKGYSRIDSHK   69 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~------~~~----~~~yn~li~~~~~~~~~~   69 (230)
                      ++|...++...+..  |+ ... ..+-..+.  +.|++++|...|+...      .++    ...|..+-..|.+.|+++
T Consensus        21 ~~A~~~~~~a~~~~--~~~~~~~~~la~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~   96 (131)
T 1elr_A           21 DTALKHYDKAKELD--PTNMTYITNQAAVYF--EKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYK   96 (131)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHhcC--CccHHHHHHHHHHHH--HhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHH
Confidence            46777888777664  43 344 77778888  9999999999998865      122    667888888999999999


Q ss_pred             HHHHHHHHHHhCCCCCCcccHHH
Q 042210           70 NGVLMYLDLLKSDVRRDNYTFPF   92 (230)
Q Consensus        70 ~a~~~~~~M~~~g~~p~~~t~~~   92 (230)
                      +|...|++..+.  .|+......
T Consensus        97 ~A~~~~~~~~~~--~~~~~~~~~  117 (131)
T 1elr_A           97 DAIHFYNKSLAE--HRTPDVLKK  117 (131)
T ss_dssp             HHHHHHHHHHHH--CCCHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCHHHHHH
Confidence            999999998774  345433333

>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=96.09  E-value=0.14  Score=40.12  Aligned_cols=132  Identities=8%  Similarity=-0.066  Sum_probs=82.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+.  .|+.. . ..+-..|.  +.|++++|...+++..   +.+...|..+-.+|.+.|++++|...|+
T Consensus        21 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~   96 (281)
T 2c2l_A           21 PEAAACYGRAITR--NPLVAVYYTNRALCYL--KMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQ   96 (281)
T ss_dssp             HHHHHHHHHHHHH--CSCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHH--HhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            4677788877765  45443 4 77778888  9999999999999876   3456788888899999999999999998


Q ss_pred             HHHhCCCCCC-cccHHHHHHHh---hhcCchhhHHHh-hhh-hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRRD-NYTFPFLFKGF---TRDIAGSLEKSC-IVM-RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p~-~~t~~~ll~~~---~~~~~~a~~~~~-~~~-~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +..+.+  |+ ...+...+...   .+...+ ...-. ... +......+-. + ..|+.++|.+.+++..+
T Consensus        97 ~al~l~--p~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~l~~-l-~~~~~~~A~~~~~~al~  163 (281)
T 2c2l_A           97 RAYSLA--KEQRLNFGDDIPSALRIAKKKRW-NSIEERRIHQESELHSYLTR-L-IAAERERELEECQRNHE  163 (281)
T ss_dssp             HHHHHH--HHTTCCCCSHHHHHHHHHHHHHH-HHHHHTCCCCCCHHHHHHHH-H-HHHHHHHHHTTTSGGGT
T ss_pred             HHHHhC--ccchhhHHHHHHHHHHHHHHHHH-HHHHHHHHhhhHHHHHHHHH-H-HHHHHHHHHHHHHhhhc
Confidence            865421  11 01111122211   111112 11001 111 4444444422 2 36899999998887765

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.03  E-value=0.08  Score=36.24  Aligned_cols=86  Identities=7%  Similarity=-0.027  Sum_probs=67.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFK   95 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~   95 (230)
                      ..+-..+.  +.|++++|...|++..  .|+    ...|..+-..|.+.|++++|...|++..+.  .| +...+..+-.
T Consensus        32 ~~~a~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~  107 (148)
T 2dba_A           32 RKEGNELF--KCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK--DGGDVKALYRRSQ  107 (148)
T ss_dssp             HHHHHHHH--TTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TSCCHHHHHHHHH
T ss_pred             HHHHHHHH--HhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CccCHHHHHHHHH
Confidence            44556677  9999999999999865  555    567888888999999999999999987664  33 4556777778


Q ss_pred             HhhhcCch--hhHHHhhhh
Q 042210           96 GFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        96 ~~~~~~~~--a~~~~~~~~  112 (230)
                      ++...|+.  |...+....
T Consensus       108 ~~~~~~~~~~A~~~~~~al  126 (148)
T 2dba_A          108 ALEKLGRLDQAVLDLQRCV  126 (148)
T ss_dssp             HHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            88888888  777777665

>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=96.03  E-value=0.072  Score=38.21  Aligned_cols=105  Identities=15%  Similarity=0.100  Sum_probs=79.2

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHH-HHhcCCh--hHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKG-YSRIDSH--KNGVL   73 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~-~~~~~~~--~~a~~   73 (230)
                      ++|...++...+..  |+. .. ..+-..|.  ..|++++|...|++..   +.+...|..+-.. +...|++  ++|..
T Consensus        27 ~~A~~~~~~al~~~--p~~~~~~~~lg~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~  102 (177)
T 2e2e_A           27 EAQLQALQDKIRAN--PQNSEQWALLGEYYL--WQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRA  102 (177)
T ss_dssp             CCCCHHHHHHHHHC--CSCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHH
T ss_pred             HHHHHHHHHHHHhC--CCcHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHH
Confidence            45666676666553  543 34 66778888  9999999999999875   4566677777777 7788998  99999


Q ss_pred             HHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh
Q 042210           74 MYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        74 ~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~  112 (230)
                      .|++..+..  | +...+..+-..+...|++  |...+....
T Consensus       103 ~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al  142 (177)
T 2e2e_A          103 MIDKALALD--SNEITALMLLASDAFMQANYAQAIELWQKVM  142 (177)
T ss_dssp             HHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhC--CCcHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            999977642  4 345677788889999998  888887766

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.02  E-value=0.0055  Score=41.31  Aligned_cols=94  Identities=12%  Similarity=0.075  Sum_probs=59.3

Q ss_pred             hhHHHHHHHHHHhcCC-CC-CcH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLL-TK-PHC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~-~~-~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|...++...+.+.. |+ ... ..+-..|.  +.|++++|...|++..   +.+...|..+-.++.+.|++++|...|
T Consensus         7 ~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~   84 (117)
T 3k9i_A            7 AQAVPYYEKAIASGLQGKDLAECYLGLGSTFR--TLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVELL   84 (117)
T ss_dssp             CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4566777776664321 32 223 55566677  8888888888888765   334567777788888888888888888


Q ss_pred             HHHHhC-CCCCCcccHHHHHHHh
Q 042210           76 LDLLKS-DVRRDNYTFPFLFKGF   97 (230)
Q Consensus        76 ~~M~~~-g~~p~~~t~~~ll~~~   97 (230)
                      ++.... .-.|+...|...+..+
T Consensus        85 ~~al~~~p~~~~~~~~~~ai~~~  107 (117)
T 3k9i_A           85 LKIIAETSDDETIQSYKQAILFY  107 (117)
T ss_dssp             HHHHHHHCCCHHHHHTHHHHHHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHH
Confidence            875443 2223333343344433

>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=96.00  E-value=0.059  Score=48.29  Aligned_cols=151  Identities=11%  Similarity=-0.081  Sum_probs=104.8

Q ss_pred             hhHHHHHHHHHHhcC---------CCC------------CcH-HHHHHHHhhhccCChHHHHHHHHhcC-C-C--ChhhH
Q 042210            2 HQLKQIHSQTIKLGL---------LTK------------PHC-PKQTRYLLLYEKGDLKYECKVFRKIT-Q-P--SVFLW   55 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~---------~~~------------~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-~-~--~~~~y   55 (230)
                      ++|+++++.+.+...         .|+            ..+ ...+....  +.|.++.|+.+|.... . |  ....|
T Consensus       395 e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~er--R~~~l~~AR~vf~~A~~~~~~~~~~ly  472 (679)
T 4e6h_A          395 PEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMK--RIQGLAASRKIFGKCRRLKKLVTPDIY  472 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHH--HHHCHHHHHHHHHHHHHTGGGSCTHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHhcCCCChHHH
Confidence            568888888876421         142            123 55556666  8899999999999875 2 2  12223


Q ss_pred             --HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh--------hHhHHHHHHHH
Q 042210           56 --NTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM--------RVFVQNALIST  123 (230)
Q Consensus        56 --n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~--------~~~~~~~li~~  123 (230)
                        .+.|.-. ..++.+.|..+|+...+. ++-+..-|...++.....|+.  |+.+|+...        ...+|...+..
T Consensus       473 i~~A~lE~~-~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~f  550 (679)
T 4e6h_A          473 LENAYIEYH-ISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFF  550 (679)
T ss_dssp             HHHHHHHHT-TTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence              3333222 135689999999996654 222344456777777778888  999999877        35789999999


Q ss_pred             HHhcCCHHHHHHHHhhccC--CChhhhHHHHHHhh
Q 042210          124 YCLCGEVDMARGIFYMSCE--DDDGLHELIRIKAV  156 (230)
Q Consensus       124 y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~~~~  156 (230)
                      -.+.|+.+.+.+|.+++.+  |+......++.-|.
T Consensus       551 E~~~G~~~~~~~v~~R~~~~~P~~~~~~~f~~ry~  585 (679)
T 4e6h_A          551 ESKVGSLNSVRTLEKRFFEKFPEVNKLEEFTNKYK  585 (679)
T ss_dssp             HHHTCCSHHHHHHHHHHHHHSTTCCHHHHHHHHTC
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHhc
Confidence            9999999999999999986  77665555665554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=95.99  E-value=0.1  Score=42.19  Aligned_cols=137  Identities=7%  Similarity=-0.080  Sum_probs=91.3

Q ss_pred             hhHHHHHHHHHHhcCCCCC-c----H-HHHHHHHhhhccCChHHHHHHHHhcC-----CCCh----hhHHHHHHHHHhcC
Q 042210            2 HQLKQIHSQTIKLGLLTKP-H----C-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSV----FLWNTMIKGYSRID   66 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~----~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~----~~yn~li~~~~~~~   66 (230)
                      ++|...++...... .++. .    . +.+-..+.  ..|++++|...+++..     ..+.    ..++.+-..+...|
T Consensus        31 ~~A~~~~~~al~~~-~~~~~~~~~~~~~~l~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G  107 (373)
T 1hz4_A           31 DEAERLAKLALEEL-PPGWFYSRIVATSVLGEVLH--CKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQG  107 (373)
T ss_dssp             HHHHHHHHHHHHTC-CTTCHHHHHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcC-CCCchhHHHHHHHHHHHHHH--hcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCC
Confidence            34566666655543 2221 1    2 33445666  8899999999988754     2232    23556666778889


Q ss_pred             ChhHHHHHHHHHHhC----CCC--CC-cccHHHHHHHhhhcCch--hhHHHhhhh----------hHhHHHHHHHHHHhc
Q 042210           67 SHKNGVLMYLDLLKS----DVR--RD-NYTFPFLFKGFTRDIAG--SLEKSCIVM----------RVFVQNALISTYCLC  127 (230)
Q Consensus        67 ~~~~a~~~~~~M~~~----g~~--p~-~~t~~~ll~~~~~~~~~--a~~~~~~~~----------~~~~~~~li~~y~~~  127 (230)
                      ++++|...+++....    +-.  |. ...+..+-..+...|++  |...+....          ....+..+-..+...
T Consensus       108 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~  187 (373)
T 1hz4_A          108 FLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLAR  187 (373)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHc
Confidence            999999999886542    222  32 23455566778888988  777776654          134577778888999


Q ss_pred             CCHHHHHHHHhhcc
Q 042210          128 GEVDMARGIFYMSC  141 (230)
Q Consensus       128 g~~~~A~~vf~~m~  141 (230)
                      |++++|...+++..
T Consensus       188 g~~~~A~~~l~~a~  201 (373)
T 1hz4_A          188 GDLDNARSQLNRLE  201 (373)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999999988764

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=95.97  E-value=0.043  Score=37.27  Aligned_cols=30  Identities=13%  Similarity=-0.063  Sum_probs=21.1

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +...+..+-..|.+.|++++|...|++..+
T Consensus        84 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           84 DIAVHAALAVSHTNEHNANAALASLRAWLL  113 (121)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455666677777777888888887776554

>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=95.94  E-value=0.04  Score=38.89  Aligned_cols=87  Identities=6%  Similarity=-0.116  Sum_probs=69.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|++++|...|+...   +.+...|..+-.+|.+.|++++|...|++..... +-+...|..+-.++..
T Consensus        25 ~~~g~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~  101 (148)
T 2vgx_A           25 YSLAFNQY--QSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQ  101 (148)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHH
Confidence            44556677  9999999999999865   4567788888889999999999999999976642 1245577778888999


Q ss_pred             cCch--hhHHHhhhh
Q 042210          100 DIAG--SLEKSCIVM  112 (230)
Q Consensus       100 ~~~~--a~~~~~~~~  112 (230)
                      .|++  |...+....
T Consensus       102 ~g~~~~A~~~~~~al  116 (148)
T 2vgx_A          102 XGELAEAESGLFLAQ  116 (148)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH
Confidence            9998  777777665

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=95.94  E-value=0.1  Score=37.06  Aligned_cols=87  Identities=7%  Similarity=-0.057  Sum_probs=69.7

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR   99 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~   99 (230)
                      ..+-..+.  +.|++++|...|++..   ..+...|..+-.+|.+.|++++|...|++..+.. +-+...|..+-.++.+
T Consensus        15 ~~~g~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~   91 (164)
T 3sz7_A           15 KSEGNAAM--ARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLARFD   91 (164)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            34446667  9999999999999865   4467788999999999999999999999976643 1245678888888999


Q ss_pred             cCch--hhHHHhhhh
Q 042210          100 DIAG--SLEKSCIVM  112 (230)
Q Consensus       100 ~~~~--a~~~~~~~~  112 (230)
                      .|++  |...+....
T Consensus        92 ~g~~~~A~~~~~~al  106 (164)
T 3sz7_A           92 MADYKGAKEAYEKGI  106 (164)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH
Confidence            9998  777777666

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=95.91  E-value=0.015  Score=50.01  Aligned_cols=86  Identities=10%  Similarity=0.065  Sum_probs=53.3

Q ss_pred             ccCChHHHHHHHHhcC-------CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhC---CCCCCcccHHHHHHHhh
Q 042210           33 EKGDLKYECKVFRKIT-------QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS---DVRRDNYTFPFLFKGFT   98 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~-------~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~---g~~p~~~t~~~ll~~~~   98 (230)
                      ..|++++|..++++..       -++    ..++|.|...|...|++++|..++++...-   -..|+.-.         
T Consensus       321 ~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~---------  391 (490)
T 3n71_A          321 SEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQ---------  391 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHH---------
T ss_pred             hCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHH---------
Confidence            6788888888776543       222    246788888888888888888888774321   11111100         


Q ss_pred             hcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           99 RDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        99 ~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                                    ...+++.|-..|...|++++|..++++-.
T Consensus       392 --------------~a~~l~nLa~~~~~~G~~~eA~~~~~~Al  420 (490)
T 3n71_A          392 --------------LGMAVMRAGLTNWHAGHIEVGHGMICKAY  420 (490)
T ss_dssp             --------------HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                          34556666667777777777776666443

>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=95.91  E-value=0.071  Score=39.96  Aligned_cols=167  Identities=7%  Similarity=-0.091  Sum_probs=108.7

Q ss_pred             HHHHHHhcC-CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcC----ch--hhHHHhhhh
Q 042210           40 ECKVFRKIT-QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDI----AG--SLEKSCIVM  112 (230)
Q Consensus        40 a~~~~~~m~-~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~----~~--a~~~~~~~~  112 (230)
                      |...|.+.- .-+...+..+=..|...+++++|...|++-.+.|   +...+..|=..|.. +    +.  |...+....
T Consensus         5 A~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~   80 (212)
T 3rjv_A            5 PGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAV   80 (212)
T ss_dssp             TTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHH
Confidence            444444433 4566677777778888999999999999987776   34456666666766 5    55  777777776


Q ss_pred             ---hHhHHHHHHHHHHh----cCCHHHHHHHHhhccCCC-----hhhhHHHHHHhhh--------cchhhhHHHHHHHhh
Q 042210          113 ---RVFVQNALISTYCL----CGEVDMARGIFYMSCEDD-----DGLHELIRIKAVD--------DDLHELFPEYLVQML  172 (230)
Q Consensus       113 ---~~~~~~~li~~y~~----~g~~~~A~~vf~~m~~~~-----~~t~n~li~~~~~--------~~~~~~~~~m~~~~~  172 (230)
                         +...+..|-..|..    .+++++|.+.|++-.+.+     ...++.|-..|..        +++++.|++-.+.+ 
T Consensus        81 ~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~-  159 (212)
T 3rjv_A           81 EAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS-  159 (212)
T ss_dssp             HTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS-
T ss_pred             HCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC-
Confidence               77778888788876    889999999999988733     4666666444433        35666666655442 


Q ss_pred             hcCchhhhhhhhhcccccCCccccc--ccCCccCCccccccccccCCC
Q 042210          173 ALPDTFMGEGLEVIPKSQAPREETP--RVGNLEEGTPQEGRPHEHSQD  218 (230)
Q Consensus       173 ~~p~~~t~~~l~~~~~~~~~~~a~~--~~g~~~~a~~i~~~~~~~~~~  218 (230)
                      -.|+  ....|..+-     ..+..  -..+.++|..++....+.|..
T Consensus       160 ~~~~--a~~~Lg~~y-----~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          160 RTGY--AEYWAGMMF-----QQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             CTTH--HHHHHHHHH-----HHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             CCHH--HHHHHHHHH-----HcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            1222  222222210     00111  123788899888888877644

>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=95.89  E-value=0.32  Score=38.50  Aligned_cols=164  Identities=5%  Similarity=-0.127  Sum_probs=107.8

Q ss_pred             hhHHHHHHHHHHhc------CCCCCc----H-HHHHHHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLG------LLTKPH----C-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKG   61 (230)
Q Consensus         2 ~~a~~~~~~m~~~g------~~~~~~----~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~   61 (230)
                      ++|.+++++..+..      +.++..    . ......|.  ..|++++|...|.+..     ..+    ...|+.+-..
T Consensus         8 ~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~   85 (307)
T 2ifu_A            8 SEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFK--NAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMM   85 (307)
T ss_dssp             HHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHH--HcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            35666676665431      134422    2 34456677  8899999999887754     122    3468888888


Q ss_pred             HHhcCChhHHHHHHHHHHhC----CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHH
Q 042210           62 YSRIDSHKNGVLMYLDLLKS----DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALIST  123 (230)
Q Consensus        62 ~~~~~~~~~a~~~~~~M~~~----g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~  123 (230)
                      |.+.|++++|...|++-...    |-.+ -..++..+-..|.+ |++  |...+....           ...+++.+-..
T Consensus        86 ~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~  164 (307)
T 2ifu_A           86 LKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRL  164 (307)
T ss_dssp             HHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHH
Confidence            99999999999999875432    2111 13466677777877 888  777776665           14678888899


Q ss_pred             HHhcCCHHHHHHHHhhccC-----CC----hhhhHHHHHHhh----hcchhhhHHHHH
Q 042210          124 YCLCGEVDMARGIFYMSCE-----DD----DGLHELIRIKAV----DDDLHELFPEYL  168 (230)
Q Consensus       124 y~~~g~~~~A~~vf~~m~~-----~~----~~t~n~li~~~~----~~~~~~~~~~m~  168 (230)
                      |.+.|++++|...|++..+     ++    ..+|..+...+.    .++|.+.|++..
T Consensus       165 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          165 LVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            9999999999999997764     22    113333333333    346666666655

>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=95.85  E-value=0.041  Score=43.80  Aligned_cols=116  Identities=9%  Similarity=-0.085  Sum_probs=85.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-------CCC--hhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-Ccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-------QPS--VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR-DNY   88 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-------~~~--~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p-~~~   88 (230)
                      +.+-..|.  +.|++++|...|++..       .+.  ..+|+.+-..|.. |++++|...|++-...    |-.+ ...
T Consensus        80 ~~lg~~~~--~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~  156 (307)
T 2ifu_A           80 EQAGMMLK--DLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAE  156 (307)
T ss_dssp             HHHHHHHH--HTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHH--hCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHH
Confidence            55667788  8899999998887643       121  2467777788888 9999999999885442    2111 134


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh-----h------HhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM-----R------VFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~-----~------~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ++..+-..+.+.|++  |...+....     +      ...+..+...|...|++++|...|++..
T Consensus       157 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          157 LIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            677788889999999  888777776     1      2356667777888899999999999765

>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=95.74  E-value=0.071  Score=45.20  Aligned_cols=55  Identities=11%  Similarity=0.111  Sum_probs=41.4

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC--CC-C---------------hhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT--QP-S---------------VFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~---------------~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      .+=..+.  +.|++++|...|++..  .| +               ...|+.+-.+|.+.|++++|...|++..+
T Consensus       273 ~~G~~~~--~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  345 (457)
T 1kt0_A          273 EKGTVYF--KGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALG  345 (457)
T ss_dssp             HHHHHHH--HTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHH--hCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            3445566  8999999999998765  22 2               46777777888888888888888887655

>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=95.64  E-value=0.074  Score=35.79  Aligned_cols=76  Identities=7%  Similarity=-0.078  Sum_probs=60.9

Q ss_pred             hhHHHHHHHHHHhcCCCCC-cH-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKP-HC-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~-~~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+..  |+. .. ..+-.+|.  +.|++++|...|++..   +.+...|..+-.++...|++++|...|+
T Consensus        21 ~~A~~~~~~al~~~--p~~~~~~~~~a~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~   96 (126)
T 3upv_A           21 PNAVKAYTEMIKRA--PEDARGYSNRAAALA--KLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLD   96 (126)
T ss_dssp             HHHHHHHHHHHHHC--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC--CCChHHHHHHHHHHH--HhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhCHHHHHHHHH
Confidence            46778888777663  543 34 77778888  9999999999999865   4456788888899999999999999999


Q ss_pred             HHHhC
Q 042210           77 DLLKS   81 (230)
Q Consensus        77 ~M~~~   81 (230)
                      +..+.
T Consensus        97 ~al~~  101 (126)
T 3upv_A           97 AARTK  101 (126)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            87653

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=95.64  E-value=0.12  Score=42.05  Aligned_cols=145  Identities=6%  Similarity=-0.144  Sum_probs=100.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCCCccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRRDNYT   89 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p~~~t   89 (230)
                      +.+-..|.  ..|++++|.+.|++..     .++    ..+++.+=..|...|++++|...|++-...    +-+....+
T Consensus       186 ~~lg~~y~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  263 (378)
T 3q15_A          186 FVIAGNYD--DFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKV  263 (378)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHH
T ss_pred             HHHHHHHH--HhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHH
Confidence            45667777  9999999999998754     222    246777888888999999999999987651    22223567


Q ss_pred             HHHHHHHhhhcCch--hhHHHhhhh----------hHhHHHHHHHHHHhcCC---HHHHHHHHhhccC-CChh-hhHHHH
Q 042210           90 FPFLFKGFTRDIAG--SLEKSCIVM----------RVFVQNALISTYCLCGE---VDMARGIFYMSCE-DDDG-LHELIR  152 (230)
Q Consensus        90 ~~~ll~~~~~~~~~--a~~~~~~~~----------~~~~~~~li~~y~~~g~---~~~A~~vf~~m~~-~~~~-t~n~li  152 (230)
                      +..+-..+.+.|+.  |...++...          ....++.+-..|...|+   +++|...|++... |+.. .+..+-
T Consensus       264 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la  343 (378)
T 3q15_A          264 LFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAA  343 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHH
Confidence            77888899999998  777777665          24456777778888888   8999999988544 2222 233333


Q ss_pred             HHhhh----cchhhhHHHHHH
Q 042210          153 IKAVD----DDLHELFPEYLV  169 (230)
Q Consensus       153 ~~~~~----~~~~~~~~~m~~  169 (230)
                      ..+..    ++|.+.|++...
T Consensus       344 ~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          344 AVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            33332    456666665543

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=95.53  E-value=0.43  Score=40.23  Aligned_cols=184  Identities=6%  Similarity=-0.113  Sum_probs=109.7

Q ss_pred             CCCCcH-HHHHHHHhhhccC---ChHHHHHHHHhcC---CCChhhHHHHHHHHHhc----CChhHHHHHHHHHHhCCCCC
Q 042210           17 LTKPHC-PKQTRYLLLYEKG---DLKYECKVFRKIT---QPSVFLWNTMIKGYSRI----DSHKNGVLMYLDLLKSDVRR   85 (230)
Q Consensus        17 ~~~~~~-~~ll~~~~~~~~~---~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~----~~~~~a~~~~~~M~~~g~~p   85 (230)
                      ..++.. ..+-..|.  +.|   +.++|.+.|...-   .++...+..+-..|...    +++++|...|+.-. .|.  
T Consensus       173 ~~~~~a~~~Lg~~~~--~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g~--  247 (452)
T 3e4b_A          173 NTTDICYVELATVYQ--KKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PGY--  247 (452)
T ss_dssp             TTCTTHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GGS--
T ss_pred             cCCHHHHHHHHHHHH--HcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CCC--
Confidence            344446 77777787  888   8888888887754   33444335555556544    68889999998876 333  


Q ss_pred             CcccHHHHHHH-h--hhcCch--hhHHHhhhh---hHhHHHHHHHHHHhcC-----CHHHHHHHHhhccCCC-hhhhHHH
Q 042210           86 DNYTFPFLFKG-F--TRDIAG--SLEKSCIVM---RVFVQNALISTYCLCG-----EVDMARGIFYMSCEDD-DGLHELI  151 (230)
Q Consensus        86 ~~~t~~~ll~~-~--~~~~~~--a~~~~~~~~---~~~~~~~li~~y~~~g-----~~~~A~~vf~~m~~~~-~~t~n~l  151 (230)
                       ...+..|=.. +  ...++.  |...+....   +...+..|=..|. .|     ++++|.+.|++-. ++ ...+..|
T Consensus       248 -~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~~A~~~L  324 (452)
T 3e4b_A          248 -PASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREVAADYYL  324 (452)
T ss_dssp             -THHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCHHHHHHH
T ss_pred             -HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCHHHHHHH
Confidence             2333333333 2  345666  777777766   6777777777776 55     9999999999888 54 3444444


Q ss_pred             HHHhhh--------cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCccccccccccCC
Q 042210          152 RIKAVD--------DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQ  217 (230)
Q Consensus       152 i~~~~~--------~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~  217 (230)
                      -..|..        +++.+.|++-.+.|  .|+....-+.....       +..-..+.++|..++....+.|-
T Consensus       325 g~~y~~G~g~~~d~~~A~~~~~~Aa~~g--~~~A~~~Lg~~y~~-------G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          325 GQIYRRGYLGKVYPQKALDHLLTAARNG--QNSADFAIAQLFSQ-------GKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             HHHHHTTTTSSCCHHHHHHHHHHHHTTT--CTTHHHHHHHHHHS-------CTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHCCCCCCcCHHHHHHHHHHHHhhC--hHHHHHHHHHHHHh-------CCCCCCCHHHHHHHHHHHHHCCC
Confidence            333322        35666666655544  23322222211111       22233466777777777666653

>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=95.49  E-value=0.33  Score=41.36  Aligned_cols=102  Identities=9%  Similarity=-0.002  Sum_probs=72.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.+++..+.  .|+.. . ..+-..|.  +.|++++|.+.+++..   +.+...|..+-.+|.+.|++++|...|+
T Consensus        23 ~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~   98 (477)
T 1wao_1           23 ENAIKFYSQAIEL--NPSNAIYYGNRSLAYL--RTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAALRDYE   98 (477)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCccHHHHHHHHHHHH--HhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            5678888877776  46544 3 77778888  9999999999999865   4456788889999999999999999999


Q ss_pred             HHHhCCCCCC-cccHHHHHHH--hhhcCch--hhHHHh
Q 042210           77 DLLKSDVRRD-NYTFPFLFKG--FTRDIAG--SLEKSC  109 (230)
Q Consensus        77 ~M~~~g~~p~-~~t~~~ll~~--~~~~~~~--a~~~~~  109 (230)
                      +..+.  .|+ ...+..+-.+  +.+.|++  |.+.++
T Consensus        99 ~al~~--~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           99 TVVKV--KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHH--STTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            97653  232 2344444444  6677777  777766

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.21  Score=41.09  Aligned_cols=138  Identities=9%  Similarity=-0.079  Sum_probs=95.8

Q ss_pred             hhHHHHHHHHHHhcCCCCC----------------cH-HHHHHHHhhhccCChHHHHHHHHhcC-----CCCh----hhH
Q 042210            2 HQLKQIHSQTIKLGLLTKP----------------HC-PKQTRYLLLYEKGDLKYECKVFRKIT-----QPSV----FLW   55 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~----------------~~-~~ll~~~~~~~~~~~~~a~~~~~~m~-----~~~~----~~y   55 (230)
                      ++|.+.+....+..-....                .. ..+...|.  +.|++++|.+.+....     .++.    .+.
T Consensus        21 ~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~   98 (434)
T 4b4t_Q           21 NEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYV--TMGAKDKLREFIPHSTEYMMQFAKSKTVKVLK   98 (434)
T ss_dssp             HHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHH--HHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHccchHHHHHHH
Confidence            4677777777665322111                12 45778888  9999999999998765     1221    122


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHh----CCCCCC-cccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHH
Q 042210           56 NTMIKGYSRIDSHKNGVLMYLDLLK----SDVRRD-NYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQ  117 (230)
Q Consensus        56 n~li~~~~~~~~~~~a~~~~~~M~~----~g~~p~-~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~  117 (230)
                      +.+=..+...|+++.+..++++...    .+..+. ..++..+-..+...|++  |..++....           ....|
T Consensus        99 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~  178 (434)
T 4b4t_Q           99 TLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVH  178 (434)
T ss_dssp             HHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHH
Confidence            2222233446889999999988643    333332 34667788889999998  777776665           56788


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          118 NALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       118 ~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..+...|...|++++|...++...
T Consensus       179 ~~~~~~~~~~~~~~~A~~~~~~al  202 (434)
T 4b4t_Q          179 LLESKVYHKLRNLAKSKASLTAAR  202 (434)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcHHHHHHHHHHHH
Confidence            999999999999999999988654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=95.40  E-value=0.48  Score=38.18  Aligned_cols=118  Identities=9%  Similarity=-0.144  Sum_probs=82.0

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--CC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc-ccHHH-
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--QP------SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN-YTFPF-   92 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--~~------~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~-~t~~~-   92 (230)
                      ..+-..+.  ..|++++|...+++..  .+      ....|..+-..+...|++++|...+++.....-.++. ..+.. 
T Consensus       139 ~~la~~~~--~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~  216 (373)
T 1hz4_A          139 RIRAQLLW--AWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISN  216 (373)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHH
T ss_pred             HHHHHHHH--HhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHH
Confidence            34556777  9999999999998753  11      1245777778888899999999999987653212211 12222 


Q ss_pred             ----HHHHhhhcCch--hhHHHhhhh---------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           93 ----LFKGFTRDIAG--SLEKSCIVM---------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        93 ----ll~~~~~~~~~--a~~~~~~~~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                          ....+...|+.  |...+....         ....+..+...|...|++++|...+++...
T Consensus       217 ~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  281 (373)
T 1hz4_A          217 ANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  281 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                22346688888  777777665         123466777889999999999999987643

>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=95.23  E-value=0.33  Score=32.98  Aligned_cols=91  Identities=10%  Similarity=0.113  Sum_probs=57.6

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhcCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRDIA  102 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~~~  102 (230)
                      ..+.  +.|++++|.+.|++..   +.+...|+.+=.+|.+.|++++|+..|++-.+.+  |+ ...|..+         
T Consensus        16 ~~~~--~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~~---------   82 (127)
T 4gcn_A           16 NAAY--KQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVG--RETRADYKLI---------   82 (127)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHTTCCHHHH---------
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhC--cccchhhHHH---------
Confidence            4455  7788888888887654   4456667777777778888888888777654321  11 1112111         


Q ss_pred             hhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          103 GSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       103 ~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                                 ..+|..+=..|...|++++|.+.|++-.
T Consensus        83 -----------a~~~~~lg~~~~~~~~~~~A~~~~~kal  110 (127)
T 4gcn_A           83 -----------AKAMSRAGNAFQKQNDLSLAVQWFHRSL  110 (127)
T ss_dssp             -----------HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -----------HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                       1234445566778888888888887643

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.12  E-value=0.16  Score=33.55  Aligned_cols=75  Identities=8%  Similarity=-0.007  Sum_probs=51.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      +.|...++...+.  .|+.. . ..+-..|.  +.|++++|...|++..   +.+...|..+-..|.+.|++++|...|+
T Consensus         2 ~~a~~~~~~al~~--~p~~~~~~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~   77 (115)
T 2kat_A            2 QAITERLEAMLAQ--GTDNMLLRFTLGKTYA--EHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWE   77 (115)
T ss_dssp             CCHHHHHHHHHTT--TCCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHh--CCCcHHHHHHHHHHHH--HccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            4455666655443  35433 3 56667777  8888888888888764   3445677777788888888888888887


Q ss_pred             HHHh
Q 042210           77 DLLK   80 (230)
Q Consensus        77 ~M~~   80 (230)
                      +..+
T Consensus        78 ~al~   81 (115)
T 2kat_A           78 SGLA   81 (115)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7544

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=95.11  E-value=0.16  Score=34.89  Aligned_cols=88  Identities=11%  Similarity=-0.008  Sum_probs=66.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-CC----cccHHHHHHHhhhcCch--hhHHHhhhh-----------hHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVR-RD----NYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVF  115 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~-p~----~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~  115 (230)
                      +|..+-..|...|++++|...+++..+..-. ++    ..++..+-..+...|++  |...+....           ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            5677777888899999999999886543111 11    13677777888888988  777776655           255


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          116 VQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .+..+-..|...|++++|.+.|++..
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~  116 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHL  116 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            67778889999999999999988765

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=95.07  E-value=0.27  Score=34.59  Aligned_cols=58  Identities=9%  Similarity=-0.101  Sum_probs=37.2

Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG  146 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~  146 (230)
                      .|..+-.++.+.|++  |...+....     +...|..+-.+|...|++++|...|+...+  |+..
T Consensus        65 ~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~  131 (162)
T 3rkv_A           65 LYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAA  131 (162)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCH
Confidence            444445555555555  444444443     566677777888888999999988887654  5543

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=94.94  E-value=0.056  Score=43.86  Aligned_cols=127  Identities=13%  Similarity=0.086  Sum_probs=57.1

Q ss_pred             HHHHhhhccCChHHHHHHHHhcC--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch
Q 042210           26 TRYLLLYEKGDLKYECKVFRKIT--QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG  103 (230)
Q Consensus        26 l~~~~~~~~~~~~~a~~~~~~m~--~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~  103 (230)
                      -..+.  +.|++++|...|++..  .|+...       +...++.+++..-+.          ...|..+-.++.+.|++
T Consensus       186 g~~~~--~~g~~~~A~~~y~~Al~~~p~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~~~~~~g~~  246 (338)
T 2if4_A          186 GNSLF--KEEKLEEAMQQYEMAIAYMGDDFM-------FQLYGKYQDMALAVK----------NPCHLNIAACLIKLKRY  246 (338)
T ss_dssp             HHHTC--SSSCCHHHHHHHHHHHHHSCHHHH-------HTCCHHHHHHHHHHH----------THHHHHHHHHHHTTTCC
T ss_pred             HHHHH--hcCCHHHHHHHHHHHHHHhccchh-------hhhcccHHHHHHHHH----------HHHHHHHHHHHHHcCCH
Confidence            34555  8899999999998754  343221       111112222211110          11344444555555555


Q ss_pred             --hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hhhhHHHHHH-----hhhcchhhhHHHHH
Q 042210          104 --SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DGLHELIRIK-----AVDDDLHELFPEYL  168 (230)
Q Consensus       104 --a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~t~n~li~~-----~~~~~~~~~~~~m~  168 (230)
                        |...+....     +...|..+-.+|...|++++|...|++..+  |+ ...++.+-..     ...+++.+.|.+|+
T Consensus       247 ~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~~~~l  326 (338)
T 2if4_A          247 DEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMYKGIF  326 (338)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC----------------------------------
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence              444444443     566677778888899999999999998765  43 3334443222     11235556666666


Q ss_pred             HHh
Q 042210          169 VQM  171 (230)
Q Consensus       169 ~~~  171 (230)
                      ...
T Consensus       327 ~~~  329 (338)
T 2if4_A          327 KGK  329 (338)
T ss_dssp             ---
T ss_pred             CCC
Confidence            544

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=94.94  E-value=0.17  Score=33.81  Aligned_cols=80  Identities=6%  Similarity=-0.049  Sum_probs=60.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCc----H-HHHHHHHhhhccCChHHHHHHHHhcC--CCC----hhhHHHHHHHHHhcCChhH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH----C-PKQTRYLLLYEKGDLKYECKVFRKIT--QPS----VFLWNTMIKGYSRIDSHKN   70 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~----~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~----~~~yn~li~~~~~~~~~~~   70 (230)
                      ++|...++...+..  |+..    . ..+-..+.  +.|++++|...|+...  .|+    ...+..+-.++.+.|++++
T Consensus        19 ~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~--~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~~~g~~~~   94 (129)
T 2xev_A           19 DDASQLFLSFLELY--PNGVYTPNALYWLGESYY--ATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQYGEGKNTE   94 (129)
T ss_dssp             HHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHH--HhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHcCCHHH
Confidence            46788888877764  4333    4 55667777  9999999999999875  344    4457777788899999999


Q ss_pred             HHHHHHHHHhCCCCCCc
Q 042210           71 GVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        71 a~~~~~~M~~~g~~p~~   87 (230)
                      |...|++.....  |+.
T Consensus        95 A~~~~~~~~~~~--p~~  109 (129)
T 2xev_A           95 AQQTLQQVATQY--PGS  109 (129)
T ss_dssp             HHHHHHHHHHHS--TTS
T ss_pred             HHHHHHHHHHHC--CCC
Confidence            999999987643  554

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=94.73  E-value=0.14  Score=44.05  Aligned_cols=57  Identities=4%  Similarity=-0.187  Sum_probs=38.4

Q ss_pred             hHhHHHHHHHHHHhcCCHHHHHHHHhhccC----------CCh-hhhHHHHHHhh----hcchhhhHHHHHH
Q 042210          113 RVFVQNALISTYCLCGEVDMARGIFYMSCE----------DDD-GLHELIRIKAV----DDDLHELFPEYLV  169 (230)
Q Consensus       113 ~~~~~~~li~~y~~~g~~~~A~~vf~~m~~----------~~~-~t~n~li~~~~----~~~~~~~~~~m~~  169 (230)
                      ...+++.|...|...|++++|..++++..+          |++ .++|.|-..|.    .++|..++++-.+
T Consensus       350 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~  421 (490)
T 3n71_A          350 VLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYA  421 (490)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            467788899999999999999998886643          333 34665544443    3456666555443

>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=94.61  E-value=0.18  Score=41.48  Aligned_cols=88  Identities=10%  Similarity=-0.002  Sum_probs=54.2

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcCC-------------------CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKITQ-------------------PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR   85 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~~-------------------~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p   85 (230)
                      +-..+.  +.|++++|.+.|++...                   .+...|+.+-.+|.+.|++++|...+++..+.  .|
T Consensus       229 ~g~~~~--~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~--~p  304 (370)
T 1ihg_A          229 IGNTFF--KSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI--DP  304 (370)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CT
T ss_pred             HHHHHH--HhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--Cc
Confidence            334555  78888888888776432                   12345666666666677777777777665542  23


Q ss_pred             CcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           86 DNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        86 ~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      +                          +...|..+-.+|.+.|++++|.+.|++..+
T Consensus       305 ~--------------------------~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~  335 (370)
T 1ihg_A          305 S--------------------------NTKALYRRAQGWQGLKEYDQALADLKKAQE  335 (370)
T ss_dssp             T--------------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             h--------------------------hHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            2                          344455555666677777777777776543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=94.33  E-value=0.18  Score=33.97  Aligned_cols=84  Identities=10%  Similarity=0.042  Sum_probs=64.2

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhc
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRD  100 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~  100 (230)
                      +-..+.  +.|++++|...|+...   +.+...|..+=.++.+.|++++|...|++-.+.  .| +...+..+-.++.+.
T Consensus        23 ~g~~~~--~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           23 EGLSML--KLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHH--HcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            335666  8999999999999875   446677888888899999999999999986653  34 344677777788888


Q ss_pred             Cch--hhHHHhhhh
Q 042210          101 IAG--SLEKSCIVM  112 (230)
Q Consensus       101 ~~~--a~~~~~~~~  112 (230)
                      |+.  |...++...
T Consensus        99 g~~~~A~~~~~~al  112 (121)
T 1hxi_A           99 HNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            888  776666543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=94.29  E-value=0.41  Score=42.90  Aligned_cols=99  Identities=11%  Similarity=0.094  Sum_probs=65.1

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhh
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCI  110 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~  110 (230)
                      ..|+++.|.++.+.+  .+...|..+-..+.+.++++.|.+.|..+..         |..+...+...++.  ...+-+.
T Consensus       664 ~~~~~~~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~  732 (814)
T 3mkq_A          664 KVGQLTLARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKD  732 (814)
T ss_dssp             HHTCHHHHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHH
Confidence            566677776766655  3446788888888888888888888887643         45555555556655  2222222


Q ss_pred             hhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          111 VMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       111 ~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ....--++.....|.++|++++|.+++.++.+
T Consensus       733 a~~~~~~~~A~~~~~~~g~~~~a~~~~~~~~~  764 (814)
T 3mkq_A          733 AETTGKFNLAFNAYWIAGDIQGAKDLLIKSQR  764 (814)
T ss_dssp             HHHTTCHHHHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHHcCchHHHHHHHHHcCCHHHHHHHHHHcCC
Confidence            22333455666778888888888888887765

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=94.07  E-value=2.5  Score=36.09  Aligned_cols=95  Identities=6%  Similarity=0.009  Sum_probs=61.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHH--HHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHH
Q 042210           55 WNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFP--FLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYC  125 (230)
Q Consensus        55 yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~--~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~  125 (230)
                      |-..+...-+.++++.|-.+|+.....+  .+...|.  +.+..... ++.  |+.+|+...     ++..|...++...
T Consensus       289 w~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~~-~d~~~ar~ife~al~~~~~~~~~~~~yid~e~  365 (493)
T 2uy1_A          289 RINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYAT-GSRATPYNIFSSGLLKHPDSTLLKEEFFLFLL  365 (493)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHHH-CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHHC-CChHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            4444444445677888999998872111  1222232  22222222 235  888888776     4666788899889


Q ss_pred             hcCCHHHHHHHHhhccCCChhhhHHHHH
Q 042210          126 LCGEVDMARGIFYMSCEDDDGLHELIRI  153 (230)
Q Consensus       126 ~~g~~~~A~~vf~~m~~~~~~t~n~li~  153 (230)
                      +.|+.+.|+.+|+... .....|...+.
T Consensus       366 ~~~~~~~aR~l~er~~-k~~~lw~~~~~  392 (493)
T 2uy1_A          366 RIGDEENARALFKRLE-KTSRMWDSMIE  392 (493)
T ss_dssp             HHTCHHHHHHHHHHSC-CBHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH-HHHHHHHHHHH
Confidence            9999999999999984 34566777664

>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=94.07  E-value=0.55  Score=39.68  Aligned_cols=101  Identities=13%  Similarity=-0.033  Sum_probs=78.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC----------------cccHHHHHHHhhhcCch--hhHHHhhhh--
Q 042210           53 FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD----------------NYTFPFLFKGFTRDIAG--SLEKSCIVM--  112 (230)
Q Consensus        53 ~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~----------------~~t~~~ll~~~~~~~~~--a~~~~~~~~--  112 (230)
                      ..|..+=..|.+.|++++|...|++-.+.  .|+                ...|..+-.++.+.|++  |...+....  
T Consensus       269 ~~~~~~G~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          269 AIVKEKGTVYFKGGKYMQAVIQYGKIVSW--LEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            45777778888999999999999987653  232                36788888899999999  888887776  


Q ss_pred             ---hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHh
Q 042210          113 ---RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKA  155 (230)
Q Consensus       113 ---~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~  155 (230)
                         +...|..+-.+|.+.|++++|...|++..+  | +...|..+-..+
T Consensus       347 ~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~  395 (457)
T 1kt0_A          347 DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQ  395 (457)
T ss_dssp             STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence               678888889999999999999999998876  4 334555554433

>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=94.06  E-value=0.31  Score=33.09  Aligned_cols=82  Identities=10%  Similarity=0.024  Sum_probs=58.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CC----C----hhhHHHHHHHHHhcCChh
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QP----S----VFLWNTMIKGYSRIDSHK   69 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~----~----~~~yn~li~~~~~~~~~~   69 (230)
                      ++|...|+...+.  .|+...  ..+-.+|.  +.|++++|.+.|++..  .|    +    ...|..+=.++...|+++
T Consensus        25 ~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~--~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~  100 (127)
T 4gcn_A           25 EKAHVHYDKAIEL--DPSNITFYNNKAAVYF--EEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLS  100 (127)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHhHHHHHH--HhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHH
Confidence            5788888887765  466544  66778888  9999999999998764  12    1    124555666777889999


Q ss_pred             HHHHHHHHHHhCCCCCCccc
Q 042210           70 NGVLMYLDLLKSDVRRDNYT   89 (230)
Q Consensus        70 ~a~~~~~~M~~~g~~p~~~t   89 (230)
                      +|.+.|++-..  ..||..+
T Consensus       101 ~A~~~~~kal~--~~~~~~~  118 (127)
T 4gcn_A          101 LAVQWFHRSLS--EFRDPEL  118 (127)
T ss_dssp             HHHHHHHHHHH--HSCCHHH
T ss_pred             HHHHHHHHHHh--hCcCHHH
Confidence            99999988654  2355433

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=93.91  E-value=0.12  Score=33.56  Aligned_cols=57  Identities=9%  Similarity=0.153  Sum_probs=45.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ..+-..+.  +.|++++|.+.|++..   +.+...|..+-.+|.+.|++++|...|++..+.
T Consensus         8 ~~~g~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            8 KEQGNSLF--KQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             HHHHHHHH--TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            34455666  8899999999998864   446677888888889999999999999887653

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=93.78  E-value=0.23  Score=40.20  Aligned_cols=102  Identities=8%  Similarity=-0.048  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A  133 (230)
                      .|..+-..+.+.|++++|...|++-...  .|+...       +...++.. .....+ ....|+.+-..|.+.|++++|
T Consensus       181 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~-~~~~~l-~~~~~~nla~~~~~~g~~~~A  249 (338)
T 2if4_A          181 RRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQ-DMALAV-KNPCHLNIAACLIKLKRYDEA  249 (338)
T ss_dssp             HHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHH-HHHHHH-HTHHHHHHHHHHHTTTCCHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHH-HHHHHH-HHHHHHHHHHHHHHcCCHHHH
Confidence            3556666777889999999999885542  232211       11222220 000111 234788888899999999999


Q ss_pred             HHHHhhccC--C-ChhhhHHHHHHhhhc----chhhhHHH
Q 042210          134 RGIFYMSCE--D-DDGLHELIRIKAVDD----DLHELFPE  166 (230)
Q Consensus       134 ~~vf~~m~~--~-~~~t~n~li~~~~~~----~~~~~~~~  166 (230)
                      ...|++..+  | +...|..+-.++...    +|.+.|++
T Consensus       250 ~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~  289 (338)
T 2if4_A          250 IGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRK  289 (338)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999997754  4 556676665666544    44444444

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=93.70  E-value=0.053  Score=35.28  Aligned_cols=63  Identities=10%  Similarity=-0.041  Sum_probs=40.7

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHH
Q 042210           52 VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVD  131 (230)
Q Consensus        52 ~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~  131 (230)
                      ...|..+-..+.+.|++++|...|++..+.  .|+                          +...|..+-..|.+.|+++
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~--------------------------~~~~~~~lg~~~~~~g~~~   55 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITA--QPQ--------------------------NPVGYSNKAMALIKLGEYT   55 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTT--------------------------CHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCC--------------------------CHHHHHHHHHHHHHhcCHH
Confidence            345556666777778888888877775442  222                          3445556666777777777


Q ss_pred             HHHHHHhhccC
Q 042210          132 MARGIFYMSCE  142 (230)
Q Consensus       132 ~A~~vf~~m~~  142 (230)
                      +|.+.|++..+
T Consensus        56 ~A~~~~~~al~   66 (111)
T 2l6j_A           56 QAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            77777776654

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=93.68  E-value=0.68  Score=38.97  Aligned_cols=143  Identities=12%  Similarity=-0.020  Sum_probs=64.6

Q ss_pred             hhHHHHHHHHHHhcCCCCCcHHHHHHHHhhhccCCh---HHHHHHHHhcCCCChhhHHHHHHHHHhcC-----ChhHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDL---KYECKVFRKITQPSVFLWNTMIKGYSRID-----SHKNGVL   73 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~~~ll~~~~~~~~~~~---~~a~~~~~~m~~~~~~~yn~li~~~~~~~-----~~~~a~~   73 (230)
                      ++|.+++....+.|-. +.. ..+=..|.  ..|+.   ++|...|.+....+...+..+-..+...+     ++++|..
T Consensus        20 ~~A~~~~~~aa~~g~~-~A~-~~Lg~~y~--~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~~~~~A~~   95 (452)
T 3e4b_A           20 VTAQQNYQQLAELGYS-EAQ-VGLADIQV--GTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEAEHHEAES   95 (452)
T ss_dssp             HHHHHHHHHHHHHTCC-TGG-GTCC------------------------------CHHHHHHHHHTC--CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCH-HHH-HHHHHHHH--ccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCcCHHHHHH
Confidence            5688888888887732 222 33333445  56666   89999998876546656666655444444     7789999


Q ss_pred             HHHHHHhCCCCCCcccHHHHHHHhhhcCch-----hhHHHhhhh---hHhHHHHHHHHHHhcC----CHHHHHHHHhhcc
Q 042210           74 MYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-----SLEKSCIVM---RVFVQNALISTYCLCG----EVDMARGIFYMSC  141 (230)
Q Consensus        74 ~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-----a~~~~~~~~---~~~~~~~li~~y~~~g----~~~~A~~vf~~m~  141 (230)
                      .|++-.+.|-..   .+..|-..|...+..     +.+.+....   +...+..|-..|...+    ..+++..++....
T Consensus        96 ~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~  172 (452)
T 3e4b_A           96 LLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHLDDVERICKAAL  172 (452)
T ss_dssp             HHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHH
Confidence            999877765432   555566666555543     222222222   4455555556666555    3444444555444


Q ss_pred             CCChhhhHHH
Q 042210          142 EDDDGLHELI  151 (230)
Q Consensus       142 ~~~~~t~n~l  151 (230)
                      ..+...+..|
T Consensus       173 ~~~~~a~~~L  182 (452)
T 3e4b_A          173 NTTDICYVEL  182 (452)
T ss_dssp             TTCTTHHHHH
T ss_pred             cCCHHHHHHH
Confidence            4333344444

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=93.61  E-value=0.33  Score=31.32  Aligned_cols=56  Identities=14%  Similarity=0.186  Sum_probs=42.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      ..+-..|.  +.|++++|...|++..   +.+...|..+-.+|.+.|++++|...|++-.+
T Consensus        11 ~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A           11 YALAQEHL--KHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            55566677  8888888888888765   33456788888888888888888888887543

>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=93.55  E-value=0.37  Score=40.68  Aligned_cols=75  Identities=7%  Similarity=-0.199  Sum_probs=38.7

Q ss_pred             CChhHHHHHHHHHHh---CCCCCC----cccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhHHHHHHHH
Q 042210           66 DSHKNGVLMYLDLLK---SDVRRD----NYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFVQNALIST  123 (230)
Q Consensus        66 ~~~~~a~~~~~~M~~---~g~~p~----~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~~~~li~~  123 (230)
                      |++++|..++++-..   .-+.|+    ..+++.|..+|...|++  |..++....             ...+++.|-..
T Consensus       312 g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          312 KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            455666666655322   112222    13444455555555555  444444433             34456666666


Q ss_pred             HHhcCCHHHHHHHHhhc
Q 042210          124 YCLCGEVDMARGIFYMS  140 (230)
Q Consensus       124 y~~~g~~~~A~~vf~~m  140 (230)
                      |...|++++|..++++-
T Consensus       392 ~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          392 YMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHTTCHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHH
Confidence            66677776666666643

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=93.50  E-value=0.11  Score=46.61  Aligned_cols=98  Identities=8%  Similarity=-0.077  Sum_probs=72.9

Q ss_pred             ccCChHHHHH-HHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHh
Q 042210           33 EKGDLKYECK-VFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~-~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~  109 (230)
                      ..+++++|.+ ++..++  +......++..+-+.|.++.|+++.++-            ..-+......|++  |.++.+
T Consensus       611 ~~~~~~~a~~~~l~~i~--~~~~~~~~~~~l~~~~~~~~a~~~~~~~------------~~~f~~~l~~~~~~~A~~~~~  676 (814)
T 3mkq_A          611 LRGEIEEAIENVLPNVE--GKDSLTKIARFLEGQEYYEEALNISPDQ------------DQKFELALKVGQLTLARDLLT  676 (814)
T ss_dssp             HTTCHHHHHHHTGGGCC--CHHHHHHHHHHHHHTTCHHHHHHHCCCH------------HHHHHHHHHHTCHHHHHHHHT
T ss_pred             HhCCHHHHHHHHHhcCC--chHHHHHHHHHHHhCCChHHheecCCCc------------chheehhhhcCCHHHHHHHHH
Confidence            6788888888 664443  1222377778888889999888876321            1224445667888  888888


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccCCC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCEDD  144 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~  144 (230)
                      .+.+...|..|-..+.+.|+++.|++.|..+.+.+
T Consensus       677 ~~~~~~~W~~la~~al~~~~~~~A~~~y~~~~d~~  711 (814)
T 3mkq_A          677 DESAEMKWRALGDASLQRFNFKLAIEAFTNAHDLE  711 (814)
T ss_dssp             TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCHH
T ss_pred             hhCcHhHHHHHHHHHHHcCCHHHHHHHHHHccChh
Confidence            77789999999999999999999999999887633

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=93.44  E-value=0.51  Score=29.03  Aligned_cols=57  Identities=12%  Similarity=0.207  Sum_probs=44.8

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ..+-..+.  +.|++++|...|++..   +.+...|..+-..+.+.|++++|...|++..+.
T Consensus        13 ~~la~~~~--~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A           13 YNLGNAYY--KQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            44556677  8899999999998764   445667888888888999999999999887653

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=93.43  E-value=0.33  Score=31.90  Aligned_cols=65  Identities=15%  Similarity=0.021  Sum_probs=41.0

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCC
Q 042210           50 PSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGE  129 (230)
Q Consensus        50 ~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~  129 (230)
                      .+...|..+-..|.+.|++++|...|++..+.  .|+                          +...|..+-..|.+.|+
T Consensus        17 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~--------------------------~~~~~~~la~~~~~~g~   68 (115)
T 2kat_A           17 DNMLLRFTLGKTYAEHEQFDAALPHLRAALDF--DPT--------------------------YSVAWKWLGKTLQGQGD   68 (115)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT--------------------------CHHHHHHHHHHHHHHTC
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CCC--------------------------cHHHHHHHHHHHHHcCC
Confidence            34556667777777777777777777775442  122                          24445556666667777


Q ss_pred             HHHHHHHHhhccC
Q 042210          130 VDMARGIFYMSCE  142 (230)
Q Consensus       130 ~~~A~~vf~~m~~  142 (230)
                      +++|...|++..+
T Consensus        69 ~~~A~~~~~~al~   81 (115)
T 2kat_A           69 RAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777766543

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=93.35  E-value=2.3  Score=34.00  Aligned_cols=197  Identities=10%  Similarity=-0.046  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccC--ChHHHHHHHHhcC---CCChhhHHHHHHHH----Hhc---CChh
Q 042210            4 LKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKG--DLKYECKVFRKIT---QPSVFLWNTMIKGY----SRI---DSHK   69 (230)
Q Consensus         4 a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~--~~~~a~~~~~~m~---~~~~~~yn~li~~~----~~~---~~~~   69 (230)
                      |.++.+.+...  .|+..+  +.==..+.  ..|  +++++.+.++.+-   +.+...|+---..+    .+.   ++++
T Consensus        52 aL~~t~~~L~~--nP~~~taWn~R~~~L~--~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~  127 (306)
T 3dra_A           52 ALHITELGINE--LASHYTIWIYRFNILK--NLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPY  127 (306)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHH--TCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTH
T ss_pred             HHHHHHHHHHH--CcHHHHHHHHHHHHHH--HcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHH
Confidence            44444444433  355444  33333444  556  7788888877765   34445565433333    333   6777


Q ss_pred             HHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch----hhHHHhhhh-----hHhHHHHHHHHHHhcCC------HHHHH
Q 042210           70 NGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG----SLEKSCIVM-----RVFVQNALISTYCLCGE------VDMAR  134 (230)
Q Consensus        70 ~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~----a~~~~~~~~-----~~~~~~~li~~y~~~g~------~~~A~  134 (230)
                      +++.+++.+.+..-+ |...|+----...+.|.+    +.+..+.+.     +-..|+.---.+.+.|+      ++++.
T Consensus       128 ~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl  206 (306)
T 3dra_A          128 REFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKKHLATDNTIDEEL  206 (306)
T ss_dssp             HHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSGGGCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccchhhhHHHHH
Confidence            888888777653211 333343333333333332    333344443     55566555555555555      67777


Q ss_pred             HHHhhccC---CChhhhHHHHHHhhh-----cchhhhHHHHHHHhhh-cCchhhhhhhhhcccccCCcccccccCCccCC
Q 042210          135 GIFYMSCE---DDDGLHELIRIKAVD-----DDLHELFPEYLVQMLA-LPDTFMGEGLEVIPKSQAPREETPRVGNLEEG  205 (230)
Q Consensus       135 ~vf~~m~~---~~~~t~n~li~~~~~-----~~~~~~~~~m~~~~~~-~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a  205 (230)
                      +.+++...   .|...|+-.-.....     .+..+++.+....+.. ..+.+....   +      ...+.+.|+.++|
T Consensus       207 ~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~---l------a~~~~~~~~~~~A  277 (306)
T 3dra_A          207 NYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALET---L------AKIYTQQKKYNES  277 (306)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHH---H------HHHHHHTTCHHHH
T ss_pred             HHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHH---H------HHHHHccCCHHHH
Confidence            77766553   355567654332221     1222233332222101 112233333   2      1155677888888


Q ss_pred             ccccccccc
Q 042210          206 TPQEGRPHE  214 (230)
Q Consensus       206 ~~i~~~~~~  214 (230)
                      .+++..+.+
T Consensus       278 ~~~~~~l~~  286 (306)
T 3dra_A          278 RTVYDLLKS  286 (306)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            888887764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.33  E-value=0.85  Score=37.38  Aligned_cols=140  Identities=7%  Similarity=-0.124  Sum_probs=88.4

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CCCh------------------hhHHHHHHHHHhcCChhHHHHHHHHHHhC-CCCC
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QPSV------------------FLWNTMIKGYSRIDSHKNGVLMYLDLLKS-DVRR   85 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~~~------------------~~yn~li~~~~~~~~~~~a~~~~~~M~~~-g~~p   85 (230)
                      ..+.  +.|++++|.+.|....  .|+.                  ..+..+...|...|++++|.+.+...... +-.+
T Consensus        12 ~~l~--~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           12 RRLV--NEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHH--HHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHH--HCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            4456  8899999999998764  1111                  13677889999999999999999986542 2222


Q ss_pred             Cccc---HHHHHH-HhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC------
Q 042210           86 DNYT---FPFLFK-GFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARGIFYMSCE------  142 (230)
Q Consensus        86 ~~~t---~~~ll~-~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~------  142 (230)
                      +..+   ....+. .+...|+.  +..++....           -..++..|...|...|++++|..++++...      
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            2221   112222 22233444  555555544           355778899999999999999999886642      


Q ss_pred             --CC-hhhhHHHHHHhhhc----chhhhHHHHH
Q 042210          143 --DD-DGLHELIRIKAVDD----DLHELFPEYL  168 (230)
Q Consensus       143 --~~-~~t~n~li~~~~~~----~~~~~~~~m~  168 (230)
                        +. ...|+.++..|...    +|...+++..
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al  202 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAAR  202 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence              22 22455556666543    4444444433

>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=93.04  E-value=0.27  Score=41.40  Aligned_cols=83  Identities=10%  Similarity=-0.100  Sum_probs=48.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhC--C-CCCC----cccHHHHHHHhhhcCch--hhHHHhhhh-------------hHhH
Q 042210           59 IKGYSRIDSHKNGVLMYLDLLKS--D-VRRD----NYTFPFLFKGFTRDIAG--SLEKSCIVM-------------RVFV  116 (230)
Q Consensus        59 i~~~~~~~~~~~a~~~~~~M~~~--g-~~p~----~~t~~~ll~~~~~~~~~--a~~~~~~~~-------------~~~~  116 (230)
                      +..+.+.|++++|..++++....  . +.|+    ..+++.|...|...|++  |..++....             ...+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            33444556777777777665432  1 2222    12455555555555665  444444443             4556


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          117 QNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       117 ~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ++.|-..|...|++++|..++++..
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            6777777888888888877776543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=92.96  E-value=2  Score=31.47  Aligned_cols=99  Identities=13%  Similarity=0.078  Sum_probs=76.4

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch-hhHHHhhh
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG-SLEKSCIV  111 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~-a~~~~~~~  111 (230)
                      ..|+++.|.++.+++  .+...|..|=....+.|+++-|.+.|+...         -|..+.-.|.-.|+. .......+
T Consensus        17 ~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~---------D~~~L~~Ly~~tg~~e~L~kla~i   85 (177)
T 3mkq_B           17 EYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQH---------SFDKLSFLYLVTGDVNKLSKMQNI   85 (177)
T ss_dssp             HTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT---------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhC---------CHHHHHHHHHHhCCHHHHHHHHHH
Confidence            899999999998887  456689999999999999999999998854         356666666667776 33333222


Q ss_pred             h-hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          112 M-RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       112 ~-~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      . ..--+|.....+.-.|+++++.++|.+..+
T Consensus        86 A~~~g~~n~af~~~l~lGdv~~~i~lL~~~~r  117 (177)
T 3mkq_B           86 AQTREDFGSMLLNTFYNNSTKERSSIFAEGGS  117 (177)
T ss_dssp             HHHTTCHHHHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHHCccHHHHHHHHHHcCCHHHHHHHHHHCCC
Confidence            2 444567777788889999999999987655

>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=92.93  E-value=0.57  Score=38.46  Aligned_cols=104  Identities=6%  Similarity=-0.092  Sum_probs=65.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhh-hHhHHHHHHHHHHhcCCHHH
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVM-RVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~-~~~~~~~li~~y~~~g~~~~  132 (230)
                      .|..+-..+.+.|++++|...|++..+.            +........ .......-. +...|+.+-..|.+.|++++
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~------------~~~~~~~~~-~~~~~~~~~~~~~~~~nla~~~~~~g~~~~  291 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRY------------VEGSRAAAE-DADGAKLQPVALSCVLNIGACKLKMSDWQG  291 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH------------HHHHHHHSC-HHHHGGGHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHH------------hhcCccccC-hHHHHHHHHHHHHHHHHHHHHHHhccCHHH
Confidence            3666777888899999999999875541            000000000 111111111 67888899999999999999


Q ss_pred             HHHHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          133 ARGIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       133 A~~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      |.+.+++..+  | +...|..+-.++..    ++|++.+++..+.
T Consensus       292 A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          292 AVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             HHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            9999998776  4 34455555444443    4666666665543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=92.23  E-value=1.4  Score=37.77  Aligned_cols=111  Identities=14%  Similarity=0.093  Sum_probs=78.9

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcCCCChhhHHH-----HHHHHHhcCChhHHHHHHHHHHhCCCCCCc-ccHHHHHHHhh
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKITQPSVFLWNT-----MIKGYSRIDSHKNGVLMYLDLLKSDVRRDN-YTFPFLFKGFT   98 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~-----li~~~~~~~~~~~a~~~~~~M~~~g~~p~~-~t~~~ll~~~~   98 (230)
                      .+....  +.+.++.|+.+|+....|+ .++..     .+... ..++++.|..+|+...+.-  |+. .-+...++-..
T Consensus       292 y~~~~~--r~~~~~~AR~i~~~A~~~~-~~~~v~i~~A~lE~~-~~~d~~~ar~ife~al~~~--~~~~~~~~~yid~e~  365 (493)
T 2uy1_A          292 HLNYVL--KKRGLELFRKLFIELGNEG-VGPHVFIYCAFIEYY-ATGSRATPYNIFSSGLLKH--PDSTLLKEEFFLFLL  365 (493)
T ss_dssp             HHHHHH--HHHCHHHHHHHHHHHTTSC-CCHHHHHHHHHHHHH-HHCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHH--HcCCHHHHHHHHHHhhCCC-CChHHHHHHHHHHHH-HCCChHHHHHHHHHHHHHC--CCCHHHHHHHHHHHH
Confidence            344444  6778999999999886443 23332     22222 2347999999999966532  332 23444566666


Q ss_pred             hcCch--hhHHHhhhh-hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           99 RDIAG--SLEKSCIVM-RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        99 ~~~~~--a~~~~~~~~-~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      +.|+.  ++.+|+... ....|...++.=.+.|+.+.++++++++.
T Consensus       366 ~~~~~~~aR~l~er~~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          366 RIGDEENARALFKRLEKTSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             HHTCHHHHHHHHHHSCCBHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            77887  899999887 78889999998889999999999998775

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=91.99  E-value=1  Score=27.50  Aligned_cols=62  Identities=16%  Similarity=0.191  Sum_probs=40.5

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHH
Q 042210           53 FLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDM  132 (230)
Q Consensus        53 ~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~  132 (230)
                      ..|..+-..+.+.|++++|...|++..+.  .|+                          +...+..+-..|.+.|++++
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~--------------------------~~~~~~~l~~~~~~~~~~~~   61 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPN--------------------------NAEAWYNLGNAYYKQGDYDE   61 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT--------------------------CHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCC--------------------------CHHHHHHHHHHHHHHhhHHH
Confidence            35566666777788888888888775542  121                          23445556666777778888


Q ss_pred             HHHHHhhccC
Q 042210          133 ARGIFYMSCE  142 (230)
Q Consensus       133 A~~vf~~m~~  142 (230)
                      |.+.|++..+
T Consensus        62 A~~~~~~a~~   71 (91)
T 1na3_A           62 AIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            8777776543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=91.94  E-value=1.1  Score=35.38  Aligned_cols=113  Identities=4%  Similarity=-0.167  Sum_probs=79.2

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh---h----HhHHHHHHHHHHhc
Q 042210           57 TMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM---R----VFVQNALISTYCLC  127 (230)
Q Consensus        57 ~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~---~----~~~~~~li~~y~~~  127 (230)
                      .....+...|++++|.++|+.....+  |+....-.+-..+.+.+++  +...+....   +    ...+..+=.++.+.
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~L  184 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANL  184 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHC
Confidence            35566778899999999999887643  5443444455578888998  888887665   1    23566667789999


Q ss_pred             CCHHHHHHHHhhccC-CC-h--h---hhHH---HHHHhhhcchhhhHHHHHHHh
Q 042210          128 GEVDMARGIFYMSCE-DD-D--G---LHEL---IRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       128 g~~~~A~~vf~~m~~-~~-~--~---t~n~---li~~~~~~~~~~~~~~m~~~~  171 (230)
                      |++++|.+.|++... |. .  .   .|+.   +...+..++|.+.|+++....
T Consensus       185 G~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          185 ALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             TCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            999999999998753 32 1  1   1221   223344578999999888765

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=91.62  E-value=4.3  Score=32.35  Aligned_cols=134  Identities=9%  Similarity=0.002  Sum_probs=76.2

Q ss_pred             CChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChh--HHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc------h
Q 042210           35 GDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHK--NGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA------G  103 (230)
Q Consensus        35 ~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~--~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~------~  103 (230)
                      ++++++.++++.+-   +.|...|+----.+.+.|.++  ++++.++.+.+.... |...|+---....+.+.      +
T Consensus       124 ~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          124 FDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             CCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhhhH
Confidence            67777777777765   556667766666666667766  788888887765433 44445444344444443      2


Q ss_pred             --hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHH-HHHHHhhccC------CChhhhHHHHHHhhh----cchhhhHH
Q 042210          104 --SLEKSCIVM-----RVFVQNALISTYCLCGEVDM-ARGIFYMSCE------DDDGLHELIRIKAVD----DDLHELFP  165 (230)
Q Consensus       104 --a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~-A~~vf~~m~~------~~~~t~n~li~~~~~----~~~~~~~~  165 (230)
                        +.+......     |...|+-+-..+.+.|+... +..+.++..+      ++...+..+...+..    ++|.+.++
T Consensus       203 ~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~  282 (306)
T 3dra_A          203 DEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYD  282 (306)
T ss_dssp             HHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Confidence              333333333     77777777777777777433 4445444332      233444444444443    35666666


Q ss_pred             HHHH
Q 042210          166 EYLV  169 (230)
Q Consensus       166 ~m~~  169 (230)
                      .+.+
T Consensus       283 ~l~~  286 (306)
T 3dra_A          283 LLKS  286 (306)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            6554

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=90.76  E-value=1.9  Score=27.54  Aligned_cols=51  Identities=18%  Similarity=0.185  Sum_probs=32.0

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhcCch
Q 042210           51 SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRDIAG  103 (230)
Q Consensus        51 ~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~~~~  103 (230)
                      +...|..+-..|.+.|++++|...|++..+..  |+ ...|..+-.++.+.|++
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~   57 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKLYERLDRT   57 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCH
Confidence            45567777778888888888888888865532  32 22344444444444444

>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=90.50  E-value=1.3  Score=31.86  Aligned_cols=88  Identities=11%  Similarity=0.007  Sum_probs=64.1

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CCC--------hh-----hHHHHHHHHHhcCChhHHHHHHHHHHhC-----CCCCC
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QPS--------VF-----LWNTMIKGYSRIDSHKNGVLMYLDLLKS-----DVRRD   86 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~~--------~~-----~yn~li~~~~~~~~~~~a~~~~~~M~~~-----g~~p~   86 (230)
                      ..+.  +.|++++|...|++.-  .|+        ..     .|+.+=.++.+.|++++|+..|++-.+.     .+.|+
T Consensus        19 ~~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           19 QRQL--VAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQD   96 (159)
T ss_dssp             HHHH--HHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTST
T ss_pred             HHHH--HCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCc
Confidence            4455  8899999999999865  333        22     7888888899999999999998875442     12343


Q ss_pred             cccHHHHHHHhhhcCchhhHHHhhhhhHhHH----HHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           87 NYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQ----NALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        87 ~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~----~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                                                +...|    ...=.++.+.|++++|..-|++-.+
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                                      23334    5556678889999999999987653

>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=90.31  E-value=1.7  Score=28.66  Aligned_cols=77  Identities=16%  Similarity=0.077  Sum_probs=54.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCcHHHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210            2 HQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ++|..+-+++...|-   ..+..+|+.-.+-..|++++|..+.+....||...|-+|  +-.+.|-.+++..-+.++..+
T Consensus        24 qEA~tIAdwL~~~~~---~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~AL--ce~rlGl~s~le~rL~~la~s   98 (116)
T 2p58_C           24 EEANCIAEWLHLKGE---EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLAL--CEYRLGLGSALESRLNRLARS   98 (116)
T ss_dssp             HHHHHHHHHHHHTTC---HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHH--HHHHHTCHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCCc---HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHH--HHHhcccHHHHHHHHHHHHhC
Confidence            356667777766653   111455544333288999999999999999999999887  556777777777777777666


Q ss_pred             CC
Q 042210           82 DV   83 (230)
Q Consensus        82 g~   83 (230)
                      |-
T Consensus        99 g~  100 (116)
T 2p58_C           99 QD  100 (116)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=89.65  E-value=1.6  Score=28.77  Aligned_cols=77  Identities=13%  Similarity=0.007  Sum_probs=55.2

Q ss_pred             hhHHHHHHHHHHhcCCCCCcHHHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210            2 HQLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ++|..+-+++...|-   ..+..+|+.-.+-..|++++|..+.+....||...|-+|  +-.+.|-.+++..-+.++..+
T Consensus        23 qEA~tIAdwL~~~~~---~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~AL--ce~rlGl~s~le~rL~~la~s   97 (115)
T 2uwj_G           23 EEALCIAEWLERLGQ---DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFAL--CEWHLGLGAALDRRLAGLGGS   97 (115)
T ss_dssp             HHHHHHHHHHHHTTC---HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHH--HHHHTTCHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhCCc---HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHH--HHHhcccHHHHHHHHHHHHhC
Confidence            356667777766653   111455544333289999999999999999999999887  566778888877777787776


Q ss_pred             CC
Q 042210           82 DV   83 (230)
Q Consensus        82 g~   83 (230)
                      |-
T Consensus        98 g~   99 (115)
T 2uwj_G           98 SD   99 (115)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=89.20  E-value=0.96  Score=31.65  Aligned_cols=56  Identities=13%  Similarity=-0.015  Sum_probs=35.1

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      ..+-.+|.  +.|++++|...++...   +.+...|..+-.+|...|++++|...|++-..
T Consensus        67 ~nla~~~~--~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           67 ANMSQCYL--NIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHHHH--HHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--hcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            44445555  6777777777766643   33455666666667777777777777766444

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=88.97  E-value=0.97  Score=28.45  Aligned_cols=53  Identities=13%  Similarity=0.322  Sum_probs=40.5

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--CC-Chh-hHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--QP-SVF-LWNTMIKGYSRIDSHKNGVLMYLDLLKS   81 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--~~-~~~-~yn~li~~~~~~~~~~~a~~~~~~M~~~   81 (230)
                      ..+.  +.|++++|...|++..  .| +.. .|..+-.+|.+.|++++|...|++..+.
T Consensus         8 ~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            8 KELI--NQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHH--HHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3455  7888999999988765  33 455 7777777888889999999998886653

>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=88.86  E-value=1.9  Score=29.54  Aligned_cols=14  Identities=7%  Similarity=0.047  Sum_probs=6.7

Q ss_pred             cCCHHHHHHHHhhc
Q 042210          127 CGEVDMARGIFYMS  140 (230)
Q Consensus       127 ~g~~~~A~~vf~~m  140 (230)
                      .++.++|.+.|++-
T Consensus        74 ~~d~~~A~~~~~~A   87 (138)
T 1klx_A           74 KKDLRKAAQYYSKA   87 (138)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHH
Confidence            44445555444443

>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=88.12  E-value=0.72  Score=38.88  Aligned_cols=54  Identities=17%  Similarity=0.114  Sum_probs=35.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC-------C---CCh-hhHHHHHHHHHhcCChhHHHHHHHHH
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT-------Q---PSV-FLWNTMIKGYSRIDSHKNGVLMYLDL   78 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~-------~---~~~-~~yn~li~~~~~~~~~~~a~~~~~~M   78 (230)
                      +.+-.+|.  ..|++++|..++++..       .   |++ .+||.|=..|...|++++|..+|++-
T Consensus       344 ~nLa~~y~--~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          344 YQAMGVCL--YMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHH--hhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            55666677  7777777777776543       2   222 35677777777777777777777663

>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=86.63  E-value=11  Score=32.69  Aligned_cols=45  Identities=16%  Similarity=0.139  Sum_probs=21.6

Q ss_pred             hHHHHHHHHhcC---CCChhhHHHHHHHHHhcC--ChhHHHHHHHHHHhC
Q 042210           37 LKYECKVFRKIT---QPSVFLWNTMIKGYSRID--SHKNGVLMYLDLLKS   81 (230)
Q Consensus        37 ~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~--~~~~a~~~~~~M~~~   81 (230)
                      ++++.+.++.+-   +.+...|+----.+.+.+  ++++++..++.+.+.
T Consensus        89 ~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~  138 (567)
T 1dce_A           89 VKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEA  138 (567)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhh
Confidence            455555555443   333444444444444444  445555555555443

>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=85.29  E-value=2.1  Score=35.91  Aligned_cols=86  Identities=3%  Similarity=-0.097  Sum_probs=63.0

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC-------CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHh-----CC-CCCC-
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT-------QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLK-----SD-VRRD-   86 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~-------~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~-----~g-~~p~-   86 (230)
                      .+..+.  +.|++++|.+++++..       .|+    ..+++.+...|...|++++|..++++...     .| --|+ 
T Consensus       293 ~ie~~~--~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~  370 (429)
T 3qwp_A          293 KIEELK--AHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVR  370 (429)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHH
T ss_pred             HHHHHH--hhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHH
Confidence            355566  8899999999997653       222    24689999999999999999999998653     22 2232 


Q ss_pred             cccHHHHHHHhhhcCch--hhHHHhhhh
Q 042210           87 NYTFPFLFKGFTRDIAG--SLEKSCIVM  112 (230)
Q Consensus        87 ~~t~~~ll~~~~~~~~~--a~~~~~~~~  112 (230)
                      ..+++.|-..|...|++  |..++....
T Consensus       371 a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          371 GVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            34677788888888888  666666554

>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=85.21  E-value=1.8  Score=35.83  Aligned_cols=64  Identities=13%  Similarity=0.143  Sum_probs=49.2

Q ss_pred             HHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh-----CCCCCCccc
Q 042210           24 KQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-----SDVRRDNYT   89 (230)
Q Consensus        24 ~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-----~g~~p~~~t   89 (230)
                      .++..+.  ..|+.++|...+....   +-+-..|-.+|.++.+.|+..+|++.|++..+     .|+.|+..+
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 AKAEAEI--ACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHH--HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHH--HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            4556666  8888888887777655   44666889999999999999999999988754     488887644

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=83.35  E-value=0.23  Score=42.76  Aligned_cols=172  Identities=12%  Similarity=0.008  Sum_probs=107.2

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~  102 (230)
                      +.|=.+..  +.+++.+|.+-|=  +..|...|..+|....+.|.+++-...++.-++..-.|  ..=+.|+.+|++.++
T Consensus        58 s~LgkAqL--~~~~v~eAIdsyI--kA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~--~IDteLi~ayAk~~r  131 (624)
T 3lvg_A           58 SQLAKAQL--QKGMVKEAIDSYI--KADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARES--YVETELIFALAKTNR  131 (624)
T ss_dssp             SSHHHHTT--TSSSCTTTTTSSC--CCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST--TTTHHHHHHHHTSCS
T ss_pred             HHHHHHHH--ccCchHHHHHHHH--hCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc--ccHHHHHHHHHhhCc
Confidence            34444444  4455555444332  23455678889999999999988777765544443334  344689999999888


Q ss_pred             h-hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC------------------------CChhhhHHHHHHhhh
Q 042210          103 G-SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE------------------------DDDGLHELIRIKAVD  157 (230)
Q Consensus       103 ~-a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~------------------------~~~~t~n~li~~~~~  157 (230)
                      + -.+=|-...+..-....=+-+-..|.++.|+-+|..+..                        .+..||-..-.+|..
T Consensus       132 L~elEefl~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd  211 (624)
T 3lvg_A          132 LAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVD  211 (624)
T ss_dssp             SSTTTSTTSCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHH
T ss_pred             HHHHHHHHcCCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhC
Confidence            7 211111122343444455666677777777777776652                        466788888888888


Q ss_pred             cchhhhHHHHHHHhhhcCchhhhhhhhhcccccCCcccccccCCccCCcccccc
Q 042210          158 DDLHELFPEYLVQMLALPDTFMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGR  211 (230)
Q Consensus       158 ~~~~~~~~~m~~~~~~~p~~~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~  211 (230)
                      .+-+++....--.-.+.||.-  ..  +       +.-|.+.|-+++-..+++.
T Consensus       212 ~~EfrLAqicGLniIvhadeL--~e--l-------v~~YE~~G~f~ELIsLlEa  254 (624)
T 3lvg_A          212 GKEFRLAQMCGLHIVVHADEL--EE--L-------INYYQDRGYFEELITMLEA  254 (624)
T ss_dssp             SCTTTTTTHHHHHHHCCSSCC--SG--G-------GSSSSTTCCCTTSTTTHHH
T ss_pred             chHHHHHHHhcchhcccHHHH--HH--H-------HHHHHhCCCHHHHHHHHHH
Confidence            888888775444443555542  22  2       3378888888887776543

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=80.65  E-value=8.6  Score=24.39  Aligned_cols=49  Identities=8%  Similarity=-0.031  Sum_probs=34.9

Q ss_pred             hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHH
Q 042210          104 SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRI  153 (230)
Q Consensus       104 a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~  153 (230)
                      +..+++...     ++.....+=..+.+.|++++|...|+.+.+  |+ ..|-.+|.
T Consensus        28 A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~-~~~~~~i~   83 (93)
T 3bee_A           28 VSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP-NLDRVTII   83 (93)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT-TCCHHHHH
T ss_pred             HHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CccHHHHH
Confidence            666666555     566666667788899999999999998876  66 44544443

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=80.09  E-value=3  Score=30.82  Aligned_cols=163  Identities=7%  Similarity=-0.122  Sum_probs=77.1

Q ss_pred             HHHHHHHHHhcCCCCCcH---HHHHHHHhhhccCChHHHHHHHHhcCCCCh----hhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            5 KQIHSQTIKLGLLTKPHC---PKQTRYLLLYEKGDLKYECKVFRKITQPSV----FLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         5 ~~~~~~m~~~g~~~~~~~---~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~----~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      .++.+.+.+.|..++...   .+.+...+  +.|+++-+..+++.-..++.    ..++.+ ...++.|+.+    +++.
T Consensus        22 ~~~~~~Ll~~g~~~~~~~~~g~t~L~~A~--~~~~~~~v~~Ll~~~~~~~~~~~~~~~t~L-~~A~~~~~~~----~v~~   94 (240)
T 3eu9_A           22 YERCRELVEAGYDVRQPDKENVTLLHWAA--INNRIDLVKYYISKGAIVDQLGGDLNSTPL-HWATRQGHLS----MVVQ   94 (240)
T ss_dssp             HHHHHHHHHTTCCTTCCCTTSCCHHHHHH--HTTCHHHHHHHHHTTCCTTCCBTTTTBCHH-HHHHHHTCHH----HHHH
T ss_pred             hHHHHHHHHcCCCcCCCCCCCCCHHHHHH--HhCCHHHHHHHHHcCCcchhhcCCcCCChh-HHHHHcCCHH----HHHH
Confidence            355677777776665432   45666667  88888888877776542221    122333 3344455544    4444


Q ss_pred             HHhCCCCCCcc---cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhc-cCCCh-
Q 042210           78 LLKSDVRRDNY---TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMS-CEDDD-  145 (230)
Q Consensus        78 M~~~g~~p~~~---t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m-~~~~~-  145 (230)
                      +.+.|..|+..   -.+.+ ...+..|+.  .+.+.+.-.     +..-.+.|..+ +..+......+++.+. ..++. 
T Consensus        95 Ll~~g~~~~~~~~~g~t~l-~~A~~~~~~~~~~~Ll~~~~~~~~~~~~g~t~l~~a-~~~~~~~~~~~~L~~~~~~~~~~  172 (240)
T 3eu9_A           95 LMKYGADPSLIDGEGCSCI-HLAAQFGHTSIVAYLIAKGQDVDMMDQNGMTPLMWA-AYRTHSVDPTRLLLTFNVSVNLG  172 (240)
T ss_dssp             HHHTTCCTTCCCTTSCCHH-HHHHHTTCHHHHHHHHHTTCCTTCCCTTSCCHHHHH-HHHCCSSTTHHHHHHTTCCTTCC
T ss_pred             HHHcCCCCcccCCCCCCHH-HHHHHcCHHHHHHHHHhcCCCccccCCCCCcHHHHH-HHhCChHHHHHHHHhcCCCcchh
Confidence            45556555432   22333 333444555  444443322     22222333333 3334433333333332 22221 


Q ss_pred             ---hhhHHHHHHhhhcchhhhHHHHHHHhhhcCchh
Q 042210          146 ---GLHELIRIKAVDDDLHELFPEYLVQMLALPDTF  178 (230)
Q Consensus       146 ---~t~n~li~~~~~~~~~~~~~~m~~~~~~~p~~~  178 (230)
                         .-++.+. ..+..+..+..+-+.+.| ..|+..
T Consensus       173 ~~~~g~t~L~-~A~~~~~~~~v~~Ll~~g-~~~~~~  206 (240)
T 3eu9_A          173 DKYHKNTALH-WAVLAGNTTVISLLLEAG-ANVDAQ  206 (240)
T ss_dssp             CTTTCCCHHH-HHHHHTCHHHHHHHHHHT-CCTTCB
T ss_pred             hccCCCcHHH-HHHHcCCHHHHHHHHHcC-CCCCCc
Confidence               1223332 223344566777777777 555533

>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=80.02  E-value=9.7  Score=25.84  Aligned_cols=104  Identities=12%  Similarity=-0.058  Sum_probs=75.4

Q ss_pred             cCChHHHHHHHHhcC-CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhh----cCch--hhH
Q 042210           34 KGDLKYECKVFRKIT-QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTR----DIAG--SLE  106 (230)
Q Consensus        34 ~~~~~~a~~~~~~m~-~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~----~~~~--a~~  106 (230)
                      .++.++|.+.|.+.- .-+....  +=..|...+..++|.+.|++-.+.|.   ...+..|=..|..    .++.  |..
T Consensus         8 ~~d~~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g~---~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACELNS---GNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHcCCC---HHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            357889999998765 3333344  55566667888889999999877653   3455555555555    5566  777


Q ss_pred             HHhhhh---hHhHHHHHHHHHHh----cCCHHHHHHHHhhccC
Q 042210          107 KSCIVM---RVFVQNALISTYCL----CGEVDMARGIFYMSCE  142 (230)
Q Consensus       107 ~~~~~~---~~~~~~~li~~y~~----~g~~~~A~~vf~~m~~  142 (230)
                      .+....   +...+..|=..|..    .++.++|.+.|+.-.+
T Consensus        83 ~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~  125 (138)
T 1klx_A           83 YYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  125 (138)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHH
Confidence            777776   77888888888888    8999999999987654

---

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	230
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.31
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.3
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.3
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.19
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	97.73
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.44
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.23
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.22
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.16
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.06
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.01
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.88
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.85
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.68
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	96.6
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.21
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	96.14
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	96.11
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.9
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	95.71
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.69
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.53
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	95.53
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	95.46
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	95.38
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.28
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	95.07
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	94.66
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	94.48
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	94.21
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.95
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	93.95
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	93.64
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	93.26
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	93.19
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	92.99
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	92.98
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	92.74
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	92.47
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	91.72
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	90.75
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	89.81
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	89.71
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	83.78
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	82.31
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	80.17

>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=98.31  E-value=4.6e-05  Score=59.81  Aligned_cols=165  Identities=8%  Similarity=-0.004  Sum_probs=120.0

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLD   77 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~   77 (230)
                      .|...++...+.  .|+...  ..+-..+.  ..|++++|...++...   ..+...|..+-..+.+.|++++|...|++
T Consensus       187 ~A~~~~~~al~~--~p~~~~~~~~l~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  262 (388)
T d1w3ba_         187 LAIHHFEKAVTL--DPNFLDAYINLGNVLK--EARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRR  262 (388)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHH--TTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CcccHHHHHHHhhhhh--ccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            455556555543  455443  66667788  9999999999998765   45566777888888999999999999998


Q ss_pred             HHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CC-hh
Q 042210           78 LLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DD-DG  146 (230)
Q Consensus        78 M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~-~~  146 (230)
                      ..+.  .| +..+|..+-..+.+.|+.  |...+....     +...+..+...|.+.|++++|.+.|++..+  |+ ..
T Consensus       263 al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~  340 (388)
T d1w3ba_         263 AIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAA  340 (388)
T ss_dssp             HHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHH
T ss_pred             HHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH
Confidence            7653  34 345777888888888988  877777766     677888889999999999999999998765  54 44


Q ss_pred             hhHHHHHHhhh----cchhhhHHHHHHHhhhcCc
Q 042210          147 LHELIRIKAVD----DDLHELFPEYLVQMLALPD  176 (230)
Q Consensus       147 t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~  176 (230)
                      +|..+-..+..    ++|.+.|++..+   ..|+
T Consensus       341 ~~~~la~~~~~~g~~~~A~~~~~~al~---l~P~  371 (388)
T d1w3ba_         341 AHSNLASVLQQQGKLQEALMHYKEAIR---ISPT  371 (388)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHT---TCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH---hCCC
Confidence            56656555544    456666655433   3465

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=1.6e-05  Score=62.18  Aligned_cols=150  Identities=9%  Similarity=0.018  Sum_probs=107.3

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CC-C-hhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-S-VFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~-~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+++...+.....+... ........  +.|+.+.|..+|+.+.  .| + ...|...+..+.+.|+.+.|.++|+
T Consensus        81 ~~a~~i~~ral~~~~p~~~~l~~~ya~~~~--~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          81 DEAANIYERAISTLLKKNMLLYFAYADYEE--SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHH--hcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            356677777665443333344 67778888  9999999999999864  33 3 3479999999999999999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHH-hhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C---
Q 042210           77 DLLKSDVRRDNYTFPFLFKG-FTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D---  143 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~-~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~---  143 (230)
                      ...+.+-. +...|...... +...|+.  |..+++...     +...|...++.+.+.|+++.|+.+|++-..  |   
T Consensus       159 ~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         159 KAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence            98765321 22223222221 2234555  888888887     788999999999999999999999998533  2   


Q ss_pred             C--hhhhHHHHHH
Q 042210          144 D--DGLHELIRIK  154 (230)
Q Consensus       144 ~--~~t~n~li~~  154 (230)
                      +  ...|...+.-
T Consensus       238 ~~~~~iw~~~~~f  250 (308)
T d2onda1         238 EKSGEIWARFLAF  250 (308)
T ss_dssp             GGCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            1  2367777653

>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=98.30  E-value=9e-06  Score=64.09  Aligned_cols=187  Identities=10%  Similarity=0.014  Sum_probs=137.5

Q ss_pred             CCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHH
Q 042210           17 LTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFP   91 (230)
Q Consensus        17 ~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~   91 (230)
                      .|+...  ..+-..+.  ..|+.++|...+++..   +.+...|..+-..+...|++++|...|++....+-. +...+.
T Consensus       165 ~~~~~~~~~~l~~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~  241 (388)
T d1w3ba_         165 QPNFAVAWSNLGCVFN--AQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPN-HAVVHG  241 (388)
T ss_dssp             CTTCHHHHHHHHHHHH--TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             CcchhHHHHhhccccc--ccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhh-HHHHHH
Confidence            455444  55667777  9999999999998764   445667888999999999999999999998765432 445677


Q ss_pred             HHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHHHHHhhh----
Q 042210           92 FLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELIRIKAVD----  157 (230)
Q Consensus        92 ~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~li~~~~~----  157 (230)
                      .+-..+.+.|++  |...+....     +...|..+-..|.+.|++++|.+.|+....  | +...+..+...+..    
T Consensus       242 ~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  321 (388)
T d1w3ba_         242 NLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNI  321 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCH
Confidence            788888999998  888888765     678899999999999999999999997765  3 44556555555554    


Q ss_pred             cchhhhHHHHHHHhhhcCchh-hhhhhhhcccccCCcccccccCCccCCccccccccccCCCcc
Q 042210          158 DDLHELFPEYLVQMLALPDTF-MGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDM  220 (230)
Q Consensus       158 ~~~~~~~~~m~~~~~~~p~~~-t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~  220 (230)
                      ++|++.+++..+   ..|+.. ++..+..         .+.+.|++++|...+..+.+.  .|+
T Consensus       322 ~~A~~~~~~al~---~~p~~~~~~~~la~---------~~~~~g~~~~A~~~~~~al~l--~P~  371 (388)
T d1w3ba_         322 EEAVRLYRKALE---VFPEFAAAHSNLAS---------VLQQQGKLQEALMHYKEAIRI--SPT  371 (388)
T ss_dssp             HHHHHHHHHHTT---SCTTCHHHHHHHHH---------HHHTTTCCHHHHHHHHHHHTT--CTT
T ss_pred             HHHHHHHHHHHH---hCCCCHHHHHHHHH---------HHHHcCCHHHHHHHHHHHHHh--CCC
Confidence            355555555432   356532 2333222         677899999999999887764  454

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=1e-05  Score=63.10  Aligned_cols=197  Identities=12%  Similarity=0.018  Sum_probs=126.1

Q ss_pred             hhHHHHHHHHHHhcCCCCCc-H-HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPH-C-PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~-~-~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|.+.|+...+.  .|+.. . ..+-..|.  ..|++++|...|++..   +-+...|..+...|...|++++|.+.++
T Consensus        36 ~~A~~~~~~al~~--~P~~~~a~~~lg~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~  111 (323)
T d1fcha_          36 PNAVLLFEAAVQQ--DPKHMEAWQYLGTTQA--ENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILR  111 (323)
T ss_dssp             HHHHHHHHHHHHS--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHHHHHH--HcCChHHHHHHHHhhhccccccccccccccccccccccccccccchh
Confidence            5678888887765  46544 3 66667788  9999999999998764   3456678888888999999999999998


Q ss_pred             HHHhCCC-CCCcccHHH-------------HHHHhhhcCch--hhHHHhhhh-------hHhHHHHHHHHHHhcCCHHHH
Q 042210           77 DLLKSDV-RRDNYTFPF-------------LFKGFTRDIAG--SLEKSCIVM-------RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        77 ~M~~~g~-~p~~~t~~~-------------ll~~~~~~~~~--a~~~~~~~~-------~~~~~~~li~~y~~~g~~~~A  133 (230)
                      +.....- .+.......             .+..+.+.+..  +...+....       +..++..+-..+.+.|++++|
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A  191 (323)
T d1fcha_         112 DWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKA  191 (323)
T ss_dssp             HHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhh
Confidence            8765321 011111100             01111111222  333433332       456777888889999999999


Q ss_pred             HHHHhhccC--CC-hhhhHHHHHHhhh----cchhhhHHHHHHHhhhcCch-hhhhhhhhcccccCCcccccccCCccCC
Q 042210          134 RGIFYMSCE--DD-DGLHELIRIKAVD----DDLHELFPEYLVQMLALPDT-FMGEGLEVIPKSQAPREETPRVGNLEEG  205 (230)
Q Consensus       134 ~~vf~~m~~--~~-~~t~n~li~~~~~----~~~~~~~~~m~~~~~~~p~~-~t~~~l~~~~~~~~~~~a~~~~g~~~~a  205 (230)
                      ...|++...  |+ ...|..+-..+..    ++|.+.|++..+.   .|+. ..+..+..         +|.+.|++++|
T Consensus       192 ~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---~p~~~~a~~~lg~---------~~~~~g~~~~A  259 (323)
T d1fcha_         192 VDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL---QPGYIRSRYNLGI---------SCINLGAHREA  259 (323)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHH---------HHHHHTCHHHH
T ss_pred             hcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHH---hhccHHHHHHHHH---------HHHHCCCHHHH
Confidence            999998654  44 5566666555443    4666777665543   4542 22333222         67788999999


Q ss_pred             ccccccccc
Q 042210          206 TPQEGRPHE  214 (230)
Q Consensus       206 ~~i~~~~~~  214 (230)
                      ...+....+
T Consensus       260 ~~~~~~al~  268 (323)
T d1fcha_         260 VEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888887666

>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=97.73  E-value=0.00023  Score=55.32  Aligned_cols=138  Identities=7%  Similarity=-0.031  Sum_probs=102.7

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH-HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHH-HHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC-PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIK-GYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~-~~~~~~~~~~a~~~~~   76 (230)
                      +.|+.+++.+.+..-.....+ ...+....  +.|+++.|+++|+...  .| +...|-.... -+...|+.+.|..+|+
T Consensus       116 ~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~--~~~~~~~ar~i~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e  193 (308)
T d2onda1         116 EKVHSIYNRLLAIEDIDPTLVYIQYMKFAR--RAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFE  193 (308)
T ss_dssp             HHHHHHHHHHHTSSSSCTHHHHHHHHHHHH--HHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCChHHHHHHHHHHHH--HcCChHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHH
Confidence            467888887765432222235 78888888  9999999999999875  22 2233322222 2334689999999999


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh---------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM---------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ..... .+-+...|...++...+.|++  |+.+|+...         ....|...+..-.+.|+++.++++++++.+
T Consensus       194 ~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         194 LGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            98764 233456788889999999999  999999875         235799999999999999999999998865

>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=97.44  E-value=0.002  Score=49.48  Aligned_cols=165  Identities=11%  Similarity=0.005  Sum_probs=113.6

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CCCh----------------hhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QPSV----------------FLWNTMIKG   61 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~~~----------------~~yn~li~~   61 (230)
                      ++|...+....+.  .|+...  ..+...|.  ..|++++|.+.++...  .|+.                ..+...+..
T Consensus        70 ~~A~~~~~~al~~--~p~~~~~~~~la~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (323)
T d1fcha_          70 LLAISALRRCLEL--KPDNQTALMALAVSFT--NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGS  145 (323)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHH
T ss_pred             HHHHHHHHhhhcc--cccccccccccccccc--ccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHH
Confidence            4677777776665  465444  66778888  9999999999998764  2221                011122233


Q ss_pred             HHhcCChhHHHHHHHHHHh-CCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHH
Q 042210           62 YSRIDSHKNGVLMYLDLLK-SDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        62 ~~~~~~~~~a~~~~~~M~~-~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A  133 (230)
                      +...+...++...|.+..+ ..-.++...+..+-..+...|++  |...+....     +...|..+-..|.+.|++++|
T Consensus       146 ~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A  225 (323)
T d1fcha_         146 LLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEA  225 (323)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhH
Confidence            3445667788888877654 33334556677778888899998  888888776     688899999999999999999


Q ss_pred             HHHHhhccC--CC-hhhhHHHHHHhh----hcchhhhHHHHHHH
Q 042210          134 RGIFYMSCE--DD-DGLHELIRIKAV----DDDLHELFPEYLVQ  170 (230)
Q Consensus       134 ~~vf~~m~~--~~-~~t~n~li~~~~----~~~~~~~~~~m~~~  170 (230)
                      .+.|++..+  |+ ..+|..+-..+.    .++|++.|++-.+-
T Consensus       226 ~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  269 (323)
T d1fcha_         226 VAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNM  269 (323)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            999998764  54 455666655544    35677777765553

>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=97.23  E-value=0.016  Score=44.67  Aligned_cols=162  Identities=9%  Similarity=-0.010  Sum_probs=102.4

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccC-ChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKG-DLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMY   75 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~-~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~   75 (230)
                      ++|.++++..++.  .|+..+  +..-..+.  +.| ++++|...++...   +.+...|+.+-..+.+.|++++|+..|
T Consensus        60 ~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~--~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~eAl~~~  135 (315)
T d2h6fa1          60 ERAFKLTRDAIEL--NAANYTVWHFRRVLLK--SLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFI  135 (315)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHH
T ss_pred             HHHHHHHHHHHHH--CCCChHHHHHHHHHHH--HhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHHHHHHHH
Confidence            4667777777665  466555  44444555  555 4788888887754   445667777777788888888888888


Q ss_pred             HHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCC------HHHHHHHHhhcc
Q 042210           76 LDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGE------VDMARGIFYMSC  141 (230)
Q Consensus        76 ~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~------~~~A~~vf~~m~  141 (230)
                      +...+.  .| +...|..+-..+.+.|++  |...++...     +...|+.+-..+.+.+.      +++|.+.+....
T Consensus       136 ~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al  213 (315)
T d2h6fa1         136 ADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMI  213 (315)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHH
T ss_pred             hhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHH
Confidence            887663  23 455677777777777877  777777666     55666666555555554      466666666554


Q ss_pred             C--C-ChhhhHHHHHHhh---hcchhhhHHHHHH
Q 042210          142 E--D-DDGLHELIRIKAV---DDDLHELFPEYLV  169 (230)
Q Consensus       142 ~--~-~~~t~n~li~~~~---~~~~~~~~~~m~~  169 (230)
                      +  | |...|+-+...+.   ..++.+.+....+
T Consensus       214 ~~~P~~~~~~~~l~~ll~~~~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         214 KLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLD  247 (315)
T ss_dssp             HHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHH
T ss_pred             HhCCCchHHHHHHHHHHHhcChHHHHHHHHHHHH
Confidence            3  4 4556665533332   2344455554433

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=0.0044  Score=44.46  Aligned_cols=108  Identities=10%  Similarity=0.033  Sum_probs=77.5

Q ss_pred             ccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch--hhHHHh
Q 042210           33 EKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG--SLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~  109 (230)
                      ..|+++.|.+.|+++..|+...|.-+=..|...|++++|.+.|++-.+.+  | +...|..+=.++.+.|+.  |..-|+
T Consensus        17 ~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld--p~~~~a~~~~g~~~~~~g~~~~A~~~~~   94 (192)
T d1hh8a_          17 DKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYFQRGMLYYQTEKYDLAIKDLK   94 (192)
T ss_dssp             HTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh--hhhhhhHHHHHHHHHhhccHHHHHHHHH
Confidence            78899999999998888888888888888888999999999998865532  3 344566666677777777  554444


Q ss_pred             hhh---------------------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVM---------------------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~---------------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ...                     ...++..+-..|.+.|++++|.+.|+...+
T Consensus        95 kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_          95 EALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             HHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            432                     123444555677788888888887776543

>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=97.16  E-value=0.0023  Score=47.49  Aligned_cols=180  Identities=8%  Similarity=-0.100  Sum_probs=112.7

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIA  102 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~  102 (230)
                      ..|.  +.|+.++|.+.|++..   +.+..+|+.+=.+|.+.|++++|...|++..+.  .| +..++..+-.++...|+
T Consensus        45 ~~y~--~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~  120 (259)
T d1xnfa_          45 VLYD--SLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGR  120 (259)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTC
T ss_pred             HHHH--HCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH--HhhhhhhHHHHHHHHHHHhh
Confidence            4556  9999999999999865   456778999999999999999999999998763  34 34467778888889999


Q ss_pred             h--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccCCCh--hhhHHHHHHhh-hcchhhhHHHHHHHhh
Q 042210          103 G--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCEDDD--GLHELIRIKAV-DDDLHELFPEYLVQML  172 (230)
Q Consensus       103 ~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~~~~--~t~n~li~~~~-~~~~~~~~~~m~~~~~  172 (230)
                      +  |...+....     +......+--.+.+.+..+.+..+......++.  ..++.. ..+. .......+........
T Consensus       121 ~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  199 (259)
T d1xnfa_         121 DKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIV-EFYLGNISEQTLMERLKADAT  199 (259)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHHHHH-HHHTTSSCHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHhhccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhhhHH-HHHHHHHHHHHHHHHHHHHHH
Confidence            8  877777766     344444444455666666666665555444332  233322 2221 1122222222222110


Q ss_pred             ----hcCch-hhhhhhhhcccccCCcccccccCCccCCccccccccccCCCcccc
Q 042210          173 ----ALPDT-FMGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEHSQDDMSL  222 (230)
Q Consensus       173 ----~~p~~-~t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~~~~~~~~  222 (230)
                          ..|+. .++..+..         .+...|++++|...+......  .|+.+
T Consensus       200 ~~~~~~~~~~~~~~~lg~---------~~~~~g~~~~A~~~~~~al~~--~p~~~  243 (259)
T d1xnfa_         200 DNTSLAEHLSETNFYLGK---------YYLSLGDLDSATALFKLAVAN--NVHNF  243 (259)
T ss_dssp             SHHHHHHHHHHHHHHHHH---------HHHHTTCHHHHHHHHHHHHTT--CCTTC
T ss_pred             HhhhcCcccHHHHHHHHH---------HHHHCCCHHHHHHHHHHHHHc--CCCCH
Confidence                11221 12222112         566889999999999887765  45443

>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=97.06  E-value=0.017  Score=42.41  Aligned_cols=76  Identities=12%  Similarity=0.046  Sum_probs=60.8

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...|+...+.  .|+...  ..+=.+|.  +.|++++|.+.|++..  .| +...|..+-..|...|++++|...|+
T Consensus        54 ~~A~~~~~~al~l--~p~~~~a~~~lg~~~~--~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~  129 (259)
T d1xnfa_          54 ALARNDFSQALAI--RPDMPEVFNYLGIYLT--QAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLL  129 (259)
T ss_dssp             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhhcc--CCCCHHHHhhhchHHH--HHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHH
Confidence            5677788877665  566544  67778888  9999999999999876  34 45678888888999999999999999


Q ss_pred             HHHhC
Q 042210           77 DLLKS   81 (230)
Q Consensus        77 ~M~~~   81 (230)
                      .-.+.
T Consensus       130 ~al~~  134 (259)
T d1xnfa_         130 AFYQD  134 (259)
T ss_dssp             HHHHH
T ss_pred             HHHhh
Confidence            87654

>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=97.01  E-value=0.0048  Score=47.85  Aligned_cols=123  Identities=6%  Similarity=-0.096  Sum_probs=98.3

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcC-ChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhh
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRID-SHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTR   99 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~-~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~   99 (230)
                      +-..+.  +.+..++|.+.+++.-  .| +...|+..-..+...| ++++|+..++...+..  | +..+|..+-..+.+
T Consensus        49 ~~~~~~--~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~--p~~~~a~~~~~~~~~~  124 (315)
T d2h6fa1          49 FRAVLQ--RDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRVLVEW  124 (315)
T ss_dssp             HHHHHH--HTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHH
T ss_pred             HHHHHH--hCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH--HhhhhHHHHHhHHHHh
Confidence            334455  8889999999999876  44 5567888877777765 5899999999875532  3 45578888888888


Q ss_pred             cCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--C-ChhhhHHH
Q 042210          100 DIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--D-DDGLHELI  151 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~-~~~t~n~l  151 (230)
                      .|+.  |...+....     +...|+.+-..|.+.|++++|...|+...+  | |...|+.+
T Consensus       125 l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r  186 (315)
T d2h6fa1         125 LRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQR  186 (315)
T ss_dssp             HTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             hccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHH
Confidence            9998  888888887     788999999999999999999999998876  4 56677754

>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=96.88  E-value=0.0066  Score=41.86  Aligned_cols=82  Identities=7%  Similarity=0.027  Sum_probs=50.7

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...|.+..   +.+...|..+-.+|.+.|++++|...|+...+.  .|+                       
T Consensus        22 ~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~p~-----------------------   76 (159)
T d1a17a_          22 KAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKK-----------------------   76 (159)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHH--ccc-----------------------
Confidence            5666666666665543   334445555555566666666666666554432  122                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                         +...|..+...|...|++++|.+.|++...
T Consensus        77 ---~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~  106 (159)
T d1a17a_          77 ---YIKGYYRRAASNMALGKFRAALRDYETVVK  106 (159)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---chHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               456677777788888888888888887664

>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=96.85  E-value=0.0085  Score=41.25  Aligned_cols=82  Identities=9%  Similarity=-0.051  Sum_probs=55.8

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210           61 GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus        61 ~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      .|.+.|++++|...|++..+.  .|+                          +...|..+-..|.+.|++++|...|+..
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~--~p~--------------------------~~~~~~~lg~~~~~~~~~~~A~~~~~ka   70 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIEL--NPS--------------------------NAIYYGNRSLAYLRTECYGYALGDATRA   70 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--STT--------------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHhhhcccc--chh--------------------------hhhhhhhhHHHHHhccccchHHHHHHHH
Confidence            455667777777777665442  132                          5777888889999999999999999987


Q ss_pred             cC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          141 CE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       141 ~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      .+  | +..+|..+..++..    ++|.+.+++...-
T Consensus        71 l~~~p~~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          71 IELDKKYIKGYYRRAASNMALGKFRAALRDYETVVKV  107 (159)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            65  5 44577766655543    4555555555443

>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=96.68  E-value=0.01  Score=38.67  Aligned_cols=85  Identities=6%  Similarity=0.056  Sum_probs=56.9

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...|++..   +.+...|+.+=.+|.+.|++++|...|+...+.  .|+                       
T Consensus        15 ~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~p~-----------------------   69 (117)
T d1elwa_          15 SVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDL--KPD-----------------------   69 (117)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHh--ccc-----------------------
Confidence            6667777777776643   344555666666666667777776666664432  122                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CCh
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYMSCE--DDD  145 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~  145 (230)
                         +...|..+-..|.+.|++++|...|+...+  |+.
T Consensus        70 ---~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~p~~  104 (117)
T d1elwa_          70 ---WGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANN  104 (117)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTC
T ss_pred             ---hhhHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCC
Confidence               466677777888888999999988887765  544

>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=96.60  E-value=0.012  Score=41.64  Aligned_cols=81  Identities=6%  Similarity=-0.017  Sum_probs=53.3

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-cccHHHHHHHhhhcCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRD-NYTFPFLFKGFTRDIA  102 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~-~~t~~~ll~~~~~~~~  102 (230)
                      ..|.  +.|++++|...|.+.-   +.+...|+-+-.+|.+.|++++|...|+.-.+  +.|+ ..+|..+-.++.+.|+
T Consensus        12 n~~~--~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~lg~~~~~l~~   87 (201)
T d2c2la1          12 NRLF--VGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFLGQCQLEMES   87 (201)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHHHHHHHHCCC
Confidence            4555  8888888888887754   45666788888888888888888888887653  3453 2244444455555555


Q ss_pred             h--hhHHHhhh
Q 042210          103 G--SLEKSCIV  111 (230)
Q Consensus       103 ~--a~~~~~~~  111 (230)
                      +  |...+...
T Consensus        88 ~~~A~~~~~~a   98 (201)
T d2c2la1          88 YDEAIANLQRA   98 (201)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            5  44444433

>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=96.21  E-value=0.029  Score=36.39  Aligned_cols=81  Identities=17%  Similarity=0.091  Sum_probs=65.6

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|..+|...++.  .|+...  ..+-.+|.  +.|++++|...++...   +.+...|..+-.++...|++++|+..|+
T Consensus        20 ~eAi~~~~~al~~--~p~~~~~~~~~a~~~~--~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~~A~~~~~   95 (117)
T d1elwa_          20 DDALQCYSEAIKL--DPHNHVLYSNRSAAYA--KKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYE   95 (117)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHH--HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CCcchhhhhccccccc--ccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHHHHHHHHH
Confidence            5688888888776  465444  66777888  9999999999999865   6677889999999999999999999999


Q ss_pred             HHHhCCCCCCcc
Q 042210           77 DLLKSDVRRDNY   88 (230)
Q Consensus        77 ~M~~~g~~p~~~   88 (230)
                      +-.+  ..|+..
T Consensus        96 ~a~~--~~p~~~  105 (117)
T d1elwa_          96 EGLK--HEANNP  105 (117)
T ss_dssp             HHHT--TCTTCH
T ss_pred             HHHH--hCCCCH
Confidence            9775  446543

>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=96.14  E-value=0.02  Score=40.30  Aligned_cols=79  Identities=8%  Similarity=-0.135  Sum_probs=41.4

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHH
Q 042210           61 GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        61 ~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A  133 (230)
                      .|.+.|++++|...|++..... +-+...|..+-.+|.+.|++  |...+....     +...|..+-.+|.+.|++++|
T Consensus        13 ~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~~~A   91 (201)
T d2c2la1          13 RLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEA   91 (201)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            4455556666666665543321 11333455555555555555  555555554     444555555556666666666


Q ss_pred             HHHHhhc
Q 042210          134 RGIFYMS  140 (230)
Q Consensus       134 ~~vf~~m  140 (230)
                      ...|+..
T Consensus        92 ~~~~~~a   98 (201)
T d2c2la1          92 IANLQRA   98 (201)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555543

>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=96.11  E-value=0.011  Score=38.15  Aligned_cols=79  Identities=10%  Similarity=0.075  Sum_probs=44.0

Q ss_pred             ccCChHHHHHHHHhcC--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT--QP-SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~-~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...|++..  .| +...|..+-.++.+.|++++|...|+...+.  .|+                       
T Consensus        28 ~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~-----------------------   82 (112)
T d1hxia_          28 KLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPK-----------------------   82 (112)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-----------------------
T ss_pred             HHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhccccccccc--ccc-----------------------
Confidence            5555555555555543  22 3445555555555555555555555543321  121                       


Q ss_pred             hhhhHhHHHHHHHHHHhcCCHHHHHHHHhh
Q 042210          110 IVMRVFVQNALISTYCLCGEVDMARGIFYM  139 (230)
Q Consensus       110 ~~~~~~~~~~li~~y~~~g~~~~A~~vf~~  139 (230)
                         +...|..+-..|.+.|+.++|.+.|++
T Consensus        83 ---~~~a~~~la~~y~~~g~~~~A~~~l~~  109 (112)
T d1hxia_          83 ---DIAVHAALAVSHTNEHNANAALASLRA  109 (112)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---cccchHHHHHHHHHCCCHHHHHHHHHH
Confidence               455666666677777777777776664

>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=95.90  E-value=0.0096  Score=42.23  Aligned_cols=65  Identities=12%  Similarity=0.142  Sum_probs=56.3

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh-----CCCCCCccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK-----SDVRRDNYT   89 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~-----~g~~p~~~t   89 (230)
                      ..+...+.  +.|++++|...++...   .-+...|..++.+|.+.|+..+|++.|++..+     .|+.|+..+
T Consensus        71 ~~la~~~~--~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          71 TAKAEAEI--ACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHH--HCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            56677888  9999999999999875   55778899999999999999999999999744     599998754

>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=95.71  E-value=0.16  Score=38.12  Aligned_cols=113  Identities=12%  Similarity=-0.065  Sum_probs=51.7

Q ss_pred             HHHHhhhccCChHHHHHHHHhcC-----CCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHh----CCC-CCCcccHH
Q 042210           26 TRYLLLYEKGDLKYECKVFRKIT-----QPS----VFLWNTMIKGYSRIDSHKNGVLMYLDLLK----SDV-RRDNYTFP   91 (230)
Q Consensus        26 l~~~~~~~~~~~~~a~~~~~~m~-----~~~----~~~yn~li~~~~~~~~~~~a~~~~~~M~~----~g~-~p~~~t~~   91 (230)
                      -..|.  ..|++++|.+.|.+..     ..+    ..+|+.+-.+|.+.|++++|...+++-..    .|- .....++.
T Consensus        44 a~~y~--~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~  121 (290)
T d1qqea_          44 ATIYR--LRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKF  121 (290)
T ss_dssp             HHHHH--HTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHH--HCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHH
Confidence            34455  5555555555555432     111    13455555555555566655555554322    111 11122333


Q ss_pred             HHHHHhhh-cCch--hhHHHhhhh-----------hHhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210           92 FLFKGFTR-DIAG--SLEKSCIVM-----------RVFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus        92 ~ll~~~~~-~~~~--a~~~~~~~~-----------~~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                      .+...|-. .|++  |.+.+....           -..++..+...|.+.|++++|...|++.
T Consensus       122 ~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~  184 (290)
T d1qqea_         122 ELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKL  184 (290)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHH
Confidence            33333422 3554  444444332           1233455555566666666666665554

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.69  E-value=0.092  Score=40.89  Aligned_cols=141  Identities=6%  Similarity=-0.044  Sum_probs=97.1

Q ss_pred             CCCcH-HHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHH
Q 042210           18 TKPHC-PKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKG   96 (230)
Q Consensus        18 ~~~~~-~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~   96 (230)
                      |+..- ..+.+.|.  +.|.++.|..++..+.     -|.-++..+.+.++++.|.+++..-  .    +..+|..+...
T Consensus        12 ~n~~d~~~i~~~c~--~~~lye~A~~lY~~~~-----d~~rl~~~~v~l~~~~~avd~~~k~--~----~~~~~k~~~~~   78 (336)
T d1b89a_          12 PNNAHIQQVGDRCY--DEKMYDAAKLLYNNVS-----NFGRLASTLVHLGEYQAAVDGARKA--N----STRTWKEVCFA   78 (336)
T ss_dssp             C------------------CTTTHHHHHHHTT-----CHHHHHHHHHTTTCHHHHHHHHHHH--T----CHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHH--HCCCHHHHHHHHHhCC-----CHHHHHHHHHhhccHHHHHHHHHHc--C----CHHHHHHHHHH
Confidence            55555 77888888  9999999999998773     3777889999999999998887643  1    45588899999


Q ss_pred             hhhcCch-hhHHHhhhh--hHhHHHHHHHHHHhcCCHHHHHHHHhhcc---CCChhhhHHHHHHhhhcchhhhHHHHHHH
Q 042210           97 FTRDIAG-SLEKSCIVM--RVFVQNALISTYCLCGEVDMARGIFYMSC---EDDDGLHELIRIKAVDDDLHELFPEYLVQ  170 (230)
Q Consensus        97 ~~~~~~~-a~~~~~~~~--~~~~~~~li~~y~~~g~~~~A~~vf~~m~---~~~~~t~n~li~~~~~~~~~~~~~~m~~~  170 (230)
                      |.+.... ..++-....  +......++..|-..|..++...+++...   .++...+|-++..++.-+..++.+.+...
T Consensus        79 l~~~~e~~la~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~~~kl~e~l~~~  158 (336)
T d1b89a_          79 CVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELF  158 (336)
T ss_dssp             HHHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhChHHHHHHHHhc
Confidence            9988776 333322222  55566789999999999999999999653   35667788999999888777777777665


Q ss_pred             h
Q 042210          171 M  171 (230)
Q Consensus       171 ~  171 (230)
                      .
T Consensus       159 s  159 (336)
T d1b89a_         159 W  159 (336)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=95.53  E-value=0.053  Score=35.57  Aligned_cols=87  Identities=6%  Similarity=-0.165  Sum_probs=47.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch-----hhHHHhhhh-------hHhHHHHHHHHH
Q 042210           58 MIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG-----SLEKSCIVM-------RVFVQNALISTY  124 (230)
Q Consensus        58 li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~-----a~~~~~~~~-------~~~~~~~li~~y  124 (230)
                      +++.+...+++++|.+.|+.-...  .| +..++..+-.++.+.++.     |..++....       ....|..|=.+|
T Consensus         5 l~n~~~~~~~l~~Ae~~Y~~aL~~--~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           5 VLNELVSVEDLLKFEKKFQSEKAA--GSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH--SCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            444445555555555555554331  12 223333333444433322     444444443       133556667788


Q ss_pred             HhcCCHHHHHHHHhhccC--CChh
Q 042210          125 CLCGEVDMARGIFYMSCE--DDDG  146 (230)
Q Consensus       125 ~~~g~~~~A~~vf~~m~~--~~~~  146 (230)
                      .+.|++++|.+.|++.-+  |+-.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~~P~~~  106 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQTEPQNN  106 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHhhhHHHHHHHHHHHHhCcCCH
Confidence            889999999999988765  6554

>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=95.53  E-value=0.13  Score=35.49  Aligned_cols=57  Identities=11%  Similarity=-0.056  Sum_probs=38.6

Q ss_pred             HHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChh
Q 042210           90 FPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDG  146 (230)
Q Consensus        90 ~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~  146 (230)
                      |+.+-.+|.+.|++  |...++...     ++..|..+-.+|...|++++|...|+...+  |+-.
T Consensus        65 ~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~  130 (170)
T d1p5qa1          65 HLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNK  130 (170)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCH
T ss_pred             HHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCH
Confidence            34444455555655  444444444     567777788889999999999999998765  6443

>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=95.46  E-value=0.033  Score=39.59  Aligned_cols=82  Identities=10%  Similarity=-0.081  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHh
Q 042210           54 LWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCL  126 (230)
Q Consensus        54 ~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~  126 (230)
                      .||--+ .+...|+++.|++.|.+.    ..|+..+|..+=.++...|++  |...|....     +...|+.+=..|.+
T Consensus         8 l~~~g~-~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~   82 (192)
T d1hh8a_           8 LWNEGV-LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQ   82 (192)
T ss_dssp             HHHHHH-HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHH-HHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHh
Confidence            355422 456789999999999864    356777888888899999999  888888887     78889999999999


Q ss_pred             cCCHHHHHHHHhhc
Q 042210          127 CGEVDMARGIFYMS  140 (230)
Q Consensus       127 ~g~~~~A~~vf~~m  140 (230)
                      .|++++|.+-|++-
T Consensus        83 ~g~~~~A~~~~~kA   96 (192)
T d1hh8a_          83 TEKYDLAIKDLKEA   96 (192)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             hccHHHHHHHHHHH
Confidence            99999999888864

>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=95.38  E-value=0.03  Score=42.31  Aligned_cols=154  Identities=6%  Similarity=-0.040  Sum_probs=94.9

Q ss_pred             hHHHHHHHHHHhcCCCCCcHHHHHHHHhhhccCChHHHHHHHHhcCCCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC-
Q 042210            3 QLKQIHSQTIKLGLLTKPHCPKQTRYLLLYEKGDLKYECKVFRKITQPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS-   81 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~~~ll~~~~~~~~~~~~~a~~~~~~m~~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~-   81 (230)
                      .+.++.+...+.+ +|...   ++..+.-+..+++++|.++|.+           .-..|...+++++|.+.|.+...- 
T Consensus         3 ~~~~~l~~aek~~-~~~~~---~~~~~~~~~~~~~~~Aa~~y~~-----------aa~~y~~~~~~~~A~~~y~kA~~~~   67 (290)
T d1qqea_           3 DPVELLKRAEKKG-VPSSG---FMKLFSGSDSYKFEEAADLCVQ-----------AATIYRLRKELNLAGDSFLKAADYQ   67 (290)
T ss_dssp             CHHHHHHHHHHHS-SCCCT---HHHHHSCCSHHHHHHHHHHHHH-----------HHHHHHHTTCTHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc-Ccchh---HHHHhcCCccccHHHHHHHHHH-----------HHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4556666655554 23322   2223320123357888887655           456788899999999999886442 


Q ss_pred             ---CCCC-CcccHHHHHHHhhhcCch--hhHHHhhhh-----------hHhHHHHHHHHHH-hcCCHHHHHHHHhhccC-
Q 042210           82 ---DVRR-DNYTFPFLFKGFTRDIAG--SLEKSCIVM-----------RVFVQNALISTYC-LCGEVDMARGIFYMSCE-  142 (230)
Q Consensus        82 ---g~~p-~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----------~~~~~~~li~~y~-~~g~~~~A~~vf~~m~~-  142 (230)
                         +-+| -..+|..+-.+|.+.|++  |...+....           ...++..+...|- ..|++++|...+.+..+ 
T Consensus        68 ~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l  147 (290)
T d1qqea_          68 KKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEW  147 (290)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHH
Confidence               2222 235788888999999998  666666554           2455566666674 46999999999987643 


Q ss_pred             ----CCh----hhhHHHHHHhh----hcchhhhHHHHHHHh
Q 042210          143 ----DDD----GLHELIRIKAV----DDDLHELFPEYLVQM  171 (230)
Q Consensus       143 ----~~~----~t~n~li~~~~----~~~~~~~~~~m~~~~  171 (230)
                          .+.    .+|+.+...+.    .++|++.+++....-
T Consensus       148 ~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~  188 (290)
T d1qqea_         148 YAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS  188 (290)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhC
Confidence                121    22333333333    356777777765543

>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=95.28  E-value=0.034  Score=35.72  Aligned_cols=73  Identities=1%  Similarity=-0.105  Sum_probs=58.9

Q ss_pred             hhHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHH
Q 042210            2 HQLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         2 ~~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~   76 (230)
                      ++|...++...+..  |+...  ..+-..+.  +.|++++|...|+...   +.+...|..+-..|...|++++|.+.|+
T Consensus        33 ~~A~~~~~~al~~~--p~~~~a~~~lg~~~~--~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~~~A~~~l~  108 (112)
T d1hxia_          33 AEAALAFEAVCQKE--PEREEAWRSLGLTQA--ENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLR  108 (112)
T ss_dssp             HHHHHHHHHHHHHS--TTCHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcccc--cccchhhhhhhhhhh--hhhhHHHhhcccccccccccccccchHHHHHHHHHCCCHHHHHHHHH
Confidence            46788888877763  65444  66667777  9999999999999865   5567789999999999999999999998


Q ss_pred             HH
Q 042210           77 DL   78 (230)
Q Consensus        77 ~M   78 (230)
                      +-
T Consensus       109 ~~  110 (112)
T d1hxia_         109 AW  110 (112)
T ss_dssp             HH
T ss_pred             HH
Confidence            74

>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=95.07  E-value=0.016  Score=38.26  Aligned_cols=86  Identities=16%  Similarity=0.038  Sum_probs=34.7

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCC---hhHHHHHHHHHHhCCCCCCc-ccHHHHHHHh
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDS---HKNGVLMYLDLLKSDVRRDN-YTFPFLFKGF   97 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~---~~~a~~~~~~M~~~g~~p~~-~t~~~ll~~~   97 (230)
                      +++.+.  ..+++++|++.|+...   +.+..++.-+-.++.+.++   .++|..+|++....+-.|+. .+|..+=.+|
T Consensus         5 l~n~~~--~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           5 VLNELV--SVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHH--HHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHhc--CHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            334444  4445555555554433   2233333333333433222   22344445444333222221 1333344444


Q ss_pred             hhcCch--hhHHHhhhh
Q 042210           98 TRDIAG--SLEKSCIVM  112 (230)
Q Consensus        98 ~~~~~~--a~~~~~~~~  112 (230)
                      .+.|++  |...|....
T Consensus        83 ~~~g~~~~A~~~~~~aL   99 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLL   99 (122)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHH
Confidence            445554  444444443

>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=94.66  E-value=0.13  Score=33.65  Aligned_cols=89  Identities=10%  Similarity=0.038  Sum_probs=56.8

Q ss_pred             HHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-CcccHHHHHHHhhhcCch
Q 042210           28 YLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRR-DNYTFPFLFKGFTRDIAG  103 (230)
Q Consensus        28 ~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p-~~~t~~~ll~~~~~~~~~  103 (230)
                      .|.  +.|++++|...|.+..   +.+...|..+-.+|.+.|++++|...+++....  .| +...|..+          
T Consensus        13 ~~~--~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l--~~~~~~~~~~~----------   78 (128)
T d1elra_          13 DAY--KKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV--GRENREDYRQI----------   78 (128)
T ss_dssp             HHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HHHSTTCHHHH----------
T ss_pred             HHH--HcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHh--CcccHHHHHHH----------
Confidence            455  7788888888887654   445667777777788888888888887775442  11 11122222          


Q ss_pred             hhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhc
Q 042210          104 SLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMS  140 (230)
Q Consensus       104 a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m  140 (230)
                                ..+|..+=..+...+++++|.+.|+.-
T Consensus        79 ----------a~~~~~lg~~~~~~~~~~~A~~~~~ka  105 (128)
T d1elra_          79 ----------AKAYARIGNSYFKEEKYKDAIHFYNKS  105 (128)
T ss_dssp             ----------HHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ----------HHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence                      234445556677778888888887653

>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=94.48  E-value=0.023  Score=43.70  Aligned_cols=197  Identities=7%  Similarity=-0.098  Sum_probs=104.1

Q ss_pred             hHHHHHHHHHHhcCCCCCcH--HHHHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHH-HHHHhcCChhHHHHHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPHC--PKQTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMI-KGYSRIDSHKNGVLMYL   76 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~~--~~ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li-~~~~~~~~~~~a~~~~~   76 (230)
                      +|..+++...+.  .|+...  ...-.++..-..++.++|...+....   +++...|...+ ..+...+.+++|+..++
T Consensus        91 ~al~~~~~~l~~--~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~  168 (334)
T d1dcea1          91 AELGFLESCLRV--NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTD  168 (334)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHH
Confidence            455566665554  354433  33434444003345788888888864   44555555444 45566788999999888


Q ss_pred             HHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh--hHhHHHHHHHHHHhcCCHHHHHHHHhhccC---CChhhhH
Q 042210           77 DLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM--RVFVQNALISTYCLCGEVDMARGIFYMSCE---DDDGLHE  149 (230)
Q Consensus        77 ~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~--~~~~~~~li~~y~~~g~~~~A~~vf~~m~~---~~~~t~n  149 (230)
                      ......-. +...|..+-..+.+.|+.  |...+....  ... ...+...+...+..+++...+.....   ++...+.
T Consensus       169 ~~i~~~p~-~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~  246 (334)
T d1dcea1         169 SLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLK-ELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCE  246 (334)
T ss_dssp             TTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHH-HHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCC
T ss_pred             HHHHcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhHHH-HHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHH
Confidence            76554321 445666666777777776  544444443  111 12233345556666666666654432   2333333


Q ss_pred             HHHHHhhh----cchhhhHHHHHHHhhhcCchh-hhhhhhhcccccCCcccccccCCccCCcccccccccc
Q 042210          150 LIRIKAVD----DDLHELFPEYLVQMLALPDTF-MGEGLEVIPKSQAPREETPRVGNLEEGTPQEGRPHEH  215 (230)
Q Consensus       150 ~li~~~~~----~~~~~~~~~m~~~~~~~p~~~-t~~~l~~~~~~~~~~~a~~~~g~~~~a~~i~~~~~~~  215 (230)
                      .+...+..    .++.+.+.+   .....|+.. ++..   +      -.++.+.|+.++|...+..+.+.
T Consensus       247 ~l~~~~~~~~~~~~a~~~~~~---~~~~~p~~~~~~~~---l------~~~~~~~~~~~eA~~~~~~ai~l  305 (334)
T d1dcea1         247 LSVEKSTVLQSELESCKELQE---LEPENKWCLLTIIL---L------MRALDPLLYEKETLQYFSTLKAV  305 (334)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHH---H------HHHHCTGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHH---HHhhCchHHHHHHH---H------HHHHHHCCCHHHHHHHHHHHHHH
Confidence            33332222    233333332   222223321 2222   1      11566788888888888777664

>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=94.21  E-value=0.2  Score=37.34  Aligned_cols=109  Identities=7%  Similarity=-0.041  Sum_probs=71.2

Q ss_pred             ccCChHHHHHHHHhcC--CCC------hhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-CcccHHHHHHHhhh
Q 042210           33 EKGDLKYECKVFRKIT--QPS------VFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR-DNYTFPFLFKGFTR   99 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~--~~~------~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p-~~~t~~~ll~~~~~   99 (230)
                      ..|++++|...+++.-  .|+      ...++.+-..|...|++++|...|++..+.    +-.+ ...++..+...+..
T Consensus        24 ~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  103 (366)
T d1hz4a_          24 NDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFA  103 (366)
T ss_dssp             HTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHH
Confidence            8899999999988753  232      235666677788889999999999886542    1111 12244445556666


Q ss_pred             cCch--hhHHHhhhh-------------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          100 DIAG--SLEKSCIVM-------------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       100 ~~~~--a~~~~~~~~-------------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .|++  +...+....             ....+..+-..|...|+++.+...+....
T Consensus       104 ~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~  160 (366)
T d1hz4a_         104 QGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGI  160 (366)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHH
Confidence            7776  444444332             23355566678888899998888887665

>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=93.95  E-value=0.55  Score=31.89  Aligned_cols=79  Identities=11%  Similarity=0.013  Sum_probs=47.0

Q ss_pred             HHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHHHHHHhhccC--CChhhhHHHHHHh------hh
Q 042210           93 LFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMARGIFYMSCE--DDDGLHELIRIKA------VD  157 (230)
Q Consensus        93 ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A~~vf~~m~~--~~~~t~n~li~~~------~~  157 (230)
                      +-.++.+.|++  |...+....     +...|..+-.+|...|++++|..-|+...+  |+.......+...      ..
T Consensus        70 la~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~  149 (168)
T d1kt1a1          70 LAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKAKEHN  149 (168)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhHH
Confidence            33344455554  444333333     566677777889999999999999998775  5544333222211      12


Q ss_pred             cchhhhHHHHHHHh
Q 042210          158 DDLHELFPEYLVQM  171 (230)
Q Consensus       158 ~~~~~~~~~m~~~~  171 (230)
                      ....+.+..|++..
T Consensus       150 e~~kk~~~~~f~~~  163 (168)
T d1kt1a1         150 ERDRRTYANMFKKF  163 (168)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhh
Confidence            34556777777665

>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=93.95  E-value=0.16  Score=38.00  Aligned_cols=108  Identities=6%  Similarity=-0.023  Sum_probs=70.4

Q ss_pred             ccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHh
Q 042210           33 EKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSC  109 (230)
Q Consensus        33 ~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~  109 (230)
                      +.|++++|...+++..   +.|...+..+...|+..|++++|...|+...+.  .|+.......+....+....-.+.+.
T Consensus         8 ~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~~l~~ll~a~~~~~~a~~   85 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGASQLRHLVKAAQARKDFAQ   85 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHhccccHHHHH
Confidence            7899999999999864   556789999999999999999999999997663  34432221111111111111111111


Q ss_pred             hhh---------hHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210          110 IVM---------RVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus       110 ~~~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                      ...         +...+......+.+.|+.++|...+++..+
T Consensus        86 ~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e  127 (264)
T d1zbpa1          86 GAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  127 (264)
T ss_dssp             SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            111         334444556677888999999999887654

>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=93.64  E-value=0.24  Score=34.54  Aligned_cols=27  Identities=11%  Similarity=0.113  Sum_probs=12.7

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          115 FVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       115 ~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      ..+..+...+.+.|++++|...++...
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al   94 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALT   94 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHH
Confidence            334444444455555555555444443

>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=93.26  E-value=0.31  Score=36.25  Aligned_cols=117  Identities=9%  Similarity=-0.130  Sum_probs=56.6

Q ss_pred             HHHHHHHhhhccCChHHHHHHHHhcC--------CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC--Ccc
Q 042210           23 PKQTRYLLLYEKGDLKYECKVFRKIT--------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKS----DVRR--DNY   88 (230)
Q Consensus        23 ~~ll~~~~~~~~~~~~~a~~~~~~m~--------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~----g~~p--~~~   88 (230)
                      ..+-..+.  ..|+++.+...+....        ......+......+...++...+...+.+....    +-.+  ...
T Consensus       137 ~~la~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~  214 (366)
T d1hz4a_         137 RIRAQLLW--AWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISN  214 (366)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHH
T ss_pred             HHHHHHHH--HhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHH
Confidence            44445555  6666666666665543        011223344444455556666666665543221    1111  111


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh---------hHhHHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM---------RVFVQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~---------~~~~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .+..+...+...|+.  +...+....         ....+..+-..|...|++++|...+++..
T Consensus       215 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  278 (366)
T d1hz4a_         215 ANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELN  278 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            233344445555555  444444333         23344445566666666666666666543

>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=93.19  E-value=0.71  Score=30.79  Aligned_cols=19  Identities=11%  Similarity=0.338  Sum_probs=10.0

Q ss_pred             HHHhcCChhHHHHHHHHHH
Q 042210           61 GYSRIDSHKNGVLMYLDLL   79 (230)
Q Consensus        61 ~~~~~~~~~~a~~~~~~M~   79 (230)
                      .+.+.|++.+|...|++..
T Consensus        26 ~~f~~~~y~~A~~~Y~~al   44 (153)
T d2fbna1          26 EFFKKNEINEAIVKYKEAL   44 (153)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            3344556666665555533

>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=92.99  E-value=0.28  Score=33.43  Aligned_cols=86  Identities=10%  Similarity=0.003  Sum_probs=51.7

Q ss_pred             HHHhhhccCChHHHHHHHHhcC-------------------CCChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT-------------------QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~-------------------~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   87 (230)
                      ..+.  +.|++++|.+.|.+.-                   +.+...|+.+-.+|.+.|++++|+..+++..+.  .|+ 
T Consensus        35 ~~~~--~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~--~p~-  109 (169)
T d1ihga1          35 NTFF--KSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI--DPS-  109 (169)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTT-
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhh--hhh-
Confidence            4455  7888888888876542                   011223344444455555555555555554332  222 


Q ss_pred             ccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           88 YTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        88 ~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                                               +...|..+-.+|.+.|++++|.+.|+...+
T Consensus       110 -------------------------~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1         110 -------------------------NTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             -------------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -------------------------hhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence                                     455666677778888888888888886654

>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=92.98  E-value=0.061  Score=41.20  Aligned_cols=66  Identities=5%  Similarity=-0.014  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHHhcCCCCCc-H-HHHH-HHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHH
Q 042210            3 QLKQIHSQTIKLGLLTKPH-C-PKQT-RYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGV   72 (230)
Q Consensus         3 ~a~~~~~~m~~~g~~~~~~-~-~~ll-~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~   72 (230)
                      .|...++...+.  .|+.. . ...+ ..+.  ..+..++|...++...   +.+...|+-+-..+.+.|++++|.
T Consensus       127 ~a~~~~~~al~~--~~~~~~~~~~~~~~~~~--~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~  198 (334)
T d1dcea1         127 RELELCARFLEA--DERNFHCWDYRRFVAAQ--AAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSG  198 (334)
T ss_dssp             HHHHHHHHHHHH--CTTCHHHHHHHHHHHHH--TCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             HHHHHHHHHHhh--CchhhhhhhhHHHHHHH--hccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHH
Confidence            445555555554  34332 2 2233 4555  7899999999999876   445667777777777777766553

>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=92.74  E-value=0.68  Score=30.91  Aligned_cols=26  Identities=12%  Similarity=-0.189  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhhcc
Q 042210          116 VQNALISTYCLCGEVDMARGIFYMSC  141 (230)
Q Consensus       116 ~~~~li~~y~~~g~~~~A~~vf~~m~  141 (230)
                      .++.+=..|.+.|++++|...|++..
T Consensus       102 a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1         102 AVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            45556677888888888888877643

>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=92.47  E-value=0.18  Score=32.89  Aligned_cols=79  Identities=6%  Similarity=-0.078  Sum_probs=44.7

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCHHHH
Q 042210           61 GYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEVDMA  133 (230)
Q Consensus        61 ~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~~~A  133 (230)
                      .+.+.|++++|...|++..+.+ +-+...|..+-.+|.+.|++  |...+....     +...|..+-.+|.+.|+...+
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~   91 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFK   91 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHH
Confidence            4555666666666666654431 12344555566666666666  555555544     344455555666666666666


Q ss_pred             HHHHhhc
Q 042210          134 RGIFYMS  140 (230)
Q Consensus       134 ~~vf~~m  140 (230)
                      ..-|++-
T Consensus        92 ~~~~~~A   98 (128)
T d1elra_          92 EEKYKDA   98 (128)
T ss_dssp             TTCHHHH
T ss_pred             hCCHHHH
Confidence            6555543

>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=91.72  E-value=1.2  Score=30.21  Aligned_cols=54  Identities=6%  Similarity=-0.077  Sum_probs=38.1

Q ss_pred             HHHHHhhhccCChHHHHHHHHhcC---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHh
Q 042210           25 QTRYLLLYEKGDLKYECKVFRKIT---QPSVFLWNTMIKGYSRIDSHKNGVLMYLDLLK   80 (230)
Q Consensus        25 ll~~~~~~~~~~~~~a~~~~~~m~---~~~~~~yn~li~~~~~~~~~~~a~~~~~~M~~   80 (230)
                      +-.+|.  +.|++++|...++...   +.++..|.-+-.+|...|++++|...|++..+
T Consensus        68 la~~y~--k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          68 LAMCHL--KLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHHHHH--HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHH--hhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            445566  7778888887777654   34566777777777778888888888777655

>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=90.75  E-value=0.31  Score=32.73  Aligned_cols=86  Identities=10%  Similarity=0.104  Sum_probs=51.4

Q ss_pred             HHHhhhccCChHHHHHHHHhcC--------CCC-----------hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT--------QPS-----------VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~--------~~~-----------~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   87 (230)
                      ..+.  +.|++++|...|.+..        .++           ..+|+-+-.+|.+.|++++|+..+++....  .|+ 
T Consensus        25 ~~~f--~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~--~p~-   99 (153)
T d2fbna1          25 NEFF--KKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI--DKN-   99 (153)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STT-
T ss_pred             HHHH--HcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccc--cch-
Confidence            3455  8899999999887643        111           112333444444455555555554443321  121 


Q ss_pred             ccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHHhhccC
Q 042210           88 YTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIFYMSCE  142 (230)
Q Consensus        88 ~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf~~m~~  142 (230)
                                               +...|..+-.+|.+.|++++|...|+...+
T Consensus       100 -------------------------~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1         100 -------------------------NVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             -------------------------CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             -------------------------hhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence                                     456666777788888888888888887654

>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=89.81  E-value=0.98  Score=30.51  Aligned_cols=101  Identities=9%  Similarity=-0.073  Sum_probs=65.7

Q ss_pred             HHHhhhccCChHHHHHHHHhcC-----CC-------------ChhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT-----QP-------------SVFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNY   88 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~-----~~-------------~~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~   88 (230)
                      ..+.  +.|++++|...|++.-     .+             ....|+-+-.+|.+.|++++|+..++...+.. +.+..
T Consensus        23 ~~~~--~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~   99 (168)
T d1kt1a1          23 TVYF--KGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-SANEK   99 (168)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHH--HcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHH
Confidence            3455  7888888888886632     11             11234555567788899999999998866532 23555


Q ss_pred             cHHHHHHHhhhcCch--hhHHHhhhh-----hHhHHHHHHHHHHhcCCH
Q 042210           89 TFPFLFKGFTRDIAG--SLEKSCIVM-----RVFVQNALISTYCLCGEV  130 (230)
Q Consensus        89 t~~~ll~~~~~~~~~--a~~~~~~~~-----~~~~~~~li~~y~~~g~~  130 (230)
                      .|..+-.++...|++  |...+....     +......+-....+.+..
T Consensus       100 a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~  148 (168)
T d1kt1a1         100 GLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKAKEH  148 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhH
Confidence            777778888888888  777777776     455555544444444433

>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=89.71  E-value=1.3  Score=29.72  Aligned_cols=102  Identities=6%  Similarity=-0.079  Sum_probs=62.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCCcccHHHHHHHhhhcCchhhHHHhhhh-hHhHHHHHHHHHHhcCCHHHHH
Q 042210           56 NTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDNYTFPFLFKGFTRDIAGSLEKSCIVM-RVFVQNALISTYCLCGEVDMAR  134 (230)
Q Consensus        56 n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~~t~~~ll~~~~~~~~~a~~~~~~~~-~~~~~~~li~~y~~~g~~~~A~  134 (230)
                      ...-..+.+.|++++|...|++..+.            +........ .......-. ....|+.+-..|.+.|++++|.
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~------------~~~~~~~~~-~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai   97 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRY------------VEGSRAAAE-DADGAKLQPVALSCVLNIGACKLKMSDWQGAV   97 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH------------HHHHHHHSC-HHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh------------hhhhhhhhh-hHHHHHhChhhHHHHHHHHHHHHhhcccchhh
Confidence            34455677889999999998875431            110000000 111111111 6667788888999999999999


Q ss_pred             HHHhhccC--C-ChhhhHHHHHHhhh----cchhhhHHHHHHH
Q 042210          135 GIFYMSCE--D-DDGLHELIRIKAVD----DDLHELFPEYLVQ  170 (230)
Q Consensus       135 ~vf~~m~~--~-~~~t~n~li~~~~~----~~~~~~~~~m~~~  170 (230)
                      ..+++..+  | +...|..+-.++..    ++|++.|++..+-
T Consensus        98 ~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          98 DSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            99998866  4 44566655555543    5677777766554

>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=83.78  E-value=1.6  Score=28.71  Aligned_cols=40  Identities=18%  Similarity=0.079  Sum_probs=24.7

Q ss_pred             HHHHHHHHhhccC--CChhhhHHHHHHhhhcchhhhHHHHHHHh
Q 042210          130 VDMARGIFYMSCE--DDDGLHELIRIKAVDDDLHELFPEYLVQM  171 (230)
Q Consensus       130 ~~~A~~vf~~m~~--~~~~t~n~li~~~~~~~~~~~~~~m~~~~  171 (230)
                      +++|.+.|+...+  |+...|..-+..+  .++.+++.+..+.|
T Consensus       102 ~~~A~~~~~kal~l~P~~~~~~~~L~~~--~ka~~~~~e~~k~~  143 (145)
T d1zu2a1         102 FDLATQFFQQAVDEQPDNTHYLKSLEMT--AKAPQLHAEAYKQG  143 (145)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHH--HTHHHHHHHHHHSS
T ss_pred             HHHhhhhhhcccccCCCHHHHHHHHHHH--HHHHHHHHHHHHHh
Confidence            5777777776654  7666555444433  45667777766654

>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=82.31  E-value=1.5  Score=26.47  Aligned_cols=57  Identities=9%  Similarity=0.045  Sum_probs=42.9

Q ss_pred             HHHhhhccCChHHHHHHHHhcC---------CCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCc
Q 042210           27 RYLLLYEKGDLKYECKVFRKIT---------QPS-VFLWNTMIKGYSRIDSHKNGVLMYLDLLKSDVRRDN   87 (230)
Q Consensus        27 ~~~~~~~~~~~~~a~~~~~~m~---------~~~-~~~yn~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   87 (230)
                      ..+.  +.|+.+.|...|++..         .++ ..+|+-+=.+|.+.|++++|...|++..+.  .|+.
T Consensus        13 ~~~~--~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~~   79 (95)
T d1tjca_          13 KVAY--TEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (95)
T ss_dssp             HHHH--HTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHH--HCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcCC
Confidence            3445  8999999999887753         111 346888888999999999999999997663  3543

>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=80.17  E-value=1.8  Score=26.02  Aligned_cols=60  Identities=18%  Similarity=0.002  Sum_probs=39.4

Q ss_pred             HHHHhcCChhHHHHHHHHHHhC-CCCCCc-ccHHHHHHHhhhcCchhhHHHhhhhhHhHHHHHHHHHHhcCCHHHHHHHH
Q 042210           60 KGYSRIDSHKNGVLMYLDLLKS-DVRRDN-YTFPFLFKGFTRDIAGSLEKSCIVMRVFVQNALISTYCLCGEVDMARGIF  137 (230)
Q Consensus        60 ~~~~~~~~~~~a~~~~~~M~~~-g~~p~~-~t~~~ll~~~~~~~~~a~~~~~~~~~~~~~~~li~~y~~~g~~~~A~~vf  137 (230)
                      ..+.+.|++++|...|++-.+. .-.+.. .+                       ...+++.|-.+|.+.|++++|.+.+
T Consensus        13 ~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~-----------------------~~~~l~~Lg~~~~~~g~~~~A~~~y   69 (95)
T d1tjca_          13 KVAYTEADYYHTELWMEQALRQLDEGEISTID-----------------------KVSVLDYLSYAVYQQGDLDKALLLT   69 (95)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSC-----------------------HHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHhhhhccCcc-----------------------HHHHHHHHhhHHHhcCChHHHHHHH
Confidence            3556678888888888774321 111110 00                       2456777888899999999999999


Q ss_pred             hhccC
Q 042210          138 YMSCE  142 (230)
Q Consensus       138 ~~m~~  142 (230)
                      ++..+
T Consensus        70 ~~aL~   74 (95)
T d1tjca_          70 KKLLE   74 (95)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88765