Citrus Sinensis ID: 040801

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320---
Protein Sequence
MAAPLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
Secondary Structure (PSIPRED)
cccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccHHHHHHHHccccccccccHHHHHHHHHccccHHHHHHHHHHHHHcccccccEEHHHHHHHHccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHHHccccccccEEEcHHHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHcccccHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHccHHHHHHHHHHHHHccccHcHcHHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccccccHHHHHHHHHHHHHcccHHHHHHHcccccccHHHHHHHHHHHHccHHHcccEEEEEEEcc
Coil and Loop (DISEMBL)
maaplplhhqtrtpalssdnsplinldninnnninsqYQAHFCLVSLEKCSTMRELKQIHAQMLRtslffdpcadYHVRLVfsqisnptiytcnsivrgytnknlhhEAFLFYHEMIVQglipdrfmfpslfKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYsscwcldqpdEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHkcvdesgfwsHVELKTTLMDAYCKCKFVSRAWDLFVKmlfpwnnygqwamsatvgpqglvgrhstahqisgpcpkkaHKLFFFSMLkkvhvpgvliqvhvpdvlf
Flexible Loop (DISEMBL)
maaplplhhqtrtpalssdnsPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTArarardlrtvkrvhkcvdesgfwshvELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQvhvpdvlf
Low Complexity Region (SEG)
MAAPLPLHHQTRTPALSSdnsplinldninnnninsQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTarararDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
Disordered region (IsUnstruct)
***********************INLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDV**
Disordered Region (DISOPRED)
*AAPLPLHHQ***************************YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
Disordered Region (DISEMBL)
MAAPLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
Disordered Region (DISPRO)
**APLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAPLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVPDVLF
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	323	2.2.26 [Sep-21-2011]
O82380	738	Pentatricopeptide repeat-	yes	no	0.712	0.311	0.279	2e-25
Q8LK93	603	Pentatricopeptide repeat-	no	no	0.656	0.351	0.286	4e-25
Q9LS72	600	Pentatricopeptide repeat-	no	no	0.659	0.355	0.304	8e-25
Q9SJZ3	681	Pentatricopeptide repeat-	no	no	0.739	0.350	0.303	1e-24
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.640	0.298	0.303	2e-22
Q9MA95	565	Putative pentatricopeptid	no	no	0.678	0.387	0.284	2e-22
Q9LUJ2	842	Pentatricopeptide repeat-	no	no	0.643	0.247	0.291	9e-21
Q9C6T2	606	Pentatricopeptide repeat-	no	no	0.690	0.367	0.281	1e-20
Q9SJG6	559	Pentatricopeptide repeat-	no	no	0.662	0.382	0.25	6e-19
Q9SN39	871	Pentatricopeptide repeat-	no	no	0.566	0.210	0.288	8e-19

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

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/279 (27%), Positives = 133/279 (47%), Gaps = 49/279 (17%)

Query: 25  NLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP------------ 72
           N  N N    N++   H  L+  E+C ++R+LKQ H  M+RT  F DP            
Sbjct: 17  NFSNPNQPTTNNERSRHISLI--ERCVSLRQLKQTHGHMIRTGTFSDPYSASKLFAMAAL 74

Query: 73  ---CADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPDRFMF 128
               +  + R VF +I  P  +  N+++R Y +      +   + +M+ +    P+++ F
Sbjct: 75  SSFASLEYARKVFDEIPKPNSFAWNTLIRAYASGPDPVLSIWAFLDMVSESQCYPNKYTF 134

Query: 129 PSLFKSCADIY---VEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ---------- 175
           P L K+ A++    + + LH  A+K  + SD F+ N+LI+ Y SC  LD           
Sbjct: 135 PFLIKAAAEVSSLSLGQSLHGMAVKSAVGSDVFVANSLIHCYFSCGDLDSACKVFTTIKE 194

Query: 176 ------------------PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRV 217
                             PD+A+++F +ME E+VK + VT+V VL+A A+ R+L   ++V
Sbjct: 195 KDVVSWNSMINGFVQKGSPDKALELFKKMESEDVKASHVTMVGVLSACAKIRNLEFGRQV 254

Query: 218 HKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM 256
              ++E+    ++ L   ++D Y KC  +  A  LF  M
Sbjct: 255 CSYIEENRVNVNLTLANAMLDMYTKCGSIEDAKRLFDAM 293

Arabidopsis thaliana (taxid: 3702)

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

 Score =  115 bits (288), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 74/258 (28%), Positives = 127/258 (49%), Gaps = 46/258 (17%)

Query: 47  LEKCSTMRELKQIHAQMLRTSL--------FFDPCADY-------HVRLVFSQISNPTIY 91
           + KC+++REL QI A  +++ +          + C +        + R +F  +S P I 
Sbjct: 36  ISKCNSLRELMQIQAYAIKSHIEDVSFVAKLINFCTESPTESSMSYARHLFEAMSEPDIV 95

Query: 92  TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA---DIYVEKQLHSQA 148
             NS+ RGY+      E F  + E++  G++PD + FPSL K+CA    +   +QLH  +
Sbjct: 96  IFNSMARGYSRFTNPLEVFSLFVEILEDGILPDNYTFPSLLKACAVAKALEEGRQLHCLS 155

Query: 149 IKFGLASDSFLHNTLINMYSSCWCLD----------------------------QPDEAI 180
           +K GL  + ++  TLINMY+ C  +D                            +P+EA+
Sbjct: 156 MKLGLDDNVYVCPTLINMYTECEDVDSARCVFDRIVEPCVVCYNAMITGYARRNRPNEAL 215

Query: 181 KIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAY 240
            +F  M+ + +KPN +TL++VL++ A    L   K +HK   +  F  +V++ T L+D +
Sbjct: 216 SLFREMQGKYLKPNEITLLSVLSSCALLGSLDLGKWIHKYAKKHSFCKYVKVNTALIDMF 275

Query: 241 CKCKFVSRAWDLFVKMLF 258
            KC  +  A  +F KM +
Sbjct: 276 AKCGSLDDAVSIFEKMRY 293

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS72|PP261_ARATH Pentatricopeptide repeat-containing protein At3g29230 OS=Arabidopsis thaliana GN=PCMP-E27 PE=2 SV=1

 Score =  114 bits (286), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 128/240 (53%), Gaps = 27/240 (11%)

Query: 44  LVSLEKCSTMRELKQIHAQMLRTSLFFDP------------CADYHVRL-VFSQISNPTI 90
           L  L KC+ + ++KQ+HAQ++R +L  D             C   ++ + VF+Q+  P +
Sbjct: 23  LQDLPKCANLNQVKQLHAQIIRRNLHEDLHIAPKLISALSLCRQTNLAVRVFNQVQEPNV 82

Query: 91  YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD---IYVEKQLHSQ 147
           + CNS++R +   +  ++AF  + EM   GL  D F +P L K+C+    + V K +H+ 
Sbjct: 83  HLCNSLIRAHAQNSQPYQAFFVFSEMQRFGLFADNFTYPFLLKACSGQSWLPVVKMMHNH 142

Query: 148 AIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR 207
             K GL+SD ++ N LI+ YS C  L   D A+K+F +M     + + V+  ++L    +
Sbjct: 143 IEKLGLSSDIYVPNALIDCYSRCGGLGVRD-AMKLFEKMS----ERDTVSWNSMLGGLVK 197

Query: 208 ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWA 267
           A +LR  +R+   + +    S      T++D Y +C+ +S+A++LF KM  P  N   W+
Sbjct: 198 AGELRDARRLFDEMPQRDLISW----NTMLDGYARCREMSKAFELFEKM--PERNTVSWS 251

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 =  114 bits (284), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 90/297 (30%), Positives = 133/297 (44%), Gaps = 58/297 (19%)

Query: 8   HHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSL-EKCSTMRELKQIHAQMLRT 66
           H Q RT +L       IN       N    +  H  L+SL EKC  +  LKQI AQM+  
Sbjct: 26  HSQRRTRSLPHHRDKPINW------NSTHSFVLHNPLLSLLEKCKLLLHLKQIQAQMIIN 79

Query: 67  SLFFDP---------CA-------DYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAF 110
            L  DP         CA       DY V+ +   I NP I++ N  +RG++      E+F
Sbjct: 80  GLILDPFASSRLIAFCALSESRYLDYSVK-ILKGIENPNIFSWNVTIRGFSESENPKESF 138

Query: 111 LFYHEMIVQGLI---PDRFMFPSLFKSCADIYVEKQLH---SQAIKFGLASDSFLHNTLI 164
           L Y +M+  G     PD F +P LFK CAD+ +    H      +K  L   S +HN  I
Sbjct: 139 LLYKQMLRHGCCESRPDHFTYPVLFKVCADLRLSSLGHMILGHVLKLRLELVSHVHNASI 198

Query: 165 NMYSSC--------------------W-CL-------DQPDEAIKIFYRMEIENVKPNAV 196
           +M++SC                    W CL        + ++AI ++  ME E VKP+ V
Sbjct: 199 HMFASCGDMENARKVFDESPVRDLVSWNCLINGYKKIGEAEKAIYVYKLMESEGVKPDDV 258

Query: 197 TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLF 253
           T++ ++++ +   DL   K  ++ V E+G    + L   LMD + KC  +  A  +F
Sbjct: 259 TMIGLVSSCSMLGDLNRGKEFYEYVKENGLRMTIPLVNALMDMFSKCGDIHEARRIF 315

Arabidopsis thaliana (taxid: 3702)

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

 Score =  106 bits (265), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/257 (30%), Positives = 116/257 (45%), Gaps = 50/257 (19%)

Query: 55  ELKQIHAQMLRTSLFFD------------PCADY-HVRLVFSQISNPTIYTCNSIVRGYT 101
           +LKQIHA++L   L F                D    R VF  +  P I+  N+I+RGY+
Sbjct: 36  QLKQIHARLLVLGLQFSGFLITKLIHASSSFGDITFARQVFDDLPRPQIFPWNAIIRGYS 95

Query: 102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADI---YVEKQLHSQAIKFGLASDSF 158
             N   +A L Y  M +  + PD F FP L K+C+ +    + + +H+Q  + G  +D F
Sbjct: 96  RNNHFQDALLMYSNMQLARVSPDSFTFPHLLKACSGLSHLQMGRFVHAQVFRLGFDADVF 155

Query: 159 LHNTLINMYSSCWCLD------------------------------QPDEAIKIFYRMEI 188
           + N LI +Y+ C  L                               +P EA++IF +M  
Sbjct: 156 VQNGLIALYAKCRRLGSARTVFEGLPLPERTIVSWTAIVSAYAQNGEPMEALEIFSQMRK 215

Query: 189 ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSR 248
            +VKP+ V LV+VL A    +DL+  + +H  V + G     +L  +L   Y KC  V+ 
Sbjct: 216 MDVKPDWVALVSVLNAFTCLQDLKQGRSIHASVVKMGLEIEPDLLISLNTMYAKCGQVAT 275

Query: 249 AWDLFVKMLFP----WN 261
           A  LF KM  P    WN
Sbjct: 276 AKILFDKMKSPNLILWN 292

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 =  106 bits (264), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 124/278 (44%), Gaps = 59/278 (21%)

Query: 44  LVSLEKCSTMRELKQIHAQMLRTSL------------FFDPCADY----HVRLVFSQISN 87
           L  LE C ++ EL Q+H  M+++S+            F   C +     + R VF  I  
Sbjct: 10  LSQLENCRSLVELNQLHGLMIKSSVIRNVIPLSRLIDFCTTCPETMNLSYARSVFESIDC 69

Query: 88  PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA---DIYVEKQL 144
           P++Y  NS++RGY+N     +A +FY EM+ +G  PD F FP + K+C+   DI     +
Sbjct: 70  PSVYIWNSMIRGYSNSPNPDKALIFYQEMLRKGYSPDYFTFPYVLKACSGLRDIQFGSCV 129

Query: 145 HSQAIKFGLASDSFLHNTLINMYSSC---------------WCL-------------DQP 176
           H   +K G   + ++   L++MY  C               W +             ++ 
Sbjct: 130 HGFVVKTGFEVNMYVSTCLLHMYMCCGEVNYGLRVFEDIPQWNVVAWGSLISGFVNNNRF 189

Query: 177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF--------WS 228
            +AI+ F  M+   VK N   +V++L A  R +D+ T K  H  +   GF          
Sbjct: 190 SDAIEAFREMQSNGVKANETIMVDLLVACGRCKDIVTGKWFHGFLQGLGFDPYFQSKVGF 249

Query: 229 HVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWNN 262
           +V L T+L+D Y KC  +  A  LF  M    L  WN+
Sbjct: 250 NVILATSLIDMYAKCGDLRTARYLFDGMPERTLVSWNS 287

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUJ2|PP249_ARATH Pentatricopeptide repeat-containing protein At3g22690 OS=Arabidopsis thaliana GN=PCMP-H56 PE=2 SV=1

 Score =  101 bits (251), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 75/257 (29%), Positives = 117/257 (45%), Gaps = 49/257 (19%)

Query: 46  SLEKCSTMRELKQIHAQMLR----------TSLFFDPCA-DYHVRLVFSQ--ISNPTIY- 91
           SL+ C T+ ELK  H  + +          T L    C       L F++    N   Y 
Sbjct: 38  SLKNCKTIDELKMFHRSLTKQGLDNDVSTITKLVARSCELGTRESLSFAKEVFENSESYG 97

Query: 92  TC---NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEK---QLH 145
           TC   NS++RGY +  L +EA L +  M+  G+ PD++ FP    +CA    +    Q+H
Sbjct: 98  TCFMYNSLIRGYASSGLCNEAILLFLRMMNSGISPDKYTFPFGLSACAKSRAKGNGIQIH 157

Query: 146 SQAIKFGLASDSFLHNTLINMYSSCWCLDQ----------------------------PD 177
              +K G A D F+ N+L++ Y+ C  LD                               
Sbjct: 158 GLIVKMGYAKDLFVQNSLVHFYAECGELDSARKVFDEMSERNVVSWTSMICGYARRDFAK 217

Query: 178 EAIKIFYRM-EIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL 236
           +A+ +F+RM   E V PN+VT+V V++A A+  DL T ++V+  +  SG   +  + + L
Sbjct: 218 DAVDLFFRMVRDEEVTPNSVTMVCVISACAKLEDLETGEKVYAFIRNSGIEVNDLMVSAL 277

Query: 237 MDAYCKCKFVSRAWDLF 253
           +D Y KC  +  A  LF
Sbjct: 278 VDMYMKCNAIDVAKRLF 294

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/274 (28%), Positives = 120/274 (43%), Gaps = 51/274 (18%)

Query: 32  NNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSL----------FFDPCADY----- 76
           NN   + Q   CL  L++C  + E KQ+HA+ ++ SL              CA       
Sbjct: 24  NNFGGKEQE--CLYLLKRCHNIDEFKQVHARFIKLSLFYSSSFSASSVLAKCAHSGWENS 81

Query: 77  --HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKS 134
             +   +F  I +P  +  N+++RGY N     EA  FY+EM+ +G  PD F +P L K+
Sbjct: 82  MNYAASIFRGIDDPCTFDFNTMIRGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCLLKA 141

Query: 135 CA---DIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP--------------- 176
           C     I   KQ+H Q  K GL +D F+ N+LINMY  C  ++                 
Sbjct: 142 CTRLKSIREGKQIHGQVFKLGLEADVFVQNSLINMYGRCGEMELSSAVFEKLESKTAASW 201

Query: 177 -------------DEAIKIFYRMEIE-NVKPNAVTLVNVLTARARARDLRTVKRVHKCVD 222
                         E + +F  M  E N+K     +V+ L A A    L     +H  + 
Sbjct: 202 SSMVSARAGMGMWSECLLLFRGMCSETNLKAEESGMVSALLACANTGALNLGMSIHGFLL 261

Query: 223 ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM 256
            +    ++ ++T+L+D Y KC  + +A  +F KM
Sbjct: 262 RNISELNIIVQTSLVDMYVKCGCLDKALHIFQKM 295

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 = 95.1 bits (235), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 74/296 (25%), Positives = 126/296 (42%), Gaps = 82/296 (27%)

Query: 49  KCSTMRELKQIHAQMLRTSLFFD--------------PCADYHVRLVFSQISNPTIYTCN 94
           +CSTMRELKQIHA +++T L  D              P    +  LVF++I++   +  N
Sbjct: 34  QCSTMRELKQIHASLIKTGLISDTVTASRVLAFCCASPSDMNYAYLVFTRINHKNPFVWN 93

Query: 95  SIVRGYTNKNLHHEAFLFYHEMIVQG--LIPDRFMFPSLFKSCADIYVEK---QLHSQAI 149
           +I+RG++  +    A   + +M+     + P R  +PS+FK+   +   +   QLH   I
Sbjct: 94  TIIRGFSRSSFPEMAISIFIDMLCSSPSVKPQRLTYPSVFKAYGRLGQARDGRQLHGMVI 153

Query: 150 KFGLASDSFLHNTLINMY-------------------------------SSCWCLDQPD- 177
           K GL  DSF+ NT+++MY                               + C  +DQ   
Sbjct: 154 KEGLEDDSFIRNTMLHMYVTCGCLIEAWRIFLGMIGFDVVAWNSMIMGFAKCGLIDQAQN 213

Query: 178 ---------------------------EAIKIFYRMEIENVKPNAVTLVNVLTARARARD 210
                                      +A+ +F  M+ ++VKP+  T+V++L A A    
Sbjct: 214 LFDEMPQRNGVSWNSMISGFVRNGRFKDALDMFREMQEKDVKPDGFTMVSLLNACAYLGA 273

Query: 211 LRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFV----KMLFPWNN 262
               + +H+ +  + F  +  + T L+D YCKC  +    ++F     K L  WN+
Sbjct: 274 SEQGRWIHEYIVRNRFELNSIVVTALIDMYCKCGCIEEGLNVFECAPKKQLSCWNS 329

Arabidopsis thaliana (taxid: 3702)

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

 Score = 94.7 bits (234), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 97/218 (44%), Gaps = 35/218 (16%)

Query: 79  RLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD- 137
           R VF +++   + + NSI+ GY +  L  +    + +M+V G+  D     S+F  CAD 
Sbjct: 250 RKVFDEMTERDVISWNSIINGYVSNGLAEKGLSVFVQMLVSGIEIDLATIVSVFAGCADS 309

Query: 138 --IYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ-------------------- 175
             I + + +HS  +K   + +    NTL++MYS C  LD                     
Sbjct: 310 RLISLGRAVHSIGVKACFSREDRFCNTLLDMYSKCGDLDSAKAVFREMSDRSVVSYTSMI 369

Query: 176 --------PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW 227
                     EA+K+F  ME E + P+  T+  VL   AR R L   KRVH+ + E+   
Sbjct: 370 AGYAREGLAGEAVKLFEEMEEEGISPDVYTVTAVLNCCARYRLLDEGKRVHEWIKENDLG 429

Query: 228 SHVELKTTLMDAYCKCKFVSRAWDLF----VKMLFPWN 261
             + +   LMD Y KC  +  A  +F    VK +  WN
Sbjct: 430 FDIFVSNALMDMYAKCGSMQEAELVFSEMRVKDIISWN 467

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	323
225445386	711	PREDICTED: pentatricopeptide repeat-cont	0.804	0.365	0.527	6e-71
224114351	660	predicted protein [Populus trichocarpa]	0.647	0.316	0.540	4e-66
297738895	580	unnamed protein product [Vitis vinifera]	0.625	0.348	0.372	3e-37
225434622	743	PREDICTED: pentatricopeptide repeat-cont	0.876	0.380	0.311	4e-33
147840590	694	hypothetical protein VITISV_032470 [Viti	0.795	0.370	0.320	6e-33
449443185	562	PREDICTED: putative pentatricopeptide re	0.777	0.446	0.338	8e-30
449455158	733	PREDICTED: pentatricopeptide repeat-cont	0.736	0.324	0.295	1e-29
356504054	563	PREDICTED: putative pentatricopeptide re	0.783	0.449	0.322	2e-29
356502930	780	PREDICTED: pentatricopeptide repeat-cont	0.752	0.311	0.314	2e-28
28558786	565	selenium binding protein-like protein [C	0.789	0.451	0.326	3e-28

>gi|225445386|ref|XP_002281711.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic [Vitis vinifera]

 Score =  273 bits (699), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 163/309 (52%), Positives = 190/309 (61%), Gaps = 49/309 (15%)

Query: 1   MAAPLPLHHQTRTPALSSDNSPL-INLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQI 59
           MA PL LHH  R P  +    PL       NNNNINSQ Q H CL+SLEKC+TM +LKQI
Sbjct: 1   MATPLSLHH-PRPPLPTEYPLPLRNAATTANNNNINSQIQLHPCLLSLEKCTTMSQLKQI 59

Query: 60  HAQMLRTSLFFDP---------CADY------HVRLVFSQISNPTIYTCNSIVRGYTNKN 104
           HAQMLRT LF DP         CA +      + RLVF+QI NPT +TCNSI+RGYTNKN
Sbjct: 60  HAQMLRTCLFVDPFSASKIVAFCALHDSGSLPYARLVFNQIPNPTTFTCNSIIRGYTNKN 119

Query: 105 LHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLI 164
           L  +A LFY  M++QGL PDRF FPSLFKSC  +   KQLH  + K G ASD+++ NTL+
Sbjct: 120 LPRQAILFYQLMMLQGLDPDRFTFPSLFKSCGVLCEGKQLHCHSTKLGFASDAYIQNTLM 179

Query: 165 NMYSSCWCL----------------------------DQPDEAIKIFYRMEIENVKPNAV 196
           NMYS+C CL                            D P EAIK+F RMEI +VKPN +
Sbjct: 180 NMYSNCGCLVSARKVFDKMVNKSVVSWATMIGAYAQWDLPHEAIKLFRRMEIASVKPNEI 239

Query: 197 TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM 256
           TLVNVLTA AR+RDL T K+VHK +DE+G   H  L + LMD YCKC     A DLF KM
Sbjct: 240 TLVNVLTACARSRDLETAKQVHKYIDETGIGFHTVLTSALMDVYCKCGCYPLARDLFNKM 299

Query: 257 ----LFPWN 261
               LF WN
Sbjct: 300 PEKNLFCWN 308

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114351|ref|XP_002332376.1| predicted protein [Populus trichocarpa] gi|222832200|gb|EEE70677.1| predicted protein [Populus trichocarpa]

 Score =  258 bits (658), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 139/257 (54%), Positives = 161/257 (62%), Gaps = 48/257 (18%)

Query: 53  MRELKQIHAQMLRTSLFFDP---------------CADYHVRLVFSQISNPTIYTCNSIV 97
           M +LKQIHAQMLRT LFFDP                +  + RLVFSQI NPT YTCNSI+
Sbjct: 1   MSQLKQIHAQMLRTGLFFDPFTASKIVAFCSLQESGSLQYARLVFSQIPNPTSYTCNSII 60

Query: 98  RGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDS 157
           RG T+KNLH EA LFY EM+VQGLIPDR+ FPSLFKSC +    KQ+H  + K G ASD+
Sbjct: 61  RGCTDKNLHQEALLFYQEMMVQGLIPDRYTFPSLFKSCRNSSEGKQIHCHSTKLGFASDT 120

Query: 158 FLHNTLINMYSSCWCL----------------------------DQPDEAIKIFYR-MEI 188
           +  NTL+NMYS+C CL                            DQP+EA+++F R M+ 
Sbjct: 121 YAQNTLMNMYSNCGCLVSARKVFDKMEDKTVVSWATMIGVHAQWDQPNEAVRLFDRMMKS 180

Query: 189 ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSR 248
           ENVKPN VTLVNVLTA ARARDL  VKR+H+ +DE GF  HV L T LMD YCKC  V  
Sbjct: 181 ENVKPNEVTLVNVLTACARARDLAMVKRIHEYIDEHGFGRHVVLNTVLMDVYCKCGCVQL 240

Query: 249 AWDLFVKM----LFPWN 261
           A DLF K     LF WN
Sbjct: 241 ARDLFDKAQEKNLFSWN 257

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738895|emb|CBI28140.3| unnamed protein product [Vitis vinifera]

 Score =  162 bits (409), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 104/279 (37%), Positives = 133/279 (47%), Gaps = 77/279 (27%)

Query: 63  MLRTSLFFDP---------CADY------HVRLVFSQISNPTIYTCNSIVRGYTNKNLHH 107
           MLRT LF DP         CA +      + RLVF+QI NPT +TCNSI+RGYTNKNL  
Sbjct: 1   MLRTCLFVDPFSASKIVAFCALHDSGSLPYARLVFNQIPNPTTFTCNSIIRGYTNKNLPR 60

Query: 108 EAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMY 167
           +A LFY  M++QGL PDRF FPSLFKSC  +   KQLH  + K G ASD+++ NTL+NMY
Sbjct: 61  QAILFYQLMMLQGLDPDRFTFPSLFKSCGVLCEGKQLHCHSTKLGFASDAYIQNTLMNMY 120

Query: 168 SSCWCL----------------------------DQPDEAIKIFYRMEI----------- 188
           S+C CL                            D P EAIK+F RMEI           
Sbjct: 121 SNCGCLVSARKVFDKMVNKSVVSWATMIGAYAQWDLPHEAIKLFRRMEIASNLFCWNIMI 180

Query: 189 ---------------------ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW 227
                                  VK + VT+ ++L A      L   K +H  +++    
Sbjct: 181 NGHVEDSDYEEALSLFNEMQLSGVKGDKVTMASLLIACTHLGALELGKWLHVYIEKEKIE 240

Query: 228 SHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQW 266
             V L T L+D Y KC  +  A  +F +M  P  +   W
Sbjct: 241 VDVALGTALVDMYAKCGSIESAMRVFQEM--PEKDVMTW 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434622|ref|XP_002279360.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Vitis vinifera]

 Score =  148 bits (373), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 107/343 (31%), Positives = 162/343 (47%), Gaps = 60/343 (17%)

Query: 1   MAAPLP-LHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQI 59
           MA P P L    R+ +L + N   I L+N      +  +  H  L  +++CS  ++LKQI
Sbjct: 1   MAIPNPCLVSLPRSHSLPTPNPNSITLNN------DRYFANHPTLSLIDQCSETKQLKQI 54

Query: 60  HAQMLRTSLFFDPCA----------------DYHVRLVFSQISNPTIYTCNSIVRGYTNK 103
           HAQMLRT LFFDP +                DY  + VF QI +P +YT N+++R Y + 
Sbjct: 55  HAQMLRTGLFFDPFSASRLITAAALSPFPSLDY-AQQVFDQIPHPNLYTWNTLIRAYASS 113

Query: 104 NLHHEAFLFYHEMIVQGL-IPDRFMFPSLFKSCADI---YVEKQLHSQAIKFGLASDSFL 159
           +  H++ L +  M+ Q    PD+F FP L K+ +++   +  K  H   IK  L SD F+
Sbjct: 114 SNPHQSLLIFLRMLHQSPDFPDKFTFPFLIKAASELEELFTGKAFHGMVIKVLLGSDVFI 173

Query: 160 HNTLINMYSSCWCLDQ----------------------------PDEAIKIFYRMEIENV 191
            N+LI+ Y+ C  L                              P+EA+++F  ME +NV
Sbjct: 174 LNSLIHFYAKCGELGLGYRVFVNIPRRDVVSWNSMITAFVQGGCPEEALELFQEMETQNV 233

Query: 192 KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWD 251
           KPN +T+V VL+A A+  D    + VH  ++ +     + L   ++D Y KC  V  A  
Sbjct: 234 KPNGITMVGVLSACAKKSDFEFGRWVHSYIERNRIGESLTLSNAMLDMYTKCGSVEDAKR 293

Query: 252 LFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKK 294
           LF KM  P  +   W  +  VG    +G +  A  I    P +
Sbjct: 294 LFDKM--PEKDIVSWT-TMLVG-YAKIGEYDAAQGIFDAMPNQ 332

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147840590|emb|CAN72716.1| hypothetical protein VITISV_032470 [Vitis vinifera]

 Score =  147 bits (371), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 101/315 (32%), Positives = 152/315 (48%), Gaps = 58/315 (18%)

Query: 1   MAAPLP-LHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQI 59
           MA P P L    R+ +L + N   I L+N      +  +  H  L  +++CS  ++LKQI
Sbjct: 1   MAIPNPCLVSLPRSHSLPTPNPNSITLNN------DRYFANHPTLSLIDQCSETKQLKQI 54

Query: 60  HAQMLRTSLFFDPCA----------------DYHVRLVFSQISNPTIYTCNSIVRGYTNK 103
           HAQMLRT LFFDP +                DY  + VF QI +P +YT N+++R Y + 
Sbjct: 55  HAQMLRTGLFFDPFSASRLITAAALSPFPSLDY-AQQVFDQIPHPNLYTWNTLIRAYASS 113

Query: 104 NLHHEAFLFYHEMIVQGL-IPDRFMFPSLFKSCADI---YVEKQLHSQAIKFGLASDSFL 159
           +  H++ L +  M+ Q    PD+F FP L K+ +++   +  K  H   IK  L SD F+
Sbjct: 114 SNPHQSLLIFLRMLHQSPDFPDKFTFPFLIKAASELEELFTGKAFHGMVIKVLLGSDVFI 173

Query: 160 HNTLINMYSSCWCLDQ----------------------------PDEAIKIFYRMEIENV 191
            N+LI+ Y+ C  L                              P+EA+++F  ME +NV
Sbjct: 174 LNSLIHFYAKCGELGLGYRVFVNXPRRDVVSWNSMITAFVQGGCPEEALELFQEMETQNV 233

Query: 192 KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWD 251
           KPN +T+V VL+A A+  D    + VH  ++ +     + L   ++D Y KC  V  A  
Sbjct: 234 KPNGITMVGVLSACAKKSDFEFGRWVHSYIERNRIXESLTLSNAMLDMYTKCGSVEDAKR 293

Query: 252 LFVKMLFPWNNYGQW 266
           LF KM  P  +   W
Sbjct: 294 LFDKM--PEKDIVSW 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443185|ref|XP_004139361.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g05240-like [Cucumis sativus] gi|449525900|ref|XP_004169954.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g05240-like [Cucumis sativus]

 Score =  137 bits (345), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 108/319 (33%), Positives = 153/319 (47%), Gaps = 68/319 (21%)

Query: 39  QAHFCLVS-LEKCSTMRELKQIHAQMLRTSL---------FFDPCAD------YHVRLVF 82
           Q ++ ++S LEKC TM+ELKQIH+ M+ TS+           D CA+       + R VF
Sbjct: 3   QNYYTVMSFLEKCKTMKELKQIHSLMITTSVVKNIIPCSRLIDFCANSELGDIEYARTVF 62

Query: 83  SQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA--DIYV 140
            QI+  T+Y  NS+++GY N      A   Y EM  +G  PD F FP + K C+  D+ V
Sbjct: 63  DQINQRTVYIWNSMIKGYCNGGDKFGALFMYEEMQRKGFSPDHFTFPFVLKVCSIIDLLV 122

Query: 141 EKQ-LHSQAIKFGLASDSFLHNTLINMYSSCWCL-------------------------- 173
             Q +H++ +K G   D +  + L+NMY SC  L                          
Sbjct: 123 YGQSVHNRIVKTGFELDVYTSSCLLNMYVSCGDLNSGLKVFEFIPKWNVVAWTSLIAGFV 182

Query: 174 --DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF----- 226
             DQP EA+++F  ME E V+PN +T+   L A AR RD+ T K VH  + + GF     
Sbjct: 183 NNDQPKEALRLFKDMENEGVEPNEITMTTALAAAARCRDIHTGKLVHDRLRQLGFDPFDT 242

Query: 227 --WSHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWNN----YGQWAMSATVGPQG 276
               +V L T +MD Y KC  +  A +LF KM    L  WN+    Y Q+      G + 
Sbjct: 243 NSCFNVILATAIMDMYAKCGKLVTARNLFDKMPQRNLVVWNSMISAYSQYGR----GAEA 298

Query: 277 LVGRHSTAHQISGPCPKKA 295
           L  R     +++G  P KA
Sbjct: 299 L--RLFVDMEMAGFVPNKA 315

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455158|ref|XP_004145320.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Cucumis sativus] gi|449470513|ref|XP_004152961.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Cucumis sativus] gi|449523079|ref|XP_004168552.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Cucumis sativus]

 Score =  136 bits (343), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 86/291 (29%), Positives = 147/291 (50%), Gaps = 53/291 (18%)

Query: 22  PLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCA------- 74
           P I+L N +  N N  ++ H  L +++KCS+ ++LK++HA+MLRT LFFDP +       
Sbjct: 7   PSISLQNFSTLNNNLLFRNHQILSTIDKCSSSKQLKEVHARMLRTGLFFDPFSASKLFTA 66

Query: 75  ---------DYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ-GLIPD 124
                    DY  R +F QI  P +YT N+++R Y + +   ++F+ + +++ +   +P+
Sbjct: 67  SALSSFSTLDY-ARNLFDQIPQPNLYTWNTLIRAYASSSDPFQSFVIFLDLLDKCEDLPN 125

Query: 125 RFMFPSLFKSCADI---YVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ------ 175
           +F FP + K+ +++    V   +H  AIK     D ++ N+L+  Y +C  L        
Sbjct: 126 KFTFPFVIKAASELKASRVGTAVHGMAIKLSFGMDLYILNSLVRFYGACGDLSMAERLFK 185

Query: 176 ----------------------PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRT 213
                                 P++A+++F +ME ENV PN+VT+V VL+A A+  DL  
Sbjct: 186 GISCKDVVSWNSMISAFAQGNCPEDALELFLKMERENVMPNSVTMVGVLSACAKKLDLEF 245

Query: 214 VKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPW 260
            + V   ++  G    + L   ++D Y KC  V  A  LF +M    +F W
Sbjct: 246 GRWVCSYIERKGIKVDLTLCNAMLDMYTKCGSVDDAQKLFDEMPERDVFSW 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504054|ref|XP_003520814.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g05240-like [Glycine max]

 Score =  136 bits (342), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 102/316 (32%), Positives = 150/316 (47%), Gaps = 63/316 (19%)

Query: 47  LEKCSTMRELKQIHAQMLRT---------SLFFDPCADY------HVRLVFSQISNPTIY 91
           L KC +MRELK++H  ++ T         S   D C D       +  LV  QI NP++Y
Sbjct: 11  LAKCKSMRELKKLHGLIVTTPTIKSIIPLSKLIDFCVDSEFGDINYADLVLRQIHNPSVY 70

Query: 92  TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSC---ADIYVEKQLHSQA 148
             NS++RG+ N +    + L Y +MI  G  PD F FP + K+C   AD    K +HS  
Sbjct: 71  IWNSMIRGFVNSHNPRMSMLLYRQMIENGYSPDHFTFPFVLKACCVIADQDCGKCIHSCI 130

Query: 149 IKFGLASDSFLHNTLINMYSSC---------------W------CL-------DQPDEAI 180
           +K G  +D++    L++MY SC               W      CL       +QP EA+
Sbjct: 131 VKSGFEADAYTATGLLHMYVSCADMKSGLKVFDNIPKWNVVAWTCLIAGYVKNNQPYEAL 190

Query: 181 KIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF-------WSHVELK 233
           K+F  M   NV+PN +T+VN L A A +RD+ T + VH+ + ++G+        S++ L 
Sbjct: 191 KVFEDMSHWNVEPNEITMVNALIACAHSRDIDTGRWVHQRIRKAGYDPFMSTSNSNIILA 250

Query: 234 TTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQI------ 287
           T +++ Y KC  +  A DLF KM  P  N   W  ++ +       RH  A  +      
Sbjct: 251 TAILEMYAKCGRLKIARDLFNKM--PQRNIVSW--NSMINAYNQYERHQEALDLFFDMWT 306

Query: 288 SGPCPKKAHKLFFFSM 303
           SG  P KA  L   S+
Sbjct: 307 SGVYPDKATFLSVLSV 322

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502930|ref|XP_003520267.1| PREDICTED: pentatricopeptide repeat-containing protein At2g29760, chloroplastic-like [Glycine max]

 Score =  132 bits (332), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 93/296 (31%), Positives = 143/296 (48%), Gaps = 53/296 (17%)

Query: 47  LEKCSTMRELKQIHAQMLRTSLFFDP----------------CADYHVRLVFSQISNPTI 90
           +++C+   +LKQIHA MLRTS F DP                C  Y  + VF+QI  P +
Sbjct: 79  IDQCTNTMQLKQIHAHMLRTSRFCDPYTASKLLTAYAISSCSCLIY-AKNVFNQIPQPNL 137

Query: 91  YTCNSIVRGYTNKNLHHEAFL-FYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHS 146
           Y  N+++RGY + +   ++FL F H +      P++F FP LFK+ + + V      LH 
Sbjct: 138 YCWNTLIRGYASSSDPTQSFLIFLHMLHSCSEFPNKFTFPFLFKAASRLKVLHLGSVLHG 197

Query: 147 QAIKFGLASDSFLHNTLINMYSSCWCLD----------------------------QPDE 178
             IK  L+SD F+ N+LIN Y S    D                             PD+
Sbjct: 198 MVIKASLSSDLFILNSLINFYGSSGAPDLAHRVFTNMPGKDVVSWNAMINAFALGGLPDK 257

Query: 179 AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD 238
           A+ +F  ME+++VKPN +T+V+VL+A A+  DL   + +   ++ +GF  H+ L   ++D
Sbjct: 258 ALLLFQEMEMKDVKPNVITMVSVLSACAKKIDLEFGRWICSYIENNGFTEHLILNNAMLD 317

Query: 239 AYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPKK 294
            Y KC  ++ A DLF KM     +   W  +  +     +G +  AH I    P K
Sbjct: 318 MYVKCGCINDAKDLFNKM--SEKDIVSW--TTMLDGHAKLGNYDEAHCIFDAMPHK 369

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|28558786|gb|AAO45757.1| selenium binding protein-like protein [Cucumis melo subsp. melo]

 Score =  132 bits (331), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 103/315 (32%), Positives = 148/315 (46%), Gaps = 60/315 (19%)

Query: 39  QAHFCLVS-LEKCSTMRELKQIHAQMLRTSL---------FFDPCAD------YHVRLVF 82
           Q+++ ++S LEKC TM+ELKQIH+ M++TS+           D CA+       + R VF
Sbjct: 3   QSYYTILSFLEKCKTMKELKQIHSLMIKTSVVKNIIPCSRLIDFCANSELGDIEYARTVF 62

Query: 83  SQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA--DIYV 140
            Q    T+Y  NS+++GY N      A   Y EM  +G  PD F FP + K C+  D+ V
Sbjct: 63  DQTDQLTVYVWNSMIKGYCNGGDKFGALFMYEEMQRKGFYPDHFTFPFVLKVCSAIDLLV 122

Query: 141 EKQ-LHSQAIKFGLASDSFLHNTLINMYSSCWCL-------------------------- 173
             Q +H++ +K G   D +  + L+NMY SC  L                          
Sbjct: 123 YGQSVHNRIVKTGFELDVYTSSCLLNMYVSCGDLNSGLKVFEFIPKWNVVAWTSLIAGFV 182

Query: 174 --DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF----- 226
             DQP EA+++F  ME E V+PN +T+   L A AR RD+ T K V   + + G      
Sbjct: 183 NNDQPKEALRLFKDMENEGVEPNEITMTTALAAAARCRDIHTGKLVRYRLRQLGLDPFHT 242

Query: 227 --WSHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWNNYGQWAMSATVGPQGLVGR 280
               +V L T +MD Y KC  +  A +LF KM    L  WN+          G + L  R
Sbjct: 243 NSRFNVILATAIMDMYAKCGKLVTARNLFDKMPQRNLVVWNSMISAFSQYGRGAEAL--R 300

Query: 281 HSTAHQISGPCPKKA 295
                +++G  P KA
Sbjct: 301 LFVDMELAGFVPNKA 315

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	323
TAIR|locus:2094812	600	AT3G29230 "AT3G29230" [Arabido	0.659	0.355	0.304	1e-23
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.430	0.204	0.349	5.5e-21
TAIR|locus:2025946	638	CRR28 "CHLORORESPIRATORY REDUC	0.380	0.192	0.345	1.2e-17
TAIR|locus:2034456	606	AT1G31920 [Arabidopsis thalian	0.278	0.148	0.419	1.6e-17
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.393	0.171	0.308	4.2e-16
TAIR|locus:2196583	866	ECB2 "EARLY CHLOROPLAST BIOGEN	0.278	0.103	0.319	7.5e-16
TAIR|locus:2144143	622	AT5G06540 [Arabidopsis thalian	0.278	0.144	0.344	1.1e-15
TAIR|locus:2045580	559	AT2G42920 [Arabidopsis thalian	0.321	0.186	0.339	4.3e-15
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.334	0.202	0.387	5.7e-14
TAIR|locus:2117084	545	AT4G18840 "AT4G18840" [Arabido	0.371	0.220	0.309	6.8e-14

TAIR|locus:2094812 AT3G29230 "AT3G29230" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.0e-23, P = 1.0e-23
 Identities = 73/240 (30%), Positives = 127/240 (52%)

Query:    44 LVSLEKCSTMRELKQIHAQMLRTSLFFD----P--------CADYHVRL-VFSQISNPTI 90
             L  L KC+ + ++KQ+HAQ++R +L  D    P        C   ++ + VF+Q+  P +
Sbjct:    23 LQDLPKCANLNQVKQLHAQIIRRNLHEDLHIAPKLISALSLCRQTNLAVRVFNQVQEPNV 82

Query:    91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD---IYVEKQLHSQ 147
             + CNS++R +   +  ++AF  + EM   GL  D F +P L K+C+    + V K +H+ 
Sbjct:    83 HLCNSLIRAHAQNSQPYQAFFVFSEMQRFGLFADNFTYPFLLKACSGQSWLPVVKMMHNH 142

Query:   148 AIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTXXXX 207
               K GL+SD ++ N LI+ YS C  L   D A+K+F +M     + + V+  ++L     
Sbjct:   143 IEKLGLSSDIYVPNALIDCYSRCGGLGVRD-AMKLFEKMS----ERDTVSWNSMLGGLVK 197

Query:   208 XXDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWA 267
               +LR  +R+   + +    S      T++D Y +C+ +S+A++LF KM  P  N   W+
Sbjct:   198 AGELRDARRLFDEMPQRDLISW----NTMLDGYARCREMSKAFELFEKM--PERNTVSWS 251

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 = 201 (75.8 bits), Expect = 5.5e-21, Sum P(2) = 5.5e-21
 Identities = 58/166 (34%), Positives = 83/166 (50%)

Query:    41 HFCLVSL-EKCSTMRELKQIHAQMLRTSLFFDP---------CA-------DYHVRLVFS 83
             H  L+SL EKC  +  LKQI AQM+   L  DP         CA       DY V+++  
Sbjct:    53 HNPLLSLLEKCKLLLHLKQIQAQMIINGLILDPFASSRLIAFCALSESRYLDYSVKIL-K 111

Query:    84 QISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLI---PDRFMFPSLFKSCADIYV 140
              I NP I++ N  +RG++      E+FL Y +M+  G     PD F +P LFK CAD+ +
Sbjct:   112 GIENPNIFSWNVTIRGFSESENPKESFLLYKQMLRHGCCESRPDHFTYPVLFKVCADLRL 171

Query:   141 EKQLH---SQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIF 183
                 H      +K  L   S +HN  I+M++SC  ++    A K+F
Sbjct:   172 SSLGHMILGHVLKLRLELVSHVHNASIHMFASCGDMEN---ARKVF 214

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2025946 CRR28 "CHLORORESPIRATORY REDUCTION28" [Arabidopsis thaliana (taxid:3702)]

 Score = 181 (68.8 bits), Expect = 1.2e-17, Sum P(3) = 1.2e-17
 Identities = 46/133 (34%), Positives = 75/133 (56%)

Query:    59 IHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNK-NLHHEAFLFYHEMI 117
             ++ ++L+ S  F    +Y  R VF  I N + +  N+++R   +  +   EAF+ Y +M+
Sbjct:    85 LYGKILQLSSSFSD-VNYAFR-VFDSIENHSSFMWNTLIRACAHDVSRKEEAFMLYRKML 142

Query:   118 VQG-LIPDRFMFPSLFKSCADIY--VE-KQLHSQAIKFGLASDSFLHNTLINMYSSCWCL 173
              +G   PD+  FP + K+CA I+   E KQ+H Q +K G   D +++N LI++Y SC CL
Sbjct:   143 ERGESSPDKHTFPFVLKACAYIFGFSEGKQVHCQIVKHGFGGDVYVNNGLIHLYGSCGCL 202

Query:   174 DQPDEAIKIFYRM 186
             D    A K+F  M
Sbjct:   203 DL---ARKVFDEM 212

GO:0005739 "mitochondrion" evidence=ISM

GO:0004519 "endonuclease activity" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA;IMP

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

 Score = 199 (75.1 bits), Expect = 1.6e-17, Sum P(2) = 1.6e-17
 Identities = 39/93 (41%), Positives = 54/93 (58%)

Query:    81 VFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA---D 137
             +F  I +P  +  N+++RGY N     EA  FY+EM+ +G  PD F +P L K+C     
Sbjct:    88 IFRGIDDPCTFDFNTMIRGYVNVMSFEEALCFYNEMMQRGNEPDNFTYPCLLKACTRLKS 147

Query:   138 IYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC 170
             I   KQ+H Q  K GL +D F+ N+LINMY  C
Sbjct:   148 IREGKQIHGQVFKLGLEADVFVQNSLINMYGRC 180

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:2205200 OTP82 "AT1G08070" [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 4.2e-16, Sum P(2) = 4.2e-16
 Identities = 45/146 (30%), Positives = 68/146 (46%)

Query:    41 HFCLVSLEKCSTMRELKQIHAQMLRTSL---------FFDPCA-DYHVR------LVFSQ 84
             H  L  L  C T++ L+ IHAQM++  L           + C    H         VF  
Sbjct:    34 HPSLSLLHNCKTLQSLRIIHAQMIKIGLHNTNYALSKLIEFCILSPHFEGLPYAISVFKT 93

Query:    85 ISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD--IYVE- 141
             I  P +   N++ RG+   +    A   Y  MI  GL+P+ + FP + KSCA    + E 
Sbjct:    94 IQEPNLLIWNTMFRGHALSSDPVSALKLYVCMISLGLLPNSYTFPFVLKSCAKSKAFKEG 153

Query:   142 KQLHSQAIKFGLASDSFLHNTLINMY 167
             +Q+H   +K G   D ++H +LI+MY
Sbjct:   154 QQIHGHVLKLGCDLDLYVHTSLISMY 179

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2196583 ECB2 "EARLY CHLOROPLAST BIOGENESIS2" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 7.5e-16, Sum P(2) = 7.5e-16
 Identities = 30/94 (31%), Positives = 50/94 (53%)

Query:    81 VFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI-VQGLIPDRFMFPSLFKSCA--- 136
             VF ++S   +++ N +V GY  +    EA   YH M+ V G+ PD + FP + ++C    
Sbjct:   151 VFGKMSERNLFSWNVLVGGYAKQGYFDEAMCLYHRMLWVGGVKPDVYTFPCVLRTCGGIP 210

Query:   137 DIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC 170
             D+   K++H   +++G   D  + N LI MY  C
Sbjct:   211 DLARGKEVHVHVVRYGYELDIDVVNALITMYVKC 244

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0009416 "response to light stimulus" evidence=IEP

TAIR|locus:2144143 AT5G06540 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 1.1e-15, Sum P(3) = 1.1e-15
 Identities = 32/93 (34%), Positives = 58/93 (62%)

Query:    81 VFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD--- 137
             +FSQI NP ++  N ++R ++      +AF FY +M+   + PD   FP L K+ ++   
Sbjct:    73 IFSQIQNPNLFVFNLLIRCFSTGAEPSKAFGFYTQMLKSRIWPDNITFPFLIKASSEMEC 132

Query:   138 IYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC 170
             + V +Q HSQ ++FG  +D ++ N+L++MY++C
Sbjct:   133 VLVGEQTHSQIVRFGFQNDVYVENSLVHMYANC 165

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 162 (62.1 bits), Expect = 4.3e-15, Sum P(2) = 4.3e-15
 Identities = 38/112 (33%), Positives = 63/112 (56%)

Query:    80 LVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG--LIPDRFMFPSLFKSCAD 137
             LVF++I++   +  N+I+RG++  +    A   + +M+     + P R  +PS+FK+   
Sbjct:    79 LVFTRINHKNPFVWNTIIRGFSRSSFPEMAISIFIDMLCSSPSVKPQRLTYPSVFKAYGR 138

Query:   138 IYVEK---QLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM 186
             +   +   QLH   IK GL  DSF+ NT+++MY +C CL    EA +IF  M
Sbjct:   139 LGQARDGRQLHGMVIKEGLEDDSFIRNTMLHMYVTCGCLI---EAWRIFLGM 187

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 202 (76.2 bits), Expect = 5.7e-14, P = 5.7e-14
 Identities = 45/116 (38%), Positives = 66/116 (56%)

Query:    75 DYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL-IPDRFMFPSLFK 133
             DY  RL F+Q+SNP ++  NSI+R YT+ +L+ +    Y +++ +   +PDRF FP +FK
Sbjct:    59 DYATRL-FNQVSNPNVFLYNSIIRAYTHNSLYCDVIRIYKQLLRKSFELPDRFTFPFMFK 117

Query:   134 SCADI---YVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM 186
             SCA +   Y+ KQ+H    KFG        N LI+MY      D   +A K+F  M
Sbjct:   118 SCASLGSCYLGKQVHGHLCKFGPRFHVVTENALIDMYMK---FDDLVDAHKVFDEM 170

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2117084 AT4G18840 "AT4G18840" [Arabidopsis thaliana (taxid:3702)]

 Score = 182 (69.1 bits), Expect = 6.8e-14, Sum P(2) = 6.8e-14
 Identities = 43/139 (30%), Positives = 73/139 (52%)

Query:    48 EKCSTMRELKQIHAQMLRTSLFFD----------------PCADYHVRLVFSQISNPTIY 91
             E+  ++ E++Q HA ML+T LF D                P    +   + ++I +P  +
Sbjct:    47 ERAKSLTEIQQAHAFMLKTGLFHDTFSASKLVAFAATNPEPKTVSYAHSILNRIGSPNGF 106

Query:    92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADI--YVE-KQLHSQA 148
             T NS++R Y N +    A   + EM++  + PD++ F  + K+CA    + E +Q+H   
Sbjct:   107 THNSVIRAYANSSTPEVALTVFREMLLGPVFPDKYSFTFVLKACAAFCGFEEGRQIHGLF 166

Query:   149 IKFGLASDSFLHNTLINMY 167
             IK GL +D F+ NTL+N+Y
Sbjct:   167 IKSGLVTDVFVENTLVNVY 185

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

Your Input: GSVIVG00016825001 SubName- Full=Chromosome chr11 scaffold_13, whole genome shotgun sequence; (711 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	323
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-20
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-19
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-17
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-15
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-09
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	7e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	0.002

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

 Score = 92.2 bits (229), Expect = 1e-20
 Identities = 57/244 (23%), Positives = 103/244 (42%), Gaps = 44/244 (18%)

Query: 57  KQIHAQMLRTSLFFD------------PCAD-YHVRLVFSQISNPTIYTCNSIVRGYTNK 103
           +++HA ++R     D             C D    RLVF ++      + N+++ GY   
Sbjct: 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFEN 266

Query: 104 NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSC---ADIYVEKQLHSQAIKFGLASDSFLH 160
               E    +  M    + PD     S+  +C    D  + +++H   +K G A D  + 
Sbjct: 267 GECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

Query: 161 NTLINMYSSCWCLDQ----------------------------PDEAIKIFYRMEIENVK 192
           N+LI MY S     +                            PD+A++ +  ME +NV 
Sbjct: 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVS 386

Query: 193 PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL 252
           P+ +T+ +VL+A A   DL    ++H+  +  G  S+V +   L++ Y KCK + +A ++
Sbjct: 387 PDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEV 446

Query: 253 FVKM 256
           F  +
Sbjct: 447 FHNI 450

Length = 857

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

 Score = 87.6 bits (217), Expect = 5e-19
 Identities = 61/216 (28%), Positives = 91/216 (42%), Gaps = 33/216 (15%)

Query: 79  RLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA-- 136
             VFS++      +  +++ GY    L  +A   Y  M    + PD     S+  +CA  
Sbjct: 343 EKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACL 402

Query: 137 -DIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIK-------------- 181
            D+ V  +LH  A + GL S   + N LI MYS C C+D+  E                 
Sbjct: 403 GDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSII 462

Query: 182 -------------IFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS 228
                        IF+R  +  +KPN+VTL+  L+A AR   L   K +H  V  +G   
Sbjct: 463 AGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGF 522

Query: 229 HVELKTTLMDAYCKCKFVSRAWDLF---VKMLFPWN 261
              L   L+D Y +C  ++ AW+ F    K +  WN
Sbjct: 523 DGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWN 558

Length = 857

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

 Score = 81.8 bits (202), Expect = 3e-17
 Identities = 49/207 (23%), Positives = 90/207 (43%), Gaps = 31/207 (14%)

Query: 81  VFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA---D 137
           VF ++    +++ N +V GY       EA   YH M+  G+ PD + FP + ++C    D
Sbjct: 143 VFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPD 202

Query: 138 IYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC--------------------WCL---- 173
           +   +++H+  ++FG   D  + N LI MY  C                    W      
Sbjct: 203 LARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISG 262

Query: 174 ----DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH 229
                +  E +++F+ M   +V P+ +T+ +V++A     D R  + +H  V ++GF   
Sbjct: 263 YFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVD 322

Query: 230 VELKTTLMDAYCKCKFVSRAWDLFVKM 256
           V +  +L+  Y        A  +F +M
Sbjct: 323 VSVCNSLIQMYLSLGSWGEAEKVFSRM 349

Length = 857

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

 Score = 76.8 bits (189), Expect = 1e-15
 Identities = 48/218 (22%), Positives = 87/218 (39%), Gaps = 35/218 (16%)

Query: 79  RLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA-- 136
           R +F ++    + +  +I+ G  +   + EAF  + EM   G   +   F  + ++ A  
Sbjct: 178 RRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGL 237

Query: 137 -DIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ-------------------- 175
                 +QLH   +K G+  D+F+   LI+MYS C  ++                     
Sbjct: 238 GSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSML 297

Query: 176 --------PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW 227
                    +EA+ ++Y M    V  +  T   ++   +R   L   K+ H  +  +GF 
Sbjct: 298 AGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFP 357

Query: 228 SHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWN 261
             +   T L+D Y K   +  A ++F +M    L  WN
Sbjct: 358 LDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWN 395

Length = 697

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

 Score = 58.3 bits (141), Expect = 2e-09
 Identities = 40/157 (25%), Positives = 63/157 (40%), Gaps = 31/157 (19%)

Query: 79  RLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSC--- 135
           R VF  +   T    NS++ GY       EA   Y+EM   G+  D+F F  + +     
Sbjct: 279 RCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRL 338

Query: 136 ADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP------------------- 176
           A +   KQ H+  I+ G   D   +  L+++YS    ++                     
Sbjct: 339 ALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALI 398

Query: 177 ---------DEAIKIFYRMEIENVKPNAVTLVNVLTA 204
                     +A+++F RM  E V PN VT + VL+A
Sbjct: 399 AGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSA 435

Length = 697

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

 Score = 56.0 bits (135), Expect = 1e-08
 Identities = 38/158 (24%), Positives = 69/158 (43%), Gaps = 31/158 (19%)

Query: 81  VFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADI-- 138
           VF  I    + +  SI+ G    N   EA +F+ +M++  L P+     +   +CA I  
Sbjct: 446 VFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LKPNSVTLIAALSACARIGA 504

Query: 139 -YVEKQLHSQAIKFGLASDSFLHNTLINMYSSC---------WCLDQPD----------- 177
               K++H+  ++ G+  D FL N L+++Y  C         +   + D           
Sbjct: 505 LMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGY 564

Query: 178 -------EAIKIFYRMEIENVKPNAVTLVNVLTARARA 208
                   A+++F RM    V P+ VT +++L A +R+
Sbjct: 565 VAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRS 602

Length = 857

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

 Score = 44.7 bits (107), Expect = 8e-07
 Identities = 13/50 (26%), Positives = 24/50 (48%)

Query: 88  PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD 137
           P + T N+++ GY  K    EA   ++EM  +G+ P+ + +  L      
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 47.5 bits (113), Expect = 6e-06
 Identities = 33/110 (30%), Positives = 47/110 (42%), Gaps = 7/110 (6%)

Query: 156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVK 215
           D F  N L+  Y+     D   EA+ +++RM    V+P+  T   VL       DL   +
Sbjct: 151 DLFSWNVLVGGYAKAGYFD---EALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGR 207

Query: 216 RVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWN 261
            VH  V   GF   V++   L+  Y KC  V  A  +F +M       WN
Sbjct: 208 EVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWN 257

Length = 857

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

 Score = 39.0 bits (92), Expect = 7e-05
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 91  YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD 124
            T N+++ G        EA   + EM  +G+ PD
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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

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

 Score = 35.8 bits (84), Expect = 0.001
 Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVT 197
           D   +NTLI+ Y       + +EA+K+F  M+   +KPN  T
Sbjct: 2   DVVTYNTLIDGYCKK---GKVEEALKLFNEMKKRGIKPNVYT 40

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

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

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 45/222 (20%), Positives = 73/222 (32%), Gaps = 37/222 (16%)

Query: 77  HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAF-LFYHEMIVQGLIPDRFMFPSLFKSC 135
             RL  +QI    +  C+ I +       H EA  LF               + +L ++C
Sbjct: 75  DARLDDTQIRKSGVSLCSQIEK-LVACGRHREALELFEILEAGCPFTLPASTYDALVEAC 133

Query: 136 A---DIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCL------------------- 173
                I   K ++      G   D ++ N ++ M+  C  L                   
Sbjct: 134 IALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWG 193

Query: 174 ---------DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES 224
                        EA  +F  M  +       T V +L A A     R  +++H CV ++
Sbjct: 194 TIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKT 253

Query: 225 GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM----LFPWNN 262
           G      +   L+D Y KC  +  A  +F  M       WN+
Sbjct: 254 GVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNS 295

Length = 697

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	323
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.65
PF13041	50	PPR_2: PPR repeat family	99.58
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.56
PF13041	50	PPR_2: PPR repeat family	99.55
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.52
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.51
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.39
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.31
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.11
PF12854	34	PPR_1: PPR repeat	99.08
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.06
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.01
PF12854	34	PPR_1: PPR repeat	98.95
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.89
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.88
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.86
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.75
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.72
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.66
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.61
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.59
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.48
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.48
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.47
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.46
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.43
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.41
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.41
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.37
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.31
PRK14574	822	hmsH outer membrane protein; Provisional	98.3
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.3
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.28
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.21
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.19
PRK12370	553	invasion protein regulator; Provisional	98.16
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.16
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.15
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.12
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.1
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.05
PRK12370	553	invasion protein regulator; Provisional	98.04
KOG1126	638	consensus DNA-binding cell division cycle control	98.0
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.0
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.96
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.96
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.91
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.9
PRK14574	822	hmsH outer membrane protein; Provisional	97.83
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.82
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.81
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.8
KOG1129	478	consensus TPR repeat-containing protein [General f	97.77
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.69
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.69
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.68
KOG1126	638	consensus DNA-binding cell division cycle control	97.67
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.61
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.6
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.54
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.52
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.52
PRK11189	296	lipoprotein NlpI; Provisional	97.45
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.42
PRK15359	144	type III secretion system chaperone protein SscB;	97.42
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.31
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.3
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.27
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.27
KOG2003	840	consensus TPR repeat-containing protein [General f	97.24
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.24
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.24
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.2
KOG1129	478	consensus TPR repeat-containing protein [General f	97.18
KOG3941	406	consensus Intermediate in Toll signal transduction	97.18
KOG2076	895	consensus RNA polymerase III transcription factor	97.14
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.12
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.1
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.07
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.03
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.02
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.97
KOG2003	840	consensus TPR repeat-containing protein [General f	96.96
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	96.92
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.88
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.88
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.83
PRK11189	296	lipoprotein NlpI; Provisional	96.77
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.76
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.73
KOG3941	406	consensus Intermediate in Toll signal transduction	96.62
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.61
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.61
KOG2076	895	consensus RNA polymerase III transcription factor	96.59
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.56
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	96.56
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.55
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.54
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.5
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.48
PRK10370	198	formate-dependent nitrite reductase complex subuni	96.42
KOG1128	777	consensus Uncharacterized conserved protein, conta	96.41
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.4
KOG0495	913	consensus HAT repeat protein [RNA processing and m	96.38
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.31
TIGR02552	135	LcrH_SycD type III secretion low calcium response	96.3
PRK15359	144	type III secretion system chaperone protein SscB;	96.3
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.21
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.18
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.16
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.16
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.14
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.12
KOG2047	835	consensus mRNA splicing factor [RNA processing and	96.04
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	96.01
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	95.96
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	95.92
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.88
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	95.86
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.74
KOG2047	835	consensus mRNA splicing factor [RNA processing and	95.69
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.67
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	95.62
KOG0495	913	consensus HAT repeat protein [RNA processing and m	95.62
PRK14720	906	transcript cleavage factor/unknown domain fusion p	95.6
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.49
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	95.49
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	95.47
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.46
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.43
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	95.35
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.25
KOG3616	1636	consensus Selective LIM binding factor [Transcript	95.21
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	95.12
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	94.85
PRK14720	906	transcript cleavage factor/unknown domain fusion p	94.78
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	94.77
PLN02789	320	farnesyltranstransferase	94.74
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	94.67
KOG1915	677	consensus Cell cycle control protein (crooked neck	94.61
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.47
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.42
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.39
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.37
KOG1128	777	consensus Uncharacterized conserved protein, conta	94.36
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	94.21
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	94.17
KOG2796	366	consensus Uncharacterized conserved protein [Funct	94.1
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.84
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	93.62
COG4700	251	Uncharacterized protein conserved in bacteria cont	93.58
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	93.54
KOG2376	652	consensus Signal recognition particle, subunit Srp	93.41
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	93.39
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	93.2
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.13
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	93.09
KOG1125	579	consensus TPR repeat-containing protein [General f	93.02
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	92.95
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	92.95
KOG3060	289	consensus Uncharacterized conserved protein [Funct	92.95
PF13371	73	TPR_9: Tetratricopeptide repeat	92.91
PF12688	120	TPR_5: Tetratrico peptide repeat	92.83
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	92.83
PRK10803	263	tol-pal system protein YbgF; Provisional	92.74
PF13929	292	mRNA_stabil: mRNA stabilisation	92.61
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	92.6
KOG2376	652	consensus Signal recognition particle, subunit Srp	92.58
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.52
PF13762	145	MNE1: Mitochondrial splicing apparatus component	92.49
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	92.14
KOG3616	1636	consensus Selective LIM binding factor [Transcript	92.01
PF13371	73	TPR_9: Tetratricopeptide repeat	91.95
PF12688	120	TPR_5: Tetratrico peptide repeat	91.92
PF13929	292	mRNA_stabil: mRNA stabilisation	91.89
PRK04841	903	transcriptional regulator MalT; Provisional	91.75
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	91.45
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	91.4
PLN02789	320	farnesyltranstransferase	91.27
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	91.23
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	91.11
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	90.96
KOG0553	304	consensus TPR repeat-containing protein [General f	90.36
PF13428	44	TPR_14: Tetratricopeptide repeat	90.16
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	89.77
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	89.39
KOG1125	579	consensus TPR repeat-containing protein [General f	89.27
PRK04841	903	transcriptional regulator MalT; Provisional	89.2
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	89.1
KOG3785	557	consensus Uncharacterized conserved protein [Funct	89.04
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	88.9
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.78
KOG2796	366	consensus Uncharacterized conserved protein [Funct	88.51
COG3629	280	DnrI DNA-binding transcriptional activator of the	88.22
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	88.03
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	87.48
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	87.25
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	87.07
COG3629	280	DnrI DNA-binding transcriptional activator of the	86.93
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	86.9
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	86.85
KOG4570	418	consensus Uncharacterized conserved protein [Funct	86.8
KOG3060	289	consensus Uncharacterized conserved protein [Funct	86.69
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	86.69
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	86.29
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	86.12
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	85.97
PF13762	145	MNE1: Mitochondrial splicing apparatus component	85.82
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.76
KOG4340	459	consensus Uncharacterized conserved protein [Funct	84.27
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.37
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	83.17
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	83.14
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	82.59
PRK10803	263	tol-pal system protein YbgF; Provisional	82.5
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	82.47
COG4700	251	Uncharacterized protein conserved in bacteria cont	81.71
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	81.39
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	80.95
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	80.71
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	80.32
KOG0553	304	consensus TPR repeat-containing protein [General f	80.24

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=3.7e-47  Score=374.66  Aligned_cols=294  Identities=12%  Similarity=0.117  Sum_probs=238.8

Q ss_pred             cccCCCCCcccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---------ccch----hHHHhcccCC----CC
Q 040801           26 LDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---------CADY----HVRLVFSQIS----NP   88 (323)
Q Consensus        26 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---------y~~~----~a~~lf~~m~----~~   88 (323)
                      +..+..+..|+..+|+.++.+|++.|+++.|.++|++|.+.|+.|+.         |+++    .|.++|++|.    .|
T Consensus       426 l~lf~~M~~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~P  505 (1060)
T PLN03218        426 FRFAKLIRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEA  505 (1060)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCC
Confidence            33344455588888999999999999999999999999999888887         5555    8888888887    68


Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHH--cCCCCchHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIK--FGLASDSFLHNTL  163 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~--~g~~~~~~~~~~l  163 (323)
                      |..+||+||.+|++.|++++|+++|++|++.|+.||..||+.||.+|++.|+   |.+++++|.+  .|+.||.++|++|
T Consensus       506 dvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaL  585 (1060)
T PLN03218        506 NVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGAL  585 (1060)
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence            8888999999999999999999999999888888998899999999888888   8888888875  5788888888888


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  243 (323)
                      |++|++.|   ++++|.++|++|.+.|+.|+..+|+++|.+|++.|++++|.++|++|.+.|+.||..+|++||++|++.
T Consensus       586 I~ay~k~G---~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~  662 (1060)
T PLN03218        586 MKACANAG---QVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHA  662 (1060)
T ss_pred             HHHHHHCC---CHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhC
Confidence            88888888   557888888888888888888888888888888888888888888888888888888888888888888


Q ss_pred             CCHHHHHHHHHhccCCCCchhhhHHHhhhccCCCCCcchhhhhhhCCCC------c-----------------hhHHHHH
Q 040801          244 KFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCP------K-----------------KAHKLFF  300 (323)
Q Consensus       244 g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~------~-----------------~~~~~~~  300 (323)
                      |++++|.++|++|.+.|..|+..+|...+..+++.|+.++|..++..+.      +                 +.+..+|
T Consensus       663 G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf  742 (1060)
T PLN03218        663 GDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVL  742 (1060)
T ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8888888888888887777777777777777777777777766654331      1                 1356667


Q ss_pred             HHHHhccCCCCeeeeecccccc
Q 040801          301 FSMLKKVHVPGVLIQVHVPDVL  322 (323)
Q Consensus       301 ~~M~~~g~~p~~~t~~~li~~l  322 (323)
                      ++|.+.|+.||..||+++|.++
T Consensus       743 ~eM~~~Gi~Pd~~Ty~sLL~a~  764 (1060)
T PLN03218        743 SEMKRLGLCPNTITYSILLVAS  764 (1060)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHH
Confidence            8888888888888888877543

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=6.9e-47  Score=372.72  Aligned_cols=286  Identities=11%  Similarity=0.120  Sum_probs=193.1

Q ss_pred             cccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---------ccch----hHHHhcccCC------CCChhhHH
Q 040801           34 INSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---------CADY----HVRLVFSQIS------NPTIYTCN   94 (323)
Q Consensus        34 ~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---------y~~~----~a~~lf~~m~------~~~~~~~~   94 (323)
                      .|+..+|+++|.+|++.|++++|..+|++|.+.|+.|+.         |++.    .|.++|++|.      .||..+|+
T Consensus       504 ~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTyn  583 (1060)
T PLN03218        504 EANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVG  583 (1060)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHH
Confidence            456666666666666666666666666666666666665         3333    6666666663      46666677


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801           95 SIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus        95 ~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                      +||.+|++.|++++|.++|++|.+.|+.|+..+|+.+|.+|++.|+   |.++|++|.+.|+.||..+|++||++|++.|
T Consensus       584 aLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G  663 (1060)
T PLN03218        584 ALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG  663 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Confidence            7777777777777777777777666777777777777777777666   6677777777777777777777777777766


Q ss_pred             CCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHH
Q 040801          172 CLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       172 ~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                         +.++|.++|++|.+.|+.||..+|++||.+|++.|++++|.++|++|.+.|+.||..+|++||.+|++.|++++|.+
T Consensus       664 ---~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAle  740 (1060)
T PLN03218        664 ---DLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE  740 (1060)
T ss_pred             ---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence               44677777777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             HHHhccCCCCchhhhHHHhhhccCCCCCcchhhhhhhCCCCc--------------------------------------
Q 040801          252 LFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPK--------------------------------------  293 (323)
Q Consensus       252 ~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~--------------------------------------  293 (323)
                      +|++|.+.|..|+..+|...+..+++.|+.++|.++++.+..                                      
T Consensus       741 lf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~  820 (1060)
T PLN03218        741 VLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGR  820 (1060)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccc
Confidence            777777666677776666666666666666666544222110                                      


Q ss_pred             --------hhHHHHHHHHHhccCCCCeeeeecccccc
Q 040801          294 --------KAHKLFFFSMLKKVHVPGVLIQVHVPDVL  322 (323)
Q Consensus       294 --------~~~~~~~~~M~~~g~~p~~~t~~~li~~l  322 (323)
                              ..+..+|++|+++|+.||..||+.+|.++
T Consensus       821 ~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl  857 (1060)
T PLN03218        821 PQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGCL  857 (1060)
T ss_pred             cccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHHh
Confidence                    12345667777778778877777777543

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2e-44  Score=357.58  Aligned_cols=247  Identities=22%  Similarity=0.329  Sum_probs=224.0

Q ss_pred             cccccCCCCCccccccCCCCCcccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------------------
Q 040801           13 TPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------------------   72 (323)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------------------   72 (323)
                      +......+....++..+..+..|+..+|+++|.++++.|++++|..+|++|.+.|+.|+.                    
T Consensus       128 i~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~  207 (857)
T PLN03077        128 LSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGR  207 (857)
T ss_pred             HHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHH
Confidence            333344455555667777788888899999999999999999999999999888888773                    


Q ss_pred             ------------------------ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC
Q 040801           73 ------------------------CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD  124 (323)
Q Consensus        73 ------------------------y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~  124 (323)
                                              |+++    .|.++|++|+.+|.++||++|.+|++.|++++|+++|++|.+.|+.||
T Consensus       208 ~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd  287 (857)
T PLN03077        208 EVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPD  287 (857)
T ss_pred             HHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence                                    4444    899999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC---------------------------
Q 040801          125 RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD---------------------------  174 (323)
Q Consensus       125 ~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~---------------------------  174 (323)
                      ..||+.+|.+|++.|+   +.+++..|.+.|+.||..+||+||++|+++|+++                           
T Consensus       288 ~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~  367 (857)
T PLN03077        288 LMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKN  367 (857)
T ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhC
Confidence            9999999999999999   9999999999999999999999999999988765                           


Q ss_pred             -ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          175 -QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       175 -~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                       ++++|+++|++|.+.|+.||..||+++|.+|++.|+++.|.++++.|.+.|+.|+..+|++||++|+++|++++|.++|
T Consensus       368 g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf  447 (857)
T PLN03077        368 GLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVF  447 (857)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHH
Confidence             6788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhccCC
Q 040801          254 VKMLFP  259 (323)
Q Consensus       254 ~~m~~~  259 (323)
                      ++|.++
T Consensus       448 ~~m~~~  453 (857)
T PLN03077        448 HNIPEK  453 (857)
T ss_pred             HhCCCC
Confidence            999876

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

Probab=100.00  E-value=2.3e-44  Score=349.66  Aligned_cols=285  Identities=21%  Similarity=0.288  Sum_probs=235.1

Q ss_pred             cccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---------ccch----hHHHhcccCCCCChhhHHHHHHHH
Q 040801           34 INSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---------CADY----HVRLVFSQISNPTIYTCNSIVRGY  100 (323)
Q Consensus        34 ~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---------y~~~----~a~~lf~~m~~~~~~~~~~li~~~  100 (323)
                      .|+..+|++++.+|++.++++.+.+++..|.+.|+.|+.         |+++    .|.++|++|+.||.++||++|.+|
T Consensus       120 ~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~  199 (697)
T PLN03081        120 TLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGL  199 (697)
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHH
Confidence            568889999999999999999999999999999999988         6666    999999999999999999999999


Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC---
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD---  174 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~---  174 (323)
                      ++.|++++|+++|++|.+.|+.||..||+.++++|++.|.   +.+++..+.+.|+.||..+||+||++|+++|+++   
T Consensus       200 ~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~  279 (697)
T PLN03081        200 VDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDAR  279 (697)
T ss_pred             HHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHH
Confidence            9999999999999999999999988888888887777776   7777777777777666666666666666666543   


Q ss_pred             -------------------------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC
Q 040801          175 -------------------------QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH  229 (323)
Q Consensus       175 -------------------------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  229 (323)
                                               +.++|+++|++|...|+.||..||+++|.+|++.|++++|.+++++|.+.|+.||
T Consensus       280 ~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d  359 (697)
T PLN03081        280 CVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLD  359 (697)
T ss_pred             HHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCC
Confidence                                     6788999999999999999999999999999999999999999999999999999


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCCCCCcchhhhhhhCCCCc----------------
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQISGPCPK----------------  293 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~----------------  293 (323)
                      ..+|++||++|+++|++++|.++|++|.++  +...|  ...+..+++.|+.++|..+++.+..                
T Consensus       360 ~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~--d~~t~--n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a  435 (697)
T PLN03081        360 IVANTALVDLYSKWGRMEDARNVFDRMPRK--NLISW--NALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSA  435 (697)
T ss_pred             eeehHHHHHHHHHCCCHHHHHHHHHhCCCC--CeeeH--HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999864  34444  4444445555566666655443321                


Q ss_pred             -------hhHHHHHHHHHh-ccCCCCeeeeecccccc
Q 040801          294 -------KAHKLFFFSMLK-KVHVPGVLIQVHVPDVL  322 (323)
Q Consensus       294 -------~~~~~~~~~M~~-~g~~p~~~t~~~li~~l  322 (323)
                             +.+..+|++|.+ .|+.|+..+|+.+|++|
T Consensus       436 ~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l  472 (697)
T PLN03081        436 CRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELL  472 (697)
T ss_pred             HhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHH
Confidence                   136667788875 47778888888887765

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

Probab=100.00  E-value=3.1e-44  Score=348.77  Aligned_cols=282  Identities=16%  Similarity=0.191  Sum_probs=257.5

Q ss_pred             CCCCCcccccccccCCCCCccccccCCCCCcccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-----------
Q 040801            4 PLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-----------   72 (323)
Q Consensus         4 p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-----------   72 (323)
                      |++..++..+......+....+...+..+..|+..+|++++.++++.|++++|..+|++|.+.|..|+.           
T Consensus       156 ~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~  235 (697)
T PLN03081        156 PDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASA  235 (697)
T ss_pred             cchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHh
Confidence            455556666666666777777788888888899999999999999999999999999999988877763           


Q ss_pred             ---------------------------------ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHH
Q 040801           73 ---------------------------------CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHE  115 (323)
Q Consensus        73 ---------------------------------y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  115 (323)
                                                       |+++    +|.++|++|+++|+++||+||.+|++.|++++|+++|++
T Consensus       236 ~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~  315 (697)
T PLN03081        236 GLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYE  315 (697)
T ss_pred             cCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHH
Confidence                                             5555    899999999999999999999999999999999999999


Q ss_pred             HHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC
Q 040801          116 MIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK  192 (323)
Q Consensus       116 m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~  192 (323)
                      |.+.|+.||..||++++.+|++.|+   |.++++.|.+.|+.||..+||+||++|+++|   ++++|.++|++|.    +
T Consensus       316 M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G---~~~~A~~vf~~m~----~  388 (697)
T PLN03081        316 MRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWG---RMEDARNVFDRMP----R  388 (697)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCC---CHHHHHHHHHhCC----C
Confidence            9999999999999999999999999   9999999999999999999999999999999   6699999999995    5


Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC-CCCchhhhHHHhh
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF-PWNNYGQWAMSAT  271 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~~~~~~  271 (323)
                      ||.+|||+||.+|++.|+.++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|.+ .|+.|+..+|...
T Consensus       389 ~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~l  468 (697)
T PLN03081        389 KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACM  468 (697)
T ss_pred             CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhH
Confidence            899999999999999999999999999999999999999999999999999999999999999986 4888988899999


Q ss_pred             hccCCCCCcchhhhhhhCCCC
Q 040801          272 VGPQGLVGRHSTAHQISGPCP  292 (323)
Q Consensus       272 ~~~~~~~~~~~~a~~l~~~~~  292 (323)
                      +..+++.|+.++|..++..++
T Consensus       469 i~~l~r~G~~~eA~~~~~~~~  489 (697)
T PLN03081        469 IELLGREGLLDEAYAMIRRAP  489 (697)
T ss_pred             HHHHHhcCCHHHHHHHHHHCC
Confidence            999999999999887766554

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.1e-42  Score=345.31  Aligned_cols=312  Identities=23%  Similarity=0.258  Sum_probs=237.1

Q ss_pred             CCCCCcccccccccCCCCCccccccCCCCCcccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-----------
Q 040801            4 PLPLHHQTRTPALSSDNSPLINLDNINNNNINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-----------   72 (323)
Q Consensus         4 p~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-----------   72 (323)
                      |.+..++..+......+....+...+..+..++..+|+++|.++++.|++++|..+|++|.+.|+.|+.           
T Consensus       220 ~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~  299 (857)
T PLN03077        220 LDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACE  299 (857)
T ss_pred             cccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHH
Confidence            334444455555555555555666666667777777777777777777777777777777777776663           


Q ss_pred             ---------------------------------ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHH
Q 040801           73 ---------------------------------CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHE  115 (323)
Q Consensus        73 ---------------------------------y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  115 (323)
                                                       |+++    .|.++|++|..||.++||++|.+|++.|++++|+++|++
T Consensus       300 ~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~  379 (857)
T PLN03077        300 LLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYAL  379 (857)
T ss_pred             hcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHH
Confidence                                             4444    899999999999999999999999999999999999999


Q ss_pred             HHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC------------------
Q 040801          116 MIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD------------------  174 (323)
Q Consensus       116 m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~------------------  174 (323)
                      |.+.|+.||..||+.+|.+|++.|+   +.++++.|.+.|+.|+..+||+||++|+++|+++                  
T Consensus       380 M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~  459 (857)
T PLN03077        380 MEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWT  459 (857)
T ss_pred             HHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHH
Confidence            9999999999999999999999999   9999999999999999999999999999999653                  


Q ss_pred             ----------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          175 ----------QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       175 ----------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                                +.++|+++|++|.. ++.||.+||+++|.+|++.|+++.+.+++..+.+.|+.+|..++++||++|+|+|
T Consensus       460 ~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G  538 (857)
T PLN03077        460 SIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCG  538 (857)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcC
Confidence                      34555555666653 5789999999999999999999999999999999998888888888888888888


Q ss_pred             CHHHHHHHHHhccCCCCchhhh-HHHhhhccCCCCCcchhhhhhhCCCC------c-----------------hhHHHHH
Q 040801          245 FVSRAWDLFVKMLFPWNNYGQW-AMSATVGPQGLVGRHSTAHQISGPCP------K-----------------KAHKLFF  300 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~~~~~~~~-~~~~~~~~~~~~~~~~~a~~l~~~~~------~-----------------~~~~~~~  300 (323)
                      ++++|.++|++| .+  +...| +++.++.   +.|+.++|..+++.+.      +                 +.+..+|
T Consensus       539 ~~~~A~~~f~~~-~~--d~~s~n~lI~~~~---~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f  612 (857)
T PLN03077        539 RMNYAWNQFNSH-EK--DVVSWNILLTGYV---AHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYF  612 (857)
T ss_pred             CHHHHHHHHHhc-CC--ChhhHHHHHHHHH---HcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHH
Confidence            888888888887 22  44444 4444444   4444444433322111      1                 1245556


Q ss_pred             HHHH-hccCCCCeeeeecccccc
Q 040801          301 FSML-KKVHVPGVLIQVHVPDVL  322 (323)
Q Consensus       301 ~~M~-~~g~~p~~~t~~~li~~l  322 (323)
                      ++|+ +.|+.|+..+|+.+++.|
T Consensus       613 ~~M~~~~gi~P~~~~y~~lv~~l  635 (857)
T PLN03077        613 HSMEEKYSITPNLKHYACVVDLL  635 (857)
T ss_pred             HHHHHHhCCCCchHHHHHHHHHH
Confidence            6666 456666666666666543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.65  E-value=4.1e-14  Score=128.91  Aligned_cols=257  Identities=11%  Similarity=-0.010  Sum_probs=185.6

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC------------ccch----hHHHhcccCC---CCChhhHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP------------CADY----HVRLVFSQIS---NPTIYTCNSIV   97 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~------------y~~~----~a~~lf~~m~---~~~~~~~~~li   97 (323)
                      ...+..+...+...|+++.|..+++.+...+..+..            |.+.    .|.++|+++.   ..+..+++.+.
T Consensus        69 ~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la  148 (389)
T PRK11788         69 VELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLL  148 (389)
T ss_pred             HHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            345677888888899999999999988875432211            2222    7888888876   45678899999


Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..+.+.|++++|.+.++.+.+.+-.++.    ..|..+...+.+.|+   |...++.+.+.. ..+...+..+...|.+.
T Consensus       149 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~  227 (389)
T PRK11788        149 EIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQ  227 (389)
T ss_pred             HHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHC
Confidence            9999999999999999999876533322    134455555666666   888888887754 22456778888999999


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  250 (323)
                      |   ++++|.++|+++...+......+++.+..+|+..|+.++|...++.+.+.  .|+...+..+...|.+.|++++|.
T Consensus       228 g---~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~la~~~~~~g~~~~A~  302 (389)
T PRK11788        228 G---DYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE--YPGADLLLALAQLLEEQEGPEAAQ  302 (389)
T ss_pred             C---CHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHhCCHHHHH
Confidence            9   66999999999987543333567888999999999999999999998876  467777788999999999999999


Q ss_pred             HHHHhccCCCCchhhhHH---HhhhccCCCCCcchhhhhhhCCCCchhHHHHHHHHHhccCCCCee
Q 040801          251 DLFVKMLFPWNNYGQWAM---SATVGPQGLVGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVL  313 (323)
Q Consensus       251 ~~~~~m~~~~~~~~~~~~---~~~~~~~~~~~~~~~a~~l~~~~~~~~~~~~~~~M~~~g~~p~~~  313 (323)
                      .+++++.+.  .|+...+   ..........|+           ..++ ...|++|.++++.|++.
T Consensus       303 ~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~-----------~~~a-~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        303 ALLREQLRR--HPSLRGFHRLLDYHLAEAEEGR-----------AKES-LLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             HHHHHHHHh--CcCHHHHHHHHHHhhhccCCcc-----------chhH-HHHHHHHHHHHHhCCCC
Confidence            999988776  3333322   222221221223           2233 34458899888876554

>PF13041 PPR_2: PPR repeat family

Probab=99.58  E-value=3.5e-15  Score=93.96  Aligned_cols=50  Identities=26%  Similarity=0.578  Sum_probs=48.9

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcc
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD  137 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~  137 (323)
                      ||+++||++|++|++.|++++|+++|++|.++|++||..||+++|++|++
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            79999999999999999999999999999999999999999999999986

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.56  E-value=2.9e-13  Score=117.66  Aligned_cols=219  Identities=13%  Similarity=0.074  Sum_probs=173.8

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC------------ccch---------------------------hHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP------------CADY---------------------------HVR   79 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~------------y~~~---------------------------~a~   79 (323)
                      +-+.|+.. -+.|...++.-+++.|...|..-+.            |...                           ...
T Consensus       118 ~E~nL~km-IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vA  196 (625)
T KOG4422|consen  118 TENNLLKM-ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVA  196 (625)
T ss_pred             chhHHHHH-HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHH
Confidence            44555554 4567788899999999988875555            1111                           344


Q ss_pred             HhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHH
Q 040801           80 LVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFL  159 (323)
Q Consensus        80 ~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~  159 (323)
                      +++.+..+.+..+|.+||.|+|+-...++|.++|++-.....+.+..+||.+|.+-+-.. ..++..+|....+.||..|
T Consensus       197 dL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~-~K~Lv~EMisqkm~Pnl~T  275 (625)
T KOG4422|consen  197 DLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSV-GKKLVAEMISQKMTPNLFT  275 (625)
T ss_pred             HHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc-cHHHHHHHHHhhcCCchHh
Confidence            477777778889999999999999999999999999999999999999999987754332 4789999999999999999


Q ss_pred             HHHHHHHHHhcCCCC-ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHH-HHHHHHHHH----HhCCcc----C
Q 040801          160 HNTLINMYSSCWCLD-QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRT-VKRVHKCVD----ESGFWS----H  229 (323)
Q Consensus       160 ~~~li~~~~~~g~~~-~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~-a~~~~~~m~----~~g~~p----~  229 (323)
                      +|+++++.++.|.+. ....|.+++.||++-|++|...+|--+|..+++.++..+ +..+..++.    -+.++|    |
T Consensus       276 fNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d  355 (625)
T KOG4422|consen  276 FNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTD  355 (625)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCch
Confidence            999999999999553 234568899999999999999999999999999998755 444444443    233444    4


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...|..-++.|.+..+.+-|..+..-+...
T Consensus       356 ~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg  385 (625)
T KOG4422|consen  356 NKFFQSAMSICSSLRDLELAYQVHGLLKTG  385 (625)
T ss_pred             hHHHHHHHHHHHHhhhHHHHHHHHHHHHcC
Confidence            556777888888999999999988776543

>PF13041 PPR_2: PPR repeat family

Probab=99.55  E-value=1.5e-14  Score=91.05  Aligned_cols=50  Identities=28%  Similarity=0.413  Sum_probs=34.1

Q ss_pred             CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc
Q 040801          155 SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR  207 (323)
Q Consensus       155 ~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  207 (323)
                      ||+++||+||++|++.|   ++++|+++|++|.+.|+.||..||+++|++||+
T Consensus         1 P~~~~yn~li~~~~~~~---~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAG---KFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCc---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            56666777777777766   446777777777766777777777777766664

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.52  E-value=1.2e-12  Score=114.01  Aligned_cols=192  Identities=15%  Similarity=0.165  Sum_probs=138.1

Q ss_pred             cccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--ccch-------hHHHhcccCC----CCChhhHHHHHHHH
Q 040801           34 INSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--CADY-------HVRLVFSQIS----NPTIYTCNSIVRGY  100 (323)
Q Consensus        34 ~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--y~~~-------~a~~lf~~m~----~~~~~~~~~li~~~  100 (323)
                      .+..-++.++|.++|+....+.|.+++.+-......-+.  +...       .-.++..+|.    .||..++|+++++.
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfNalL~c~  283 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFNALLSCA  283 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHHHHHHHH
Confidence            345568899999999999999999999988765543333  1111       2345555554    78888888888888


Q ss_pred             HhCCChHH----HHHHHHHHHHCCCCCCcccHHHHHHHhcchhh----HHHHHHHH----HHcCCCC----chHHHHHHH
Q 040801          101 TNKNLHHE----AFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV----EKQLHSQA----IKFGLAS----DSFLHNTLI  164 (323)
Q Consensus       101 ~~~g~~~~----A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~----a~~~~~~m----~~~g~~~----~~~~~~~li  164 (323)
                      .+.|+++.    |++++.+|++-|+.|...+|..+|+.+++.++    +..+..++    -...++|    |...|-+-|
T Consensus       284 akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM  363 (625)
T KOG4422|consen  284 AKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAM  363 (625)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHH
Confidence            88887664    46677888888888888888888888888877    33333333    3333444    334455555


Q ss_pred             HHHHhcCCCC---------------------------------------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHH
Q 040801          165 NMYSSCWCLD---------------------------------------QPDEAIKIFYRMEIENVKPNAVTLVNVLTAR  205 (323)
Q Consensus       165 ~~~~~~g~~~---------------------------------------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  205 (323)
                      +.|.+..+..                                       ..+..++.++.|.-.-+-|+..+..-++++.
T Consensus       364 ~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~  443 (625)
T KOG4422|consen  364 SICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLLRAL  443 (625)
T ss_pred             HHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHHHHH
Confidence            5555444333                                       4566677777777666778999999999999


Q ss_pred             hccCChHHHHHHHHHHHHhC
Q 040801          206 ARARDLRTVKRVHKCVDESG  225 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~g  225 (323)
                      ...|.++-.-++|.+++..|
T Consensus       444 ~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  444 DVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             hhcCcchhHHHHHHHHHHhh
Confidence            99999999999999888777

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.51  E-value=2.1e-12  Score=117.64  Aligned_cols=232  Identities=10%  Similarity=0.025  Sum_probs=173.1

Q ss_pred             HHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC-CCC------hhhHHHHHHHHHhC
Q 040801           45 VSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS-NPT------IYTCNSIVRGYTNK  103 (323)
Q Consensus        45 ~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~-~~~------~~~~~~li~~~~~~  103 (323)
                      ......|+++.|...|+.+.+.+  |+.          |.+.    .|.++++.+. .++      ...+..+...|.+.
T Consensus        43 ~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~  120 (389)
T PRK11788         43 LNFLLNEQPDKAIDLFIEMLKVD--PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKA  120 (389)
T ss_pred             HHHHhcCChHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHC
Confidence            34456789999999999999863  444          2221    7888887765 222      25678889999999


Q ss_pred             CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc----hHHHHHHHHHHHhcCCCCCh
Q 040801          104 NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD----SFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~----~~~~~~li~~~~~~g~~~~~  176 (323)
                      |++++|.++|+++.+. -+++..++..+...+.+.|+   |.+.++.+.+.+-.+.    ...|..+...+.+.|   ++
T Consensus       121 g~~~~A~~~~~~~l~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~---~~  196 (389)
T PRK11788        121 GLLDRAEELFLQLVDE-GDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARG---DL  196 (389)
T ss_pred             CCHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCC---CH
Confidence            9999999999999875 33567889999999999998   8999999887664332    224566777888888   66


Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ++|.+.|+++.... ..+...+..+...+.+.|++++|..+++++.+.+-.....+++.+..+|++.|+.++|...++++
T Consensus       197 ~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        197 DAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999999998754 33466888888999999999999999999987643333567889999999999999999999998


Q ss_pred             cCCCCchhhhHHHhhhccCCCCCcchhhh
Q 040801          257 LFPWNNYGQWAMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       257 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~  285 (323)
                      .+..  |+...+......+.+.|+.++|.
T Consensus       276 ~~~~--p~~~~~~~la~~~~~~g~~~~A~  302 (389)
T PRK11788        276 LEEY--PGADLLLALAQLLEEQEGPEAAQ  302 (389)
T ss_pred             HHhC--CCchHHHHHHHHHHHhCCHHHHH
Confidence            8752  22222223333334445555443

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

Probab=99.39  E-value=6e-11  Score=118.64  Aligned_cols=212  Identities=9%  Similarity=-0.012  Sum_probs=128.3

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGY  100 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~  100 (323)
                      ..+..+...+.+.|+++.|..+++.+.+..  |+.          |...    .|.+.|+++.   +.+...|..+...+
T Consensus       568 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  645 (899)
T TIGR02917       568 EPALALAQYYLGKGQLKKALAILNEAADAA--PDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAY  645 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH
Confidence            344556666677777777777777766532  222          1111    5666665543   33455666666777


Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      .+.|++++|.+.|+++.+.. +.+..++..+...+...|+   |.++++.+.+.+ ..+...+..+...+.+.|   +++
T Consensus       646 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g---~~~  720 (899)
T TIGR02917       646 AVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQK---DYP  720 (899)
T ss_pred             HHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCC---CHH
Confidence            77777777777776665531 2335566666666666666   666666666554 334555666666666666   456


Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +|.+.|+++...+  |+..++..+...+.+.|+.++|...++.+.+.. +.+...+..+...|.+.|+.++|.+.|+++.
T Consensus       721 ~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  797 (899)
T TIGR02917       721 AAIQAYRKALKRA--PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVV  797 (899)
T ss_pred             HHHHHHHHHHhhC--CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            7777776666543  444556666666666677777666666665542 3345566666666666677777776666665


Q ss_pred             CC
Q 040801          258 FP  259 (323)
Q Consensus       258 ~~  259 (323)
                      +.
T Consensus       798 ~~  799 (899)
T TIGR02917       798 KK  799 (899)
T ss_pred             Hh
Confidence            44

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

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

Probab=99.31  E-value=3.9e-10  Score=112.81  Aligned_cols=238  Identities=12%  Similarity=-0.058  Sum_probs=176.4

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVR   98 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~   98 (323)
                      +...+..+...+...|+++.|...++.+.+..  |+.          |.+.    .|.++|+++.   +.+...|..+..
T Consensus       600 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~  677 (899)
T TIGR02917       600 SPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ--PDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQ  677 (899)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            45578888889999999999999999998764  333          2111    7888887654   456788899999


Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCC
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~  175 (323)
                      .+...|++++|.++++.+.+.+ +.+...+..+...+.+.|+   |.+.++.+.+.+  |+..++..+..++.+.|   +
T Consensus       678 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~g---~  751 (899)
T TIGR02917       678 LLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLHRALLASG---N  751 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHCC---C
Confidence            9999999999999999988764 4566777777777877777   888888877765  55567777888888888   5


Q ss_pred             hHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          176 PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      +++|.+.++++.... ..+...+..+...|...|+.++|...++++.+.. +.+...++.+...|.+.|+ ++|...+++
T Consensus       752 ~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~-~~A~~~~~~  828 (899)
T TIGR02917       752 TAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAWLYLELKD-PRALEYAEK  828 (899)
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCc-HHHHHHHHH
Confidence            688888888887654 4567788888888888888888888888887764 4467778888888888888 778888887


Q ss_pred             ccCC-CCchhhh-HHHhhhccCCCCCcchhhhhh
Q 040801          256 MLFP-WNNYGQW-AMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       256 m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~~l  287 (323)
                      ..+. +..+..+ .+...+   ...|+.++|...
T Consensus       829 ~~~~~~~~~~~~~~~~~~~---~~~g~~~~A~~~  859 (899)
T TIGR02917       829 ALKLAPNIPAILDTLGWLL---VEKGEADRALPL  859 (899)
T ss_pred             HHhhCCCCcHHHHHHHHHH---HHcCCHHHHHHH
Confidence            7654 3344444 333333   334556666443

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

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

Probab=99.11  E-value=7.1e-10  Score=104.47  Aligned_cols=208  Identities=15%  Similarity=0.043  Sum_probs=150.8

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      .||.++|..+|.-||..|+.+.|- +|.-|+-+....+...|+.++.+....++++.       .. .|...+|+.|..+
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~En-------pk-ep~aDtyt~Ll~a   92 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAEN-------PK-EPLADTYTNLLKA   92 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccC-------CC-CCchhHHHHHHHH
Confidence            788899999999999999999998 99999888888899999999999998887221       11 7899999999999


Q ss_pred             HHhcCCCCChHHHHHHHHHHHH----cCCC-----------------CChHH----------HHHHHHHHh------ccC
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEI----ENVK-----------------PNAVT----------LVNVLTARA------RAR  209 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~----~g~~-----------------p~~~t----------~~~li~~~~------~~~  209 (323)
                      |...|++..++.+.+.+.....    .|+.                 ||..+          |..++.-+.      ..+
T Consensus        93 yr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~~~  172 (1088)
T KOG4318|consen   93 YRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAWNA  172 (1088)
T ss_pred             HHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccccc
Confidence            9999999888888775555532    2332                 22221          111111110      000


Q ss_pred             -----------ChHHHHHHHHHHHHhCC-ccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCCC
Q 040801          210 -----------DLRTVKRVHKCVDESGF-WSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGL  277 (323)
Q Consensus       210 -----------~~~~a~~~~~~m~~~g~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~  277 (323)
                                 +..-.+++.+..+. +. .|+..+|.+++++-..+|+++.|..++.+|+++|..+..+.+...+...+ 
T Consensus       173 p~~vfLrqnv~~ntpvekLl~~cks-l~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g~~-  250 (1088)
T KOG4318|consen  173 PFQVFLRQNVVDNTPVEKLLNMCKS-LVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLGIN-  250 (1088)
T ss_pred             hHHHHHHHhccCCchHHHHHHHHHH-hhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhcCc-
Confidence                       11112233333322 22 49999999999999999999999999999999987777665555554422 


Q ss_pred             CCcchhhhhhhCCCCchhHHHHHHHHHhccCCCCeeeeeccc
Q 040801          278 VGRHSTAHQISGPCPKKAHKLFFFSMLKKVHVPGVLIQVHVP  319 (323)
Q Consensus       278 ~~~~~~a~~l~~~~~~~~~~~~~~~M~~~g~~p~~~t~~~li  319 (323)
                                    ...+++.+...|.+.|+.|+..||...+
T Consensus       251 --------------~~q~~e~vlrgmqe~gv~p~seT~adyv  278 (1088)
T KOG4318|consen  251 --------------AAQVFEFVLRGMQEKGVQPGSETQADYV  278 (1088)
T ss_pred             --------------cchHHHHHHHHHHHhcCCCCcchhHHHH
Confidence                          2345677778999999999999987544

>PF12854 PPR_1: PPR repeat

Probab=99.08  E-value=1.7e-10  Score=65.69  Aligned_cols=34  Identities=38%  Similarity=0.570  Sum_probs=26.1

Q ss_pred             hCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          224 SGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       224 ~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +|+.||..||++||++||+.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3677778888888888888888888888877774

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

Probab=99.06  E-value=1.9e-09  Score=101.65  Aligned_cols=209  Identities=15%  Similarity=0.029  Sum_probs=148.5

Q ss_pred             HHHHHHHHhcCCCCC--ccch----------hHHHhcccCC----CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCC
Q 040801           58 QIHAQMLRTSLFFDP--CADY----------HVRLVFSQIS----NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL  121 (323)
Q Consensus        58 ~i~~~m~~~~~~~~~--y~~~----------~a~~lf~~m~----~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~  121 (323)
                      ..+..+...|+.|+.  |.+.          .|..+|.-|.    ..+...|+.++.+....|+.+.+.           
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaatif~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAATIFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCccccchhhhhcccccccchhHHHHHhcccccccccCCC-----------
Confidence            356678889999998  3333          4555888887    456788999999999999988877           


Q ss_pred             CCCcccHHHHHHHhcchhh--HHHHHHH-HHH-------cCC-----------------CCchH----------HHHHHH
Q 040801          122 IPDRFMFPSLFKSCADIYV--EKQLHSQ-AIK-------FGL-----------------ASDSF----------LHNTLI  164 (323)
Q Consensus       122 ~p~~~ty~~ll~~~~~~~~--a~~~~~~-m~~-------~g~-----------------~~~~~----------~~~~li  164 (323)
                      .|...||+.|+.+|...||  ..+..+. |+.       .|+                 -||..          .|..++
T Consensus        80 ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqll  159 (1088)
T KOG4318|consen   80 EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLL  159 (1088)
T ss_pred             CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999999  2222222 221       121                 12221          122233


Q ss_pred             HHHHhcCCCC--------------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          165 NMYSSCWCLD--------------QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       165 ~~~~~~g~~~--------------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      ....+.-...              +.....++....+...-.|++.+|..++.+-..+|+++.|..++.+|++.|+..+.
T Consensus       160 kll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~  239 (1088)
T KOG4318|consen  160 KLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRA  239 (1088)
T ss_pred             HHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCccc
Confidence            3332111110              22233333333222111599999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCCCCCc
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGR  280 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~  280 (323)
                      +-|-.|+-+   .|+..-++.+++-|.+.|..|++.|+...+..+.+++.
T Consensus       240 HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  240 HYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             ccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            988888776   89999999999999999999999887777766666444

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

Probab=99.01  E-value=2.2e-09  Score=93.43  Aligned_cols=227  Identities=11%  Similarity=0.044  Sum_probs=103.8

Q ss_pred             hHHHhhcCCCchHHHHHHHHHHHhcCCCCC------ccch--------hHHHhcccCC---CCChhhHHHHHHHHHhCCC
Q 040801           43 CLVSLEKCSTMRELKQIHAQMLRTSLFFDP------CADY--------HVRLVFSQIS---NPTIYTCNSIVRGYTNKNL  105 (323)
Q Consensus        43 li~~~~~~~~~~~a~~i~~~m~~~~~~~~~------y~~~--------~a~~lf~~m~---~~~~~~~~~li~~~~~~g~  105 (323)
                      +...+.+.|+++.|++++..-......|+.      ++..        .|.+.++++.   +.+...+..++.. ...++
T Consensus        14 ~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l-~~~~~   92 (280)
T PF13429_consen   14 LARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQL-LQDGD   92 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccc
Confidence            455566677888888888655444322333      2211        5666666655   3355667777777 79999


Q ss_pred             hHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcC-CCCchHHHHHHHHHHHhcCCCCChHHHHH
Q 040801          106 HHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFG-LASDSFLHNTLINMYSSCWCLDQPDEAIK  181 (323)
Q Consensus       106 ~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~g~~~~~~~a~~  181 (323)
                      +++|.++++...+..  ++...+..++..+.+.++   +.++++.+.+.. ...+...|..+-..+.+.|   +.++|++
T Consensus        93 ~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G---~~~~A~~  167 (280)
T PF13429_consen   93 PEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLG---DPDKALR  167 (280)
T ss_dssp             ---------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCC---HHHHHHH
T ss_pred             ccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcC---CHHHHHH
Confidence            999999998875543  556667777777777777   777777776433 4567888999999999999   7799999


Q ss_pred             HHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-
Q 040801          182 IFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-  259 (323)
Q Consensus       182 ~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-  259 (323)
                      .+++.....  | |....+.++..+...|+.+++..+++...+.. +.|...+..+..+|...|+.++|...|++..+. 
T Consensus       168 ~~~~al~~~--P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~  244 (280)
T PF13429_consen  168 DYRKALELD--PDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN  244 (280)
T ss_dssp             HHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcC--CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc
Confidence            999998754  5 57788899999999999999999999987765 667788899999999999999999999998764 


Q ss_pred             CCchhhh-HHHhhhccCCCC
Q 040801          260 WNNYGQW-AMSATVGPQGLV  278 (323)
Q Consensus       260 ~~~~~~~-~~~~~~~~~~~~  278 (323)
                      +.+|... .+..++...|+.
T Consensus       245 p~d~~~~~~~a~~l~~~g~~  264 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRK  264 (280)
T ss_dssp             TT-HHHHHHHHHHHT-----
T ss_pred             cccccccccccccccccccc
Confidence            3445444 677777666653

>PF12854 PPR_1: PPR repeat

Probab=98.95  E-value=8.7e-10  Score=62.73  Aligned_cols=32  Identities=38%  Similarity=0.497  Sum_probs=17.1

Q ss_pred             CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          152 GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       152 g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                      |+.||.++||+||++||+.|   +.++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G---~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAG---RVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCC---CHHHHHHHHHhC
Confidence            45555555555555555555   335555555554

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.89  E-value=4.3e-07  Score=88.16  Aligned_cols=154  Identities=13%  Similarity=-0.025  Sum_probs=89.0

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~  176 (323)
                      +...|++++|.++++.+.+..-.++...+..+...+.+.|+   |...++...+.. ..+...+..+-..|...|+.   
T Consensus       187 l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~---  262 (656)
T PRK15174        187 FLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRS---  262 (656)
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCc---
Confidence            44445555555555554433222222333333344444444   555555555443 22345556666667776743   


Q ss_pred             HH----HHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          177 DE----AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       177 ~~----a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      ++    |...|++..... ..+...+..+-..+...|++++|...+++..+.. +-+...+..+..+|.+.|++++|...
T Consensus       263 ~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~  340 (656)
T PRK15174        263 REAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDE  340 (656)
T ss_pred             hhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            43    677777666532 2245577777777777778888877777776653 12344566667777778888888888


Q ss_pred             HHhccCC
Q 040801          253 FVKMLFP  259 (323)
Q Consensus       253 ~~~m~~~  259 (323)
                      ++++.+.
T Consensus       341 l~~al~~  347 (656)
T PRK15174        341 FVQLARE  347 (656)
T ss_pred             HHHHHHh
Confidence            8777654

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.88  E-value=5.5e-07  Score=87.43  Aligned_cols=235  Identities=12%  Similarity=-0.032  Sum_probs=162.1

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYT  101 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~  101 (323)
                      ....+..+....|+++.|...++.+.+.  .|+.          |...    .|.+.+++..   +.+...+..+...+.
T Consensus        78 ~l~~l~~~~l~~g~~~~A~~~l~~~l~~--~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~  155 (656)
T PRK15174         78 LLRRWVISPLASSQPDAVLQVVNKLLAV--NVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLV  155 (656)
T ss_pred             HHHHHhhhHhhcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            4555666667789999999999998876  3444          1111    6777777654   446677888889999


Q ss_pred             hCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHH
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      ..|++++|...++.+....  |+.......+..+...|+   |..+++.+.+..-.++...+..+...+...|   ++++
T Consensus       156 ~~g~~~eA~~~~~~~~~~~--P~~~~a~~~~~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g---~~~e  230 (656)
T PRK15174        156 LMDKELQAISLARTQAQEV--PPRGDMIATCLSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVG---KYQE  230 (656)
T ss_pred             HCCChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCC---CHHH
Confidence            9999999999998876543  332222222233555666   8888888766543344455556677888888   6689


Q ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHH----HHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHH
Q 040801          179 AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRT----VKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFV  254 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~----a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  254 (323)
                      |++.|++..... ..+...+..+-..+...|+.++    |...++...+.. +-+...+..+...+.+.|+.++|...++
T Consensus       231 A~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~  308 (656)
T PRK15174        231 AIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQ  308 (656)
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999988754 3356777888888999999885    788888887753 2356678888899999999999999999


Q ss_pred             hccCC-CCchhhh-HHHhhhccCCCCCcchhhh
Q 040801          255 KMLFP-WNNYGQW-AMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       255 ~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~  285 (323)
                      +..+. +..+..+ .+...+.   ..|+.++|.
T Consensus       309 ~al~l~P~~~~a~~~La~~l~---~~G~~~eA~  338 (656)
T PRK15174        309 QSLATHPDLPYVRAMYARALR---QVGQYTAAS  338 (656)
T ss_pred             HHHHhCCCCHHHHHHHHHHHH---HCCCHHHHH
Confidence            88765 2333333 3333333   345555554

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.86  E-value=1.7e-06  Score=72.14  Aligned_cols=196  Identities=9%  Similarity=-0.104  Sum_probs=145.2

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+..+...+...|+++.|...+++..+..                   +.+...+..+-..+...|++++|.+.+++..
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-------------------p~~~~~~~~la~~~~~~~~~~~A~~~~~~al   92 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHD-------------------PDDYLAYLALALYYQQLGELEKAEDSFRRAL   92 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------------------cccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            345666777788889999999998887663                   3456677888888999999999999998887


Q ss_pred             HCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCC-CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          118 VQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLA-SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      +.. +.+...+..+-..+...|+   |.+.++...+.... .....+..+-..+...|   ++++|.+.|++..... ..
T Consensus        93 ~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~-~~  167 (234)
T TIGR02521        93 TLN-PNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAG---DFDKAEKYLTRALQID-PQ  167 (234)
T ss_pred             hhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-cC
Confidence            653 2234556666666666666   78888887764322 23455666777788888   6689999998877643 22


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +...+..+...+...|++++|...+++..+. .+.+...+..+...+.+.|+.++|..+.+.+..
T Consensus       168 ~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       168 RPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            4567778888888899999999999988776 344566677788888888999999888877654

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.

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

Probab=98.75  E-value=1.1e-07  Score=82.61  Aligned_cols=211  Identities=10%  Similarity=-0.080  Sum_probs=107.6

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCC-CCCccch----------hHHHhcccCC--CCChhhHHHHHHHHHhCCChH
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLF-FDPCADY----------HVRLVFSQIS--NPTIYTCNSIVRGYTNKNLHH  107 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~-~~~y~~~----------~a~~lf~~m~--~~~~~~~~~li~~~~~~g~~~  107 (323)
                      ..+.......++++.|...++.+...+-. |..|.+.          .|.+++.+.-  .++...+..++..+.+.++++
T Consensus        48 ~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l~~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  127 (280)
T PF13429_consen   48 RLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQLLQDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYD  127 (280)
T ss_dssp             ----------------------------------------------------------------------H-HHHTT-HH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhHHHHHHHHHhHHH
Confidence            34444555678999999999999877643 2221111          6666665442  566777889999999999999


Q ss_pred             HHHHHHHHHHHCC-CCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHHHHHH
Q 040801          108 EAFLFYHEMIVQG-LIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDEAIKI  182 (323)
Q Consensus       108 ~A~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~  182 (323)
                      ++.++++...+.. ...+...|..+-..+.+.|+   |.+.++...+..  | |....+.++..+...|   +.+++.++
T Consensus       128 ~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--P~~~~~~~~l~~~li~~~---~~~~~~~~  202 (280)
T PF13429_consen  128 EAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELD--PDDPDARNALAWLLIDMG---DYDEAREA  202 (280)
T ss_dssp             HHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHCTTC---HHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCC---ChHHHHHH
Confidence            9999999987543 45677778888888888888   999999888865  6 4778899999999988   66888888


Q ss_pred             HHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          183 FYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       183 ~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ++...... ..|...+..+-.++...|+.++|...++...+.. +.|......+.+++...|+.++|.++.++.-+
T Consensus       203 l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  203 LKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT-----------------
T ss_pred             HHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-cccccccccccccccccccccccccccccccc
Confidence            88877654 5677788899999999999999999999988753 34788888999999999999999999887643

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.72  E-value=2.6e-08  Score=57.08  Aligned_cols=35  Identities=29%  Similarity=0.525  Sum_probs=33.2

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR  125 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~  125 (323)
                      .+||++|++|++.|++++|.++|++|.+.|+.||.
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.

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.66  E-value=4.1e-06  Score=69.75  Aligned_cols=165  Identities=11%  Similarity=0.025  Sum_probs=131.2

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLIN  165 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~  165 (323)
                      ....+..+-..+...|++++|.+.+++..+.. +-+...+..+-..+...|+   |.+.++...+.. ..+...+..+..
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~  107 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGT  107 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHH
Confidence            34567888899999999999999999987652 2335666777777777777   888888887765 234567888888


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCC-CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENV-KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      .|...|   ++++|.+.|++...... ......+..+-..+...|+.++|...+++..+.. +.+...+..+...+.+.|
T Consensus       108 ~~~~~g---~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  183 (234)
T TIGR02521       108 FLCQQG---KYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRG  183 (234)
T ss_pred             HHHHcc---cHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcC
Confidence            999999   66999999999886432 2244567778888999999999999999988763 224667888999999999


Q ss_pred             CHHHHHHHHHhccCC
Q 040801          245 FVSRAWDLFVKMLFP  259 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~  259 (323)
                      +.++|...+++..+.
T Consensus       184 ~~~~A~~~~~~~~~~  198 (234)
T TIGR02521       184 QYKDARAYLERYQQT  198 (234)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998764

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.

>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=98.61  E-value=1.2e-05  Score=77.99  Aligned_cols=232  Identities=9%  Similarity=-0.125  Sum_probs=144.6

Q ss_pred             hcCCCchHHHHHHHHHHHhc-CCCCC----------cc-ch---hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHH
Q 040801           48 EKCSTMRELKQIHAQMLRTS-LFFDP----------CA-DY---HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEA  109 (323)
Q Consensus        48 ~~~~~~~~a~~i~~~m~~~~-~~~~~----------y~-~~---~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A  109 (323)
                      ...+++++|...|+...+.+ ..|..          |. ..   .|.+.|++..   +.+...|..+-..+...|++++|
T Consensus       305 ~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA  384 (615)
T TIGR00990       305 KADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKA  384 (615)
T ss_pred             hhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHH
Confidence            44567888888888887765 23333          11 11   6666666543   33455777777788888888888


Q ss_pred             HHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          110 FLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       110 ~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                      .+.|++..+.. +-+..+|..+-..+...|+   |...++...+.. ..+...+..+-..+.+.|   ++++|+..|++.
T Consensus       385 ~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~~~la~~~~~~g---~~~eA~~~~~~a  459 (615)
T TIGR00990       385 EEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSHIQLGVTQYKEG---SIASSMATFRRC  459 (615)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHHHHHHHHHHHCC---CHHHHHHHHHHH
Confidence            88888876642 2234666666666777777   777777776654 224566777777788888   568888888887


Q ss_pred             HHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh------hHHHHHHHHHhcCCHHHHHHHHHhccCCC
Q 040801          187 EIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE------LKTTLMDAYCKCKFVSRAWDLFVKMLFPW  260 (323)
Q Consensus       187 ~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~------~~~~li~~~~~~g~~~~a~~~~~~m~~~~  260 (323)
                      .... .-+...|+.+-..+...|++++|...++...+..-..+..      .++.....|...|++++|.+++++..+. 
T Consensus       460 l~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l-  537 (615)
T TIGR00990       460 KKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALII-  537 (615)
T ss_pred             HHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhc-
Confidence            6532 2346677778888888888888888888877643111111      1222222344468888888888886543 


Q ss_pred             Cchhhh-HHHhhhccCCCCCcchhhhhh
Q 040801          261 NNYGQW-AMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       261 ~~~~~~-~~~~~~~~~~~~~~~~~a~~l  287 (323)
                       +|... .+...-..+...|+.++|...
T Consensus       538 -~p~~~~a~~~la~~~~~~g~~~eAi~~  564 (615)
T TIGR00990       538 -DPECDIAVATMAQLLLQQGDVDEALKL  564 (615)
T ss_pred             -CCCcHHHHHHHHHHHHHccCHHHHHHH
Confidence             22222 233333333444555555433

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.59  E-value=9e-08  Score=54.50  Aligned_cols=34  Identities=26%  Similarity=0.438  Sum_probs=32.3

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP  123 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p  123 (323)
                      +.+||.+|++|++.|+++.|+++|++|++.|++|
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            3689999999999999999999999999999988

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.48  E-value=4.5e-05  Score=76.81  Aligned_cols=209  Identities=7%  Similarity=-0.109  Sum_probs=145.8

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------cc---c--h-hHHHhcccCC--CCChhhHHHHHHHHHhC
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------CA---D--Y-HVRLVFSQIS--NPTIYTCNSIVRGYTNK  103 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------y~---~--~-~a~~lf~~m~--~~~~~~~~~li~~~~~~  103 (323)
                      .+..+-..+.. +++++|...+.......  |+.       +.   .  . .|...|+++.  .++...+..+-..+.+.
T Consensus       479 a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~  555 (987)
T PRK09782        479 AWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAA  555 (987)
T ss_pred             HHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHC
Confidence            44555555555 78888999888777653  444       11   1  1 6777776554  34445566667778888


Q ss_pred             CChHHHHHHHHHHHHCCCCCCc-ccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHH
Q 040801          104 NLHHEAFLFYHEMIVQGLIPDR-FMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      |++++|.+.|++..+..  |+. ..+..+.......|+   |...++...+..  |+...|..+-..+.+.|   +.++|
T Consensus       556 Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~lG---~~deA  628 (987)
T PRK09782        556 GNGAARDRWLQQAEQRG--LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIA--PSANAYVARATIYRQRH---NVPAA  628 (987)
T ss_pred             CCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHHCC---CHHHH
Confidence            99999999998887653  333 222222233322244   888888777654  66778888888888988   66899


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++.|++..... .-+...++.+-..+...|+.++|...++...+.. +-+...+..+-.+|.+.|++++|...+++..+.
T Consensus       629 ~~~l~~AL~l~-Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~-P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l  706 (987)
T PRK09782        629 VSDLRAALELE-PNNSNYQAALGYALWDSGDIAQSREMLERAHKGL-PDDPALIRQLAYVNQRLDDMAATQHYARLVIDD  706 (987)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            99998887754 2345667777778888999999999988887753 224667788888899999999999999887654

>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=98.48  E-value=4.7e-05  Score=73.77  Aligned_cols=211  Identities=11%  Similarity=-0.114  Sum_probs=155.0

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGY  100 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~  100 (323)
                      ..+..+-..+...|+++.|...++...+.  .|+.          |...    .|.+.|++..   +.+...|..+-..+
T Consensus       332 ~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~  409 (615)
T TIGR00990       332 IALNLRGTFKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLH  409 (615)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            34566666677889999999999998865  3443          1111    6777777553   45678899999999


Q ss_pred             HhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCCh
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~  176 (323)
                      ...|++++|.+.|++..+.  .| +...+..+-..+.+.|+   |...++...+.. ..+...|+.+-..+...|   ++
T Consensus       410 ~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g---~~  483 (615)
T TIGR00990       410 FIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQN---KF  483 (615)
T ss_pred             HHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcc---CH
Confidence            9999999999999998764  34 34556666666666776   888888877643 234678889999999999   67


Q ss_pred             HHHHHHHHHHHHcCCCC-----ChH-HHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHH
Q 040801          177 DEAIKIFYRMEIENVKP-----NAV-TLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p-----~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a  249 (323)
                      ++|++.|++-....-..     +.. .++..+..+-..|++++|..++++..+..  |+ ...+..+...|.+.|++++|
T Consensus       484 ~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~--p~~~~a~~~la~~~~~~g~~~eA  561 (615)
T TIGR00990       484 DEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIID--PECDIAVATMAQLLLQQGDVDEA  561 (615)
T ss_pred             HHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHccCHHHH
Confidence            99999999977643111     111 12222223334699999999999987764  43 45688999999999999999


Q ss_pred             HHHHHhccC
Q 040801          250 WDLFVKMLF  258 (323)
Q Consensus       250 ~~~~~~m~~  258 (323)
                      .+.|++..+
T Consensus       562 i~~~e~A~~  570 (615)
T TIGR00990       562 LKLFERAAE  570 (615)
T ss_pred             HHHHHHHHH
Confidence            999998754

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.47  E-value=3.9e-05  Score=70.21  Aligned_cols=227  Identities=10%  Similarity=-0.045  Sum_probs=149.6

Q ss_pred             hcCCCchHHHHHHHHHHHhcCCCCCc---------cch----hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHH
Q 040801           48 EKCSTMRELKQIHAQMLRTSLFFDPC---------ADY----HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFL  111 (323)
Q Consensus        48 ~~~~~~~~a~~i~~~m~~~~~~~~~y---------~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~  111 (323)
                      .+.|+++.|...+.++.+..-.+..+         -..    .|.+.++++.   +.+......+...|.+.|++++|.+
T Consensus       129 ~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~  208 (398)
T PRK10747        129 QQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLD  208 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHH
Confidence            66788888988888887643222211         111    6667766655   5567778888999999999999999


Q ss_pred             HHHHHHHCCCCCCc-------ccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHH
Q 040801          112 FYHEMIVQGLIPDR-------FMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIK  181 (323)
Q Consensus       112 ~~~~m~~~g~~p~~-------~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~  181 (323)
                      ++..+.+.+..++.       .+|..++....+..+   ..++++.+.+. ...+......+...+...|   +.++|.+
T Consensus       209 ~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g---~~~~A~~  284 (398)
T PRK10747        209 ILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECD---DHDTAQQ  284 (398)
T ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            99999887655322       123333333222222   44444444221 2446777888999999999   6699999


Q ss_pred             HHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCC
Q 040801          182 IFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWN  261 (323)
Q Consensus       182 ~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  261 (323)
                      ++++....  .||...  .++.+.+..++.+++....+...+.. +-|.....++-..+.+.|++++|.+.|+...+...
T Consensus       285 ~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~~-P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P  359 (398)
T PRK10747        285 IILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQH-GDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRP  359 (398)
T ss_pred             HHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            99888763  444422  24455556689999999998887652 23455677888999999999999999999987632


Q ss_pred             chhh-hHHHhhhccCCCCCcchhhhh
Q 040801          262 NYGQ-WAMSATVGPQGLVGRHSTAHQ  286 (323)
Q Consensus       262 ~~~~-~~~~~~~~~~~~~~~~~~a~~  286 (323)
                      +... ..+...+..   .|+.++|..
T Consensus       360 ~~~~~~~La~~~~~---~g~~~~A~~  382 (398)
T PRK10747        360 DAYDYAWLADALDR---LHKPEEAAA  382 (398)
T ss_pred             CHHHHHHHHHHHHH---cCCHHHHHH
Confidence            2222 244444444   445555543

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.46  E-value=6.9e-05  Score=75.49  Aligned_cols=192  Identities=10%  Similarity=-0.024  Sum_probs=136.3

Q ss_pred             hHHHhcccCC--CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHc
Q 040801           77 HVRLVFSQIS--NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF  151 (323)
Q Consensus        77 ~a~~lf~~m~--~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~  151 (323)
                      +|...|.+-.  .|+......+...+...|++++|...|+++...  .|+...+..+...+.+.|+   |...++...+.
T Consensus       494 eAi~a~~~Al~~~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l  571 (987)
T PRK09782        494 VALYAWLQAEQRQPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQR  571 (987)
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            5666554433  455433333344446899999999999997554  4555556566666777777   88888888876


Q ss_pred             CCCCch-HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          152 GLASDS-FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       152 g~~~~~-~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      +  |+. ..+..+...+.+.|   ++++|...+++..+  ..|+...|..+-..+.+.|+.++|...++...+.. +-+.
T Consensus       572 ~--P~~~~l~~~La~~l~~~G---r~~eAl~~~~~AL~--l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~-Pd~~  643 (987)
T PRK09782        572 G--LGDNALYWWLHAQRYIPG---QPELALNDLTRSLN--IAPSANAYVARATIYRQRHNVPAAVSDLRAALELE-PNNS  643 (987)
T ss_pred             C--CccHHHHHHHHHHHHhCC---CHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCH
Confidence            5  433 33333333444557   67999999999876  45788899999999999999999999999998873 2245


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLV  278 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~  278 (323)
                      ..++.+-..+...|+.++|...+++..+. +..+..+ ....++...|+.
T Consensus       644 ~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~  693 (987)
T PRK09782        644 NYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDM  693 (987)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCH
Confidence            66777778999999999999999988764 4444444 555566555543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.43  E-value=3.2e-07  Score=52.42  Aligned_cols=33  Identities=27%  Similarity=0.409  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN  194 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~  194 (323)
                      +||++|++|++.|   ++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~---~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAG---RVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCC---CHHHHHHHHHHHHHcCCCCC
Confidence            4555555555555   33555555555555555554

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.41  E-value=4.8e-05  Score=78.95  Aligned_cols=205  Identities=9%  Similarity=-0.003  Sum_probs=134.9

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHHHhCC
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTNKN  104 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~~g  104 (323)
                      .+...+...|++++|.+.+++..+..  |+.          |.+.    +|.+.|++..   +.+...+-.+-..+...+
T Consensus       466 ~~a~~~~~~g~~~eA~~~~~~Al~~~--P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~  543 (1157)
T PRK11447        466 QQAEALENQGKWAQAAELQRQRLALD--PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSD  543 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCC
Confidence            34455667899999999999988763  443          2111    6666666543   223333433444556677


Q ss_pred             ChHHHHHHHHHHHHCCCCCCccc---------HHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC
Q 040801          105 LHHEAFLFYHEMIVQGLIPDRFM---------FPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~~p~~~t---------y~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      +.++|++.++.+......++...         +..+...+...|+   |.++++   .  ...+...+..+-..|.+.| 
T Consensus       544 ~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~---~--~p~~~~~~~~La~~~~~~g-  617 (1157)
T PRK11447        544 RDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLR---Q--QPPSTRIDLTLADWAQQRG-  617 (1157)
T ss_pred             CHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHH---h--CCCCchHHHHHHHHHHHcC-
Confidence            78888777776543322222111         1122334444555   444444   1  2344556777888888888 


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHH
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                        +.++|++.|++..... ..+...+..+...+...|+.++|...++.+.+.  .| +...+..+..++.+.|+.++|.+
T Consensus       618 --~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~--~p~~~~~~~~la~~~~~~g~~~eA~~  692 (1157)
T PRK11447        618 --DYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQGDLAAARAQLAKLPAT--ANDSLNTQRRVALAWAALGDTAAAQR  692 (1157)
T ss_pred             --CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCChHHHHHHHHHHHhCCCHHHHHH
Confidence              6689999999888754 336778888999999999999999999977654  34 34556667778889999999999


Q ss_pred             HHHhccCC
Q 040801          252 LFVKMLFP  259 (323)
Q Consensus       252 ~~~~m~~~  259 (323)
                      +++++...
T Consensus       693 ~~~~al~~  700 (1157)
T PRK11447        693 TFNRLIPQ  700 (1157)
T ss_pred             HHHHHhhh
Confidence            99988764

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

Probab=98.41  E-value=3.6e-07  Score=50.70  Aligned_cols=31  Identities=32%  Similarity=0.541  Sum_probs=29.3

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCC
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL  121 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~  121 (323)
                      ++||++|++|++.|++++|.++|++|++.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4899999999999999999999999999885

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.37  E-value=6.9e-07  Score=50.74  Aligned_cols=32  Identities=25%  Similarity=0.243  Sum_probs=15.5

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          197 TLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       197 t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                      ||+++|.+|++.|+++.|.++|++|.+.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            44444444444444444444444444444443

>TIGR00540 hemY_coli hemY protein

Probab=98.31  E-value=0.00014  Score=66.90  Aligned_cols=234  Identities=11%  Similarity=-0.026  Sum_probs=149.9

Q ss_pred             HHHhhcCCCchHHHHHHHHHHHhcCCCCC-----ccch--------hHHHhcccCC---CCChhhHHHHHHHHHhCCChH
Q 040801           44 LVSLEKCSTMRELKQIHAQMLRTSLFFDP-----CADY--------HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHH  107 (323)
Q Consensus        44 i~~~~~~~~~~~a~~i~~~m~~~~~~~~~-----y~~~--------~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~  107 (323)
                      ..+....|+++.|...+....+..-.+..     +++.        .|.+.++++.   +.+......+...+...|+++
T Consensus       125 A~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~  204 (409)
T TIGR00540       125 AEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQ  204 (409)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHH
Confidence            34455668999999999988765422221     2221        6777777765   456778889999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCcccHHHHHHHh---cchhh---HHHHHHHHHHcC---CCCchHHHHHHHHHHHhcCCCCChHH
Q 040801          108 EAFLFYHEMIVQGLIPDRFMFPSLFKSC---ADIYV---EKQLHSQAIKFG---LASDSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       108 ~A~~~~~~m~~~g~~p~~~ty~~ll~~~---~~~~~---a~~~~~~m~~~g---~~~~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      +|.+++....+.++.+....-..-..++   ...+.   +.+.+..+.+..   ...+...+-.+...+...|   +.++
T Consensus       205 ~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g---~~~~  281 (409)
T TIGR00540       205 ALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCD---DHDS  281 (409)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCC---ChHH
Confidence            9999999999987643332212222222   11111   223333433332   1137788899999999999   6699


Q ss_pred             HHHHHHHHHHcCCCCChHH---HHHHHHHHhccCChHHHHHHHHHHHHhCCccCh---hhHHHHHHHHHhcCCHHHHHHH
Q 040801          179 AIKIFYRMEIENVKPNAVT---LVNVLTARARARDLRTVKRVHKCVDESGFWSHV---ELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t---~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~---~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      |.+++++.....  ||...   .....-.....++.+.+...++...+.  .|+.   ....++-..+.+.|++++|.+.
T Consensus       282 A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~  357 (409)
T TIGR00540       282 AQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCINRALGQLLMKHGEFIEAADA  357 (409)
T ss_pred             HHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHHHHHHHHHHHHcccHHHHHHH
Confidence            999999988754  44432   122222234457888888888887654  4544   4556788889999999999999


Q ss_pred             HHh--ccCC-CCchhhhHHHhhhccCCCCCcchhhhhh
Q 040801          253 FVK--MLFP-WNNYGQWAMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       253 ~~~--m~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~l  287 (323)
                      |+.  ..+. +...+...+...+...|   +.++|..+
T Consensus       358 le~a~a~~~~p~~~~~~~La~ll~~~g---~~~~A~~~  392 (409)
T TIGR00540       358 FKNVAACKEQLDANDLAMAADAFDQAG---DKAEAAAM  392 (409)
T ss_pred             HHHhHHhhcCCCHHHHHHHHHHHHHcC---CHHHHHHH
Confidence            994  4333 32333335555555544   45555443

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.30  E-value=0.00013  Score=72.04  Aligned_cols=85  Identities=15%  Similarity=0.033  Sum_probs=69.6

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC-----CccChhhHHHHHHHHHhcCCHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG-----FWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g-----~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                      ++.++++.|+.+...|.+.-..+--.+..+|...++.++|+.++..+....     ..++......|.-+|...+++++|
T Consensus       307 r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A  386 (822)
T PRK14574        307 QTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKA  386 (822)
T ss_pred             hHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHH
Confidence            678999999999988866455577789999999999999999999986542     223444467899999999999999


Q ss_pred             HHHHHhccCC
Q 040801          250 WDLFVKMLFP  259 (323)
Q Consensus       250 ~~~~~~m~~~  259 (323)
                      ..+++++.+.
T Consensus       387 ~~~l~~~~~~  396 (822)
T PRK14574        387 YQFAVNYSEQ  396 (822)
T ss_pred             HHHHHHHHhc
Confidence            9999999873

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

Probab=98.30  E-value=4.8e-06  Score=60.06  Aligned_cols=76  Identities=11%  Similarity=0.100  Sum_probs=59.5

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCC-CCCcccHHHHHHHhcchhh-----------HHHHHHHHHHcCCCCchHHHH
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGL-IPDRFMFPSLFKSCADIYV-----------EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~-~p~~~ty~~ll~~~~~~~~-----------a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      ...|..+...+++.....+|..++++|+ .|+..+|+.+|++.++..-           ...++++|...+++|+..+||
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            3456667777999999999999999999 8999999999998886543           666777777777777777777


Q ss_pred             HHHHHHHh
Q 040801          162 TLINMYSS  169 (323)
Q Consensus       162 ~li~~~~~  169 (323)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            77776655

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 [, , ].

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.28  E-value=0.00019  Score=74.52  Aligned_cols=209  Identities=8%  Similarity=-0.035  Sum_probs=154.9

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----ccch----------hHHHhcccCCCC----Ch---------
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----CADY----------HVRLVFSQISNP----TI---------   90 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----y~~~----------~a~~lf~~m~~~----~~---------   90 (323)
                      ..+..+...+.+.|+++.|...++...+.  .|+.    |...          +|.+.++.++..    +.         
T Consensus       496 ~~~~~LA~~~~~~G~~~~A~~~l~~al~~--~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~  573 (1157)
T PRK11447        496 WLTYRLAQDLRQAGQRSQADALMRRLAQQ--KPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQS  573 (1157)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhh
Confidence            34566778889999999999999998864  3433    2211          788888877621    11         


Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      ..+..+...+...|+.++|.++++.     .+.+...+..+-..+.+.|+   |.+.++...+.. ..+...+..+...|
T Consensus       574 ~~~l~~a~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~  647 (1157)
T PRK11447        574 DQVLETANRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVD  647 (1157)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            1123456678899999999999872     34455566667777777777   889999888764 23578899999999


Q ss_pred             HhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc--c---ChhhHHHHHHHHHh
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW--S---HVELKTTLMDAYCK  242 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~--p---~~~~~~~li~~~~~  242 (323)
                      ...|   +.++|.+.++...... ..+..++..+-.++...|+.++|.++++.+.+..-.  |   +...+..+...+.+
T Consensus       648 ~~~g---~~~eA~~~l~~ll~~~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~  723 (1157)
T PRK11447        648 IAQG---DLAAARAQLAKLPATA-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQ  723 (1157)
T ss_pred             HHCC---CHHHHHHHHHHHhccC-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHH
Confidence            9999   6699999999776532 234456667778888999999999999999875322  2   22456666788999


Q ss_pred             cCCHHHHHHHHHhccC
Q 040801          243 CKFVSRAWDLFVKMLF  258 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~  258 (323)
                      .|+.++|...|++...
T Consensus       724 ~G~~~~A~~~y~~Al~  739 (1157)
T PRK11447        724 TGQPQQALETYKDAMV  739 (1157)
T ss_pred             cCCHHHHHHHHHHHHh
Confidence            9999999999998753

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.21  E-value=0.00048  Score=68.49  Aligned_cols=199  Identities=9%  Similarity=-0.039  Sum_probs=141.3

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCC-hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPT-IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-  124 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-  124 (323)
                      +...++++.|.+.|+.+.+.+-.                 .|+ ...+  +-..|...|++++|...|++..+..  |. 
T Consensus       247 Ll~~g~~~eA~~~~~~ll~~~~~-----------------~P~~a~~~--la~~yl~~g~~e~A~~~l~~~l~~~--p~~  305 (765)
T PRK10049        247 LLARDRYKDVISEYQRLKAEGQI-----------------IPPWAQRW--VASAYLKLHQPEKAQSILTELFYHP--ETI  305 (765)
T ss_pred             HHHhhhHHHHHHHHHHhhccCCC-----------------CCHHHHHH--HHHHHHhcCCcHHHHHHHHHHhhcC--CCC
Confidence            34556777777777777665420                 122 2222  4568889999999999999987542  22 


Q ss_pred             ----cccHHHHHHHhcchhh---HHHHHHHHHHcC-----------CCCc---hHHHHHHHHHHHhcCCCCChHHHHHHH
Q 040801          125 ----RFMFPSLFKSCADIYV---EKQLHSQAIKFG-----------LASD---SFLHNTLINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       125 ----~~ty~~ll~~~~~~~~---a~~~~~~m~~~g-----------~~~~---~~~~~~li~~~~~~g~~~~~~~a~~~~  183 (323)
                          ...+..+..++.+.++   |..+++.+.+..           -.|+   ...+..+...+...|   +.++|++++
T Consensus       306 ~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g---~~~eA~~~l  382 (765)
T PRK10049        306 ADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSN---DLPQAEMRA  382 (765)
T ss_pred             CCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcC---CHHHHHHHH
Confidence                2345566667777777   888888877652           1223   234566777888888   669999999


Q ss_pred             HHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CC
Q 040801          184 YRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WN  261 (323)
Q Consensus       184 ~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~  261 (323)
                      +++.... +-+...+..+...+...|+.++|+..+++..+..  |+ ...+..+...+.+.|++++|+.+++++.+. +.
T Consensus       383 ~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~--Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd  459 (765)
T PRK10049        383 RELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEVLE--PRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQ  459 (765)
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC
Confidence            9997653 4467788888999999999999999999988764  65 566777777899999999999999999876 33


Q ss_pred             chhhhHHHhhh
Q 040801          262 NYGQWAMSATV  272 (323)
Q Consensus       262 ~~~~~~~~~~~  272 (323)
                      ++....+-...
T Consensus       460 ~~~~~~~~~~~  470 (765)
T PRK10049        460 DPGVQRLARAR  470 (765)
T ss_pred             CHHHHHHHHHH
Confidence            34333333333

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=98.19  E-value=2.2e-05  Score=63.70  Aligned_cols=118  Identities=16%  Similarity=0.170  Sum_probs=83.2

Q ss_pred             CCChhhHHHHHHHHHhC-----CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHH
Q 040801           87 NPTIYTCNSIVRGYTNK-----NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~-----g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      ..|-.+|..+|+.|.+.     |.++=...-++.|.+-|+.-|..+|+.||..+-+ |.            +.|... +-
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~------------fvp~n~-fQ  109 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GK------------FVPRNF-FQ  109 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CC------------cccccH-HH
Confidence            66777888888888765     5566667778888999999999999999888875 22            223222 22


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC-hHHHHHHHHHHHH
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD-LRTVKRVHKCVDE  223 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~-~~~a~~~~~~m~~  223 (323)
                      ++.--|-+     +-+-|++++++|...|+-||..|+..|++.+++.+. +.+..++.-.|-+
T Consensus       110 ~~F~hyp~-----Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmmYWmpk  167 (228)
T PF06239_consen  110 AEFMHYPR-----QQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRMMYWMPK  167 (228)
T ss_pred             HHhccCcH-----HHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHHHHHHHH
Confidence            22223444     337788899999989999999999999999988775 3445555555544

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

>PRK12370 invasion protein regulator; Provisional

Probab=98.16  E-value=0.00036  Score=66.71  Aligned_cols=173  Identities=11%  Similarity=-0.077  Sum_probs=114.7

Q ss_pred             hHHHhcccCC--CC-ChhhHHHHHHHHH---------hCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---
Q 040801           77 HVRLVFSQIS--NP-TIYTCNSIVRGYT---------NKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---  140 (323)
Q Consensus        77 ~a~~lf~~m~--~~-~~~~~~~li~~~~---------~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---  140 (323)
                      .|.++|++..  .| +...|..+-.++.         ..+++++|.+.+++..+.  .| +...+..+-..+...|+   
T Consensus       279 ~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~l--dP~~~~a~~~lg~~~~~~g~~~~  356 (553)
T PRK12370        279 QALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATEL--DHNNPQALGLLGLINTIHSEYIV  356 (553)
T ss_pred             HHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHccCHHH
Confidence            5666665544  33 3344544433333         234578899888887764  34 33455555445555555   


Q ss_pred             HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh-HHHHHHHHHHhccCChHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA-VTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                      |...++...+..  |+ ...|..+-..|...|   ++++|...+++..+..  |+. ..+..+...+...|+.++|...+
T Consensus       357 A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~G---~~~eAi~~~~~Al~l~--P~~~~~~~~~~~~~~~~g~~eeA~~~~  429 (553)
T PRK12370        357 GSLLFKQANLLS--PISADIKYYYGWNLFMAG---QLEEALQTINECLKLD--PTRAAAGITKLWITYYHTGIDDAIRLG  429 (553)
T ss_pred             HHHHHHHHHHhC--CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHhccCHHHHHHHH
Confidence            888888887765  43 556777788888888   5689999998887744  432 23334455566788899999988


Q ss_pred             HHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          219 KCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       219 ~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +++.+.. .| +...+..+-.+|...|+.++|...++++...
T Consensus       430 ~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~  470 (553)
T PRK12370        430 DELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ  470 (553)
T ss_pred             HHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc
Confidence            8876653 34 3445666777888899999999999887655

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

Probab=98.16  E-value=2.5e-06  Score=47.24  Aligned_cols=20  Identities=5%  Similarity=0.147  Sum_probs=7.0

Q ss_pred             HHHHHhccCChHHHHHHHHH
Q 040801          201 VLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       201 li~~~~~~~~~~~a~~~~~~  220 (323)
                      +|++|++.|++++|.++|++
T Consensus         6 li~~~~~~~~~~~a~~~~~~   25 (31)
T PF01535_consen    6 LISGYCKMGQFEEALEVFDE   25 (31)
T ss_pred             HHHHHHccchHHHHHHHHHH
Confidence            33333333333333333333

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.

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

Probab=98.15  E-value=0.00015  Score=62.14  Aligned_cols=158  Identities=12%  Similarity=0.089  Sum_probs=103.0

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCch----HHHHHHHHHHH
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDS----FLHNTLINMYS  168 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~----~~~~~li~~~~  168 (323)
                      |=+-|.+.|-+|+|.++|..+.+.|. .-....-.|+..|-...+   |.++-..+.+.|-.+..    ..|..|-..+.
T Consensus       113 L~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~  191 (389)
T COG2956         113 LGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQAL  191 (389)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHh
Confidence            44566777888888888887776442 122445666777766666   77777777666644432    22344444444


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHH-HHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVL-TARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      ...   +.+.|..++++-.+.+  |+.+-=++++ +.....|++.+|.+.++.+.+.+..--..+...|..+|...|+.+
T Consensus       192 ~~~---~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~  266 (389)
T COG2956         192 ASS---DVDRARELLKKALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPA  266 (389)
T ss_pred             hhh---hHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHH
Confidence            444   5577788877766543  3333333333 455677888888888888887766556677788888888888888


Q ss_pred             HHHHHHHhccCC
Q 040801          248 RAWDLFVKMLFP  259 (323)
Q Consensus       248 ~a~~~~~~m~~~  259 (323)
                      +....+.++.+.
T Consensus       267 ~~~~fL~~~~~~  278 (389)
T COG2956         267 EGLNFLRRAMET  278 (389)
T ss_pred             HHHHHHHHHHHc
Confidence            888888877665

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.12  E-value=0.00022  Score=66.25  Aligned_cols=234  Identities=13%  Similarity=0.024  Sum_probs=149.6

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhh-HHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYT-CNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~-~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      ..-+...|...|+++.|..++.+..+.=.           +.+. +.-+.+.+ -+.+=..|...+++++|..+|+++..
T Consensus       202 ~~~La~~y~~~g~~e~A~~l~k~Al~~l~-----------k~~G-~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~  269 (508)
T KOG1840|consen  202 LRNLAEMYAVQGRLEKAEPLCKQALRILE-----------KTSG-LKHLVVASMLNILALVYRSLGKYDEAVNLYEEALT  269 (508)
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHHHH-----------HccC-ccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            34478889999999999999998876610           0000 11222222 23455678888999999999998843


Q ss_pred             ---CCCCCCcccH----HHHHHHhcchhh---HHHHHHHHH-----HcCC-CCch-HHHHHHHHHHHhcCCCCChHHHHH
Q 040801          119 ---QGLIPDRFMF----PSLFKSCADIYV---EKQLHSQAI-----KFGL-ASDS-FLHNTLINMYSSCWCLDQPDEAIK  181 (323)
Q Consensus       119 ---~g~~p~~~ty----~~ll~~~~~~~~---a~~~~~~m~-----~~g~-~~~~-~~~~~li~~~~~~g~~~~~~~a~~  181 (323)
                         ...-++....    +.|-.+|.+.|+   |...++...     ..|. .|.+ ..++.+...++..+   .+++|..
T Consensus       270 i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~---~~Eea~~  346 (508)
T KOG1840|consen  270 IREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMN---EYEEAKK  346 (508)
T ss_pred             HHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhc---chhHHHH
Confidence               3344555444    444445778887   333333221     1222 2333 33566667777777   5588888


Q ss_pred             HHHHHHH---cCCCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHhC----Cc--c-ChhhHHHHHHHHHhcCCHH
Q 040801          182 IFYRMEI---ENVKPN----AVTLVNVLTARARARDLRTVKRVHKCVDESG----FW--S-HVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       182 ~~~~m~~---~g~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g----~~--p-~~~~~~~li~~~~~~g~~~  247 (323)
                      +++.-..   .-..++    ..+++.|-..|-..|++++|+.+++...+..    -.  + .-..++.|-..|.+.++.+
T Consensus       347 l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~  426 (508)
T KOG1840|consen  347 LLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYE  426 (508)
T ss_pred             HHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccc
Confidence            8876543   112232    2589999999999999999999999986431    11  1 2445778888899999999


Q ss_pred             HHHHHHHhcc----CCC-Cchhhh-HHHhhhccCCCCCcchhhhhhh
Q 040801          248 RAWDLFVKML----FPW-NNYGQW-AMSATVGPQGLVGRHSTAHQIS  288 (323)
Q Consensus       248 ~a~~~~~~m~----~~~-~~~~~~-~~~~~~~~~~~~~~~~~a~~l~  288 (323)
                      +|.++|.+-.    ..| ..|+.. +|......+...|+.++|..+.
T Consensus       427 ~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~  473 (508)
T KOG1840|consen  427 EAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELE  473 (508)
T ss_pred             hHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHH
Confidence            9999988743    222 233443 7777777777777777776553

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.10  E-value=0.0008  Score=61.62  Aligned_cols=233  Identities=7%  Similarity=-0.073  Sum_probs=140.0

Q ss_pred             hhHHHhhc--CCCchHHHHHHHHHHHhcCCCCC-c--------cch---hHHHhcccCC--CCChhhHH--HHHHHHHhC
Q 040801           42 FCLVSLEK--CSTMRELKQIHAQMLRTSLFFDP-C--------ADY---HVRLVFSQIS--NPTIYTCN--SIVRGYTNK  103 (323)
Q Consensus        42 ~li~~~~~--~~~~~~a~~i~~~m~~~~~~~~~-y--------~~~---~a~~lf~~m~--~~~~~~~~--~li~~~~~~  103 (323)
                      .+..++..  .|+++.|.+......+.+-.|.. |        ...   .|.+.|.++.  .|+...+-  ..-..+...
T Consensus        87 ~~~~gl~a~~eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~  166 (398)
T PRK10747         87 QTEQALLKLAEGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLAR  166 (398)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHC
Confidence            34444333  37888888777765554322333 1        111   6777776665  34433332  224577778


Q ss_pred             CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCch-------HHHHHHHHHHHhcCCC
Q 040801          104 NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDS-------FLHNTLINMYSSCWCL  173 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~-------~~~~~li~~~~~~g~~  173 (323)
                      |++++|.+.+++..+.. +-+...+..+...+.+.|+   +.+++..+.+.+..++.       .+|..++.......  
T Consensus       167 g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~--  243 (398)
T PRK10747        167 NENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQ--  243 (398)
T ss_pred             CCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhc--
Confidence            88888888888887653 2345667777777888887   77778888877654322       12333333333322  


Q ss_pred             CChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          174 DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       174 ~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                       +.+...+++++.-.. .+.+......+...+...|+.++|..++++..+.  .||..  -.++.+.+..|+.+++.+..
T Consensus       244 -~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~al~~~  317 (398)
T PRK10747        244 -GSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTNNPEQLEKVL  317 (398)
T ss_pred             -CHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCCChHHHHHHH
Confidence             334445555444222 3456777778888888889999999888888774  34432  12334445568888888888


Q ss_pred             HhccCC-CCchhhh-HHHhhhccCCCCCcchh
Q 040801          254 VKMLFP-WNNYGQW-AMSATVGPQGLVGRHST  283 (323)
Q Consensus       254 ~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~  283 (323)
                      ++..++ +.++... ++...+...++.++..+
T Consensus       318 e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~  349 (398)
T PRK10747        318 RQQIKQHGDTPLLWSTLGQLLMKHGEWQEASL  349 (398)
T ss_pred             HHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            887765 4455544 55666655555444433

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.05  E-value=0.0014  Score=65.20  Aligned_cols=216  Identities=11%  Similarity=0.050  Sum_probs=120.2

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------ccch----hHHHhcccCC---CCChhhHHHHHHHHHhC
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTNK  103 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~~  103 (323)
                      ...-++....-.|+.+.|.+++.......-.+..        |...    .|.++|++..   +.+...+..+...+...
T Consensus        17 ~~~d~~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~   96 (765)
T PRK10049         17 QIADWLQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADA   96 (765)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC
Confidence            4455666677777777777777776652211111        1111    6666666632   44455566677777777


Q ss_pred             CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCC-----
Q 040801          104 NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLD-----  174 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~-----  174 (323)
                      |++++|...+++..+.  .|+...+..+-..+...|+   |...++...+..  |+ ...+..+...+...|..+     
T Consensus        97 g~~~eA~~~l~~~l~~--~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~~--P~~~~~~~~la~~l~~~~~~e~Al~~  172 (765)
T PRK10049         97 GQYDEALVKAKQLVSG--APDKANLLALAYVYKRAGRHWDELRAMTQALPRA--PQTQQYPTEYVQALRNNRLSAPALGA  172 (765)
T ss_pred             CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCChHHHHHH
Confidence            7777777777777654  3332225555555555555   666666666543  32 233333444444443210     


Q ss_pred             -----------------------------------Ch---HHHHHHHHHHHHc-CCCCChH-HHH----HHHHHHhccCC
Q 040801          175 -----------------------------------QP---DEAIKIFYRMEIE-NVKPNAV-TLV----NVLTARARARD  210 (323)
Q Consensus       175 -----------------------------------~~---~~a~~~~~~m~~~-g~~p~~~-t~~----~li~~~~~~~~  210 (323)
                                                         .+   ++|++.++.+... .-.|+.. .+.    ..+.++...|+
T Consensus       173 l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~  252 (765)
T PRK10049        173 IDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDR  252 (765)
T ss_pred             HHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhh
Confidence                                               01   3455555555532 1223221 111    11344556788


Q ss_pred             hHHHHHHHHHHHHhCCc-cChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          211 LRTVKRVHKCVDESGFW-SHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       211 ~~~a~~~~~~m~~~g~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .++|...|+.+.+.+-. |+- .-..+..+|...|++++|..+|+++.+.
T Consensus       253 ~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~  301 (765)
T PRK10049        253 YKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYH  301 (765)
T ss_pred             HHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhc
Confidence            88888888888776521 321 1122466788888899998888887654

>PRK12370 invasion protein regulator; Provisional

Probab=98.04  E-value=0.00064  Score=65.02  Aligned_cols=171  Identities=10%  Similarity=-0.037  Sum_probs=120.1

Q ss_pred             hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHH
Q 040801           77 HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAI  149 (323)
Q Consensus        77 ~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~  149 (323)
                      .|.+.+++..   +.+...|..+=..+...|++++|...|++..+.  .|+ ...+..+-..+...|+   |...++...
T Consensus       322 ~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al  399 (553)
T PRK12370        322 KAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLL--SPISADIKYYYGWNLFMAGQLEEALQTINECL  399 (553)
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555555433   456677888877888999999999999998875  354 4456666667777777   888888887


Q ss_pred             HcCCCCch-HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc
Q 040801          150 KFGLASDS-FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       150 ~~g~~~~~-~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                      +..  |+. ..+..+...+...|   ++++|.+.+++..... .|+ ...+..+-..+...|+.++|...+.++...  .
T Consensus       400 ~l~--P~~~~~~~~~~~~~~~~g---~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~  471 (553)
T PRK12370        400 KLD--PTRAAAGITKLWITYYHT---GIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--E  471 (553)
T ss_pred             hcC--CCChhhHHHHHHHHHhcc---CHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--c
Confidence            765  442 22333444566677   5699999999987643 343 445666777888999999999999887554  3


Q ss_pred             cC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          228 SH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       228 p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      |+ ....+.+...|++.|  ++|...++++.+.
T Consensus       472 ~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~  502 (553)
T PRK12370        472 ITGLIAVNLLYAEYCQNS--ERALPTIREFLES  502 (553)
T ss_pred             chhHHHHHHHHHHHhccH--HHHHHHHHHHHHH
Confidence            43 334455666778888  4888877777653

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

Probab=98.00  E-value=0.00012  Score=68.11  Aligned_cols=224  Identities=10%  Similarity=-0.031  Sum_probs=144.1

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCC-CC---ccch------------hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHH
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFF-DP---CADY------------HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAF  110 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~-~~---y~~~------------~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~  110 (323)
                      +..-++++.|+++|+...+..-.. +.   |+..            .|.++.+.. +-...+|.++=.+|.-.++++.|+
T Consensus       363 yFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Ai  441 (638)
T KOG1126|consen  363 YFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAI  441 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHH
Confidence            333356777788887776653211 11   4333            333333332 345678999999999999999999


Q ss_pred             HHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHH---HHHHHHhcCCCCChHHHHHHH
Q 040801          111 LFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNT---LINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       111 ~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~---li~~~~~~g~~~~~~~a~~~~  183 (323)
                      +.|++-.+  +.| ..++|+.+=+-+....+   |..-|+.    .+..|...||+   |--.|.|.+   +++.|+-.|
T Consensus       442 k~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~----Al~~~~rhYnAwYGlG~vy~Kqe---k~e~Ae~~f  512 (638)
T KOG1126|consen  442 KCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRK----ALGVDPRHYNAWYGLGTVYLKQE---KLEFAEFHF  512 (638)
T ss_pred             HHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHh----hhcCCchhhHHHHhhhhheeccc---hhhHHHHHH
Confidence            99988765  445 55666665433333333   5554443    34466666665   455678888   668999999


Q ss_pred             HHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCch
Q 040801          184 YRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNY  263 (323)
Q Consensus       184 ~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~  263 (323)
                      +.-.+-+ .-|.+....+-..+-+.|+.++|.+++++.....-+ |+..--.-...+...++.++|.+.++++++-  .|
T Consensus       513 qkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~~~~~~il~~~~~~~eal~~LEeLk~~--vP  588 (638)
T KOG1126|consen  513 QKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCKYHRASILFSLGRYVEALQELEELKEL--VP  588 (638)
T ss_pred             HhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhHHHHHHHHHhhcchHHHHHHHHHHHHh--Cc
Confidence            8776533 236677777778888999999999999998765422 3333334456677889999999999999875  34


Q ss_pred             hhh-HHHhhhccCCCCCcchhh
Q 040801          264 GQW-AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       264 ~~~-~~~~~~~~~~~~~~~~~a  284 (323)
                      ... .+...-..+.+.|+.+.|
T Consensus       589 ~es~v~~llgki~k~~~~~~~A  610 (638)
T KOG1126|consen  589 QESSVFALLGKIYKRLGNTDLA  610 (638)
T ss_pred             chHHHHHHHHHHHHHHccchHH
Confidence            333 222222233344444444

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

Probab=98.00  E-value=0.00014  Score=52.61  Aligned_cols=79  Identities=13%  Similarity=0.078  Sum_probs=59.2

Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCC-CCChHHHHHHHHHHhccC--------ChHHHHHHHHHHHHhCCccChhh
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENV-KPNAVTLVNVLTARARAR--------DLRTVKRVHKCVDESGFWSHVEL  232 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~~--------~~~~a~~~~~~m~~~g~~p~~~~  232 (323)
                      ..|..+...+   ++.....+|+..++.|+ -|++.+|+.++.+.++..        .+-....++..|...+++|+..+
T Consensus        30 ~~I~~~~~~~---d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   30 DNINSCFENE---DYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHhhc---chHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            3444444446   55788888888888888 888888888888887653        24456778888888888888888


Q ss_pred             HHHHHHHHHhc
Q 040801          233 KTTLMDAYCKC  243 (323)
Q Consensus       233 ~~~li~~~~~~  243 (323)
                      |+.++..+.+.
T Consensus       107 Ynivl~~Llkg  117 (120)
T PF08579_consen  107 YNIVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHHHh
Confidence            88888877653

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 [, , ].

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

Probab=97.96  E-value=0.0036  Score=55.16  Aligned_cols=201  Identities=14%  Similarity=0.031  Sum_probs=122.2

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCC---cc-------ch---hHHHhcc---cCCCCChhhHHHHHHHHHhCCChHHHHHH
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDP---CA-------DY---HVRLVFS---QISNPTIYTCNSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~---y~-------~~---~a~~lf~---~m~~~~~~~~~~li~~~~~~g~~~~A~~~  112 (323)
                      .-||.+.+-..+.+..+..-.+..   -.       +.   .|++-.+   +|.+.+...-....+.|.+.|++.+...+
T Consensus       130 qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~  209 (400)
T COG3071         130 QRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAI  209 (400)
T ss_pred             hcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHH
Confidence            335677777777666655222222   01       01   3333333   34477888899999999999999999999


Q ss_pred             HHHHHHCCCCCCc-------ccHHHHHHHhcchhhHHH---HHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHH
Q 040801          113 YHEMIVQGLIPDR-------FMFPSLFKSCADIYVEKQ---LHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKI  182 (323)
Q Consensus       113 ~~~m~~~g~~p~~-------~ty~~ll~~~~~~~~a~~---~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~  182 (323)
                      ...|.+.|+--|.       .+|..++.=....+.++.   .|+..-. ..+-+...-.+++.-+..+|   +.++|.++
T Consensus       210 l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr-~lr~~p~l~~~~a~~li~l~---~~~~A~~~  285 (400)
T COG3071         210 LPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPR-KLRNDPELVVAYAERLIRLG---DHDEAQEI  285 (400)
T ss_pred             HHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccH-HhhcChhHHHHHHHHHHHcC---ChHHHHHH
Confidence            9999999876555       577777777777666333   4444422 23445556677888888888   66899998


Q ss_pred             HHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH-HhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          183 FYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD-ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       183 ~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~-~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .++-..++..|+..+    +-.+.+.++.+.-.+..+.-. +.+-.|  -.+.+|=..|.+.+.+.+|.+.|+...+.
T Consensus       286 i~~~Lk~~~D~~L~~----~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl~~  357 (400)
T COG3071         286 IEDALKRQWDPRLCR----LIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALEAALKL  357 (400)
T ss_pred             HHHHHHhccChhHHH----HHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHHhc
Confidence            888877776655222    123334444444444444332 222222  44444555555555555555555544443

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

Probab=97.96  E-value=0.0012  Score=56.65  Aligned_cols=199  Identities=11%  Similarity=0.057  Sum_probs=136.6

Q ss_pred             hHHHhcccCCCCChhhH---HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHH-------hcchhh---HHH
Q 040801           77 HVRLVFSQISNPTIYTC---NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKS-------CADIYV---EKQ  143 (323)
Q Consensus        77 ~a~~lf~~m~~~~~~~~---~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~-------~~~~~~---a~~  143 (323)
                      .|..+|-+|.+.|..+|   -+|=+-|-+.|..|+|+++-..+.++   ||. |+.-=+.+       |...|-   |++
T Consensus        53 KAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdl-T~~qr~lAl~qL~~Dym~aGl~DRAE~  128 (389)
T COG2956          53 KAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDL-TFEQRLLALQQLGRDYMAAGLLDRAED  128 (389)
T ss_pred             hHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCC-chHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence            45555555544444444   34556788899999999999888765   543 44444333       333443   999


Q ss_pred             HHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh----HHHHHHHHHHhccCChHHHHHHHH
Q 040801          144 LHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA----VTLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       144 ~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      +|..+.+.|. .-...--.|+..|-...   ++++|+++-++....|-.+..    ..|.-+...+....+++.|..++.
T Consensus       129 ~f~~L~de~e-fa~~AlqqLl~IYQ~tr---eW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         129 IFNQLVDEGE-FAEGALQQLLNIYQATR---EWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHHhcchh-hhHHHHHHHHHHHHHhh---HHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            9999887552 22445677899999988   779999999988876544433    356666667777889999999999


Q ss_pred             HHHHhCCccChhhHH-HHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCCCCCcchhhh
Q 040801          220 CVDESGFWSHVELKT-TLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       220 ~m~~~g~~p~~~~~~-~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~  285 (323)
                      +..+..  |+.+=-+ .+=+.+...|++++|.+.++...+...+..+......+..+...|+.++..
T Consensus       205 kAlqa~--~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~  269 (389)
T COG2956         205 KALQAD--KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGL  269 (389)
T ss_pred             HHHhhC--ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHH
Confidence            987763  4433333 344578899999999999999998855555555555555555555555543

>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=97.91  E-value=5.4e-05  Score=61.46  Aligned_cols=114  Identities=11%  Similarity=0.133  Sum_probs=74.1

Q ss_pred             CCCcccHHHHHHHhcchhh--------HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          122 IPDRFMFPSLFKSCADIYV--------EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       122 ~p~~~ty~~ll~~~~~~~~--------a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      .-|..+|..++..+.+...        ....+..|.+.|+.-|..+|+.|++.+=+ |.+    .--.+|+.+-      
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~f----vp~n~fQ~~F------  112 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKF----VPRNFFQAEF------  112 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCc----ccccHHHHHh------
Confidence            3455566666666554421        55556677777777777777777777665 322    1112222221      


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC-HHHHHHHHHhcc
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF-VSRAWDLFVKML  257 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~-~~~a~~~~~~m~  257 (323)
                              .   -...+-+-|..++++|...|+.||..|+..|++.|++.+. +.+..++.--|.
T Consensus       113 --------~---hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rmmYWmp  166 (228)
T PF06239_consen  113 --------M---HYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRMMYWMP  166 (228)
T ss_pred             --------c---cCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence                    1   1334677899999999999999999999999999998886 344444444443

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

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

Probab=97.90  E-value=0.00013  Score=66.30  Aligned_cols=119  Identities=14%  Similarity=0.096  Sum_probs=97.7

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC--CCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ--GLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      ..+......++..+.+.-+++++.+++...+..  ....-..|..++++.|.+.|.   +..++..=...|+-||.+++|
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            445666777888888888899999998888765  333344566799999999887   777777778889999999999


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA  208 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~  208 (323)
                      .||+.+.+.|   ++..|.++..+|...+...+..|+...+.+|.+.
T Consensus       143 ~Lmd~fl~~~---~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  143 LLMDHFLKKG---NYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHhhcc---cHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            9999999999   6699999999999888778888888888887766

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 [].

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.83  E-value=0.0044  Score=61.57  Aligned_cols=194  Identities=11%  Similarity=-0.032  Sum_probs=132.4

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC-
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG-  120 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g-  120 (323)
                      -.+.++.+.++++++.+-++.+...+.                  +.-..+=-.+-++|...+.+++|..+|+...... 
T Consensus       297 Drl~aL~~r~r~~~vi~~y~~l~~~~~------------------~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~  358 (822)
T PRK14574        297 DRLGALLVRHQTADLIKEYEAMEAEGY------------------KMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDG  358 (822)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHhhhcCC------------------CCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccc
Confidence            345566666777777777777777665                  2122234566777888888888888888775432 


Q ss_pred             ----CCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCC-----------CC--ch-HHHHHHHHHHHhcCCCCChHHH
Q 040801          121 ----LIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGL-----------AS--DS-FLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       121 ----~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-----------~~--~~-~~~~~li~~~~~~g~~~~~~~a  179 (323)
                          ..++......|.-++...++   |..+++.+.+.--           .|  |- ..+..++..+...|   +..+|
T Consensus       359 ~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~g---dl~~A  435 (822)
T PRK14574        359 KTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALN---DLPTA  435 (822)
T ss_pred             cccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcC---CHHHH
Confidence                22233335667777777777   7777777766210           11  11 22344566677778   55899


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ++.++++.... +-|......+-..+...|....|+..++.....  .| +..+......++...|++++|..+.++..+
T Consensus       436 e~~le~l~~~a-P~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l--~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~  512 (822)
T PRK14574        436 QKKLEDLSSTA-PANQNLRIALASIYLARDLPRKAEQELKAVESL--APRSLILERAQAETAMALQEWHQMELLTDDVIS  512 (822)
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh--CCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence            99998886654 457778888888888889999999988666554  44 456677788888888999999888877765


Q ss_pred             C
Q 040801          259 P  259 (323)
Q Consensus       259 ~  259 (323)
                      .
T Consensus       513 ~  513 (822)
T PRK14574        513 R  513 (822)
T ss_pred             h
Confidence            4

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.82  E-value=0.0013  Score=61.27  Aligned_cols=202  Identities=14%  Similarity=0.093  Sum_probs=135.4

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH---
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV---  118 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---  118 (323)
                      .+-..+...+++++|..+|+.+..--           .++|.++.+.-..+++.|=..|++.|++++|..++++-.+   
T Consensus       246 ~~a~~y~~~~k~~eAv~ly~~AL~i~-----------e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~  314 (508)
T KOG1840|consen  246 ILALVYRSLGKYDEAVNLYEEALTIR-----------EEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYE  314 (508)
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHH-----------HHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHH
Confidence            35556666677777777777776432           1233343344456677777889999999999988877432   


Q ss_pred             C--C-CCCCcc-cHHHHHHHhcchhh---HHHHHHHHHHc---CCCC----chHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 040801          119 Q--G-LIPDRF-MFPSLFKSCADIYV---EKQLHSQAIKF---GLAS----DSFLHNTLINMYSSCWCLDQPDEAIKIFY  184 (323)
Q Consensus       119 ~--g-~~p~~~-ty~~ll~~~~~~~~---a~~~~~~m~~~---g~~~----~~~~~~~li~~~~~~g~~~~~~~a~~~~~  184 (323)
                      .  | ..|.+. -++.+...++..++   |..+++...+.   -..+    -.-+++.|-..|-+.|   ++++|.++|+
T Consensus       315 ~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~g---k~~ea~~~~k  391 (508)
T KOG1840|consen  315 KLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMG---KYKEAEELYK  391 (508)
T ss_pred             HhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhc---chhHHHHHHH
Confidence            2  1 122222 23333444444444   55555544322   1122    2467899999999999   5699999999


Q ss_pred             HHHHc-----C-CCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHH----hCCc-c-ChhhHHHHHHHHHhcCCHHHHHH
Q 040801          185 RMEIE-----N-VKPN-AVTLVNVLTARARARDLRTVKRVHKCVDE----SGFW-S-HVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       185 ~m~~~-----g-~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~-p-~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                      +....     | ..+. -..++.+-..|.+.+....|.++|.+...    .|.. | ...+|..|...|-+.|++++|.+
T Consensus       392 ~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~  471 (508)
T KOG1840|consen  392 KAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEE  471 (508)
T ss_pred             HHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHH
Confidence            88642     1 1222 45677788899999999999999888753    3322 2 25679999999999999999999


Q ss_pred             HHHhcc
Q 040801          252 LFVKML  257 (323)
Q Consensus       252 ~~~~m~  257 (323)
                      +.+...
T Consensus       472 ~~~~~~  477 (508)
T KOG1840|consen  472 LEEKVL  477 (508)
T ss_pred             HHHHHH
Confidence            988775

>TIGR00540 hemY_coli hemY protein

Probab=97.81  E-value=0.0056  Score=56.32  Aligned_cols=235  Identities=9%  Similarity=-0.116  Sum_probs=141.7

Q ss_pred             hhhHHHhhc--CCCchHHHHHHHHHHHhcCCCCC---------ccch---hHHHhcccCC--CCCh--hhHHHHHHHHHh
Q 040801           41 HFCLVSLEK--CSTMRELKQIHAQMLRTSLFFDP---------CADY---HVRLVFSQIS--NPTI--YTCNSIVRGYTN  102 (323)
Q Consensus        41 ~~li~~~~~--~~~~~~a~~i~~~m~~~~~~~~~---------y~~~---~a~~lf~~m~--~~~~--~~~~~li~~~~~  102 (323)
                      ..+..++..  .|+++.|.+.+....+..-.|..         ....   .|.+.+.+..  .|+.  ..--.....+..
T Consensus        86 ~~~~~glla~~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~  165 (409)
T TIGR00540        86 KQTEEALLKLAEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLA  165 (409)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHH
Confidence            334444433  47899999999876665322222         1111   6777776643  2333  233334777888


Q ss_pred             CCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHH---HhcCCCCCh
Q 040801          103 KNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMY---SSCWCLDQP  176 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~---~~~g~~~~~  176 (323)
                      .|++++|.+.++++.+.. +-+...+..+...+...|+   +.+++..+.+.+..+....-..-..++   ...+   ..
T Consensus       166 ~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~---~~  241 (409)
T TIGR00540       166 QNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEA---MA  241 (409)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH---HH
Confidence            999999999999998864 2244577788888888888   888899998887543332211111111   2222   11


Q ss_pred             HHHHHHHHHHHHcC---CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhH-HHHHH--HHHhcCCHHHHH
Q 040801          177 DEAIKIFYRMEIEN---VKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELK-TTLMD--AYCKCKFVSRAW  250 (323)
Q Consensus       177 ~~a~~~~~~m~~~g---~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~-~~li~--~~~~~g~~~~a~  250 (323)
                      +++.+.+.++....   .+.+...+..+...+...|+.++|..++++..+..  ||.... ..++.  .....++.+++.
T Consensus       242 ~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~--pd~~~~~~~~l~~~~~l~~~~~~~~~  319 (409)
T TIGR00540       242 DEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKL--GDDRAISLPLCLPIPRLKPEDNEKLE  319 (409)
T ss_pred             hcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhC--CCcccchhHHHHHhhhcCCCChHHHH
Confidence            23334454444432   12377888888899999999999999999988864  333310 01223  234457888888


Q ss_pred             HHHHhccCC-CCch--hhh-HHHhhhccCCCCCcc
Q 040801          251 DLFVKMLFP-WNNY--GQW-AMSATVGPQGLVGRH  281 (323)
Q Consensus       251 ~~~~~m~~~-~~~~--~~~-~~~~~~~~~~~~~~~  281 (323)
                      +.+++..+. +.++  ... ++...+...++.++.
T Consensus       320 ~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A  354 (409)
T TIGR00540       320 KLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEA  354 (409)
T ss_pred             HHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHH
Confidence            888877654 4455  332 555555454443333

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.

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

Probab=97.80  E-value=0.00051  Score=62.39  Aligned_cols=129  Identities=7%  Similarity=0.004  Sum_probs=104.1

Q ss_pred             HHHHHHH---CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHc--CCCCchHHHHHHHHHHHhcCCCCChHHHHHHH
Q 040801          112 FYHEMIV---QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF--GLASDSFLHNTLINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       112 ~~~~m~~---~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~--g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~  183 (323)
                      ++.+|.+   ++.+.+......+++.+....+   +..++...+..  ....-..|..++|..|.+.|   ..+++++++
T Consensus        50 ~~~~l~~k~~~~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~---~~~~~l~~L  126 (429)
T PF10037_consen   50 LYSELDKKFERKKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELG---AEDELLELL  126 (429)
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcC---CHHHHHHHH
Confidence            5555533   4566778888899999888888   66666666544  33333455679999999999   669999999


Q ss_pred             HHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc
Q 040801          184 YRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       184 ~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  243 (323)
                      +.-..-|+-||..|||.||..+.+.|++..|.+|..+|...+...+..|+..-+.+|.+.
T Consensus       127 ~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  127 KNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999998877777888888777777776

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 [].

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

Probab=97.77  E-value=0.00073  Score=58.09  Aligned_cols=176  Identities=12%  Similarity=-0.013  Sum_probs=109.9

Q ss_pred             hHHHhcccCC--CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHH-Hhcchhh---HHHHHHHHHH
Q 040801           77 HVRLVFSQIS--NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFK-SCADIYV---EKQLHSQAIK  150 (323)
Q Consensus        77 ~a~~lf~~m~--~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~-~~~~~~~---a~~~~~~m~~  150 (323)
                      +|.+.|+.-.  .|-+.+|-.|-++|.+..+++.|+.+|.+-.+.  .|..+||-.=+- .+-..++   +.++++...+
T Consensus       241 ~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk  318 (478)
T KOG1129|consen  241 RAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEAMEQQEDALQLYKLVLK  318 (478)
T ss_pred             hhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHh
Confidence            6666665433  566677777777777777777777777766543  455555543221 1111111   6666766665


Q ss_pred             cCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-
Q 040801          151 FGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-  229 (323)
Q Consensus       151 ~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-  229 (323)
                      .. ..++....++-.+|.-.+   ++|-|++.++.+.+.|+. +...|+.+=-+|...++++.+..-|.+....--.|+ 
T Consensus       319 ~~-~~nvEaiAcia~~yfY~~---~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~  393 (478)
T KOG1129|consen  319 LH-PINVEAIACIAVGYFYDN---NPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQ  393 (478)
T ss_pred             cC-CccceeeeeeeeccccCC---ChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcch
Confidence            43 223444455555565555   667788888877777754 667777777777777777777777777765443343 


Q ss_pred             -hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          230 -VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       230 -~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                       ..+|-.|=...+..|++.-|.+.|+-....
T Consensus       394 aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~  424 (478)
T KOG1129|consen  394 AADVWYNLGFVAVTIGDFNLAKRCFRLALTS  424 (478)
T ss_pred             hhhhhhccceeEEeccchHHHHHHHHHHhcc
Confidence             234555555666777777777777766654

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

Probab=97.69  E-value=0.00078  Score=62.58  Aligned_cols=231  Identities=17%  Similarity=0.048  Sum_probs=141.1

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC--CCChhhHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS--NPTIYTCNSIVRGY  100 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~--~~~~~~~~~li~~~  100 (323)
                      .-+|.-+-+.+...|++++|...++.+++..  |+-          +.+.    .|...|.+-.  .|+.....+-+..+
T Consensus       116 ae~ysn~aN~~kerg~~~~al~~y~~aiel~--p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnL  193 (966)
T KOG4626|consen  116 AEAYSNLANILKERGQLQDALALYRAAIELK--PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNL  193 (966)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHHHHHhcC--chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHH
Confidence            3456778889999999999999999998763  222          1111    4444444333  34333333333333


Q ss_pred             Hh-CCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCC
Q 040801          101 TN-KNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus       101 ~~-~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~  175 (323)
                      .+ .|++++|...|.+-.+..- --...|+.|=..+-..|+   |.+.|++..+  +.|+ ...|-.|=..|...+   .
T Consensus       194 lka~Grl~ea~~cYlkAi~~qp-~fAiawsnLg~~f~~~Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~---~  267 (966)
T KOG4626|consen  194 LKAEGRLEEAKACYLKAIETQP-CFAIAWSNLGCVFNAQGEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEAR---I  267 (966)
T ss_pred             HHhhcccchhHHHHHHHHhhCC-ceeeeehhcchHHhhcchHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHh---c
Confidence            33 4667777777666544311 112344444444445555   5555555444  3344 234555555666666   4


Q ss_pred             hHHHHHHHHHHHHcCCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          176 PDEAIKIFYRMEIENVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                      +++|+.-+.+-..  .+|+ .+.|..+--.|-..|+++.|...+++..+.  .|+ ...|+.|-.++-..|++.+|+..+
T Consensus       268 ~d~Avs~Y~rAl~--lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~~cY  343 (966)
T KOG4626|consen  268 FDRAVSCYLRALN--LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCY  343 (966)
T ss_pred             chHHHHHHHHHHh--cCCcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHH
Confidence            4677766655443  4454 467777777777888899988888887765  454 567888999999999999999999


Q ss_pred             HhccCC-CCchhhh-HHHhhhccCCCCC
Q 040801          254 VKMLFP-WNNYGQW-AMSATVGPQGLVG  279 (323)
Q Consensus       254 ~~m~~~-~~~~~~~-~~~~~~~~~~~~~  279 (323)
                      ++...- ++.++.. .+..+++..++.+
T Consensus       344 nkaL~l~p~hadam~NLgni~~E~~~~e  371 (966)
T KOG4626|consen  344 NKALRLCPNHADAMNNLGNIYREQGKIE  371 (966)
T ss_pred             HHHHHhCCccHHHHHHHHHHHHHhccch
Confidence            887654 4444444 5555555555433

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

Probab=97.69  E-value=0.018  Score=53.91  Aligned_cols=204  Identities=14%  Similarity=0.094  Sum_probs=124.8

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-----------ccch---hHHHhcccCC--CCC-hhhHHHHHHHHHhCC
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-----------CADY---HVRLVFSQIS--NPT-IYTCNSIVRGYTNKN  104 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-----------y~~~---~a~~lf~~m~--~~~-~~~~~~li~~~~~~g  104 (323)
                      -|=..+...+.++.|...+.....  ..|+.           |...   .|-.-+++-.  +|+ ...||.|-.++-..|
T Consensus       257 NLGnV~ke~~~~d~Avs~Y~rAl~--lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G  334 (966)
T KOG4626|consen  257 NLGNVYKEARIFDRAVSCYLRALN--LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKG  334 (966)
T ss_pred             hHHHHHHHHhcchHHHHHHHHHHh--cCCcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhcc
Confidence            333445555566666666655433  23443           2222   3444443322  333 356777777777777


Q ss_pred             ChHHHHHHHHHHHHCCCCCCc-ccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCChHHH
Q 040801          105 LHHEAFLFYHEMIVQGLIPDR-FMFPSLFKSCADIYV---EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      ++.+|.+.|+.-...  -|+. .+.+.|-..+...|.   |..+|....+.  .|+ ...+|.|-..|-..|   +.++|
T Consensus       335 ~V~ea~~cYnkaL~l--~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqg---nl~~A  407 (966)
T KOG4626|consen  335 SVTEAVDCYNKALRL--CPNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQG---NLDDA  407 (966)
T ss_pred             chHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcc---cHHHH
Confidence            777777777766543  2322 445556566665555   66655555443  333 455677777777777   44777


Q ss_pred             HHHHHHHHHcCCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          180 IKIFYRMEIENVKPNA-VTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +.-+++..+  +.|+- ..|+.+=..|-..|+++.|.+.+.+....  .|. ....+.|-..|-..|++.+|..-+++..
T Consensus       408 i~~Ykealr--I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~--nPt~AeAhsNLasi~kDsGni~~AI~sY~~aL  483 (966)
T KOG4626|consen  408 IMCYKEALR--IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQI--NPTFAEAHSNLASIYKDSGNIPEAIQSYRTAL  483 (966)
T ss_pred             HHHHHHHHh--cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhc--CcHHHHHHhhHHHHhhccCCcHHHHHHHHHHH
Confidence            777777655  66664 56777777777777888887777776664  343 4456677777778888888888887765


Q ss_pred             C
Q 040801          258 F  258 (323)
Q Consensus       258 ~  258 (323)
                      +
T Consensus       484 k  484 (966)
T KOG4626|consen  484 K  484 (966)
T ss_pred             c
Confidence            4

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

Probab=97.68  E-value=0.02  Score=50.65  Aligned_cols=173  Identities=7%  Similarity=-0.048  Sum_probs=130.5

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      +.....|..-..+--..|+.++|-+++.+..+.--.++...+-+.-+.....|+   |..-...+.+.+- .+..+-...
T Consensus       115 e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~p-r~~~vlrLa  193 (400)
T COG3071         115 EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMTP-RHPEVLRLA  193 (400)
T ss_pred             cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCc-CChHHHHHH
Confidence            445566777778888889999999999998775334555555556666777776   6666677766653 346678899


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCC-------hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPN-------AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~-------~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ..+|.+.|   ++.....+..+|...|.--|       ..+|+.+++-....++.+.-...|+....+ .+-++..-.++
T Consensus       194 ~r~y~~~g---~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~  269 (400)
T COG3071         194 LRAYIRLG---AWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK-LRNDPELVVAY  269 (400)
T ss_pred             HHHHHHhc---cHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH-hhcChhHHHHH
Confidence            99999999   66899999999998886443       348888888888888877777777776443 34567777888


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCCCCchh
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFPWNNYG  264 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~~~~~~  264 (323)
                      +.-+.++|+.++|.++..+-.++.-++.
T Consensus       270 a~~li~l~~~~~A~~~i~~~Lk~~~D~~  297 (400)
T COG3071         270 AERLIRLGDHDEAQEIIEDALKRQWDPR  297 (400)
T ss_pred             HHHHHHcCChHHHHHHHHHHHHhccChh
Confidence            8899999999999999988877654555

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

Probab=97.67  E-value=0.0013  Score=61.50  Aligned_cols=172  Identities=13%  Similarity=0.021  Sum_probs=106.9

Q ss_pred             hHHHhcccCC--CCChh-hHHHHHHHHHhCCChHHHHHHHHHHHHCC--CCCCcccHHHHHHHhcchhhHHHHHHHHHHc
Q 040801           77 HVRLVFSQIS--NPTIY-TCNSIVRGYTNKNLHHEAFLFYHEMIVQG--LIPDRFMFPSLFKSCADIYVEKQLHSQAIKF  151 (323)
Q Consensus        77 ~a~~lf~~m~--~~~~~-~~~~li~~~~~~g~~~~A~~~~~~m~~~g--~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~  151 (323)
                      +|...|..++  .+|+. .-.-+=++|...+++++|.++|+..++..  ..-+...|.+.|-.+-+.-.---+-+++.+.
T Consensus       337 ~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~  416 (638)
T KOG1126|consen  337 EALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDT  416 (638)
T ss_pred             HHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhh
Confidence            7888887766  44554 22345568888999999999999987642  3457788888877766554411222333332


Q ss_pred             CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          152 GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       152 g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      . .-...+|-++=++|+-.+   +.+.|++.|++-.+  +.| ...+|+.+=.-+.....+|+|...|+...    ..|+
T Consensus       417 ~-~~sPesWca~GNcfSLQk---dh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al----~~~~  486 (638)
T KOG1126|consen  417 D-PNSPESWCALGNCFSLQK---DHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKAL----GVDP  486 (638)
T ss_pred             C-CCCcHHHHHhcchhhhhh---HHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhhh----cCCc
Confidence            2 234577888888888887   66888888877665  344 44566555455555556666666665533    2345


Q ss_pred             hhHHHHHH---HHHhcCCHHHHHHHHHhccC
Q 040801          231 ELKTTLMD---AYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       231 ~~~~~li~---~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..|+++-.   .|.|.++++.|+-.|++..+
T Consensus       487 rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~  517 (638)
T KOG1126|consen  487 RHYNAWYGLGTVYLKQEKLEFAEFHFQKAVE  517 (638)
T ss_pred             hhhHHHHhhhhheeccchhhHHHHHHHhhhc
Confidence            55554433   46666666666666666554

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

Probab=97.61  E-value=0.0091  Score=60.49  Aligned_cols=204  Identities=10%  Similarity=0.013  Sum_probs=97.7

Q ss_pred             CcccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHH
Q 040801           33 NINSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        33 ~~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~  112 (323)
                      ..++...|-.+++..-..++.+.|++++++.... +.+..           +  +--.-.|.++++--.-.|.-+...++
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~t-IN~RE-----------e--eEKLNiWiA~lNlEn~yG~eesl~kV 1519 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKT-INFRE-----------E--EEKLNIWIAYLNLENAYGTEESLKKV 1519 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhh-CCcch-----------h--HHHHHHHHHHHhHHHhhCcHHHHHHH
Confidence            3345556666777777778888888888877654 21111           0  01112344444444444455555555


Q ss_pred             HHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc
Q 040801          113 YHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE  189 (323)
Q Consensus       113 ~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~  189 (323)
                      |++..+..-  -...|..|..-|.+.+.   |.++++.|.+. +.-...+|-...+.+.+..   +-+.|.+++.+-...
T Consensus      1520 FeRAcqycd--~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~n---e~~aa~~lL~rAL~~ 1593 (1710)
T KOG1070|consen 1520 FERACQYCD--AYTVHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQN---EAEAARELLKRALKS 1593 (1710)
T ss_pred             HHHHHHhcc--hHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhccc---HHHHHHHHHHHHHhh
Confidence            555544311  11334444444444444   55555555432 1133444555555555544   224445555443321


Q ss_pred             CCCCC---hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          190 NVKPN---AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       190 g~~p~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                        -|-   +....-.+..=.+.||.+.+..+|+.....- +--.-.|+..|++=.+.|+.+.+..+|++....
T Consensus      1594 --lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l 1663 (1710)
T KOG1070|consen 1594 --LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIEL 1663 (1710)
T ss_pred             --cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhc
Confidence              121   2222222333335555555555555554431 112445555555555555555555555555444

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

Probab=97.60  E-value=0.02  Score=53.94  Aligned_cols=34  Identities=15%  Similarity=0.087  Sum_probs=20.3

Q ss_pred             cccchhh-hhhHHHhhcCCCchHHHHHHHHHHHhc
Q 040801           34 INSQYQA-HFCLVSLEKCSTMRELKQIHAQMLRTS   67 (323)
Q Consensus        34 ~~~~~~~-~~li~~~~~~~~~~~a~~i~~~m~~~~   67 (323)
                      +.|..++ ......+.+.|+.++|..++..+.+++
T Consensus        34 I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN   68 (517)
T PF12569_consen   34 ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN   68 (517)
T ss_pred             CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            3444433 344455666677777777777777764

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 [], [].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.54  E-value=0.015  Score=48.99  Aligned_cols=164  Identities=13%  Similarity=-0.022  Sum_probs=103.4

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHHhcchhh---HHHHHHHHHHcCCC-Cch-HH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKSCADIYV---EKQLHSQAIKFGLA-SDS-FL  159 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~~-~~  159 (323)
                      ....+-.+...+.+.|++++|...|++....  .|+.    .++..+-.++...|+   |...++.+.+..-. +.. .+
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESR--YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            3445556666777788888888888777553  2332    234445555555566   77777777654311 111 12


Q ss_pred             HHHHHHHHHhc--------CCCCChHHHHHHHHHHHHcCCCCChH-HH-----------------HHHHHHHhccCChHH
Q 040801          160 HNTLINMYSSC--------WCLDQPDEAIKIFYRMEIENVKPNAV-TL-----------------VNVLTARARARDLRT  213 (323)
Q Consensus       160 ~~~li~~~~~~--------g~~~~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~li~~~~~~~~~~~  213 (323)
                      +..+-.++...        |   +.++|.+.|++.....  |+.. .+                 -.+-..+.+.|+..+
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~---~~~~A~~~~~~~~~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~  184 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQT---AAREAFEAFQELIRRY--PNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVA  184 (235)
T ss_pred             HHHHHHHHHHhcccccCCHH---HHHHHHHHHHHHHHHC--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHH
Confidence            33333333322        3   5578888888887643  3321 11                 134456778899999


Q ss_pred             HHHHHHHHHHhC--CccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          214 VKRVHKCVDESG--FWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       214 a~~~~~~m~~~g--~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      |...++...+..  -+.....+..+..+|.+.|+.++|...++.+..+
T Consensus       185 A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       185 AINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            999999987652  1223567888999999999999999999888765

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).

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

Probab=97.52  E-value=0.023  Score=51.32  Aligned_cols=245  Identities=13%  Similarity=0.049  Sum_probs=165.2

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCC-----------ccch-------hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHH
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDP-----------CADY-------HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAF  110 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~-----------y~~~-------~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~  110 (323)
                      ..+|+|.|..+|+++.+..  |-.           |.+.       .|..+++ +.+--..|+.++-.-|.-.++.++|.
T Consensus       274 ~~rDfD~a~s~Feei~knD--PYRl~dmdlySN~LYv~~~~skLs~LA~~v~~-idKyR~ETCCiIaNYYSlr~eHEKAv  350 (559)
T KOG1155|consen  274 NQRDFDQAESVFEEIRKND--PYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSN-IDKYRPETCCIIANYYSLRSEHEKAV  350 (559)
T ss_pred             hhhhHHHHHHHHHHHHhcC--CCcchhHHHHhHHHHHHhhhHHHHHHHHHHHH-hccCCccceeeehhHHHHHHhHHHHH
Confidence            3468999999999999873  222           3333       3444432 23444567777778888889999999


Q ss_pred             HHHHHHHHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          111 LFYHEMIVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       111 ~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                      .+|+.-.+-  -|. ...|+.+=+-|....+   |.+-+....+.. ..|-..|-.|=.+|.-.+   .+.=|+-.|++-
T Consensus       351 ~YFkRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~---Mh~YaLyYfqkA  424 (559)
T KOG1155|consen  351 MYFKRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMK---MHFYALYYFQKA  424 (559)
T ss_pred             HHHHHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhc---chHHHHHHHHHH
Confidence            999887663  233 3456666566666655   666666666644 346778888888888877   446777777776


Q ss_pred             HHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC----C-
Q 040801          187 EIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP----W-  260 (323)
Q Consensus       187 ~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~-  260 (323)
                      ..  ++| |...|.+|=++|.+.++.++|.+.|......| ..+...+..|-+.|-+.++..+|...|++..+.    | 
T Consensus       425 ~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~-dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~  501 (559)
T KOG1155|consen  425 LE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLG-DTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGE  501 (559)
T ss_pred             Hh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcc
Confidence            55  445 67899999999999999999999999998876 224578899999999999999999998887653    2 


Q ss_pred             Cchhhh-HHHhhhccCCCCCcchhhhh----hh-CCCCchhHHHHHHHHHh
Q 040801          261 NNYGQW-AMSATVGPQGLVGRHSTAHQ----IS-GPCPKKAHKLFFFSMLK  305 (323)
Q Consensus       261 ~~~~~~-~~~~~~~~~~~~~~~~~a~~----l~-~~~~~~~~~~~~~~M~~  305 (323)
                      .++... +..-.-.-+.+.++.++|..    .. +....++++.++.+..+
T Consensus       502 ~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~~~~e~eeak~LlReir~  552 (559)
T KOG1155|consen  502 IDDETIKARLFLAEYFKKMKDFDEASYYATLVLKGETECEEAKALLREIRK  552 (559)
T ss_pred             cchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhcCCchHHHHHHHHHHHHH
Confidence            222222 22223333445666666632    22 22223445555555544

>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=97.52  E-value=0.005  Score=53.67  Aligned_cols=95  Identities=16%  Similarity=0.085  Sum_probs=44.5

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhh
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVEL  232 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~  232 (323)
                      .-.....|..|.+.+   +++.|.+.++.|.+-  ..| .+...+..+++.    ...+..|..+|+++.+. +.+++.+
T Consensus       131 lE~~al~Vqi~L~~~---R~dlA~k~l~~~~~~--~eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~  203 (290)
T PF04733_consen  131 LELLALAVQILLKMN---RPDLAEKELKNMQQI--DED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKL  203 (290)
T ss_dssp             HHHHHHHHHHHHHTT----HHHHHHHHHHHHCC--SCC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHH
T ss_pred             ccHHHHHHHHHHHcC---CHHHHHHHHHHHHhc--CCc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHH
Confidence            334444555555555   335555555555432  222 222233333332    12355555556555432 3445555


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          233 KTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       233 ~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .+.+..++...|++++|.+++++..+
T Consensus       204 lng~A~~~l~~~~~~eAe~~L~~al~  229 (290)
T PF04733_consen  204 LNGLAVCHLQLGHYEEAEELLEEALE  229 (290)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            55555555556666666665555443

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.

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.45  E-value=0.036  Score=48.58  Aligned_cols=161  Identities=10%  Similarity=-0.033  Sum_probs=102.1

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNT  162 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~  162 (323)
                      +.+...|+.+=..+...|++++|.+.|+...+  +.|+ ..+|..+-..+...|+   |.+.++...+..  |+......
T Consensus        95 P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~--l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~~~~  170 (296)
T PRK11189         95 PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLE--LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--PNDPYRAL  170 (296)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHH
Confidence            45678899999999999999999999999876  3454 3455555555555666   777777776654  54332222


Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh---C--Ccc-ChhhHHHH
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES---G--FWS-HVELKTTL  236 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~---g--~~p-~~~~~~~l  236 (323)
                      ....+...+   +.++|.+.|.+..... .|+...+ .+  .....|+...+ ..+..+.+.   .  +.| ....|..+
T Consensus       171 ~~~l~~~~~---~~~~A~~~l~~~~~~~-~~~~~~~-~~--~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~L  242 (296)
T PRK11189        171 WLYLAESKL---DPKQAKENLKQRYEKL-DKEQWGW-NI--VEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYL  242 (296)
T ss_pred             HHHHHHccC---CHHHHHHHHHHHHhhC-CccccHH-HH--HHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHH
Confidence            121222334   6789999997755332 3333222 22  22235555554 355555431   1  111 24578888


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -..|.+.|+.++|...|++..+.
T Consensus       243 g~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        243 AKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh
Confidence            88999999999999999998765

>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=97.42  E-value=0.0058  Score=53.25  Aligned_cols=150  Identities=9%  Similarity=0.005  Sum_probs=107.3

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh--cCC
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS--CWC  172 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~--~g~  172 (323)
                      ..+...|++++|++++..-      .+.......+..+.+.++   |.+.++.|.+..  .|.. -..|..++..  .|.
T Consensus       110 ~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~~-l~qLa~awv~l~~g~  180 (290)
T PF04733_consen  110 TILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQQID--EDSI-LTQLAEAWVNLATGG  180 (290)
T ss_dssp             HHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCHH-HHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHH-HHHHHHHHHHHHhCc
Confidence            3566679999999888642      455677777888888888   999999998754  4443 3344444443  232


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCH-HHHHH
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFV-SRAWD  251 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~-~~a~~  251 (323)
                       +.+++|..+|+++.+. ..++..+.|.+..++...|++++|+.++.+..+.+ +-+..+...+|-...-.|+. +.+.+
T Consensus       181 -e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~  257 (290)
T PF04733_consen  181 -EKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAER  257 (290)
T ss_dssp             -TCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHH
T ss_pred             -hhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHH
Confidence             2679999999998654 56889999999999999999999999999976543 22455666677777777777 78889


Q ss_pred             HHHhccCC
Q 040801          252 LFVKMLFP  259 (323)
Q Consensus       252 ~~~~m~~~  259 (323)
                      .+.+++..
T Consensus       258 ~l~qL~~~  265 (290)
T PF04733_consen  258 YLSQLKQS  265 (290)
T ss_dssp             HHHHCHHH
T ss_pred             HHHHHHHh
Confidence            99998864

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.

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.42  E-value=0.0046  Score=47.92  Aligned_cols=117  Identities=8%  Similarity=-0.122  Sum_probs=91.0

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      -+.+++...+..  |+.  +..+-..+...|   ++++|.+.|+...... ..+...|..+-..+...|++++|...|+.
T Consensus        12 ~~~~~~~al~~~--p~~--~~~~g~~~~~~g---~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~   83 (144)
T PRK15359         12 PEDILKQLLSVD--PET--VYASGYASWQEG---DYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGH   83 (144)
T ss_pred             HHHHHHHHHHcC--HHH--HHHHHHHHHHcC---CHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            455555555543  553  445666778888   6699999999988754 34778889999999999999999999999


Q ss_pred             HHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh
Q 040801          221 VDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW  266 (323)
Q Consensus       221 m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~  266 (323)
                      ..+.. +.+...+..+-.++.+.|+.++|...|+...+. +.++..|
T Consensus        84 Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~  129 (144)
T PRK15359         84 ALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWS  129 (144)
T ss_pred             HHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHH
Confidence            99764 346788888999999999999999999998764 3444444

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

Probab=97.31  E-value=0.038  Score=45.51  Aligned_cols=183  Identities=12%  Similarity=-0.002  Sum_probs=139.1

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      .-|=-+|...|+...|..-+++-.+.  .| +..++..+-..|-+.|+   |.+-|+...+.. .-+..+.|..=-.+|.
T Consensus        39 lqLal~YL~~gd~~~A~~nlekAL~~--DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC~  115 (250)
T COG3063          39 LQLALGYLQQGDYAQAKKNLEKALEH--DPSYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLCA  115 (250)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHHh
Confidence            33445899999999999999998775  34 44677888888888888   888888877654 2245566777777889


Q ss_pred             cCCCCChHHHHHHHHHHHHcC-CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIEN-VKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSR  248 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~  248 (323)
                      .|   .+++|...|++-...- +.--..||..+--+-.+.|+.+.|+..+++..+..-. ...+.-.+.+...+.|+.-.
T Consensus       116 qg---~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y~~  191 (250)
T COG3063         116 QG---RPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDYAP  191 (250)
T ss_pred             CC---ChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccchH
Confidence            99   6699999998887642 3334568888888888999999999999999886421 35567788889999999999


Q ss_pred             HHHHHHhccCCCCchhhhHHHhhhccCCCCCcchhh
Q 040801          249 AWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       249 a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a  284 (323)
                      |...++....++. +...++...++.-...|+...+
T Consensus       192 Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a  226 (250)
T COG3063         192 ARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAA  226 (250)
T ss_pred             HHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHH
Confidence            9999999998864 5555666666666666665443

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

Probab=97.30  E-value=0.014  Score=52.67  Aligned_cols=131  Identities=11%  Similarity=-0.041  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      |...|+...+.+ .-....|+-+=+-|..-.   +...|.+-++.-.+-+ +-|-..|=.|=++|.-.+...-|...|.+
T Consensus       349 Av~YFkRALkLN-p~~~~aWTLmGHEyvEmK---Nt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqk  423 (559)
T KOG1155|consen  349 AVMYFKRALKLN-PKYLSAWTLMGHEYVEMK---NTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQK  423 (559)
T ss_pred             HHHHHHHHHhcC-cchhHHHHHhhHHHHHhc---ccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHH
Confidence            555555555544 122455666666666655   4466666666655432 33556666677777777777777777777


Q ss_pred             HHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCc--hhhhHHHhhhccCCC
Q 040801          221 VDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNN--YGQWAMSATVGPQGL  277 (323)
Q Consensus       221 m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~--~~~~~~~~~~~~~~~  277 (323)
                      ..+.. +-|...|.+|=+.|.+.+++++|.+.|.....-+..  ...|.....+..+++
T Consensus       424 A~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d  481 (559)
T KOG1155|consen  424 ALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKD  481 (559)
T ss_pred             HHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHh
Confidence            66642 347999999999999999999999999988765422  222344444444443

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

Probab=97.27  E-value=0.04  Score=56.12  Aligned_cols=187  Identities=12%  Similarity=0.064  Sum_probs=140.9

Q ss_pred             CCC-hhhHHHHHHHHHhCCChHHHHHHHHHHHHC-CCCCC---cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchH
Q 040801           87 NPT-IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ-GLIPD---RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSF  158 (323)
Q Consensus        87 ~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-g~~p~---~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~  158 (323)
                      .|| ...|-..|......++.++|.+++++-... ++.-.   ...|.++++.-.-.|.   ..++|+..-+..  ---.
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~ 1531 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYT 1531 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHH
Confidence            444 467999999999999999999999997653 11111   1345555554444443   788888877653  3356


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC---hhhHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH---VELKTT  235 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~  235 (323)
                      +|..|...|.+.+   .+++|.++++.|..+ +.-....|...+..+.+..+-+.|..++.+..+.  -|.   .....-
T Consensus      1532 V~~~L~~iy~k~e---k~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~Isk 1605 (1710)
T KOG1070|consen 1532 VHLKLLGIYEKSE---KNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISK 1605 (1710)
T ss_pred             HHHHHHHHHHHhh---cchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHH
Confidence            7999999999999   669999999999864 2356789999999999999999999999998765  333   445566


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcc
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRH  281 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~  281 (323)
                      .+..=.++|+.+++..+|+..... +-..+.| .|+.+-..++....+
T Consensus      1606 fAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~v 1653 (1710)
T KOG1070|consen 1606 FAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYV 1653 (1710)
T ss_pred             HHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHH
Confidence            677778999999999999988764 5567889 788887777754333

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

Probab=97.27  E-value=0.042  Score=50.63  Aligned_cols=148  Identities=10%  Similarity=0.092  Sum_probs=112.4

Q ss_pred             hHHHHHHHHHHHHCC-CCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHHHH
Q 040801          106 HHEAFLFYHEMIVQG-LIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDEAI  180 (323)
Q Consensus       106 ~~~A~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~a~  180 (323)
                      .+...+.+++....- +.| ..+|..+|+..-+...   |..+|....+.+..+ ++++++++|.-||..    +.+-|.
T Consensus       347 ~~~~~~~~~~ll~~~~~~~-tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~csk----D~~~Af  421 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDL-TLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSK----DKETAF  421 (656)
T ss_pred             hhhhHHHHHHHHhhhccCC-ceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcC----ChhHHH
Confidence            556666777765543 444 4567777776666544   999999999998877 899999999999986    557899


Q ss_pred             HHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC--hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          181 KIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH--VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       181 ~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ++|+-=... ..-+..--...+.-+...++-..+..+|++..+.++.||  ...|..+|+-=...|++..+.++-+++..
T Consensus       422 rIFeLGLkk-f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  422 RIFELGLKK-FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHHHHHh-cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            999654332 233334445677888889999999999999998877765  57899999999999999999998887654


Q ss_pred             C
Q 040801          259 P  259 (323)
Q Consensus       259 ~  259 (323)
                      .
T Consensus       501 a  501 (656)
T KOG1914|consen  501 A  501 (656)
T ss_pred             h
Confidence            3

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

Probab=97.24  E-value=0.049  Score=49.19  Aligned_cols=161  Identities=9%  Similarity=0.017  Sum_probs=99.3

Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHH
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      -..|++++|++.|-.+..- +.-+....-.+-..|-...+ +..+--.|....+.| |..+.+.|-+.|-+.|   +-..
T Consensus       535 e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~slip~dp~ilskl~dlydqeg---dksq  610 (840)
T KOG2003|consen  535 EALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLADLYDQEG---DKSQ  610 (840)
T ss_pred             HHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHHHHhhccc---chhh
Confidence            3445566666665544321 11122223333333333333 222222233444444 6777888888888888   4467


Q ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHH-hcCCHHHHHHHHHhcc
Q 040801          179 AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYC-KCKFVSRAWDLFVKML  257 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~-~~g~~~~a~~~~~~m~  257 (323)
                      |++..-+--+ =+.-|..|...|-.-|....-.+++...|++..-  +.|+..-|..+|..|. +.|++.+|.+++++..
T Consensus       611 afq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~h  687 (840)
T KOG2003|consen  611 AFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIH  687 (840)
T ss_pred             hhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            7766544322 2445777888888888888888888888887543  5799999999888655 5899999999999998


Q ss_pred             CC-CCchhhhHH
Q 040801          258 FP-WNNYGQWAM  268 (323)
Q Consensus       258 ~~-~~~~~~~~~  268 (323)
                      ++ +-+.....+
T Consensus       688 rkfpedldclkf  699 (840)
T KOG2003|consen  688 RKFPEDLDCLKF  699 (840)
T ss_pred             HhCccchHHHHH
Confidence            76 334444433

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

Probab=97.24  E-value=0.16  Score=46.44  Aligned_cols=216  Identities=11%  Similarity=-0.003  Sum_probs=138.5

Q ss_pred             hhHHHhhcCC-CchHHHHHHHHHH---HhcCCCCCccch---------hHHHhcccCC------CCChhhHHHHHHHHHh
Q 040801           42 FCLVSLEKCS-TMRELKQIHAQML---RTSLFFDPCADY---------HVRLVFSQIS------NPTIYTCNSIVRGYTN  102 (323)
Q Consensus        42 ~li~~~~~~~-~~~~a~~i~~~m~---~~~~~~~~y~~~---------~a~~lf~~m~------~~~~~~~~~li~~~~~  102 (323)
                      .=+..+.+.| ++....+.|+.+.   ..+-.|+.|-..         ++++.-++++      .++...+...+.+...
T Consensus       207 ~Gi~~L~raGydp~gM~~ff~rl~~~~~~~~~~p~yl~THPlp~~RIa~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~  286 (484)
T COG4783         207 IGITTLVRAGYDPQGMPEFFERLADQLRYGGQPPEYLLTHPLPEERIADLRNRAEQSPPYNKLDSPDFQLARARIRAKYE  286 (484)
T ss_pred             HHHHHHHHcCCCchhHHHHHHHHHHHHhcCCCCChHHhcCCCchhHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhc
Confidence            3355566666 5667778888877   344444443333         5666666776      5566667777776665


Q ss_pred             CCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh--HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHH
Q 040801          103 KNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV--EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAI  180 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~--a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~  180 (323)
                      ...-..+-.++.+-.+.+  -...-|..-+..+-...-  |+..+..+.+.- .-|.+.+....+.+.+.+   +.++|.
T Consensus       287 ~~~~~~~~~~~~~~~~~~--~~aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~i~~~~n---k~~~A~  360 (484)
T COG4783         287 ALPNQQAADLLAKRSKRG--GLAAQYGRALQTYLAGQYDEALKLLQPLIAAQ-PDNPYYLELAGDILLEAN---KAKEAI  360 (484)
T ss_pred             cccccchHHHHHHHhCcc--chHHHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcC---ChHHHH
Confidence            555444444443332211  122334444444322211  888888876643 335566667778888888   558899


Q ss_pred             HHHHHHHHcCCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          181 KIFYRMEIENVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       181 ~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +.++.+...  .|+ ....-++-+++.+.|+..+|.++++...... +-|+..|..|-.+|...|+..++.....++...
T Consensus       361 e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~~  437 (484)
T COG4783         361 ERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEGYAL  437 (484)
T ss_pred             HHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHHHHh
Confidence            989888764  455 4555567788888999998888888876542 457888999999999999988888888777654


Q ss_pred             CCchhhh
Q 040801          260 WNNYGQW  266 (323)
Q Consensus       260 ~~~~~~~  266 (323)
                      -.....|
T Consensus       438 ~G~~~~A  444 (484)
T COG4783         438 AGRLEQA  444 (484)
T ss_pred             CCCHHHH
Confidence            3234444

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

Probab=97.24  E-value=0.023  Score=50.93  Aligned_cols=153  Identities=11%  Similarity=-0.048  Sum_probs=102.5

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCcc-cHHHHHHHhcch----hh---HHHHHHHHHHcCCCCch-HHHHHHHHHHH
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDRF-MFPSLFKSCADI----YV---EKQLHSQAIKFGLASDS-FLHNTLINMYS  168 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~-ty~~ll~~~~~~----~~---a~~~~~~m~~~g~~~~~-~~~~~li~~~~  168 (323)
                      ..+...|++++|.+++++..+.  .|+.. .+.. ...+...    +.   +.+.+..  .....|+. .....+-..+.
T Consensus        51 ~~~~~~g~~~~A~~~~~~~l~~--~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~  125 (355)
T cd05804          51 LSAWIAGDLPKALALLEQLLDD--YPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLE  125 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHH
Confidence            3556789999999999998765  34332 3331 1112122    22   3333333  22233433 34445566778


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC-ccCh--hhHHHHHHHHHhcCC
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF-WSHV--ELKTTLMDAYCKCKF  245 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~--~~~~~li~~~~~~g~  245 (323)
                      ..|   ++++|.+.+++..... +.+...+..+-..+...|++++|...++...+..- .|+.  ..|..+...+...|+
T Consensus       126 ~~G---~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~  201 (355)
T cd05804         126 EAG---QYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGD  201 (355)
T ss_pred             HcC---CHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCC
Confidence            888   6699999999998754 33466777888889999999999999998876421 2232  345678889999999


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      .++|..++++....
T Consensus       202 ~~~A~~~~~~~~~~  215 (355)
T cd05804         202 YEAALAIYDTHIAP  215 (355)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999997543

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.

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

Probab=97.20  E-value=0.017  Score=52.35  Aligned_cols=108  Identities=14%  Similarity=0.012  Sum_probs=86.4

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      |..+++.+.+..  |+..  ..|...+...+   +-.+|++++++..... +-|......-.+.|.+.++.+.|..+.++
T Consensus       188 ai~lle~L~~~~--pev~--~~LA~v~l~~~---~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~  259 (395)
T PF09295_consen  188 AIELLEKLRERD--PEVA--VLLARVYLLMN---EEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSKKKYELALEIAKK  259 (395)
T ss_pred             HHHHHHHHHhcC--CcHH--HHHHHHHHhcC---cHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            888999988776  6543  34777777666   5589999998888643 33566666666778899999999999999


Q ss_pred             HHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          221 VDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       221 m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +.+.  .|+ ..+|..|..+|.+.|++++|...++.+..
T Consensus       260 av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  260 AVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             HHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            9886  454 56999999999999999999999998863

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

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

Probab=97.18  E-value=0.014  Score=50.54  Aligned_cols=207  Identities=14%  Similarity=-0.012  Sum_probs=148.6

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCC-------ccch----hHHHhcccCC--CCChhhH-HHHHHHHHhCCChHHHHHH
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDP-------CADY----HVRLVFSQIS--NPTIYTC-NSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~-------y~~~----~a~~lf~~m~--~~~~~~~-~~li~~~~~~g~~~~A~~~  112 (323)
                      +-+-|-+.+|.+-++.-.++--.|++       |.+.    .|+.+|.+-.  -|-.++| .-+-+.+-..++.++|.++
T Consensus       233 ylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~l  312 (478)
T KOG1129|consen  233 YLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQL  312 (478)
T ss_pred             HHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHH
Confidence            33446678888888877777667777       6666    8999998765  4444444 4456677778999999999


Q ss_pred             HHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc
Q 040801          113 YHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE  189 (323)
Q Consensus       113 ~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~  189 (323)
                      |++..+. ..-+++...++-.+|.-.++   |...+..+.+.|+. +...|+.+--+|.-.+   ++|-++--|..-...
T Consensus       313 Yk~vlk~-~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaq---Q~D~~L~sf~RAlst  387 (478)
T KOG1129|consen  313 YKLVLKL-HPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQ---QIDLVLPSFQRALST  387 (478)
T ss_pred             HHHHHhc-CCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhc---chhhhHHHHHHHHhh
Confidence            9987654 23355555555555554444   99999999999964 4555666666666666   557787777766553


Q ss_pred             CCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          190 NVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       190 g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      --.|+  ...|-.|=...+..||+..|.+.|......+-. ....+|.|--.-.+.|++++|..+++.....
T Consensus       388 at~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  388 ATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             ccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            32233  345666777778899999999999998876422 3567888888888999999999999987764

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

Probab=97.18  E-value=0.0044  Score=52.41  Aligned_cols=95  Identities=15%  Similarity=0.126  Sum_probs=71.2

Q ss_pred             hHHHhcccCC--CCChhhHHHHHHHHHhC-----CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---------
Q 040801           77 HVRLVFSQIS--NPTIYTCNSIVRGYTNK-----NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---------  140 (323)
Q Consensus        77 ~a~~lf~~m~--~~~~~~~~~li~~~~~~-----g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---------  140 (323)
                      ..++.|...+  ++|-.+|-+.+..|...     +.++=...-++.|++.|+.-|..+|+.||+.+-+-.-         
T Consensus        52 ~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~  131 (406)
T KOG3941|consen   52 HVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKV  131 (406)
T ss_pred             chhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHH
Confidence            5667777776  78888888888888654     4566666677889999999999999999888765332         


Q ss_pred             ----------HHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801          141 ----------EKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus       141 ----------a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                                +.+++++|+..|+.||.-+-..||+++++.+
T Consensus       132 F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~  172 (406)
T KOG3941|consen  132 FLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWN  172 (406)
T ss_pred             HhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccc
Confidence                      6667777777777777777777777776665

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

Probab=97.14  E-value=0.059  Score=52.47  Aligned_cols=166  Identities=10%  Similarity=0.056  Sum_probs=108.9

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC----------------------cccHHH----HHHHhcchhh-
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD----------------------RFMFPS----LFKSCADIYV-  140 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~----------------------~~ty~~----ll~~~~~~~~-  140 (323)
                      -+...+|++...|.+...++.|......+......+|                      ...|..    +.-++.+... 
T Consensus       314 ~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~  393 (895)
T KOG2076|consen  314 ASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLKER  393 (895)
T ss_pred             ccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhccccc
Confidence            3445677777888888888888887777766222222                      122211    1111222222 


Q ss_pred             --HHHHHHHHHHcC--CCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHH
Q 040801          141 --EKQLHSQAIKFG--LASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKR  216 (323)
Q Consensus       141 --a~~~~~~m~~~g--~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~  216 (323)
                        .+-+...+.+..  ..-+.-.|.-+.++|...|   .+.+|+++|......-.--+...|-.+-++|-..|..+.|.+
T Consensus       394 e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~---~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e  470 (895)
T KOG2076|consen  394 ELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIG---KYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIE  470 (895)
T ss_pred             chHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcc---cHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHH
Confidence              555555555655  3345667888888888888   558888888888775444467788888888888888888888


Q ss_pred             HHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          217 VHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       217 ~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .++.....  .|+ .-.--.|-..|-+.|+.++|.++++.|..
T Consensus       471 ~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~  511 (895)
T KOG2076|consen  471 FYEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQIIN  511 (895)
T ss_pred             HHHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccC
Confidence            88888765  233 33334556677788888888888888753

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

Probab=97.12  E-value=0.009  Score=41.13  Aligned_cols=94  Identities=19%  Similarity=0.049  Sum_probs=74.5

Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHH
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDA  239 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  239 (323)
                      +..+...+...|   ++++|.++|++..... ..+...+..+...+...+++++|...++...+.. ..+...+..+...
T Consensus         3 ~~~~a~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~   77 (100)
T cd00189           3 LLNLGNLYYKLG---DYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLA   77 (100)
T ss_pred             HHHHHHHHHHHh---cHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHH
Confidence            455667777888   6699999999987653 2344677788888889999999999999987754 3344678888899


Q ss_pred             HHhcCCHHHHHHHHHhccC
Q 040801          240 YCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       240 ~~~~g~~~~a~~~~~~m~~  258 (323)
                      +...|+.++|...+++..+
T Consensus        78 ~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          78 YYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHHHhHHHHHHHHHHHHc
Confidence            9999999999999988754

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

Probab=97.10  E-value=0.016  Score=44.00  Aligned_cols=98  Identities=8%  Similarity=-0.106  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ......+...+...|   ++++|.+.|+.....+ ..+...+..+-..+...|++++|..+++...+.+ +.+...+..+
T Consensus        17 ~~~~~~~a~~~~~~~---~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l   91 (135)
T TIGR02552        17 LEQIYALAYNLYQQG---RYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHA   91 (135)
T ss_pred             HHHHHHHHHHHHHcc---cHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHH
Confidence            344666777788888   6699999999887755 3467788888888889999999999999887764 3456777778


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -..|...|+.++|...|+...+.
T Consensus        92 a~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        92 AECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            88999999999999999988765

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

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

Probab=97.07  E-value=0.0054  Score=53.29  Aligned_cols=111  Identities=13%  Similarity=0.118  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHcC-CCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHH
Q 040801          141 EKQLHSQAIKFG-LASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       141 a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      +..+|...++.+ +..++++..++|.-++..    +.+.|.++|+..... +.-+...|..-+.-+.+.++.+.|..+|+
T Consensus        20 aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~----d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l~~~~d~~~aR~lfe   94 (280)
T PF05843_consen   20 ARKVFKRARKDKRCTYHVYVAYALMEYYCNK----DPKRARKIFERGLKK-FPSDPDFWLEYLDFLIKLNDINNARALFE   94 (280)
T ss_dssp             HHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-----HHHHHHHHHHHHHH-HTT-HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHhCC----CHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence            444444444332 233444444444333221    223355555444432 23344444444455555555555555555


Q ss_pred             HHHHhCCcc---ChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          220 CVDESGFWS---HVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       220 ~m~~~g~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +.... +.+   ....|...++-=.+.|+++.+..+.+++.
T Consensus        95 r~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~  134 (280)
T PF05843_consen   95 RAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAE  134 (280)
T ss_dssp             HHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHH
T ss_pred             HHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            54432 111   12345555555555555555555554443

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.

>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=97.03  E-value=0.023  Score=51.47  Aligned_cols=120  Identities=14%  Similarity=0.099  Sum_probs=91.8

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      -..|++.+...++++.|.++|+++.+..  |+  ....+.+.+...++   |.+++.+..+.. .-+......-...|.+
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHh
Confidence            3456667777799999999999999875  54  44456666655555   777777776432 3356666666777888


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNA-VTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      .+   +.+.|+++.++...  ..|+. .+|..|..+|...|+++.|...++-+-
T Consensus       247 k~---~~~lAL~iAk~av~--lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  247 KK---KYELALEIAKKAVE--LSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             cC---CHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            88   66999999999987  45665 599999999999999999999888764

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

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

Probab=97.02  E-value=0.033  Score=43.12  Aligned_cols=108  Identities=13%  Similarity=0.024  Sum_probs=73.4

Q ss_pred             HHHHHHHHHHcCCCCch----HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh--HHHHHHHHHHhccCChHHH
Q 040801          141 EKQLHSQAIKFGLASDS----FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA--VTLVNVLTARARARDLRTV  214 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~~~~~~a  214 (323)
                      +...++.+.+..  |+.    ...-.+-..+...|   ++++|...|+........|+.  ...-.+...+...|++++|
T Consensus        30 ~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~~~g---~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~A  104 (145)
T PF09976_consen   30 AEAAAEQLAKDY--PSSPYAALAALQLAKAAYEQG---DYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEA  104 (145)
T ss_pred             HHHHHHHHHHHC--CCChHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            555666666543  222    22333456777778   668999999998886633332  2444466778888999999


Q ss_pred             HHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          215 KRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       215 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      ...++......+  ....+...=+.|.+.|+.++|...|++
T Consensus       105 l~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  105 LATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            999877544333  344566777789999999999998875

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

Probab=96.97  E-value=0.13  Score=42.18  Aligned_cols=146  Identities=15%  Similarity=0.022  Sum_probs=102.5

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      -+-.|...|+++.+..-.+.+..    |. ..|+       ..++   +...++...+.. ..|...|..|-..|...| 
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~~----~~-~~~~-------~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g-   87 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLAD----PL-HQFA-------SQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRN-   87 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHhC----cc-cccc-------CchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCC-
Confidence            34578899998886433322211    11 1111       1222   333344444433 356788999999999999 


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHH-hccCC--hHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHH
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTAR-ARARD--LRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~-~~~~~--~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                        ++++|...|++..... .-+...+..+-.++ ...|+  .++|..++++..+.+- -+...+..+-..+.+.|++++|
T Consensus        88 --~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP-~~~~al~~LA~~~~~~g~~~~A  163 (198)
T PRK10370         88 --DYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALDA-NEVTALMLLASDAFMQADYAQA  163 (198)
T ss_pred             --CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC-CChhHHHHHHHHHHHcCCHHHH
Confidence              6699999999887754 23667777777764 67677  5999999999988752 2567888888899999999999


Q ss_pred             HHHHHhccCC
Q 040801          250 WDLFVKMLFP  259 (323)
Q Consensus       250 ~~~~~~m~~~  259 (323)
                      ...|+++.+.
T Consensus       164 i~~~~~aL~l  173 (198)
T PRK10370        164 IELWQKVLDL  173 (198)
T ss_pred             HHHHHHHHhh
Confidence            9999999775

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

Probab=96.96  E-value=0.043  Score=49.51  Aligned_cols=187  Identities=12%  Similarity=0.095  Sum_probs=130.5

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCC-----------ccch-hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHH
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDP-----------CADY-HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFY  113 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~-----------y~~~-~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~  113 (323)
                      ..|++++|...+.+......+-..           .++. +|++.|-.+.   .-+..+.-.+-..|-...++.+|.+++
T Consensus       502 ~ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             ecCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            457888888888877655432211           1222 7777776665   556666666777888888999999887


Q ss_pred             HHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Q 040801          114 HEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       114 ~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~  188 (323)
                      -+  ...+.| |....+.|-..|-+.|+   |.+.+-+  ....-| +..+..=|-.-|....   -+++++..|+.-.-
T Consensus       582 ~q--~~slip~dp~ilskl~dlydqegdksqafq~~yd--syryfp~nie~iewl~ayyidtq---f~ekai~y~ekaal  654 (840)
T KOG2003|consen  582 MQ--ANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYD--SYRYFPCNIETIEWLAAYYIDTQ---FSEKAINYFEKAAL  654 (840)
T ss_pred             HH--hcccCCCCHHHHHHHHHHhhcccchhhhhhhhhh--cccccCcchHHHHHHHHHHHhhH---HHHHHHHHHHHHHh
Confidence            44  444445 56777888888888888   4444333  333334 4444444555566655   55899999987543


Q ss_pred             cCCCCChHHHHHHHHHHh-ccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC
Q 040801          189 ENVKPNAVTLVNVLTARA-RARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF  245 (323)
Q Consensus       189 ~g~~p~~~t~~~li~~~~-~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  245 (323)
                        +.|+.+-|..+|..|. +.|++.+|..+++...++ ++-|.....-|++.+...|.
T Consensus       655 --iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  655 --IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             --cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccc
Confidence              7899999999998887 579999999999998765 56677777888887777663

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=96.92  E-value=0.2  Score=42.07  Aligned_cols=162  Identities=10%  Similarity=-0.062  Sum_probs=109.2

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCC-ChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNP-TIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      .+..+...+...|+++.|...+++.....-  +               .+ ....+..+-..+.+.|++++|.+.|++..
T Consensus        35 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p--~---------------~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l   97 (235)
T TIGR03302        35 ELYEEAKEALDSGDYTEAIKYFEALESRYP--F---------------SPYAEQAQLDLAYAYYKSGDYAEAIAAADRFI   97 (235)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--C---------------chhHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            455566677788889999998888876531  0               11 12456777788899999999999999997


Q ss_pred             HCCCCCCcc----cHHHHHHHhcch--------hh---HHHHHHHHHHcCCCCchH-HH-----------------HHHH
Q 040801          118 VQGLIPDRF----MFPSLFKSCADI--------YV---EKQLHSQAIKFGLASDSF-LH-----------------NTLI  164 (323)
Q Consensus       118 ~~g~~p~~~----ty~~ll~~~~~~--------~~---a~~~~~~m~~~g~~~~~~-~~-----------------~~li  164 (323)
                      +.  .|+..    ++..+-.++.+.        |+   |.+.++.+.+..  |+.. .+                 -.+-
T Consensus        98 ~~--~p~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~~a  173 (235)
T TIGR03302        98 RL--HPNHPDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRY--PNSEYAPDAKKRMDYLRNRLAGKELYVA  173 (235)
T ss_pred             HH--CcCCCchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHC--CCChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            64  23322    222222222221        33   777777776653  3321 11                 1344


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcC--CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIEN--VKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ..|.+.|   ++++|...+++.....  -......+..+..++...|+.++|...++.+...
T Consensus       174 ~~~~~~g---~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       174 RFYLKRG---AYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHcC---ChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            5677888   6699999999988753  1224578889999999999999999998887654

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).

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

Probab=96.88  E-value=0.24  Score=45.87  Aligned_cols=109  Identities=16%  Similarity=0.142  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHHHHHh-ccCCCCchhhh-HHHhhh
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWDLFVK-MLFPWNNYGQW-AMSATV  272 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~-m~~~~~~~~~~-~~~~~~  272 (323)
                      .+|...++.--+..-+..|..+|.++.+.+..+ ++.+++++|.-||. ++.+-|.++|+- |+.-|+.|..- .|+..+
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            456677777778888999999999998887777 88899999998876 567888999985 44446666555 777777


Q ss_pred             ccCCCCCcchhh-hhhhCC-CCchhHHHHHHHHHh
Q 040801          273 GPQGLVGRHSTA-HQISGP-CPKKAHKLFFFSMLK  305 (323)
Q Consensus       273 ~~~~~~~~~~~a-~~l~~~-~~~~~~~~~~~~M~~  305 (323)
                      ...++-.++... +.++.. .+-....++++.|++
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            777765554322 333322 222233455566654

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

Probab=96.88  E-value=0.0037  Score=43.42  Aligned_cols=78  Identities=14%  Similarity=0.091  Sum_probs=57.9

Q ss_pred             ChHHHHHHHHHHHHcCC-CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENV-KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      ++++|+.+|+++....- .++...+-.+-.++.+.|++++|..+++. .+  ..++ ....-.+-.+|.+.|++++|.++
T Consensus         4 ~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~--~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    4 NYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LK--LDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             -HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HT--HHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             cHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hC--CCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            67899999999988653 23455566688999999999999999988 32  2332 23344557789999999999999


Q ss_pred             HHh
Q 040801          253 FVK  255 (323)
Q Consensus       253 ~~~  255 (323)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            876

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

Probab=96.83  E-value=0.042  Score=46.27  Aligned_cols=152  Identities=9%  Similarity=-0.013  Sum_probs=87.5

Q ss_pred             HHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCCchHHHHHHHHHHHhc--CCC
Q 040801           97 VRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLASDSFLHNTLINMYSSC--WCL  173 (323)
Q Consensus        97 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~~~~~~~~li~~~~~~--g~~  173 (323)
                      ...|+..|++++|++....    |-..+....+.-|..-...-+ |++.++.|.+..   +-.|.+.|-.++.+.  |..
T Consensus       115 a~i~~~~~~~deAl~~~~~----~~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~id---ed~tLtQLA~awv~la~gge  187 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHL----GENLEAAALNVQILLKMHRFDLAEKELKKMQQID---EDATLTQLAQAWVKLATGGE  187 (299)
T ss_pred             hHHhhcCCChHHHHHHHhc----cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHHhccch
Confidence            3467778888888877655    222233333333332222233 777777776643   445555555555442  111


Q ss_pred             CChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhH-HHHHHHHHhcCCHHHHHHH
Q 040801          174 DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELK-TTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       174 ~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~-~~li~~~~~~g~~~~a~~~  252 (323)
                       ...+|+-+|++|-+ ...|+..+.+-...++...|++++|+.++++...+.-+ ++.+. |.++.+.-...+.+-..+.
T Consensus       188 -k~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~Nliv~a~~~Gkd~~~~~r~  264 (299)
T KOG3081|consen  188 -KIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLANLIVLALHLGKDAEVTERN  264 (299)
T ss_pred             -hhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCCChHHHHHH
Confidence             45788888888754 25678888888888888888888888888888765433 23333 3333333333344444555


Q ss_pred             HHhccC
Q 040801          253 FVKMLF  258 (323)
Q Consensus       253 ~~~m~~  258 (323)
                      +..++.
T Consensus       265 l~QLk~  270 (299)
T KOG3081|consen  265 LSQLKL  270 (299)
T ss_pred             HHHHHh
Confidence            555544

>PRK11189 lipoprotein NlpI; Provisional

Probab=96.77  E-value=0.33  Score=42.52  Aligned_cols=125  Identities=10%  Similarity=-0.136  Sum_probs=91.8

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTLINM  166 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~li~~  166 (323)
                      ..|..+=..|.+.|+.++|...|++..+.. +-+...|+.+-..+...|+   |...++...+..  | +...|..+-..
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~  141 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAYLNRGIA  141 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH
Confidence            456666678889999999999999987752 2345778888888888888   888888877654  5 35677788888


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      +...|   ++++|.+.|+.-...  .|+..........+...++.++|...++....
T Consensus       142 l~~~g---~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~  193 (296)
T PRK11189        142 LYYGG---RYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYE  193 (296)
T ss_pred             HHHCC---CHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            88888   669999999998764  35443222222234466789999999977654

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

Probab=96.76  E-value=0.023  Score=49.36  Aligned_cols=143  Identities=12%  Similarity=0.098  Sum_probs=108.7

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCC-CCCCcccHHHHHHHhc-chhh-HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPDRFMFPSLFKSCA-DIYV-EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~~~ty~~ll~~~~-~~~~-a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      .+|-.+|+..-+.+..+.|..+|++-++.+ +..+.....++|..++ +..+ |.++|+...+. +..+...|...++.+
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHH
Confidence            468899999999999999999999998653 5566777777786664 4444 99999998765 456778899999999


Q ss_pred             HhcCCCCChHHHHHHHHHHHHcCCCCCh---HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIENVKPNA---VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAY  240 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~g~~p~~---~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  240 (323)
                      .+.|   +.+.|..+|++.... +.++.   ..|...|+-=.+.|+++.+..+.+++.+.  .|+......+++-|
T Consensus        81 ~~~~---d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   81 IKLN---DINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHTT----HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHhC---cHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            9998   669999999998754 33322   59999999889999999999999999875  45555555555544

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.73  E-value=0.06  Score=39.50  Aligned_cols=98  Identities=7%  Similarity=-0.154  Sum_probs=75.6

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC--CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc--cChhhHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV--KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW--SHVELKT  234 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~--~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~--p~~~~~~  234 (323)
                      ++-.+...+.+.|   ++++|.+.|++.....-  ......+..+...+.+.|+++.|...++.+.+..-.  .....+.
T Consensus         4 ~~~~~~~~~~~~~---~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~   80 (119)
T TIGR02795         4 AYYDAALLVLKAG---DYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALL   80 (119)
T ss_pred             HHHHHHHHHHHcC---CHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHH
Confidence            4566677788888   67999999999986431  112346667888999999999999999999875311  1245677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+..+|.+.|+.++|...++++.+.
T Consensus        81 ~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        81 KLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHHH
Confidence            7888899999999999999998876

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.

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

Probab=96.62  E-value=0.01  Score=50.28  Aligned_cols=82  Identities=21%  Similarity=0.188  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC-------------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD-------------QPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR  207 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~-------------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~  207 (323)
                      ....+..|.+.|++.|..+|+.||+.+=|..-..             +-+-+++++++|...|+.||..+--.|++++++
T Consensus        91 Iy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr  170 (406)
T KOG3941|consen   91 IYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGR  170 (406)
T ss_pred             HHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcc
Confidence            4455678899999999999999999887654333             445678889999989999999998899999888


Q ss_pred             cCCh-HHHHHHHHHHH
Q 040801          208 ARDL-RTVKRVHKCVD  222 (323)
Q Consensus       208 ~~~~-~~a~~~~~~m~  222 (323)
                      .+-. .+..++.-.|-
T Consensus       171 ~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  171 WNFPTKKVKRMLYWMP  186 (406)
T ss_pred             ccccHHHHHHHHHhhh
Confidence            7643 33444444443

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

Probab=96.61  E-value=0.21  Score=41.89  Aligned_cols=155  Identities=12%  Similarity=-0.068  Sum_probs=105.5

Q ss_pred             HHHHHHhcchhhHHHHHHHHHHcCCC--CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHh
Q 040801          129 PSLFKSCADIYVEKQLHSQAIKFGLA--SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARA  206 (323)
Q Consensus       129 ~~ll~~~~~~~~a~~~~~~m~~~g~~--~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  206 (323)
                      ..+-+.+.-.|++..-...+.+..+.  -|...-+.+.....+.|   ++.+|+..|++..... .+|..+|+-+=-+|-
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g---~~~~A~~~~rkA~~l~-p~d~~~~~~lgaald  145 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNG---NFGEAVSVLRKAARLA-PTDWEAWNLLGAALD  145 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhc---chHHHHHHHHHHhccC-CCChhhhhHHHHHHH
Confidence            33444445555533333334343333  34456666888889999   6689999998876543 678899999999999


Q ss_pred             ccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCCCCCcchhhhh
Q 040801          207 RARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQ  286 (323)
Q Consensus       207 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  286 (323)
                      +.|+++.|..-+.+..+... -+...+|.|--.|.-.|+.++|..++......+. .+.-.-.......+..|+..+|..
T Consensus       146 q~Gr~~~Ar~ay~qAl~L~~-~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~  223 (257)
T COG5010         146 QLGRFDEARRAYRQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAED  223 (257)
T ss_pred             HccChhHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHh
Confidence            99999999999998877532 2456677777778888999999999998876532 122223333334555677777877


Q ss_pred             hhC
Q 040801          287 ISG  289 (323)
Q Consensus       287 l~~  289 (323)
                      +..
T Consensus       224 i~~  226 (257)
T COG5010         224 IAV  226 (257)
T ss_pred             hcc
Confidence            654

>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=96.61  E-value=0.21  Score=47.21  Aligned_cols=96  Identities=9%  Similarity=-0.013  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      ++.-|-..|-..|   +.++|++++++-.+.  .|+ +..|.+--+.+-+.|++.+|...++...+... -|...-+--+
T Consensus       196 ~~~~lAqhyd~~g---~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DRyiNsK~a  269 (517)
T PF12569_consen  196 TLYFLAQHYDYLG---DYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDLKEAAEAMDEARELDL-ADRYINSKCA  269 (517)
T ss_pred             HHHHHHHHHHHhC---CHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhHHHHHHHH
Confidence            3355566677777   668888888877764  455 56777777888888888888888888877652 3666777777


Q ss_pred             HHHHhcCCHHHHHHHHHhccCCC
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFPW  260 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~~  260 (323)
                      ..+.|+|++++|.+++....+.+
T Consensus       270 Ky~LRa~~~e~A~~~~~~Ftr~~  292 (517)
T PF12569_consen  270 KYLLRAGRIEEAEKTASLFTRED  292 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhcCCC
Confidence            88888888888888888887664

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 [], [].

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

Probab=96.59  E-value=0.42  Score=46.87  Aligned_cols=239  Identities=8%  Similarity=-0.032  Sum_probs=139.3

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC----CCChh----hH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS----NPTIY----TC   93 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~----~~~~~----~~   93 (323)
                      +..-|-.+-....+.|.++.|.-+|...++..  |+.          |.+.    .|.+-|.++-    +.|..    .-
T Consensus       206 d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~--p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i  283 (895)
T KOG2076|consen  206 DYELWKRLADLSEQLGNINQARYCYSRAIQAN--PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLI  283 (895)
T ss_pred             ChHHHHHHHHHHHhcccHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHH
Confidence            34455666666666666777777777666652  333          2222    5555555543    22222    22


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHH-CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHH---------
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIV-QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLH---------  160 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~-~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~---------  160 (323)
                      -.+++.|...++-+.|++.++.-.. .+-..+...++++...+.+...   +......+.....++|..-|         
T Consensus       284 ~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~  363 (895)
T KOG2076|consen  284 RRVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREE  363 (895)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhcccc
Confidence            3345667777777888888877655 2334455556666665555554   43333333332112221111         


Q ss_pred             -------------H----HHHHHHHhcCCCCChHHHHHHHHHHHHcC--CCCChHHHHHHHHHHhccCChHHHHHHHHHH
Q 040801          161 -------------N----TLINMYSSCWCLDQPDEAIKIFYRMEIEN--VKPNAVTLVNVLTARARARDLRTVKRVHKCV  221 (323)
Q Consensus       161 -------------~----~li~~~~~~g~~~~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  221 (323)
                                   +    -++-++....   ..+...-+..-.....  +.-+...|.-+.+++...|.++.|..++..+
T Consensus       364 ~~~~~~~~~~~s~~l~v~rl~icL~~L~---~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i  440 (895)
T KOG2076|consen  364 PNALCEVGKELSYDLRVIRLMICLVHLK---ERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPI  440 (895)
T ss_pred             ccccccCCCCCCccchhHhHhhhhhccc---ccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence                         1    1222222222   1222333333333344  4446678888889999999999999999998


Q ss_pred             HHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCC
Q 040801          222 DESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVG  279 (323)
Q Consensus       222 ~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~  279 (323)
                      ......-+...|--+-.+|-..|..++|.+.+++.... +...+.- ++...+...|+..
T Consensus       441 ~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~E  500 (895)
T KOG2076|consen  441 TNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHE  500 (895)
T ss_pred             hcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHH
Confidence            87655556788888899999999999999999988765 3333333 6666666665533

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

Probab=96.56  E-value=0.11  Score=43.76  Aligned_cols=148  Identities=11%  Similarity=-0.096  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Q 040801          109 AFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       109 A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~  188 (323)
                      --++++++...-..-+......-...|++.++-.+.++.... |-..+....|.-|  +.+..   ..+-|.+.++.|.+
T Consensus        92 ~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~-~~~lE~~Al~VqI--~lk~~---r~d~A~~~lk~mq~  165 (299)
T KOG3081|consen   92 LASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHL-GENLEAAALNVQI--LLKMH---RFDLAEKELKKMQQ  165 (299)
T ss_pred             HHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhc-cchHHHHHHHHHH--HHHHH---HHHHHHHHHHHHHc
Confidence            344556665554444434444445556777773333333333 3334444444333  23333   45889999999985


Q ss_pred             cCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCch
Q 040801          189 ENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNY  263 (323)
Q Consensus       189 ~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~  263 (323)
                         --+..|.+-|.+++.+    .+.+..|..+|++|.++ ..|+..+-+....++...|++++|+.++++...+ ..+|
T Consensus       166 ---ided~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dp  241 (299)
T KOG3081|consen  166 ---IDEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDP  241 (299)
T ss_pred             ---cchHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCH
Confidence               3466777777776654    45688999999999874 5789999999999999999999999999998876 3344


Q ss_pred             hhh
Q 040801          264 GQW  266 (323)
Q Consensus       264 ~~~  266 (323)
                      ...
T Consensus       242 etL  244 (299)
T KOG3081|consen  242 ETL  244 (299)
T ss_pred             HHH
Confidence            443

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

Probab=96.56  E-value=0.083  Score=51.97  Aligned_cols=210  Identities=10%  Similarity=0.011  Sum_probs=147.0

Q ss_pred             hHHHhhcCCCchHHHHHHHHHHHhcCCCCC---ccch-----------hHHHhcccCC---CCChhhHHHHHHHHHhCCC
Q 040801           43 CLVSLEKCSTMRELKQIHAQMLRTSLFFDP---CADY-----------HVRLVFSQIS---NPTIYTCNSIVRGYTNKNL  105 (323)
Q Consensus        43 li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~-----------~a~~lf~~m~---~~~~~~~~~li~~~~~~g~  105 (323)
                      +-..+-.-++++.|.+++....+.  .|+-   |-+.           +|-..+++..   ..|...++.+=..+.+...
T Consensus       502 larl~E~l~~~~~A~e~Yk~Ilke--hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~  579 (1018)
T KOG2002|consen  502 LARLLEELHDTEVAEEMYKSILKE--HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSE  579 (1018)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHHH--CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhh
Confidence            444444556888899999888765  3333   2222           5666666554   4455555555557888888


Q ss_pred             hHHHHHHHHHHHHCC-CCCCcccHHHHHHHhcc-------hhh--------HHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801          106 HHEAFLFYHEMIVQG-LIPDRFMFPSLFKSCAD-------IYV--------EKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus       106 ~~~A~~~~~~m~~~g-~~p~~~ty~~ll~~~~~-------~~~--------a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      +.-|.+-|+...+.- ..+|.++.-.|=+.|..       .+.        |.++|....+.. .-|.+.-|-+=-.++.
T Consensus       580 ~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~  658 (1018)
T KOG2002|consen  580 WKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAE  658 (1018)
T ss_pred             hcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhh
Confidence            888888777765432 22454444444332221       111        777777776654 3466777777777888


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH-hCCccChhhHHHHHHHHHhcCCHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE-SGFWSHVELKTTLMDAYCKCKFVSR  248 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~~~li~~~~~~g~~~~  248 (323)
                      +|   ++.+|.++|.+..+... -+..+|-.+-+.|...|++..|.++|+...+ .+-.-+..+.++|-+++-++|.+.+
T Consensus       659 kg---~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~e  734 (1018)
T KOG2002|consen  659 KG---RFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQE  734 (1018)
T ss_pred             cc---CchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHH
Confidence            88   55899999999988664 3667888999999999999999999998865 4444568888999999999999999


Q ss_pred             HHHHHHhccCC
Q 040801          249 AWDLFVKMLFP  259 (323)
Q Consensus       249 a~~~~~~m~~~  259 (323)
                      |.+.+-.....
T Consensus       735 ak~~ll~a~~~  745 (1018)
T KOG2002|consen  735 AKEALLKARHL  745 (1018)
T ss_pred             HHHHHHHHHHh
Confidence            99988776544

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

Probab=96.55  E-value=0.41  Score=43.80  Aligned_cols=54  Identities=13%  Similarity=0.152  Sum_probs=43.2

Q ss_pred             hHHHhccc-CC-CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHH
Q 040801           77 HVRLVFSQ-IS-NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLF  132 (323)
Q Consensus        77 ~a~~lf~~-m~-~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll  132 (323)
                      .|+++|.. |. +|+...|++.|+.=.+-+.++.|..+|+...-  +.|++.+|--..
T Consensus       159 gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikya  214 (677)
T KOG1915|consen  159 GARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYA  214 (677)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHH
Confidence            78888865 44 99999999999999999999999999988754  347666655443

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

Probab=96.54  E-value=0.18  Score=46.19  Aligned_cols=160  Identities=14%  Similarity=0.040  Sum_probs=71.3

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      |..+|-+==+.+.-.+++++|..=|++-++  +.| +...|..+--+.-+.+.   ++..|++.++. +.-.+-+||-.-
T Consensus       393 n~dvYyHRgQm~flL~q~e~A~aDF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fA  469 (606)
T KOG0547|consen  393 NPDVYYHRGQMRFLLQQYEEAIADFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFA  469 (606)
T ss_pred             CCchhHhHHHHHHHHHHHHHHHHHHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHH
Confidence            344444444444444555555555554443  122 12223222222223333   55555555432 333344555555


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcC-----CC--CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIEN-----VK--PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g-----~~--p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      ..+...+   ++++|++-|+.-.+..     +-  +....--.++-.= -.+++..|..+++...+..- -....|.+|-
T Consensus       470 eiLtDqq---qFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~Dp-kce~A~~tla  544 (606)
T KOG0547|consen  470 EILTDQQ---QFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIELDP-KCEQAYETLA  544 (606)
T ss_pred             HHHhhHH---hHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHccCc-hHHHHHHHHH
Confidence            5555555   4456666665554311     10  1111111111111 22556666666665554421 1234556666


Q ss_pred             HHHHhcCCHHHHHHHHHhc
Q 040801          238 DAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m  256 (323)
                      ..-...|++++|.++|++-
T Consensus       545 q~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  545 QFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             HHHHHHhhHHHHHHHHHHH
Confidence            6666666666666666654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.50  E-value=0.028  Score=49.16  Aligned_cols=172  Identities=15%  Similarity=0.153  Sum_probs=103.5

Q ss_pred             hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcch--hh----------HHHH
Q 040801           77 HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADI--YV----------EKQL  144 (323)
Q Consensus        77 ~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~--~~----------a~~~  144 (323)
                      .|++++-.+-+.=+..--.|+--|.+.+++.+|..+.+++.-  ..|    |.-++++....  |.          |.+.
T Consensus       272 gALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~P--ttP----~EyilKgvv~aalGQe~gSreHlKiAqqf  345 (557)
T KOG3785|consen  272 GALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDP--TTP----YEYILKGVVFAALGQETGSREHLKIAQQF  345 (557)
T ss_pred             cHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCC--CCh----HHHHHHHHHHHHhhhhcCcHHHHHHHHHH
Confidence            455555433322223334566678899999999998877642  223    55555554332  22          7777


Q ss_pred             HHHHHHcCCCCchHHHHHHHHH-HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          145 HSQAIKFGLASDSFLHNTLINM-YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       145 ~~~m~~~g~~~~~~~~~~li~~-~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      |+..-+.+.+-|+..-..-+.+ +.-.-   ++|+++-.++....-=..-|.+-|| +.++.+..|...+|+++|-.+..
T Consensus       346 fqlVG~Sa~ecDTIpGRQsmAs~fFL~~---qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~  421 (557)
T KOG3785|consen  346 FQLVGESALECDTIPGRQSMASYFFLSF---QFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISG  421 (557)
T ss_pred             HHHhcccccccccccchHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcC
Confidence            7776666665554433222222 22222   4577777777776544444555554 67788888888888888877655


Q ss_pred             hCCccChhhHH-HHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          224 SGFWSHVELKT-TLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       224 ~g~~p~~~~~~-~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..++ |..+|. .|.++|.++++.+-|++++-++...
T Consensus       422 ~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t~  457 (557)
T KOG3785|consen  422 PEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTNTP  457 (557)
T ss_pred             hhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcCCc
Confidence            4443 445554 4556788888888888877776543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.48  E-value=0.076  Score=46.38  Aligned_cols=193  Identities=10%  Similarity=0.140  Sum_probs=118.7

Q ss_pred             CchHHHHHHHHHHH-hcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHh--CCChHHHHHHHHHHHHCCCCCCcccH
Q 040801           52 TMRELKQIHAQMLR-TSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTN--KNLHHEAFLFYHEMIVQGLIPDRFMF  128 (323)
Q Consensus        52 ~~~~a~~i~~~m~~-~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~--~g~~~~A~~~~~~m~~~g~~p~~~ty  128 (323)
                      +.+.-..+-+.+++ .|+             |+........++.+++..-..  ...+++.+++++.|++.|++-+..+|
T Consensus        34 d~~~~~~~~~~IK~~t~~-------------fS~lr~~~~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~  100 (297)
T PF13170_consen   34 DAERFKEISKYIKKNTGW-------------FSPLRGNHRFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLY  100 (297)
T ss_pred             CHHHHHHHHHHHHHcccc-------------cccccccHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHH
Confidence            45555555555555 232             333333344445555544333  12266778899999999999999888


Q ss_pred             HHHHHHhcc--hhh-------HHHHHHHHHHcCC---CCchHHHHHHHHHHHhcCCCC-ChHHHHHHHHHHHHcCCCCCh
Q 040801          129 PSLFKSCAD--IYV-------EKQLHSQAIKFGL---ASDSFLHNTLINMYSSCWCLD-QPDEAIKIFYRMEIENVKPNA  195 (323)
Q Consensus       129 ~~ll~~~~~--~~~-------a~~~~~~m~~~g~---~~~~~~~~~li~~~~~~g~~~-~~~~a~~~~~~m~~~g~~p~~  195 (323)
                      -+..-....  ..+       +..+++.|++...   .++-+++..|+..  ...+.+ -.+.+.+.|+.+...|+..+-
T Consensus       101 laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kgn  178 (297)
T PF13170_consen  101 LAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKGN  178 (297)
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCCc
Confidence            874444433  122       9999999998753   4667888888766  333222 346778888888887876533


Q ss_pred             -HHHHHHHHHHhcc-CC--hHHHHHHHHHHHHhCCccChhhHHHH-HHHHHhcCC---HHHHHHHHHhccCC
Q 040801          196 -VTLVNVLTARARA-RD--LRTVKRVHKCVDESGFWSHVELKTTL-MDAYCKCKF---VSRAWDLFVKMLFP  259 (323)
Q Consensus       196 -~t~~~li~~~~~~-~~--~~~a~~~~~~m~~~g~~p~~~~~~~l-i~~~~~~g~---~~~a~~~~~~m~~~  259 (323)
                       .-+.+-|-+++.. .+  +..+..+++.+.+.|+++....|..+ +-++...+.   +++..++.+.+.+.
T Consensus       179 ~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~~~~~~~~i~ev~~~L~~~  250 (297)
T PF13170_consen  179 DLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDPEEKIVEEIKEVIDELKEQ  250 (297)
T ss_pred             HHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCchHHHHHHHHHHHHHHhhC
Confidence             2333333344433 22  44678889999999999988877644 223344444   55556666666554

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

Probab=96.42  E-value=0.21  Score=40.98  Aligned_cols=32  Identities=16%  Similarity=0.093  Sum_probs=20.4

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      +.|...|..+-..|...|++++|.+.|++-.+
T Consensus        70 P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~  101 (198)
T PRK10370         70 PQNSEQWALLGEYYLWRNDYDNALLAYRQALQ  101 (198)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44556666666666666666666666665544

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

Probab=96.41  E-value=0.08  Score=50.52  Aligned_cols=202  Identities=11%  Similarity=0.014  Sum_probs=123.1

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--ccch----hHHHhcc-cCC-CCChhhHHHHHHHHHhCCChHHHHHH
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--CADY----HVRLVFS-QIS-NPTIYTCNSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--y~~~----~a~~lf~-~m~-~~~~~~~~~li~~~~~~g~~~~A~~~  112 (323)
                      ..+...+.++|-..+|..|++..-.-.  |-.  |...    .|.++.. ++. +||...|..+-+......-+++|+++
T Consensus       402 ~~laell~slGitksAl~I~Erlemw~--~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawEl  479 (777)
T KOG1128|consen  402 RLLAELLLSLGITKSALVIFERLEMWD--PVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWEL  479 (777)
T ss_pred             HHHHHHHHHcchHHHHHHHHHhHHHHH--HHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHH
Confidence            456667888888899998888653221  111  2222    3333332 223 55666666666666665666666666


Q ss_pred             HHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc
Q 040801          113 YHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE  189 (323)
Q Consensus       113 ~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~  189 (323)
                      .+....+.    ...++.++   .+.++   +.+.++.-.+.. .....+|-.+=.+.-+.+   +++.|.+-|..-.. 
T Consensus       480 sn~~sarA----~r~~~~~~---~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqle---k~q~av~aF~rcvt-  547 (777)
T KOG1128|consen  480 SNYISARA----QRSLALLI---LSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLE---KEQAAVKAFHRCVT-  547 (777)
T ss_pred             hhhhhHHH----HHhhcccc---ccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHh---hhHHHHHHHHHHhh-
Confidence            65543220    00001000   11222   333333322221 012233333333344444   66888888877664 


Q ss_pred             CCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          190 NVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       190 g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                       ..|| ...||++-.+|.+.++-.+|...+.+..+.. .-+-..|...+..-.+.|.+++|.+.++.+..
T Consensus       548 -L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  548 -LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             -cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence             3454 5789999999999999999999999999887 44577888888899999999999999998754

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.40  E-value=0.019  Score=43.29  Aligned_cols=46  Identities=11%  Similarity=0.138  Sum_probs=22.1

Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHH-hCCccChhhHHHHHH
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDE-SGFWSHVELKTTLMD  238 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p~~~~~~~li~  238 (323)
                      |+..+..+++.+|+..+++..|.++.+...+ -+++.+..+|..|++
T Consensus        50 Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   50 PTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE   96 (126)
T ss_pred             CCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4455555555555555555555555554432 234444444444444

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

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

Probab=96.38  E-value=0.66  Score=44.23  Aligned_cols=211  Identities=9%  Similarity=-0.050  Sum_probs=104.9

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-----------ccch-hHHHhcccCC---CCChhhHHHHHHHHHhCC
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-----------CADY-HVRLVFSQIS---NPTIYTCNSIVRGYTNKN  104 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-----------y~~~-~a~~lf~~m~---~~~~~~~~~li~~~~~~g  104 (323)
                      |..-...|.+.+-++-|+.||....+--....+           |++. ....+|++..   +.....|-...+.+-..|
T Consensus       519 w~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~ag  598 (913)
T KOG0495|consen  519 WLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAG  598 (913)
T ss_pred             HhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcC
Confidence            333444555555667777777766654221111           3333 3444444432   334455666666666777


Q ss_pred             ChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHH
Q 040801          105 LHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIK  181 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~  181 (323)
                      ++-.|..++...-+..- -+...|-.-++.-..+..   |..++......  .|+..+|.--++.--..+   +.++|.+
T Consensus       599 dv~~ar~il~~af~~~p-nseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld---~~eeA~r  672 (913)
T KOG0495|consen  599 DVPAARVILDQAFEANP-NSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLD---NVEEALR  672 (913)
T ss_pred             CcHHHHHHHHHHHHhCC-CcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhh---hHHHHHH
Confidence            77777777766655321 133445555555554444   66666665553  355555544444333333   4467777


Q ss_pred             HHHHHHHcCCCCChH-HHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          182 IFYRMEIENVKPNAV-TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       182 ~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++++-..  .-|+-. .|..+=+.+-+.++++.|...|..=.+ .++-.+..|-.|.+.=-+.|.+-+|..++++-+-+
T Consensus       673 llEe~lk--~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k-~cP~~ipLWllLakleEk~~~~~rAR~ildrarlk  748 (913)
T KOG0495|consen  673 LLEEALK--SFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTK-KCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLK  748 (913)
T ss_pred             HHHHHHH--hCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccc-cCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhc
Confidence            7755543  223332 232222333334444444433332111 12223445555555555566666666666655543

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

Probab=96.31  E-value=1.1  Score=44.06  Aligned_cols=206  Identities=11%  Similarity=0.071  Sum_probs=132.9

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCC-ccch-------------hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHH
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDP-CADY-------------HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFL  111 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~-y~~~-------------~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~  111 (323)
                      ..+++..|.+-.+.+.++  .|+. |++.             +|.++++...   ..|..+-..+-.+|.+.|+.++|..
T Consensus        21 d~~qfkkal~~~~kllkk--~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~   98 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKK--HPNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVH   98 (932)
T ss_pred             hhHHHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHH
Confidence            345667777777766655  4444 3333             6777776654   5588889999999999999999999


Q ss_pred             HHHHHHHCCCCCCcccHHHHHHHhcchhh-------HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC-------ChH
Q 040801          112 FYHEMIVQGLIPDRFMFPSLFKSCADIYV-------EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD-------QPD  177 (323)
Q Consensus       112 ~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-------a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~-------~~~  177 (323)
                      +|+...+.  -|+..-...+..+|.+.+.       |.+++.     .+.-+.+.+=++|+.+...-.-.       -.-
T Consensus        99 ~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-----~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~  171 (932)
T KOG2053|consen   99 LYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYK-----NFPKRAYYFWSVISLILQSIFSENELLDPILLA  171 (932)
T ss_pred             HHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----hCCcccchHHHHHHHHHHhccCCcccccchhHH
Confidence            99988764  5778888899999999888       444444     22233444445555554432111       112


Q ss_pred             HHHHHHHHHHHcC-CCCChHHHHHHHHHHhccCChHHHHHHHHH-HHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          178 EAIKIFYRMEIEN-VKPNAVTLVNVLTARARARDLRTVKRVHKC-VDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       178 ~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~~a~~~~~~-m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      -|.+.++.+..++ -.-+..-.-.-+..+-..|..++|..++.. ..+.-..-+...-+--++.+.+.+++.+..++-.+
T Consensus       172 LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~  251 (932)
T KOG2053|consen  172 LAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSR  251 (932)
T ss_pred             HHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHH
Confidence            3444555555443 222333333333444567789999998843 33443333455556677888999999999999888


Q ss_pred             ccCCCCch
Q 040801          256 MLFPWNNY  263 (323)
Q Consensus       256 m~~~~~~~  263 (323)
                      +..++++.
T Consensus       252 Ll~k~~Dd  259 (932)
T KOG2053|consen  252 LLEKGNDD  259 (932)
T ss_pred             HHHhCCcc
Confidence            88886554

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

Probab=96.30  E-value=0.18  Score=38.07  Aligned_cols=93  Identities=10%  Similarity=0.018  Sum_probs=44.8

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      .....+...+...|++++|.+.|+.....+ +.+...+..+-..+.+.|+   |...++...+.+ ..+...+..+-..|
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~   95 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECL   95 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHH
Confidence            344455566666777777777776665532 1233344444444444444   444444444332 12233344444444


Q ss_pred             HhcCCCCChHHHHHHHHHHHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~  188 (323)
                      ...|   +.++|++.|++..+
T Consensus        96 ~~~g---~~~~A~~~~~~al~  113 (135)
T TIGR02552        96 LALG---EPESALKALDLAIE  113 (135)
T ss_pred             HHcC---CHHHHHHHHHHHHH
Confidence            4444   33555555544443

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

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=96.30  E-value=0.15  Score=39.41  Aligned_cols=63  Identities=6%  Similarity=-0.033  Sum_probs=29.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ...|..+-..+.+.|   ++++|...|+...... ..+...+..+-.++...|+.++|...++...+
T Consensus        58 ~~a~~~lg~~~~~~g---~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         58 WRAHIALAGTWMMLK---EYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HHHHHHHHHHHHHHh---hHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444444444   3345555555544422 22344444444455555555555555555444

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=96.21  E-value=0.027  Score=42.47  Aligned_cols=66  Identities=18%  Similarity=0.156  Sum_probs=53.1

Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHH---------------HhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVD---------------ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~---------------~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      |..++.++|.++++.|+++....+.+..-               .....|+..+..+++.+|+.+|++..|.++++...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            45677778888888888887777776552               123568899999999999999999999999999877


Q ss_pred             C
Q 040801          259 P  259 (323)
Q Consensus       259 ~  259 (323)
                      .
T Consensus        81 ~   81 (126)
T PF12921_consen   81 K   81 (126)
T ss_pred             H
Confidence            6

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

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.18  E-value=0.12  Score=44.44  Aligned_cols=206  Identities=14%  Similarity=0.095  Sum_probs=124.5

Q ss_pred             HhhcCCCchHHHHHHHHHHHhc-CCCCC--------ccch---hHHHhcccCC-CCChhhHHHHHHHHHhCCChHHHHHH
Q 040801           46 SLEKCSTMRELKQIHAQMLRTS-LFFDP--------CADY---HVRLVFSQIS-NPTIYTCNSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        46 ~~~~~~~~~~a~~i~~~m~~~~-~~~~~--------y~~~---~a~~lf~~m~-~~~~~~~~~li~~~~~~g~~~~A~~~  112 (323)
                      ++-+.+.+.+|+.+...|.+.. +....        |+..   .++.+.++.+ +-+..+-+..=--..+.|+++.|++-
T Consensus        87 SLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqk  166 (459)
T KOG4340|consen   87 SLYKACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQK  166 (459)
T ss_pred             HHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHH
Confidence            4445566666766666655421 10000        5544   5666677766 33444333333344578999999999


Q ss_pred             HHHHHH-CCCCCCcccHHHHHHHhcchhh--HHHHHHHHHHcCCCC-------------ch--------HHHHHHHHHH-
Q 040801          113 YHEMIV-QGLIPDRFMFPSLFKSCADIYV--EKQLHSQAIKFGLAS-------------DS--------FLHNTLINMY-  167 (323)
Q Consensus       113 ~~~m~~-~g~~p~~~ty~~ll~~~~~~~~--a~~~~~~m~~~g~~~-------------~~--------~~~~~li~~~-  167 (323)
                      |.+-.+ .|..| ...|+..+-.|.+...  |.++..++.++|++-             |+        ..-+.++.++ 
T Consensus       167 FqaAlqvsGyqp-llAYniALaHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfN  245 (459)
T KOG4340|consen  167 FQAALQVSGYQP-LLAYNLALAHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFN  245 (459)
T ss_pred             HHHHHhhcCCCc-hhHHHHHHHHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhh
Confidence            988766 55655 5789988888877666  889999988887632             21        1123344333 


Q ss_pred             ------HhcCCCCChHHHHHHHHHHHHc-CCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHH
Q 040801          168 ------SSCWCLDQPDEAIKIFYRMEIE-NVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAY  240 (323)
Q Consensus       168 ------~~~g~~~~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  240 (323)
                            -+.|   +++.|.+-+.+|--+ .-+.|.+|...+.-.=. .+++....+=+..+.+..- .-..||..++-.|
T Consensus       246 LKaAIeyq~~---n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nP-fP~ETFANlLlly  320 (459)
T KOG4340|consen  246 LKAAIEYQLR---NYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNP-FPPETFANLLLLY  320 (459)
T ss_pred             hhhhhhhhcc---cHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCC-CChHHHHHHHHHH
Confidence                  3334   667777777777432 23457777665543322 2334444444444444432 3467888888889


Q ss_pred             HhcCCHHHHHHHHHhcc
Q 040801          241 CKCKFVSRAWDLFVKML  257 (323)
Q Consensus       241 ~~~g~~~~a~~~~~~m~  257 (323)
                      ||+.-++-|-.++.+=.
T Consensus       321 CKNeyf~lAADvLAEn~  337 (459)
T KOG4340|consen  321 CKNEYFDLAADVLAENA  337 (459)
T ss_pred             hhhHHHhHHHHHHhhCc
Confidence            99999998888877644

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.16  E-value=0.025  Score=37.17  Aligned_cols=53  Identities=15%  Similarity=0.100  Sum_probs=36.7

Q ss_pred             hccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          206 ARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...|++++|..+++.+.+.. +-+...+-.+..+|.+.|++++|.++++++...
T Consensus         2 l~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hhccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34677777888877776653 225666667777888888888888888877765

...

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

Probab=96.16  E-value=0.31  Score=44.68  Aligned_cols=149  Identities=14%  Similarity=0.069  Sum_probs=108.2

Q ss_pred             hCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcC-CCCchHHHHHHHHHHHhcCCCCChH
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFG-LASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      -.|+...|.+-|+..+...-.++.. |--+-..|....+   .++.|+...+.. -.||++....-|.....     +++
T Consensus       338 L~g~~~~a~~d~~~~I~l~~~~~~l-yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~-----q~e  411 (606)
T KOG0547|consen  338 LKGDSLGAQEDFDAAIKLDPAFNSL-YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQ-----QYE  411 (606)
T ss_pred             hcCCchhhhhhHHHHHhcCcccchH-HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHH-----HHH
Confidence            3588889999999988765444332 5555556666666   777777776655 34566555555555444     779


Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +|..=|++-.... .-+...|.-+--+.-+.+.++.++..|++.+++ ++-.+.+|+-.-..+...+++++|.+-|+...
T Consensus       412 ~A~aDF~Kai~L~-pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai  489 (606)
T KOG0547|consen  412 EAIADFQKAISLD-PENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAI  489 (606)
T ss_pred             HHHHHHHHHhhcC-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHH
Confidence            9999998887633 224456655555556888999999999998775 56668999999999999999999999999765


Q ss_pred             C
Q 040801          258 F  258 (323)
Q Consensus       258 ~  258 (323)
                      +
T Consensus       490 ~  490 (606)
T KOG0547|consen  490 E  490 (606)
T ss_pred             h
Confidence            4

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

Probab=96.14  E-value=0.28  Score=44.84  Aligned_cols=142  Identities=14%  Similarity=0.133  Sum_probs=106.6

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHH-HHHhcchhh---HHHHHHHHHHcCCCCc-hHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSL-FKSCADIYV---EKQLHSQAIKFGLASD-SFLHNTLIN  165 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~l-l~~~~~~~~---a~~~~~~m~~~g~~~~-~~~~~~li~  165 (323)
                      .-|..-+..| ..|++++|+..+..+...  .||...|..+ ...+.+.++   |.+.++.+...  .|+ ....-.+-.
T Consensus       308 a~YG~A~~~~-~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~  382 (484)
T COG4783         308 AQYGRALQTY-LAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQ  382 (484)
T ss_pred             HHHHHHHHHH-HhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHH
Confidence            3355555544 789999999999998765  4555555444 555666666   66767666654  466 566677888


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF  245 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  245 (323)
                      +|.+.|   ++.+|+++++...... +-|...|..|-++|...|+..++.....                  ++|...|+
T Consensus       383 all~~g---~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~A------------------E~~~~~G~  440 (484)
T COG4783         383 ALLKGG---KPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARA------------------EGYALAGR  440 (484)
T ss_pred             HHHhcC---ChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHH------------------HHHHhCCC
Confidence            899999   6689999999987654 6689999999999999999998865544                  45677899


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      ++.|...+...+++
T Consensus       441 ~~~A~~~l~~A~~~  454 (484)
T COG4783         441 LEQAIIFLMRASQQ  454 (484)
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999988887765

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.12  E-value=0.4  Score=47.07  Aligned_cols=158  Identities=11%  Similarity=-0.008  Sum_probs=117.1

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCccc-HHHHHHHhcchhh---HHHHHHHHHHcCCCCc-hHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFM-FPSLFKSCADIYV---EKQLHSQAIKFGLASD-SFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~t-y~~ll~~~~~~~~---a~~~~~~m~~~g~~~~-~~~~~  161 (323)
                      ..++..+-.|-....+.|.+++|.++++...+  +.||... ...+...+.+.++   |....+...+..  |+ ....+
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~~~~~~~  158 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG--SSSAREIL  158 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CCCHHHHH
Confidence            34577788888899999999999999999887  4676643 4445555666666   777777776654  54 55567


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHH
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYC  241 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  241 (323)
                      .+-.++.+.|   ++++|..+|++....+ .-+..++..+-.++-..|+.++|...|+...+.- .+...-|+.++    
T Consensus       159 ~~a~~l~~~g---~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~-~~~~~~~~~~~----  229 (694)
T PRK15179        159 LEAKSWDEIG---QSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI-GDGARKLTRRL----  229 (694)
T ss_pred             HHHHHHHHhc---chHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh-CcchHHHHHHH----
Confidence            7778888888   6699999999998743 2347888889999999999999999999997652 34445666544    


Q ss_pred             hcCCHHHHHHHHHhccCC
Q 040801          242 KCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       242 ~~g~~~~a~~~~~~m~~~  259 (323)
                        +++..-..+++++.-.
T Consensus       230 --~~~~~~~~~~~~~~~~  245 (694)
T PRK15179        230 --VDLNADLAALRRLGVE  245 (694)
T ss_pred             --HHHHHHHHHHHHcCcc
Confidence              4556667777777544

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

Probab=96.04  E-value=1.4  Score=41.91  Aligned_cols=107  Identities=11%  Similarity=0.034  Sum_probs=75.6

Q ss_pred             hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC------CCCCCcccHHHHHHHhcchhh------HHHH
Q 040801           77 HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ------GLIPDRFMFPSLFKSCADIYV------EKQL  144 (323)
Q Consensus        77 ~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------g~~p~~~ty~~ll~~~~~~~~------a~~~  144 (323)
                      .+.+++..-.+.++..-+-.|..+++.+++++|-+.++.....      .-+-+...|..+....++..+      +..+
T Consensus       156 ts~rvyrRYLk~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdai  235 (835)
T KOG2047|consen  156 TSIRVYRRYLKVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAI  235 (835)
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHH
Confidence            5566666555666666788899999999999999998877542      244566677777777776666      4554


Q ss_pred             HHHHHHcCCCCc--hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Q 040801          145 HSQAIKFGLASD--SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       145 ~~~m~~~g~~~~--~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~  188 (323)
                      +..+...  -+|  ...|++|-+-|.+.|   .+++|.++|++-.+
T Consensus       236 iR~gi~r--ftDq~g~Lw~SLAdYYIr~g---~~ekarDvyeeai~  276 (835)
T KOG2047|consen  236 IRGGIRR--FTDQLGFLWCSLADYYIRSG---LFEKARDVYEEAIQ  276 (835)
T ss_pred             HHhhccc--CcHHHHHHHHHHHHHHHHhh---hhHHHHHHHHHHHH
Confidence            4444332  234  467999999999999   45788888877654

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

Probab=96.01  E-value=0.33  Score=37.47  Aligned_cols=116  Identities=10%  Similarity=-0.050  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC--hhh
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP--NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH--VEL  232 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~  232 (323)
                      ...|..++..+. .+   +...+.+.++.+....-.-  .....-.+-..+...|++++|...|+.+.+..-.|+  ...
T Consensus        12 ~~~y~~~~~~~~-~~---~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a   87 (145)
T PF09976_consen   12 SALYEQALQALQ-AG---DPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLA   87 (145)
T ss_pred             HHHHHHHHHHHH-CC---CHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHH
Confidence            456777777775 55   5688888898888754221  123333455788899999999999999998763332  234


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhh-HHHhhhccCC
Q 040801          233 KTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQW-AMSATVGPQG  276 (323)
Q Consensus       233 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~~~~~~~  276 (323)
                      .-.|...+...|++++|...++........+..+ ....++...|
T Consensus        88 ~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g  132 (145)
T PF09976_consen   88 RLRLARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQG  132 (145)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCC
Confidence            4567788999999999999998866554444444 4444444444

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

Probab=95.96  E-value=1.1  Score=39.98  Aligned_cols=27  Identities=7%  Similarity=0.166  Sum_probs=12.7

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+..+-..|...|++++|.+++++..
T Consensus       149 ~~~~~la~i~~~~g~~~eA~~~l~~~l  175 (355)
T cd05804         149 WAVHAVAHVLEMQGRFKEGIAFMESWR  175 (355)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHhhh
Confidence            334444444445555555555544443

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.

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

Probab=95.92  E-value=0.49  Score=39.79  Aligned_cols=159  Identities=12%  Similarity=-0.020  Sum_probs=101.2

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      .-+=..+--.|+-+.+..+....... -.-|........+...+.|+   |...+.+..... .+|...||.+=-+|-+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHc
Confidence            33444555566666666554443211 12233344446677777777   666666665533 56777888888888888


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  250 (323)
                      |   ++++|..-|.+-.+-. .-+...+|.+--.+.-.|+.+.|+.++......+ .-|...-..|.-+....|++++|+
T Consensus       148 G---r~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~A~  222 (257)
T COG5010         148 G---RFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFREAE  222 (257)
T ss_pred             c---ChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHHHH
Confidence            8   4477777777666532 1244566777777777788888888888777654 225666677777788888888888


Q ss_pred             HHHHhccCC
Q 040801          251 DLFVKMLFP  259 (323)
Q Consensus       251 ~~~~~m~~~  259 (323)
                      .+...-...
T Consensus       223 ~i~~~e~~~  231 (257)
T COG5010         223 DIAVQELLS  231 (257)
T ss_pred             hhccccccc
Confidence            877655543

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.88  E-value=0.43  Score=37.98  Aligned_cols=99  Identities=12%  Similarity=-0.039  Sum_probs=68.7

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      ...+..+-..|...|   ++++|...|++....+..+.  ...+..+-..+.+.|+.++|...+.+..+.. +-+...+.
T Consensus        35 a~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~  110 (172)
T PRK02603         35 AFVYYRDGMSAQADG---EYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALN  110 (172)
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHH
Confidence            455677777788888   66899999988876432222  4677788888889999999999988887752 12355566


Q ss_pred             HHHHHHHhcCC--------------HHHHHHHHHhccCC
Q 040801          235 TLMDAYCKCKF--------------VSRAWDLFVKMLFP  259 (323)
Q Consensus       235 ~li~~~~~~g~--------------~~~a~~~~~~m~~~  259 (323)
                      .+...|...|+              +++|.+++++....
T Consensus       111 ~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~  149 (172)
T PRK02603        111 NIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRL  149 (172)
T ss_pred             HHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhh
Confidence            66667777776              45566666555543

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=95.86  E-value=0.54  Score=46.17  Aligned_cols=96  Identities=8%  Similarity=0.054  Sum_probs=48.3

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA-VTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELK  233 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~  233 (323)
                      ++..+--|-......|+   .++|..+++...+  ..||. .....+...+.+.+.+++|....+...+.  .|+ ....
T Consensus        85 ~~~~~~~La~i~~~~g~---~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~  157 (694)
T PRK15179         85 TELFQVLVARALEAAHR---SDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREI  157 (694)
T ss_pred             cHHHHHHHHHHHHHcCC---cHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHH
Confidence            34445555555555552   2555555555544  23332 34444555555555555555555555544  233 2233


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          234 TTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       234 ~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..+-.++.+.|+.++|..+|++...
T Consensus       158 ~~~a~~l~~~g~~~~A~~~y~~~~~  182 (694)
T PRK15179        158 LLEAKSWDEIGQSEQADACFERLSR  182 (694)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHh
Confidence            3444455555555555555555554

>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=95.74  E-value=0.048  Score=35.82  Aligned_cols=63  Identities=11%  Similarity=0.016  Sum_probs=48.0

Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      +.|   ++++|+++|++.....- -|...+-.+..+|.+.|++++|..+++.+...  .|+...|..++
T Consensus         3 ~~~---~~~~A~~~~~~~l~~~p-~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    3 KQG---DYDEAIELLEKALQRNP-DNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HTT---HHHHHHHHHHHHHHHTT-TSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             hcc---CHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            456   67999999999987652 26777778999999999999999999998876  46645555443

...

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

Probab=95.69  E-value=2.1  Score=40.94  Aligned_cols=215  Identities=15%  Similarity=0.108  Sum_probs=128.0

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccch----------------------hHHHhcccCC--CCCh--hhH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADY----------------------HVRLVFSQIS--NPTI--YTC   93 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~----------------------~a~~lf~~m~--~~~~--~~~   93 (323)
                      -.-+|..+++.+++++|.+.+...+...--.+.+++.                      ....++..+.  -+|.  ..|
T Consensus       172 ~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw  251 (835)
T KOG2047|consen  172 REEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLW  251 (835)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHH
Confidence            4667788888888888888887765333211112222                      3334444433  2233  459


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh--HHHHHHHHH--HcCCCCchH-------HHHH
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV--EKQLHSQAI--KFGLASDSF-------LHNT  162 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~--a~~~~~~m~--~~g~~~~~~-------~~~~  162 (323)
                      ++|-+-|.+.|.+++|.++|++-.+.  ..++.-|+.+..+|+.-..  .....+ +.  +.|-.-+..       .+..
T Consensus       252 ~SLAdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~FEE~~~~~~me-~a~~~~~n~ed~~dl~~~~a~~e~  328 (835)
T KOG2047|consen  252 CSLADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQFEESCVAAKME-LADEESGNEEDDVDLELHMARFES  328 (835)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHHHHHHHHHHHHh-hhhhcccChhhhhhHHHHHHHHHH
Confidence            99999999999999999999997765  3455667888888776554  111111 11  112111111       1222


Q ss_pred             HHHH-------HHhcCCCC--------------ChHHHHHHHHHHHHcCCCC------ChHHHHHHHHHHhccCChHHHH
Q 040801          163 LINM-------YSSCWCLD--------------QPDEAIKIFYRMEIENVKP------NAVTLVNVLTARARARDLRTVK  215 (323)
Q Consensus       163 li~~-------~~~~g~~~--------------~~~~a~~~~~~m~~~g~~p------~~~t~~~li~~~~~~~~~~~a~  215 (323)
                      ||+.       -+-..+..              +..+...++.+.... +.|      -...|..+-.-|-..|+++.|.
T Consensus       329 lm~rr~~~lNsVlLRQn~~nV~eW~kRV~l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aR  407 (835)
T KOG2047|consen  329 LMNRRPLLLNSVLLRQNPHNVEEWHKRVKLYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDAR  407 (835)
T ss_pred             HHhccchHHHHHHHhcCCccHHHHHhhhhhhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHH
Confidence            2211       11111010              345556666665432 222      2346777778888899999999


Q ss_pred             HHHHHHHHhCCccC---hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          216 RVHKCVDESGFWSH---VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       216 ~~~~~m~~~g~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .+|+...+-.++--   ..+|...-++=.+..+++.|.++.++...
T Consensus       408 vifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~  453 (835)
T KOG2047|consen  408 VIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATH  453 (835)
T ss_pred             HHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhc
Confidence            99998876544332   34566666666677788888888887643

>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=95.67  E-value=0.051  Score=42.01  Aligned_cols=73  Identities=15%  Similarity=0.038  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH-----HhCCccChh
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD-----ESGFWSHVE  231 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~-----~~g~~p~~~  231 (323)
                      ..+...++..+...|   ++++|.++.+...... +.|...|..+|.++...|+...|.++|+.+.     +.|+.|+..
T Consensus        62 ~~~~~~l~~~~~~~~---~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~  137 (146)
T PF03704_consen   62 LDALERLAEALLEAG---DYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPE  137 (146)
T ss_dssp             HHHHHHHHHHHHHTT----HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HH
T ss_pred             HHHHHHHHHHHHhcc---CHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHH
Confidence            445555666666666   5577777777766644 3466677777777777777777777776663     346666655


Q ss_pred             hH
Q 040801          232 LK  233 (323)
Q Consensus       232 ~~  233 (323)
                      +-
T Consensus       138 ~~  139 (146)
T PF03704_consen  138 TR  139 (146)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

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

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

Probab=95.62  E-value=1.8  Score=40.60  Aligned_cols=208  Identities=15%  Similarity=0.090  Sum_probs=123.1

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----ccch----------hHHHhcccCCCC---ChhhHHHHHHHHHhC
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----CADY----------HVRLVFSQISNP---TIYTCNSIVRGYTNK  103 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----y~~~----------~a~~lf~~m~~~---~~~~~~~li~~~~~~  103 (323)
                      -.-|..+...|+..+..-+=..|++.  .|+.    |+-.          +|++.|+.-...   =...|-.+=..|+-.
T Consensus       282 ~~~ia~l~el~~~n~Lf~lsh~LV~~--yP~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e  359 (611)
T KOG1173|consen  282 PLHIACLYELGKSNKLFLLSHKLVDL--YPSKALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGE  359 (611)
T ss_pred             HHHHHHHHHhcccchHHHHHHHHHHh--CCCCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhc
Confidence            33455666667766666666666655  3333    1111          788888765522   225677777788888


Q ss_pred             CChHHHHHHHHHHHH--CC-CCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHH
Q 040801          104 NLHHEAFLFYHEMIV--QG-LIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       104 g~~~~A~~~~~~m~~--~g-~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      |..|+|+..|..--+  .| ..|  ..|..+=-+..+.-+ |+++|.+...  +.| |+.+.+-+=-..-..+   .+.+
T Consensus       360 ~EhdQAmaaY~tAarl~~G~hlP--~LYlgmey~~t~n~kLAe~Ff~~A~a--i~P~Dplv~~Elgvvay~~~---~y~~  432 (611)
T KOG1173|consen  360 GEHDQAMAAYFTAARLMPGCHLP--SLYLGMEYMRTNNLKLAEKFFKQALA--IAPSDPLVLHELGVVAYTYE---EYPE  432 (611)
T ss_pred             chHHHHHHHHHHHHHhccCCcch--HHHHHHHHHHhccHHHHHHHHHHHHh--cCCCcchhhhhhhheeehHh---hhHH
Confidence            888888877765433  12 233  223222222222222 7776665543  344 4555555444344344   4567


Q ss_pred             HHHHHHHHHH--cCC----CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          179 AIKIFYRMEI--ENV----KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       179 a~~~~~~m~~--~g~----~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      |..+|+.-..  +.+    ..-..+++.|=.+|.+.+..++|...+++..... +-+..+|.++--.|...|+++.|.+.
T Consensus       433 A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~-~k~~~~~asig~iy~llgnld~Aid~  511 (611)
T KOG1173|consen  433 ALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLS-PKDASTHASIGYIYHLLGNLDKAIDH  511 (611)
T ss_pred             HHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcC-CCchhHHHHHHHHHHHhcChHHHHHH
Confidence            7777766552  111    1234456777777778888888888888776642 34667777777777888888888888


Q ss_pred             HHhccC
Q 040801          253 FVKMLF  258 (323)
Q Consensus       253 ~~~m~~  258 (323)
                      |++-..
T Consensus       512 fhKaL~  517 (611)
T KOG1173|consen  512 FHKALA  517 (611)
T ss_pred             HHHHHh
Confidence            887654

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

Probab=95.62  E-value=2.2  Score=40.84  Aligned_cols=127  Identities=13%  Similarity=0.052  Sum_probs=84.1

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC-----------
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG-----------  225 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g-----------  225 (323)
                      .-.|-.|...=-+.|   .+-.|..+|+.-..++ .-|...|-..|+.=.+.|+.+.|+.++.+..+..           
T Consensus       719 ipLWllLakleEk~~---~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI  794 (913)
T KOG0495|consen  719 IPLWLLLAKLEEKDG---QLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAI  794 (913)
T ss_pred             chHHHHHHHHHHHhc---chhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHH
Confidence            344555655556666   4578888888877666 4478899999999999999999998888776531           


Q ss_pred             ------------------CccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCC-Cchhhh-HHHhhhccCCCCCcchhhh
Q 040801          226 ------------------FWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPW-NNYGQW-AMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       226 ------------------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~-~~~~~~~~~~~~~~~~~a~  285 (323)
                                        ++.|.++.-++-..|-...++++|.+.|++..+.. ..-+.| -+......+|...+-.+..
T Consensus       795 ~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~  874 (913)
T KOG0495|consen  795 WLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVL  874 (913)
T ss_pred             HhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHH
Confidence                              34455555566666666777888888888877652 223455 3344444555444444443


Q ss_pred             hh
Q 040801          286 QI  287 (323)
Q Consensus       286 ~l  287 (323)
                      ..
T Consensus       875 ~~  876 (913)
T KOG0495|consen  875 KK  876 (913)
T ss_pred             HH
Confidence            33

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

Probab=95.60  E-value=0.61  Score=46.78  Aligned_cols=129  Identities=12%  Similarity=0.097  Sum_probs=90.4

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHH-hcchhh---------------------HHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKS-CADIYV---------------------EKQL  144 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~-~~~~~~---------------------a~~~  144 (323)
                      ..+...|-.||..+-+.+++++|.++.++-.+  ..|+...+-.+.-. +...++                     ++.+
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~--~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~  105 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLK--EHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHI  105 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH--hCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHH
Confidence            56778899999999999999999999986544  34554433322222 111111                     2222


Q ss_pred             HHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          145 HSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       145 ~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ...|...+  -+...+-.|-.+|-+.|   +.+++..++++..+-. .-|....|.+-..+... ++++|.+++....+.
T Consensus       106 ~~~i~~~~--~~k~Al~~LA~~Ydk~g---~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~  178 (906)
T PRK14720        106 CDKILLYG--ENKLALRTLAEAYAKLN---ENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR  178 (906)
T ss_pred             HHHHHhhh--hhhHHHHHHHHHHHHcC---ChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH
Confidence            33333322  23356667788888888   6699999999999876 45788999999999988 999999998888765

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

Probab=95.49  E-value=0.19  Score=45.34  Aligned_cols=83  Identities=12%  Similarity=-0.107  Sum_probs=52.7

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFV  254 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  254 (323)
                      ++++|++.|++..... .-+...|..+-.+|...|++++|...++.+.+.. +.+...|..+-.+|...|++++|...|+
T Consensus        17 ~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA~~~~~   94 (356)
T PLN03088         17 DFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTAKAALE   94 (356)
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            5567777777766543 2245566666666777777777777777766543 1234556666666777777777777777


Q ss_pred             hccCC
Q 040801          255 KMLFP  259 (323)
Q Consensus       255 ~m~~~  259 (323)
                      +..+.
T Consensus        95 ~al~l   99 (356)
T PLN03088         95 KGASL   99 (356)
T ss_pred             HHHHh
Confidence            66543

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

Probab=95.49  E-value=2.2  Score=39.96  Aligned_cols=253  Identities=13%  Similarity=0.035  Sum_probs=148.3

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhc-CCCCC--------ccch-------hHHHhcccCCCCChhhHHHHHHHHHhC
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTS-LFFDP--------CADY-------HVRLVFSQISNPTIYTCNSIVRGYTNK  103 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~-~~~~~--------y~~~-------~a~~lf~~m~~~~~~~~~~li~~~~~~  103 (323)
                      ......-+....++....++.+...+.. +.++-        |-..       .++++.+.- +....+|=++=--|...
T Consensus       247 l~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~YYl~i  325 (611)
T KOG1173|consen  247 LAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGCYYLMI  325 (611)
T ss_pred             HHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHHHHHHh
Confidence            3445556667789999999999887653 33333        1111       333333332 33556777777777888


Q ss_pred             CChHHHHHHHHHH--HHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHc--C-CCCchHHHHHHHHHHHhcCCCCC
Q 040801          104 NLHHEAFLFYHEM--IVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF--G-LASDSFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus       104 g~~~~A~~~~~~m--~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~--g-~~~~~~~~~~li~~~~~~g~~~~  175 (323)
                      |+..+|.+.|.+-  ......|-...|.   ++++-.+.   |...+...-+.  | ..|.  .|-.+=  |.+.+   +
T Consensus       326 ~k~seARry~SKat~lD~~fgpaWl~fg---hsfa~e~EhdQAmaaY~tAarl~~G~hlP~--LYlgme--y~~t~---n  395 (611)
T KOG1173|consen  326 GKYSEARRYFSKATTLDPTFGPAWLAFG---HSFAGEGEHDQAMAAYFTAARLMPGCHLPS--LYLGME--YMRTN---N  395 (611)
T ss_pred             cCcHHHHHHHHHHhhcCccccHHHHHHh---HHhhhcchHHHHHHHHHHHHHhccCCcchH--HHHHHH--HHHhc---c
Confidence            9999999999774  3344555444444   44444444   44444433222  2 2343  343333  44555   5


Q ss_pred             hHHHHHHHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh--CCcc----ChhhHHHHHHHHHhcCCHHH
Q 040801          176 PDEAIKIFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDES--GFWS----HVELKTTLMDAYCKCKFVSR  248 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p----~~~~~~~li~~~~~~g~~~~  248 (323)
                      .+-|.++|.+-..  +.| |....+-+=-.....+.+.+|...|....+.  ...+    -..+++.|=++|-+.++.++
T Consensus       396 ~kLAe~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~e  473 (611)
T KOG1173|consen  396 LKLAEKFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEE  473 (611)
T ss_pred             HHHHHHHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHH
Confidence            6899999987654  555 4455555544444578888998888887621  1111    23457788889999999999


Q ss_pred             HHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhh-hhhhCCCCch-hHHHHHHHHHh
Q 040801          249 AWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTA-HQISGPCPKK-AHKLFFFSMLK  305 (323)
Q Consensus       249 a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a-~~l~~~~~~~-~~~~~~~~M~~  305 (323)
                      |...+++-... +.++..+ +....+...|+.+.+.+. .+-+..-+++ -+..++..+++
T Consensus       474 AI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  474 AIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAIE  534 (611)
T ss_pred             HHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            99999987654 3444444 444445555555444333 3444455554 33344444443

>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=95.47  E-value=0.27  Score=33.29  Aligned_cols=27  Identities=15%  Similarity=0.117  Sum_probs=18.9

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHC
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      |..+...+...|++++|.+++++..+.
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~   29 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALEL   29 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            445566677778888888887777653

>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=95.46  E-value=0.14  Score=39.50  Aligned_cols=70  Identities=14%  Similarity=-0.066  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-----CCchhhh
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-----WNNYGQW  266 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~  266 (323)
                      .+...++..+...|+.+.|..+...+.... +.|...|..+|.+|.+.|+..+|.++|+++.+.     |..|...
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~  137 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPE  137 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHH
Confidence            355667777888889999999988888764 447778889999999999999999998887543     6666654

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

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.43  E-value=1.1  Score=39.32  Aligned_cols=157  Identities=13%  Similarity=0.133  Sum_probs=97.0

Q ss_pred             chHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC---CCCCcccHH
Q 040801           53 MRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG---LIPDRFMFP  129 (323)
Q Consensus        53 ~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g---~~p~~~ty~  129 (323)
                      ++....+++.|++.|+..+.|.-..|.-+..+.++.+.   .         -...+|.++|+.|++.-   -.++..++.
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~---~---------~~~~ra~~iy~~mKk~H~fLTs~~D~~~a  145 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDY---D---------EIIQRAKEIYKEMKKKHPFLTSPEDYPFA  145 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccH---H---------HHHHHHHHHHHHHHHhCccccCccchhHH
Confidence            56778999999999994444332222222222111110   0         12468999999998753   357788888


Q ss_pred             HHHHHhcchhh-----HHHHHHHHHHcCCCCchH-HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          130 SLFKSCADIYV-----EKQLHSQAIKFGLASDSF-LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       130 ~ll~~~~~~~~-----a~~~~~~m~~~g~~~~~~-~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      .+|..-.+.-+     ++..++.+.+.|+..+-. -+-+-|-+++....-+...++.++++.+.++|+++....|. +|.
T Consensus       146 ~lLA~~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp-~lG  224 (297)
T PF13170_consen  146 ALLAMTSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYP-TLG  224 (297)
T ss_pred             HHHhcccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCcccccccc-HHH
Confidence            88777444333     889999999989766433 34444444444332212357899999999999998888876 444


Q ss_pred             HHhccCC-----hHHHHHHHHHHH
Q 040801          204 ARARARD-----LRTVKRVHKCVD  222 (323)
Q Consensus       204 ~~~~~~~-----~~~a~~~~~~m~  222 (323)
                      .++-.++     ++....+.+.+.
T Consensus       225 lLall~~~~~~~~~~i~ev~~~L~  248 (297)
T PF13170_consen  225 LLALLEDPEEKIVEEIKEVIDELK  248 (297)
T ss_pred             HHHhcCCchHHHHHHHHHHHHHHh
Confidence            4443333     334445555554

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

Probab=95.35  E-value=2.6  Score=42.03  Aligned_cols=217  Identities=9%  Similarity=-0.006  Sum_probs=132.8

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------ccch--------hHHHhcccCC--CCC--hhhHHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------CADY--------HVRLVFSQIS--NPT--IYTCNSI   96 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------y~~~--------~a~~lf~~m~--~~~--~~~~~~l   96 (323)
                      ++...+.|.+-+.--|+++.++.+..++......-..       ++|+        .|...|.+-.  .+|  +-.+--|
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~Gl  348 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGL  348 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccch
Confidence            3445677888888889999999999988877632222       3333        5666665443  233  2334557


Q ss_pred             HHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-------HHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           97 VRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-------EKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        97 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-------a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      -+.|.+.|+++++...|+..... .+-+..|.-+|=..|...+.       |..+.....+.- ..|...|-.+-..|-.
T Consensus       349 gQm~i~~~dle~s~~~fEkv~k~-~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~~a~l~laql~e~  426 (1018)
T KOG2002|consen  349 GQMYIKRGDLEESKFCFEKVLKQ-LPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDSEAWLELAQLLEQ  426 (1018)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHh-CcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccHHHHHHHHHHHHh
Confidence            88889999999999999888654 23344556555555555532       444444433322 2345555555555544


Q ss_pred             cCCCCChHHHHHHHH----HHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh---CCccChh-------hHHH
Q 040801          170 CWCLDQPDEAIKIFY----RMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES---GFWSHVE-------LKTT  235 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~----~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~~~-------~~~~  235 (323)
                      .    ++..++..|.    .+...+..+-....|.+-.-....|++.+|...|......   ...+|..       -|| 
T Consensus       427 ~----d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN-  501 (1018)
T KOG2002|consen  427 T----DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN-  501 (1018)
T ss_pred             c----ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH-
Confidence            3    3334455443    3334555577788888888888888888888888887654   2334432       222 


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +-..+-..++.+.|.+.+..+.+.
T Consensus       502 larl~E~l~~~~~A~e~Yk~Ilke  525 (1018)
T KOG2002|consen  502 LARLLEELHDTEVAEEMYKSILKE  525 (1018)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHHH
Confidence            333444556777788888777765

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.25  E-value=0.66  Score=36.71  Aligned_cols=102  Identities=11%  Similarity=-0.082  Sum_probs=71.4

Q ss_pred             HcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc
Q 040801          150 KFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP--NAVTLVNVLTARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       150 ~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                      ..+..-....|..+...+...|   ++++|+..|++.......|  ...+|..+-..+...|+.++|...++...+.. +
T Consensus        28 ~~~~~~~a~~~~~~g~~~~~~g---~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~  103 (168)
T CHL00033         28 TTSGEKEAFTYYRDGMSAQSEG---EYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-P  103 (168)
T ss_pred             CCchhHHHHHHHHHHHHHHHcC---CHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-c
Confidence            3333334667778888888888   6799999999887643222  23578888889999999999999999987652 2


Q ss_pred             cChhhHHHHHHHHH-------hcCCHHHHHHHHHh
Q 040801          228 SHVELKTTLMDAYC-------KCKFVSRAWDLFVK  255 (323)
Q Consensus       228 p~~~~~~~li~~~~-------~~g~~~~a~~~~~~  255 (323)
                      .....+..+...|.       +.|++++|...+++
T Consensus       104 ~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        104 FLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             CcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHH
Confidence            23445666666666       77787755555543

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=95.21  E-value=0.65  Score=44.85  Aligned_cols=110  Identities=17%  Similarity=0.108  Sum_probs=82.4

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFV  254 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  254 (323)
                      .+.+|+.+++.+++...  -+--|..+...|+..|+++.|+++|.+.         ..++--|++|.++|+++.|.++-.
T Consensus       747 ew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~my~k~~kw~da~kla~  815 (1636)
T KOG3616|consen  747 EWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWEDAFKLAE  815 (1636)
T ss_pred             hhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHHHHHHHHH
Confidence            66888888888876543  3445778889999999999999999763         346677899999999999999988


Q ss_pred             hccCCCCchhhhHHHhhhccCCCCCcchhhhhhh--CCCCchhHH
Q 040801          255 KMLFPWNNYGQWAMSATVGPQGLVGRHSTAHQIS--GPCPKKAHK  297 (323)
Q Consensus       255 ~m~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~l~--~~~~~~~~~  297 (323)
                      +...+  ......|+.-.......|++.+|+++-  =..|+++++
T Consensus       816 e~~~~--e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiq  858 (1636)
T KOG3616|consen  816 ECHGP--EATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQ  858 (1636)
T ss_pred             HhcCc--hhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHH
Confidence            87754  555556776666777778888887663  234555443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=95.12  E-value=0.87  Score=33.11  Aligned_cols=28  Identities=4%  Similarity=-0.045  Sum_probs=19.5

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHC
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      ++-.+...+.+.|++++|.+.|+.+.+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~   31 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKK   31 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3445566677778888888888777653

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.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=94.85  E-value=2.4  Score=40.33  Aligned_cols=137  Identities=8%  Similarity=-0.090  Sum_probs=91.0

Q ss_pred             CCCCCCcccHHHHHHHhcchhh--------HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCC-----ChHHHHHHHH
Q 040801          119 QGLIPDRFMFPSLFKSCADIYV--------EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLD-----QPDEAIKIFY  184 (323)
Q Consensus       119 ~g~~p~~~ty~~ll~~~~~~~~--------a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~-----~~~~a~~~~~  184 (323)
                      .+.+.|...|...+++......        |..+|++..+..  |+ ...|..+..+|.....+.     +...+.+...
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld--P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~  408 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSE--PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELD  408 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHH
Confidence            4456677888888888654322        777777777654  54 344554444443332221     1123333333


Q ss_pred             HHHHc-CCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          185 RMEIE-NVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       185 ~m~~~-g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..... ....+...|..+--.....|++++|...+++..+..  |+...|..+-..|...|+.++|.+.+++..+-
T Consensus       409 ~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        409 NIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             HhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            32221 123455777777666667799999999999998875  68888999999999999999999999987654

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

Probab=94.78  E-value=3.7  Score=41.44  Aligned_cols=242  Identities=10%  Similarity=0.013  Sum_probs=122.7

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----ccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----CADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~  112 (323)
                      .-.+..|+..+...+++++|.++.+.-.+  ..|+.    |.  .+. ++.+..+.+-..--.++.......++.-...+
T Consensus        31 ~~a~~~Li~~~~~~~~~deai~i~~~~l~--~~P~~i~~yy~--~G~-l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~  105 (906)
T PRK14720         31 FKELDDLIDAYKSENLTDEAKDICEEHLK--EHKKSISALYI--SGI-LSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHI  105 (906)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH--hCCcceehHHH--HHH-HHHhhcchhhhhhhhhhhhcccccchhHHHHH
Confidence            34567899999999999999999995444  35555    11  111 22222211111111444444444445333333


Q ss_pred             HHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc
Q 040801          113 YHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE  189 (323)
Q Consensus       113 ~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~  189 (323)
                      +..|...+-  +...+-.+-.+|-+.|+   +..+++.+.+.. .-|..+.|.+-..|+.. +   .++|.+++..-...
T Consensus       106 ~~~i~~~~~--~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-d---L~KA~~m~~KAV~~  178 (906)
T PRK14720        106 CDKILLYGE--NKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-D---KEKAITYLKKAIYR  178 (906)
T ss_pred             HHHHHhhhh--hhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-h---HHHHHHHHHHHHHH
Confidence            344443221  22345555555545454   666666666655 33555666666666665 3   35666666555432


Q ss_pred             CC---CCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHh-CCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCch
Q 040801          190 NV---KPN--AVTLVNVLTARARARDLRTVKRVHKCVDES-GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNY  263 (323)
Q Consensus       190 g~---~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~  263 (323)
                      -+   +++  ...|..++.  +..-+++.-.++.+.+... |..--..++--|-..|-+..+++++..+++.+.+.- .-
T Consensus       179 ~i~~kq~~~~~e~W~k~~~--~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~-~~  255 (906)
T PRK14720        179 FIKKKQYVGIEEIWSKLVH--YNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHD-NK  255 (906)
T ss_pred             HHhhhcchHHHHHHHHHHh--cCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcC-Cc
Confidence            11   000  001111111  1112233333344444322 444445566667777888888888888888887652 11


Q ss_pred             hhh----HHHhhhccCCCCCcchhhhhhhCCCCc
Q 040801          264 GQW----AMSATVGPQGLVGRHSTAHQISGPCPK  293 (323)
Q Consensus       264 ~~~----~~~~~~~~~~~~~~~~~a~~l~~~~~~  293 (323)
                      +.|    .....-..++.....++++.+.+.-..
T Consensus       256 n~~a~~~l~~~y~~kY~~~~~~ee~l~~s~l~~~  289 (906)
T PRK14720        256 NNKAREELIRFYKEKYKDHSLLEDYLKMSDIGNN  289 (906)
T ss_pred             chhhHHHHHHHHHHHccCcchHHHHHHHhccccC
Confidence            222    222222455556666777777664433

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

Probab=94.77  E-value=5  Score=40.58  Aligned_cols=188  Identities=11%  Similarity=0.141  Sum_probs=112.4

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------------ccchhHHHhcccCCCCChhhHHHHHHHHHhCCCh
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------------CADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLH  106 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------------y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~  106 (323)
                      ..-+.++...+-+.+..++++..+-..-..+.              +.+....+..+++..-|.   -.+-..+..++-+
T Consensus       988 S~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAikad~trVm~YI~rLdnyDa---~~ia~iai~~~Ly 1064 (1666)
T KOG0985|consen  988 SVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIKADRTRVMEYINRLDNYDA---PDIAEIAIENQLY 1064 (1666)
T ss_pred             HHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhhcChHHHHHHHHHhccCCc---hhHHHHHhhhhHH
Confidence            44455566666666666666665532211111              111144555555442222   1223445567778


Q ss_pred             HHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          107 HEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       107 ~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                      ++|+.+|+..-     .+......||.-.....+|.++-+..      -...+|+.+-.+-...|.+   .+|++-|-+ 
T Consensus      1065 EEAF~ifkkf~-----~n~~A~~VLie~i~~ldRA~efAe~~------n~p~vWsqlakAQL~~~~v---~dAieSyik- 1129 (1666)
T KOG0985|consen 1065 EEAFAIFKKFD-----MNVSAIQVLIENIGSLDRAYEFAERC------NEPAVWSQLAKAQLQGGLV---KDAIESYIK- 1129 (1666)
T ss_pred             HHHHHHHHHhc-----ccHHHHHHHHHHhhhHHHHHHHHHhh------CChHHHHHHHHHHHhcCch---HHHHHHHHh-
Confidence            99999987653     34455666666555444433332222      2245688888888887744   667665532 


Q ss_pred             HHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          187 EIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       187 ~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                           .-|...|..+|+...+.|.+++-.+.+-...++..+|...  +.||-+|++.|++.+.++++
T Consensus      1130 -----adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi 1189 (1666)
T KOG0985|consen 1130 -----ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI 1189 (1666)
T ss_pred             -----cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh
Confidence                 2466778888888888888888888777777776666544  46778888888887776654

>PLN02789 farnesyltranstransferase

Probab=94.74  E-value=2.8  Score=37.13  Aligned_cols=197  Identities=10%  Similarity=-0.007  Sum_probs=88.2

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCcc----ch-----------hHHHhcccCC---CCChhhHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCA----DY-----------HVRLVFSQIS---NPTIYTCNSIVRGYT  101 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~----~~-----------~a~~lf~~m~---~~~~~~~~~li~~~~  101 (323)
                      +..+-..+.+.++.+.|+.+.++.++..  |+.|.    |.           ++.+.++++.   +.+...|+.---.+.
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~  117 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHH
Confidence            3455556666778889999888887653  33310    00           3333333332   334444554333333


Q ss_pred             hCCCh--HHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC---C
Q 040801          102 NKNLH--HEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWC---L  173 (323)
Q Consensus       102 ~~g~~--~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~---~  173 (323)
                      +.|+.  ++++++++.+.+..- -|..+|+..--.+.+.|+   +.+.+..+.+.+. -+...|+..--.+.+.|.   .
T Consensus       118 ~l~~~~~~~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~-~N~sAW~~R~~vl~~~~~l~~~  195 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDV-RNNSAWNQRYFVITRSPLLGGL  195 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCC-CchhHHHHHHHHHHhccccccc
Confidence            34432  445555555554321 233444443333333333   5555555555442 223334443333333211   1


Q ss_pred             C-ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc----CChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh
Q 040801          174 D-QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA----RDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK  242 (323)
Q Consensus       174 ~-~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~----~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  242 (323)
                      . ..++.++..++..... .-|...|+-+-..+...    +...+|.....+..+.+ ..+......|++.|+.
T Consensus       196 ~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        196 EAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             cccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence            0 1133444444444332 22445555555444442    22233444544443322 1234455555666654

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=94.67  E-value=4.7  Score=39.30  Aligned_cols=202  Identities=12%  Similarity=-0.011  Sum_probs=90.7

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHE  115 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  115 (323)
                      +...|+.|.-++..+|+++.+-+.|++....-+.                   ....|+.+=..|...|.-..|..+.++
T Consensus       322 d~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-------------------~~e~w~~~als~saag~~s~Av~ll~~  382 (799)
T KOG4162|consen  322 DAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-------------------EHERWYQLALSYSAAGSDSKAVNLLRE  382 (799)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-------------------hHHHHHHHHHHHHHhccchHHHHHHHh
Confidence            5556777777777888888777777777655442                   223455555555555555555555544


Q ss_pred             HHHCCCCC-CcccHHHHHHHhcchhh--------HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC--------ChHH
Q 040801          116 MIVQGLIP-DRFMFPSLFKSCADIYV--------EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD--------QPDE  178 (323)
Q Consensus       116 m~~~g~~p-~~~ty~~ll~~~~~~~~--------a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~--------~~~~  178 (323)
                      -....-.| |...+-..-+.|.+.-.        |.++........-......|-.+=-+|...-.-.        ...+
T Consensus       383 ~~~~~~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~k  462 (799)
T KOG4162|consen  383 SLKKSEQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKK  462 (799)
T ss_pred             hcccccCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHH
Confidence            32221112 22222222222222221        2222221100000111112222222222111000        1234


Q ss_pred             HHHHHHHHHHc-CCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          179 AIKIFYRMEIE-NVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       179 a~~~~~~m~~~-g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +++.+++-.+. +-.|++.-|-++-.  +..++++.|.....+..+.+-.-+...|..|.-.+...+++.+|+.+++...
T Consensus       463 slqale~av~~d~~dp~~if~lalq~--A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al  540 (799)
T KOG4162|consen  463 SLQALEEAVQFDPTDPLVIFYLALQY--AEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAAL  540 (799)
T ss_pred             HHHHHHHHHhcCCCCchHHHHHHHHH--HHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            44444444442 23444444443332  2344566666666555555444455556666666666666666666655443


Q ss_pred             C
Q 040801          258 F  258 (323)
Q Consensus       258 ~  258 (323)
                      +
T Consensus       541 ~  541 (799)
T KOG4162|consen  541 E  541 (799)
T ss_pred             H
Confidence            3

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

Probab=94.61  E-value=3.7  Score=37.90  Aligned_cols=210  Identities=11%  Similarity=0.062  Sum_probs=150.7

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---ccchhHHHhcccCCCCChhhH-HHHHHHHHhCCChHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---CADYHVRLVFSQISNPTIYTC-NSIVRGYTNKNLHHEAFLF  112 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~~a~~lf~~m~~~~~~~~-~~li~~~~~~g~~~~A~~~  112 (323)
                      --+|-.++......|+.+...++++..+.. ++|-.   |=+-            -+..| |-.+-.=....+++.+.++
T Consensus       322 YDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~R------------YIYLWinYalyeEle~ed~ertr~v  388 (677)
T KOG1915|consen  322 YDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRR------------YIYLWINYALYEELEAEDVERTRQV  388 (677)
T ss_pred             chHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHH------------HHHHHHHHHHHHHHHhhhHHHHHHH
Confidence            335566777888889999999999988765 33322   0000            00000 1122222345678899999


Q ss_pred             HHHHHHCCCCCCcccHHHHHHHhcchhh-------HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 040801          113 YHEMIVQGLIPDRFMFPSLFKSCADIYV-------EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYR  185 (323)
Q Consensus       113 ~~~m~~~g~~p~~~ty~~ll~~~~~~~~-------a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~  185 (323)
                      |..-.. =|+-...||.-+=-.|++-.-       |.+++...  -|..|-..+|-..|..=.+.+   ++|.+.++++.
T Consensus       389 yq~~l~-lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~A--IG~cPK~KlFk~YIelElqL~---efDRcRkLYEk  462 (677)
T KOG1915|consen  389 YQACLD-LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNA--IGKCPKDKLFKGYIELELQLR---EFDRCRKLYEK  462 (677)
T ss_pred             HHHHHh-hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHH--hccCCchhHHHHHHHHHHHHh---hHHHHHHHHHH
Confidence            988877 355567888877555554221       66666654  366799999999999888888   66999999999


Q ss_pred             HHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh-CCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchh
Q 040801          186 MEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES-GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYG  264 (323)
Q Consensus       186 m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~  264 (323)
                      -..-+ +-|..+|...-.-=-..|+.+.|..+|+...+. .+..-...|.+.|+-=...|.+++|..+++.+.++....-
T Consensus       463 fle~~-Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~h~k  541 (677)
T KOG1915|consen  463 FLEFS-PENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQHVK  541 (677)
T ss_pred             HHhcC-hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhcccch
Confidence            88765 347788888887778899999999999999764 3444567788888888899999999999999988754455


Q ss_pred             hh
Q 040801          265 QW  266 (323)
Q Consensus       265 ~~  266 (323)
                      .|
T Consensus       542 vW  543 (677)
T KOG1915|consen  542 VW  543 (677)
T ss_pred             HH
Confidence            77

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

Probab=94.47  E-value=0.14  Score=33.20  Aligned_cols=54  Identities=11%  Similarity=-0.053  Sum_probs=31.3

Q ss_pred             HHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          203 TARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       203 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      ..+...|++++|...|+.+.+.. +-+...+..+-..+.+.|++++|...|++..
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34555666666666666666553 2245555555566666666666666666654

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.42  E-value=1.7  Score=33.15  Aligned_cols=87  Identities=10%  Similarity=0.129  Sum_probs=46.2

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                      .-..+|..+.+.+.++....+++.+...+. .+...++.++..+++... .++.+.+..   ..+.+....++..|.+.+
T Consensus         9 ~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~~-~~ll~~l~~---~~~~yd~~~~~~~c~~~~   83 (140)
T smart00299        9 DVSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYDP-QKEIERLDN---KSNHYDIEKVGKLCEKAK   83 (140)
T ss_pred             CHHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHCH-HHHHHHHHh---ccccCCHHHHHHHHHHcC
Confidence            345567777777777777777777766653 555666666666665443 111122221   122333334555555544


Q ss_pred             CCCChHHHHHHHHHH
Q 040801          172 CLDQPDEAIKIFYRM  186 (323)
Q Consensus       172 ~~~~~~~a~~~~~~m  186 (323)
                         .++++.-++..+
T Consensus        84 ---l~~~~~~l~~k~   95 (140)
T smart00299       84 ---LYEEAVELYKKD   95 (140)
T ss_pred             ---cHHHHHHHHHhh
Confidence               335555555444

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=94.39  E-value=0.15  Score=34.43  Aligned_cols=62  Identities=11%  Similarity=0.038  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHh----CC-ccC-hhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDES----GF-WSH-VELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~-~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      .+|+.+-..|...|++++|...+++..+.    |- .|+ ..++..+-..|.+.|+.++|.+.+++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            56778888888888888888888888643    11 122 5567788888999999999999888653

...

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

Probab=94.37  E-value=0.58  Score=42.62  Aligned_cols=128  Identities=13%  Similarity=0.127  Sum_probs=95.1

Q ss_pred             cccHHHHHHHhcchhh---HHHHHHHHHHcC-CCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHH-H
Q 040801          125 RFMFPSLFKSCADIYV---EKQLHSQAIKFG-LASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTL-V  199 (323)
Q Consensus       125 ~~ty~~ll~~~~~~~~---a~~~~~~m~~~g-~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~-~  199 (323)
                      ...|...|+...+...   |..+|-...+.| +.+++++++++|.-+|..    ++.-|.++|+-=...  -||+..| +
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~----d~~ta~~ifelGl~~--f~d~~~y~~  470 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATG----DRATAYNIFELGLLK--FPDSTLYKE  470 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcC----CcchHHHHHHHHHHh--CCCchHHHH
Confidence            3456666666655444   999999999999 788999999999999875    456899999654332  3444433 4


Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCccC--hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          200 NVLTARARARDLRTVKRVHKCVDESGFWSH--VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       200 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -.+.-+.+.++-..|..+|+...++ +.-+  ...|..+|+-=...|++..+..+=+.|.+.
T Consensus       471 kyl~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         471 KYLLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH
Confidence            5677788899999999999966542 1222  567999999989999999988887777654

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

Probab=94.36  E-value=0.77  Score=44.16  Aligned_cols=153  Identities=17%  Similarity=-0.000  Sum_probs=87.0

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      .|..+|.+|+..|+.++|.++..+-.+  -+||...|..+....-...-   |+++.+..-..    -...++-++   .
T Consensus       426 mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s~yEkawElsn~~sar----A~r~~~~~~---~  496 (777)
T KOG1128|consen  426 MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPSLYEKAWELSNYISAR----AQRSLALLI---L  496 (777)
T ss_pred             HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChHHHHHHHHHhhhhhHH----HHHhhcccc---c
Confidence            455566666666666666665555544  24555555555444333222   44443332211    001111111   1


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHH
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~  247 (323)
                      +.+   +++++.+.|+.-..-+ .....||=..=.+..+.+++..+.+.|......  .|| ...||.+-.+|.+.|+..
T Consensus       497 ~~~---~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~aF~rcvtL--~Pd~~eaWnNls~ayi~~~~k~  570 (777)
T KOG1128|consen  497 SNK---DFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTL--EPDNAEAWNNLSTAYIRLKKKK  570 (777)
T ss_pred             cch---hHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHHHHHHhhc--CCCchhhhhhhhHHHHHHhhhH
Confidence            123   5566666665544321 112233333323334667888888888887764  454 678999999999999999


Q ss_pred             HHHHHHHhccCC
Q 040801          248 RAWDLFVKMLFP  259 (323)
Q Consensus       248 ~a~~~~~~m~~~  259 (323)
                      +|...+.+..+-
T Consensus       571 ra~~~l~EAlKc  582 (777)
T KOG1128|consen  571 RAFRKLKEALKC  582 (777)
T ss_pred             HHHHHHHHHhhc
Confidence            999999998765

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

Probab=94.21  E-value=3.7  Score=36.34  Aligned_cols=87  Identities=16%  Similarity=0.024  Sum_probs=63.1

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      +.+.-|.-+...|   +...|.++-++-+    -|+..-|-.-|.+++..+++++.+++-.   +   +-.+.-|.-+++
T Consensus       179 Sl~~Ti~~li~~~---~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~---s---kKsPIGyepFv~  245 (319)
T PF04840_consen  179 SLNDTIRKLIEMG---QEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAK---S---KKSPIGYEPFVE  245 (319)
T ss_pred             CHHHHHHHHHHCC---CHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHh---C---CCCCCChHHHHH
Confidence            3444455666667   4477777766553    4788888888999999999888766532   2   224577888899


Q ss_pred             HHHhcCCHHHHHHHHHhccC
Q 040801          239 AYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       239 ~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ++.+.|+..+|...+.++..
T Consensus       246 ~~~~~~~~~eA~~yI~k~~~  265 (319)
T PF04840_consen  246 ACLKYGNKKEASKYIPKIPD  265 (319)
T ss_pred             HHHHCCCHHHHHHHHHhCCh
Confidence            99999999999988888654

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

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=94.17  E-value=0.29  Score=32.08  Aligned_cols=61  Identities=20%  Similarity=-0.004  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC-CHHHHHHHHHhc
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK-FVSRAWDLFVKM  256 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g-~~~~a~~~~~~m  256 (323)
                      ..+|..+=..+...|++++|...|++..+.. +-+...|..+-.+|.+.| +.++|.+.+++.
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            3455555556666666666666666666543 223445555555666666 466666666554

...

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.10  E-value=1.2  Score=37.73  Aligned_cols=151  Identities=11%  Similarity=0.032  Sum_probs=99.5

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      +|..+-.....+.-+++|++-...       ..++++..+-..++   ..+++..+.+..-+.+....+.|...-...| 
T Consensus       155 ii~~~e~~~~~ESsv~lW~KRl~~-------Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~G-  226 (366)
T KOG2796|consen  155 ILANLEQGLAEESSIRLWRKRLGR-------VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIG-  226 (366)
T ss_pred             HHHHHHhccchhhHHHHHHHHHHH-------HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcc-
Confidence            444454445557778888765442       23444444444444   7777888888776778888888888888888 


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHH-----HHhccCChHHHHHHHHHHHHhCCccChhhHH--HHHHHHHhcCC
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLT-----ARARARDLRTVKRVHKCVDESGFWSHVELKT--TLMDAYCKCKF  245 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~-----~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~--~li~~~~~~g~  245 (323)
                        |.+.|...|++.....-..|..+++.+..     .+.-.+++..|...+.++.... .-|+...|  +|+..|  .|+
T Consensus       227 --D~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllY--lg~  301 (366)
T KOG2796|consen  227 --DIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLY--LGK  301 (366)
T ss_pred             --cHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHH--HHH
Confidence              55888888887766544556666655543     4455677777877787776543 12233333  444444  488


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      ..+|.+..+.|...
T Consensus       302 l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  302 LKDALKQLEAMVQQ  315 (366)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999999876

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.84  E-value=2  Score=32.48  Aligned_cols=138  Identities=9%  Similarity=-0.039  Sum_probs=81.2

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHH---HHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLH---NTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~---~~li~~~~~~g~~~~~  176 (323)
                      +.-.|.+++..++..+...+   -+..-||.+|-.....-+..-+++.+..-|--.|....   -.+|.+|++.|     
T Consensus        12 ~ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n-----   83 (161)
T PF09205_consen   12 RILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRN-----   83 (161)
T ss_dssp             HHHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT-----
T ss_pred             HHHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhc-----
Confidence            34468888888888887653   23345666666555555566677777766644444332   23455555544     


Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                                      -+..-+...+..+...|.-++-.++..++.+.+ ++++...-.+-.+|.+.|+..++.+++.+.
T Consensus        84 ----------------~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~A  146 (161)
T PF09205_consen   84 ----------------KLSEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEA  146 (161)
T ss_dssp             -------------------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             ----------------chHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence                            233344556777778888888888888776532 566777777788888888888888888877


Q ss_pred             cCCCCc
Q 040801          257 LFPWNN  262 (323)
Q Consensus       257 ~~~~~~  262 (323)
                      -++|..
T Consensus       147 CekG~k  152 (161)
T PF09205_consen  147 CEKGLK  152 (161)
T ss_dssp             HHTT-H
T ss_pred             HHhchH
Confidence            766643

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=93.62  E-value=1.5  Score=34.30  Aligned_cols=89  Identities=8%  Similarity=-0.007  Sum_probs=67.8

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChH-HHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAV-TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  243 (323)
                      .-+...|   ++++|.++|+-...  +.|... -|-.|=-.|-..|++++|...+........ -|+..+-.+-.+|.+.
T Consensus        43 ~~ly~~G---~l~~A~~~f~~L~~--~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~l  116 (157)
T PRK15363         43 MQLMEVK---EFAGAARLFQLLTI--YDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLAC  116 (157)
T ss_pred             HHHHHCC---CHHHHHHHHHHHHH--hCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHc
Confidence            3345667   66999999988876  345444 444455555577999999999999988763 4677888888899999


Q ss_pred             CCHHHHHHHHHhccCC
Q 040801          244 KFVSRAWDLFVKMLFP  259 (323)
Q Consensus       244 g~~~~a~~~~~~m~~~  259 (323)
                      |+.+.|.+.|+.....
T Consensus       117 G~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        117 DNVCYAIKALKAVVRI  132 (157)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999876653

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=93.58  E-value=2.7  Score=33.90  Aligned_cols=103  Identities=11%  Similarity=-0.007  Sum_probs=59.2

Q ss_pred             CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC---Ccc
Q 040801          152 GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG---FWS  228 (323)
Q Consensus       152 g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g---~~p  228 (323)
                      .+.|++..--.|-.+....|   +..+|...|.+-...-+.-|....-.+.++....+++..|...++.+-+..   -.|
T Consensus        84 ~~ApTvqnr~rLa~al~elG---r~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~p  160 (251)
T COG4700          84 AIAPTVQNRYRLANALAELG---RYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSP  160 (251)
T ss_pred             hhchhHHHHHHHHHHHHHhh---hhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCC
Confidence            44555555556666666666   446666666665443344455566666666666666666666666665432   122


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          229 HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      |  +--.+-+.|...|+...|+..|+....-
T Consensus       161 d--~~Ll~aR~laa~g~~a~Aesafe~a~~~  189 (251)
T COG4700         161 D--GHLLFARTLAAQGKYADAESAFEVAISY  189 (251)
T ss_pred             C--chHHHHHHHHhcCCchhHHHHHHHHHHh
Confidence            2  2334445666666666666666665543

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

Probab=93.54  E-value=3.8  Score=34.12  Aligned_cols=192  Identities=10%  Similarity=-0.074  Sum_probs=140.3

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCC
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL  121 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~  121 (323)
                      -|--.+-..|++..|+.-++...+..                   +-+..+|..+-..|-+.|..+.|.+-|+.-.+.  
T Consensus        40 qLal~YL~~gd~~~A~~nlekAL~~D-------------------Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--   98 (250)
T COG3063          40 QLALGYLQQGDYAQAKKNLEKALEHD-------------------PSYYLAHLVRAHYYQKLGENDLADESYRKALSL--   98 (250)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-------------------cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--
Confidence            44456777788888888888888774                   456678999999999999999999999987653  


Q ss_pred             CCCc-ccHHHHHHHhcchhh---HHHHHHHHHHc-CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChH
Q 040801          122 IPDR-FMFPSLFKSCADIYV---EKQLHSQAIKF-GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAV  196 (323)
Q Consensus       122 ~p~~-~ty~~ll~~~~~~~~---a~~~~~~m~~~-g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~  196 (323)
                      .|+. ...|..=.-+|..|+   +...|+..... ..---..+|..+.-+-.+.|   +++.|.+.|++-.+.. +-...
T Consensus        99 ~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~g---q~~~A~~~l~raL~~d-p~~~~  174 (250)
T COG3063          99 APNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAG---QFDQAEEYLKRALELD-PQFPP  174 (250)
T ss_pred             CCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcC---CchhHHHHHHHHHHhC-cCCCh
Confidence            3332 223333333455555   66666665543 22223567777777788888   6689999999887754 22445


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          197 TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       197 t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +.-.+.+.....|+...|...++.....+- ++....-..|+.--+.|+-+.+.+.=..+.+.
T Consensus       175 ~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         175 ALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            777888889999999999999999887765 78887778888888889988888776666554

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

Probab=93.41  E-value=3.6  Score=38.87  Aligned_cols=119  Identities=12%  Similarity=0.026  Sum_probs=69.3

Q ss_pred             HHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHH--HHHHHHhcCCCC
Q 040801           97 VRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNT--LINMYSSCWCLD  174 (323)
Q Consensus        97 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~--li~~~~~~g~~~  174 (323)
                      |+-+.+.|++++|......+...+ +-|...+..=+-++...+.-.+.+...+..+.   ..+++.  +=.+||.-. ++
T Consensus        19 ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~---~~~~~~~~fEKAYc~Yr-ln   93 (652)
T KOG2376|consen   19 LNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGA---LLVINSFFFEKAYCEYR-LN   93 (652)
T ss_pred             HHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcch---hhhcchhhHHHHHHHHH-cc
Confidence            455666777888888888877665 33445555556666666663344444444442   112222  356666554 22


Q ss_pred             ChHHHHHHHHHHHHcCCCCChH-HHHHHHHHHhccCChHHHHHHHHHHHHhC
Q 040801          175 QPDEAIKIFYRMEIENVKPNAV-TLVNVLTARARARDLRTVKRVHKCVDESG  225 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~g  225 (323)
                      ..|+|+..++     |..++.. +.-.=-..|-+.+++++|..++..+.+.+
T Consensus        94 k~Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~  140 (652)
T KOG2376|consen   94 KLDEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNN  140 (652)
T ss_pred             cHHHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            5677777666     3333332 44444456667788888888888776553

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

Probab=93.39  E-value=1.6  Score=39.42  Aligned_cols=99  Identities=8%  Similarity=-0.044  Sum_probs=59.9

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD  174 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~  174 (323)
                      ..+...|++++|+++|++..+..- -+...|..+-.++.+.|+   |...++...+.. ..+...|..+-.+|...|   
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg---   84 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLE---   84 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhC---
Confidence            345677888888888888876421 233445555555555666   666666665543 124555666666777777   


Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      ++++|...|++...  +.|+.......+.
T Consensus        85 ~~~eA~~~~~~al~--l~P~~~~~~~~l~  111 (356)
T PLN03088         85 EYQTAKAALEKGAS--LAPGDSRFTKLIK  111 (356)
T ss_pred             CHHHHHHHHHHHHH--hCCCCHHHHHHHH
Confidence            55777777777665  3355444444443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=93.20  E-value=1.6  Score=34.40  Aligned_cols=97  Identities=13%  Similarity=0.064  Sum_probs=55.8

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..|..+...+...|++++|+..|++.....  |+..                            ....+|..+-..|...
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~--~~~~----------------------------~~~~~~~~lg~~~~~~   85 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLE--IDPY----------------------------DRSYILYNIGLIHTSN   85 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcc--ccch----------------------------hhHHHHHHHHHHHHHc
Confidence            445666666666777777777776665431  1110                            0123566666667777


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHh-------ccCChHHHHHHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARA-------RARDLRTVKRVHKCV  221 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~-------~~~~~~~a~~~~~~m  221 (323)
                      |   ++++|++.+++..... +....++..+...+.       ..|+++.|...+++.
T Consensus        86 g---~~~eA~~~~~~Al~~~-~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033         86 G---EHTKALEYYFQALERN-PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             C---CHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            7   5577887777766532 223344555555555       666777666555544

>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=93.13  E-value=0.73  Score=30.09  Aligned_cols=65  Identities=17%  Similarity=0.033  Sum_probs=54.5

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccC-ChHHHHHHHHHHHHh
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARAR-DLRTVKRVHKCVDES  224 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~-~~~~a~~~~~~m~~~  224 (323)
                      ++.+|..+=..+...|   ++++|+..|++..+.. .-+...|..+-.++...| +.++|...++...+.
T Consensus         2 ~a~~~~~~g~~~~~~~---~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQG---DYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            4567888888899999   7799999999998865 336778888889999999 799999999988764

...

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

Probab=93.09  E-value=6.4  Score=36.19  Aligned_cols=145  Identities=11%  Similarity=0.081  Sum_probs=108.7

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCC-CCCCcccHHHHHHHhcchhh--HHHHHHH-HHHcCCCCchHHH-HHHH
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPDRFMFPSLFKSCADIYV--EKQLHSQ-AIKFGLASDSFLH-NTLI  164 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~~~ty~~ll~~~~~~~~--a~~~~~~-m~~~g~~~~~~~~-~~li  164 (323)
                      ..+|...|..-.+..-++.|..+|-+.+..| +.+++..++++|.-++....  |..+|+. |+..   ||...| +..+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d~~ta~~ifelGl~~f---~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYNIFELGLLKF---PDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHHHHHHHHHhC---CCchHHHHHHH
Confidence            3568889999999999999999999999999 78999999999999998777  8888876 3333   444333 4556


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK  242 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  242 (323)
                      .-+.+-+   +-+.|..+|+.-..+ +.-+  ...|..+|.-=..-|++..+..+-++|.+.  .|-..+...+...|+-
T Consensus       474 ~fLi~in---de~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry~i  547 (660)
T COG5107         474 LFLIRIN---DEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRYAI  547 (660)
T ss_pred             HHHHHhC---cHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHHhh
Confidence            6667766   558899999855432 2223  568999999889999999988888877664  4555566666666554


Q ss_pred             c
Q 040801          243 C  243 (323)
Q Consensus       243 ~  243 (323)
                      .
T Consensus       548 k  548 (660)
T COG5107         548 K  548 (660)
T ss_pred             h
Confidence            3

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=93.02  E-value=5.6  Score=37.44  Aligned_cols=199  Identities=14%  Similarity=0.086  Sum_probs=131.7

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCC---ccch-----------hHHHhcc---cCCCCChhhHHHHHHHHHhCCChHHH
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDP---CADY-----------HVRLVFS---QISNPTIYTCNSIVRGYTNKNLHHEA  109 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~-----------~a~~lf~---~m~~~~~~~~~~li~~~~~~g~~~~A  109 (323)
                      +-+.|++..|.-.|+..++..  |..   ..+.           .|..-+.   ++.+.|....-.|--.|...|.=.+|
T Consensus       295 lm~nG~L~~A~LafEAAVkqd--P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD--PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC--hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHH
Confidence            456688888888888877763  333   1111           2222222   22255777788888899999999999


Q ss_pred             HHHHHHHHHCCC-----CC---CcccHHHHHHHhcchhh---HHHHHHH-HHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801          110 FLFYHEMIVQGL-----IP---DRFMFPSLFKSCADIYV---EKQLHSQ-AIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       110 ~~~~~~m~~~g~-----~p---~~~ty~~ll~~~~~~~~---a~~~~~~-m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      ++.++.-.....     .+   +..+=+.  +.+.....   ..++|-+ ..+.+.++|..++..|=-.|--.|   +++
T Consensus       373 l~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~---efd  447 (579)
T KOG1125|consen  373 LKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSG---EFD  447 (579)
T ss_pred             HHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcch---HHH
Confidence            999988755321     11   1111100  12222222   4444444 456675566666666666677777   669


Q ss_pred             HHHHHHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          178 EAIKIFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      +|++-|+....  ++| |...||-|=..++...+.++|...+.+..+.  +|+ +...-.|--+|...|.+++|.+.|=.
T Consensus       448 raiDcf~~AL~--v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~  523 (579)
T KOG1125|consen  448 RAVDCFEAALQ--VKPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLE  523 (579)
T ss_pred             HHHHHHHHHHh--cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHH
Confidence            99999998876  455 6689999999999999999999999999876  454 34444455568999999999888765


Q ss_pred             c
Q 040801          256 M  256 (323)
Q Consensus       256 m  256 (323)
                      .
T Consensus       524 A  524 (579)
T KOG1125|consen  524 A  524 (579)
T ss_pred             H
Confidence            3

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

Probab=92.95  E-value=0.3  Score=33.62  Aligned_cols=75  Identities=9%  Similarity=0.023  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHcCC-CCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHH
Q 040801          141 EKQLHSQAIKFGL-ASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       141 a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      |..+++.+.+..- .++...+-.+-.+|.+.|   ++++|+++++. ...+. .+....-.+-.+|.+.|+.++|..+++
T Consensus         8 Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~---~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen    8 AIKYYEKLLELDPTNPNSAYLYNLAQCYFQQG---KYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             HHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTT---HHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCChhHHHHHHHHHHHHHCC---CHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            5555555554442 124444555778888888   66888888877 22111 122333344677778888888888876


Q ss_pred             H
Q 040801          220 C  220 (323)
Q Consensus       220 ~  220 (323)
                      +
T Consensus        83 ~   83 (84)
T PF12895_consen   83 K   83 (84)
T ss_dssp             H
T ss_pred             c
Confidence            5

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

Probab=92.95  E-value=0.73  Score=29.74  Aligned_cols=57  Identities=12%  Similarity=-0.084  Sum_probs=46.2

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      -..+.+.|   ++++|.+.|++..... .-+...+..+-..+...|++++|..+++++.+.
T Consensus         4 a~~~~~~g---~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQG---DYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCT---HHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcC---CHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34577778   7799999999998766 236678888888999999999999999998765

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.95  E-value=5.1  Score=33.90  Aligned_cols=79  Identities=14%  Similarity=0.059  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ++|+++++...+.+ +.|.++|--=+...-..|.--+|.+-+....+. +.-|...|.-|-+.|...|++++|.-.++++
T Consensus       103 ~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~  180 (289)
T KOG3060|consen  103 KEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEEL  180 (289)
T ss_pred             hhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            45555555555444 334444443333333333333333333333222 3345555555555555555555555555554


Q ss_pred             c
Q 040801          257 L  257 (323)
Q Consensus       257 ~  257 (323)
                      .
T Consensus       181 l  181 (289)
T KOG3060|consen  181 L  181 (289)
T ss_pred             H
Confidence            4

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=92.91  E-value=0.44  Score=31.59  Aligned_cols=56  Identities=13%  Similarity=-0.066  Sum_probs=34.3

Q ss_pred             HHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          203 TARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       203 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..+.+.++++.|..+++.+.+.+ +.+...|...-..|.+.|++++|.+.|+...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            34556666666666666666653 224555555666666667777776666666544

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=92.83  E-value=3.1  Score=31.03  Aligned_cols=87  Identities=14%  Similarity=0.078  Sum_probs=55.5

Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC----hhhHHHHHHH
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH----VELKTTLMDA  239 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~  239 (323)
                      ++-..|   +.++|+.+|++-...|....  ...+-.+-..+-..|+.++|..+++......  |+    ......+.-+
T Consensus        10 a~d~~G---~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen   10 AHDSLG---REEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALA   84 (120)
T ss_pred             HHHhcC---CHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHH
Confidence            344455   56888888888877775544  2355556667777888888888888776542  33    1222223346


Q ss_pred             HHhcCCHHHHHHHHHhcc
Q 040801          240 YCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       240 ~~~~g~~~~a~~~~~~m~  257 (323)
                      +...|+.++|.+.+-...
T Consensus        85 L~~~gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEAL  102 (120)
T ss_pred             HHHCCCHHHHHHHHHHHH
Confidence            677788888887775543

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=92.83  E-value=7.4  Score=37.05  Aligned_cols=138  Identities=10%  Similarity=-0.111  Sum_probs=91.6

Q ss_pred             CCChhhHHHHHHHHHhCC-----ChHHHHHHHHHHHHCCCCCCc-ccHHHHHHHhcch--------hhHHHHHHHHHH--
Q 040801           87 NPTIYTCNSIVRGYTNKN-----LHHEAFLFYHEMIVQGLIPDR-FMFPSLFKSCADI--------YVEKQLHSQAIK--  150 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g-----~~~~A~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~--------~~a~~~~~~m~~--  150 (323)
                      ..|...|...+++.....     ..++|.++|++-.+.  .||- ..|..+..++...        .+.....+...+  
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            457788999999865433     277999999998774  5654 3333332222111        111222232222  


Q ss_pred             -c-CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          151 -F-GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       151 -~-g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                       . ....+...|..+--.....|   ++++|...+++..+.+  |+...|..+-..+...|+.++|...+++....  .|
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g---~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~P  484 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKG---KTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--RP  484 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcC---CHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CC
Confidence             1 12334566776655555567   7799999999998855  78899999999999999999999999998765  45


Q ss_pred             ChhhH
Q 040801          229 HVELK  233 (323)
Q Consensus       229 ~~~~~  233 (323)
                      ...+|
T Consensus       485 ~~pt~  489 (517)
T PRK10153        485 GENTL  489 (517)
T ss_pred             CCchH
Confidence            54444

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=92.74  E-value=2  Score=36.92  Aligned_cols=98  Identities=9%  Similarity=-0.060  Sum_probs=72.5

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh----HHHHHHHHHHhccCChHHHHHHHHHHHHhCC--ccCh
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA----VTLVNVLTARARARDLRTVKRVHKCVDESGF--WSHV  230 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~--~p~~  230 (323)
                      ...|..-+..+.+.|   ++++|...|+.....-  |+.    ..+-.+-..+...|+.+.|...|+.+.+.--  ....
T Consensus       143 ~~~Y~~A~~l~~~~~---~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~  217 (263)
T PRK10803        143 NTDYNAAIALVQDKS---RQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAA  217 (263)
T ss_pred             HHHHHHHHHHHHhcC---CHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchh
Confidence            445777666666667   6799999999998753  443    4566788889999999999999999986521  1123


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..+-.+...|.+.|+.++|..++++..+.
T Consensus       218 dAl~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        218 DAMFKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            33344456677899999999999998765

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=92.61  E-value=2.8  Score=36.17  Aligned_cols=127  Identities=7%  Similarity=-0.063  Sum_probs=86.0

Q ss_pred             HHHHHHHhcchhhHHHHHHHHHH-cCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc-CCCCChHHHHHHHHHH
Q 040801          128 FPSLFKSCADIYVEKQLHSQAIK-FGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE-NVKPNAVTLVNVLTAR  205 (323)
Q Consensus       128 y~~ll~~~~~~~~a~~~~~~m~~-~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~-g~~p~~~t~~~li~~~  205 (323)
                      |..|++.-.-.-+|.++++.... ..+--|..+...|++......+. ....-.++.+-+... |-.++..+..++|+.+
T Consensus       134 Y~~LVk~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~-~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L  212 (292)
T PF13929_consen  134 YWDLVKRNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENT-KLNALYEVVDFLVSTFSKSLTRNVIISILEIL  212 (292)
T ss_pred             HHHHHHhhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhcccc-chhhHHHHHHHHHhccccCCChhHHHHHHHHH
Confidence            66665432222224444443221 23556777777777777773222 333444555555443 4578888888999999


Q ss_pred             hccCChHHHHHHHHHHHHh-CCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          206 ARARDLRTVKRVHKCVDES-GFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      +..+++.+-.++|+..... +..-|...|..+|+.....|+..-...+.++
T Consensus       213 ~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  213 AESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            9999999999988887654 6667888999999999999998888888775

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=92.60  E-value=12  Score=37.24  Aligned_cols=75  Identities=5%  Similarity=-0.059  Sum_probs=46.4

Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhc
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVG  273 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~  273 (323)
                      |...|...-.-+-..|+.+.|..+++..+         .|-++++..|-.|+.++|-++-++-.   .....+.+...|.
T Consensus       911 d~~L~~WWgqYlES~GemdaAl~~Y~~A~---------D~fs~VrI~C~qGk~~kAa~iA~esg---d~AAcYhlaR~YE  978 (1416)
T KOG3617|consen  911 DESLYSWWGQYLESVGEMDAALSFYSSAK---------DYFSMVRIKCIQGKTDKAARIAEESG---DKAACYHLARMYE  978 (1416)
T ss_pred             chHHHHHHHHHHhcccchHHHHHHHHHhh---------hhhhheeeEeeccCchHHHHHHHhcc---cHHHHHHHHHHhh
Confidence            44455555555556677777777776643         36677777788888888887766543   3445555555555


Q ss_pred             cCCCCCc
Q 040801          274 PQGLVGR  280 (323)
Q Consensus       274 ~~~~~~~  280 (323)
                      ..|+.++
T Consensus       979 n~g~v~~  985 (1416)
T KOG3617|consen  979 NDGDVVK  985 (1416)
T ss_pred             hhHHHHH
Confidence            5554433

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

Probab=92.58  E-value=9.6  Score=36.16  Aligned_cols=49  Identities=16%  Similarity=0.106  Sum_probs=30.9

Q ss_pred             ccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          207 RARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       207 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +.|+.++|..+++++.+.. ++|..+...++.+|++. ++++|..+-..+.
T Consensus       470 r~G~~~ea~s~leel~k~n-~~d~~~l~~lV~a~~~~-d~eka~~l~k~L~  518 (652)
T KOG2376|consen  470 RHGNEEEASSLLEELVKFN-PNDTDLLVQLVTAYARL-DPEKAESLSKKLP  518 (652)
T ss_pred             hcCchHHHHHHHHHHHHhC-CchHHHHHHHHHHHHhc-CHHHHHHHhhcCC
Confidence            5567777777777766643 45666666777777665 4566666655553

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.52  E-value=3.7  Score=31.22  Aligned_cols=114  Identities=17%  Similarity=0.176  Sum_probs=69.2

Q ss_pred             HHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHH
Q 040801          129 PSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTAR  205 (323)
Q Consensus       129 ~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  205 (323)
                      ..++..+...+.   ...+++.+.+.+ ..+...+|.+|..|++..    .++.++.++.      ..+......+++.|
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~----~~~ll~~l~~------~~~~yd~~~~~~~c   79 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD----PQKEIERLDN------KSNHYDIEKVGKLC   79 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC----HHHHHHHHHh------ccccCCHHHHHHHH
Confidence            344555543333   556666666665 367778888888888763    3555666553      23444555577888


Q ss_pred             hccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc-CCHHHHHHHHHhccCCCCchhhh
Q 040801          206 ARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC-KFVSRAWDLFVKMLFPWNNYGQW  266 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~~~~~~~~  266 (323)
                      -+.+-++++..++.++..         |...++.+... ++++.|.+.+.+-.    ++..|
T Consensus        80 ~~~~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~~~----~~~lw  128 (140)
T smart00299       80 EKAKLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVKQN----NPELW  128 (140)
T ss_pred             HHcCcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHhCC----CHHHH
Confidence            888877777777766432         33334444444 77787877777622    45555

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=92.49  E-value=3.4  Score=31.83  Aligned_cols=102  Identities=9%  Similarity=0.031  Sum_probs=76.8

Q ss_pred             HHHHHHHHcCCCCch--HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcC-----CCCChHHHHHHHHHHhccCC-hHHH
Q 040801          143 QLHSQAIKFGLASDS--FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIEN-----VKPNAVTLVNVLTARARARD-LRTV  214 (323)
Q Consensus       143 ~~~~~m~~~g~~~~~--~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g-----~~p~~~t~~~li~~~~~~~~-~~~a  214 (323)
                      +....|++.+..++.  ...|+++.-....+   ++...+.+++.+..-.     -.-+..+|.+++.+.++..- --.+
T Consensus        23 ~~~~y~~~~~~~~~~k~~fiN~iL~hl~~~~---nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~   99 (145)
T PF13762_consen   23 SHLPYMQEENASQSTKTIFINCILNHLASYQ---NFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTS   99 (145)
T ss_pred             HHHHHhhhcccChhHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHH
Confidence            444666777777765  44688888888777   5578888888874321     13467789999999987776 5557


Q ss_pred             HHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          215 KRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       215 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      ..+|+.|++.+.+++...|..||.+..+....+
T Consensus       100 ~~Lf~~Lk~~~~~~t~~dy~~li~~~l~g~~~~  132 (145)
T PF13762_consen  100 LTLFNFLKKNDIEFTPSDYSCLIKAALRGYFHD  132 (145)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCCc
Confidence            788999999999999999999999888764443

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

Probab=92.14  E-value=1.3  Score=39.12  Aligned_cols=52  Identities=8%  Similarity=-0.031  Sum_probs=25.9

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          197 TLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       197 t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      +.+..|.-|...|+...|.++-.+   .+ .||..-|-.-|.+|+..|++++-+.+
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~---Fk-v~dkrfw~lki~aLa~~~~w~eL~~f  230 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKE---FK-VPDKRFWWLKIKALAENKDWDELEKF  230 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHH---cC-CcHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            344444455555555554444332   22 24555555555555555555555544

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

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=92.01  E-value=2  Score=41.74  Aligned_cols=143  Identities=9%  Similarity=0.054  Sum_probs=91.1

Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCC
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~  175 (323)
                      +......+.+|+.+++.+..+...  ..-|..+-..|+..|+   |+++|-+   .|      .++--|.+|.+.|   .
T Consensus       741 aai~akew~kai~ildniqdqk~~--s~yy~~iadhyan~~dfe~ae~lf~e---~~------~~~dai~my~k~~---k  806 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNIQDQKTA--SGYYGEIADHYANKGDFEIAEELFTE---AD------LFKDAIDMYGKAG---K  806 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHhhhhccc--cccchHHHHHhccchhHHHHHHHHHh---cc------hhHHHHHHHhccc---c
Confidence            444556777888888888766442  3458888889999988   6666643   23      3677789999999   6


Q ss_pred             hHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH----------HhCCc-----------cC--hhh
Q 040801          176 PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD----------ESGFW-----------SH--VEL  232 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~----------~~g~~-----------p~--~~~  232 (323)
                      +++|.++-.+.  .|-+..++.|.+-.+-+-+.|.+.+|++++-.+.          +.|..           |+  ..|
T Consensus       807 w~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv~k~h~d~l~dt  884 (1636)
T KOG3616|consen  807 WEDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLVEKHHGDHLHDT  884 (1636)
T ss_pred             HHHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHHHHhChhhhhHH
Confidence            68998876554  4555566777777777777777777766542211          11111           11  223


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          233 KTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       233 ~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      -..+-.-|-..|++..|++-|-+..
T Consensus       885 ~~~f~~e~e~~g~lkaae~~flea~  909 (1636)
T KOG3616|consen  885 HKHFAKELEAEGDLKAAEEHFLEAG  909 (1636)
T ss_pred             HHHHHHHHHhccChhHHHHHHHhhh
Confidence            3445555666677777777665543

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=91.95  E-value=1.7  Score=28.58  Aligned_cols=62  Identities=8%  Similarity=-0.057  Sum_probs=49.2

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVEL  232 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  232 (323)
                      ..|.+.+   ++++|.++++.+...+ +.+...+...-..+.+.|++++|...++...+.+  |+...
T Consensus         3 ~~~~~~~---~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~--p~~~~   64 (73)
T PF13371_consen    3 QIYLQQE---DYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS--PDDPD   64 (73)
T ss_pred             HHHHhCC---CHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC--CCcHH
Confidence            4577777   7799999999998865 3366777778888899999999999999998764  44443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=91.92  E-value=0.95  Score=33.73  Aligned_cols=59  Identities=10%  Similarity=-0.048  Sum_probs=49.2

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHhCCccC--hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          201 VLTARARARDLRTVKRVHKCVDESGFWSH--VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       201 li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +-.++-..|+.++|..+++...+.|....  ...+-.+-..|-..|++++|..++++....
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~   67 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEE   67 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34566688999999999999999987765  445667777899999999999999998765

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=91.89  E-value=7.7  Score=33.51  Aligned_cols=102  Identities=10%  Similarity=0.122  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHHH-cCCCCChHHHHHHHHHHhc-cC-ChHHHHHHHHHHH-HhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          177 DEAIKIFYRMEI-ENVKPNAVTLVNVLTARAR-AR-DLRTVKRVHKCVD-ESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       177 ~~a~~~~~~m~~-~g~~p~~~t~~~li~~~~~-~~-~~~~a~~~~~~m~-~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      .+|+++|+.... +.+--|..+...+++.... .+ ....-.++.+.+. +.|-.++..+....|+.+++.+++.+-.++
T Consensus       145 v~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~~f  224 (292)
T PF13929_consen  145 VEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLFQF  224 (292)
T ss_pred             HHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHHHH
Confidence            578888874333 3456677777777777766 22 3334445555554 345678888899999999999999999999


Q ss_pred             HHhccCC---CCchhhh-HHHhhhccCCCC
Q 040801          253 FVKMLFP---WNNYGQW-AMSATVGPQGLV  278 (323)
Q Consensus       253 ~~~m~~~---~~~~~~~-~~~~~~~~~~~~  278 (323)
                      ++.....   +.++-+| .++..+...|+.
T Consensus       225 W~~~~~~~~~~~D~rpW~~FI~li~~sgD~  254 (292)
T PF13929_consen  225 WEQCIPNSVPGNDPRPWAEFIKLIVESGDQ  254 (292)
T ss_pred             HHHhcccCCCCCCCchHHHHHHHHHHcCCH
Confidence            9877544   5677888 777777776653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.75  E-value=17  Score=37.17  Aligned_cols=163  Identities=10%  Similarity=-0.063  Sum_probs=86.8

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHC--CCCCC--cccHHHHHHHhcchhh---HHHHHHHHHHcCCC-CchHHH----
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQ--GLIPD--RFMFPSLFKSCADIYV---EKQLHSQAIKFGLA-SDSFLH----  160 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~--g~~p~--~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~~~~~----  160 (323)
                      +..+-..+...|++++|.+.+.+....  ...+.  ..++..+-......|+   |.+.++......-. .....+    
T Consensus       576 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~  655 (903)
T PRK04841        576 LRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANA  655 (903)
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHH
Confidence            333444556668888888777765432  11121  1222223333344444   55555555332100 011111    


Q ss_pred             -HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh---HHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccC-hh
Q 040801          161 -NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA---VTLVNVLTARARARDLRTVKRVHKCVDES----GFWSH-VE  231 (323)
Q Consensus       161 -~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~---~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~  231 (323)
                       ...+..+...|   +.+.|.+++.+..........   ..+..+..++...|+.++|...++...+.    |..++ ..
T Consensus       656 ~~~~~~~~~~~g---~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~  732 (903)
T PRK04841        656 DKVRLIYWQMTG---DKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNR  732 (903)
T ss_pred             HHHHHHHHHHCC---CHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHH
Confidence             11123344455   557777776554432111111   11345666778889999998888887543    33332 23


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +...+-.+|.+.|+.++|...+.+..+
T Consensus       733 ~~~~la~a~~~~G~~~~A~~~L~~Al~  759 (903)
T PRK04841        733 NLILLNQLYWQQGRKSEAQRVLLEALK  759 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            555666788899999999888887754

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=91.45  E-value=3.8  Score=40.43  Aligned_cols=67  Identities=15%  Similarity=0.170  Sum_probs=39.7

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFV  254 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~  254 (323)
                      ++|.|+.++..-++         |=++.+..|-.|++++|-++-++   .|   |....-.|-+.|-..|++.+|..+|-
T Consensus       927 emdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~e---sg---d~AAcYhlaR~YEn~g~v~~Av~FfT  991 (1416)
T KOG3617|consen  927 EMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEE---SG---DKAACYHLARMYENDGDVVKAVKFFT  991 (1416)
T ss_pred             chHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHh---cc---cHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence            44666666654432         33456666677777777666554   22   44555566666666666666666665


Q ss_pred             hc
Q 040801          255 KM  256 (323)
Q Consensus       255 ~m  256 (323)
                      +.
T Consensus       992 rA  993 (1416)
T KOG3617|consen  992 RA  993 (1416)
T ss_pred             HH
Confidence            54

>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=91.40  E-value=0.61  Score=31.41  Aligned_cols=64  Identities=20%  Similarity=0.140  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc--CCC---CC-hHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE--NVK---PN-AVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~--g~~---p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ..+|+.+-..|...|   ++++|++.|++..+-  ...   |+ ..++..+-..+...|+.++|...+++..+
T Consensus         5 a~~~~~la~~~~~~~---~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELG---RYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            357888999999999   779999999888752  122   33 56888888999999999999999998754

...

>PLN02789 farnesyltranstransferase

Probab=91.27  E-value=10  Score=33.66  Aligned_cols=129  Identities=5%  Similarity=-0.111  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      +...++.+.+..- -+..+|+.---.+.+.|.. ..++++.+++++.+.. .-|..+|+---..+...|+++++...+++
T Consensus        91 eL~~~~~~i~~np-knyqaW~~R~~~l~~l~~~-~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~  167 (320)
T PLN02789         91 ELDFAEDVAEDNP-KNYQIWHHRRWLAEKLGPD-AANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQ  167 (320)
T ss_pred             HHHHHHHHHHHCC-cchHHhHHHHHHHHHcCch-hhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            5555555544431 1223344332223333321 1245677777776654 23667777777777777788888888888


Q ss_pred             HHHhCCccChhhHHHHHHHHHhc---CCH----HHHHHHHHh-ccCCCCchhhhHHHhhhc
Q 040801          221 VDESGFWSHVELKTTLMDAYCKC---KFV----SRAWDLFVK-MLFPWNNYGQWAMSATVG  273 (323)
Q Consensus       221 m~~~g~~p~~~~~~~li~~~~~~---g~~----~~a~~~~~~-m~~~~~~~~~~~~~~~~~  273 (323)
                      +.+.+.. +...|+..-..+.+.   |..    ++..+...+ +...+.+...|.|...+-
T Consensus       168 ~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll  227 (320)
T PLN02789        168 LLEEDVR-NNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLF  227 (320)
T ss_pred             HHHHCCC-chhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHH
Confidence            8776532 345555544444333   222    345555533 444466777785555443

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

Probab=91.23  E-value=11  Score=34.21  Aligned_cols=160  Identities=9%  Similarity=-0.025  Sum_probs=87.9

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHHhcchhhHHHHHHHHHHcC-CCCchHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKSCADIYVEKQLHSQAIKFG-LASDSFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~~~a~~~~~~m~~~g-~~~~~~~~~  161 (323)
                      .-|+.....+-+.+...|+.++|...|+.-+.-  .|+.    ..|..|+.-=++..+...+...+.... .....+.-.
T Consensus       229 r~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~ta~~wfV~  306 (564)
T KOG1174|consen  229 RCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVKYTASHWFVH  306 (564)
T ss_pred             CccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhhcchhhhhhh
Confidence            557777888888889999999999888876542  2322    234444433333333333333332221 112122112


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHH
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYC  241 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  241 (323)
                      .-+..+.|     +++.|+.+-++-.+.. .-++..|-.==+.+...+++++|.--|+...... +-+...|..|++.|.
T Consensus       307 ~~~l~~~K-----~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYL  379 (564)
T KOG1174|consen  307 AQLLYDEK-----KFERALNFVEKCIDSE-PRNHEALILKGRLLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYL  379 (564)
T ss_pred             hhhhhhhh-----hHHHHHHHHHHHhccC-cccchHHHhccHHHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHH
Confidence            22222233     5567777666555422 1122222111144556777777777777765542 235677888888888


Q ss_pred             hcCCHHHHHHHHHh
Q 040801          242 KCKFVSRAWDLFVK  255 (323)
Q Consensus       242 ~~g~~~~a~~~~~~  255 (323)
                      ..|++.+|...-++
T Consensus       380 A~~~~kEA~~~An~  393 (564)
T KOG1174|consen  380 AQKRFKEANALANW  393 (564)
T ss_pred             hhchHHHHHHHHHH
Confidence            88888887765544

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

Probab=91.11  E-value=11  Score=38.25  Aligned_cols=82  Identities=15%  Similarity=0.210  Sum_probs=64.9

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh-C----------CccChhhHHHHHHHHHhc
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES-G----------FWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~-g----------~~p~~~~~~~li~~~~~~  243 (323)
                      .++++++.++.|...+++-|..+.-.+..-|+..=..+...++|+..+.. |          +.-|+.+.--.|.+-|+.
T Consensus       658 sve~s~eclkaml~~NirqNlQi~VQvatky~eqlg~~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA~kt  737 (1666)
T KOG0985|consen  658 SVEDSLECLKAMLSANIRQNLQIVVQVATKYHEQLGAQALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAACKT  737 (1666)
T ss_pred             CHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCHHHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHHHhh
Confidence            67899999999999999989888888888887776667777777766542 2          445666667789999999


Q ss_pred             CCHHHHHHHHHhc
Q 040801          244 KFVSRAWDLFVKM  256 (323)
Q Consensus       244 g~~~~a~~~~~~m  256 (323)
                      |++.+.+++-++-
T Consensus       738 ~QikEvERicres  750 (1666)
T KOG0985|consen  738 GQIKEVERICRES  750 (1666)
T ss_pred             ccHHHHHHHHhcc
Confidence            9999999987764

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

Probab=90.96  E-value=12  Score=34.05  Aligned_cols=208  Identities=13%  Similarity=-0.017  Sum_probs=105.3

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC------ccch------------hHHHhcccCCCCChhhHHHHHHHHHh
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP------CADY------------HVRLVFSQISNPTIYTCNSIVRGYTN  102 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~------y~~~------------~a~~lf~~m~~~~~~~~~~li~~~~~  102 (323)
                      ..+-..+...|+.+.|.-.|+...-  +.|..      |+-.            ....+|..- +.....|-.-......
T Consensus       236 ~~lak~~~~~Gdn~~a~~~Fe~~~~--~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~  312 (564)
T KOG1174|consen  236 MALGKCLYYNGDYFQAEDIFSSTLC--ANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYD  312 (564)
T ss_pred             HHHhhhhhhhcCchHHHHHHHHHhh--CChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhh
Confidence            4455555566788888877776543  33433      2222            233333321 2233344444455556


Q ss_pred             CCChHHHHHHHHHHHHCC--CCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCC-CchHHHHHHHHHHHhcCCCCChHHH
Q 040801          103 KNLHHEAFLFYHEMIVQG--LIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLA-SDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g--~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      ..+++.|+.+-++-++..  ..|-...=..++....+...|.-.|.....  +. -+..+|-.|+++|...|..   .+|
T Consensus       313 ~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~--Lap~rL~~Y~GL~hsYLA~~~~---kEA  387 (564)
T KOG1174|consen  313 EKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQM--LAPYRLEIYRGLFHSYLAQKRF---KEA  387 (564)
T ss_pred             hhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhhchH---HHH
Confidence            677777777776655421  111111111222222222224444444333  33 3567888888888888844   454


Q ss_pred             HHHHHHHHHc----------------------------------CCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          180 IKIFYRMEIE----------------------------------NVKPNA-VTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       180 ~~~~~~m~~~----------------------------------g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .-+-++-...                                  .++|+- -..+.+.+-|...|..+.+..+++.-...
T Consensus       388 ~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~  467 (564)
T KOG1174|consen  388 NALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII  467 (564)
T ss_pred             HHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh
Confidence            4333222110                                  123332 23344445555556666666666554443


Q ss_pred             CCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          225 GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       225 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                        .||....+.|-+.+...+.+.+|.+-|....+
T Consensus       468 --~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  468 --FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             --ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence              46666666666666666666666666665544

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=90.36  E-value=3.5  Score=35.61  Aligned_cols=82  Identities=16%  Similarity=0.012  Sum_probs=57.0

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                      ++++|++.|.+-..-. .-|.+-|..=-.+|++.|..+.|.+--+...+.  .| ....|..|=.+|...|++++|.+.|
T Consensus        96 ~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~~A~~ay  172 (304)
T KOG0553|consen   96 DYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYEEAIEAY  172 (304)
T ss_pred             hHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHHHHHHHH
Confidence            6678888887776633 236677777788888888887776655554443  23 3566777777888888888888888


Q ss_pred             HhccCC
Q 040801          254 VKMLFP  259 (323)
Q Consensus       254 ~~m~~~  259 (323)
                      ++-.+-
T Consensus       173 kKaLel  178 (304)
T KOG0553|consen  173 KKALEL  178 (304)
T ss_pred             Hhhhcc
Confidence            776653

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=90.16  E-value=0.62  Score=27.59  Aligned_cols=35  Identities=20%  Similarity=0.144  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW  266 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~  266 (323)
                      ++..+-..|.+.|++++|.++|++..+. +.++..|
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~   38 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAW   38 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHH
Confidence            4566677777777777777777777654 3344444

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

Probab=89.77  E-value=5.7  Score=39.43  Aligned_cols=116  Identities=17%  Similarity=0.117  Sum_probs=75.4

Q ss_pred             HHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          149 IKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       149 ~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                      ++.+-.+.+.++.+|+.  .+.|   ..++|..+++.....+.. |..|..++-..|-..++.+++..+|++..+.  .|
T Consensus        37 kk~Pn~~~a~vLkaLsl--~r~g---k~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P  108 (932)
T KOG2053|consen   37 KKHPNALYAKVLKALSL--FRLG---KGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YP  108 (932)
T ss_pred             HHCCCcHHHHHHHHHHH--HHhc---CchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CC
Confidence            44444444555555542  3444   447888888777665544 7788888888888888888888888887765  46


Q ss_pred             ChhhHHHHHHHHHhcCCHHH----HHHHHHhccCCCCchhhhHHHhhhcc
Q 040801          229 HVELKTTLMDAYCKCKFVSR----AWDLFVKMLFPWNNYGQWAMSATVGP  274 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~----a~~~~~~m~~~~~~~~~~~~~~~~~~  274 (323)
                      +......+.-+|+|.+.+.+    |.+++....++  ..-.|++...+-.
T Consensus       109 ~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk~--~yyfWsV~Slilq  156 (932)
T KOG2053|consen  109 SEELLYHLFMAYVREKSYKKQQKAALQLYKNFPKR--AYYFWSVISLILQ  156 (932)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcc--cchHHHHHHHHHH
Confidence            67777777778888877655    44444444443  4455655544433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=89.39  E-value=2.3  Score=39.09  Aligned_cols=95  Identities=11%  Similarity=-0.063  Sum_probs=65.2

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh----HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA----VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE  231 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  231 (323)
                      +...|+.+-.+|.+.|   ++++|+..|++-.+  +.|+.    .+|..+-.+|...|+.++|...+++..+.+ .+   
T Consensus        74 ~a~a~~NLG~AL~~lG---ryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALels-n~---  144 (453)
T PLN03098         74 TAEDAVNLGLSLFSKG---RVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDY-NL---  144 (453)
T ss_pred             CHHHHHHHHHHHHHcC---CHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc-ch---
Confidence            4667888888898888   66899999988766  35664    358888889999999999999999988762 11   


Q ss_pred             hHHHHHH--HHHhcCCHHHHHHHHHhccCC
Q 040801          232 LKTTLMD--AYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       232 ~~~~li~--~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .|..+..  .+....+.++..+++++..+-
T Consensus       145 ~f~~i~~DpdL~plR~~pef~eLlee~rk~  174 (453)
T PLN03098        145 KFSTILNDPDLAPFRASPEFKELQEEARKG  174 (453)
T ss_pred             hHHHHHhCcchhhhcccHHHHHHHHHHHHh
Confidence            2322221  122333445667777766554

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=89.27  E-value=20  Score=33.94  Aligned_cols=82  Identities=7%  Similarity=-0.055  Sum_probs=56.9

Q ss_pred             hHHHHHHHHHHHH-cCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          176 PDEAIKIFYRMEI-ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       176 ~~~a~~~~~~m~~-~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                      ..+..++|-++.. .+.++|....+.|=--|--.|++++|...|+...+.  +| |..+||-|=-.++...+.++|...|
T Consensus       410 l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v--~Pnd~~lWNRLGAtLAN~~~s~EAIsAY  487 (579)
T KOG1125|consen  410 LAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQV--KPNDYLLWNRLGATLANGNRSEEAISAY  487 (579)
T ss_pred             HHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhc--CCchHHHHHHhhHHhcCCcccHHHHHHH
Confidence            3455566666654 342344444444444455678888888888888765  44 6778888888888888999999999


Q ss_pred             HhccCC
Q 040801          254 VKMLFP  259 (323)
Q Consensus       254 ~~m~~~  259 (323)
                      ++..+-
T Consensus       488 ~rALqL  493 (579)
T KOG1125|consen  488 NRALQL  493 (579)
T ss_pred             HHHHhc
Confidence            888764

>PRK04841 transcriptional regulator MalT; Provisional

Probab=89.20  E-value=16  Score=37.32  Aligned_cols=156  Identities=8%  Similarity=-0.115  Sum_probs=95.6

Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHHhcchhh---HHHHHHHHHHc----CC-CCchHHHHHHHHH
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKSCADIYV---EKQLHSQAIKF----GL-ASDSFLHNTLINM  166 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~-~~~~~~~~~li~~  166 (323)
                      .+...|++++|...+++-.+.--..+.    .+.+.+-..+...|+   +...++.....    |- .....++..+-..
T Consensus       461 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        461 VAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            456789999999999887653111111    122333333444555   66666665432    21 1123445556667


Q ss_pred             HHhcCCCCChHHHHHHHHHHHH----cCCC--C-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh--CCcc--ChhhHHH
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEI----ENVK--P-NAVTLVNVLTARARARDLRTVKRVHKCVDES--GFWS--HVELKTT  235 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~----~g~~--p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p--~~~~~~~  235 (323)
                      +...|   ++++|.+.+++...    .|..  + ....+..+-..+...|++++|...+.+....  ...+  ....+..
T Consensus       541 ~~~~G---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  617 (903)
T PRK04841        541 LFAQG---FLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAM  617 (903)
T ss_pred             HHHCC---CHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHH
Confidence            78888   66899998877654    2211  1 2234445556677789999999998887543  1112  2334445


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcc
Q 040801          236 LMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +...+...|+.++|.+.+++..
T Consensus       618 la~~~~~~G~~~~A~~~l~~a~  639 (903)
T PRK04841        618 LAKISLARGDLDNARRYLNRLE  639 (903)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHH
Confidence            6667889999999999888763

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=89.10  E-value=5.2  Score=36.84  Aligned_cols=96  Identities=9%  Similarity=-0.103  Sum_probs=63.3

Q ss_pred             CCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCch----HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh
Q 040801          123 PDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDS----FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA  195 (323)
Q Consensus       123 p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~----~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~  195 (323)
                      .+...++.+-.+|.+.|+   |...++...+.  .|+.    .+|..+-.+|.+.|   +.++|++.+++..+.+ .|  
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LG---r~dEAla~LrrALels-n~--  144 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYRE---EGKKAADCLRTALRDY-NL--  144 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhc-ch--
Confidence            345677777778888888   77777777775  4764    46999999999999   6699999999988742 11  


Q ss_pred             HHHHHHHH--HHhccCChHHHHHHHHHHHHhCCc
Q 040801          196 VTLVNVLT--ARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       196 ~t~~~li~--~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                       -|..+..  .+...++.....++++.+.+.|..
T Consensus       145 -~f~~i~~DpdL~plR~~pef~eLlee~rk~G~~  177 (453)
T PLN03098        145 -KFSTILNDPDLAPFRASPEFKELQEEARKGGED  177 (453)
T ss_pred             -hHHHHHhCcchhhhcccHHHHHHHHHHHHhCCc
Confidence             2322221  111223444666677777666643

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.04  E-value=16  Score=32.59  Aligned_cols=180  Identities=16%  Similarity=0.091  Sum_probs=106.9

Q ss_pred             hHHHhcccCCCCChhhHHHHHHH--HHhCCC-------hHHHHHHHHHHHHCCCC----CCcccHHHHHHHhcchhhHHH
Q 040801           77 HVRLVFSQISNPTIYTCNSIVRG--YTNKNL-------HHEAFLFYHEMIVQGLI----PDRFMFPSLFKSCADIYVEKQ  143 (323)
Q Consensus        77 ~a~~lf~~m~~~~~~~~~~li~~--~~~~g~-------~~~A~~~~~~m~~~g~~----p~~~ty~~ll~~~~~~~~a~~  143 (323)
                      +|..+.++..+.++.-|  ++++  ++..|+       ..-|.++|.-.-+++..    |...+..+.+-.+-+-.++.-
T Consensus       303 eA~~L~Kdl~PttP~Ey--ilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~  380 (557)
T KOG3785|consen  303 EAISLCKDLDPTTPYEY--ILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLT  380 (557)
T ss_pred             HHHHHHhhcCCCChHHH--HHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHH
Confidence            77777777765444333  3332  223332       55667777555455543    333333333333333333444


Q ss_pred             HHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHH-HHHhccCChHHHHHHHHHHH
Q 040801          144 LHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVL-TARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       144 ~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~~~~~~a~~~~~~m~  222 (323)
                      .+...+..=..-|.+.|| +-.+++..|   ++.+|.++|-......++ |..+|.+++ ++|.+.+....|+.++=.+ 
T Consensus       381 YlnSi~sYF~NdD~Fn~N-~AQAk~atg---ny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~-  454 (557)
T KOG3785|consen  381 YLNSIESYFTNDDDFNLN-LAQAKLATG---NYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKT-  454 (557)
T ss_pred             HHHHHHHHhcCcchhhhH-HHHHHHHhc---ChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhc-
Confidence            444444433344455444 678888888   668999999776544444 667777665 6777888888876665444 


Q ss_pred             HhCCccChhhHHHH-HHHHHhcCCHHHHHHHHHhccCCCCchhhh
Q 040801          223 ESGFWSHVELKTTL-MDAYCKCKFVSRAWDLFVKMLFPWNNYGQW  266 (323)
Q Consensus       223 ~~g~~p~~~~~~~l-i~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  266 (323)
                        .-..+....-.+ ..-|-++|.+=-|-+.|+++......|..|
T Consensus       455 --~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~pEnW  497 (557)
T KOG3785|consen  455 --NTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTPENW  497 (557)
T ss_pred             --CCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCcccc
Confidence              323344444444 446888999988888998887764456666

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=88.90  E-value=10  Score=30.02  Aligned_cols=49  Identities=14%  Similarity=0.186  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD  210 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~  210 (323)
                      ..+..+-..|.+.|   ++++|.+.+++..... .-+...+..+-..+...|+
T Consensus        73 ~~~~~la~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~  121 (172)
T PRK02603         73 YILYNMGIIYASNG---EHDKALEYYHQALELN-PKQPSALNNIAVIYHKRGE  121 (172)
T ss_pred             HHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCC
Confidence            45666666777777   5577777777766532 1134445455555555444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.78  E-value=1.3  Score=38.52  Aligned_cols=48  Identities=15%  Similarity=0.172  Sum_probs=25.1

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      ++++++-++..-.+-|+-||-+|++.+|+.+.+.+++..|.++...|.
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            344555555555555555555555555555555555555555544443

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.51  E-value=15  Score=31.47  Aligned_cols=99  Identities=8%  Similarity=-0.030  Sum_probs=70.1

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      .+.++++..+.-.|   .+.-.+..+++.....-+-+..-...|.+.-.+.||++.|...|++..+..=+.|..+.+.++
T Consensus       178 ~Vmy~~~~~llG~k---Ey~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V  254 (366)
T KOG2796|consen  178 RVMYSMANCLLGMK---EYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMV  254 (366)
T ss_pred             HHHHHHHHHHhcch---hhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHH
Confidence            45566666666666   345677777777776656677788888888888889888888888876544445555555544


Q ss_pred             H-----HHHhcCCHHHHHHHHHhccCC
Q 040801          238 D-----AYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       238 ~-----~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .     .|...++..+|...+.++.++
T Consensus       255 ~~n~a~i~lg~nn~a~a~r~~~~i~~~  281 (366)
T KOG2796|consen  255 LMNSAFLHLGQNNFAEAHRFFTEILRM  281 (366)
T ss_pred             HhhhhhheecccchHHHHHHHhhcccc
Confidence            3     366677888888888887765

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

Probab=88.22  E-value=6.8  Score=33.85  Aligned_cols=78  Identities=13%  Similarity=0.110  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH-----hCCccChhh
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE-----SGFWSHVEL  232 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~-----~g~~p~~~~  232 (323)
                      .++..++..+..+|   +.+.+.+.+++..... .-|...|..+|.+|.+.|+...|.+.++.+.+     .|+.|...+
T Consensus       154 ~~l~~lae~~~~~~---~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~  229 (280)
T COG3629         154 KALTKLAEALIACG---RADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPEL  229 (280)
T ss_pred             HHHHHHHHHHHhcc---cHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHH
Confidence            44566666666666   4466666666666544 34666777777777777777777766666643     466666665


Q ss_pred             HHHHHHH
Q 040801          233 KTTLMDA  239 (323)
Q Consensus       233 ~~~li~~  239 (323)
                      .......
T Consensus       230 ~~~y~~~  236 (280)
T COG3629         230 RALYEEI  236 (280)
T ss_pred             HHHHHHH
Confidence            5544444

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

Probab=88.03  E-value=26  Score=33.76  Aligned_cols=216  Identities=8%  Similarity=-0.037  Sum_probs=116.0

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcC-CCCC--ccch-----------------hHHHhcccCC--CCChhhH-
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSL-FFDP--CADY-----------------HVRLVFSQIS--NPTIYTC-   93 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~-~~~~--y~~~-----------------~a~~lf~~m~--~~~~~~~-   93 (323)
                      ...|-.+..+..-.|+...|..+.++..+... .|+.  |.+.                 .|.+-+....  ..|-..| 
T Consensus       143 ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~  222 (700)
T KOG1156|consen  143 RASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFE  222 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHh
Confidence            44666777777778999999999999998764 3333  2222                 3444333332  1222222 


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhc-chhh---HH-HHHHHHHHc---CCCCc---------
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCA-DIYV---EK-QLHSQAIKF---GLASD---------  156 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~-~~~~---a~-~~~~~m~~~---g~~~~---------  156 (323)
                      .+--.-+.+.+++++|..+|..+...  .||..-|...+..+. +..+   +. .+++...+.   .-.|-         
T Consensus       223 e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~  300 (700)
T KOG1156|consen  223 ETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNG  300 (700)
T ss_pred             hhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCc
Confidence            23344667889999999999998775  477766666554444 3333   22 334433322   11111         


Q ss_pred             -------------------hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH--cCC------------CCChHHHH--HH
Q 040801          157 -------------------SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI--ENV------------KPNAVTLV--NV  201 (323)
Q Consensus       157 -------------------~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~--~g~------------~p~~~t~~--~l  201 (323)
                                         ..++..+.+-|-.-.   ..+-..++.-++..  .|-            .|+...|+  -+
T Consensus       301 eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~---k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~l  377 (700)
T KOG1156|consen  301 EELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPE---KVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFL  377 (700)
T ss_pred             chhHHHHHHHHHHHhhcCCCchhhhhHHHHhchh---HhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHH
Confidence                               112222222222111   00111111111111  111            34444333  35


Q ss_pred             HHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          202 LTARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       202 i~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +..+-+.|+++.|+..++....+  .|+ +..|-.=-+.+.-+|++++|..++++..+-
T Consensus       378 aqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~el  434 (700)
T KOG1156|consen  378 AQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQEL  434 (700)
T ss_pred             HHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhc
Confidence            56667778888888888876665  333 223334446777888888888888877654

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=87.48  E-value=18  Score=31.30  Aligned_cols=208  Identities=11%  Similarity=0.078  Sum_probs=118.1

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---ccch--hHHHhcccCC-CCChhhHHHHHHHHHhCCChHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---CADY--HVRLVFSQIS-NPTIYTCNSIVRGYTNKNLHHEAFLFY  113 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~--~a~~lf~~m~-~~~~~~~~~li~~~~~~g~~~~A~~~~  113 (323)
                      |.---..+...++++.|...|....+.-...+.   -++.  .|..++.+.. ..-+..|.-.+..|...|++..|-+++
T Consensus        38 y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~  117 (282)
T PF14938_consen   38 YEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKGDPDEAIECYEKAIEIYREAGRFSQAAKCL  117 (282)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHCT-HHHHHHHH
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            444555666677888888888877654432222   1111  5666666653 112355777888888888888888777


Q ss_pred             HHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHH----HcCCCC--chHHHHHHHHHHHhcCCCCChHHHHHHHHHHH
Q 040801          114 HEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAI----KFGLAS--DSFLHNTLINMYSSCWCLDQPDEAIKIFYRME  187 (323)
Q Consensus       114 ~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~----~~g~~~--~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~  187 (323)
                      .++-+-=. ....-+..          |.+.|+...    ..| .+  -..++..+...+.+.|   ++++|.++|++..
T Consensus       118 ~~lA~~ye-~~~~d~e~----------Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~---~y~~A~~~~e~~~  182 (282)
T PF14938_consen  118 KELAEIYE-EQLGDYEK----------AIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLG---RYEEAIEIYEEVA  182 (282)
T ss_dssp             HHHHHHHC-CTT--HHH----------HHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHH
T ss_pred             HHHHHHHH-HHcCCHHH----------HHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhC---CHHHHHHHHHHHH
Confidence            77633100 00011222          444444332    223 22  2455677888899988   7799999999987


Q ss_pred             HcCC-----CCChH-HHHHHHHHHhccCChHHHHHHHHHHHHh--CCccC--hhhHHHHHHHHHhc--CCHHHHHHHHHh
Q 040801          188 IENV-----KPNAV-TLVNVLTARARARDLRTVKRVHKCVDES--GFWSH--VELKTTLMDAYCKC--KFVSRAWDLFVK  255 (323)
Q Consensus       188 ~~g~-----~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~--~~~~~~li~~~~~~--g~~~~a~~~~~~  255 (323)
                      ....     +.+.. .|-..+-.+...||...|...+++..+.  ++..+  ..+...||++|-..  ..+.+|..-|+.
T Consensus       183 ~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~  262 (282)
T PF14938_consen  183 KKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDS  262 (282)
T ss_dssp             HTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTT
T ss_pred             HHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcc
Confidence            6432     22332 2333344556678999999999998754  44433  34566777776543  345566665655


Q ss_pred             ccCCCCchhhh
Q 040801          256 MLFPWNNYGQW  266 (323)
Q Consensus       256 m~~~~~~~~~~  266 (323)
                      +.    ..+.|
T Consensus       263 ~~----~ld~w  269 (282)
T PF14938_consen  263 IS----RLDNW  269 (282)
T ss_dssp             SS-------HH
T ss_pred             cC----ccHHH
Confidence            55    45667

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=87.25  E-value=24  Score=34.19  Aligned_cols=207  Identities=10%  Similarity=0.035  Sum_probs=105.5

Q ss_pred             hhhHHHhhcCCCchHHHHHH--HHHHHhcCCCCC--------ccch--hHHHhcccCCCC--ChhhHHH-----HHHHHH
Q 040801           41 HFCLVSLEKCSTMRELKQIH--AQMLRTSLFFDP--------CADY--HVRLVFSQISNP--TIYTCNS-----IVRGYT  101 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~--~~m~~~~~~~~~--------y~~~--~a~~lf~~m~~~--~~~~~~~-----li~~~~  101 (323)
                      ++-=.++.+.++....+-|.  ++|+++|-.|+.        |..-  +|.++|.+-...  -...|+-     ..+-|.
T Consensus       602 ~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iLlA~~~Ay~gKF~EAAklFk~~G~enRAlEmyTDlRMFD~aQE~~  681 (1081)
T KOG1538|consen  602 ETARKAYIRVRDLRYLELISELEERKKRGETPNDLLLADVFAYQGKFHEAAKLFKRSGHENRALEMYTDLRMFDYAQEFL  681 (1081)
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHHHHHHHHhhhhHHHHHHHHHHcCchhhHHHHHHHHHHHHHHHHHh
Confidence            44445666666655444443  467788888887        5444  888888765422  1122221     123333


Q ss_pred             hCCChHHHHHHHHHHHH--CCCCCCcccHHHHHHHhcchhhH-----HH-HHHHHHHcCCCCchHHHHHHHHHHHhcCCC
Q 040801          102 NKNLHHEAFLFYHEMIV--QGLIPDRFMFPSLFKSCADIYVE-----KQ-LHSQAIKFGLASDSFLHNTLINMYSSCWCL  173 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~--~g~~p~~~ty~~ll~~~~~~~~a-----~~-~~~~m~~~g~~~~~~~~~~li~~~~~~g~~  173 (323)
                      ..|..++-..+.++--+  ..++-- ..-..++-..+...+|     .. ..+.+.+-+.+.|..--.+|...-.....+
T Consensus       682 ~~g~~~eKKmL~RKRA~WAr~~keP-kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l  760 (1081)
T KOG1538|consen  682 GSGDPKEKKMLIRKRADWARNIKEP-KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKL  760 (1081)
T ss_pred             hcCChHHHHHHHHHHHHHhhhcCCc-HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhc
Confidence            44444333333322111  111111 1111122111211111     11 112223333334433333333222222222


Q ss_pred             CChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh-----------hHHHHHHHHHh
Q 040801          174 DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE-----------LKTTLMDAYCK  242 (323)
Q Consensus       174 ~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-----------~~~~li~~~~~  242 (323)
                      +.+.-|-++|..|-+.         .++.+.....+++++|..+-+..-+.  .||+.           -|.---.+|.|
T Consensus       761 ~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLAE~DrFeEAqkAfhk  829 (1081)
T KOG1538|consen  761 DSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLAENDRFEEAQKAFHK  829 (1081)
T ss_pred             cccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhhhhhhHHHHHHHHHH
Confidence            2456788888887542         25677788889999988877665432  33332           24455578999


Q ss_pred             cCCHHHHHHHHHhccCC
Q 040801          243 CKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~~  259 (323)
                      +|+-.+|..+++++...
T Consensus       830 AGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  830 AGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hcchHHHHHHHHHhhhh
Confidence            99999999999998654

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=87.07  E-value=18  Score=30.71  Aligned_cols=55  Identities=7%  Similarity=-0.040  Sum_probs=32.3

Q ss_pred             HHHHhccCChHHHHHHHHHHHHh--CCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          202 LTARARARDLRTVKRVHKCVDES--GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       202 i~~~~~~~~~~~a~~~~~~m~~~--g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      .+-|.+.|.+..|..=++.+.+.  +-+......-.++++|.+.|..++|..+...+
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l  238 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKII  238 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            33455666666666666666653  22233444556666777777777776665544

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

Probab=86.93  E-value=2.7  Score=36.25  Aligned_cols=71  Identities=14%  Similarity=-0.069  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-----CCchhhh
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-----WNNYGQW  266 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~  266 (323)
                      ..++..+++.+...|+.+.+...++++.+.. +-+...|..+|.+|.+.|+...|...++.+.+.     |+.|..-
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~  228 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPE  228 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHH
Confidence            4567788889999999999999999998864 458899999999999999999999999988652     5555443

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

Probab=86.90  E-value=31  Score=33.33  Aligned_cols=102  Identities=10%  Similarity=-0.013  Sum_probs=76.8

Q ss_pred             CCchHHHH--HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChH-HHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          154 ASDSFLHN--TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAV-TLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       154 ~~~~~~~~--~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      .|.+..|.  .++..|=+.|   +++.|...++.-.+  -.|+.+ -|.+=-+.+...|+++.|...+++..+.. .+|.
T Consensus       366 ~PttllWt~y~laqh~D~~g---~~~~A~~yId~AId--HTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD-~aDR  439 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLG---DYEVALEYIDLAID--HTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELD-TADR  439 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcc---cHHHHHHHHHHHhc--cCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhcc-chhH
Confidence            45555554  5777788888   67999999988765  356553 55556688999999999999999998765 3555


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCCCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFPWN  261 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  261 (323)
                      ..-.-=..-..+++++++|.++.....+.|.
T Consensus       440 ~INsKcAKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  440 AINSKCAKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             HHHHHHHHHHHHccccHHHHHHHHHhhhccc
Confidence            5544555667789999999999998887753

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=86.85  E-value=16  Score=31.57  Aligned_cols=28  Identities=18%  Similarity=0.223  Sum_probs=14.7

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      |...|-.|=..|...|+++.|..-|.+-
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A  182 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNA  182 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHH
Confidence            4455555555555555555555555444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.80  E-value=6.2  Score=34.49  Aligned_cols=100  Identities=9%  Similarity=0.115  Sum_probs=72.6

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC---CCCCcccHHHHHHHhcchhh--HHHHHHHHHHcCCCCchHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG---LIPDRFMFPSLFKSCADIYV--EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g---~~p~~~ty~~ll~~~~~~~~--a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      .....+-..++..-....+++.+..++-.++.+-   ..|+...|. +++.|-+...  +.-++..=.+.|+-||.++++
T Consensus        61 ~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~-~irlllky~pq~~i~~l~npIqYGiF~dqf~~c  139 (418)
T KOG4570|consen   61 PVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHT-WIRLLLKYDPQKAIYTLVNPIQYGIFPDQFTFC  139 (418)
T ss_pred             CcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHH-HHHHHHccChHHHHHHHhCcchhccccchhhHH
Confidence            4455555666776667788999999888887642   445554443 3444444333  666777777899999999999


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcC
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIEN  190 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g  190 (323)
                      .+|+.+.+.+   +..+|.++..+|....
T Consensus       140 ~l~D~flk~~---n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  140 LLMDSFLKKE---NYKDAASVVTEVMMQE  165 (418)
T ss_pred             HHHHHHHhcc---cHHHHHHHHHHHHHHH
Confidence            9999999999   6688888888877654

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.69  E-value=19  Score=30.65  Aligned_cols=187  Identities=9%  Similarity=-0.026  Sum_probs=128.2

Q ss_pred             CCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCCh-hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc----
Q 040801           51 STMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTI-YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR----  125 (323)
Q Consensus        51 ~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~-~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~----  125 (323)
                      ++++...+++.++....-.-              ...++. ..|--++-+....|+.+.|...++.+..+-  |.+    
T Consensus        26 rnseevv~l~~~~~~~~k~~--------------~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~   89 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSG--------------ALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVG   89 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhc--------------ccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHH
Confidence            35677777777776322100              003333 346667778889999999999999998763  544    


Q ss_pred             ccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHH
Q 040801          126 FMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTAR  205 (323)
Q Consensus       126 ~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~  205 (323)
                      ..+..++.+-..-++|.++++.+.+.. .-|.++|--=+...-..|   ..-+|++-+.+..+. +.-|...|--+-+.|
T Consensus        90 ~lkam~lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~G---K~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY  164 (289)
T KOG3060|consen   90 KLKAMLLEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQG---KNLEAIKELNEYLDK-FMNDQEAWHELAEIY  164 (289)
T ss_pred             HHHHHHHHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcC---CcHHHHHHHHHHHHH-hcCcHHHHHHHHHHH
Confidence            334556677666666999999998877 456777765555555556   335788877777654 467999999999999


Q ss_pred             hccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC---CHHHHHHHHHhccCC
Q 040801          206 ARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK---FVSRAWDLFVKMLFP  259 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~m~~~  259 (323)
                      ...|++++|...++++.-.. +.+..-+..+-+.+--.|   +++-|.+.+..-.+-
T Consensus       165 ~~~~~f~kA~fClEE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  165 LSEGDFEKAAFCLEELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HhHhHHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            99999999999999997652 223444455555443333   566677777766553

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=86.69  E-value=24  Score=31.93  Aligned_cols=168  Identities=11%  Similarity=0.033  Sum_probs=99.8

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCC-C-CCC-cccHHHHHHHhcc---hhh---HHHHHHHHHHcCCCCchHHHHHHHH
Q 040801           95 SIVRGYTNKNLHHEAFLFYHEMIVQG-L-IPD-RFMFPSLFKSCAD---IYV---EKQLHSQAIKFGLASDSFLHNTLIN  165 (323)
Q Consensus        95 ~li~~~~~~g~~~~A~~~~~~m~~~g-~-~p~-~~ty~~ll~~~~~---~~~---a~~~~~~m~~~g~~~~~~~~~~li~  165 (323)
                      .++-+|....+++...++++.|..-- + .++ ...--...-++.+   .|+   |.+++..+....-.++..+|..+-.
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            44446889999999999999997641 1 111 1111112223333   455   8888888666666677777766555


Q ss_pred             HHH----hcCC--CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC----hHHHHHHH----HHHHHhCCc---c
Q 040801          166 MYS----SCWC--LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD----LRTVKRVH----KCVDESGFW---S  228 (323)
Q Consensus       166 ~~~----~~g~--~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~----~~~a~~~~----~~m~~~g~~---p  228 (323)
                      .|-    ..+.  ....++|.+.|++--+  +.||..+--.+..-+...|.    -.+..++-    ....++|..   .
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kgFe--~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~  303 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKGFE--IEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKMQ  303 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHHHc--CCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccccc
Confidence            552    2221  1145677777765543  33555443333333333332    22233333    222234432   3


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhh
Q 040801          229 HVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQW  266 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  266 (323)
                      |-..+.++.++..-.|+.++|.+..++|.+.  .|..|
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l--~~~~W  339 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKAFKL--KPPAW  339 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc--CCcch
Confidence            5556789999999999999999999999976  56677

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=86.29  E-value=1.5  Score=24.66  Aligned_cols=25  Identities=12%  Similarity=0.073  Sum_probs=20.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      +|+.|-+.|.+.|++++|.+++++.
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            4677888999999999999999874

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=86.12  E-value=1.5  Score=24.56  Aligned_cols=26  Identities=19%  Similarity=0.345  Sum_probs=21.8

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      +|+.|=..|.+.|++++|.++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46788899999999999999999843

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=85.97  E-value=15  Score=29.41  Aligned_cols=98  Identities=17%  Similarity=0.127  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh--HHHHHHHHHHhccCChHHHHHHHHHHHHh---CCccC--
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA--VTLVNVLTARARARDLRTVKRVHKCVDES---GFWSH--  229 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~--~t~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~p~--  229 (323)
                      ...+..+.+-|++.|   +.++|++.|.++.+....+..  ..+-.+|+.....+++..+.....+....   |-.++  
T Consensus        36 r~~~~~l~~~~~~~G---d~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~  112 (177)
T PF10602_consen   36 RMALEDLADHYCKIG---DLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERR  112 (177)
T ss_pred             HHHHHHHHHHHHHhh---hHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHH
Confidence            466889999999999   669999999999887655544  56778999999999999999998888643   22222  


Q ss_pred             --hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          230 --VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       230 --~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                        ...|..|.  +...|++.+|-+.|-+....
T Consensus       113 nrlk~~~gL~--~l~~r~f~~AA~~fl~~~~t  142 (177)
T PF10602_consen  113 NRLKVYEGLA--NLAQRDFKEAAELFLDSLST  142 (177)
T ss_pred             HHHHHHHHHH--HHHhchHHHHHHHHHccCcC
Confidence              22333333  33468999999988887654

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=85.82  E-value=10  Score=29.22  Aligned_cols=80  Identities=14%  Similarity=0.029  Sum_probs=58.8

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCC---C--CCCcccHHHHHHHhcchhh----HHHHHHHHHHcCCCCchHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQG---L--IPDRFMFPSLFKSCADIYV----EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g---~--~p~~~ty~~ll~~~~~~~~----a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      ...|.++.-....+.+...+++++.+..-.   +  .-+..+|.+++++.++..-    +..+|..|++.+.+++..-|.
T Consensus        40 ~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~  119 (145)
T PF13762_consen   40 IFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYS  119 (145)
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            346888888888899999888888883311   1  2456778888888866555    777788887777778888888


Q ss_pred             HHHHHHHhc
Q 040801          162 TLINMYSSC  170 (323)
Q Consensus       162 ~li~~~~~~  170 (323)
                      .||.++.+.
T Consensus       120 ~li~~~l~g  128 (145)
T PF13762_consen  120 CLIKAALRG  128 (145)
T ss_pred             HHHHHHHcC
Confidence            888776654

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=85.76  E-value=16  Score=28.97  Aligned_cols=52  Identities=8%  Similarity=0.022  Sum_probs=24.3

Q ss_pred             HHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHH
Q 040801          112 FYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus       112 ~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      +..-+.+.|+.|+...|..++..+.+.|. ...+..+.+.++-+|.......+
T Consensus        16 YirSl~~~~i~~~~~L~~lli~lLi~~~~-~~~L~qllq~~Vi~DSk~lA~~L   67 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDLLIRNGQ-FSQLHQLLQYHVIPDSKPLACQL   67 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHcCC-HHHHHHHHhhcccCCcHHHHHHH
Confidence            33444445555555555555555555554 22223334444444444444443

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.27  E-value=28  Score=30.45  Aligned_cols=209  Identities=12%  Similarity=0.035  Sum_probs=119.8

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------ccch----hHHHhcccCC--CCChhhHHH-HHHHHHhCC
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------CADY----HVRLVFSQIS--NPTIYTCNS-IVRGYTNKN  104 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------y~~~----~a~~lf~~m~--~~~~~~~~~-li~~~~~~g  104 (323)
                      +.+.+..+-+-.++++|.+++..--++.-..-.        |-+.    .|..-++++.  .|...-|.. --+.+.+.+
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~   92 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKAC   92 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhc
Confidence            445566666777888888887766554321111        1111    4555555554  333333332 234556677


Q ss_pred             ChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcch--hh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHH
Q 040801          105 LHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADI--YV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~--~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      .+..|+++...|..+   |+...=..=+.+..+-  ++   +..+.++....|   +..+.+..-...-+.|   +.+.|
T Consensus        93 i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykeg---qyEaA  163 (459)
T KOG4340|consen   93 IYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEG---QYEAA  163 (459)
T ss_pred             ccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccc---cHHHH
Confidence            777777777766543   2222222223332221  22   444444443222   2222222222334556   77999


Q ss_pred             HHHHHHHHH-cCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-------------cChh--------hHHHHH
Q 040801          180 IKIFYRMEI-ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW-------------SHVE--------LKTTLM  237 (323)
Q Consensus       180 ~~~~~~m~~-~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-------------p~~~--------~~~~li  237 (323)
                      ++-|.+-.+ .|..| ...||..+ +..+.|+.+.|.+...++.++|++             ||+.        .-+.++
T Consensus       164 vqkFqaAlqvsGyqp-llAYniAL-aHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~  241 (459)
T KOG4340|consen  164 VQKFQAALQVSGYQP-LLAYNLAL-AHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALV  241 (459)
T ss_pred             HHHHHHHHhhcCCCc-hhHHHHHH-HHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHH
Confidence            999988877 56654 56787655 445678999999999999888754             2211        234555


Q ss_pred             HH-------HHhcCCHHHHHHHHHhccCC
Q 040801          238 DA-------YCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       238 ~~-------~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+       +.+.|+.+.|.+.+-+|.-+
T Consensus       242 eAfNLKaAIeyq~~n~eAA~eaLtDmPPR  270 (459)
T KOG4340|consen  242 EAFNLKAAIEYQLRNYEAAQEALTDMPPR  270 (459)
T ss_pred             HHhhhhhhhhhhcccHHHHHHHhhcCCCc
Confidence            54       45779999999999999754

>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=83.37  E-value=1.1  Score=34.36  Aligned_cols=86  Identities=17%  Similarity=0.076  Sum_probs=56.0

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK  242 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  242 (323)
                      +|+.+.+.+   .++...++++.....+..-+....+.++..|++.++.++...+++       ..+..-...+++.+-+
T Consensus        13 vi~~~~~~~---~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~-------~~~~yd~~~~~~~c~~   82 (143)
T PF00637_consen   13 VISAFEERN---QPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK-------TSNNYDLDKALRLCEK   82 (143)
T ss_dssp             CHHHCTTTT----GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT-------SSSSS-CTHHHHHHHT
T ss_pred             HHHHHHhCC---CHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc-------cccccCHHHHHHHHHh
Confidence            455555555   446777777777766655667777888888888877677666665       1222444566677777


Q ss_pred             cCCHHHHHHHHHhccC
Q 040801          243 CKFVSRAWDLFVKMLF  258 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~  258 (323)
                      .|.+++|.-++.++..
T Consensus        83 ~~l~~~a~~Ly~~~~~   98 (143)
T PF00637_consen   83 HGLYEEAVYLYSKLGN   98 (143)
T ss_dssp             TTSHHHHHHHHHCCTT
T ss_pred             cchHHHHHHHHHHccc
Confidence            7777777777777654

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.

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=83.17  E-value=15  Score=30.09  Aligned_cols=73  Identities=21%  Similarity=0.154  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH---hCCccChhhHHHHHHHHHhcCCHHHHH
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE---SGFWSHVELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~---~g~~p~~~~~~~li~~~~~~g~~~~a~  250 (323)
                      ++|.+.|-.+...+.- +....-.-+..|-...|.+++.+++....+   .+-.+|+..+..|...|-+.|+.+.|.
T Consensus       123 ~~A~~~fL~~E~~~~l-~t~elq~aLAtyY~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  123 QEALRRFLQLEGTPEL-ETAELQYALATYYTKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHHHHHcCCCCC-CCHHHHHHHHHHHHccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            4666666666555533 333333334444445566666666666543   222556666666666666666666664

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=83.14  E-value=28  Score=30.15  Aligned_cols=97  Identities=12%  Similarity=0.040  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHhc-CCCCChHHHHHHHHHHHH----cCCCC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc----
Q 040801          159 LHNTLINMYSSC-WCLDQPDEAIKIFYRMEI----ENVKP--NAVTLVNVLTARARARDLRTVKRVHKCVDESGFW----  227 (323)
Q Consensus       159 ~~~~li~~~~~~-g~~~~~~~a~~~~~~m~~----~g~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~----  227 (323)
                      ++..+-..|-.. |   ++++|++.|++-.+    .| .+  -..++..+...+.+.|++++|..+|++....-..    
T Consensus       116 ~~~~lA~~ye~~~~---d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~  191 (282)
T PF14938_consen  116 CLKELAEIYEEQLG---DYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLL  191 (282)
T ss_dssp             HHHHHHHHHCCTT-----HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTT
T ss_pred             HHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhccccc
Confidence            444455555555 5   56788887776643    23 22  2346677778888999999999999988764332    


Q ss_pred             -cChh-hHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          228 -SHVE-LKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       228 -p~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                       .+.. .|-..+-++...|++..|...+++....
T Consensus       192 ~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  192 KYSAKEYFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             GHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             chhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             2222 2233344566678999999999987654

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=82.59  E-value=22  Score=28.15  Aligned_cols=119  Identities=8%  Similarity=0.001  Sum_probs=82.3

Q ss_pred             HHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          143 QLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       143 ~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      +...-+.+.|+.|+...|..+|+.+.+.|.       ...+..+...++-+|+......+-.+..  ....+.++=-+|.
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~-------~~~L~qllq~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDML   85 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQ-------FSQLHQLLQYHVIPDSKPLACQLLSLGN--QYPPAYQLGLDML   85 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCC-------HHHHHHHHhhcccCCcHHHHHHHHHhHc--cChHHHHHHHHHH
Confidence            555666788999999999999999999883       3456667778888888887766655443  3344555544443


Q ss_pred             Hh-CCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccCC
Q 040801          223 ES-GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQG  276 (323)
Q Consensus       223 ~~-g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~~  276 (323)
                      ++ |     ..+..+++.+...|++-+|.++.+..... .++....+..+....+
T Consensus        86 kRL~-----~~~~~iievLL~~g~vl~ALr~ar~~~~~-~~~~~~~fLeAA~~~~  134 (167)
T PF07035_consen   86 KRLG-----TAYEEIIEVLLSKGQVLEALRYARQYHKV-DSVPARKFLEAAANSN  134 (167)
T ss_pred             HHhh-----hhHHHHHHHHHhCCCHHHHHHHHHHcCCc-ccCCHHHHHHHHHHcC
Confidence            32 2     24788889999999999999999886432 2334444554444433

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=82.50  E-value=6.1  Score=33.96  Aligned_cols=63  Identities=5%  Similarity=-0.102  Sum_probs=50.4

Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh----hhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV----ELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...|...+.-..+.|++++|...|+.+.+.  .|+.    ..+--+-..|...|++++|...|+.+.+.
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~  209 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKN  209 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            456766666666779999999999999886  3443    45667778899999999999999999865

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=82.47  E-value=7.9  Score=29.40  Aligned_cols=68  Identities=18%  Similarity=0.159  Sum_probs=39.6

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                      +.-....-++.+.+.|   .-|.-.++..+....+ +++....-.+-.+|.+.|+..++..++.+..+.|++
T Consensus        85 ~se~vD~ALd~lv~~~---kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   85 LSEYVDLALDILVKQG---KKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             --HHHHHHHHHHHHTT----HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             hHHHHHHHHHHHHHhc---cHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            4444566677777777   4466666666665422 566666667777777777777777777777777654

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=81.71  E-value=27  Score=28.40  Aligned_cols=97  Identities=12%  Similarity=-0.039  Sum_probs=43.7

Q ss_pred             CCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcC---CCCCh
Q 040801          122 IPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIEN---VKPNA  195 (323)
Q Consensus       122 ~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g---~~p~~  195 (323)
                      .|+..---.|-.++.+.|+   |...|++....=+.-|....-.+-.+....+   ++..|..++++..+..   -.|| 
T Consensus        86 ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~---~~A~a~~tLe~l~e~~pa~r~pd-  161 (251)
T COG4700          86 APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQ---EFAAAQQTLEDLMEYNPAFRSPD-  161 (251)
T ss_pred             chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhc---cHHHHHHHHHHHhhcCCccCCCC-
Confidence            3444444444444444444   4445554444334444444444444444444   3345555555544422   1222 


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                       +--.+-+.+...|....|+.-|+....
T Consensus       162 -~~Ll~aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         162 -GHLLFARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             -chHHHHHHHHhcCCchhHHHHHHHHHH
Confidence             222333444455555555555555444

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=81.39  E-value=3.4  Score=33.13  Aligned_cols=92  Identities=14%  Similarity=0.057  Sum_probs=56.6

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc--ccHHHHHHHhcchhh---HHHHHHHHHHc---CCCCc----hH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR--FMFPSLFKSCADIYV---EKQLHSQAIKF---GLASD----SF  158 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~--~ty~~ll~~~~~~~~---a~~~~~~m~~~---g~~~~----~~  158 (323)
                      ..+..+-.-|++.|+.++|++.|.+++.....+..  ..+-.+|+.....++   +..........   |-..+    ..
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            45788999999999999999999999887555543  334555666666666   33333333222   21121    23


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRME  187 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~  187 (323)
                      +|..|.....+     ++.+|-+.|-+..
T Consensus       117 ~~~gL~~l~~r-----~f~~AA~~fl~~~  140 (177)
T PF10602_consen  117 VYEGLANLAQR-----DFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHhc-----hHHHHHHHHHccC
Confidence            34444433332     6788888776654

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=80.95  E-value=47  Score=30.81  Aligned_cols=138  Identities=6%  Similarity=-0.010  Sum_probs=74.9

Q ss_pred             HhCCChHHHHHHHHHHHHCC-CCC---C-cccHHHHHHHhcchhh--HHHHHHHHHH-cCCCCchHHHHHHHHHHHhcCC
Q 040801          101 TNKNLHHEAFLFYHEMIVQG-LIP---D-RFMFPSLFKSCADIYV--EKQLHSQAIK-FGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g-~~p---~-~~ty~~ll~~~~~~~~--a~~~~~~m~~-~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      -+.+++.+|.++|.+.-++. -.|   . .+--+.+|++|--.+-  .+.....+++ .|-.+-...+-.|+.  -+.+ 
T Consensus        17 qkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~--Y~~k-   93 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLNNLDLMEKQLMELRQQFGKSAYLPLFKALVA--YKQK-   93 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHhhHHHHHHHHHHHHHhcCCchHHHHHHHHHH--HHhh-
Confidence            35677888888887764431 111   1 2334456666665544  4444444433 333332222333221  1223 


Q ss_pred             CCChHHHHHHHHHHHHc--CCCC------------ChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccChhhHH
Q 040801          173 LDQPDEAIKIFYRMEIE--NVKP------------NAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWSHVELKT  234 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~--g~~p------------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~~~~~  234 (323)
                        .+++|++.+..-...  +..|            |..-=+..++++...|.+.++..+++++...    .+..+..+|+
T Consensus        94 --~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd  171 (549)
T PF07079_consen   94 --EYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYD  171 (549)
T ss_pred             --hHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHH
Confidence              556777776655543  3222            2233345566777888888888887777653    3447788888


Q ss_pred             HHHHHHHhc
Q 040801          235 TLMDAYCKC  243 (323)
Q Consensus       235 ~li~~~~~~  243 (323)
                      .++-.+++.
T Consensus       172 ~~vlmlsrS  180 (549)
T PF07079_consen  172 RAVLMLSRS  180 (549)
T ss_pred             HHHHHHhHH
Confidence            777666654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=80.71  E-value=46  Score=31.32  Aligned_cols=158  Identities=12%  Similarity=0.005  Sum_probs=98.8

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHC-CCCC-----CcccHHHHHHHhcch--hh-----HHHHHHHHHHcCCCCchHHH
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQ-GLIP-----DRFMFPSLFKSCADI--YV-----EKQLHSQAIKFGLASDSFLH  160 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~-g~~p-----~~~ty~~ll~~~~~~--~~-----a~~~~~~m~~~g~~~~~~~~  160 (323)
                      ..++...+=.||-+.+++++.+-.+. ++.-     -..+|..++..++..  .+     ++++++.+.+.  -|+...|
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lf  269 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALF  269 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHH
Confidence            45666666778888888888765442 2322     224566666666665  33     88888887764  3777666


Q ss_pred             HHHHHH-HHhcCCCCChHHHHHHHHHHHHcC---CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          161 NTLINM-YSSCWCLDQPDEAIKIFYRMEIEN---VKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       161 ~~li~~-~~~~g~~~~~~~a~~~~~~m~~~g---~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      .-.-.- +...|   +.++|++.|++.....   -+.....+=-+.-.+....++++|...|..+.+..-. +..+|.-+
T Consensus       270 l~~~gR~~~~~g---~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~W-Ska~Y~Y~  345 (468)
T PF10300_consen  270 LFFEGRLERLKG---NLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKW-SKAFYAYL  345 (468)
T ss_pred             HHHHHHHHHHhc---CHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcccc-HHHHHHHH
Confidence            543322 34445   6799999998755311   1122333334555677788999999999999775422 34444433


Q ss_pred             HH-HHHhcCCH-------HHHHHHHHhcc
Q 040801          237 MD-AYCKCKFV-------SRAWDLFVKML  257 (323)
Q Consensus       237 i~-~~~~~g~~-------~~a~~~~~~m~  257 (323)
                      .. +|...|+.       ++|.++|.+..
T Consensus       346 ~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  346 AAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            33 45567777       88888888764

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=80.32  E-value=19  Score=25.89  Aligned_cols=60  Identities=13%  Similarity=0.148  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      +..+-++.+....+-|+.....+.|++|-+.+|+..|.++++-++.+- ......|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHH
Confidence            444444444445566777777777777777777777777777765431 222336665554

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=80.24  E-value=8.2  Score=33.43  Aligned_cols=122  Identities=14%  Similarity=-0.018  Sum_probs=79.3

Q ss_pred             HHHHHHHHHHhcCC----CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          159 LHNTLINMYSSCWC----LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       159 ~~~~li~~~~~~g~----~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      ..+.+++++-...+    ....++...+-++++.+|        |    -..+.+++.+|...|.+.++.. +-|.+-|.
T Consensus        53 ~~~~~l~~~~~~~~~~~~~~~~~e~~~~AE~LK~eG--------N----~~m~~~~Y~eAv~kY~~AI~l~-P~nAVyyc  119 (304)
T KOG0553|consen   53 EGTTLLDSFESAERHPVEILTPEEDKALAESLKNEG--------N----KLMKNKDYQEAVDKYTEAIELD-PTNAVYYC  119 (304)
T ss_pred             ccccHHHHHHHhccCcccccChHhHHHHHHHHHHHH--------H----HHHHhhhHHHHHHHHHHHHhcC-CCcchHHH
Confidence            34556666555554    112224666667777666        2    2346789999999999998863 23567777


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccCCCCchhhh-HHHhhhccCCCCCcchhhhhh----hCCCCchh
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQW-AMSATVGPQGLVGRHSTAHQI----SGPCPKKA  295 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~~~~~~~~~~~~~~a~~l----~~~~~~~~  295 (323)
                      .=-.+|++.|..+.|++--+....  ++|..| +|...=..+-..|+.++|..-    ++..|+++
T Consensus       120 NRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~~A~~aykKaLeldP~Ne  183 (304)
T KOG0553|consen  120 NRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYEEAIEAYKKALELDPDNE  183 (304)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHHHHHHHHHhhhccCCCcH
Confidence            778899999999999987777665  377777 444433333334455555433    77777764

---

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	323
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.87
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.85
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.83
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.8
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.52
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.45
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.4
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.38
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.33
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.32
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.31
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.3
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.28
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.28
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.25
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.21
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.2
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.18
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.17
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.16
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.14
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.08
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.07
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.07
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.05
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.04
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.03
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.02
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.02
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.01
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.01
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.98
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.98
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.95
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.94
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.92
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.91
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.91
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.86
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.84
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.8
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.79
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.79
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.75
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.73
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.7
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.69
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.68
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.68
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.67
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.64
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.63
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.62
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.58
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.53
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.51
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.51
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.44
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.42
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.4
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.37
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.3
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.29
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.24
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.2
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.18
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.17
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.09
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.09
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.07
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.07
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.06
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.06
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.05
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.04
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.03
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.02
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.02
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.01
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.01
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.0
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.0
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.96
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	97.93
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.9
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.89
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.89
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.89
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.88
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.87
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.86
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.84
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.84
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.83
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.82
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.81
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.8
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.8
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.79
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.79
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.78
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.77
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.76
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.73
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.72
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.72
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.68
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.68
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.68
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	97.67
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.67
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	97.67
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.66
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.66
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.65
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.65
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.61
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.6
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.59
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.57
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.56
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.55
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.53
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.51
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.5
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	97.46
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.43
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.41
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.41
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.4
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.4
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.38
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.28
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.26
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.24
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.22
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.21
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.19
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.19
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.16
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.14
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.06
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.06
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.06
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.04
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.01
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	96.93
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	96.87
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	96.86
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.79
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.76
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	96.75
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	96.74
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.73
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.72
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.7
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	96.7
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	96.64
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.63
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.61
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.59
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	96.58
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.56
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.54
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.46
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.45
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.37
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.34
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	96.34
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	96.32
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	96.32
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.22
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	96.16
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	96.16
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.14
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.1
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.09
3k9i_A	117	BH0479 protein; putative protein binding protein,	96.07
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.05
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.02
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	95.95
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.77
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.73
1klx_A	138	Cysteine rich protein B; structural genomics, heli	95.63
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.59
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	95.54
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	95.39
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.35
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	95.07
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	95.01
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	94.93
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	94.82
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	94.82
1klx_A	138	Cysteine rich protein B; structural genomics, heli	94.74
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	94.66
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	94.46
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	93.99
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	93.99
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	93.56
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	93.38
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	92.34
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.2
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	92.14
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	92.07
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	92.05
1pc2_A	152	Mitochondria fission protein; unknown function; NM	91.96
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	91.72
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	91.59
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	91.12
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	90.84
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	90.72
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	89.2
1pc2_A	152	Mitochondria fission protein; unknown function; NM	88.02
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	87.51
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	85.17
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	84.59
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	84.54
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	84.34
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	82.72
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	81.61
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	80.75
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	80.59
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	80.22

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=1.5e-35  Score=275.84  Aligned_cols=183  Identities=12%  Similarity=0.061  Sum_probs=172.3

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh------------HHHHHHHHHHcCCCCch
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV------------EKQLHSQAIKFGLASDS  157 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~------------a~~~~~~m~~~g~~~~~  157 (323)
                      ...++.+|++|++.|++++|+++|++|.+.|+.||..|||+||.+|++.+.            |.++|++|.+.|+.||.
T Consensus        26 e~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~  105 (501)
T 4g26_A           26 EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE  105 (501)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCH
Confidence            346899999999999999999999999999999999999999999987542            89999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      +|||+||++|++.|   ++++|.++|++|...|+.||..|||++|.+|++.|++++|.++|++|.+.|+.||..||++||
T Consensus       106 ~tyn~lI~~~~~~g---~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li  182 (501)
T 4g26_A          106 ATFTNGARLAVAKD---DPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALL  182 (501)
T ss_dssp             HHHHHHHHHHHHHT---CHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            99999999999999   669999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccC
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQ  275 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~  275 (323)
                      ++|++.|++++|.++|++|++.+..|+..|+......+
T Consensus       183 ~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F  220 (501)
T 4g26_A          183 KVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWF  220 (501)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHH
T ss_pred             HHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHH
Confidence            99999999999999999999988888887766655443

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=1.5e-34  Score=269.02  Aligned_cols=186  Identities=12%  Similarity=0.076  Sum_probs=179.0

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCC---------hHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNL---------HHE  108 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~---------~~~  108 (323)
                      ..++.+|.+|++.|++++|.++|++|.+.|+                  .||..+||+||.+|++.+.         +++
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv------------------~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~   88 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGV------------------QLSQYHYNVLLYVCSLAEAATESSPNPGLSR   88 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTC------------------CCCHHHHHHHHHHHTTCCCCSSSSCCHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC------------------CCCHhHHHHHHHHHHhCCchhhhhhcchHHH
Confidence            3578899999999999999999999999999                  9999999999999998765         689


Q ss_pred             HHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 040801          109 AFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYR  185 (323)
Q Consensus       109 A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~  185 (323)
                      |+++|++|.+.|+.||..||++||.+|++.|+   |.+++++|.+.|+.||..+||+||.+|++.|   +.++|.++|++
T Consensus        89 A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g---~~~~A~~l~~~  165 (501)
T 4g26_A           89 GFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG---DADKAYEVDAH  165 (501)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCC---CHHHHHHHHHH
Confidence            99999999999999999999999999999999   9999999999999999999999999999999   66999999999


Q ss_pred             HHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          186 MEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       186 m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      |.+.|+.||..||++||.+|++.|++++|.+++++|.+.|+.|+..||+.+++.|++.+
T Consensus       166 M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          166 MVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             HHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            99999999999999999999999999999999999999999999999999999998743

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.87  E-value=6.6e-23  Score=197.69  Aligned_cols=148  Identities=14%  Similarity=0.015  Sum_probs=126.1

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHH---HCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHH
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMI---VQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      ..+||+||++||+.|++++|.++|++|.   ..|+.||..|||+||.+||+.|+   |.++|++|.+.|+.||.+|||+|
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            3689999999999999999999998876   45899999999999999999999   99999999999999999999999


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC------hhhHHHHH
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH------VELKTTLM  237 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~------~~~~~~li  237 (323)
                      |+++|+.|+.  .++|.++|++|.+.|+.||.+||+.+|.++.+.+-++.    .+++ ..++.|+      ..+...|.
T Consensus       207 I~glcK~G~~--~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~----Vrkv-~P~f~p~~~~~~~~~t~~LL~  279 (1134)
T 3spa_A          207 LQCMGRQDQD--AGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKA----VHKV-KPTFSLPPQLPPPVNTSKLLR  279 (1134)
T ss_dssp             HHHHHHHTCC--HHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHH----HGGG-CCCCCCCCCCCCCCCCCTTTH
T ss_pred             HHHHHhCCCc--HHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHH----HHHh-CcccCCCCCCcccccchHHHH
Confidence            9999999943  37899999999999999999999999976665433333    2222 3456655      56677888


Q ss_pred             HHHHhcC
Q 040801          238 DAYCKCK  244 (323)
Q Consensus       238 ~~~~~~g  244 (323)
                      +.|.+.+
T Consensus       280 dl~s~d~  286 (1134)
T 3spa_A          280 DVYAKDG  286 (1134)
T ss_dssp             HHHCCCS
T ss_pred             HHHccCC
Confidence            8888776

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.85  E-value=5.9e-22  Score=191.12  Aligned_cols=130  Identities=10%  Similarity=0.113  Sum_probs=115.5

Q ss_pred             CcccHHHHHHHhcchhh---HHHHHHHHH---HcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHH
Q 040801          124 DRFMFPSLFKSCADIYV---EKQLHSQAI---KFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVT  197 (323)
Q Consensus       124 ~~~ty~~ll~~~~~~~~---a~~~~~~m~---~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t  197 (323)
                      -..||++||.+||+.|+   |.++|++|.   +.|+.||++|||+||++||+.|   +.++|.++|++|.+.|+.||.+|
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G---~~~eA~~Lf~eM~~~G~~PDvvT  202 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQG---AFKELVYVLFMVKDAGLTPDLLS  202 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCC---CHHHHHHHHHHHHHcCCCCcHHH
Confidence            34689999999999999   999998876   4589999999999999999999   66999999999999999999999


Q ss_pred             HHHHHHHHhccCCh-HHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          198 LVNVLTARARARDL-RTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       198 ~~~li~~~~~~~~~-~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ||+||.++|+.|+. +.|.++|++|.+.|+.||..+|++++.++.+.+-++.+.++..++
T Consensus       203 YntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f  262 (1134)
T 3spa_A          203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTF  262 (1134)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCC
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCccc
Confidence            99999999999985 789999999999999999999999998887775555554443333

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.83  E-value=1.1e-18  Score=165.49  Aligned_cols=241  Identities=7%  Similarity=-0.121  Sum_probs=200.0

Q ss_pred             cccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCC------------------------------------------
Q 040801           34 INSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFD------------------------------------------   71 (323)
Q Consensus        34 ~~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~------------------------------------------   71 (323)
                      ..+..+++.+..++.+.|++++|..+|++|.+.+....                                          
T Consensus       197 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  276 (597)
T 2xpi_A          197 KLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYM  276 (597)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHH
Confidence            34577899999999999999999999999988652210                                          


Q ss_pred             ----Cccch----hHHHhcccCCC--CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-
Q 040801           72 ----PCADY----HVRLVFSQISN--PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-  140 (323)
Q Consensus        72 ----~y~~~----~a~~lf~~m~~--~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-  140 (323)
                          .|.+.    +|.++|+++..  ++..+|+.++..|.+.|++++|.++|++|.+.+ +.+..++..++.++.+.|+ 
T Consensus       277 ~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~  355 (597)
T 2xpi_A          277 LKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEK  355 (597)
T ss_dssp             TTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCH
T ss_pred             HHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCH
Confidence                03333    89999999984  899999999999999999999999999998765 3478899999999999999 


Q ss_pred             --HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHH
Q 040801          141 --EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       141 --a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                        |.++++.+.+.. ..+..+|+.+..+|.+.|   ++++|.++|+++.... ..+..+|+.++.++.+.|++++|..+|
T Consensus       356 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~  430 (597)
T 2xpi_A          356 NKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVN---KISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAY  430 (597)
T ss_dssp             HHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhc---cHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence              999999998654 457889999999999999   6799999999998754 346789999999999999999999999


Q ss_pred             HHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhh
Q 040801          219 KCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       219 ~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a  284 (323)
                      +++.+.+ +.+..+|..+..+|.+.|++++|.++|+++.+. +.++..| .+...+..   .|+.++|
T Consensus       431 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A  494 (597)
T 2xpi_A          431 TTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFN---KSDMQTA  494 (597)
T ss_dssp             HHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH---TTCHHHH
T ss_pred             HHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH---hCCHHHH
Confidence            9998764 447899999999999999999999999999764 3344444 44444444   4454444

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.80  E-value=9.6e-18  Score=158.95  Aligned_cols=236  Identities=12%  Similarity=-0.075  Sum_probs=196.3

Q ss_pred             ccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------ccch----hHHHhcccCC---CCChhhHHHHHHH
Q 040801           35 NSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------CADY----HVRLVFSQIS---NPTIYTCNSIVRG   99 (323)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------y~~~----~a~~lf~~m~---~~~~~~~~~li~~   99 (323)
                      ++..++..++..+.+.|++++|..+|+.+.+.+-....        |.+.    +|.++|+++.   +.+..+|+.+...
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  382 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIY  382 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHH
Confidence            56778999999999999999999999999987532111        2222    8888888775   5678899999999


Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~  176 (323)
                      |.+.|++++|.++|+++.+.. +.+..+|+.+..++.+.|+   |.++++.+.+.+ ..+..+|+.+..+|.+.|   ++
T Consensus       383 ~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g---~~  457 (597)
T 2xpi_A          383 YLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLG---NI  457 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHT---CH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcC---CH
Confidence            999999999999999998742 2356799999999999999   999999998765 347889999999999999   67


Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccC--hhhHHHHHHHHHhcCCHHHHH
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWSH--VELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~--~~~~~~li~~~~~~g~~~~a~  250 (323)
                      ++|.++|+++.... ..+..+|+.+...|.+.|++++|..+|+++.+.    +..|+  ..+|..+..+|.+.|++++|.
T Consensus       458 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  536 (597)
T 2xpi_A          458 LLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAI  536 (597)
T ss_dssp             HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHH
Confidence            99999999998765 347899999999999999999999999999876    77887  789999999999999999999


Q ss_pred             HHHHhccCC-CCchhhh-HHHhhhccCC
Q 040801          251 DLFVKMLFP-WNNYGQW-AMSATVGPQG  276 (323)
Q Consensus       251 ~~~~~m~~~-~~~~~~~-~~~~~~~~~~  276 (323)
                      ++++++.+. +.++..| .+...+...|
T Consensus       537 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g  564 (597)
T 2xpi_A          537 DALNQGLLLSTNDANVHTAIALVYLHKK  564 (597)
T ss_dssp             HHHHHHHHHSSCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhC
Confidence            999998764 2344444 4555554444

>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=99.52  E-value=3.8e-12  Score=114.08  Aligned_cols=212  Identities=11%  Similarity=0.004  Sum_probs=149.1

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYT  101 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~  101 (323)
                      .+..+...+.+.|+++.|...++.+.+..  |+.          |...    +|.+.|+++.   +.+..+|+.+-..+.
T Consensus       103 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~  180 (388)
T 1w3b_A          103 GYINLAAALVAAGDMEGAVQAYVSALQYN--PDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFN  180 (388)
T ss_dssp             HHHHHHHHHHHHSCSSHHHHHHHHHHHHC--TTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            34555556666666666666666665542  333          1111    6666666554   334566777777777


Q ss_pred             hCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHH
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      +.|++++|.+.|+++.+.. +-+...|..+-..+...|+   |...++...+.. ..+..++..+...|.+.|   ++++
T Consensus       181 ~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g---~~~~  255 (388)
T 1w3b_A          181 AQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQG---LIDL  255 (388)
T ss_dssp             TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcC---CHHH
Confidence            7777777777777776532 1223455555566666666   666666666543 124677888888899988   6689


Q ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          179 AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      |.+.|+++...+ +.+..+|..+...+.+.|++++|...++++.+.. +.+..++..+...|.+.|++++|...++++.+
T Consensus       256 A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  333 (388)
T 1w3b_A          256 AIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALE  333 (388)
T ss_dssp             HHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            999999988754 2356788889999999999999999999988763 45678889999999999999999999999877


Q ss_pred             C
Q 040801          259 P  259 (323)
Q Consensus       259 ~  259 (323)
                      .
T Consensus       334 ~  334 (388)
T 1w3b_A          334 V  334 (388)
T ss_dssp             S
T ss_pred             c
Confidence            5

>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=99.45  E-value=5.4e-12  Score=115.02  Aligned_cols=213  Identities=8%  Similarity=-0.095  Sum_probs=153.9

Q ss_pred             ccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHH
Q 040801           35 NSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIV   97 (323)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li   97 (323)
                      .+...+..+...+.+.|+++.|..+|+.+.+.  .|+.          |...    .|.+.|+++.   +.+...|..+.
T Consensus        24 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~  101 (450)
T 2y4t_A           24 ADVEKHLELGKKLLAAGQLADALSQFHAAVDG--DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRG  101 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHH
Confidence            34556788888999999999999999999876  3443          2222    7888887765   45678889999


Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHH------------hcchhh---HHHHHHHHHHcCCCCchH
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKS------------CADIYV---EKQLHSQAIKFGLASDSF  158 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~------------~~~~~~---a~~~~~~m~~~g~~~~~~  158 (323)
                      ..|.+.|++++|.+.|+++.+.  .|+.    .++..+...            +.+.|+   |...++.+.+.. ..+..
T Consensus       102 ~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~  178 (450)
T 2y4t_A          102 HLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAE  178 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChH
Confidence            9999999999999999998764  3443    444444333            555555   888888877654 33567


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC-hhhHHHH-
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH-VELKTTL-  236 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~l-  236 (323)
                      ++..+..+|.+.|   ++++|.+.|+++.... ..+..+|..+...+...|++++|...++.+.+.  .|+ ...+..+ 
T Consensus       179 ~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~  252 (450)
T 2y4t_A          179 LRELRAECFIKEG---EPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYK  252 (450)
T ss_dssp             HHHHHHHHHHHTT---CGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHH
Confidence            7888888888888   5578888888877643 345677888888888888888888888887754  333 3333333 


Q ss_pred             -----------HHHHHhcCCHHHHHHHHHhccC
Q 040801          237 -----------MDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       237 -----------i~~~~~~g~~~~a~~~~~~m~~  258 (323)
                                 ...|.+.|++++|...|+++.+
T Consensus       253 ~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~  285 (450)
T 2y4t_A          253 QVKKLNKLIESAEELIRDGRYTDATSKYESVMK  285 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                       6677777888888888877754

>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=99.40  E-value=3.5e-11  Score=107.69  Aligned_cols=237  Identities=12%  Similarity=-0.066  Sum_probs=161.5

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC--CC-ChhhHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS--NP-TIYTCNSIVRG   99 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~--~~-~~~~~~~li~~   99 (323)
                      ...+..+...+.+.|++++|...|+.+.+.  .|+.          |.+.    .|.+.|.++.  .| +...+..+-..
T Consensus        67 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  144 (388)
T 1w3b_A           67 AEAYSNLGNVYKERGQLQEAIEHYRHALRL--KPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNL  144 (388)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHH
Confidence            345667777777777888888887777764  3443          1111    6666666554  33 34456666667


Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~  176 (323)
                      +...|++++|.++|+++.+.. +-+..+|..+-..+.+.|+   |...++.+.+.+ ..+...|..+-..+...|   ++
T Consensus       145 ~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~---~~  219 (388)
T 1w3b_A          145 LKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEAR---IF  219 (388)
T ss_dssp             HHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTT---CT
T ss_pred             HHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcC---CH
Confidence            777788888888887776542 2234667777777777777   777777777654 223566777777777777   45


Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ++|.+.|++..... +-+..++..+...+.+.|++++|...++++.+.. +-+..+|..+...|.+.|++++|.+.++++
T Consensus       220 ~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  297 (388)
T 1w3b_A          220 DRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTA  297 (388)
T ss_dssp             THHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            78888887776643 2357788889999999999999999999988763 224678889999999999999999999988


Q ss_pred             cCC-CCchhhh-HHHhhhccCCCCCcchhhh
Q 040801          257 LFP-WNNYGQW-AMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       257 ~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~  285 (323)
                      .+. +..+..| .....+   ...|+.++|.
T Consensus       298 l~~~p~~~~~~~~l~~~~---~~~g~~~~A~  325 (388)
T 1w3b_A          298 LRLCPTHADSLNNLANIK---REQGNIEEAV  325 (388)
T ss_dssp             HHHCTTCHHHHHHHHHHH---HTTTCHHHHH
T ss_pred             HhhCcccHHHHHHHHHHH---HHcCCHHHHH
Confidence            754 2333444 333333   3445555554

>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=99.38  E-value=1.6e-11  Score=111.82  Aligned_cols=235  Identities=8%  Similarity=-0.038  Sum_probs=176.7

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC--CC-Ch---hhHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS--NP-TI---YTCNS   95 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~--~~-~~---~~~~~   95 (323)
                      +...+..+...+...|+++.|...++.+.+.+  |+.          |.+.    .|.+.|+++.  .| +.   ..|..
T Consensus        59 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  136 (450)
T 2y4t_A           59 NYIAYYRRATVFLAMGKSKAALPDLTKVIQLK--MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSENEEKEAQSQ  136 (450)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChhhHHHHHH
Confidence            45567788888999999999999999998874  443          2222    8888888775  33 33   56666


Q ss_pred             HHHH------------HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHH
Q 040801           96 IVRG------------YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLH  160 (323)
Q Consensus        96 li~~------------~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~  160 (323)
                      +...            +.+.|++++|.+.|+++.+.. +.+..++..+...+.+.|+   |.+.++.+.+.. ..+..+|
T Consensus       137 l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~  214 (450)
T 2y4t_A          137 LIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAF  214 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence            6444            889999999999999997642 3466778888888888888   888888887764 3467889


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC-hHHHHHH------------HHHHhccCChHHHHHHHHHHHHhCCc
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN-AVTLVNV------------LTARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~-~~t~~~l------------i~~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                      ..+...|...|   ++++|++.|+++...  .|+ ...+..+            ...+.+.|++++|...++.+.+.  .
T Consensus       215 ~~l~~~~~~~g---~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~  287 (450)
T 2y4t_A          215 YKISTLYYQLG---DHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--E  287 (450)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--C
T ss_pred             HHHHHHHHHcC---CHHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--C
Confidence            99999999999   679999999999864  343 3444444            78888999999999999999875  3


Q ss_pred             cC-----hhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhh
Q 040801          228 SH-----VELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       228 p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a  284 (323)
                      |+     ...|..+...|.+.|++++|...++++.+. +..+..| .....+...   |+.++|
T Consensus       288 p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~---~~~~~A  348 (450)
T 2y4t_A          288 PSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAYLIE---EMYDEA  348 (450)
T ss_dssp             CSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT---TCHHHH
T ss_pred             CcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHh---cCHHHH
Confidence            44     447888899999999999999999987643 3344444 444445444   445544

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.33  E-value=1.4e-10  Score=102.60  Aligned_cols=215  Identities=10%  Similarity=-0.008  Sum_probs=169.1

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRG   99 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~   99 (323)
                      ...+..+-..+...|+++.|...++.+.+.  .|+.          |...    .|.+.|++..   +.+...|..+...
T Consensus        64 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~  141 (368)
T 1fch_A           64 HPQPFEEGLRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVS  141 (368)
T ss_dssp             CSSHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            445667788889999999999999999876  3444          2222    7888887654   5678899999999


Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHH---------------HHHHhcchhh---HHHHHHHHHHcCCCC-chHHH
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPS---------------LFKSCADIYV---EKQLHSQAIKFGLAS-DSFLH  160 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~---------------ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~  160 (323)
                      |...|++++|.+.|+++.+..-. +...+..               .+..+...|+   |...++.+.+..-.. +..++
T Consensus       142 ~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~  220 (368)
T 1fch_A          142 FTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQ  220 (368)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHH
Confidence            99999999999999999875321 1111111               1223335555   889999888765321 57889


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHH
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAY  240 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  240 (323)
                      ..+...|.+.|   ++++|.+.|++..... +.+..+|..+...+...|++++|...++++.+.. +.+...+..+...|
T Consensus       221 ~~l~~~~~~~g---~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~  295 (368)
T 1fch_A          221 CGLGVLFNLSG---EYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISC  295 (368)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            99999999999   7799999999988754 3467899999999999999999999999998763 33577899999999


Q ss_pred             HhcCCHHHHHHHHHhccCC
Q 040801          241 CKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       241 ~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.|++++|...|++..+.
T Consensus       296 ~~~g~~~~A~~~~~~al~~  314 (368)
T 1fch_A          296 INLGAHREAVEHFLEALNM  314 (368)
T ss_dssp             HHHTCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHh
Confidence            9999999999999988653

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.32  E-value=3.4e-10  Score=94.77  Aligned_cols=198  Identities=8%  Similarity=-0.083  Sum_probs=164.8

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ...+..+...+...|+++.|...++...+..                   +.+...|..+...|...|++++|.+.|++.
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~a   97 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-------------------PSSADAHAALAVVFQTEMEPKLADEEYRKA   97 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-------------------CChHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4456777788889999999999999998874                   456778999999999999999999999998


Q ss_pred             HHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC
Q 040801          117 IVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK  192 (323)
Q Consensus       117 ~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~  192 (323)
                      .+.. +.+...+..+...+...|+   |.+.++.+.+.+..| +...+..+...|...|   ++++|.+.|++..... .
T Consensus        98 ~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~~~~~~~~~-~  172 (252)
T 2ho1_A           98 LASD-SRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMK---KPAQAKEYFEKSLRLN-R  172 (252)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-S
T ss_pred             HHHC-cCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcC---CHHHHHHHHHHHHhcC-c
Confidence            7653 2356777788888888888   888888887744445 5677888999999999   6799999999988754 3


Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+...+..+...+...|+.++|...++.+.+.. +.+...+..+...|.+.|+.++|.+.++++.+.
T Consensus       173 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          173 NQPSVALEMADLLYKEREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            467889999999999999999999999987753 345677888999999999999999999998764

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.31  E-value=7.5e-11  Score=104.57  Aligned_cols=217  Identities=13%  Similarity=-0.036  Sum_probs=167.9

Q ss_pred             ccchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHH
Q 040801           35 NSQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIV   97 (323)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li   97 (323)
                      .+...+..+...+.+.|+++.|..+|+.+.+..  |+.          |...    .|.+.|++..   +.+...|..+.
T Consensus        63 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~  140 (365)
T 4eqf_A           63 KDWPGAFEEGLKRLKEGDLPVTILFMEAAILQD--PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALA  140 (365)
T ss_dssp             TTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence            345567788888999999999999999999874  444          2222    7888887765   55688899999


Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCC---------CCcccHHHHHHHhcchhh---HHHHHHHHHHcCCC-CchHHHHHHH
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLI---------PDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLA-SDSFLHNTLI  164 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~---------p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~~~~~~~li  164 (323)
                      ..|...|++++|.+.|++..+..-.         .....+..+...+.+.|+   |...++.+.+..-. .+..+|..+.
T Consensus       141 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~  220 (365)
T 4eqf_A          141 VSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLG  220 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHH
T ss_pred             HHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHH
Confidence            9999999999999999998764210         012233445677777888   99999998877522 2688999999


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      ..|.+.|   ++++|.+.|++..... +.+..+|..+...+...|++++|...++++.+.. +.+...|..+...|.+.|
T Consensus       221 ~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g  295 (365)
T 4eqf_A          221 VLFHLSG---EFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLG  295 (365)
T ss_dssp             HHHHHHT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHCC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCC
Confidence            9999999   7799999999998764 3467899999999999999999999999998863 234788999999999999


Q ss_pred             CHHHHHHHHHhccC
Q 040801          245 FVSRAWDLFVKMLF  258 (323)
Q Consensus       245 ~~~~a~~~~~~m~~  258 (323)
                      ++++|...|++..+
T Consensus       296 ~~~~A~~~~~~al~  309 (365)
T 4eqf_A          296 AYREAVSNFLTALS  309 (365)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999998865

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.30  E-value=5.7e-10  Score=96.71  Aligned_cols=245  Identities=11%  Similarity=-0.003  Sum_probs=180.8

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVR   98 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~   98 (323)
                      +...+......+...|++++|..+++.+.+..  |+.          |...    .|.+.|++..   +.+...|..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHH
Confidence            33455667778888999999999999998863  434          1111    7788887664   557788999999


Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCc-ccHHHH--------------HH-Hhcchhh---HHHHHHHHHHcCCCCchHH
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDR-FMFPSL--------------FK-SCADIYV---EKQLHSQAIKFGLASDSFL  159 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~-~ty~~l--------------l~-~~~~~~~---a~~~~~~m~~~g~~~~~~~  159 (323)
                      .|...|++++|.+.|++..+..  |+. ..+..+              -. .+...|+   |.+.++.+.+.. ..+..+
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  174 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQ--PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQL  174 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTS--TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHH
Confidence            9999999999999999998752  332 333332              11 2666666   888888888765 236788


Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHH
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDA  239 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  239 (323)
                      +..+...|.+.|   ++++|.+.+++..... ..+..++..+...+...|++++|...++++.+.. +.+...+..+...
T Consensus       175 ~~~la~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~  249 (327)
T 3cv0_A          175 HASLGVLYNLSN---NYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVS  249 (327)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc---cHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHH
Confidence            999999999999   7799999999998764 3467889999999999999999999999998764 3357789999999


Q ss_pred             HHhcCCHHHHHHHHHhccCCCCch-----------hhhHHHhhhccCCCCCcchhhhhhhCC
Q 040801          240 YCKCKFVSRAWDLFVKMLFPWNNY-----------GQWAMSATVGPQGLVGRHSTAHQISGP  290 (323)
Q Consensus       240 ~~~~g~~~~a~~~~~~m~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~a~~l~~~  290 (323)
                      |.+.|++++|.+.+++..+.....           ....+......+...|+.++|..+...
T Consensus       250 ~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  311 (327)
T 3cv0_A          250 YSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQ  311 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTC
T ss_pred             HHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            999999999999999886541110           122333333334445666666666553

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.28  E-value=5.5e-10  Score=96.49  Aligned_cols=188  Identities=9%  Similarity=-0.061  Sum_probs=142.3

Q ss_pred             HHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHH-HHHhcchhh---HHHHHHHHHHcCC
Q 040801           78 VRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSL-FKSCADIYV---EKQLHSQAIKFGL  153 (323)
Q Consensus        78 a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~l-l~~~~~~~~---a~~~~~~m~~~g~  153 (323)
                      |..-++....|+..++..+...+.+.|+.++|++.++++...+..|+...+..+ -..+...|+   |.+.++.      
T Consensus        53 al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------  126 (291)
T 3mkr_A           53 VLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------  126 (291)
T ss_dssp             HHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------
T ss_pred             HHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------
Confidence            333333333667788999999999999999999999999988877776555444 477777787   6665554      


Q ss_pred             CCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHH---HHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          154 ASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTL---VNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       154 ~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~---~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      ..+...+..+...|.+.|   ++++|.+.|+++....  |+....   ...+..+...|++++|..+|+++.+. .+.+.
T Consensus       127 ~~~~~~~~~l~~~~~~~g---~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~  200 (291)
T 3mkr_A          127 GDSLECMAMTVQILLKLD---RLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTL  200 (291)
T ss_dssp             CCSHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCH
T ss_pred             CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcH
Confidence            467788999999999999   6699999999998864  654322   12334444568999999999999887 45678


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGL  277 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~  277 (323)
                      ..++.+..+|.+.|++++|...|++..+. +.++..+ .....+...|+
T Consensus       201 ~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~  249 (291)
T 3mkr_A          201 LLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGK  249 (291)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            88999999999999999999999997653 5566666 44445545443

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.28  E-value=5.3e-10  Score=97.02  Aligned_cols=242  Identities=10%  Similarity=-0.071  Sum_probs=183.4

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----ccch--------hHHHhcccCC---CCChhhHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----CADY--------HVRLVFSQIS---NPTIYTCNSIVRGYT  101 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----y~~~--------~a~~lf~~m~---~~~~~~~~~li~~~~  101 (323)
                      ...+..+...+...|+++.|..+++.+.+..-....    ++.+        .|.++|+++.   +.+...|..+-..+.
T Consensus        22 ~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  101 (330)
T 3hym_B           22 LDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYL  101 (330)
T ss_dssp             CTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHH
Confidence            345566777788889999999999999876432222    1111        7777777665   557788999999999


Q ss_pred             hCC-ChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801          102 NKN-LHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       102 ~~g-~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      ..| ++++|.+.|++..+.. +.+...|..+-..+...|+   |...++...+..- .+...+..+...|...|   +++
T Consensus       102 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~---~~~  176 (330)
T 3hym_B          102 MVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLTN---NSK  176 (330)
T ss_dssp             HSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHTT---CHH
T ss_pred             HhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHh---hHH
Confidence            999 9999999999988653 2346778888888888888   8888888887652 24566777999999999   779


Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC--------CccChhhHHHHHHHHHhcCCHHHH
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG--------FWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g--------~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                      +|.+.|++..... +.+..++..+...+...|++++|...++.+.+..        .......+..+...|.+.|++++|
T Consensus       177 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  255 (330)
T 3hym_B          177 LAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEA  255 (330)
T ss_dssp             HHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHH
Confidence            9999999988754 4467889999999999999999999999997642        133467899999999999999999


Q ss_pred             HHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhhhhh
Q 040801          250 WDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       250 ~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~~l  287 (323)
                      ...+++..+. +..+..| .+...+..   .|+.++|...
T Consensus       256 ~~~~~~a~~~~~~~~~~~~~la~~~~~---~g~~~~A~~~  292 (330)
T 3hym_B          256 LDYHRQALVLIPQNASTYSAIGYIHSL---MGNFENAVDY  292 (330)
T ss_dssp             HHHHHHHHHHSTTCSHHHHHHHHHHHH---HTCHHHHHHH
T ss_pred             HHHHHHHHhhCccchHHHHHHHHHHHH---hccHHHHHHH
Confidence            9999998754 2333444 34444433   4555555433

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.25  E-value=3.6e-09  Score=86.37  Aligned_cols=198  Identities=6%  Similarity=-0.143  Sum_probs=159.0

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ...+..+...+...|+++.|...++...+..                   +.+...|..+...|...|++++|.+.|++.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a   68 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSD-------------------PKNELAWLVRAEIYQYLKVNDKAQESFRQA   68 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-------------------ccchHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            4456777788888999999999999988874                   445778888999999999999999999998


Q ss_pred             HHCCCCCCcccHHHHHHHhcch-hh---HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC
Q 040801          117 IVQGLIPDRFMFPSLFKSCADI-YV---EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV  191 (323)
Q Consensus       117 ~~~g~~p~~~ty~~ll~~~~~~-~~---a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~  191 (323)
                      .+.. +.+..++..+...+... |+   |...++.+.+.+..|+ ...+..+...|...|   ++++|.+.|++..... 
T Consensus        69 ~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~A~~~~~~~~~~~-  143 (225)
T 2vq2_A           69 LSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQG---QFGLAEAYLKRSLAAQ-  143 (225)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHS-
T ss_pred             HHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-
Confidence            7642 23566778888888888 77   8888888877433343 577888888999988   6799999999988754 


Q ss_pred             CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          192 KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       192 ~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..+...+..+...+...|++++|...++.+.+..-..+...+..+...+.+.|+.++|..+++.+.+
T Consensus       144 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          144 PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            3357888889999999999999999999987764224667788888888999999999999998864

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.21  E-value=6.9e-10  Score=92.06  Aligned_cols=197  Identities=11%  Similarity=0.033  Sum_probs=150.1

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ...+..+-..+...|+++.|...++...+..                   +.+...|..+-..|.+.|++++|.+.|++.
T Consensus        23 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~   83 (243)
T 2q7f_A           23 SMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-------------------KEDAIPYINFANLLSSVNELERALAFYDKA   83 (243)
T ss_dssp             -------------------CCTTHHHHHTTC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-------------------cccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4456666777888899999999999988753                   456788899999999999999999999998


Q ss_pred             HHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          117 IVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       117 ~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      .+.. +.+..++..+...+...|+   |.+.++...+.. ..+...+..+...|.+.|   ++++|.+.+++..... ..
T Consensus        84 ~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~---~~~~A~~~~~~~~~~~-~~  157 (243)
T 2q7f_A           84 LELD-SSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLE---QPKLALPYLQRAVELN-EN  157 (243)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTS---CHHHHHHHHHHHHHHC-TT
T ss_pred             HHcC-CcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhc---cHHHHHHHHHHHHHhC-Cc
Confidence            7652 2356777778888888887   888898888765 346778899999999999   7799999999988754 34


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +...+..+...+...|++++|...++.+.+.. +.+...+..+...|.+.|+.++|.+.+++..+.
T Consensus       158 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          158 DTEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             CHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc
Confidence            67889999999999999999999999998764 335778999999999999999999999998764

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.20  E-value=7.2e-09  Score=89.78  Aligned_cols=220  Identities=11%  Similarity=-0.035  Sum_probs=175.7

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------------cc-ch-hHHHhcccCC---CCChhhHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------------CA-DY-HVRLVFSQIS---NPTIYTCNSIVRGY  100 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------------y~-~~-~a~~lf~~m~---~~~~~~~~~li~~~  100 (323)
                      .+..+...+...|+++.|..+++.+.+..  |+.             -+ .. .|.+.|++..   +.+...|..+-..+
T Consensus        58 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~  135 (330)
T 3hym_B           58 CLPVHIGTLVELNKANELFYLSHKLVDLY--PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSF  135 (330)
T ss_dssp             THHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhhhHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            44556778888899999999999998864  333             11 12 6888887654   45678899999999


Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      ...|++++|.+.|++..+.. +.+...+..+-..+...|+   |.+.++...+.. ..+..++..+...|...|   +++
T Consensus       136 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~---~~~  210 (330)
T 3hym_B          136 AVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNG---EWK  210 (330)
T ss_dssp             HHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTT---CHH
T ss_pred             HHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcc---cHH
Confidence            99999999999999987753 2345667778788888887   888888887764 345788999999999999   779


Q ss_pred             HHHHHHHHHHHcC--------CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHH
Q 040801          178 EAIKIFYRMEIEN--------VKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       178 ~a~~~~~~m~~~g--------~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                      +|.+.|++.....        ...+..++..+...+...|++++|...+++..+.. +.+...+..+...|.+.|+.++|
T Consensus       211 ~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A  289 (330)
T 3hym_B          211 TAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENA  289 (330)
T ss_dssp             HHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHH
Confidence            9999999987632        13446799999999999999999999999998864 33678899999999999999999


Q ss_pred             HHHHHhccCC-CCchhhh
Q 040801          250 WDLFVKMLFP-WNNYGQW  266 (323)
Q Consensus       250 ~~~~~~m~~~-~~~~~~~  266 (323)
                      .+.+++..+. +..+..+
T Consensus       290 ~~~~~~al~~~p~~~~~~  307 (330)
T 3hym_B          290 VDYFHTALGLRRDDTFSV  307 (330)
T ss_dssp             HHHHHTTTTTCSCCHHHH
T ss_pred             HHHHHHHHccCCCchHHH
Confidence            9999999875 3344444

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.18  E-value=6.9e-11  Score=106.33  Aligned_cols=220  Identities=10%  Similarity=0.021  Sum_probs=103.7

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---ccch----hHHHhcccCC--CCChhhHHHHHHHHHhCCChHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---CADY----HVRLVFSQIS--NPTIYTCNSIVRGYTNKNLHHE  108 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~----~a~~lf~~m~--~~~~~~~~~li~~~~~~g~~~~  108 (323)
                      ..|..+..++.+.|++++|...|.........-..   +...    +|.+.++...  .++..+.+.++.+|.+.|++++
T Consensus        33 ~vWs~La~A~l~~g~~~eAIdsfika~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e  112 (449)
T 1b89_A           33 AVWSQLAKAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAE  112 (449)
T ss_dssp             ----------------------------------------------------------------------------CHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHhCCHHH
Confidence            48889999999999999999999654221111111   2222    6666555444  4556789999999999999999


Q ss_pred             HHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 040801          109 AFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYR  185 (323)
Q Consensus       109 A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~  185 (323)
                      +.++++       .|+..+|..+-..|...|.   |...|..+         ..|..|.+++++.|   ++++|++.+++
T Consensus       113 ~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg---~yq~AVea~~K  173 (449)
T 1b89_A          113 LEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLG---EYQAAVDGARK  173 (449)
T ss_dssp             HTTTTT-------CC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTT---CHHHHHHHHHH
T ss_pred             HHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhc---cHHHHHHHHHH
Confidence            998885       3788899999999999999   88888866         47999999999999   67999999998


Q ss_pred             HHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchh
Q 040801          186 MEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYG  264 (323)
Q Consensus       186 m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~  264 (323)
                      +      -++.||..++.+|+..|+++.|......     +...+.-...++..|.+.|++++|..+++....- +....
T Consensus       174 A------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-----L~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le~ah~~  242 (449)
T 1b89_A          174 A------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMG  242 (449)
T ss_dssp             H------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHH
T ss_pred             c------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCcHHHHH
Confidence            7      3789999999999999999999554443     2223334557999999999999999999987643 33445


Q ss_pred             hhHHHhhhccCCCCCcchhhhhh
Q 040801          265 QWAMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~a~~l  287 (323)
                      .|+-+..+-..-+-++..+.+++
T Consensus       243 ~ftel~il~~ky~p~k~~ehl~~  265 (449)
T 1b89_A          243 MFTELAILYSKFKPQKMREHLEL  265 (449)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHH
Confidence            56544444444445555555444

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.17  E-value=1.5e-11  Score=110.70  Aligned_cols=208  Identities=5%  Similarity=-0.035  Sum_probs=58.0

Q ss_pred             HhhcCCCchHHHHHHHHHHHhcCCCCC---ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           46 SLEKCSTMRELKQIHAQMLRTSLFFDP---CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        46 ~~~~~~~~~~a~~i~~~m~~~~~~~~~---y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+.++|++++|.+.++.+....++...   |.+.    +|.+.|..  .+|...|..++.++...|++++|.++++..++
T Consensus        12 ll~~~~~ld~A~~fae~~~~~~vWs~La~A~l~~g~~~eAIdsfik--a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark   89 (449)
T 1b89_A           12 LIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARK   89 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHccCHHHHHHHHHhCCChHHHHHHHHHHHHcCCHHHHHHHHHc--CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            345667778888888777443322222   2222    55555543  45555677777777777777777775544444


Q ss_pred             CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh
Q 040801          119 QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA  195 (323)
Q Consensus       119 ~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~  195 (323)
                      .  .++..+.+.++.+|.+.|+   +.++++       .|+..+|+.+-+.|...|   .+++|...|..+         
T Consensus        90 ~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g---~yeeA~~~Y~~a---------  148 (449)
T 1b89_A           90 K--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEK---MYDAAKLLYNNV---------  148 (449)
T ss_dssp             ---------------------CHHHHTTTTT-------CC-------------------CTTTHHHHHHHT---------
T ss_pred             h--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcC---CHHHHHHHHHHh---------
Confidence            2  3446667777777777766   332221       255667777777777777   446777777655         


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhhHHHhhhccC
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQWAMSATVGPQ  275 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~~~~~  275 (323)
                      ..|..+..++++.|+++.|.+.+.++      .++.+|..++.+|+..|+++.|......+..   .|...  ..++..+
T Consensus       149 ~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~---~ad~l--~~lv~~Y  217 (449)
T 1b89_A          149 SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIVV---HADEL--EELINYY  217 (449)
T ss_dssp             TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTTT---CHHHH--HHHHHHH
T ss_pred             hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHHh---CHhhH--HHHHHHH
Confidence            36677777777777777777777765      2567777777777777777777555544332   22221  1222333


Q ss_pred             CCCCcchhhhhh
Q 040801          276 GLVGRHSTAHQI  287 (323)
Q Consensus       276 ~~~~~~~~a~~l  287 (323)
                      .+.|+.+++..+
T Consensus       218 ek~G~~eEai~l  229 (449)
T 1b89_A          218 QDRGYFEELITM  229 (449)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             HHCCCHHHHHHH
Confidence            445556666444

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.16  E-value=5.3e-09  Score=90.24  Aligned_cols=190  Identities=9%  Similarity=-0.018  Sum_probs=137.2

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCC-ChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNP-TIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      +...+...+...++.+.|.+.++.+...+.                  .| +...+..+-..+...|++++|++.+++  
T Consensus        67 a~~~la~~~~~~~~~~~A~~~l~~ll~~~~------------------~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--  126 (291)
T 3mkr_A           67 AVRMFAEYLASHSRRDAIVAELDREMSRSV------------------DVTNTTFLLMAASIYFYDQNPDAALRTLHQ--  126 (291)
T ss_dssp             HHHHHHHHHHCSTTHHHHHHHHHHHHHSCC------------------CCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHHHhccc------------------CCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--
Confidence            334444444444455555555555444432                  34 444555566889999999999999987  


Q ss_pred             HCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHH---HHHHHHHHhcCCCCChHHHHHHHHHHHHcCC
Q 040801          118 VQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLH---NTLINMYSSCWCLDQPDEAIKIFYRMEIENV  191 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~---~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~  191 (323)
                          +.+...+..+...+.+.|+   |.+.++.+.+..  |+....   ..++..+...|   ++++|..+|+++.... 
T Consensus       127 ----~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~---~~~eA~~~~~~~l~~~-  196 (291)
T 3mkr_A          127 ----GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD--EDATLTQLATAWVSLAAGGE---KLQDAYYIFQEMADKC-  196 (291)
T ss_dssp             ----CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTT---HHHHHHHHHHHHHHHS-
T ss_pred             ----CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhCch---HHHHHHHHHHHHHHhC-
Confidence                4667788888888888888   888888888775  654322   22334444446   6799999999998873 


Q ss_pred             CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHH-HHHHHHhccCC
Q 040801          192 KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSR-AWDLFVKMLFP  259 (323)
Q Consensus       192 ~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~-a~~~~~~m~~~  259 (323)
                      +.+...++.+-.++.+.|++++|+..+++..+.. +-+..++..++..+...|+.++ +.++++++.+.
T Consensus       197 p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          197 SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            5678889999999999999999999999988763 2367788889999999999876 57888887653

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.14  E-value=1e-08  Score=84.34  Aligned_cols=190  Identities=10%  Similarity=-0.063  Sum_probs=105.6

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+..+-..+.+.|++++|...++...+..                   +.+...|..+-..+.+.|++++|.+.|++..+
T Consensus         7 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   67 (217)
T 2pl2_A            7 NPLRLGVQLYALGRYDAALTLFERALKEN-------------------PQDPEALYWLARTQLKLGLVNPALENGKTLVA   67 (217)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTS-------------------SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44555556666777777777777766553                   34556666777777777777777777777665


Q ss_pred             CCCCCC-cccHHHHHHHhcch-----------hh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHH
Q 040801          119 QGLIPD-RFMFPSLFKSCADI-----------YV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       119 ~g~~p~-~~ty~~ll~~~~~~-----------~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~  183 (323)
                      .  .|+ ...+..+-..+...           |+   |...++...+.. .-+...|..+-..|...|   ++++|++.|
T Consensus        68 ~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g---~~~~A~~~~  141 (217)
T 2pl2_A           68 R--TPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLG---ERDKAEASL  141 (217)
T ss_dssp             H--CTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             h--CCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcC---ChHHHHHHH
Confidence            3  233 34555555555555           55   555555555543 113455555666666666   446666666


Q ss_pred             HHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          184 YRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       184 ~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ++..+..  .+...+..+-..+...|++++|...++...+.. +-+...+..+...|.+.|+.++|...+++.
T Consensus       142 ~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          142 KQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            6666555  455666666666666666666666666665542 223455556666666666666666665543

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.08  E-value=8.6e-09  Score=86.08  Aligned_cols=164  Identities=9%  Similarity=-0.011  Sum_probs=138.2

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      ...|..+-..+...|++++|.+.|++..+.. +.+..++..+...+...|+   |.+.++...+.. ..+...+..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            5668888899999999999999999987753 3356778888888888888   889999888765 2367889999999


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF  245 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  245 (323)
                      |...|   ++++|.+.|++....+..| +...+..+...+...|++++|...++++.+.. +.+...+..+...|.+.|+
T Consensus       115 ~~~~g---~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~  190 (252)
T 2ho1_A          115 LYEQK---RYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKERE  190 (252)
T ss_dssp             HHHTT---CHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHh---HHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCC
Confidence            99999   7799999999998743445 56788888999999999999999999998764 3357888999999999999


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      .++|...+++..+.
T Consensus       191 ~~~A~~~~~~~~~~  204 (252)
T 2ho1_A          191 YVPARQYYDLFAQG  204 (252)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999998765

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.07  E-value=6.3e-09  Score=96.00  Aligned_cols=237  Identities=7%  Similarity=-0.134  Sum_probs=165.8

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---------ccch----hHHHhcccCC---CCChhhHHHHHHHHHh
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTN  102 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~  102 (323)
                      .+...-..+.+.|+++.|...|+++.+..  |+.         |.+.    .|.+.|++..   +.+...|..+...|.+
T Consensus         8 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~   85 (514)
T 2gw1_A            8 ALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEG   85 (514)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHH
Confidence            34455567778899999999999998876  454         2211    7777777654   5567889999999999


Q ss_pred             CCChHHHHHHHHHHHHCCCCCCcccH------------------------------------------------------
Q 040801          103 KNLHHEAFLFYHEMIVQGLIPDRFMF------------------------------------------------------  128 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g~~p~~~ty------------------------------------------------------  128 (323)
                      .|++++|.+.|+++...+- ++....                                                      
T Consensus        86 ~g~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           86 LGKFADAMFDLSVLSLNGD-FNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             TTCHHHHHHHHHHHHHSSS-CCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HhhHHHHHHHHHHHHhcCC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            9999999999999876542 111111                                                      


Q ss_pred             -----------------------HHHHHH--hc---chhh---HHHHHHHHHH-----cCCC--------CchHHHHHHH
Q 040801          129 -----------------------PSLFKS--CA---DIYV---EKQLHSQAIK-----FGLA--------SDSFLHNTLI  164 (323)
Q Consensus       129 -----------------------~~ll~~--~~---~~~~---a~~~~~~m~~-----~g~~--------~~~~~~~~li  164 (323)
                                             ..+..+  +.   +.|+   |..+++.+.+     ..-.        .+..++..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (514)
T 2gw1_A          165 ASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTG  244 (514)
T ss_dssp             HHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHH
Confidence                                   111111  11   2455   8888888877     3212        2356788888


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      ..|...|   ++++|.+.|++.....  |+..++..+...+...|++++|...++.+.+.. +.+...|..+...|.+.|
T Consensus       245 ~~~~~~~---~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  318 (514)
T 2gw1_A          245 IFKFLKN---DPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQ  318 (514)
T ss_dssp             HHHHHSS---CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHCC---CHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhC
Confidence            8899999   6799999999988765  338888888899999999999999999887753 335677888888999999


Q ss_pred             CHHHHHHHHHhccCC-CCchhhhHHHhhhccCCCCCcchhhhh
Q 040801          245 FVSRAWDLFVKMLFP-WNNYGQWAMSATVGPQGLVGRHSTAHQ  286 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~  286 (323)
                      ++++|...+++..+. +..+..+  ......+...|+.++|..
T Consensus       319 ~~~~A~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~A~~  359 (514)
T 2gw1_A          319 NYDQAGKDFDKAKELDPENIFPY--IQLACLAYRENKFDDCET  359 (514)
T ss_dssp             CTTHHHHHHHHHHHTCSSCSHHH--HHHHHHTTTTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHhChhhHHHH--HHHHHHHHHcCCHHHHHH
Confidence            999999999988654 2223333  222333344556665543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.07  E-value=3.2e-08  Score=80.62  Aligned_cols=166  Identities=10%  Similarity=0.002  Sum_probs=138.1

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHH
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      .+...|..+...+...|++++|.+.|++..+.. +.+...+..+...+...|+   |.+.++...+.. ..+..++..+.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~   83 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYG   83 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            355678889999999999999999999987742 2346678888888888888   888888888765 33677889999


Q ss_pred             HHHHhc-CCCCChHHHHHHHHHHHHcCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh
Q 040801          165 NMYSSC-WCLDQPDEAIKIFYRMEIENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK  242 (323)
Q Consensus       165 ~~~~~~-g~~~~~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  242 (323)
                      ..|... |   ++++|.+.|++....+..| +...+..+...+...|++++|...++++.+.. +.+...+..+...|.+
T Consensus        84 ~~~~~~~~---~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  159 (225)
T 2vq2_A           84 WFLCGRLN---RPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKML  159 (225)
T ss_dssp             HHHHTTTC---CHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHhcC---cHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHH
Confidence            999999 9   7799999999998733334 36788889999999999999999999998764 2357788999999999


Q ss_pred             cCCHHHHHHHHHhccCC
Q 040801          243 CKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~~  259 (323)
                      .|++++|...+++..+.
T Consensus       160 ~~~~~~A~~~~~~~~~~  176 (225)
T 2vq2_A          160 AGQLGDADYYFKKYQSR  176 (225)
T ss_dssp             HTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHh
Confidence            99999999999998754

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.05  E-value=1.9e-09  Score=95.49  Aligned_cols=193  Identities=7%  Similarity=-0.081  Sum_probs=140.2

Q ss_pred             hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHH
Q 040801           77 HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIK  150 (323)
Q Consensus        77 ~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~  150 (323)
                      .|.++|++..   +.+...|..+-..|.+.|++++|.+.|++..+.. +.+..+|..+...+...|+   |...++.+.+
T Consensus        83 ~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  161 (365)
T 4eqf_A           83 VTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWIK  161 (365)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHHH
Confidence            7777777664   5577888999999999999999999999887642 2346778888888888888   8888888776


Q ss_pred             cCCCCc-----------hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC-CChHHHHHHHHHHhccCChHHHHHHH
Q 040801          151 FGLASD-----------SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK-PNAVTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       151 ~g~~~~-----------~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                      ..  |+           ...+..+...|.+.|   ++++|.+.|+++....-. ++..++..+...+...|++++|...+
T Consensus       162 ~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~  236 (365)
T 4eqf_A          162 QN--PKYKYLVKNKKGSPGLTRRMSKSPVDSS---VLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAF  236 (365)
T ss_dssp             HC--HHHHCC-------------------CCH---HHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             hC--ccchHHHhhhccchHHHHHHHHHHhhhh---hHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            53  22           233344577788888   668999999998875422 26889999999999999999999999


Q ss_pred             HHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCC
Q 040801          219 KCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQG  276 (323)
Q Consensus       219 ~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~  276 (323)
                      +++.+.. +.+..+|..+...|.+.|++++|...|++..+. +..+..| .+...+...|
T Consensus       237 ~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g  295 (365)
T 4eqf_A          237 NAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLG  295 (365)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCC
Confidence            9998863 335788999999999999999999999998764 2334444 4444444444

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.04  E-value=1.2e-08  Score=83.85  Aligned_cols=190  Identities=11%  Similarity=-0.016  Sum_probs=142.6

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHH
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      ++...|..+-..+.+.|++++|...|++..+.. +-+...+..+-..+.+.|+   |...++...+.. ..+...+..+-
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            456678888889999999999999999987642 2355677777777777777   888888888765 23467788888


Q ss_pred             HHHHhc-----------CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhH
Q 040801          165 NMYSSC-----------WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELK  233 (323)
Q Consensus       165 ~~~~~~-----------g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  233 (323)
                      ..|.+.           |   ++++|++.|++..+.. +-+...+..+-..+...|++++|...+++..+..  .+...+
T Consensus        81 ~~~~~~~~~~~~~~~~~g---~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~  154 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKG---YLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIR  154 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHH---HHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHH
T ss_pred             HHHHHhhhhhhhhccccc---CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHH
Confidence            889988           8   6799999999988754 2356788888899999999999999999999987  688899


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhhhhhh
Q 040801          234 TTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTAHQIS  288 (323)
Q Consensus       234 ~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~~l~  288 (323)
                      ..+-..|...|++++|...|++..+. +..+..+ .+...+   ...|+.++|...+
T Consensus       155 ~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~---~~~g~~~~A~~~~  208 (217)
T 2pl2_A          155 SALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASAL---LLKGKAEEAARAA  208 (217)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHH---TC-----------
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHH---HHccCHHHHHHHH
Confidence            99999999999999999999998764 3333333 333333   3445555554433

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.03  E-value=5.5e-09  Score=90.41  Aligned_cols=215  Identities=8%  Similarity=-0.119  Sum_probs=165.0

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHH--
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSI--   96 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~l--   96 (323)
                      +...+..+...+...|+++.|...++...+..  |+.          |...    .|.+.|++..   +.+...+..+  
T Consensus        54 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~  131 (327)
T 3cv0_A           54 REEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQ  131 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTTTC------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhH
Confidence            34456677788889999999999999998873  443          2111    7777776654   2333334333  


Q ss_pred             ------------HH-HHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHH
Q 040801           97 ------------VR-GYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLH  160 (323)
Q Consensus        97 ------------i~-~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~  160 (323)
                                  -. .+...|++++|.+.+++..+.. +.+..++..+...+.+.|+   |.+.++...+.. ..+..+|
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  209 (327)
T 3cv0_A          132 ADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLW  209 (327)
T ss_dssp             --------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHH
Confidence                        22 3778899999999999997753 2366788888888888888   888888887764 3357889


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-----------C
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-----------H  229 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-----------~  229 (323)
                      ..+...|...|   ++++|.+.|++..... ..+..++..+...+...|++++|...++.+.+..-..           +
T Consensus       210 ~~l~~~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  285 (327)
T 3cv0_A          210 NKLGATLANGN---RPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREAT  285 (327)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHH
T ss_pred             HHHHHHHHHcC---CHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcC
Confidence            99999999999   7799999999988754 3467889999999999999999999999997753221           4


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ...|..+..+|.+.|+.++|..++++..+
T Consensus       286 ~~~~~~l~~~~~~~g~~~~A~~~~~~~l~  314 (327)
T 3cv0_A          286 RSMWDFFRMLLNVMNRPDLVELTYAQNVE  314 (327)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHTTCCSH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            67899999999999999999999886554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.02  E-value=4.4e-08  Score=81.58  Aligned_cols=204  Identities=10%  Similarity=-0.061  Sum_probs=152.6

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC---------ccch----hHHHhcccCC--CC----C----hhhHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP---------CADY----HVRLVFSQIS--NP----T----IYTCNS   95 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~---------y~~~----~a~~lf~~m~--~~----~----~~~~~~   95 (323)
                      .+..+-..+...|+++.|...++...+..  .+.         |...    .|.+.|.+..  .|    +    ...|..
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45667778888999999999999999887  333         1111    6666666543  11    1    577888


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      +-..|.+.|++++|.+.|++..+.  .|+..       .+.+.|+   +...++...+.. ..+...|..+...|...| 
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~-------~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-  153 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTE--HRTAD-------ILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFTKS-  153 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CCCHH-------HHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhc--CchhH-------HHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHhc-
Confidence            888888999999999998888763  34422       2333344   777777776643 224567888888888988 


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                        ++++|.+.|++..... +.+..+|..+...+...|++++|...++...+.. +.+...|..+...|.+.|+.++|.+.
T Consensus       154 --~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (258)
T 3uq3_A          154 --DWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALET  229 (258)
T ss_dssp             --CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             --CHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence              6699999999988754 3467888889999999999999999999988764 33477788888999999999999999


Q ss_pred             HHhccCC
Q 040801          253 FVKMLFP  259 (323)
Q Consensus       253 ~~~m~~~  259 (323)
                      +++..+.
T Consensus       230 ~~~a~~~  236 (258)
T 3uq3_A          230 LDAARTK  236 (258)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9887653

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.02  E-value=4.3e-08  Score=85.69  Aligned_cols=194  Identities=7%  Similarity=-0.147  Sum_probs=156.8

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+..+-..+...|+++.|...++...+..                   +.+...|..+-..+...|++++|.+.|++..+
T Consensus         5 ~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-------------------p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~   65 (359)
T 3ieg_A            5 KHLELGKKLLAAGQLADALSQFHAAVDGD-------------------PDNYIAYYRRATVFLAMGKSKAALPDLTKVIA   65 (359)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC-------------------cccHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            44556677888999999999999999874                   45677888899999999999999999999876


Q ss_pred             CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC----chHHHHHH------------HHHHHhcCCCCChHHH
Q 040801          119 QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS----DSFLHNTL------------INMYSSCWCLDQPDEA  179 (323)
Q Consensus       119 ~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~----~~~~~~~l------------i~~~~~~g~~~~~~~a  179 (323)
                      .. +-+...+..+-..+...|+   |...++...+..  |    +...+..+            ...+...|   ++++|
T Consensus        66 ~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~---~~~~A  139 (359)
T 3ieg_A           66 LK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN--PSEQEEKEAESQLVKADEMQRLRSQALDAFDGA---DYTAA  139 (359)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---CHHHH
T ss_pred             hC-CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHHcc---CHHHH
Confidence            42 2245677777888888887   888888887654  4    34444444            47788888   77999


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.|++..... +.+...+..+...+...|++++|...++.+.+.. +.+...+..+...|.+.|++++|...+++..+.
T Consensus       140 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  217 (359)
T 3ieg_A          140 ITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  217 (359)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            99999998764 3467888999999999999999999999998763 346788999999999999999999999988754

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.01  E-value=8.4e-09  Score=91.05  Aligned_cols=213  Identities=10%  Similarity=-0.092  Sum_probs=164.6

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHH---
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNS---   95 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~---   95 (323)
                      +...+..+...+...|+++.|...++...+..  |+.          |...    .|.+.|++..   +.+...+..   
T Consensus        97 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  174 (368)
T 1fch_A           97 HMEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEE  174 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC----
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            34466778888999999999999999998874  444          2222    7777777654   222222321   


Q ss_pred             ------------HHHHHHhCCChHHHHHHHHHHHHCCCC-CCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHH
Q 040801           96 ------------IVRGYTNKNLHHEAFLFYHEMIVQGLI-PDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFL  159 (323)
Q Consensus        96 ------------li~~~~~~g~~~~A~~~~~~m~~~g~~-p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~  159 (323)
                                  .+..+...|++++|.+.|+++.+..-. ++..++..+-..+.+.|+   |...++...+.. ..+..+
T Consensus       175 ~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~  253 (368)
T 1fch_A          175 GAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLL  253 (368)
T ss_dssp             -----------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHH
Confidence                        245555899999999999999774321 146788888888888888   888998888764 235788


Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc----------C
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS----------H  229 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p----------~  229 (323)
                      |..+...|.+.|   ++++|.+.|++..... +.+..++..+...+.+.|++++|...++.+.+..-..          .
T Consensus       254 ~~~l~~~~~~~g---~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  329 (368)
T 1fch_A          254 WNKLGATLANGN---QSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMS  329 (368)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCC
T ss_pred             HHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchh
Confidence            999999999999   7799999999998754 3467899999999999999999999999997642111          1


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      ...|..+..+|.+.|+.++|..++++
T Consensus       330 ~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          330 ENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             hHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            57899999999999999999998874

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.01  E-value=1.7e-08  Score=86.65  Aligned_cols=208  Identities=11%  Similarity=-0.033  Sum_probs=150.7

Q ss_pred             cchhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHH
Q 040801           36 SQYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHE  115 (323)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  115 (323)
                      ....+..+...+...|+++.|..+++...+..-           +....-.......+..+-..|...|++++|.+.|++
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~-----------~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~   94 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLE-----------KTSGHDHPDVATMLNILALVYRDQNKYKDAANLLND   94 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----------HHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-----------HHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            445677888889999999999999998887411           000000033456788888999999999999999998


Q ss_pred             HHHC------C-CCCCcccHHHHHHHhcchhh---HHHHHHHHHHc------CCCC-chHHHHHHHHHHHhcCCCCChHH
Q 040801          116 MIVQ------G-LIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF------GLAS-DSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       116 m~~~------g-~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~------g~~~-~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      ..+.      + ......++..+-..+...|+   |...++...+.      +-.| ...++..+-..|...|   ++++
T Consensus        95 al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~---~~~~  171 (311)
T 3nf1_A           95 ALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQG---KYEE  171 (311)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT---CHHH
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcC---CHHH
Confidence            8653      1 12234667777778888887   77777777654      3223 4566888888999988   6799


Q ss_pred             HHHHHHHHHHc------CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC--------------------------
Q 040801          179 AIKIFYRMEIE------NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESG--------------------------  225 (323)
Q Consensus       179 a~~~~~~m~~~------g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g--------------------------  225 (323)
                      |.+.|++....      +-.| ...++..+...+...|++++|...++++.+..                          
T Consensus       172 A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  251 (311)
T 3nf1_A          172 VEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECK  251 (311)
T ss_dssp             HHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhc
Confidence            99999988764      2233 34578888899999999999999999987531                          


Q ss_pred             ----------------------CccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          226 ----------------------FWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       226 ----------------------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                                            -..+..++..+...|.+.|++++|.+.+++..
T Consensus       252 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  305 (311)
T 3nf1_A          252 GKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAM  305 (311)
T ss_dssp             ------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                                  12234567777788888888888888887654

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.98  E-value=4.7e-08  Score=90.07  Aligned_cols=217  Identities=10%  Similarity=-0.095  Sum_probs=166.0

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------ccch----hHHHhcccCC---CCChhhHHHHHHHHHh
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTN  102 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~  102 (323)
                      ...+..+...+...|+++.|...++...+..-.+..       |...    .|.+.|++..   +.+...|..+...|..
T Consensus       237 ~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  316 (514)
T 2gw1_A          237 AISLEHTGIFKFLKNDPLGAHEDIKKAIELFPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFI  316 (514)
T ss_dssp             HHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHH
Confidence            345566777888899999999999999887644111       1111    6666666543   4567788889999999


Q ss_pred             CCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHH
Q 040801          103 KNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      .|++++|.+.|++..+.. +.+..++..+...+...|+   |...++.+.+.. ..+..+|..+...|.+.|   ++++|
T Consensus       317 ~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~---~~~~A  391 (514)
T 2gw1_A          317 LQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKN---DFDKA  391 (514)
T ss_dssp             TTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTT---CHHHH
T ss_pred             hCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCC---CHHHH
Confidence            999999999999987753 2356778888888888888   888888887654 235677888888999988   66899


Q ss_pred             HHHHHHHHHcCC-CCC----hHHHHHHHHHHhc---cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHH
Q 040801          180 IKIFYRMEIENV-KPN----AVTLVNVLTARAR---ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       180 ~~~~~~m~~~g~-~p~----~~t~~~li~~~~~---~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                      .+.|++...... .++    ..+|..+...+..   .|++++|...++.+.+.. +.+...+..+...|.+.|++++|..
T Consensus       392 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~  470 (514)
T 2gw1_A          392 LKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAIT  470 (514)
T ss_dssp             HHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHH
Confidence            999988876321 122    3488888889999   999999999999988763 3356778888899999999999999


Q ss_pred             HHHhccCC
Q 040801          252 LFVKMLFP  259 (323)
Q Consensus       252 ~~~~m~~~  259 (323)
                      .|++..+.
T Consensus       471 ~~~~a~~~  478 (514)
T 2gw1_A          471 LFEESADL  478 (514)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            99988764

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.98  E-value=2e-08  Score=84.70  Aligned_cols=165  Identities=7%  Similarity=-0.110  Sum_probs=108.1

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      +.+...|..+-..|...|++++|.+.|++..+.. +.+..++..+-..+.+.|+   |...++.+.+..  |+.......
T Consensus        74 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~~~~~~~~~  150 (275)
T 1xnf_A           74 PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD--PNDPFRSLW  150 (275)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCChHHHHH
Confidence            4456777777778888888888888887776642 2245667777777777777   777777776643  444444444


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc--c-ChhhHHHHHHHH
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW--S-HVELKTTLMDAY  240 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~--p-~~~~~~~li~~~  240 (323)
                      +..+...|   ++++|.+.+++..... .++...+. +...+...++.++|...+....+....  | +...|..+...|
T Consensus       151 ~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~  225 (275)
T 1xnf_A          151 LYLAEQKL---DEKQAKEVLKQHFEKS-DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYY  225 (275)
T ss_dssp             HHHHHHHH---CHHHHHHHHHHHHHHS-CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhc---CHHHHHHHHHHHHhcC-CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHH
Confidence            44555556   5678888887666543 33444443 666666777777777777766443211  1 146677777888


Q ss_pred             HhcCCHHHHHHHHHhccCC
Q 040801          241 CKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       241 ~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.|++++|...|++..+.
T Consensus       226 ~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          226 LSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHcCCHHHHHHHHHHHHhC
Confidence            8888888888888887765

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.95  E-value=2.1e-08  Score=83.58  Aligned_cols=180  Identities=12%  Similarity=-0.033  Sum_probs=133.4

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcC--CCCc----hHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFG--LASD----SFLHN  161 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g--~~~~----~~~~~  161 (323)
                      ..|..+-..+...|++++|.++|++..+..  .+..+|..+-..+...|+   |.+.++...+..  ..++    ..+|.
T Consensus         6 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   83 (258)
T 3uq3_A            6 DKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFA   83 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHH
Confidence            456777778888888888888888887766  777788888888887777   777777766543  1112    57788


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcC------------------------CCC-ChHHHHHHHHHHhccCChHHHHH
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIEN------------------------VKP-NAVTLVNVLTARARARDLRTVKR  216 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g------------------------~~p-~~~t~~~li~~~~~~~~~~~a~~  216 (323)
                      .+...|...|   ++++|.+.|++.....                        ..| +...+..+...+...|++++|..
T Consensus        84 ~l~~~~~~~~---~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~  160 (258)
T 3uq3_A           84 RIGNAYHKLG---DLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVK  160 (258)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHcc---cHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHH
Confidence            8888888888   6688888888877632                        222 45678888889999999999999


Q ss_pred             HHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCC
Q 040801          217 VHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQG  276 (323)
Q Consensus       217 ~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~  276 (323)
                      .++.+.+.. +.+...|..+...|.+.|++++|...+++..+. +..+..| .....+...|
T Consensus       161 ~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g  221 (258)
T 3uq3_A          161 AYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVK  221 (258)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHh
Confidence            999998764 336788999999999999999999999998754 2334444 3334443333

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.94  E-value=1.7e-07  Score=81.82  Aligned_cols=236  Identities=8%  Similarity=-0.052  Sum_probs=171.2

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC--CC----ChhhHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS--NP----TIYTCNSI   96 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~--~~----~~~~~~~l   96 (323)
                      ...+..+...+...|+++.|...++...+..  |+.          |...    .|.+.|++..  .|    +...+..+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l  114 (359)
T 3ieg_A           37 YIAYYRRATVFLAMGKSKAALPDLTKVIALK--MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQL  114 (359)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHH
Confidence            3466777788888999999999999998773  444          2111    7888887764  33    44555555


Q ss_pred             ------------HHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHH
Q 040801           97 ------------VRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        97 ------------i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~  161 (323)
                                  ...+...|++++|.++|++..+.. +.+...+..+-..+...|+   |...++...+.. ..+..++.
T Consensus       115 ~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  192 (359)
T 3ieg_A          115 VKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFY  192 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHH
Confidence                        478899999999999999987652 3456777788888888888   888888887754 34678889


Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHH------------HHHHHhccCChHHHHHHHHHHHHhCCccC
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVN------------VLTARARARDLRTVKRVHKCVDESGFWSH  229 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~------------li~~~~~~~~~~~a~~~~~~m~~~g~~p~  229 (323)
                      .+...|...|   ++++|.+.|++..... ..+...+..            +...+.+.|++++|...++.+.+..  |+
T Consensus       193 ~la~~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~  266 (359)
T 3ieg_A          193 KISTLYYQLG---DHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PS  266 (359)
T ss_dssp             HHHHHHHHHT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CS
T ss_pred             HHHHHHHHcC---CHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CC
Confidence            9999999999   6799999999988754 223333332            2556889999999999999998764  33


Q ss_pred             h-----hhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhhh
Q 040801          230 V-----ELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       230 ~-----~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~  285 (323)
                      .     ..+..+...|.+.|++++|...+++..+. +..+..| .....+..   .|+.++|.
T Consensus       267 ~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~A~  326 (359)
T 3ieg_A          267 VAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLI---EEMYDEAI  326 (359)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH---TTCHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH---cCCHHHHH
Confidence            2     23556778999999999999999999874 3344444 34444433   45555553

>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=98.92  E-value=6.7e-07  Score=75.67  Aligned_cols=213  Identities=13%  Similarity=-0.047  Sum_probs=161.2

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHh----CCChHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTN----KNLHHEAFLFY  113 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~----~g~~~~A~~~~  113 (323)
                      ..+..+-..+...+++++|...|+...+.+.                     ...+..+-..|..    .+++++|.+.|
T Consensus         7 ~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~~---------------------~~a~~~lg~~~~~g~~~~~~~~~A~~~~   65 (273)
T 1ouv_A            7 KELVGLGAKSYKEKDFTQAKKYFEKACDLKE---------------------NSGCFNLGVLYYQGQGVEKNLKKAASFY   65 (273)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC---------------------HHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCC---------------------HHHHHHHHHHHHcCCCcCCCHHHHHHHH
Confidence            3455566677788899999999998887542                     3566777778888    99999999999


Q ss_pred             HHHHHCCCCCCcccHHHHHHHhcc----hhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh----cCCCCChHHHHHH
Q 040801          114 HEMIVQGLIPDRFMFPSLFKSCAD----IYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS----CWCLDQPDEAIKI  182 (323)
Q Consensus       114 ~~m~~~g~~p~~~ty~~ll~~~~~----~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~~~~a~~~  182 (323)
                      ++-.+.+   +...+..+-..+..    .++   |.+.++...+.+   +...+..+-..|..    .|   ++++|++.
T Consensus        66 ~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~---~~~~A~~~  136 (273)
T 1ouv_A           66 AKACDLN---YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTR---DFKKAVEY  136 (273)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCC---CHHHHHHH
T ss_pred             HHHHHCC---CHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCccc---CHHHHHHH
Confidence            9988876   56667777666665    566   888888888875   67788888888888    77   77999999


Q ss_pred             HHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh----cCCHHHHHHHHH
Q 040801          183 FYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK----CKFVSRAWDLFV  254 (323)
Q Consensus       183 ~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~~~~  254 (323)
                      |++..+.+   +...+..+-..+..    .++.++|...+++..+.+   +...+..+-..|.+    .++.++|...|+
T Consensus       137 ~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~  210 (273)
T 1ouv_A          137 FTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYS  210 (273)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHH
T ss_pred             HHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHH
Confidence            99988866   56677777777777    899999999999998875   46777888888999    999999999999


Q ss_pred             hccCCCCchhhh-HHHhhhcc-CCCCCcchhhhhh
Q 040801          255 KMLFPWNNYGQW-AMSATVGP-QGLVGRHSTAHQI  287 (323)
Q Consensus       255 ~m~~~~~~~~~~-~~~~~~~~-~~~~~~~~~a~~l  287 (323)
                      +..+.+. +..+ .+...+.. .+..++.++|...
T Consensus       211 ~a~~~~~-~~a~~~l~~~~~~g~~~~~~~~~A~~~  244 (273)
T 1ouv_A          211 KACELEN-GGGCFNLGAMQYNGEGVTRNEKQAIEN  244 (273)
T ss_dssp             HHHHTTC-HHHHHHHHHHHHTTSSSSCCSTTHHHH
T ss_pred             HHHhCCC-HHHHHHHHHHHHcCCCcccCHHHHHHH
Confidence            9887654 3333 33333332 2334555555433

>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=98.91  E-value=1.2e-07  Score=74.41  Aligned_cols=162  Identities=10%  Similarity=-0.056  Sum_probs=134.3

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      ..|..+-..+...|++++|.+.|++..+.. +.+..++..+...+...|+   |.+.++...+.. ..+...+..+...|
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            457778888999999999999998886542 2356677777778888877   888888887764 34577888899999


Q ss_pred             HhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      ...|   ++++|.+.|++..... ..+...+..+...+...|++++|...++.+.+.. +.+...+..+...|.+.|+.+
T Consensus        87 ~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~  161 (186)
T 3as5_A           87 VQVQ---KYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHE  161 (186)
T ss_dssp             HHHT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHhc---CHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHH
Confidence            9999   7799999999988764 4577888899999999999999999999998764 345788999999999999999


Q ss_pred             HHHHHHHhccCC
Q 040801          248 RAWDLFVKMLFP  259 (323)
Q Consensus       248 ~a~~~~~~m~~~  259 (323)
                      +|...+++..+.
T Consensus       162 ~A~~~~~~~~~~  173 (186)
T 3as5_A          162 EALPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc
Confidence            999999987653

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.91  E-value=1.6e-08  Score=83.59  Aligned_cols=183  Identities=10%  Similarity=-0.020  Sum_probs=127.8

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      ......|..+-..+...|++++|.++|++..+.. +.+...+..+...+...|+   |.+.++...+.. ..+..++..+
T Consensus        20 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l   97 (243)
T 2q7f_A           20 HMASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGA   97 (243)
T ss_dssp             ----------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHH
Confidence            3455667888888999999999999999998742 3356777777788888887   888888888765 3467888999


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  243 (323)
                      ...|...|   ++++|.+.|++..... ..+...+..+...+...|++++|...++++.+.. +.+...+..+...|.+.
T Consensus        98 a~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  172 (243)
T 2q7f_A           98 GNVYVVKE---MYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANE  172 (243)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhc---cHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHc
Confidence            99999999   7799999999998765 3467889999999999999999999999998763 33677889999999999


Q ss_pred             CCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCC
Q 040801          244 KFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQG  276 (323)
Q Consensus       244 g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~  276 (323)
                      |++++|...+++..+. +..+..| .+...+...+
T Consensus       173 ~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~  207 (243)
T 2q7f_A          173 GMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKE  207 (243)
T ss_dssp             TCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcc
Confidence            9999999999998754 2334444 4444444444

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.86  E-value=1.1e-06  Score=76.08  Aligned_cols=166  Identities=8%  Similarity=-0.032  Sum_probs=132.0

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcc--cHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRF--MFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~--ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      +.+...|..+...+.+.|++++|.++|++..+  +.|+..  .|..+...+.+.|+   |..+|+...+..- .+...|.
T Consensus        96 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~  172 (308)
T 2ond_A           96 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYV  172 (308)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHH
T ss_pred             cccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC-CCHHHHH
Confidence            44667899999999999999999999999987  456543  68888888887777   8889998887642 2344454


Q ss_pred             HHHHHHH-hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC-Ccc--ChhhHHHHH
Q 040801          162 TLINMYS-SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG-FWS--HVELKTTLM  237 (323)
Q Consensus       162 ~li~~~~-~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p--~~~~~~~li  237 (323)
                      ....... ..|   +.++|.++|++..... .-+...|..++..+.+.|+.++|..+|++..+.. +.|  ....|..++
T Consensus       173 ~~a~~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~  248 (308)
T 2ond_A          173 TAALMEYYCSK---DKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFL  248 (308)
T ss_dssp             HHHHHHHHTSC---CHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHH
T ss_pred             HHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence            3333322 246   7799999999987753 2367889999999999999999999999999873 565  366899999


Q ss_pred             HHHHhcCCHHHHHHHHHhccCC
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..+.+.|+.++|..+++++.+.
T Consensus       249 ~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          249 AFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999999999999998764

>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=98.84  E-value=7.1e-07  Score=82.75  Aligned_cols=158  Identities=12%  Similarity=-0.073  Sum_probs=114.8

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      |..+-..+...|++++|.+.|++..+.  .|+..++..+-..+...|+   |...++...+.. ..+..+|..+...|..
T Consensus       246 ~~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  322 (537)
T 3fp2_A          246 LCYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFI  322 (537)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHh
Confidence            445556677777888888888877663  4556677777777777777   777777776654 2346677778888888


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                      .|   ++++|.+.|++..... ..+..+|..+...+...|++++|...++.+.+.. +.+...+..+...|.+.|++++|
T Consensus       323 ~~---~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A  397 (537)
T 3fp2_A          323 LQ---DYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTA  397 (537)
T ss_dssp             TT---CHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHH
T ss_pred             cC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHH
Confidence            87   6688888888877654 2345677778888888888888888888887663 33456777788888888888888


Q ss_pred             HHHHHhccC
Q 040801          250 WDLFVKMLF  258 (323)
Q Consensus       250 ~~~~~~m~~  258 (323)
                      ...+++..+
T Consensus       398 ~~~~~~a~~  406 (537)
T 3fp2_A          398 IKQYDIAKR  406 (537)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888887654

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.80  E-value=8e-07  Score=70.35  Aligned_cols=164  Identities=13%  Similarity=-0.048  Sum_probs=133.2

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLIN  165 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~  165 (323)
                      +...|..+=..|.+.|++++|.+.|++..+.. +-+..++..+-..+.+.|+   +...+....+... -+...+..+-.
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHHH
Confidence            56678888899999999999999999987642 2245677777778888887   7777777766552 34566777777


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF  245 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  245 (323)
                      .+...+   +++.+.+.+.+..... .-+...+..+-..+.+.|++++|...+++..+.. +-+...|..+-.+|.+.|+
T Consensus        82 ~~~~~~---~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~  156 (184)
T 3vtx_A           82 ANFMID---EKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGL  156 (184)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHcC---CHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCC
Confidence            888888   7799999999887754 3467788888999999999999999999998864 3357789999999999999


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      .++|.+.|++..+.
T Consensus       157 ~~~A~~~~~~al~~  170 (184)
T 3vtx_A          157 RDEAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999998765

>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=98.79  E-value=5e-07  Score=83.80  Aligned_cols=214  Identities=10%  Similarity=-0.052  Sum_probs=157.4

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------ccch----hHHHhcccCC---CCChhhHHHHHHHHHhCCC
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTNKNL  105 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~~g~  105 (323)
                      +..+-..+...|+++.|...++...+..-.+..       |...    .|.+.|.+..   +.+...|..+-..+...|+
T Consensus       246 ~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  325 (537)
T 3fp2_A          246 LCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQD  325 (537)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCC
Confidence            445556777789999999999999887533222       2222    7777777654   4567788888899999999


Q ss_pred             hHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHH
Q 040801          106 HHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKI  182 (323)
Q Consensus       106 ~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~  182 (323)
                      +++|.+.|++..+.. +-+..++..+-..+...|+   |...++...+.. ..+...+..+-..|...|   ++++|.+.
T Consensus       326 ~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g---~~~~A~~~  400 (537)
T 3fp2_A          326 YKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRG---DFDTAIKQ  400 (537)
T ss_dssp             HHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhC---CHHHHHHH
Confidence            999999999887642 2245677777788877777   888888887764 334667888888888888   66899999


Q ss_pred             HHHHHHcC-----CCCChHHHHHHHHHHhcc----------CChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          183 FYRMEIEN-----VKPNAVTLVNVLTARARA----------RDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       183 ~~~m~~~g-----~~p~~~t~~~li~~~~~~----------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      |++.....     .......+......+...          |++++|...++.+.+.. +.+...+..+...|.+.|+.+
T Consensus       401 ~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~  479 (537)
T 3fp2_A          401 YDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKID  479 (537)
T ss_dssp             HHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHH
Confidence            98876532     111222344445566666          89999999999988763 235677888889999999999


Q ss_pred             HHHHHHHhccCC
Q 040801          248 RAWDLFVKMLFP  259 (323)
Q Consensus       248 ~a~~~~~~m~~~  259 (323)
                      +|.+.|++..+.
T Consensus       480 ~A~~~~~~al~~  491 (537)
T 3fp2_A          480 EAIELFEDSAIL  491 (537)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999987654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.79  E-value=4.1e-07  Score=76.51  Aligned_cols=189  Identities=10%  Similarity=-0.091  Sum_probs=149.1

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcc
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRF  126 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~  126 (323)
                      ....++++.|...++++.+.....               ++.+...|..+-..+...|++++|.+.|++..+.. +.+..
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~---------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~   78 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALT---------------DDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPE   78 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCC---------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHH
T ss_pred             cCccchHHHHHHHHHHHHhccccc---------------CchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHH
Confidence            445578899999999888763200               02246778899999999999999999999998752 23567


Q ss_pred             cHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          127 MFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       127 ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      +|..+-..+...|+   |.+.++...+.. ..+..++..+...|.+.|   ++++|.+.|++....  .|+.......+.
T Consensus        79 ~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~g---~~~~A~~~~~~a~~~--~~~~~~~~~~~~  152 (275)
T 1xnf_A           79 VFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYGG---RDKLAQDDLLAFYQD--DPNDPFRSLWLY  152 (275)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTT---CHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHhc---cHHHHHHHHHHHHHh--CCCChHHHHHHH
Confidence            88888888888888   999999988764 235788999999999999   779999999999874  466656666666


Q ss_pred             HHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          204 ARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       204 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+...|+.++|...++...+.. +++...+ .+...+...++.++|...+++..+.
T Consensus       153 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~  206 (275)
T 1xnf_A          153 LAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATD  206 (275)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCS
T ss_pred             HHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcc
Confidence            7778899999999998887753 3344444 4778888999999999999998876

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.75  E-value=8.9e-07  Score=81.65  Aligned_cols=193  Identities=11%  Similarity=-0.004  Sum_probs=133.5

Q ss_pred             hhhhhHHHhhcCCCc-hHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTM-RELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        39 ~~~~li~~~~~~~~~-~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      .+..+-..+...|++ +.|...++...+..                   +.+...|..+-..|.+.|++++|.+.|++..
T Consensus       104 ~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al  164 (474)
T 4abn_A          104 ALMLKGKALNVTPDYSPEAEVLLSKAVKLE-------------------PELVEAWNQLGEVYWKKGDVTSAHTCFSGAL  164 (474)
T ss_dssp             HHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccHHHHHHHHHHHHhhC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            344444555556666 66666666666553                   3456777888888888888888888888877


Q ss_pred             HCCCCCCcccHHHHHHHhcch---------hh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc--------CCCCChH
Q 040801          118 VQGLIPDRFMFPSLFKSCADI---------YV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC--------WCLDQPD  177 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~---------~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~--------g~~~~~~  177 (323)
                      +.  .|+...+..+-..+...         |+   |.+.++...+.. .-+...|..+-.+|...        |   +++
T Consensus       165 ~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g---~~~  238 (474)
T 4abn_A          165 TH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPK---ISQ  238 (474)
T ss_dssp             TT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHH---HHH
T ss_pred             hh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccc---hHH
Confidence            64  36667777777777777         66   777777776654 22466777777777776        6   567


Q ss_pred             HHHHHHHHHHHcCCC--CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          178 EAIKIFYRMEIENVK--PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~--p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      +|++.|++.....-.  -+...|..+-..+...|++++|...|++..+.. +-+...+..+-..+...|++++|.+.+.+
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~~eAi~~~~~  317 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRLTSLLESKGK  317 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            888888877764310  366777778888888888888888888877653 22355677777778888888888776665


Q ss_pred             cc
Q 040801          256 ML  257 (323)
Q Consensus       256 m~  257 (323)
                      +.
T Consensus       318 ~~  319 (474)
T 4abn_A          318 TK  319 (474)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.73  E-value=1.5e-07  Score=79.33  Aligned_cols=196  Identities=12%  Similarity=-0.044  Sum_probs=136.1

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC------CC-
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ------GL-  121 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------g~-  121 (323)
                      ..|+++.|...+++..+.--           ++...-.+.....|..+-..|...|++++|.+.|++..+.      +- 
T Consensus        13 ~~~~~~~A~~~~~~al~~~~-----------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   81 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLE-----------KTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDH   81 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHH-----------HHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHH-----------HhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcc
Confidence            34566677766666554310           1111111234567888999999999999999999988653      11 


Q ss_pred             CCCcccHHHHHHHhcchhh---HHHHHHHHHHc------CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc--
Q 040801          122 IPDRFMFPSLFKSCADIYV---EKQLHSQAIKF------GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE--  189 (323)
Q Consensus       122 ~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~------g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~--  189 (323)
                      .....++..+-..+...|+   |...++...+.      .-.| ...++..+-..|...|   ++++|.+.|++....  
T Consensus        82 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~~~~al~~~~  158 (283)
T 3edt_B           82 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQG---KAEEVEYYYRRALEIYA  158 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHH
Confidence            2234677778888888888   77777776654      1123 4677888999999999   679999999988764  


Q ss_pred             ----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC---------------------------------------
Q 040801          190 ----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESG---------------------------------------  225 (323)
Q Consensus       190 ----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g---------------------------------------  225 (323)
                          +-.| ...++..+-..+...|++++|...+++..+..                                       
T Consensus       159 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (283)
T 3edt_B          159 TRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYG  238 (283)
T ss_dssp             HHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC--------
T ss_pred             HhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHH
Confidence                1123 35688888999999999999999999987531                                       


Q ss_pred             ---------CccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          226 ---------FWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       226 ---------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                               .......+..+...|.+.|++++|...+++..+
T Consensus       239 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          239 SWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                     111234566777777777888888777776543

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.70  E-value=1.3e-07  Score=87.19  Aligned_cols=217  Identities=7%  Similarity=-0.119  Sum_probs=163.7

Q ss_pred             hHHHhcccCC---CCChhhHHHHHHHHHhCCCh-HHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHH
Q 040801           77 HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLH-HEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAI  149 (323)
Q Consensus        77 ~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~-~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~  149 (323)
                      .+.+.+++..   +.+...|..+=..|...|++ ++|.+.|++..+.. +-+...|..+-..+.+.|+   |.+.++...
T Consensus        86 ~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al  164 (474)
T 4abn_A           86 KTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTCFSGAL  164 (474)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4445554433   45778888888999999999 99999999987642 2246788888888888888   888888887


Q ss_pred             HcCCCCchHHHHHHHHHHHhc---------CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc--------CChH
Q 040801          150 KFGLASDSFLHNTLINMYSSC---------WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA--------RDLR  212 (323)
Q Consensus       150 ~~g~~~~~~~~~~li~~~~~~---------g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~--------~~~~  212 (323)
                      +..  |+...+..+-..|...         |   ++++|++.|++..+.. .-+...|..+-.++...        |+++
T Consensus       165 ~~~--p~~~~~~~lg~~~~~~~~~~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          165 THC--KNKVSLQNLSMVLRQLQTDSGDEHSR---HVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             TTC--CCHHHHHHHHHHHTTCCCSCHHHHHH---HHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             hhC--CCHHHHHHHHHHHHHhccCChhhhhh---hHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            764  7778899999999988         8   6799999999998764 33678899999999988        9999


Q ss_pred             HHHHHHHHHHHhCCc--cChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhhhhhh
Q 040801          213 TVKRVHKCVDESGFW--SHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTAHQIS  288 (323)
Q Consensus       213 ~a~~~~~~m~~~g~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a~~l~  288 (323)
                      +|...+++..+..-.  -+...|..+-.+|.+.|++++|.+.|++..+. +..+..| .....+   ...++.++|....
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~---~~lg~~~eAi~~~  315 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLL---EFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH---HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH---HHHHHHHHHHHHh
Confidence            999999999886311  37888999999999999999999999998654 3333333 233333   3345667776666


Q ss_pred             CCCCchhHHHHHHHH
Q 040801          289 GPCPKKAHKLFFFSM  303 (323)
Q Consensus       289 ~~~~~~~~~~~~~~M  303 (323)
                      +....+....+...+
T Consensus       316 ~~~~~~~l~~~~~~l  330 (474)
T 4abn_A          316 GKTKPKKLQSMLGSL  330 (474)
T ss_dssp             TTCCHHHHHHHHHTC
T ss_pred             ccccCccHHHHHHhc
Confidence            655555444444443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.69  E-value=1.9e-06  Score=72.42  Aligned_cols=191  Identities=10%  Similarity=-0.121  Sum_probs=147.2

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG  120 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g  120 (323)
                      ...-..+...|+++.|...++...+..                   +.+...|..+-..|...|++++|.+.|++..+.+
T Consensus         7 ~~~a~~~~~~~~~~~A~~~~~~~l~~~-------------------p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~   67 (272)
T 3u4t_A            7 FRYADFLFKNNNYAEAIEVFNKLEAKK-------------------YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV   67 (272)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHTT-------------------CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhC-------------------CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc
Confidence            344566778899999999999998764                   3456688889999999999999999999998844


Q ss_pred             CCCCccc----HHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          121 LIPDRFM----FPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       121 ~~p~~~t----y~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                        ++...    |..+-..+...|+   |.+.++...+.. ..+..+|..+-..|...|   ++++|.+.|++..... ..
T Consensus        68 --~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~---~~~~A~~~~~~al~~~-~~  140 (272)
T 3u4t_A           68 --NATKAKSADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKG---NFPLAIQYMEKQIRPT-TT  140 (272)
T ss_dssp             --CTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTT---CHHHHHHHHGGGCCSS-CC
T ss_pred             --CchhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcc---CHHHHHHHHHHHhhcC-CC
Confidence              33333    6777777887777   888888888765 235678999999999999   7799999999887652 33


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC---HHHHHHHHHhccC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF---VSRAWDLFVKMLF  258 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m~~  258 (323)
                      +...|..+-..+...+++++|...++.+.+.. +.+...+..+...+...|+   .++|...+++..+
T Consensus       141 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~  207 (272)
T 3u4t_A          141 DPKVFYELGQAYYYNKEYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIE  207 (272)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHH
Confidence            45566666525555669999999999998863 2236677778888888888   7778877777654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.68  E-value=1.2e-07  Score=81.28  Aligned_cols=167  Identities=17%  Similarity=0.053  Sum_probs=130.9

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHC-------CCCCCcccHHHHHHHhcchhh---HHHHHHHHHHc------C
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ-------GLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF------G  152 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-------g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~------g  152 (323)
                      +...|..+-..+...|++++|.++|++..+.       .......++..+-..+...|+   |...++...+.      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            4567888999999999999999999998762       223344667777777777777   77777777654      2


Q ss_pred             CCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc------CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          153 LAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE------NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       153 ~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~------g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      -.| ...++..+...|...|   ++++|.+.|++....      +-.| ....+..+-..+...|++++|...++++.+.
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  182 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRG---KYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEI  182 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcC---cHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            223 4677889999999999   779999999988764      2223 4567888889999999999999999999764


Q ss_pred             ------CCcc-ChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          225 ------GFWS-HVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       225 ------g~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                            +-.| ...++..+...|.+.|++++|.+.+++..+
T Consensus       183 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          183 YQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             HHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                  2223 355788899999999999999999998874

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.68  E-value=1e-05  Score=69.92  Aligned_cols=197  Identities=10%  Similarity=0.001  Sum_probs=144.9

Q ss_pred             hHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHH-------hCCCh-------HHHHHHHHHHHHC
Q 040801           54 RELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYT-------NKNLH-------HEAFLFYHEMIVQ  119 (323)
Q Consensus        54 ~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~-------~~g~~-------~~A~~~~~~m~~~  119 (323)
                      +.|..+|++..+..                   +.+...|..+...+.       +.|++       ++|.++|++-.+.
T Consensus        33 ~~a~~~~~~al~~~-------------------p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~   93 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-------------------GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST   93 (308)
T ss_dssp             HHHHHHHHHHHHHH-------------------TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHc-------------------CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH
Confidence            56677777777653                   556777887777765       45886       9999999998874


Q ss_pred             CCCCCc-ccHHHHHHHhcchhh---HHHHHHHHHHcCCCCch-H-HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          120 GLIPDR-FMFPSLFKSCADIYV---EKQLHSQAIKFGLASDS-F-LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       120 g~~p~~-~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~-~-~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                       +.|+. ..|..+...+.+.|+   |.++|+...+.  .|+. . +|..+...+.+.|   ++++|.++|++....+ .+
T Consensus        94 -~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~---~~~~A~~~~~~a~~~~-p~  166 (308)
T 2ond_A           94 -LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAE---GIKSGRMIFKKAREDA-RT  166 (308)
T ss_dssp             -TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHH---CHHHHHHHHHHHHTST-TC
T ss_pred             -hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhc---CHHHHHHHHHHHHhcC-CC
Confidence             34544 477788877777777   99999998874  4543 3 8999999999999   6699999999988754 23


Q ss_pred             ChHHHHHHHHHHh-ccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCC-Cc----hhhh-
Q 040801          194 NAVTLVNVLTARA-RARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPW-NN----YGQW-  266 (323)
Q Consensus       194 ~~~t~~~li~~~~-~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~-~~----~~~~-  266 (323)
                      +...|........ ..|+.++|..+|+...+.. +-+...|..++..+.+.|++++|..+|++..+.. .+    ...| 
T Consensus       167 ~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~  245 (308)
T 2ond_A          167 RHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWA  245 (308)
T ss_dssp             CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHH
Confidence            4455544433322 3699999999999998752 2357889999999999999999999999998742 23    3345 


Q ss_pred             HHHhhhccCCC
Q 040801          267 AMSATVGPQGL  277 (323)
Q Consensus       267 ~~~~~~~~~~~  277 (323)
                      .+.......|+
T Consensus       246 ~~~~~~~~~g~  256 (308)
T 2ond_A          246 RFLAFESNIGD  256 (308)
T ss_dssp             HHHHHHHHHSC
T ss_pred             HHHHHHHHcCC
Confidence            45555555443

>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=98.67  E-value=5.6e-06  Score=69.91  Aligned_cols=183  Identities=11%  Similarity=-0.059  Sum_probs=141.2

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcc----hhh---HHHHHHHHHHcCCCCchHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCAD----IYV---EKQLHSQAIKFGLASDSFLHN  161 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~~~---a~~~~~~m~~~g~~~~~~~~~  161 (323)
                      +...+..+=..|...|++++|.+.|++..+.+   +..++..+-..+..    .++   |...++...+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            55667778888999999999999999988733   34556666666665    565   889999988876   677888


Q ss_pred             HHHHHHHh----cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhH
Q 040801          162 TLINMYSS----CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELK  233 (323)
Q Consensus       162 ~li~~~~~----~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~  233 (323)
                      .+-..|..    .+   ++++|++.|++....+   +...+..+-..+..    .++.++|...+++..+.+   +...+
T Consensus        79 ~lg~~~~~g~~~~~---~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~  149 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQ---NTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGC  149 (273)
T ss_dssp             HHHHHHHHTSSSCC---CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             HHHHHHhCCCCccc---CHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHH
Confidence            88888888    77   7799999999998865   77888888888888    999999999999999876   56677


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHHhccCCCCchhhh-HHHhhhcc-CCCCCcchhhhhh
Q 040801          234 TTLMDAYCK----CKFVSRAWDLFVKMLFPWNNYGQW-AMSATVGP-QGLVGRHSTAHQI  287 (323)
Q Consensus       234 ~~li~~~~~----~g~~~~a~~~~~~m~~~~~~~~~~-~~~~~~~~-~~~~~~~~~a~~l  287 (323)
                      ..+-..|.+    .++.++|...|++..+.+. +..+ .+...+.. .+..++.++|...
T Consensus       150 ~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~a~~~lg~~~~~g~~~~~~~~~A~~~  208 (273)
T 1ouv_A          150 TILGSLYDAGRGTPKDLKKALASYDKACDLKD-SPGCFNAGNMYHHGEGATKNFKEALAR  208 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHTCSSCCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC-HHHHHHHHHHHHcCCCCCccHHHHHHH
Confidence            788888888    9999999999999887653 3333 33333322 2335666666443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.64  E-value=5.8e-06  Score=65.28  Aligned_cols=163  Identities=12%  Similarity=-0.042  Sum_probs=130.2

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ...|..+=..+.+.|++++|...|+...+..                   +.+...|..+-..|.+.|++++|.+.+...
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~la~~~~~~~~~~~a~~~~~~~   65 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-------------------PNNVETLLKLGKTYMDIGLPNDAIESLKKF   65 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3456677778888999999999999998875                   557788999999999999999999999998


Q ss_pred             HHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          117 IVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       117 ~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      ..... -+...+..+-..+...++   +...+....+.. .-+...+..+-..|.+.|   ++++|++.|++..+.. +-
T Consensus        66 ~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g---~~~~A~~~~~~~l~~~-p~  139 (184)
T 3vtx_A           66 VVLDT-TSAEAYYILGSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMG---EHDKAIEAYEKTISIK-PG  139 (184)
T ss_dssp             HHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TT
T ss_pred             HhcCc-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhC---CchhHHHHHHHHHHhc-ch
Confidence            76422 233444444455555555   777777776654 335778888999999999   7799999999988754 34


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +..+|..+-..+.+.|+.++|...|++..+.
T Consensus       140 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          140 FIRAYQSIGLAYEGKGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             hhhHHHHHHHHHHHCCCHHHHHHHHHHHHhC
Confidence            6788999999999999999999999998875

>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=98.63  E-value=1.6e-06  Score=67.95  Aligned_cols=161  Identities=9%  Similarity=-0.073  Sum_probs=128.5

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+..+...+...|+++.|...++.+.+..                   +.+...|..+...+...|++++|.+.+++..+
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~   70 (186)
T 3as5_A           10 YYRDKGISHAKAGRYSQAVMLLEQVYDAD-------------------AFDVDVALHLGIAYVKTGAVDRGTELLERSLA   70 (186)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTTTCCTT-------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-------------------ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            34455556666777777777776655432                   45677889999999999999999999999876


Q ss_pred             CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh
Q 040801          119 QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA  195 (323)
Q Consensus       119 ~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~  195 (323)
                      .. +.+...+..+...+...|+   |.+.++...+.. ..+...+..+...|...|   ++++|.+.+++..... ..+.
T Consensus        71 ~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~---~~~~A~~~~~~~~~~~-~~~~  144 (186)
T 3as5_A           71 DA-PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLG---RFDEAIDSFKIALGLR-PNEG  144 (186)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCH
T ss_pred             cC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcC---cHHHHHHHHHHHHhcC-ccch
Confidence            52 3356677777778887777   888888887764 346778889999999999   7799999999988765 3467


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .++..+...+...|+.++|...++.+.+.
T Consensus       145 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          145 KVHRAIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            88999999999999999999999998765

>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=98.62  E-value=2.4e-06  Score=62.91  Aligned_cols=129  Identities=19%  Similarity=0.111  Sum_probs=86.8

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                      .|..+...+...|++++|.++|+++.+..  |                               .+...+..+...+...|
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~-------------------------------~~~~~~~~~a~~~~~~~   49 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD--P-------------------------------RSAEAWYNLGNAYYKQG   49 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC--T-------------------------------TCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC--C-------------------------------cchhHHHHHHHHHHHhc
Confidence            46677778888888888888888776531  1                               12334555566666666


Q ss_pred             CCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHH
Q 040801          172 CLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       172 ~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                         ++++|.+.|+++...+ ..+...+..+...+...|++++|...++.+.+.. +.+...+..+...|.+.|+.++|..
T Consensus        50 ---~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  124 (136)
T 2fo7_A           50 ---DYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIE  124 (136)
T ss_dssp             ---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             ---CHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHH
Confidence               5577777777776544 3345666677777777777777777777776653 2245666777777777777777777


Q ss_pred             HHHhccC
Q 040801          252 LFVKMLF  258 (323)
Q Consensus       252 ~~~~m~~  258 (323)
                      .++++.+
T Consensus       125 ~~~~~~~  131 (136)
T 2fo7_A          125 YYQKALE  131 (136)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHc
Confidence            7776643

>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=98.58  E-value=4.1e-06  Score=61.65  Aligned_cols=123  Identities=19%  Similarity=0.045  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      ..|..+...|...|   ++++|.++|+++...+ ..+...+..+...+...|++++|...++++.+.+ +.+...+..+.
T Consensus         2 ~~~~~l~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   76 (136)
T 2fo7_A            2 EAWYNLGNAYYKQG---DYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLG   76 (136)
T ss_dssp             HHHHHHHHHHHHHT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHcC---cHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHH
Confidence            35778888999999   7799999999998765 3467888889999999999999999999998764 33567888999


Q ss_pred             HHHHhcCCHHHHHHHHHhccCCC-Cchhhh-HHHhhhccCCCCCcchhhhhhh
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFPW-NNYGQW-AMSATVGPQGLVGRHSTAHQIS  288 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~-~~~~~~~~~~~~~~~~~a~~l~  288 (323)
                      ..|.+.|++++|...++++.+.. ..+..+ .+...+   ...|+.++|...+
T Consensus        77 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~---~~~~~~~~A~~~~  126 (136)
T 2fo7_A           77 NAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAY---YKQGDYDEAIEYY  126 (136)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH---HTTTCHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHH---HHHccHHHHHHHH
Confidence            99999999999999999987642 233333 333333   3456677765544

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.53  E-value=2.7e-05  Score=69.60  Aligned_cols=190  Identities=6%  Similarity=-0.056  Sum_probs=154.1

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCC-hHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNL-HHEAFLFYHEMI  117 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~-~~~A~~~~~~m~  117 (323)
                      .+..+-..+.+.|+++.|...++...+..                   +.+...|+.+-..+.+.|+ +++|++.|++..
T Consensus        99 a~~~lg~~~~~~g~~~~Al~~~~~al~l~-------------------P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al  159 (382)
T 2h6f_A           99 VYDYFRAVLQRDERSERAFKLTRDAIELN-------------------AANYTVWHFRRVLLKSLQKDLHEEMNYITAII  159 (382)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHhC-------------------ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHH
Confidence            35556667777889999999999998874                   5577889999999999997 999999999998


Q ss_pred             HCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          118 VQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       118 ~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      +.  .| +...|..+-..+...|+   |...++...+.. .-+...|..+-.++.+.|   ++++|++.|++...... -
T Consensus       160 ~l--~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g---~~~eAl~~~~~al~l~P-~  232 (382)
T 2h6f_A          160 EE--QPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFK---LWDNELQYVDQLLKEDV-R  232 (382)
T ss_dssp             HH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHT---CCTTHHHHHHHHHHHCT-T
T ss_pred             HH--CCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcC---ChHHHHHHHHHHHHhCC-C
Confidence            74  34 45677777777777777   999999998865 236788999999999999   45899999999998653 3


Q ss_pred             ChHHHHHHHHHHhc-cCChHHH-----HHHHHHHHHhCCcc-ChhhHHHHHHHHHhcC--CHHHHHHHHHhc
Q 040801          194 NAVTLVNVLTARAR-ARDLRTV-----KRVHKCVDESGFWS-HVELKTTLMDAYCKCK--FVSRAWDLFVKM  256 (323)
Q Consensus       194 ~~~t~~~li~~~~~-~~~~~~a-----~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g--~~~~a~~~~~~m  256 (323)
                      +...|+.+-..+.. .|..++|     ...+++..+.  .| +...|..+-..|.+.|  +.++|.+.++++
T Consensus       233 ~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~  302 (382)
T 2h6f_A          233 NNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL  302 (382)
T ss_dssp             CHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHh
Confidence            77899999899988 6665777     4777777765  34 4678888888899988  699999999998

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.51  E-value=1.8e-05  Score=73.67  Aligned_cols=166  Identities=8%  Similarity=0.027  Sum_probs=127.0

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc--ccHHHHHHHhcchhh---HHHHHHHHHHcCC-CCchHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR--FMFPSLFKSCADIYV---EKQLHSQAIKFGL-ASDSFLH  160 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~--~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-~~~~~~~  160 (323)
                      +.+...|..+...+.+.|++++|.++|++..+  +.|+.  ..|..+...+.+.|+   |.++++...+..- .+.....
T Consensus       318 p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~  395 (530)
T 2ooe_A          318 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVT  395 (530)
T ss_dssp             SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHH
T ss_pred             cccHHHHHHHHHHHHhcCCHHHHHHHHHHHhC--ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHH
Confidence            44678899999999999999999999999987  45654  367777777777777   8888888876531 1112222


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC-CccC--hhhHHHHH
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG-FWSH--VELKTTLM  237 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~--~~~~~~li  237 (323)
                      ..++. +...|   +.++|.++|++..... .-+...|..++..+.+.|+.+.|..+|++..+.+ ..|+  ...|...+
T Consensus       396 ~a~~~-~~~~~---~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~  470 (530)
T 2ooe_A          396 AALME-YYCSK---DKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFL  470 (530)
T ss_dssp             HHHHH-HHHTC---CHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHH
T ss_pred             HHHHH-HHHcC---ChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence            22332 33567   6799999999887643 2357889999999999999999999999998863 2332  44788889


Q ss_pred             HHHHhcCCHHHHHHHHHhccCC
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ....+.|+.+.+..+++++.+.
T Consensus       471 ~~e~~~G~~~~~~~~~~r~~~~  492 (530)
T 2ooe_A          471 AFESNIGDLASILKVEKRRFTA  492 (530)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            9888999999999999988764

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.51  E-value=7.3e-06  Score=68.76  Aligned_cols=163  Identities=10%  Similarity=-0.070  Sum_probs=126.8

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc--hHHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD--SFLHNTLIN  165 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~--~~~~~~li~  165 (323)
                      ..+-..-..+...|++++|.+.|++..+.. +-+...+..+-..+...|+   |.+.++...+..-.++  ...|..+-.
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            345556678899999999999999998752 2244588888888888888   8888988887443332  334888999


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF  245 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~  245 (323)
                      .|...|   ++++|.+.|++..... +.+..+|..+-..+...|++++|...+++..+.. +-+...|..+-..+...++
T Consensus        83 ~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~  157 (272)
T 3u4t_A           83 ILMKKG---QDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYYNKE  157 (272)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHcc---cHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHHHHH
Confidence            999999   7799999999998754 3366889999999999999999999999987762 2345666666624444569


Q ss_pred             HHHHHHHHHhccCC
Q 040801          246 VSRAWDLFVKMLFP  259 (323)
Q Consensus       246 ~~~a~~~~~~m~~~  259 (323)
                      +++|.+.|++..+.
T Consensus       158 ~~~A~~~~~~a~~~  171 (272)
T 3u4t_A          158 YVKADSSFVKVLEL  171 (272)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99999999998764

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.44  E-value=2.6e-05  Score=69.66  Aligned_cols=202  Identities=12%  Similarity=0.016  Sum_probs=154.7

Q ss_pred             hhhhhhHHHhhcCCC-chHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCST-MRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        38 ~~~~~li~~~~~~~~-~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ..|+.+-..+...|+ ++.|...++...+..                   +.+...|+.+=..+.+.|++++|+..|++.
T Consensus       132 ~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-------------------P~~~~a~~~~g~~~~~~g~~~eAl~~~~ka  192 (382)
T 2h6f_A          132 TVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-------------------PKNYQVWHHRRVLVEWLRDPSQELEFIADI  192 (382)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-------------------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-------------------CCCHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            345566667777786 999999999888875                   567888999999999999999999999999


Q ss_pred             HHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh-cCCCCChHHH-----HHHHHHHH
Q 040801          117 IVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS-CWCLDQPDEA-----IKIFYRME  187 (323)
Q Consensus       117 ~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~-~g~~~~~~~a-----~~~~~~m~  187 (323)
                      .+.. +-+...|..+-.++.+.|+   |...++.+.+..- -+...|+.+-..|.+ .|.   .++|     ++.|++..
T Consensus       193 l~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~~---~~eA~~~~el~~~~~Al  267 (382)
T 2h6f_A          193 LNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGY---NDRAVLEREVQYTLEMI  267 (382)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCS---CSHHHHHHHHHHHHHHH
T ss_pred             HHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCc---chHHHHHHHHHHHHHHH
Confidence            8742 2355677777777777777   9999999988762 357889999999998 553   2566     57888877


Q ss_pred             HcCCCCChHHHHHHHHHHhccC--ChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC---------CHHHHHHHHHhc
Q 040801          188 IENVKPNAVTLVNVLTARARAR--DLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK---------FVSRAWDLFVKM  256 (323)
Q Consensus       188 ~~g~~p~~~t~~~li~~~~~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g---------~~~~a~~~~~~m  256 (323)
                      ... .-+...|+.+-..+...|  +.++|...+.++ +. -..+...+..+.+.|.+.|         .+++|.++++++
T Consensus       268 ~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          268 KLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEIL  344 (382)
T ss_dssp             HHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             HHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHH
Confidence            644 235678888888888888  688998888887 22 2335678889999999874         369999999999


Q ss_pred             -cCC-CCchhhh
Q 040801          257 -LFP-WNNYGQW  266 (323)
Q Consensus       257 -~~~-~~~~~~~  266 (323)
                       .+. +.....|
T Consensus       345 ~~~~DP~r~~~w  356 (382)
T 2h6f_A          345 AKEKDTIRKEYW  356 (382)
T ss_dssp             HHTTCGGGHHHH
T ss_pred             HHHhCchhHHHH
Confidence             443 4555666

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.42  E-value=9.6e-06  Score=78.45  Aligned_cols=160  Identities=10%  Similarity=-0.016  Sum_probs=135.8

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCC-chHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS-DSFLHNTL  163 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~-~~~~~~~l  163 (323)
                      +...|+.|=..|.+.|++++|++.|++-.+.  .|+ ..+|..+-..+.+.|+   |.+.++...+..  | +...|+.+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~--P~~~~a~~nL   83 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS--PTFADAYSNM   83 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHH
Confidence            4567899999999999999999999998764  454 5678888888888888   888898888764  4 47789999


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHh
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCK  242 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~  242 (323)
                      -..|.+.|   ++++|++.|++..+.. .-+...|+.+-..+...|++++|...+++..+.  .| +...|..|...|..
T Consensus        84 g~~l~~~g---~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~  157 (723)
T 4gyw_A           84 GNTLKEMQ---DVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQI  157 (723)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHh
Confidence            99999999   6799999999988754 235689999999999999999999999999886  35 47789999999999


Q ss_pred             cCCHHHHHHHHHhccC
Q 040801          243 CKFVSRAWDLFVKMLF  258 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~  258 (323)
                      .|++++|.+.+++..+
T Consensus       158 ~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          158 VCDWTDYDERMKKLVS  173 (723)
T ss_dssp             TTCCTTHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHH
Confidence            9999999999887653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.40  E-value=2.3e-05  Score=72.95  Aligned_cols=185  Identities=10%  Similarity=-0.002  Sum_probs=135.5

Q ss_pred             CCChhhHHHHHHHHHh-------CCChH-------HHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTN-------KNLHH-------EAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAI  149 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~-------~g~~~-------~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~  149 (323)
                      +.+...|..+...+.+       .|+++       +|.++|++-.+.-.+-+...|..+...+.+.|+   |..+++...
T Consensus       269 p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al  348 (530)
T 2ooe_A          269 GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLL  348 (530)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence            4567788888888775       79987       899999988763233346677777777777777   999999998


Q ss_pred             HcCCCCc--hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHH-HhccCChHHHHHHHHHHHHhCC
Q 040801          150 KFGLASD--SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTA-RARARDLRTVKRVHKCVDESGF  226 (323)
Q Consensus       150 ~~g~~~~--~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~-~~~~~~~~~a~~~~~~m~~~g~  226 (323)
                      +.  .|+  ...|..+...+.+.|   +.++|.++|++-.... ..+...|...... +...|+.++|..+|+...+.. 
T Consensus       349 ~~--~p~~~~~~~~~~~~~~~~~~---~~~~A~~~~~~Al~~~-~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~-  421 (530)
T 2ooe_A          349 AI--EDIDPTLVYIQYMKFARRAE---GIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-  421 (530)
T ss_dssp             HS--SSSCHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHTCT-TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH-
T ss_pred             Cc--cccCchHHHHHHHHHHHHhc---CHHHHHHHHHHHHhcc-CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC-
Confidence            85  454  358999999999988   6699999999987643 1223333332222 335899999999999998753 


Q ss_pred             ccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchh----hh-HHHhhhccCCCC
Q 040801          227 WSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYG----QW-AMSATVGPQGLV  278 (323)
Q Consensus       227 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~----~~-~~~~~~~~~~~~  278 (323)
                      +-+...|..+++.+.+.|+.++|..+|++.... +.+|.    .| .+......+|+.
T Consensus       422 p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~  479 (530)
T 2ooe_A          422 GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDL  479 (530)
T ss_dssp             TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCH
T ss_pred             CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCH
Confidence            235788999999999999999999999998765 23343    56 556665555543

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=98.37  E-value=2.2e-05  Score=64.26  Aligned_cols=152  Identities=13%  Similarity=-0.067  Sum_probs=114.0

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHH
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      .|...|...=..+.+.|++++|.+.|++..+..-.++...+..+-..+...|+   |.+.++...+.. .-+...|..+-
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHH
Confidence            35567777788899999999999999998876443666667667777777777   888888877654 22567788888


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCCh-------HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC---hhhHH
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNA-------VTLVNVLTARARARDLRTVKRVHKCVDESGFWSH---VELKT  234 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~-------~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~  234 (323)
                      ..|...|   ++++|++.|++..... +-+.       ..|..+=..+...|++++|...++...+.  .|+   ...|.
T Consensus        84 ~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~  157 (228)
T 4i17_A           84 AAYRDMK---NNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALY  157 (228)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHH
T ss_pred             HHHHHcc---cHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHH
Confidence            8999988   6799999998887743 1233       45666667778889999999999988765  444   45667


Q ss_pred             HHHHHHHhcCCH
Q 040801          235 TLMDAYCKCKFV  246 (323)
Q Consensus       235 ~li~~~~~~g~~  246 (323)
                      .+-..|...|+.
T Consensus       158 ~l~~~~~~~~~~  169 (228)
T 4i17_A          158 SLGVLFYNNGAD  169 (228)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            777777776665

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.30  E-value=2.3e-06  Score=71.90  Aligned_cols=156  Identities=15%  Similarity=-0.003  Sum_probs=116.2

Q ss_pred             HHhCCChHHHHHHHHHHHH-------CCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHc------CCCC-chHHHHH
Q 040801          100 YTNKNLHHEAFLFYHEMIV-------QGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKF------GLAS-DSFLHNT  162 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~-------~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~------g~~~-~~~~~~~  162 (323)
                      ....|++++|.++|++-.+       ...+....++..+-..+...|+   |...++...+.      +-.| ...++..
T Consensus        11 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   90 (283)
T 3edt_B           11 SSGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNN   90 (283)
T ss_dssp             --CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            3456777777777766544       1222345667777777777777   88888777654      3233 4667899


Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHc------CC-CCChHHHHHHHHHHhccCChHHHHHHHHHHHHh------CCcc-
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIE------NV-KPNAVTLVNVLTARARARDLRTVKRVHKCVDES------GFWS-  228 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~------g~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p-  228 (323)
                      +-..|...|   ++++|.+.|++....      .- .....++..+-..+...|++++|...++++.+.      +-.| 
T Consensus        91 l~~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  167 (283)
T 3edt_B           91 LAVLYGKRG---KYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPN  167 (283)
T ss_dssp             HHHHHHTTT---CHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHH
T ss_pred             HHHHHHHhc---cHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHH
Confidence            999999999   779999999988764      11 234678888999999999999999999999765      1122 


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          229 HVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ...++..+...|.+.|++++|...+++..+
T Consensus       168 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          168 VAKTKNNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            356788899999999999999999998764

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.29  E-value=3.6e-06  Score=75.29  Aligned_cols=245  Identities=10%  Similarity=-0.042  Sum_probs=127.8

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------------ccch----hHHHhccc-------CC--CCChhh
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------------CADY----HVRLVFSQ-------IS--NPTIYT   92 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------------y~~~----~a~~lf~~-------m~--~~~~~~   92 (323)
                      +..+-..+...|+++.|...++...+.+  |+.              |...    .|.+.|++       ..  ......
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            3445556778899999999999999874  222              1111    33333332       22  123345


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHC----CCC-CCcccHHHHHHHhcchhh--------------------HHHHHHH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQ----GLI-PDRFMFPSLFKSCADIYV--------------------EKQLHSQ  147 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~----g~~-p~~~ty~~ll~~~~~~~~--------------------a~~~~~~  147 (323)
                      |..+-..|...|++++|.+.|++..+.    +-. ....++..+-..+...|+                    |.+.++.
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~  208 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQE  208 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHH
Confidence            666666677777777777777665432    100 112233333333333322                    4444444


Q ss_pred             HHHc----CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC-CCC----hHHHHHHHHHHhccCChHHHHHH
Q 040801          148 AIKF----GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV-KPN----AVTLVNVLTARARARDLRTVKRV  217 (323)
Q Consensus       148 m~~~----g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~-~p~----~~t~~~li~~~~~~~~~~~a~~~  217 (323)
                      ..+.    +-.+ ...++..+-..|...|   ++++|.+.|++.....- .++    ..++..+...+...|++++|...
T Consensus       209 al~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  285 (411)
T 4a1s_A          209 NLKLMRDLGDRGAQGRACGNLGNTYYLLG---DFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEH  285 (411)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcC---ChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHH
Confidence            3322    1111 2235666666666666   55677777766654210 011    12566666667777777777777


Q ss_pred             HHHHHHhCCc-----cChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCC----chhhh-HHHhhhccCCCCCcchhhhhh
Q 040801          218 HKCVDESGFW-----SHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWN----NYGQW-AMSATVGPQGLVGRHSTAHQI  287 (323)
Q Consensus       218 ~~~m~~~g~~-----p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~~~~~-~~~~~~~~~~~~~~~~~a~~l  287 (323)
                      +++..+..-.     ....++..+...|.+.|++++|...+++..+...    ..... .+...-..+...|+.++|...
T Consensus       286 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  365 (411)
T 4a1s_A          286 YKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKY  365 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHH
Confidence            7666542111     1134566666677777777777777777665411    11111 333333444445555555444


Q ss_pred             hC
Q 040801          288 SG  289 (323)
Q Consensus       288 ~~  289 (323)
                      +.
T Consensus       366 ~~  367 (411)
T 4a1s_A          366 AE  367 (411)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.24  E-value=5.7e-05  Score=64.98  Aligned_cols=141  Identities=9%  Similarity=-0.013  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCC-CCchHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 040801          109 AFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGL-ASDSFLHNTLINMYSSCWCLDQPDEAIKIFY  184 (323)
Q Consensus       109 A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~  184 (323)
                      |...|++..+.+ .++..++..+-.++...|+   |.+++....+.|- .-+...+..++..|.+.|   +.+.|.+.++
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~---r~d~A~k~l~  160 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNN---NVSTASTIFD  160 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCC---CHHHHHHHHH
Confidence            444555444433 2333333344444444444   4444444333331 123444555555555555   3455666665


Q ss_pred             HHHHcCCCC-----ChHHHHHHHHHHh--ccC--ChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          185 RMEIENVKP-----NAVTLVNVLTARA--RAR--DLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       185 ~m~~~g~~p-----~~~t~~~li~~~~--~~~--~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      +|.+.  .|     +..+...+..+++  ..|  +...|..+|+++.+.  .|+..+-..|+.++.+.|++++|++.++.
T Consensus       161 ~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~  236 (310)
T 3mv2_B          161 NYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVEL  236 (310)
T ss_dssp             HHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHH
Confidence            55442  34     2344444444422  122  555555555555433  23322223333355555666666665554


Q ss_pred             cc
Q 040801          256 ML  257 (323)
Q Consensus       256 m~  257 (323)
                      +.
T Consensus       237 l~  238 (310)
T 3mv2_B          237 LL  238 (310)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.20  E-value=7.6e-05  Score=72.18  Aligned_cols=161  Identities=12%  Similarity=0.034  Sum_probs=135.3

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEM  116 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  116 (323)
                      ...++.|-..+.+.|++++|.+.|++..+..                   +.+...|+.+=..|.+.|++++|++.|++.
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~-------------------P~~~~a~~nLg~~l~~~g~~~eA~~~~~~A   69 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVF-------------------PEFAAAHSNLASVLQQQGKLQEALMHYKEA   69 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4467788889999999999999999998874                   456788999999999999999999999998


Q ss_pred             HHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC
Q 040801          117 IVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK  192 (323)
Q Consensus       117 ~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~  192 (323)
                      .+.  .|+ ...|..+-..+.+.|+   |.+.++...+.. .-+...|+.+-..|.+.|   ++++|++.|++..+.. .
T Consensus        70 l~l--~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g---~~~eAi~~~~~Al~l~-P  142 (723)
T 4gyw_A           70 IRI--SPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSG---NIPEAIASYRTALKLK-P  142 (723)
T ss_dssp             HHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-S
T ss_pred             HHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-C
Confidence            763  454 5678888888888888   888888887764 224778999999999999   6799999999988754 2


Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      -+...|..+...+...|++++|.+.++++.+
T Consensus       143 ~~~~a~~~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          143 DFPDAYCNLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             CCHHHHHHHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             CChHHHhhhhhHHHhcccHHHHHHHHHHHHH
Confidence            2568899999999999999999999888764

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.18  E-value=0.00034  Score=64.35  Aligned_cols=196  Identities=11%  Similarity=0.034  Sum_probs=130.4

Q ss_pred             CCCchHHHHHHHHHHHhcCCCCC------ccc----h----hHHHhcccCC-CCChhhHHHHHHHHHh----CCChHHHH
Q 040801           50 CSTMRELKQIHAQMLRTSLFFDP------CAD----Y----HVRLVFSQIS-NPTIYTCNSIVRGYTN----KNLHHEAF  110 (323)
Q Consensus        50 ~~~~~~a~~i~~~m~~~~~~~~~------y~~----~----~a~~lf~~m~-~~~~~~~~~li~~~~~----~g~~~~A~  110 (323)
                      .++++.|...|+...+.|...-.      |..    .    .|.+.|.+.. .-+...+..|=..|..    .+++++|.
T Consensus        56 ~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~  135 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESV  135 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             CcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            67888999999888876532111      322    1    6777776544 4466666667677777    77888999


Q ss_pred             HHHHHHHHCCCCCCcccHHHHHHHhcc----hhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHh----cCCCCChHHH
Q 040801          111 LFYHEMIVQGLIPDRFMFPSLFKSCAD----IYV---EKQLHSQAIKFGLASDSFLHNTLINMYSS----CWCLDQPDEA  179 (323)
Q Consensus       111 ~~~~~m~~~g~~p~~~ty~~ll~~~~~----~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~----~g~~~~~~~a  179 (323)
                      +.|++-.+.|   +...+..|-..|..    .++   |.+.++...+.|   +...+..|-..|..    .+   +.++|
T Consensus       136 ~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~---~~~~A  206 (490)
T 2xm6_A          136 KWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVER---NDAIS  206 (490)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCC---CHHHH
T ss_pred             HHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCc---CHHHH
Confidence            8888887765   33444444444433    233   777777777765   46666667667766    44   67888


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh----cCCHHHHHH
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK----CKFVSRAWD  251 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~~~a~~  251 (323)
                      .+.|++-.+.|   +...+..+-..+..    .++.++|...++...+.|   +...+..|-..|..    .++.++|.+
T Consensus       207 ~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~  280 (490)
T 2xm6_A          207 AQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALE  280 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHH
Confidence            88888777654   44556666666654    678888888888877665   34455555566666    778888888


Q ss_pred             HHHhccCCC
Q 040801          252 LFVKMLFPW  260 (323)
Q Consensus       252 ~~~~m~~~~  260 (323)
                      .|++..+.+
T Consensus       281 ~~~~a~~~~  289 (490)
T 2xm6_A          281 WYRKSAEQG  289 (490)
T ss_dssp             HHHHHHTTT
T ss_pred             HHHHHHHcC
Confidence            888777664

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.17  E-value=0.00018  Score=66.19  Aligned_cols=198  Identities=13%  Similarity=0.009  Sum_probs=111.6

Q ss_pred             CCCchHHHHHHHHHHHhcCCCCC-------ccc------h--hHHHhcccCC-CCChhhHHHHHHHHHh----CCChHHH
Q 040801           50 CSTMRELKQIHAQMLRTSLFFDP-------CAD------Y--HVRLVFSQIS-NPTIYTCNSIVRGYTN----KNLHHEA  109 (323)
Q Consensus        50 ~~~~~~a~~i~~~m~~~~~~~~~-------y~~------~--~a~~lf~~m~-~~~~~~~~~li~~~~~----~g~~~~A  109 (323)
                      .++++.|...|+...+.|. +..       |..      .  .|.+.|++.. .-+...+..|=..|..    .+++++|
T Consensus        92 ~~~~~~A~~~~~~a~~~~~-~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A  170 (490)
T 2xm6_A           92 PQDYAQAVIWYKKAALKGL-PQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMA  170 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCC-HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            5677888888877776652 111       222      1  5666665543 3455556666666665    6777788


Q ss_pred             HHHHHHHHHCCCCCCcccHHHHHHHhcc----hhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc-CCCCChHHHHH
Q 040801          110 FLFYHEMIVQGLIPDRFMFPSLFKSCAD----IYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC-WCLDQPDEAIK  181 (323)
Q Consensus       110 ~~~~~~m~~~g~~p~~~ty~~ll~~~~~----~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-g~~~~~~~a~~  181 (323)
                      .+.|++..+.|   +...+..+-..+..    .++   |.++++...+.|   +...+..|-..|... |...+.++|.+
T Consensus       171 ~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~  244 (490)
T 2xm6_A          171 REWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRV  244 (490)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            87777776654   34444444444433    333   666666666654   344555555555541 11125667777


Q ss_pred             HHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc-----CCHHHHHHH
Q 040801          182 IFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC-----KFVSRAWDL  252 (323)
Q Consensus       182 ~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~-----g~~~~a~~~  252 (323)
                      +|++..+.|   +...+..+-..+..    .++.++|...++...+.|   +...+..|-..|...     ++.++|...
T Consensus       245 ~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~  318 (490)
T 2xm6_A          245 LFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISW  318 (490)
T ss_dssp             HHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHH
Confidence            776665543   23344444444444    566666766666666554   334455555555555     666666666


Q ss_pred             HHhccCCC
Q 040801          253 FVKMLFPW  260 (323)
Q Consensus       253 ~~~m~~~~  260 (323)
                      +++..+.+
T Consensus       319 ~~~a~~~~  326 (490)
T 2xm6_A          319 YTKSAEQG  326 (490)
T ss_dssp             HHHHHHTT
T ss_pred             HHHHHhcC
Confidence            66665543

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.09  E-value=3.3e-05  Score=66.24  Aligned_cols=200  Identities=11%  Similarity=-0.035  Sum_probs=95.3

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCC--hhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPT--IYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      ...-..+...|+++.|...+++..+..-  +.               +.  ...|..+-..|...|++++|.+.+++..+
T Consensus         9 ~~~g~~~~~~g~~~~A~~~~~~al~~~~--~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   71 (338)
T 3ro2_A            9 ALEGERLCKSGDCRAGVSFFEAAVQVGT--ED---------------LKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLT   71 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCC--SC---------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhhCc--cc---------------HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3344566778999999999999988742  11               00  23455555555556666666655555422


Q ss_pred             C----CCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCC-CCc----hHHHHHHHHHHHhcCCCC-----------
Q 040801          119 Q----GLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGL-ASD----SFLHNTLINMYSSCWCLD-----------  174 (323)
Q Consensus       119 ~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-~~~----~~~~~~li~~~~~~g~~~-----------  174 (323)
                      .    +-.| ...++..+-..+...|+   |...++...+..- .++    ..++..+-..|...|+..           
T Consensus        72 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  151 (338)
T 3ro2_A           72 LARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEF  151 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----C
T ss_pred             HhhcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhh
Confidence            1    1111 12333444444444444   4444444332210 011    224555555555555200           


Q ss_pred             ------ChHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-c----ChhhHHHHHH
Q 040801          175 ------QPDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFW-S----HVELKTTLMD  238 (323)
Q Consensus       175 ------~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p----~~~~~~~li~  238 (323)
                            .+++|.+.+++....    +-.+ ...++..+-..+...|++++|...+++..+..-. +    ....+..+..
T Consensus       152 ~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~  231 (338)
T 3ro2_A          152 PEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGN  231 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHH
Confidence                  045555555444321    1111 1234555555555556666666555555432100 0    1224555555


Q ss_pred             HHHhcCCHHHHHHHHHhcc
Q 040801          239 AYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       239 ~~~~~g~~~~a~~~~~~m~  257 (323)
                      .|...|++++|...+++..
T Consensus       232 ~~~~~g~~~~A~~~~~~al  250 (338)
T 3ro2_A          232 AYIFLGEFETASEYYKKTL  250 (338)
T ss_dssp             HHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            5556666666665555543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.09  E-value=1.7e-05  Score=70.34  Aligned_cols=95  Identities=13%  Similarity=-0.077  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC-CC----ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC----Ccc-
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV-KP----NAVTLVNVLTARARARDLRTVKRVHKCVDESG----FWS-  228 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~-~p----~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g----~~p-  228 (323)
                      ++..+-..|...|   ++++|.+.|++.....- .+    ...++..+-..+...|++++|...+++..+..    -.+ 
T Consensus       189 ~~~~la~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  265 (406)
T 3sf4_A          189 AFGNLGNTHYLLG---NFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAV  265 (406)
T ss_dssp             HHHHHHHHHHHHT---BHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHcc---CHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchH
Confidence            4555555555555   44555555555543100 01    12255555555555566666555555554321    000 


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          229 HVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ...++..+-..|.+.|++++|...+++.
T Consensus       266 ~~~~~~~la~~~~~~g~~~~A~~~~~~a  293 (406)
T 3sf4_A          266 EAQSCYSLGNTYTLLQDYEKAIDYHLKH  293 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCcHHHHHHHHHHH
Confidence            0334455555555556655555555554

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.07  E-value=3.2e-05  Score=68.53  Aligned_cols=198  Identities=11%  Similarity=-0.024  Sum_probs=142.6

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCC----hhhHHHHHHHHHhCCChHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPT----IYTCNSIVRGYTNKNLHHEAFLFYH  114 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~----~~~~~~li~~~~~~g~~~~A~~~~~  114 (323)
                      .+...-..+...|+++.|...++...+.+-                   .+    ...|..+-..|...|++++|.+.|+
T Consensus        11 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~~-------------------~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~   71 (406)
T 3sf4_A           11 ELALEGERLCKSGDCRAGVSFFEAAVQVGT-------------------EDLKTLSAIYSQLGNAYFYLHDYAKALEYHH   71 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-------------------SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcCc-------------------ccHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            444556677888999999999999988742                   22    3568888899999999999999998


Q ss_pred             HHHHC----CCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chHHHHHHHHHHHhcCCCCC------
Q 040801          115 EMIVQ----GLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSFLHNTLINMYSSCWCLDQ------  175 (323)
Q Consensus       115 ~m~~~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~g~~~~------  175 (323)
                      +....    +-.| ...++..+-..+...|+   |...++...+.    +-.+ ...++..+-..|...|   +      
T Consensus        72 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~~~~  148 (406)
T 3sf4_A           72 HDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKG---KSFGCPG  148 (406)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHH---HTCC---
T ss_pred             HHHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcC---Ccccccc
Confidence            86432    2122 13456666666777777   66666665443    2111 2457888888899988   5      


Q ss_pred             --------------hHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-cC----hh
Q 040801          176 --------------PDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFW-SH----VE  231 (323)
Q Consensus       176 --------------~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~----~~  231 (323)
                                    +++|.+.+++....    +-.| ...++..+-..+...|++++|...+++..+..-. ++    ..
T Consensus       149 ~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  228 (406)
T 3sf4_A          149 PQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERR  228 (406)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHH
Confidence                          68899888876542    2112 2357888888999999999999999998653111 11    33


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .+..+...|...|++++|...+++..+
T Consensus       229 ~~~~la~~~~~~g~~~~A~~~~~~al~  255 (406)
T 3sf4_A          229 AYSNLGNAYIFLGEFETASEYYKKTLL  255 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            788889999999999999999998753

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.07  E-value=0.00057  Score=58.25  Aligned_cols=161  Identities=11%  Similarity=-0.038  Sum_probs=116.4

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCC-CCCCcc----cHHHHHHHhcchhh---HHHHHHHHHHcCCC-Cc----hHHH
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPDRF----MFPSLFKSCADIYV---EKQLHSQAIKFGLA-SD----SFLH  160 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~~~----ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~----~~~~  160 (323)
                      ...+..+.+.|++++|.+++++..... ..|+..    .|..+...+...++   |...++...+.... ++    ..+|
T Consensus        79 ~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 3u3w_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHH
Confidence            334778999999999999999987642 223321    22334445555554   88888888874322 23    3368


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHH----c-CCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccC-
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEI----E-NVKPNA-VTLVNVLTARARARDLRTVKRVHKCVDES----GFWSH-  229 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~----~-g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-  229 (323)
                      +.+-..|...|   ++++|++.|++...    . +..+.. .+|..+-..|.+.|++++|...+++..+.    +-.+. 
T Consensus       159 ~~lg~~y~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~  235 (293)
T 3u3w_A          159 NAIANIYAENG---YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTH
T ss_pred             HHHHHHHHHcC---CHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHH
Confidence            99999999999   77999999999874    1 222223 48888999999999999999999988653    22222 


Q ss_pred             hhhHHHHHHHHHhcCC-HHHHHHHHHhcc
Q 040801          230 VELKTTLMDAYCKCKF-VSRAWDLFVKML  257 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~-~~~a~~~~~~m~  257 (323)
                      ...|..+-.+|.+.|+ .++|.+.+++..
T Consensus       236 ~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            5678888889999994 699998888765

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.06  E-value=0.00014  Score=62.47  Aligned_cols=175  Identities=7%  Similarity=-0.050  Sum_probs=125.7

Q ss_pred             HHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCC-CCCcccHHHHHHHhcchhh---HHHHHHHHHH
Q 040801           78 VRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL-IPDRFMFPSLFKSCADIYV---EKQLHSQAIK  150 (323)
Q Consensus        78 a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~-~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~  150 (323)
                      |.+.|++..   .++..++..+-..+...|++++|++++.+-...|- .-+...+..++..+.+.|+   |.+.++.|.+
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~  164 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTN  164 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            445555443   35555566777899999999999999998766543 2356778888888999888   9999999987


Q ss_pred             cCCCC-----chHHHHHHHHHHHh--cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          151 FGLAS-----DSFLHNTLINMYSS--CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       151 ~g~~~-----~~~~~~~li~~~~~--~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      .  .|     +..+...|..+++.  .|. ++.++|+.+|+++.+.  .|+..+-..++.++.+.|++++|+..++.+.+
T Consensus       165 ~--~~d~~~~~d~~l~~Laea~v~l~~g~-~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          165 A--IEDTVSGDNEMILNLAESYIKFATNK-ETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             H--SCHHHHHHHHHHHHHHHHHHHHHHTC-STTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             c--CccccccchHHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6  36     35566666666333  231 1569999999998654  36645555666689999999999999997765


Q ss_pred             h-----CC---cc-ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          224 S-----GF---WS-HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       224 ~-----g~---~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .     ..   .| |..+.-.+|......|+  +|.++++++.+.
T Consensus       240 ~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          240 DYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             HHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             hcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            3     11   23 45666455555555676  889999999875

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.06  E-value=9.9e-05  Score=65.49  Aligned_cols=194  Identities=8%  Similarity=-0.091  Sum_probs=97.2

Q ss_pred             HhhcCCCchHHHHHHHHHHHhcC-CCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC-CCC
Q 040801           46 SLEKCSTMRELKQIHAQMLRTSL-FFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIP  123 (323)
Q Consensus        46 ~~~~~~~~~~a~~i~~~m~~~~~-~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p  123 (323)
                      .+...|+++.|...++...+.-- .++.              ......|..+=..|...|++++|.+.+++-.+-- -.+
T Consensus       112 ~~~~~g~~~~A~~~~~~al~~~~~~~~~--------------~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~  177 (383)
T 3ulq_A          112 YELDQREYLSAIKFFKKAESKLIFVKDR--------------IEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHE  177 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCH--------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCS
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhCCCH--------------HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCc
Confidence            45567899999999988775421 0111              0022345555555666666666666665543310 001


Q ss_pred             C-----cccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc-
Q 040801          124 D-----RFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE-  189 (323)
Q Consensus       124 ~-----~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~-  189 (323)
                      +     ..+++.+-..+...|+   |.+.++...+.    +-.+ ...++..+-..|...|   ++++|.+.|++.... 
T Consensus       178 ~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g---~~~~A~~~~~~al~~~  254 (383)
T 3ulq_A          178 AYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQS---QYEDAIPYFKRAIAVF  254 (383)
T ss_dssp             TTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHH
Confidence            1     2344444445555554   44444444322    1111 1234555556666666   446666666555441 


Q ss_pred             ---CC-CCChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccChhhHHHHHHHHHhcCC---HHHHHHHHHhc
Q 040801          190 ---NV-KPNAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWSHVELKTTLMDAYCKCKF---VSRAWDLFVKM  256 (323)
Q Consensus       190 ---g~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~~~~~~li~~~~~~g~---~~~a~~~~~~m  256 (323)
                         +. .....++..+-..+.+.|+.++|...+++..+.    +-......+..+-..|.+.|+   +++|..++++.
T Consensus       255 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~  332 (383)
T 3ulq_A          255 EESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK  332 (383)
T ss_dssp             HHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT
T ss_pred             HhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence               22 223455666666666666666666666655432    111112224445555556666   55555555555

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.05  E-value=9.7e-05  Score=63.18  Aligned_cols=193  Identities=9%  Similarity=-0.088  Sum_probs=121.0

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHH----CCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chHH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIV----QGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSFL  159 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~----~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~~  159 (323)
                      |+-....|...|++++|.+.|.+-.+    .|-.++ ..+|+.+-..+.+.|+   |...++...+.    |-.. -..+
T Consensus        40 ~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~  119 (292)
T 1qqe_A           40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (292)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            44444556666777777777765533    121111 3456666666666655   55555544332    2111 1456


Q ss_pred             HHHHHHHHHhc-CCCCChHHHHHHHHHHHHcC--C-CC-C-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh--
Q 040801          160 HNTLINMYSSC-WCLDQPDEAIKIFYRMEIEN--V-KP-N-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE--  231 (323)
Q Consensus       160 ~~~li~~~~~~-g~~~~~~~a~~~~~~m~~~g--~-~p-~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~--  231 (323)
                      ++.+-..|... |   ++++|++.|++.....  . .+ . ..+|+.+-..+.+.|++++|...+++..+........  
T Consensus       120 ~~~lg~~~~~~lg---~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  196 (292)
T 1qqe_A          120 KFELGEILENDLH---DYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (292)
T ss_dssp             HHHHHHHHHHTTC---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHHHHHhhc---CHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccH
Confidence            88888889886 8   6799999998876521  1 11 1 3578889999999999999999999998864333221  


Q ss_pred             ----hHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh---H---HHhhhccCCCCCcchhhhhhhC
Q 040801          232 ----LKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW---A---MSATVGPQGLVGRHSTAHQISG  289 (323)
Q Consensus       232 ----~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~---~---~~~~~~~~~~~~~~~~a~~l~~  289 (323)
                          .|..+..+|...|++++|...|++..+- +......   .   +...+ ..++.+++.+|.....
T Consensus       197 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~-~~~~~~~~~~A~~~~~  264 (292)
T 1qqe_A          197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAV-NEGDSEQLSEHCKEFD  264 (292)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHH-HTTCTTTHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH-HcCCHHHHHHHHHHhc
Confidence                5677788899999999999999998764 1111111   1   22222 2345677777766554

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.04  E-value=1.6e-05  Score=68.18  Aligned_cols=204  Identities=10%  Similarity=-0.071  Sum_probs=97.6

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+..+...+...|+++.|...++...+..-..+.             .......+..+-..|...|++++|.+.+++..
T Consensus        44 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~-------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  110 (338)
T 3ro2_A           44 AIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGD-------------QLGEAKASGNLGNTLKVLGNFDEAIVCCQRHL  110 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC-------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccc-------------cHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            35667777888889999999999887644210000             01112345555555556666666666655543


Q ss_pred             HCCC-CCC----cccHHHHHHHhcchhh-----------------------HHHHHHHHHH----cCCCC-chHHHHHHH
Q 040801          118 VQGL-IPD----RFMFPSLFKSCADIYV-----------------------EKQLHSQAIK----FGLAS-DSFLHNTLI  164 (323)
Q Consensus       118 ~~g~-~p~----~~ty~~ll~~~~~~~~-----------------------a~~~~~~m~~----~g~~~-~~~~~~~li  164 (323)
                      +..- .++    ..++..+-..+...|+                       |.+.++...+    .+..+ ...++..+-
T Consensus       111 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~  190 (338)
T 3ro2_A          111 DISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLG  190 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            2110 011    1133333333332221                       3333322221    11111 123455555


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHc----CC-CCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC----cc-ChhhHH
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIE----NV-KPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF----WS-HVELKT  234 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~----g~-~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~----~p-~~~~~~  234 (323)
                      ..|...|   ++++|.+.+++....    +. .....++..+...+...|++++|...+++..+..-    .+ ...++.
T Consensus       191 ~~~~~~~---~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  267 (338)
T 3ro2_A          191 NTHYLLG---NFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCY  267 (338)
T ss_dssp             HHHHHHT---CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHhC---CHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHH
Confidence            5555555   445666555554321    11 11234555555556666666666666555543210    00 133455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcc
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      .+...|.+.|++++|...+++..
T Consensus       268 ~la~~~~~~g~~~~A~~~~~~a~  290 (338)
T 3ro2_A          268 SLGNTYTLLQDYEKAIDYHLKHL  290 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHH
Confidence            55555666666666666655543

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.03  E-value=1.5e-05  Score=71.18  Aligned_cols=217  Identities=12%  Similarity=-0.047  Sum_probs=151.0

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhc--C--CCCC----------ccch----hHHHhcccCC---------CCChh
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTS--L--FFDP----------CADY----HVRLVFSQIS---------NPTIY   91 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~--~--~~~~----------y~~~----~a~~lf~~m~---------~~~~~   91 (323)
                      .+..+-..+...|+++.|...+++..+..  .  .+..          |...    .|.+.|.+..         .....
T Consensus        88 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  167 (411)
T 4a1s_A           88 IYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGR  167 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHH
Confidence            45666677778899999999999887542  1  1111          1111    4555544432         12345


Q ss_pred             hHHHHHHHHHhCCC-----------------hHHHHHHHHHHHHC----CCCC-CcccHHHHHHHhcchhh---HHHHHH
Q 040801           92 TCNSIVRGYTNKNL-----------------HHEAFLFYHEMIVQ----GLIP-DRFMFPSLFKSCADIYV---EKQLHS  146 (323)
Q Consensus        92 ~~~~li~~~~~~g~-----------------~~~A~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~  146 (323)
                      .|..+-..|...|+                 +++|.+.+++..+.    +-.+ ...++..+-..+...|+   |...++
T Consensus       168 ~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  247 (411)
T 4a1s_A          168 ALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQ  247 (411)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            78888889999999                 99999999886432    1111 22466666677777777   777777


Q ss_pred             HHHHcCCC-Cc----hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcC--CC---CChHHHHHHHHHHhccCChHHHHH
Q 040801          147 QAIKFGLA-SD----SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIEN--VK---PNAVTLVNVLTARARARDLRTVKR  216 (323)
Q Consensus       147 ~m~~~g~~-~~----~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g--~~---p~~~t~~~li~~~~~~~~~~~a~~  216 (323)
                      ...+..-. .+    ..++..+-..|...|   ++++|.+.|++.....  ..   ....++..+-..+...|++++|..
T Consensus       248 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  324 (411)
T 4a1s_A          248 ERLRIAREFGDRAAERRANSNLGNSHIFLG---QFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIE  324 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHHCc---CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            76543211 11    347888999999999   7799999998876532  11   125678888899999999999999


Q ss_pred             HHHHHHHhC----Cc-cChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          217 VHKCVDESG----FW-SHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       217 ~~~~m~~~g----~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .+++..+..    -. .....+..+...|.+.|+.++|.+.+++..+
T Consensus       325 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          325 YHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            999986531    11 1245788899999999999999999998765

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.02  E-value=0.00014  Score=57.02  Aligned_cols=58  Identities=3%  Similarity=-0.153  Sum_probs=37.0

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .....+.+.|+++.|...++...+..                   +.+...|..+-..+.+.|++++|.+.|+...+
T Consensus        11 ~~a~~~~~~g~~~~A~~~~~~al~~~-------------------P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~   68 (176)
T 2r5s_A           11 KQVSELLQQGEHAQALNVIQTLSDEL-------------------QSRGDVKLAKADCLLETKQFELAQELLATIPL   68 (176)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTSCHHH-------------------HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCG
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHC-------------------CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhh
Confidence            33445556666777766666655543                   34556677777777777777777777766543

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.02  E-value=0.00028  Score=58.94  Aligned_cols=166  Identities=12%  Similarity=0.005  Sum_probs=121.8

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC----cccHHHHHHHhcchhh---HHHHHHHHHHcCC-CC-ch
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD----RFMFPSLFKSCADIYV---EKQLHSQAIKFGL-AS-DS  157 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~----~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-~~-~~  157 (323)
                      +.+...+-.+-..+.+.|++++|.+.|++..+..  |+    ...+..+-.++.+.|+   |...++...+..- .| ..
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~   89 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVP   89 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhH
Confidence            4455666667778889999999999999998753  43    3456666677777777   8898998887631 12 24


Q ss_pred             HHHHHHHHHHHh--------cCCCCChHHHHHHHHHHHHcCCCCC-hHHH-----------------HHHHHHHhccCCh
Q 040801          158 FLHNTLINMYSS--------CWCLDQPDEAIKIFYRMEIENVKPN-AVTL-----------------VNVLTARARARDL  211 (323)
Q Consensus       158 ~~~~~li~~~~~--------~g~~~~~~~a~~~~~~m~~~g~~p~-~~t~-----------------~~li~~~~~~~~~  211 (323)
                      ..+..+-.+|..        .|   ++++|.+.|++.....  |+ ....                 ..+-..+.+.|++
T Consensus        90 ~a~~~lg~~~~~~~~~~~~~~~---~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~  164 (261)
T 3qky_A           90 QAEYERAMCYYKLSPPYELDQT---DTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELY  164 (261)
T ss_dssp             HHHHHHHHHHHHHCCCTTSCCH---HHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhcccccccch---hHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCH
Confidence            556667777777        77   7799999999998754  32 2333                 3456778899999


Q ss_pred             HHHHHHHHHHHHhCCcc--ChhhHHHHHHHHHhc----------CCHHHHHHHHHhccCC
Q 040801          212 RTVKRVHKCVDESGFWS--HVELKTTLMDAYCKC----------KFVSRAWDLFVKMLFP  259 (323)
Q Consensus       212 ~~a~~~~~~m~~~g~~p--~~~~~~~li~~~~~~----------g~~~~a~~~~~~m~~~  259 (323)
                      ++|...++.+.+..-..  ....+..+..+|.+.          |++++|...+++..+.
T Consensus       165 ~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          165 EAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            99999999998763111  234677777788866          8999999999998764

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.01  E-value=0.00014  Score=52.37  Aligned_cols=98  Identities=21%  Similarity=0.060  Sum_probs=83.5

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ...|..+...+...|   ++++|.+.|++..... ..+..++..+...+...|++++|..+++++.+.. +.+...+..+
T Consensus         9 ~~~~~~~~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l   83 (125)
T 1na0_A            9 AEAWYNLGNAYYKQG---DYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNL   83 (125)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHH
Confidence            567888888999999   7799999999998754 3467788899999999999999999999998764 3367788899


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...|.+.|++++|...++++.+.
T Consensus        84 a~~~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           84 GNAYYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHh
Confidence            99999999999999999988654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.01  E-value=0.00032  Score=59.93  Aligned_cols=200  Identities=10%  Similarity=-0.075  Sum_probs=133.6

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCC--ChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNP--TIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      |......+...|+++.|...|....+.               +.+...+  ...+|+.+-..|.+.|++++|++.|++-.
T Consensus        40 ~~~a~~~~~~~g~~~~A~~~~~~al~~---------------~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al  104 (292)
T 1qqe_A           40 CVQAATIYRLRKELNLAGDSFLKAADY---------------QKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAI  104 (292)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHH---------------HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH---------------HHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344444555666666666666655443               2222222  24678899999999999999999998865


Q ss_pred             HC----CCCC-CcccHHHHHHHhcch-hh---HHHHHHHHHHcCC----CCc-hHHHHHHHHHHHhcCCCCChHHHHHHH
Q 040801          118 VQ----GLIP-DRFMFPSLFKSCADI-YV---EKQLHSQAIKFGL----ASD-SFLHNTLINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       118 ~~----g~~p-~~~ty~~ll~~~~~~-~~---a~~~~~~m~~~g~----~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~  183 (323)
                      +-    |-.. -..+|..+-..+... |+   |...++...+..-    ... ..+++.+-..|.+.|   ++++|++.|
T Consensus       105 ~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g---~~~~A~~~~  181 (292)
T 1qqe_A          105 QIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDG---QYIEASDIY  181 (292)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhC---CHHHHHHHH
Confidence            42    1110 124677777777764 66   7777777665321    111 456888999999999   779999999


Q ss_pred             HHHHHcCCCCCh------HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh------hhHHHHHHHHH--hcCCHHHH
Q 040801          184 YRMEIENVKPNA------VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV------ELKTTLMDAYC--KCKFVSRA  249 (323)
Q Consensus       184 ~~m~~~g~~p~~------~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~------~~~~~li~~~~--~~g~~~~a  249 (323)
                      ++..........      ..|..+-.++...|+.++|...+++..+.  .|+.      ..+..++.+|.  ..+++++|
T Consensus       182 ~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A  259 (292)
T 1qqe_A          182 SKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDAVNEGDSEQLSEH  259 (292)
T ss_dssp             HHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTTCTTTHHHH
T ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999875433222      15677778888999999999999997653  2321      13455666665  45779999


Q ss_pred             HHHHHhccCC
Q 040801          250 WDLFVKMLFP  259 (323)
Q Consensus       250 ~~~~~~m~~~  259 (323)
                      ...|+++..-
T Consensus       260 ~~~~~~~~~l  269 (292)
T 1qqe_A          260 CKEFDNFMRL  269 (292)
T ss_dssp             HHHHTTSSCC
T ss_pred             HHHhccCCcc
Confidence            9998887653

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=98.00  E-value=0.00022  Score=72.32  Aligned_cols=186  Identities=12%  Similarity=-0.023  Sum_probs=115.8

Q ss_pred             hHHHhhcCCCchHHHHHHHHHHHhcCCCCC-ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           43 CLVSLEKCSTMRELKQIHAQMLRTSLFFDP-CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        43 li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      +-..+...|.+++|..+|+......-..+. +...    +|.++..+.  .+..+|..+=.++.+.|++++|.+.|.+- 
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~~~~~A~~VLie~i~nldrAiE~Aerv--n~p~vWsqLAKAql~~G~~kEAIdsYiKA- 1131 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERC--NEPAVWSQLAKAQLQKGMVKEAIDSYIKA- 1131 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCHHHHHHHHHhc-
Confidence            445566667888888888774211100000 1111    455555543  33556777777888888888888887442 


Q ss_pred             HCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC
Q 040801          118 VQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN  194 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~  194 (323)
                           -|...|.-+...+.+.|+   +.+.+...++..  ++....+.+..+|++.++   +++... |   ..   .|+
T Consensus      1132 -----dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~r---leele~-f---I~---~~n 1194 (1630)
T 1xi4_A         1132 -----DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNR---LAELEE-F---IN---GPN 1194 (1630)
T ss_pred             -----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcC---HHHHHH-H---Hh---CCC
Confidence                 456677777888887777   556555555443  444444557777777763   343222 2   11   345


Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      ...|..+-..|...|++++|..+|...         ..|..+...|++.|++++|.+.+++..
T Consensus      1195 ~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA~ 1248 (1630)
T 1xi4_A         1195 NAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN 1248 (1630)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHhC
Confidence            566666777777777777777777774         367777777777777777777777664

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.00  E-value=0.00014  Score=70.04  Aligned_cols=152  Identities=8%  Similarity=-0.193  Sum_probs=123.9

Q ss_pred             HhCCChHHHHHHHHHHHH------CCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801          101 TNKNLHHEAFLFYHEMIV------QGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~------~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ...|++++|++.+++..+      ....| +...+..+-..+...|+   |.+.++...+.. .-+...|..+-..|...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHHc
Confidence            788999999999999872      12334 45667777777888888   888888887764 23567888888899999


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  250 (323)
                      |   ++++|.+.|++..+.. .-+...|..+-..+.+.|++++ ...+++..+.. +-+...|..+-.+|.+.|++++|.
T Consensus       481 g---~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~  554 (681)
T 2pzi_A          481 G---DYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAV  554 (681)
T ss_dssp             T---CHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             C---CHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHH
Confidence            9   7799999999988754 2356788889999999999999 99999998864 225678889999999999999999


Q ss_pred             HHHHhccCC
Q 040801          251 DLFVKMLFP  259 (323)
Q Consensus       251 ~~~~~m~~~  259 (323)
                      +.|++..+.
T Consensus       555 ~~~~~al~l  563 (681)
T 2pzi_A          555 RTLDEVPPT  563 (681)
T ss_dssp             HHHHTSCTT
T ss_pred             HHHHhhccc
Confidence            999999875

>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=97.96  E-value=0.00018  Score=67.51  Aligned_cols=142  Identities=10%  Similarity=-0.062  Sum_probs=73.6

Q ss_pred             hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHH
Q 040801           77 HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIK  150 (323)
Q Consensus        77 ~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~  150 (323)
                      +|.+.|++..   +.+...|..+-..|.+.|++++|.+.|++..+.. +-+...+..+-..+...|+   |.+.++...+
T Consensus         7 ~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   85 (568)
T 2vsy_A            7 RELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVLLQQASD   85 (568)
T ss_dssp             --------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            3444454433   3345556666666666677777777776665531 1223445555555555555   5555555555


Q ss_pred             cCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc---CChHHHHHHHHHHHHh
Q 040801          151 FGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA---RDLRTVKRVHKCVDES  224 (323)
Q Consensus       151 ~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~---~~~~~a~~~~~~m~~~  224 (323)
                      .. ..+...+..+-..|.+.|   ++++|.+.|++..+.. .-+...+..+...+...   |+.++|...+++..+.
T Consensus        86 ~~-p~~~~~~~~la~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           86 AA-PEHPGIALWLGHALEDAG---QAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             cC-CCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            43 123455566666666666   4466666666655533 12345555566666666   6666666666666554

>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=97.93  E-value=0.0012  Score=53.64  Aligned_cols=187  Identities=10%  Similarity=-0.113  Sum_probs=132.9

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+...-..+...|+++.|...|+...+..-                  .++...|..+-.++...|++++|.+.|++..
T Consensus         8 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~------------------~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al   69 (228)
T 4i17_A            8 NQLKNEGNDALNAKNYAVAFEKYSEYLKLTN------------------NQDSVTAYNCGVCADNIKKYKEAADYFDIAI   69 (228)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT------------------TCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhccC------------------CCCcHHHHHHHHHHHHhhcHHHHHHHHHHHH
Confidence            4555566677888999999999999998752                  3677777778889999999999999999988


Q ss_pred             HCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc-h-------HHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 040801          118 VQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD-S-------FLHNTLINMYSSCWCLDQPDEAIKIFYR  185 (323)
Q Consensus       118 ~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~-~-------~~~~~li~~~~~~g~~~~~~~a~~~~~~  185 (323)
                      +.  .| +...|..+-..+...|+   |...++...+..  |+ .       ..|..+=..+...|   ++++|++.|++
T Consensus        70 ~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~---~~~~A~~~~~~  142 (228)
T 4i17_A           70 KK--NYNLANAYIGKSAAYRDMKNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAG---NIEKAEENYKH  142 (228)
T ss_dssp             HT--TCSHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             Hh--CcchHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhc---cHHHHHHHHHH
Confidence            64  33 44567777777777777   888888887764  33 3       44667777778888   77999999999


Q ss_pred             HHHcCCCCC---hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          186 MEIENVKPN---AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       186 m~~~g~~p~---~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ....  .|+   ...|..+-..+...     +...++.+...+ ..+...|....  ....+.+++|...+++..+.
T Consensus       143 al~~--~p~~~~~~~~~~l~~~~~~~-----~~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l  209 (228)
T 4i17_A          143 ATDV--TSKKWKTDALYSLGVLFYNN-----GADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTL  209 (228)
T ss_dssp             HTTS--SCHHHHHHHHHHHHHHHHHH-----HHHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhc--CCCcccHHHHHHHHHHHHHH-----HHHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhc
Confidence            8764  565   45666666666543     334445554443 22334444433  23456688999999888654

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.90  E-value=0.00022  Score=60.81  Aligned_cols=169  Identities=5%  Similarity=-0.096  Sum_probs=115.1

Q ss_pred             HhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCC
Q 040801           80 LVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLAS  155 (323)
Q Consensus        80 ~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~  155 (323)
                      +.+++..+.+...+..+-..+.+.|++++|.+.|++..+.  .| +...+..+-..+...|+   |..+++...+..  |
T Consensus       107 ~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p  182 (287)
T 3qou_A          107 ALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--Q  182 (287)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--C
T ss_pred             HHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--c
Confidence            3333333445555666777788889999999999888663  34 34566667777777777   777777665443  4


Q ss_pred             chHHHHHHH-HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-cChhhH
Q 040801          156 DSFLHNTLI-NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW-SHVELK  233 (323)
Q Consensus       156 ~~~~~~~li-~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~~~~~  233 (323)
                      +........ ..+...+   +.++|.+.|++..... ..+...+..+-..+...|+.++|...+.++.+..-. .+...+
T Consensus       183 ~~~~~~~~~~~~l~~~~---~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~  258 (287)
T 3qou_A          183 DTRYQGLVAQIELLXQA---ADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTR  258 (287)
T ss_dssp             SHHHHHHHHHHHHHHHH---TSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHH
T ss_pred             chHHHHHHHHHHHHhhc---ccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHH
Confidence            443322222 2244555   3367888888877654 346677888888888899999999999888876422 125678


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhc
Q 040801          234 TTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       234 ~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ..|...|...|+.++|...+++-
T Consensus       259 ~~l~~~~~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          259 XTFQEILAALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHH
Confidence            88888888889888888877753

>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=97.89  E-value=0.00056  Score=54.83  Aligned_cols=125  Identities=10%  Similarity=-0.063  Sum_probs=67.1

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      .+..+-..+...|++++|.+.|++.    +.|+...|..+-..+.+.|+   |.+.++...+.. ..+...|..+-.+|.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            3445556677888888888888765    34455555555555555555   555555554433 223445555555555


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCC--------------C-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVK--------------P-NAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~--------------p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ..|   ++++|.+.|++.....-.              | +...+..+-..+...|+.++|...++...+.
T Consensus        83 ~~~---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           83 QTE---KYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HTT---CHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             Hcc---cHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            555   445566555555542210              1 1134444555555555555555555555443

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.89  E-value=0.0011  Score=58.37  Aligned_cols=25  Identities=8%  Similarity=-0.118  Sum_probs=15.4

Q ss_pred             hhhHHHhhcCCCchHHHHHHHHHHH
Q 040801           41 HFCLVSLEKCSTMRELKQIHAQMLR   65 (323)
Q Consensus        41 ~~li~~~~~~~~~~~a~~i~~~m~~   65 (323)
                      ..+-..+...|+++.|...+++..+
T Consensus        57 ~~l~~~~~~~g~~~~A~~~~~~al~   81 (373)
T 1hz4_A           57 SVLGEVLHCKGELTRSLALMQQTEQ   81 (373)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            3344455566777777777776654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.89  E-value=0.00028  Score=62.49  Aligned_cols=192  Identities=9%  Similarity=-0.075  Sum_probs=99.9

Q ss_pred             hhcCCCchHHHHHHHHHHHhcC-CCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC--CC--
Q 040801           47 LEKCSTMRELKQIHAQMLRTSL-FFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ--GL--  121 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~-~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--g~--  121 (323)
                      +...|+++.|...+++..+..- .++.              ......+..+-..|...|++++|.+.+++-.+.  ..  
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~--------------~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~  176 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDD--------------IEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPL  176 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCH--------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTT
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCCh--------------HHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCC
Confidence            3466888888888888765421 0110              011234555555666666666666666654331  00  


Q ss_pred             -CC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH---
Q 040801          122 -IP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI---  188 (323)
Q Consensus       122 -~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~---  188 (323)
                       .+ ...+++.+-..+...|+   |.+.++...+.    +-.+ ...+++.+-..|...|   ++++|.+.|++...   
T Consensus       177 ~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~---~~~~A~~~~~~al~~~~  253 (378)
T 3q15_A          177 YSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSG---DDQMAVEHFQKAAKVSR  253 (378)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHH
Confidence             11 12344455555555555   55555444332    1111 1234555666666666   45666666666554   


Q ss_pred             -cCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc----cChhhHHHHHHHHHhcCC---HHHHHHHHHh
Q 040801          189 -ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW----SHVELKTTLMDAYCKCKF---VSRAWDLFVK  255 (323)
Q Consensus       189 -~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~----p~~~~~~~li~~~~~~g~---~~~a~~~~~~  255 (323)
                       .+......++..+-..+.+.|+.++|...+++..+..-.    .....+..+-..|...|+   +++|...+++
T Consensus       254 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~  328 (378)
T 3q15_A          254 EKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK  328 (378)
T ss_dssp             HHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHH
T ss_pred             hhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh
Confidence             022223556666666666666666666666666543211    112234444455555666   6666666665

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.88  E-value=0.0013  Score=53.65  Aligned_cols=160  Identities=9%  Similarity=-0.032  Sum_probs=109.5

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCc----ccHHHHHHHhcchhh---HHHHHHHHHHcCCC-Cch-HHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDR----FMFPSLFKSCADIYV---EKQLHSQAIKFGLA-SDS-FLHN  161 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~-~~~-~~~~  161 (323)
                      ..+-.+-..+.+.|++++|.+.|+++.+.  .|+.    ..+..+-.++.+.|+   |...++.+.+..-. +.. ..+-
T Consensus         5 ~~~~~~a~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            5 NEIYATAQQKLQDGNWRQAITQLEALDNR--YPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            34444556678888999999999888764  2332    355566667777777   88888887765421 111 1233


Q ss_pred             HHHHHHHh------------------cCCCCChHHHHHHHHHHHHcCCCCChH-HH-----------------HHHHHHH
Q 040801          162 TLINMYSS------------------CWCLDQPDEAIKIFYRMEIENVKPNAV-TL-----------------VNVLTAR  205 (323)
Q Consensus       162 ~li~~~~~------------------~g~~~~~~~a~~~~~~m~~~g~~p~~~-t~-----------------~~li~~~  205 (323)
                      .+-.+|..                  .|   +.++|.+.|++.....  |+.. .+                 -.+-..+
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~A~~~~~~~l~~~--P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~  157 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQ---QARAAFSDFSKLVRGY--PNSQYTTDATKRLVFLKDRLAKYEYSVAEYY  157 (225)
T ss_dssp             HHHHHHHHHHC--------------CCH---HHHHHHHHHHHHHTTC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcH---HHHHHHHHHHHHHHHC--cCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33333332                  34   6789999999988643  4332 22                 2344567


Q ss_pred             hccCChHHHHHHHHHHHHhCCccC----hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          206 ARARDLRTVKRVHKCVDESGFWSH----VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       206 ~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.|++++|...++.+.+.-  |+    ...+..+..+|.+.|+.++|.+.++.+...
T Consensus       158 ~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~  213 (225)
T 2yhc_A          158 TERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAAN  213 (225)
T ss_dssp             HHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             HHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh
Confidence            88999999999999998763  43    256888899999999999999999988765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.87  E-value=0.00021  Score=63.35  Aligned_cols=164  Identities=12%  Similarity=-0.025  Sum_probs=122.0

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCC-CCCC----cccHHHHHHHhcchhh---HHHHHHHHHHc----CC-C-Cch
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPD----RFMFPSLFKSCADIYV---EKQLHSQAIKF----GL-A-SDS  157 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~----~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~-~-~~~  157 (323)
                      .|-..=..+...|++++|.+.|++..+.- -.+|    ..+|..+-..+...|+   |...+....+.    +- . ...
T Consensus       105 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  184 (383)
T 3ulq_A          105 FNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLL  184 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHH
Confidence            45555667789999999999999986631 1233    3567777777777777   66666665543    11 1 124


Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CC-c
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDES----GF-W  227 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~-~  227 (323)
                      .+++.+-..|...|   ++++|.+.|++....    +-.+ ...++..+-..+...|++++|...+++..+.    +- +
T Consensus       185 ~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~  261 (383)
T 3ulq_A          185 QCHSLFATNFLDLK---QYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILP  261 (383)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHhc---CHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccch
Confidence            67888889999999   779999999887653    1111 2258999999999999999999999998762    33 3


Q ss_pred             cChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          228 SHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       228 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ....++..+-..|.+.|++++|...+++..+
T Consensus       262 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          262 SLPQAYFLITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3467788999999999999999999998754

>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=97.86  E-value=0.00069  Score=68.84  Aligned_cols=213  Identities=7%  Similarity=0.003  Sum_probs=136.8

Q ss_pred             cCCCchHHHHHHHHHHHhcCCCCC---ccch--------hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           49 KCSTMRELKQIHAQMLRTSLFFDP---CADY--------HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        49 ~~~~~~~a~~i~~~m~~~~~~~~~---y~~~--------~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+++++|.++.+...    .|..   +++.        +|.+-|..  ..|...|.-++.+|.+.|++++|.++|..-+
T Consensus      1088 ~i~nldrAiE~Aervn----~p~vWsqLAKAql~~G~~kEAIdsYiK--AdD~say~eVa~~~~~lGkyEEAIeyL~mAr 1161 (1630)
T 1xi4_A         1088 HIGNLDRAYEFAERCN----EPAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMAR 1161 (1630)
T ss_pred             HHhhHHHHHHHHHhcC----CHHHHHHHHHHHHhCCCHHHHHHHHHh--cCChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            6677888887777441    2222   3333        55555543  5777889999999999999999999997655


Q ss_pred             HCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHH
Q 040801          118 VQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVT  197 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t  197 (323)
                      +..  ++....+.+..+|++.++-.+ ++...+   .++...|..+=+.|-..|   ++++|..+|...         ..
T Consensus      1162 k~~--~e~~Idt~LafaYAKl~rlee-le~fI~---~~n~ad~~~iGd~le~eg---~YeeA~~~Y~kA---------~n 1223 (1630)
T 1xi4_A         1162 KKA--RESYVETELIFALAKTNRLAE-LEEFIN---GPNNAHIQQVGDRCYDEK---MYDAAKLLYNNV---------SN 1223 (1630)
T ss_pred             hhc--ccccccHHHHHHHHhhcCHHH-HHHHHh---CCCHHHHHHHHHHHHhcC---CHHHHHHHHHhh---------hH
Confidence            543  454445568888888877222 333332   345555666777777777   557777777663         36


Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHh----------------------C--CccChhhHHHHHHHHHhcCCHHHHHHHH
Q 040801          198 LVNVLTARARARDLRTVKRVHKCVDES----------------------G--FWSHVELKTTLMDAYCKCKFVSRAWDLF  253 (323)
Q Consensus       198 ~~~li~~~~~~~~~~~a~~~~~~m~~~----------------------g--~~p~~~~~~~li~~~~~~g~~~~a~~~~  253 (323)
                      |..+...+++.|+++.|.+.+++....                      |  +.-+...+..++..|-+.|.+++|..++
T Consensus      1224 y~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~Ll 1303 (1630)
T 1xi4_A         1224 FGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITML 1303 (1630)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            777777777777777777666554221                      1  2235566778899999999999999999


Q ss_pred             HhccCC-CCchhhhHHHhhhccCCCCCcchhhh
Q 040801          254 VKMLFP-WNNYGQWAMSATVGPQGLVGRHSTAH  285 (323)
Q Consensus       254 ~~m~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~  285 (323)
                      +.-..- +.....|+....+...-+-+++.++.
T Consensus      1304 E~aL~LeraH~gmftELaiLyaKy~peklmEhl 1336 (1630)
T 1xi4_A         1304 EAALGLERAHMGMFTELAILYSKFKPQKMREHL 1336 (1630)
T ss_pred             HHHhccChhHhHHHHHHHHHHHhCCHHHHHHHH
Confidence            876543 22333344333333333444444443

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.84  E-value=0.0009  Score=55.76  Aligned_cols=168  Identities=8%  Similarity=-0.092  Sum_probs=118.0

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ..+..+-..+.+.|+++.|...|+...+..-  +.              ......+..+-.+|.+.|++++|.+.|++..
T Consensus        16 ~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p--~~--------------~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l   79 (261)
T 3qky_A           16 QEAFERAMEFYNQGKYDRAIEYFKAVFTYGR--TH--------------EWAADAQFYLARAYYQNKEYLLAASEYERFI   79 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHGGGCS--CS--------------TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC--CC--------------cchHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            3445566677788999999999999987631  00              1115567778888999999999999999987


Q ss_pred             HCCCCCC----cccHHHHHHHhcc--------hhh---HHHHHHHHHHcCCCCc-hHHH-----------------HHHH
Q 040801          118 VQGLIPD----RFMFPSLFKSCAD--------IYV---EKQLHSQAIKFGLASD-SFLH-----------------NTLI  164 (323)
Q Consensus       118 ~~g~~p~----~~ty~~ll~~~~~--------~~~---a~~~~~~m~~~g~~~~-~~~~-----------------~~li  164 (323)
                      +..  |+    ...+..+-.++..        .|+   |...++...+..  |+ ....                 ..+-
T Consensus        80 ~~~--p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la  155 (261)
T 3qky_A           80 QIY--QIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAA  155 (261)
T ss_dssp             HHC--TTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHC--CCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            742  32    2334444455544        566   888888887754  32 2233                 4557


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCC--ChHHHHHHHHHHhcc----------CChHHHHHHHHHHHHhCCccCh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKP--NAVTLVNVLTARARA----------RDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~----------~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      ..|.+.|   ++++|+..|++........  ....+..+..++...          |++++|...++.+.+.  .|+.
T Consensus       156 ~~~~~~g---~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~  228 (261)
T 3qky_A          156 RLYERRE---LYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI--FPDS  228 (261)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHHHcc---CHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH--CCCC
Confidence            7788888   7799999999998753211  245677777778766          8899999999999876  3553

>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=97.84  E-value=0.00029  Score=67.81  Aligned_cols=190  Identities=9%  Similarity=-0.120  Sum_probs=137.0

Q ss_pred             hcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC-Ccc
Q 040801           48 EKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRF  126 (323)
Q Consensus        48 ~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~  126 (323)
                      ...+++++|.+.+++..+..+.           .-.+..+.+...|..+-..|.+.|++++|.+.|++..+.  .| +..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~-----------~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~  468 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALD-----------ADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--VGWRWR  468 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC------------------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCCCHH
T ss_pred             ccccCHHHHHHHHHHhhhhccc-----------ccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--CcchHH
Confidence            5667788888888777621110           000001445677888889999999999999999998764  34 446


Q ss_pred             cHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          127 MFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       127 ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      .|..+-..+...|+   |.+.|+...+.. .-+...|..+-.+|.+.|++   ++ ++.|++..+.+ .-+...|..+-.
T Consensus       469 a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~---~~-~~~~~~al~~~-P~~~~a~~~lg~  542 (681)
T 2pzi_A          469 LVWYRAVAELLTGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNT---DE-HKFYQTVWSTN-DGVISAAFGLAR  542 (681)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCC---CT-TCHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCh---HH-HHHHHHHHHhC-CchHHHHHHHHH
Confidence            67777677777777   888898888765 22567788999999999955   67 88898887754 336678999999


Q ss_pred             HHhccCChHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCC--------HHHHHHHHHhccC
Q 040801          204 ARARARDLRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKF--------VSRAWDLFVKMLF  258 (323)
Q Consensus       204 ~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~--------~~~a~~~~~~m~~  258 (323)
                      ++.+.|+.++|...+++..+.  .|+ ...|..+..+|...|+        +++|.+.++.+..
T Consensus       543 ~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~~  604 (681)
T 2pzi_A          543 ARSAEGDRVGAVRTLDEVPPT--SRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALPP  604 (681)
T ss_dssp             HHHHTTCHHHHHHHHHTSCTT--STTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSCT
T ss_pred             HHHHcCCHHHHHHHHHhhccc--CcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCCC
Confidence            999999999999999987665  354 5667777777766554        6777777776653

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.83  E-value=0.0028  Score=57.41  Aligned_cols=208  Identities=8%  Similarity=-0.097  Sum_probs=134.1

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhc-ccCCCCChhhHHHHHHHHHhCCChHHHHHHHHH
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVF-SQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHE  115 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf-~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  115 (323)
                      ...|+.+-..+...|+.++|.+.|++..+.--           +.. ++.......+|+.+-..|...|++++|...+++
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~-----------~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~k  119 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQ-----------QEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDK  119 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH-----------HHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH-----------hcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHH
Confidence            34567777788888999999999987654310           000 011134567899999999999999999999987


Q ss_pred             HHHC----C--CCCC-cccHHHHHHHhcchh--h---HHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCChHHHHHH
Q 040801          116 MIVQ----G--LIPD-RFMFPSLFKSCADIY--V---EKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQPDEAIKI  182 (323)
Q Consensus       116 m~~~----g--~~p~-~~ty~~ll~~~~~~~--~---a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~  182 (323)
                      ..+-    .  ..++ ..+|...-.++.+.|  +   |...|+...+..  |+ ...+..+...+.+.+..++.++|++.
T Consensus       120 a~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~--p~~~~~~~~~~~~~~~l~~~~~~~~al~~  197 (472)
T 4g1t_A          120 VKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK--PKNPEFTSGLAIASYRLDNWPPSQNAIDP  197 (472)
T ss_dssp             HHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHSCCCCCTHHH
T ss_pred             HHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhcCchHHHHHHHH
Confidence            6431    1  1111 234443333333322  2   888888887764  43 44455555554443333355788988


Q ss_pred             HHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          183 FYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       183 ~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +++..... +.+..++..+-..+..    .++.++|..++++..+.. +.+...+..+-..|.+.|+.++|.+.+++..+
T Consensus       198 ~~~al~l~-p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  275 (472)
T 4g1t_A          198 LRQAIRLN-PDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALE  275 (472)
T ss_dssp             HHHHHHHC-SSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhcC-CcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            88877643 2345556555544443    467888999999887764 33567788899999999999999999998765


Q ss_pred             C
Q 040801          259 P  259 (323)
Q Consensus       259 ~  259 (323)
                      .
T Consensus       276 ~  276 (472)
T 4g1t_A          276 Y  276 (472)
T ss_dssp             H
T ss_pred             h
Confidence            4

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.82  E-value=0.0029  Score=57.62  Aligned_cols=210  Identities=14%  Similarity=-0.002  Sum_probs=107.1

Q ss_pred             hHHHhhcCCCchHHHHHHHHHHHhcCCCCC------ccch-------hHHHhcccCCCCChhhHHHHHHHHHhCC-----
Q 040801           43 CLVSLEKCSTMRELKQIHAQMLRTSLFFDP------CADY-------HVRLVFSQISNPTIYTCNSIVRGYTNKN-----  104 (323)
Q Consensus        43 li~~~~~~~~~~~a~~i~~~m~~~~~~~~~------y~~~-------~a~~lf~~m~~~~~~~~~~li~~~~~~g-----  104 (323)
                      +-....+.|+++.|..+|+...+.|...-.      |...       +|.+.|.+....+...+..+=..+...|     
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~   88 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELGYSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEA   88 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCTGGGTCC----------------------------CHHHHHHHHHTC--CCHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCc
Confidence            455566778999999999999888742222      2111       6777776655446666666666555655     


Q ss_pred             ChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh------HHHHHHHHHHcCC-------------------------
Q 040801          105 LHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV------EKQLHSQAIKFGL-------------------------  153 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~------a~~~~~~m~~~g~-------------------------  153 (323)
                      ++++|++.|++-.+.|...   .+..|-..|...+.      +.+.+....+.|.                         
T Consensus        89 ~~~~A~~~~~~Aa~~g~~~---A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~~~a~  165 (452)
T 3e4b_A           89 EHHEAESLLKKAFANGEGN---TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHLDDVE  165 (452)
T ss_dssp             HHHHHHHHHHHHHHTTCSS---CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHH---HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCHHHHH
Confidence            7889999999887766432   33333222222111      2222222222221                         


Q ss_pred             -------CCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc----CChHHHHHHHHHHH
Q 040801          154 -------ASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA----RDLRTVKRVHKCVD  222 (323)
Q Consensus       154 -------~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~----~~~~~a~~~~~~m~  222 (323)
                             ..+...+..|-..|.+.|...+.++|++.|++-.+.| .++...+..+-..|...    ++.++|...|+...
T Consensus       166 ~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa  244 (452)
T 3e4b_A          166 RICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA  244 (452)
T ss_dssp             HHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc
Confidence                   2233355666666666663334567777777766665 33444434444444433    56666666666655


Q ss_pred             HhCCccChhhHHHHHHH-H--HhcCCHHHHHHHHHhccCCC
Q 040801          223 ESGFWSHVELKTTLMDA-Y--CKCKFVSRAWDLFVKMLFPW  260 (323)
Q Consensus       223 ~~g~~p~~~~~~~li~~-~--~~~g~~~~a~~~~~~m~~~~  260 (323)
                       .|   +...+..|-.. |  ...|+.++|.+.|++..+.|
T Consensus       245 -~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g  281 (452)
T 3e4b_A          245 -PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD  281 (452)
T ss_dssp             -GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT
T ss_pred             -CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC
Confidence             22   33444444443 2  34566666666666665554

>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=97.81  E-value=0.00017  Score=56.49  Aligned_cols=158  Identities=9%  Similarity=-0.033  Sum_probs=110.8

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHH-
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINM-  166 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~-  166 (323)
                      .+...-..+.+.|++++|...|++..+.  .| +...+..+-..+...|+   |...++...+..  |+...+..+... 
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~   83 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDE--LQSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLE   83 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHH--HHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHH
Confidence            4555667888999999999999887552  23 44667777777777777   777776665443  333333222111 


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCC
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKF  245 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~  245 (323)
                      +...+   ...+|.+.|++..... +-+...+..+-..+...|++++|...++++.+..-.+ +...+..+...|...|+
T Consensus        84 ~~~~~---~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~  159 (176)
T 2r5s_A           84 LHQQA---AESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQ  159 (176)
T ss_dssp             HHHHH---TSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCS
T ss_pred             HHhhc---ccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCC
Confidence            12222   1245788888877643 2257888888899999999999999999988764322 35678889999999999


Q ss_pred             HHHHHHHHHhcc
Q 040801          246 VSRAWDLFVKML  257 (323)
Q Consensus       246 ~~~a~~~~~~m~  257 (323)
                      .++|...|++..
T Consensus       160 ~~~A~~~y~~al  171 (176)
T 2r5s_A          160 GNAIASKYRRQL  171 (176)
T ss_dssp             SCHHHHHHHHHH
T ss_pred             CCcHHHHHHHHH
Confidence            999999988653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.80  E-value=0.0015  Score=55.56  Aligned_cols=164  Identities=9%  Similarity=-0.070  Sum_probs=113.6

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-c----ccHHHHHHHhcchhh---HHHHHHHHHHcCCC---Cc--h
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-R----FMFPSLFKSCADIYV---EKQLHSQAIKFGLA---SD--S  157 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~----~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~---~~--~  157 (323)
                      ..+...+..+...|++++|.+.+++..+..-..+ .    ..+..+-..+...|+   |...++...+....   +.  .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            4456678889999999999999988776432111 1    112223333444445   77777776643211   11  4


Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHH---c-CCCC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC----c
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEI---E-NVKP--NAVTLVNVLTARARARDLRTVKRVHKCVDESGF----W  227 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~---~-g~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~----~  227 (323)
                      .+|+.+-..|...|   ++++|.+.|++...   . +-.+  ...+|..+-..|...|++++|...+++..+..-    .
T Consensus       156 ~~~~~lg~~y~~~~---~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~  232 (293)
T 2qfc_A          156 YIENAIANIYAENG---YLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSM  232 (293)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBC
T ss_pred             HHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcH
Confidence            58889999999999   77999999988763   1 1111  225888899999999999999999998865321    1


Q ss_pred             c-ChhhHHHHHHHHHhcCCHHHH-HHHHHhcc
Q 040801          228 S-HVELKTTLMDAYCKCKFVSRA-WDLFVKML  257 (323)
Q Consensus       228 p-~~~~~~~li~~~~~~g~~~~a-~~~~~~m~  257 (323)
                      . -..+|..+-..|.+.|+.++| ...+++..
T Consensus       233 ~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          233 ALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             SSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            1 156778888899999999999 77676643

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.80  E-value=0.0013  Score=53.19  Aligned_cols=165  Identities=10%  Similarity=-0.061  Sum_probs=119.3

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchh----h---HHHHHHHHHHcCCCCchHHH
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIY----V---EKQLHSQAIKFGLASDSFLH  160 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~----~---a~~~~~~m~~~g~~~~~~~~  160 (323)
                      -+...+..+=..|...+++++|++.|++-.+.|   +...+..|=..+.. +    +   |.++++...+.|   +...+
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~   88 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGE   88 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            456677777788888999999999999988876   44556666666666 4    3   888888887765   45566


Q ss_pred             HHHHHHHHh-cCCCCChHHHHHHHHHHHHcCCC-CChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          161 NTLINMYSS-CWCLDQPDEAIKIFYRMEIENVK-PNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       161 ~~li~~~~~-~g~~~~~~~a~~~~~~m~~~g~~-p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      ..|-..|.. .|...++++|++.|++-.+.|.. -+...+..|=..|..    .++.++|...+++..+.  ..+...+.
T Consensus        89 ~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~  166 (212)
T 3rjv_A           89 IVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEY  166 (212)
T ss_dssp             HHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHH
T ss_pred             HHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHH
Confidence            666666654 11122789999999988766521 126677777777777    78899999999999876  23455666


Q ss_pred             HHHHHHHhc-C-----CHHHHHHHHHhccCCCC
Q 040801          235 TLMDAYCKC-K-----FVSRAWDLFVKMLFPWN  261 (323)
Q Consensus       235 ~li~~~~~~-g-----~~~~a~~~~~~m~~~~~  261 (323)
                      .|-..|... |     +.++|...|++..+.|.
T Consensus       167 ~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          167 WAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            677777654 3     89999999998877653

>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=97.79  E-value=0.00062  Score=63.84  Aligned_cols=147  Identities=7%  Similarity=-0.082  Sum_probs=81.4

Q ss_pred             CChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHH
Q 040801          104 NLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      |++++|.+.|++..+.  .| +...|..+-..+...|+   |.+.++...+.. ..+...|..+-..|...|   ++++|
T Consensus         3 g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g---~~~~A   76 (568)
T 2vsy_A            3 ADGPRELLQLRAAVRH--RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQ---RHAEA   76 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             ccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCC---CHHHH
Confidence            5667777777666543  23 34555555566666666   666666665543 123556666777777777   55777


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc---CCHHHHHHHHHhc
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC---KFVSRAWDLFVKM  256 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~---g~~~~a~~~~~~m  256 (323)
                      .+.|++..+.. .-+...+..+-..+.+.|+.++|...+++..+.. +-+...+..+...|.+.   |+.++|.+.+++.
T Consensus        77 ~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~a  154 (568)
T 2vsy_A           77 AVLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAA  154 (568)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            77777766543 2245666667777777777777777777776653 22355666677777777   7777777777766


Q ss_pred             cC
Q 040801          257 LF  258 (323)
Q Consensus       257 ~~  258 (323)
                      .+
T Consensus       155 l~  156 (568)
T 2vsy_A          155 VA  156 (568)
T ss_dssp             HH
T ss_pred             Hh
Confidence            44

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.79  E-value=0.0029  Score=55.53  Aligned_cols=193  Identities=8%  Similarity=-0.086  Sum_probs=115.2

Q ss_pred             HhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCCh----hhHHHHHHHHHhCCChHHHHHHHHHHHHCCC
Q 040801           46 SLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTI----YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL  121 (323)
Q Consensus        46 ~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~----~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~  121 (323)
                      .+...|+++.|...+++.....-                  ..+.    ..++.+-..+...|++++|.+.+++..+..-
T Consensus        23 ~~~~~g~~~~A~~~~~~al~~~~------------------~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~   84 (373)
T 1hz4_A           23 VAINDGNPDEAERLAKLALEELP------------------PGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMAR   84 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCC------------------TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCC------------------CCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHH
Confidence            44567899999999988776531                  1111    2345555667778888888888877644210


Q ss_pred             -CCCc----ccHHHHHHHhcchhh---HHHHHHHHHHc----CCC--C-chHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          122 -IPDR----FMFPSLFKSCADIYV---EKQLHSQAIKF----GLA--S-DSFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       122 -~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~--~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                       .++.    .++..+-..+...|+   |...++...+.    +..  | ....+..+-..|...|   ++++|.+.+++.
T Consensus        85 ~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~~~~a  161 (373)
T 1hz4_A           85 QHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWA---RLDEAEASARSG  161 (373)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTT---CHHHHHHHHHHH
T ss_pred             hcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhc---CHHHHHHHHHHH
Confidence             1111    123334444555555   55555555432    222  2 2345566777777777   668888888777


Q ss_pred             HHcCC--CC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh-hhHH-----HHHHHHHhcCCHHHHHHHHHhc
Q 040801          187 EIENV--KP--NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV-ELKT-----TLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       187 ~~~g~--~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~-----~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      ....-  .+  ...+|..+-..+...|++++|...+++..+..-.++. ..+.     .....+...|+.++|...+++.
T Consensus       162 l~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a  241 (373)
T 1hz4_A          162 IEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHT  241 (373)
T ss_dssp             HHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            65321  11  2346667777778888888888888887654222211 1122     2334467888888888888887


Q ss_pred             cCC
Q 040801          257 LFP  259 (323)
Q Consensus       257 ~~~  259 (323)
                      ...
T Consensus       242 ~~~  244 (373)
T 1hz4_A          242 AKP  244 (373)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.78  E-value=0.0016  Score=59.01  Aligned_cols=215  Identities=12%  Similarity=0.043  Sum_probs=140.1

Q ss_pred             chhhhhhHHHhhcCCCchHHHHHHHHHHHhc--C-CC---CC-------------ccch---hHHHhcccCC--CC-Chh
Q 040801           37 QYQAHFCLVSLEKCSTMRELKQIHAQMLRTS--L-FF---DP-------------CADY---HVRLVFSQIS--NP-TIY   91 (323)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~i~~~m~~~~--~-~~---~~-------------y~~~---~a~~lf~~m~--~~-~~~   91 (323)
                      ..+|+-+-..+...|++++|...++...+..  + .+   ..             +++.   .|.+.|++..  .| +..
T Consensus        94 ~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~  173 (472)
T 4g1t_A           94 LVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPE  173 (472)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHH
Confidence            3456777778889999999999998776432  1 11   11             1111   7888887654  33 444


Q ss_pred             hHHHHHHH---HHhCCChHHHHHHHHHHHHCCCCCC-cccHHHHHHHhcchh----h---HHHHHHHHHHcCCCCchHHH
Q 040801           92 TCNSIVRG---YTNKNLHHEAFLFYHEMIVQGLIPD-RFMFPSLFKSCADIY----V---EKQLHSQAIKFGLASDSFLH  160 (323)
Q Consensus        92 ~~~~li~~---~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~----~---a~~~~~~m~~~g~~~~~~~~  160 (323)
                      .+..+-..   +...++.++|++.|++-.+.  .|+ ..++..+-..+...+    +   |.+.++...+.. ..+..++
T Consensus       174 ~~~~~~~~~~~l~~~~~~~~al~~~~~al~l--~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~  250 (472)
T 4g1t_A          174 FTSGLAIASYRLDNWPPSQNAIDPLRQAIRL--NPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVL  250 (472)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTHHHHHHHHHH--CSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHH
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHHHHHHhhc--CCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHH
Confidence            44444333   45567888899888877653  343 344444433333322    2   888888877654 3456778


Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc-------------------cCChHHHHHHHHHH
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR-------------------ARDLRTVKRVHKCV  221 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~-------------------~~~~~~a~~~~~~m  221 (323)
                      ..+-..|.+.|   ++++|.+.|++..... +-+..++..+-..|..                   .+..+.|...++..
T Consensus       251 ~~lg~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a  326 (472)
T 4g1t_A          251 RSAAKFYRRKD---EPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKA  326 (472)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---chHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            88999999999   6799999999887643 2244555554443322                   12345566666666


Q ss_pred             HHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          222 DESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       222 ~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.. +.+...+..+-..|.+.|++++|.+.|++..+.
T Consensus       327 ~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~  363 (472)
T 4g1t_A          327 DEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSK  363 (472)
T ss_dssp             HHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             hhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc
Confidence            6543 234667888999999999999999999987654

>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=97.77  E-value=0.0012  Score=46.77  Aligned_cols=99  Identities=13%  Similarity=-0.117  Sum_probs=83.6

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTT  235 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~  235 (323)
                      ....+..+...+...|   ++++|.+.|++..... +.+...+..+...+...|++++|...+++..+.. +.+...+..
T Consensus         3 ~~~~~~~~~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~   77 (118)
T 1elw_A            3 QVNELKEKGNKALSVG---NIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSR   77 (118)
T ss_dssp             HHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHcc---cHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHH
Confidence            3556778888888999   7799999999988754 3367888888999999999999999999998764 235778888


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +...|.+.|++++|.+.+++..+.
T Consensus        78 ~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           78 KAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHc
Confidence            999999999999999999998765

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.76  E-value=0.00084  Score=57.17  Aligned_cols=156  Identities=12%  Similarity=0.012  Sum_probs=114.7

Q ss_pred             hhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCC
Q 040801           42 FCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL  121 (323)
Q Consensus        42 ~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~  121 (323)
                      .+-..+...|+++.|...++...+..                   +.+...+..+-..+.+.|++++|.+.+++....  
T Consensus       122 ~~a~~~~~~g~~~~A~~~~~~al~~~-------------------P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--  180 (287)
T 3qou_A          122 QQAMQLMQESNYTDALPLLXDAWQLS-------------------NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--  180 (287)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHT-------------------TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHhC-------------------CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--
Confidence            34444556677777777777766653                   456778899999999999999999999988654  


Q ss_pred             CCCcccHHHHHHH--hcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC-CCh
Q 040801          122 IPDRFMFPSLFKS--CADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK-PNA  195 (323)
Q Consensus       122 ~p~~~ty~~ll~~--~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~-p~~  195 (323)
                      .|+.. +..+..+  +...++   +...++...+.. ..+...+..+-..|...|   ++++|++.|++.....-. .+.
T Consensus       181 ~p~~~-~~~~~~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g---~~~~A~~~l~~~l~~~p~~~~~  255 (287)
T 3qou_A          181 DQDTR-YQGLVAQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVG---RNEEALELLFGHLRXDLTAADG  255 (287)
T ss_dssp             GCSHH-HHHHHHHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHCTTGGGG
T ss_pred             hcchH-HHHHHHHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcc---cHHHHHHHHHHHHhcccccccc
Confidence            45543 2222222  333333   777777777654 235778899999999999   679999999999886422 236


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          196 VTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       196 ~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ..+..+...+...|+.+.|...+++...
T Consensus       256 ~a~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          256 QTRXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            7899999999999999999888877643

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.73  E-value=0.00097  Score=48.63  Aligned_cols=100  Identities=13%  Similarity=-0.023  Sum_probs=84.5

Q ss_pred             CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          155 SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       155 ~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      .+...|..+-..+...|   ++++|.+.|++..... ..+...+..+...+...|++++|...+++..+.. +.+...+.
T Consensus        14 ~~~~~~~~~~~~~~~~~---~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~   88 (133)
T 2lni_A           14 DLALMVKNKGNECFQKG---DYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYT   88 (133)
T ss_dssp             CHHHHHHHHHHHHHHTT---CSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             ccHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHH
Confidence            45677888899999999   5699999999987653 3367888899999999999999999999998763 23577888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+...|.+.|++++|.+.|++..+.
T Consensus        89 ~la~~~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           89 RKAAALEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            8999999999999999999988654

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.72  E-value=0.00081  Score=48.71  Aligned_cols=99  Identities=13%  Similarity=-0.080  Sum_probs=81.7

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTT  235 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~  235 (323)
                      +...+..+...+...|   ++++|.+.|++..... ..+...+..+...+...|++++|...++...+.. +.+...+..
T Consensus        11 ~~~~~~~~~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~   85 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVE---NFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGR   85 (131)
T ss_dssp             HHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             hhHHHHHHHHHHHHcc---CHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHH
Confidence            4566777888888888   6799999999987754 3467788888899999999999999999998763 234677888


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +...|.+.|++++|...+++..+.
T Consensus        86 ~~~~~~~~~~~~~A~~~~~~~~~~  109 (131)
T 2vyi_A           86 MGLALSSLNKHVEAVAYYKKALEL  109 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            888999999999999999987654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.72  E-value=0.00036  Score=55.32  Aligned_cols=154  Identities=10%  Similarity=-0.146  Sum_probs=99.8

Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHH----cCCCC-chHHHHHHHHHHHhcCC
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIK----FGLAS-DSFLHNTLINMYSSCWC  172 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~----~g~~~-~~~~~~~li~~~~~~g~  172 (323)
                      ...|++++|.+.++..... ......++..+-..+...|+   |...++...+    .|..+ ...++..+-..|...| 
T Consensus         3 ~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g-   80 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG-   80 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT-
T ss_pred             cccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC-
Confidence            4567788888754444321 11233455555555666666   6666655543    22222 3466788888899999 


Q ss_pred             CCChHHHHHHHHHHHHc----CCCC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCcc-ChhhHHHHHHHHH
Q 040801          173 LDQPDEAIKIFYRMEIE----NVKP--NAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWS-HVELKTTLMDAYC  241 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~----g~~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~  241 (323)
                        ++++|.+.+++....    +-.|  ....+..+-..+...|++++|...+++..+.    +-.. -..++..+-..|.
T Consensus        81 --~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  158 (203)
T 3gw4_A           81 --NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQ  158 (203)
T ss_dssp             --CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             --CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence              679999999887653    2111  2456777888889999999999999988643    2111 1334677888899


Q ss_pred             hcCCHHHHHHHHHhccC
Q 040801          242 KCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       242 ~~g~~~~a~~~~~~m~~  258 (323)
                      +.|++++|...+++..+
T Consensus       159 ~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          159 QEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            99999999999887654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.68  E-value=0.00099  Score=50.99  Aligned_cols=98  Identities=9%  Similarity=-0.084  Sum_probs=82.7

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ...+..+-..+.+.|   ++++|.+.|++..... +-+...|..+-.++...|++++|...|++..+.. +-+...|..+
T Consensus        36 ~~~~~~lg~~~~~~g---~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~l  110 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKG---RIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHT  110 (151)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHH
Confidence            456777778888889   6799999999998764 3467888889999999999999999999998874 2357788899


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -.+|.+.|++++|...|++..+.
T Consensus       111 g~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          111 GQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999999988764

>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=97.68  E-value=0.00043  Score=52.86  Aligned_cols=97  Identities=14%  Similarity=-0.083  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      ..+..+-..+...|   ++++|.+.|++..... ..+..++..+...+...|++++|...++...+.. +.+...|..+-
T Consensus        14 ~~~~~~a~~~~~~~---~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a   88 (166)
T 1a17_A           14 EELKTQANDYFKAK---DYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRA   88 (166)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcc---CHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence            44566666677777   6678888887776643 2356677777777778888888888888777653 23456677777


Q ss_pred             HHHHhcCCHHHHHHHHHhccCC
Q 040801          238 DAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..|.+.|++++|...+++..+.
T Consensus        89 ~~~~~~~~~~~A~~~~~~a~~~  110 (166)
T 1a17_A           89 ASNMALGKFRAALRDYETVVKV  110 (166)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHh
Confidence            7788888888888888777653

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.68  E-value=0.0017  Score=52.29  Aligned_cols=24  Identities=13%  Similarity=0.202  Sum_probs=19.5

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      .-..+.+.|++++|.+.|++..+.
T Consensus        10 ~g~~~~~~g~~~~A~~~~~~al~~   33 (208)
T 3urz_A           10 KVSAAIEAGQNGQAVSYFRQTIAL   33 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh
Confidence            344677899999999999998763

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=97.67  E-value=0.0018  Score=46.34  Aligned_cols=114  Identities=19%  Similarity=0.117  Sum_probs=78.0

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      ...|..+...+...|++++|.++|++..+..  |                               .+..++..+...|.+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~-------------------------------~~~~~~~~la~~~~~   55 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD--P-------------------------------NNAEAWYNLGNAYYK   55 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------------------------TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--c-------------------------------CcHHHHHHHHHHHHH
Confidence            4567777888888888888888888776431  1                               123456667777777


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYC  241 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  241 (323)
                      .|   ++++|...|+++.... ..+..++..+...+...|++++|...++++.+.. +.+...+..+-..+.
T Consensus        56 ~~---~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~  122 (125)
T 1na0_A           56 QG---DYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             TT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             hC---CHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            77   6688888888877654 3456777788888888888888888888887653 123344444444443

>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=97.67  E-value=0.00062  Score=58.54  Aligned_cols=162  Identities=7%  Similarity=-0.052  Sum_probs=110.9

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHC----CCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chH
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQ----GLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSF  158 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~  158 (323)
                      .|+.....|...|++++|.+.|.+..+-    |-.+ -..+|+.+-..+.+.|+   |...++...+.    |-.. -..
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            3555667788889999999988876442    1111 12466666667766666   66666655433    2111 245


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccC
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWSH  229 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~  229 (323)
                      +++.+-..|.. |   ++++|++.|++....    |-.+ ...+++.+-..+.+.|++++|...+++..+.    +..+.
T Consensus       118 ~~~~lg~~~~~-g---~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  193 (307)
T 2ifu_A          118 ALDRAGKLMEP-L---DLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPT  193 (307)
T ss_dssp             HHHHHHHHHTT-T---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHc-C---CHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhH
Confidence            67778888877 7   679999999887642    1111 1467888889999999999999999998753    22222


Q ss_pred             -hhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          230 -VELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       230 -~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                       ...+..+...+...|++++|...|++..
T Consensus       194 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          194 CYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence             2356677778888899999999999987

>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=97.67  E-value=0.0025  Score=50.96  Aligned_cols=118  Identities=17%  Similarity=-0.037  Sum_probs=94.0

Q ss_pred             Hhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC
Q 040801          134 SCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD  210 (323)
Q Consensus       134 ~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~  210 (323)
                      .+...|+   |...++..    +.|+...|..+-..|.+.|   ++++|++.|++..... ..+...|..+-..+...|+
T Consensus        15 ~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A           15 LAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILK---NMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            3444455   55555544    4678889999999999999   7799999999988754 3467889999999999999


Q ss_pred             hHHHHHHHHHHHHhC--------------Ccc-ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          211 LRTVKRVHKCVDESG--------------FWS-HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       211 ~~~a~~~~~~m~~~g--------------~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +++|...++...+..              ..| ....+..+-.+|.+.|++++|.+.|++..+.
T Consensus        87 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           87 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            999999999998743              112 1267888888999999999999999998765

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.66  E-value=0.00091  Score=49.32  Aligned_cols=102  Identities=9%  Similarity=-0.022  Sum_probs=84.4

Q ss_pred             CCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh
Q 040801          153 LASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE  231 (323)
Q Consensus       153 ~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  231 (323)
                      +.|+ ...+...=..|.+.|   ++++|++.|++..... +.+...|..+-.++.+.|++++|...++...+.. +.+..
T Consensus         8 inP~~a~~~~~~G~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~   82 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKG---DYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIK   82 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HCHHHHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhH
Confidence            3443 345666777888999   7799999999988754 3477899999999999999999999999998864 23577


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .|..+-.+|...|++++|.+.|++..+-
T Consensus        83 a~~~lg~~~~~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           83 GYIRKAACLVAMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            8889999999999999999999998764

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.66  E-value=0.00053  Score=48.30  Aligned_cols=99  Identities=8%  Similarity=-0.172  Sum_probs=82.3

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc--ChhhH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS--HVELK  233 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p--~~~~~  233 (323)
                      +...|..+-..+...|   ++++|...|++..... ..+...|..+-..+...|++++|...+++..+.. +.  +...+
T Consensus         5 ~~~~~~~~~~~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~   79 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAG---NYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVW   79 (112)
T ss_dssp             STTGGGGHHHHHHSSC---CHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHH
T ss_pred             cHHHHHHHHHHHHHhh---hHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHH
Confidence            3456777888888888   7799999999988754 3467788888899999999999999999998763 22  47788


Q ss_pred             HHHHHHHHhc-CCHHHHHHHHHhccCC
Q 040801          234 TTLMDAYCKC-KFVSRAWDLFVKMLFP  259 (323)
Q Consensus       234 ~~li~~~~~~-g~~~~a~~~~~~m~~~  259 (323)
                      ..+...|.+. |+.++|.+.+++....
T Consensus        80 ~~l~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           80 AAKADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHHHHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHhhc
Confidence            8899999999 9999999999998765

>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=97.65  E-value=0.0011  Score=63.61  Aligned_cols=178  Identities=11%  Similarity=-0.006  Sum_probs=128.9

Q ss_pred             hHH-HhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCC---------CCCC------------cccHHHH
Q 040801           77 HVR-LVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQG---------LIPD------------RFMFPSL  131 (323)
Q Consensus        77 ~a~-~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g---------~~p~------------~~ty~~l  131 (323)
                      .|. ++|+.-.   +.+...|-..+...-+.|++++|.++|+......         -.|+            ...|...
T Consensus       361 ~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y  440 (679)
T 4e6h_A          361 TVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVY  440 (679)
T ss_dssp             THHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHH
Confidence            443 5554433   4566668888888899999999999999987631         0142            2346666


Q ss_pred             HHHhcchhh---HHHHHHHHHHc-C-CCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHh
Q 040801          132 FKSCADIYV---EKQLHSQAIKF-G-LASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARA  206 (323)
Q Consensus       132 l~~~~~~~~---a~~~~~~m~~~-g-~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~  206 (323)
                      ++...+.|.   |..+|....+. + ..+..++..+.+.-.+ .+   +.+.|.++|+...+. ..-+...+...+....
T Consensus       441 ~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~---d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~  515 (679)
T 4e6h_A          441 MNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SK---DTKTACKVLELGLKY-FATDGEYINKYLDFLI  515 (679)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TS---CCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CC---CHHHHHHHHHHHHHH-CCCchHHHHHHHHHHH
Confidence            666656665   99999998876 3 3445555555554332 23   458999999988875 3335566778888888


Q ss_pred             ccCChHHHHHHHHHHHHhCCcc--ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          207 RARDLRTVKRVHKCVDESGFWS--HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       207 ~~~~~~~a~~~~~~m~~~g~~p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..|+.+.|..+|++..+..-.+  ....|...++--.+.|+.+.+..+.+++.+.
T Consensus       516 ~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~  570 (679)
T 4e6h_A          516 YVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK  570 (679)
T ss_dssp             HHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            8999999999999988765322  3568899999889999999999999999865

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.65  E-value=0.00068  Score=59.95  Aligned_cols=163  Identities=13%  Similarity=-0.021  Sum_probs=120.9

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCC-CCCC----cccHHHHHHHhcchhh---HHHHHHHHHHc----CC-CC-chH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQG-LIPD----RFMFPSLFKSCADIYV---EKQLHSQAIKF----GL-AS-DSF  158 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~----~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~-~~-~~~  158 (323)
                      |-..=..+...|++++|.+.|++..+.. -.+|    ..++..+-..+...|+   |...+....+.    +- .+ ...
T Consensus       104 ~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  183 (378)
T 3q15_A          104 LFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQ  183 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHH
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHH
Confidence            4444556788999999999999986532 1233    3566677777777777   66666665433    21 11 256


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHH----cCCC-CChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCccC
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEI----ENVK-PNAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWSH  229 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~----~g~~-p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~  229 (323)
                      +++.+-..|...|   ++++|.+.|++...    .+-. ....++..+-..+...|+.++|...+++..+.    +-+..
T Consensus       184 ~~~~lg~~y~~~~---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~  260 (378)
T 3q15_A          184 SLFVIAGNYDDFK---HYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLL  260 (378)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGH
T ss_pred             HHHHHHHHHHHhC---CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhH
Confidence            7888899999999   77999999988765    2333 34568899999999999999999999998761    32333


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..++..+-..|.+.|+.++|...+++..+
T Consensus       261 ~~~~~~la~~~~~~g~~~~A~~~~~~al~  289 (378)
T 3q15_A          261 PKVLFGLSWTLCKAGQTQKAFQFIEEGLD  289 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            67788899999999999999999998643

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.61  E-value=0.0015  Score=49.55  Aligned_cols=99  Identities=5%  Similarity=-0.119  Sum_probs=82.3

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTT  235 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~  235 (323)
                      +...+..+-..+.+.|   ++++|...|++..... ..+...|..+-.++...|++++|...+++..+.. +-+...|..
T Consensus        20 ~~~~~~~~g~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~   94 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSG---XYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFH   94 (148)
T ss_dssp             HHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHH
T ss_pred             hHHHHHHHHHHHHHcC---ChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHH
Confidence            3456677788888999   7799999999988754 3477788888889999999999999999998864 235678888


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +-.+|...|++++|...|++..+.
T Consensus        95 lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           95 AAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            899999999999999999988653

>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=97.60  E-value=0.0011  Score=48.06  Aligned_cols=99  Identities=15%  Similarity=0.085  Sum_probs=81.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC--ccC----h
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF--WSH----V  230 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~--~p~----~  230 (323)
                      ...|..+-..+...|   ++++|...|++..... ..+...+..+...+...|++++|...++...+..-  .++    .
T Consensus         4 ~~~~~~l~~~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~   79 (131)
T 1elr_A            4 ALKEKELGNDAYKKK---DFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIA   79 (131)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhc---CHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHH
Confidence            356777888888988   7799999999988754 34678888899999999999999999999976531  122    6


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..|..+...|.+.|++++|.+.|++..+.
T Consensus        80 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           80 KAYARIGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            67888899999999999999999988765

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.59  E-value=0.0022  Score=47.25  Aligned_cols=100  Identities=12%  Similarity=-0.102  Sum_probs=85.0

Q ss_pred             CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          155 SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       155 ~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      .+...|..+-..+...|   ++++|...|++..... ..+...|..+-..+...|++++|...++...+.. +-+...|.
T Consensus         7 ~~~~~~~~~g~~~~~~~---~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~   81 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGR---KYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHF   81 (137)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             ccHHHHHHHHHHHHHhC---cHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHH
Confidence            45678888889999999   7799999999988754 3467888999999999999999999999998864 23577888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+-.+|.+.|++++|...|++..+.
T Consensus        82 ~l~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           82 FLGQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            9999999999999999999988754

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.57  E-value=0.0021  Score=46.81  Aligned_cols=98  Identities=13%  Similarity=-0.084  Sum_probs=82.2

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ...|..+-..+.+.|   ++++|++.|++..... ..+...|..+-.++.+.|++++|...++...+.. +-+...|..+
T Consensus         4 a~~~~~~g~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l   78 (126)
T 3upv_A            4 AEEARLEGKEYFTKS---DWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRK   78 (126)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhc---CHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHH
Confidence            345667777888888   7799999999988754 3467889999999999999999999999998864 2347788889


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -.+|...|++++|...|++..+.
T Consensus        79 g~~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           79 ATAQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCHHHHHHHHHHHHHh
Confidence            99999999999999999988754

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.56  E-value=0.002  Score=48.27  Aligned_cols=98  Identities=10%  Similarity=-0.114  Sum_probs=80.8

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ...+..+-..+.+.|   ++++|.+.|++..... +.+...|..+-.++...|++++|...++...+.. +-+...+..+
T Consensus        18 ~~~~~~~a~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l   92 (142)
T 2xcb_A           18 LEQLYALGFNQYQAG---KWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHA   92 (142)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHH
T ss_pred             HHHHHHHHHHHHHHc---cHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHH
Confidence            344556667788888   7799999999988754 3467788888889999999999999999998874 3356778888


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -.+|...|++++|...|++..+.
T Consensus        93 g~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           93 AECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            89999999999999999988654

>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=97.55  E-value=0.003  Score=47.96  Aligned_cols=129  Identities=15%  Similarity=-0.021  Sum_probs=90.9

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..|..+-..+...|++++|.+.|++..+.  .|                               .+..++..+-..|...
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~--~~-------------------------------~~~~~~~~~a~~~~~~   60 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIEL--NP-------------------------------SNAIYYGNRSLAYLRT   60 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--ST-------------------------------TCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh--CC-------------------------------CChHHHHHHHHHHHHc
Confidence            44666667777778888888777776542  12                               1245566777778888


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhH--HHHHHHHHhcCCHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELK--TTLMDAYCKCKFVSR  248 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~--~~li~~~~~~g~~~~  248 (323)
                      |   ++++|.+.|++..... ..+...|..+-..+...|++++|...+++..+..- -+...+  -.+...+.+.|++++
T Consensus        61 ~---~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~  135 (166)
T 1a17_A           61 E---CYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFER  135 (166)
T ss_dssp             T---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C---CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHH
Confidence            8   6689999888887654 34567788888888899999999999988877631 233344  334444778889999


Q ss_pred             HHHHHHhcc
Q 040801          249 AWDLFVKML  257 (323)
Q Consensus       249 a~~~~~~m~  257 (323)
                      |.+.+++..
T Consensus       136 A~~~~~~~~  144 (166)
T 1a17_A          136 AIAGDEHKR  144 (166)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHcccchH
Confidence            988887654

>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=97.53  E-value=0.0029  Score=54.28  Aligned_cols=190  Identities=11%  Similarity=0.009  Sum_probs=124.3

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCC--ChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNP--TIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      |......+...|+++.|...|.+..+..               .+...+  -...|+.+-..|.+.|++++|.+.|++-.
T Consensus        39 ~~~a~~~~~~~g~~~~A~~~~~~al~~~---------------~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al  103 (307)
T 2ifu_A           39 YAKAAVAFKNAKQLEQAKDAYLQEAEAH---------------ANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKAS  103 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHH---------------HHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHH---------------HHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3444455566667777776666655432               222211  13568888889999999999999998764


Q ss_pred             HC----CCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 040801          118 VQ----GLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIFY  184 (323)
Q Consensus       118 ~~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~~  184 (323)
                      +-    |-.. -..++..+-..+.. |+   |...++...+.    |-.. ...+++.+-..|.+.|   ++++|++.|+
T Consensus       104 ~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g---~~~~A~~~~~  179 (307)
T 2ifu_A          104 VMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQ---KFDEAAASLQ  179 (307)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcC---CHHHHHHHHH
Confidence            32    2111 12456666667766 77   77777766543    2111 1467888999999999   7799999999


Q ss_pred             HHHHc----CCCCCh-HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh------hhHHHHHHHHHhcCCHHHHHHH
Q 040801          185 RMEIE----NVKPNA-VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV------ELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       185 ~m~~~----g~~p~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~------~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      +....    +..++. .++..+...+...|+.++|...+++.. .  .|+.      .....++.+| ..|+.+.+.++
T Consensus       180 ~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al-~--~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          180 KEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY-S--IPGFSGSEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT-T--STTSTTSHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh-C--CCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            88752    222222 366667777778899999999999987 3  3421      2345566655 67888777774

>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=97.51  E-value=0.0022  Score=49.74  Aligned_cols=113  Identities=12%  Similarity=-0.021  Sum_probs=86.3

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHH-HhccCCh--HHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTA-RARARDL--RTVKRV  217 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~-~~~~~~~--~~a~~~  217 (323)
                      |...++...+.. ..+...|..+-..|...|   ++++|.+.|++..... ..+...+..+-.. +...|+.  ++|...
T Consensus        29 A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A~~~  103 (177)
T 2e2e_A           29 QLQALQDKIRAN-PQNSEQWALLGEYYLWQN---DYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQTRAM  103 (177)
T ss_dssp             CCHHHHHHHHHC-CSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHHHHH
Confidence            566666665543 235677888888888988   6799999999887654 2356677777777 6688888  999999


Q ss_pred             HHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          218 HKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       218 ~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++.+.+.. +-+...+..+...|.+.|++++|...|++..+.
T Consensus       104 ~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A          104 IDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            99988763 224677888888999999999999999987654

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.50  E-value=0.0022  Score=49.22  Aligned_cols=99  Identities=12%  Similarity=-0.074  Sum_probs=83.7

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTT  235 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~  235 (323)
                      +...|..+-..|.+.|   ++++|++.|++..... .-+...|..+-.++.+.|++++|...+++..+.. +-+...|..
T Consensus        10 ~a~~~~~~g~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~   84 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARK---EYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSR   84 (164)
T ss_dssp             HHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHH
Confidence            4567788888899999   7799999999988754 3377888899999999999999999999998874 235778889


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccCC
Q 040801          236 LMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +-.+|.+.|++++|...|++..+.
T Consensus        85 lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           85 LGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999999988754

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=97.46  E-value=0.022  Score=46.19  Aligned_cols=161  Identities=9%  Similarity=-0.079  Sum_probs=111.5

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      +..+-..+.+.|+++.|...|+.+.+..-  +.              ......+..+-.+|.+.|++++|.+.|++..+.
T Consensus         7 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~p--~~--------------~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~   70 (225)
T 2yhc_A            7 IYATAQQKLQDGNWRQAITQLEALDNRYP--FG--------------PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   70 (225)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCT--TS--------------TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CC--------------hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            34455567778999999999999988632  00              112345777788999999999999999998764


Q ss_pred             CCCCCcc----cHHHHHHHhc------------------chhh---HHHHHHHHHHcCCCCch-HHH-------------
Q 040801          120 GLIPDRF----MFPSLFKSCA------------------DIYV---EKQLHSQAIKFGLASDS-FLH-------------  160 (323)
Q Consensus       120 g~~p~~~----ty~~ll~~~~------------------~~~~---a~~~~~~m~~~g~~~~~-~~~-------------  160 (323)
                        .|+..    .+-.+-.++.                  ..|+   |...++.+.+.-  |+. ..+             
T Consensus        71 --~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--P~~~~a~~a~~~l~~~~~~~  146 (225)
T 2yhc_A           71 --NPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY--PNSQYTTDATKRLVFLKDRL  146 (225)
T ss_dssp             --CTTCTTHHHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC--TTCTTHHHHHHHHHHHHHHH
T ss_pred             --CcCCCcHHHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC--cCChhHHHHHHHHHHHHHHH
Confidence              34432    2222222222                  1334   778888877653  432 222             


Q ss_pred             ----HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHhC
Q 040801          161 ----NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN----AVTLVNVLTARARARDLRTVKRVHKCVDESG  225 (323)
Q Consensus       161 ----~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g  225 (323)
                          -.+-..|.+.|   ++++|+..|++.....  |+    ...+..+..++.+.|+.++|...++.+...+
T Consensus       147 ~~~~~~~a~~~~~~~---~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          147 AKYEYSVAEYYTERG---AWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHcC---cHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence                23455678888   7799999999998753  33    2568888999999999999999999888764

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.43  E-value=0.0018  Score=52.09  Aligned_cols=68  Identities=12%  Similarity=0.210  Sum_probs=38.6

Q ss_pred             HHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           45 VSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        45 ~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      ..+...|+++.|...|+...+..-  +.   ..+.-. ..+.   ......++.+-..|.+.|++++|.+.|++..+
T Consensus        12 ~~~~~~g~~~~A~~~~~~al~~~p--~~---~~~~~~-~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A           12 SAAIEAGQNGQAVSYFRQTIALNI--DR---TEMYYW-TNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCH--HH---HHHHHH-HHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCC--CC---hHHHHH-hhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345677999999999999887631  10   000000 0000   00011122266777788888888888877665

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.41  E-value=0.0047  Score=44.80  Aligned_cols=120  Identities=13%  Similarity=-0.026  Sum_probs=76.1

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      ..+...|..+-..+.+.|++++|.+.|++..+.  .|+                               +...+..+-..
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~~~-------------------------------~~~~~~~la~~   59 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKR--NPK-------------------------------DAKLYSNRAAC   59 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTT--CTT-------------------------------CHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCC-------------------------------cHHHHHHHHHH
Confidence            445567888888888999999999998887653  221                               12344555555


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      |...|   ++++|.+.|++..... ..+...+..+-..+.+.|++++|...+++..+.. +-+...+..+...+.+.|
T Consensus        60 ~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           60 YTKLL---EFQLALKDCEECIQLE-PTFIKGYTRKAAALEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HTTTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHHHT
T ss_pred             HHHhc---cHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhc
Confidence            66666   5577777776666543 2245666666667777777777777777766542 123445555555555544

>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=97.41  E-value=0.0039  Score=59.73  Aligned_cols=202  Identities=11%  Similarity=-0.040  Sum_probs=135.3

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHH-HHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcC---------C
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAF-LFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFG---------L  153 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~-~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g---------~  153 (323)
                      ..+...|-....-+-+.|+.++|. ++|++-... ++.+...|-..+...-+.|+   |.++++.+.+..         -
T Consensus       340 p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~  418 (679)
T 4e6h_A          340 CFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMED  418 (679)
T ss_dssp             TTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence            446677777788888889999997 999988753 33343334444444445555   888888887641         0


Q ss_pred             CC------------chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc-C-CCCChHHHHHHHHHHhccCChHHHHHHHH
Q 040801          154 AS------------DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE-N-VKPNAVTLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       154 ~~------------~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~-g-~~p~~~t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      .|            ...+|-..+....+.|   +.+.|.++|...... + ..+......+.|.-.+ .++.+.|..+|+
T Consensus       419 ~p~~~~~~~~~~~~~~~vWi~y~~~erR~~---~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife  494 (679)
T 4e6h_A          419 DPTNESAINQLKSKLTYVYCVYMNTMKRIQ---GLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLE  494 (679)
T ss_dssp             STTCHHHHHHHHHHHHHHHHHHHHHHHHHH---CHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHH
T ss_pred             cCcchhhhhhhccchHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHH
Confidence            13            2346888888888888   569999999998775 2 2233333333444322 356999999999


Q ss_pred             HHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCCCC----chhhh-HHHhhhccCCCCCcchhh-hhhhCCCCc
Q 040801          220 CVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFPWN----NYGQW-AMSATVGPQGLVGRHSTA-HQISGPCPK  293 (323)
Q Consensus       220 ~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~~~~~-~~~~~~~~~~~~~~~~~a-~~l~~~~~~  293 (323)
                      ...+. ++-+...|...++...+.|+.+.|..+|+.......    ....| .+...-..+|....+... ......+|+
T Consensus       495 ~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~  573 (679)
T 4e6h_A          495 LGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPE  573 (679)
T ss_dssp             HHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTT
T ss_pred             HHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            99886 444667778999988999999999999999887632    23445 566666666655444333 233344444


Q ss_pred             h
Q 040801          294 K  294 (323)
Q Consensus       294 ~  294 (323)
                      +
T Consensus       574 ~  574 (679)
T 4e6h_A          574 V  574 (679)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.40  E-value=0.0037  Score=45.07  Aligned_cols=120  Identities=13%  Similarity=-0.049  Sum_probs=81.0

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      +...|..+-..+...|++++|.+.|++..+.  .|+                               +...+..+...|.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~-------------------------------~~~~~~~~a~~~~   57 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIEL--NPA-------------------------------NAVYFCNRAAAYS   57 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-------------------------------CHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHc--CCC-------------------------------CHHHHHHHHHHHH
Confidence            3456777777888888888888888776643  121                               2344556666677


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCH
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFV  246 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~  246 (323)
                      ..|   ++++|.+.+++..... ..+...+..+-..+...|++++|...+++..+.. +.+...+..+...+.+.|+.
T Consensus        58 ~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           58 KLG---NYAGAVQDCERAICID-PAYSKAYGRMGLALSSLNKHVEAVAYYKKALELD-PDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTTC
T ss_pred             Hhh---chHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHhcC
Confidence            777   5678888887776643 2346677777777888888888888888877653 22455666677777766653

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.40  E-value=0.0043  Score=46.03  Aligned_cols=98  Identities=12%  Similarity=-0.076  Sum_probs=82.4

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChh
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN----AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVE  231 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  231 (323)
                      +...+..+-..+...|   ++++|.+.|++....  .|+    ...|..+-..+...|++++|...++...+.. +.+..
T Consensus        27 ~~~~~~~~a~~~~~~~---~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~  100 (148)
T 2dba_A           27 SVEQLRKEGNELFKCG---DYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVK  100 (148)
T ss_dssp             CHHHHHHHHHHHHTTT---CHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHH
T ss_pred             HHHHHHHHHHHHHHhC---CHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHH
Confidence            5677888888899989   779999999998764  465    6788888889999999999999999998763 23567


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          232 LKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       232 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+..+-.+|.+.|+.++|...|++..+.
T Consensus       101 ~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          101 ALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            7888889999999999999999988654

>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=97.38  E-value=0.001  Score=50.59  Aligned_cols=102  Identities=8%  Similarity=-0.067  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLM  237 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li  237 (323)
                      .+-.+-..|.+.|   ++++|++.|++..... +-+..+|..+-..+...|++++|...|+...+.  .| +...|..+-
T Consensus        33 ~~~~la~~y~~~~---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la  106 (150)
T 4ga2_A           33 KGFYFAKLYYEAK---EYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIA  106 (150)
T ss_dssp             THHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            3445666677777   5577777777776643 225567777777777777777777777777665  23 355677777


Q ss_pred             HHHHhcCCHHHHHHH-HHhccC-CCCchhhh
Q 040801          238 DAYCKCKFVSRAWDL-FVKMLF-PWNNYGQW  266 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~-~~~m~~-~~~~~~~~  266 (323)
                      ..|.+.|+.++|.+. +++..+ .+..+..+
T Consensus       107 ~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~  137 (150)
T 4ga2_A          107 ELLCKNDVTDGRAKYWVERAAKLFPGSPAVY  137 (150)
T ss_dssp             HHHHHHCSSSSHHHHHHHHHHHHSTTCHHHH
T ss_pred             HHHHHcCChHHHHHHHHHHHHHhCcCCHHHH
Confidence            777777777655443 454433 23344444

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.28  E-value=0.059  Score=48.86  Aligned_cols=226  Identities=8%  Similarity=-0.037  Sum_probs=131.8

Q ss_pred             CchHHHHHHHHHHHhcCCCCC------ccch-------hHHHhcccCC-CCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           52 TMRELKQIHAQMLRTSLFFDP------CADY-------HVRLVFSQIS-NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        52 ~~~~a~~i~~~m~~~~~~~~~------y~~~-------~a~~lf~~m~-~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      ++++|...++...+.|...-.      |...       .+.+.+.... .-+...+..+-..|...+.++++.+-.+...
T Consensus        89 ~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~  168 (452)
T 3e4b_A           89 EHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHLDDVERIC  168 (452)
T ss_dssp             HHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCHHHHHHHH
Confidence            678899999988887643322      1111       2333332222 2344556666667777775555555544443


Q ss_pred             HCCCCCCcccHHHHHHHhcchh---h---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc-CCCCChHHHHHHHHHHHHcC
Q 040801          118 VQGLIPDRFMFPSLFKSCADIY---V---EKQLHSQAIKFGLASDSFLHNTLINMYSSC-WCLDQPDEAIKIFYRMEIEN  190 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~---~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-g~~~~~~~a~~~~~~m~~~g  190 (323)
                      +.-...+...+..|-..+.+.|   +   |.+.++...+.|. ++...+..|-..|... |...+.++|++.|++.. .|
T Consensus       169 ~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g  246 (452)
T 3e4b_A          169 KAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG  246 (452)
T ss_dssp             HHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG
T ss_pred             HHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC
Confidence            3222333346666766666666   4   7778888777773 4444445555555433 11127788999988876 33


Q ss_pred             CCCChHHHHHHHHH-H--hccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC-----CHHHHHHHHHhccCCCCc
Q 040801          191 VKPNAVTLVNVLTA-R--ARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK-----FVSRAWDLFVKMLFPWNN  262 (323)
Q Consensus       191 ~~p~~~t~~~li~~-~--~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g-----~~~~a~~~~~~m~~~~~~  262 (323)
                         +...+..+-.. +  ...++.++|...|++..+.|   +...+..|-..|. .|     +.++|.+.|++.. .+..
T Consensus       247 ---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~  318 (452)
T 3e4b_A          247 ---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREV  318 (452)
T ss_dssp             ---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCH
T ss_pred             ---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCH
Confidence               34444444444 3  45788999999999888877   5556666666666 45     8999999998888 5433


Q ss_pred             hhhhHHHhhhcc-CCCCCcchhhhhh
Q 040801          263 YGQWAMSATVGP-QGLVGRHSTAHQI  287 (323)
Q Consensus       263 ~~~~~~~~~~~~-~~~~~~~~~a~~l  287 (323)
                      .....+...+.. .+...+.++|..+
T Consensus       319 ~A~~~Lg~~y~~G~g~~~d~~~A~~~  344 (452)
T 3e4b_A          319 AADYYLGQIYRRGYLGKVYPQKALDH  344 (452)
T ss_dssp             HHHHHHHHHHHTTTTSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCCcCHHHHHHH
Confidence            333333333322 2223455555433

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.26  E-value=0.011  Score=47.61  Aligned_cols=172  Identities=11%  Similarity=-0.085  Sum_probs=116.4

Q ss_pred             HHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHH
Q 040801          108 EAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFY  184 (323)
Q Consensus       108 ~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~  184 (323)
                      +|++.|++..+.|   +...+..|=..+...++   |.+.++...+.|   +...+..|=..|...|...+.++|++.|+
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIRNPQQADYPQARQLAE   77 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTSSTTSCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            4667777776664   44555555555555556   888898888876   45566666666776443337899999999


Q ss_pred             HHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCc-cChhhHHHHHHHHHh----cCCHHHHHHHHHh
Q 040801          185 RMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFW-SHVELKTTLMDAYCK----CKFVSRAWDLFVK  255 (323)
Q Consensus       185 ~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~-p~~~~~~~li~~~~~----~g~~~~a~~~~~~  255 (323)
                      +-.+.|   +...+..|-..|..    .++.++|...+++..+.|.. -+...+..|-..|..    .++.++|...|++
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   56677777777776    88999999999998887632 125677778888888    7899999999999


Q ss_pred             ccCCCCchhhh-HHHhhhccC-C--CCCcchhhhhhh
Q 040801          256 MLFPWNNYGQW-AMSATVGPQ-G--LVGRHSTAHQIS  288 (323)
Q Consensus       256 m~~~~~~~~~~-~~~~~~~~~-~--~~~~~~~a~~l~  288 (323)
                      ..+.+..+... .+...+... +  ...+.++|...+
T Consensus       155 A~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~  191 (212)
T 3rjv_A          155 SSSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWL  191 (212)
T ss_dssp             HHHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHH
Confidence            87763334333 443443222 2  233555554443

>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=97.24  E-value=0.0027  Score=49.31  Aligned_cols=117  Identities=9%  Similarity=-0.009  Sum_probs=73.0

Q ss_pred             hCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHH-HHhcCCCCCh-
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINM-YSSCWCLDQP-  176 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~-~~~~g~~~~~-  176 (323)
                      ..|++++|.+.+++..+.. +.+...|..+-..+...|+   |...++...+.. ..+...+..+-.. |...|   ++ 
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~---~~~   96 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQAS---QHM   96 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTT---TCC
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcC---Ccc
Confidence            4556666666666654431 1233455555555555555   666666655443 1245556666666 66777   54 


Q ss_pred             -HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          177 -DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       177 -~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                       ++|.+.|++..... .-+...+..+-..+...|++++|...++.+.+.
T Consensus        97 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           97 TAQTRAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             CHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence             88999998887754 234677777888888899999999999888775

>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=97.22  E-value=0.0074  Score=52.55  Aligned_cols=146  Identities=13%  Similarity=-0.026  Sum_probs=110.0

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      +...|..+=..|.+.|++++|.+.|++..+..  |+...+         ... +.++-.        ....+|..+-.+|
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~---------~~~~~~~~~~--------~~~~~~~nla~~~  206 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSF---------SNEEAQKAQA--------LRLASHLNLAMCH  206 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCC---------CSHHHHHHHH--------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccC---------ChHHHHHHHH--------HHHHHHHHHHHHH
Confidence            45678888889999999999999999887632  332211         011 111110        1246788899999


Q ss_pred             HhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      .+.|   ++++|++.|++..... ..+...|..+-.++...|++++|...|++..+.. +-+...+..+-..+.+.|+.+
T Consensus       207 ~~~g---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~  281 (336)
T 1p5q_A          207 LKLQ---AFSAAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQL  281 (336)
T ss_dssp             HHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHcC---CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHH
Confidence            9999   7799999999998764 3477889999999999999999999999998863 235678888999999999999


Q ss_pred             HH-HHHHHhccC
Q 040801          248 RA-WDLFVKMLF  258 (323)
Q Consensus       248 ~a-~~~~~~m~~  258 (323)
                      +| ...+++|..
T Consensus       282 ~a~~~~~~~~~~  293 (336)
T 1p5q_A          282 AREKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            98 456666643

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.21  E-value=0.0041  Score=45.31  Aligned_cols=95  Identities=7%  Similarity=-0.130  Sum_probs=77.9

Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHH
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDA  239 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  239 (323)
                      +-.+-..+.+.|   ++++|+..|++..... .-+...|..+-..+...|+.++|...+++..+.. +-+...+..+-.+
T Consensus        20 ~~~~g~~~~~~g---~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~   94 (121)
T 1hxi_A           20 PMEEGLSMLKLA---NLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVS   94 (121)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC---CHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            444556778888   7799999999998754 2367788888889999999999999999998864 2256788889999


Q ss_pred             HHhcCCHHHHHHHHHhccCC
Q 040801          240 YCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       240 ~~~~g~~~~a~~~~~~m~~~  259 (323)
                      |.+.|+.++|...+++..+.
T Consensus        95 ~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           95 HTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999998764

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.19  E-value=0.0069  Score=44.46  Aligned_cols=99  Identities=13%  Similarity=0.002  Sum_probs=77.4

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC--ccC----h
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF--WSH----V  230 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~--~p~----~  230 (323)
                      ...+..|=..+.+.|   ++++|++.|++..+.. +-+...|+.+-.+|...|++++|...++...+..-  .++    .
T Consensus         8 A~a~~~lG~~~~~~~---~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a   83 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQK---DFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIA   83 (127)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHH
Confidence            345666777888899   7799999999988754 33578899999999999999999999999876421  111    2


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..|..+-.+|...|++++|.+.|++..+.
T Consensus        84 ~~~~~lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           84 KAMSRAGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            35666777888999999999999987643

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.19  E-value=0.012  Score=40.91  Aligned_cols=99  Identities=8%  Similarity=-0.129  Sum_probs=67.5

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      +...|..+-..+.+.|++++|.+.|++..+..  |                               .+...|..+-..|.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--~-------------------------------~~~~~~~~~a~~~~   51 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD--P-------------------------------EESKYWLMKGKALY   51 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC--C-------------------------------CCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC--c-------------------------------CCHHHHHHHHHHHH
Confidence            44556667777778888888888877765431  1                               12344556666677


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCC--ChHHHHHHHHHHhcc-CChHHHHHHHHHHHHh
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKP--NAVTLVNVLTARARA-RDLRTVKRVHKCVDES  224 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~-~~~~~a~~~~~~m~~~  224 (323)
                      ..|   ++++|.+.|++..... ..  +...+..+...+... |+.++|.+.++...+.
T Consensus        52 ~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           52 NLE---RYEEAVDCYNYVINVI-EDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HTT---CHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             Hcc---CHHHHHHHHHHHHHhC-cccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhc
Confidence            777   5678888887776643 22  466777777788888 8888888888877665

>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=97.16  E-value=0.0045  Score=53.92  Aligned_cols=100  Identities=10%  Similarity=-0.062  Sum_probs=84.1

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC--------------hHHHHHHHHHHhccCChHHHHHHHHHH
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN--------------AVTLVNVLTARARARDLRTVKRVHKCV  221 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--------------~~t~~~li~~~~~~~~~~~a~~~~~~m  221 (323)
                      +...|..+-..|.+.|   ++++|++.|++.....-...              ...|..+-.++.+.|++++|...++..
T Consensus       146 ~a~~~~~~g~~~~~~g---~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~a  222 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEG---KYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKA  222 (336)
T ss_dssp             HHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3566788888899999   77999999999887542211              489999999999999999999999999


Q ss_pred             HHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          222 DESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       222 ~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+.. +-+...|..+-.+|.+.|++++|...|++..+.
T Consensus       223 l~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  259 (336)
T 1p5q_A          223 LELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  259 (336)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            8874 336788899999999999999999999998754

>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=97.14  E-value=0.01  Score=50.31  Aligned_cols=160  Identities=11%  Similarity=-0.051  Sum_probs=108.4

Q ss_pred             HHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCCh----hhHHHHHHHHHhCCChHHHHHHHHHHHHC
Q 040801           44 LVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTI----YTCNSIVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        44 i~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~----~~~~~li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      +..+...++++.|..+++...+...                 ..++.    ..+..+-..+...|++++|++.|++....
T Consensus        82 i~~~~~~~~y~~a~~~~~~~l~~~~-----------------~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~  144 (293)
T 3u3w_A           82 VIMLCKQKRYKEIYNKVWNELKKEE-----------------YHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQ  144 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCC-----------------CCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcccc-----------------CChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHH
Confidence            4445556666666666666654321                 01221    12344666777788999999999999874


Q ss_pred             CCC-CCc----ccHHHHHHHhcchhh---HHHHHHHHHH----c-CCCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHH
Q 040801          120 GLI-PDR----FMFPSLFKSCADIYV---EKQLHSQAIK----F-GLASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYR  185 (323)
Q Consensus       120 g~~-p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~----~-g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~  185 (323)
                      ... ++.    .+|+.+-..+...|+   |...++...+    . +..+. ..+|..+-..|.+.|   ++++|.+.+++
T Consensus       145 ~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~---~y~~A~~~~~~  221 (293)
T 3u3w_A          145 QLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDS---RYEESLYQVNK  221 (293)
T ss_dssp             CCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             hcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHh---HHHHHHHHHHH
Confidence            332 222    257777777877777   8888877763    2 22222 347889999999999   77999999988


Q ss_pred             HHHc----CCCCC-hHHHHHHHHHHhccCC-hHHHHHHHHHHHH
Q 040801          186 MEIE----NVKPN-AVTLVNVLTARARARD-LRTVKRVHKCVDE  223 (323)
Q Consensus       186 m~~~----g~~p~-~~t~~~li~~~~~~~~-~~~a~~~~~~m~~  223 (323)
                      ....    +..+. ..+|..+-..+.+.|+ .++|...+++..+
T Consensus       222 al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          222 AIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            7642    22222 5688888888889994 6999988888754

>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=97.06  E-value=0.0065  Score=46.01  Aligned_cols=134  Identities=9%  Similarity=-0.074  Sum_probs=72.4

Q ss_pred             hCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      +.|++++|++.+......  .| +...+-.+-..|.+.|+   |.+.++...+.. .-+..+|..+-.+|.+.|   +++
T Consensus         9 ~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~---~~~   82 (150)
T 4ga2_A            9 SKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEE---NTD   82 (150)
T ss_dssp             CHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHH
T ss_pred             HcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcC---chH
Confidence            345566666666554332  12 22334445555555555   666666666553 224556666666666666   556


Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHH-HHHHHHhCCcc-ChhhHHHHHHHHHhcC
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRV-HKCVDESGFWS-HVELKTTLMDAYCKCK  244 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~-~~~m~~~g~~p-~~~~~~~li~~~~~~g  244 (323)
                      +|+..|++..+.. +-+...|..+-..+.+.|+.+++... +++..+.  .| +...|...-..+.+.|
T Consensus        83 ~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A           83 KAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhC
Confidence            7777776666533 12455666666666666666554433 4555543  23 3444554444444444

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.06  E-value=0.044  Score=48.77  Aligned_cols=203  Identities=12%  Similarity=0.029  Sum_probs=133.9

Q ss_pred             HHhhcCCCchHHHHHHHHHHHhcCCCCC-ccch----hHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHC
Q 040801           45 VSLEKCSTMRELKQIHAQMLRTSLFFDP-CADY----HVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQ  119 (323)
Q Consensus        45 ~~~~~~~~~~~a~~i~~~m~~~~~~~~~-y~~~----~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  119 (323)
                      ..+.+.|++++|.+.+....+..-.... +...    ...+.       -...+..+...|.+.|++++|.+++......
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-------~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~   84 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNE-------QETSILELGQLYVTMGAKDKLREFIPHSTEY   84 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHH-------HHHHHHHHHHHHHHHTCHHHHHHHHHHTHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhh-------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            3466779999999999998876432222 1111    11110       1124678899999999999999999887542


Q ss_pred             -CCCCCccc---HHHHHHHhc-chhh---HHHHHHHHH----HcCCCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Q 040801          120 -GLIPDRFM---FPSLFKSCA-DIYV---EKQLHSQAI----KFGLASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYRM  186 (323)
Q Consensus       120 -g~~p~~~t---y~~ll~~~~-~~~~---a~~~~~~m~----~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~m  186 (323)
                       +-.++..+   ....+..+. ..|+   +..++....    +.+..+. ..++..|...|...|   ++++|.+++++.
T Consensus        85 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g---~~~~A~~~l~~~  161 (434)
T 4b4t_Q           85 MMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKK---QYKDSLALINDL  161 (434)
T ss_dssp             HHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHT---CHHHHHHHHHHH
T ss_pred             HHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHcc---ChHHHHHHHHHH
Confidence             11222211   122222222 2232   555555543    3343333 567888999999999   679999999988


Q ss_pred             HHc--CC--CC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh--CCc-c-C--hhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          187 EIE--NV--KP-NAVTLVNVLTARARARDLRTVKRVHKCVDES--GFW-S-H--VELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       187 ~~~--g~--~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~-p-~--~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      ...  +.  .+ ...+|..+.+.|...|++++|..+++...+.  .+. | .  ...+..+...+...|++++|...|.+
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~  241 (434)
T 4b4t_Q          162 LREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFE  241 (434)
T ss_dssp             HHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHH
T ss_pred             HHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            653  21  12 2458888999999999999999999988642  222 1 1  34567777788899999999888876


Q ss_pred             cc
Q 040801          256 ML  257 (323)
Q Consensus       256 m~  257 (323)
                      ..
T Consensus       242 a~  243 (434)
T 4b4t_Q          242 SF  243 (434)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.06  E-value=0.0037  Score=49.30  Aligned_cols=135  Identities=6%  Similarity=-0.105  Sum_probs=94.6

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHH----CCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CCC
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV----QGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GLA  154 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~  154 (323)
                      ......++.+-..+...|++++|.+.+++..+    .|..| ...++..+-..+...|+   |.+.++...+.    +-.
T Consensus        23 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~  102 (203)
T 3gw4_A           23 ATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPED  102 (203)
T ss_dssp             TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCcc
Confidence            34567788888999999999999999998765    22222 23455555566666666   66666665443    322


Q ss_pred             C--chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc---CCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          155 S--DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE---NVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       155 ~--~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~---g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +  ....+..+-..+...|   ++++|.+.+++....   .-.+.  ..++..+-..+...|+.++|...+++..+.
T Consensus       103 ~~~~~~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  176 (203)
T 3gw4_A          103 PLAASANAYEVATVALHFG---DLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDI  176 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhC---CHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            2  2456788888999999   679999999887642   11122  234677788888999999999998887653

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.04  E-value=0.00084  Score=48.53  Aligned_cols=97  Identities=9%  Similarity=0.009  Sum_probs=67.9

Q ss_pred             ChHHHHHHHHHHHHcC--CCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          175 QPDEAIKIFYRMEIEN--VKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g--~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      ++++|+..|++....+  -+-+...+..+-..+...|++++|...+++..+.. +-+...+..+-.+|.+.|+.++|...
T Consensus         5 ~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~   83 (117)
T 3k9i_A            5 LEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVEL   83 (117)
T ss_dssp             --CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHHH
Confidence            5578888888887643  12245677778888888899999999999888764 22466777888888999999999998


Q ss_pred             HHhccCC-CCchhhhHHHhhh
Q 040801          253 FVKMLFP-WNNYGQWAMSATV  272 (323)
Q Consensus       253 ~~~m~~~-~~~~~~~~~~~~~  272 (323)
                      +++..+. +.++....+..++
T Consensus        84 ~~~al~~~p~~~~~~~~~~ai  104 (117)
T 3k9i_A           84 LLKIIAETSDDETIQSYKQAI  104 (117)
T ss_dssp             HHHHHHHHCCCHHHHHTHHHH
T ss_pred             HHHHHHhCCCcHHHHHHHHHH
Confidence            8887654 3334333333333

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.01  E-value=0.019  Score=41.42  Aligned_cols=90  Identities=10%  Similarity=-0.077  Sum_probs=72.4

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh----HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC----hhhHH
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA----VTLVNVLTARARARDLRTVKRVHKCVDESGFWSH----VELKT  234 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~----~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~  234 (323)
                      +-..+...|   ++++|.+.|++.....  |+.    ..+..+-..+...|++++|...++...+..  |+    ...+.
T Consensus         8 ~a~~~~~~~---~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~   80 (129)
T 2xev_A            8 VAFDALKNG---KYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLL   80 (129)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHH
T ss_pred             HHHHHHHhC---CHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHH
Confidence            445667778   7799999999988754  332    477778888999999999999999998764  33    45677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+-.+|.+.|+.++|...|++..+.
T Consensus        81 ~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           81 KLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            8888999999999999999998764

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=96.93  E-value=0.11  Score=44.46  Aligned_cols=224  Identities=11%  Similarity=-0.015  Sum_probs=148.4

Q ss_pred             hhhHHHhhcCCC-chHHHHHHHHHHHhcCCCCC-------------cc--ch-hHHHhcccCC---CCChhhHHHHHHHH
Q 040801           41 HFCLVSLEKCST-MRELKQIHAQMLRTSLFFDP-------------CA--DY-HVRLVFSQIS---NPTIYTCNSIVRGY  100 (323)
Q Consensus        41 ~~li~~~~~~~~-~~~a~~i~~~m~~~~~~~~~-------------y~--~~-~a~~lf~~m~---~~~~~~~~~li~~~  100 (323)
                      ...+.+..+.+. .++|+.+.+.+...  .|+.             -.  .. ++.+.++.+.   +.+...|+.--..+
T Consensus        36 ~~~~~a~~~~~e~s~~aL~~t~~~L~~--nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL  113 (306)
T 3dra_A           36 MGLLLALMKAEEYSERALHITELGINE--LASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLII  113 (306)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHH--CcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHH
Confidence            344444445554 57899999999876  4555             11  22 5566665554   55667777654444


Q ss_pred             ----HhC---CChHHHHHHHHHHHHCCCCCCcccHHHH---HHHhcchh--hHHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801          101 ----TNK---NLHHEAFLFYHEMIVQGLIPDRFMFPSL---FKSCADIY--VEKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus       101 ----~~~---g~~~~A~~~~~~m~~~g~~p~~~ty~~l---l~~~~~~~--~a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                          .+.   +++++++++++.+.+.. +-|..+|+.-   +..+..-.  ++.+.+..+.+... -|-..|+.--..+.
T Consensus       114 ~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~  191 (306)
T 3dra_A          114 GQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLF  191 (306)
T ss_dssp             HHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence                455   78999999999998742 2344444433   44444444  47778888887653 45666776555555


Q ss_pred             hcCCC---CChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCCh-HHHHHHHHHHHHhC--CccChhhHHHHHHHHHh
Q 040801          169 SCWCL---DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDL-RTVKRVHKCVDESG--FWSHVELKTTLMDAYCK  242 (323)
Q Consensus       169 ~~g~~---~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~-~~a~~~~~~m~~~g--~~p~~~~~~~li~~~~~  242 (323)
                      +.|..   ..++++++.+++...... -|...|+-.-..+.+.|+. +.+..+...+.+.+  -..+...+..+.+.|.+
T Consensus       192 ~l~~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~  270 (306)
T 3dra_A          192 SKKHLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQ  270 (306)
T ss_dssp             SSGGGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHH
T ss_pred             hccccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHc
Confidence            55520   016899999999988763 4788888877777777763 33555666554432  13367889999999999


Q ss_pred             cCCHHHHHHHHHhccC--CCCchhhhHHH
Q 040801          243 CKFVSRAWDLFVKMLF--PWNNYGQWAMS  269 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~--~~~~~~~~~~~  269 (323)
                      .|+.++|.++++.+.+  .++....|.+.
T Consensus       271 ~~~~~~A~~~~~~l~~~~Dpir~~yW~~~  299 (306)
T 3dra_A          271 QKKYNESRTVYDLLKSKYNPIRSNFWDYQ  299 (306)
T ss_dssp             TTCHHHHHHHHHHHHHTTCGGGHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhccChHHHHHHHHH
Confidence            9999999999999985  35666777543

>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=96.87  E-value=0.0083  Score=43.17  Aligned_cols=110  Identities=5%  Similarity=-0.024  Sum_probs=65.7

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..|..+-..+...|++++|.+.|++..+..  |+                               +...+..+-..|...
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~-------------------------------~~~~~~~la~~~~~~   51 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD--PT-------------------------------NMTYITNQAAVYFEK   51 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-------------------------------CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--Cc-------------------------------cHHHHHHHHHHHHHh
Confidence            456777778888888888888888876532  21                               123444555555566


Q ss_pred             CCCCChHHHHHHHHHHHHcCC--CCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENV--KPN----AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~--~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      |   ++++|...|++......  .++    ..+|..+-..+...|++++|...++...+..  |+......+-.
T Consensus        52 ~---~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~  120 (131)
T 1elr_A           52 G---DYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQ  120 (131)
T ss_dssp             T---CHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHH
T ss_pred             c---cHHHHHHHHHHHHhhccccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHH
Confidence            6   45666666666655321  112    5556666666666677777777766666542  34444444433

>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=96.86  E-value=0.042  Score=38.39  Aligned_cols=98  Identities=11%  Similarity=-0.058  Sum_probs=61.0

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      ...|..+-..+...|++++|.+.|++....  .|+                               +...+..+-..|..
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~-------------------------------~~~~~~~~a~~~~~   50 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKL--DPH-------------------------------NHVLYSNRSAAYAK   50 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-------------------------------CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCC-------------------------------cHHHHHHHHHHHHh
Confidence            455677777888888888888888887653  121                               23344445555555


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .|   ++++|.+.+++..... ..+...+..+...+...|++++|...++...+.
T Consensus        51 ~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           51 KG---DYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hc---cHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            56   4566666666665543 224555666666666666666666666666543

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.79  E-value=0.083  Score=44.52  Aligned_cols=128  Identities=10%  Similarity=-0.095  Sum_probs=91.5

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCCCC-CC----cccHHHHHHHhcchhh---HHHHHHHHHHc----CCCC--chH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQGLI-PD----RFMFPSLFKSCADIYV---EKQLHSQAIKF----GLAS--DSF  158 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g~~-p~----~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~~~--~~~  158 (323)
                      +..+-..+...|++++|++.+++..+.... .+    ..+|+.+-..|...|+   |...++...+.    +-.+  ...
T Consensus       118 ~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~  197 (293)
T 2qfc_A          118 QYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVK  197 (293)
T ss_dssp             HHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHH
Confidence            344556678889999999999987653211 12    2367777777777777   88888877622    2112  225


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHH-HHHHHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTV-KRVHKCVDE  223 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a-~~~~~~m~~  223 (323)
                      +|+.+-..|.+.|   ++++|++.+++....    +... -..+|..+-..+.+.|+.++| ...+++..+
T Consensus       198 ~~~nlg~~y~~~~---~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          198 VRYNHAKALYLDS---RYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHHh---hHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            8889999999999   779999999887642    1111 257888888999999999999 777777653

>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=96.76  E-value=0.011  Score=50.03  Aligned_cols=187  Identities=9%  Similarity=-0.061  Sum_probs=109.6

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+..+-..+.+.|+++.|...++...+..                   +.+...|..+-..|.+.|++++|.+.+++..+
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-------------------p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~   66 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRN-------------------PLVAVYYTNRALCYLKMQQPEQALADCRRALE   66 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------------------CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            45556667778888888888888888764                   34667788888888888888888888888765


Q ss_pred             CCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCch-HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC
Q 040801          119 QGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDS-FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP  193 (323)
Q Consensus       119 ~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~-~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p  193 (323)
                      .  .| +...+..+-.++...|+   |...++...+..  |+. ..+...+....+..      ++.. +......-...
T Consensus        67 ~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~~~~~~~~~~------~~~~-~~~~~~~~~~~  135 (281)
T 2c2l_A           67 L--DGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLA--KEQRLNFGDDIPSALRIA------KKKR-WNSIEERRIHQ  135 (281)
T ss_dssp             S--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHTTCCCCSHHHHHHHHH------HHHH-HHHHHHTCCCC
T ss_pred             h--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHHHH------HHHH-HHHHHHHHHhh
Confidence            4  33 34556666666666666   777776665432  211 11112222222211      1111 12222222333


Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh-hhHHHHHHHHHhc-CCHHHHHHHHHhccCC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV-ELKTTLMDAYCKC-KFVSRAWDLFVKMLFP  259 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~-g~~~~a~~~~~~m~~~  259 (323)
                      +.... ..+..+. .|+.++|...++...+.  .|+. .....+-..+.+. +.+++|.++|++..+.
T Consensus       136 ~~~i~-~~l~~l~-~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          136 ESELH-SYLTRLI-AAERERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             CCHHH-HHHHHHH-HHHHHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             hHHHH-HHHHHHH-HHHHHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            33333 3333332 57777777777665543  4543 3334444445555 6788999999988764

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=96.75  E-value=0.023  Score=48.03  Aligned_cols=113  Identities=13%  Similarity=-0.084  Sum_probs=76.5

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC--hHHHHHHHHHHhccCChHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN--AVTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                      |.++++.+...+  |+....-.+-..+.+.+   ++++|+..|+...... .|.  ...+..+=.++...|++++|...|
T Consensus       121 A~~~l~~~~~~~--p~~~~~~~~a~l~~~~~---r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~~LG~~~eAl~~l  194 (282)
T 4f3v_A          121 AMEALEAAPVAG--SEHLVAWMKAVVYGAAE---RWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAANLALFTEAERRL  194 (282)
T ss_dssp             HHHHHTSSCCTT--CHHHHHHHHHHHHHHTT---CHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CchHHHHHHHHHHHHcC---CHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            666666665533  54434444445677777   6689999997443211 111  235666777888999999999999


Q ss_pred             HHHHHhCCccC--hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          219 KCVDESGFWSH--VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       219 ~~m~~~g~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++.......|.  .......-.++.+.|+.++|..+|+++...
T Consensus       195 ~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          195 TEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            98875443253  234555666788899999999999999875

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=96.74  E-value=0.064  Score=40.74  Aligned_cols=99  Identities=13%  Similarity=0.035  Sum_probs=75.5

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      +...|..+-..+.+.|++++|++.|++..+.  .|+                               +...|..+-.+|.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~-------------------------------~~~~~~~l~~~~~   56 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSI--APA-------------------------------NPIYLSNRAAAYS   56 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STT-------------------------------CHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCc-------------------------------CHHHHHHHHHHHH
Confidence            4456677777888888888888888776652  121                               3556777778888


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +.|   ++++|++.|++..... .-+...|..+-..+...|++++|...|++..+.
T Consensus        57 ~~g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           57 ASG---QHEKAAEDAELATVVD-PKYSKAWSRLGLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             Hcc---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            888   6689999998887754 335778888888899999999999999988775

>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=96.73  E-value=0.023  Score=47.90  Aligned_cols=92  Identities=8%  Similarity=-0.129  Sum_probs=53.5

Q ss_pred             HHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHH
Q 040801          128 FPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTA  204 (323)
Q Consensus       128 y~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~  204 (323)
                      +..+-..+.+.|+   |...+....+.. ..+...|..+-.+|.+.|   ++++|++.+++..... .-+...+..+-.+
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   81 (281)
T 2c2l_A            7 LKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQ---QPEQALADCRRALELD-GQSVKAHFFLGQC   81 (281)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHTTSC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhc---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            3344444444555   666666665543 124556666666666666   5567777666665432 2244566666666


Q ss_pred             HhccCChHHHHHHHHHHHHh
Q 040801          205 RARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       205 ~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +...|++++|...++...+.
T Consensus        82 ~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            66677777777766666543

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.72  E-value=0.01  Score=44.31  Aligned_cols=137  Identities=11%  Similarity=-0.044  Sum_probs=94.2

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      .++..+-..|...|++++|.+.+++..+..-.               .++.            ..-..++..+-..|...
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~---------------~~~~------------~~~~~~~~~l~~~~~~~   62 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKE---------------FGDK------------AAERIAYSNLGNAYIFL   62 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH---------------HTCH------------HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH---------------hCCc------------hHHHHHHHHHHHHHHHc
Confidence            45677777888899999999999887642100               0000            00124566777778888


Q ss_pred             CCCCChHHHHHHHHHHHHc----CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHh----CCcc-ChhhHHHHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIE----NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDES----GFWS-HVELKTTLMDAY  240 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~----g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~  240 (323)
                      |   ++++|.+.+++....    +-.+ ....+..+-..+...|++++|...+++..+.    +-.+ ....+..+-..|
T Consensus        63 g---~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~  139 (164)
T 3ro3_A           63 G---EFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAY  139 (164)
T ss_dssp             T---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             C---CHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHH
Confidence            8   668888888876542    1111 2567888888888999999999888887643    2111 245677888889


Q ss_pred             HhcCCHHHHHHHHHhcc
Q 040801          241 CKCKFVSRAWDLFVKML  257 (323)
Q Consensus       241 ~~~g~~~~a~~~~~~m~  257 (323)
                      ...|+.++|.+.+++..
T Consensus       140 ~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A          140 TALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHTCHHHHHHHHHHHH
T ss_pred             HHccCHHHHHHHHHHHH
Confidence            99999999999988754

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.70  E-value=0.011  Score=44.10  Aligned_cols=129  Identities=14%  Similarity=-0.006  Sum_probs=89.5

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC---CC--ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC----Cc
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV---KP--NAVTLVNVLTARARARDLRTVKRVHKCVDESG----FW  227 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~---~p--~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g----~~  227 (323)
                      ..++..+-..|...|   ++++|.+.+++.....-   .+  -..++..+-..+...|++++|...++...+..    -.
T Consensus         9 ~~~~~~l~~~~~~~~---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~   85 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLG---NFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDR   85 (164)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhc---CHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCc
Confidence            567888888899999   67999999988765311   11  12588889999999999999999999986532    11


Q ss_pred             c-ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC----CCchh-hhHHHhhhccCCCCCcchhhhhhh
Q 040801          228 S-HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP----WNNYG-QWAMSATVGPQGLVGRHSTAHQIS  288 (323)
Q Consensus       228 p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~~~-~~~~~~~~~~~~~~~~~~~a~~l~  288 (323)
                      + ....+..+-..|...|++++|.+.+++..+.    +..+. .+.+...-..+...|+.++|...+
T Consensus        86 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  152 (164)
T 3ro3_A           86 AVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFA  152 (164)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHH
Confidence            1 1456778888999999999999999887532    22221 223333333444456666665543

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.70  E-value=0.07  Score=39.16  Aligned_cols=104  Identities=9%  Similarity=-0.106  Sum_probs=71.9

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      ..+...|..+-..+.+.|++++|.+.|++..+.  .|+..                            .....|..+-..
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~----------------------------~~~~~~~~~a~~   74 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQ----------------------------DQAVLHRNRAAC   74 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHH----------------------------HHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccch----------------------------HHHHHHHHHHHH
Confidence            446677888888999999999999999988764  34310                            013445556666


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      |...|   ++++|.+.+++..... ..+...+..+-..+...|+.++|...+++..+.
T Consensus        75 ~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           75 HLKLE---DYDKAETEASKAIEKD-GGDVKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHTT---CHHHHHHHHHHHHHHT-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHc---cHHHHHHHHHHHHhhC-ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            66766   5577777777766543 224566667777777777888887777777665

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=96.64  E-value=0.048  Score=39.78  Aligned_cols=96  Identities=10%  Similarity=0.022  Sum_probs=63.7

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                      .|...=..|.+.|++++|++.|++..+.  .|                               .+...|..+-.+|.+.|
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~--~p-------------------------------~~~~~~~~~~~~~~~~~   61 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKR--DP-------------------------------ENAILYSNRAACLTKLM   61 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT-------------------------------TCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CC-------------------------------CCHHHHHHHhhHHHhhc
Confidence            3444555677788888888887776542  12                               23445566666677777


Q ss_pred             CCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          172 CLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       172 ~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                         ++++|++.|++....+ ..+...|..+-.++...|++++|...|++..+.
T Consensus        62 ---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           62 ---EFQRALDDCDTCIRLD-SKFIKGYIRKAACLVAMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             ---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ---cHHHHHHHHHHHHHhh-hhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence               5577777777776643 235567777777777777777777777777665

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.63  E-value=0.085  Score=46.88  Aligned_cols=184  Identities=10%  Similarity=-0.062  Sum_probs=118.9

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCC-Cc---------------ccHHHHHHHhcchhh---HHHHHHHHHHc-CCCCch
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIP-DR---------------FMFPSLFKSCADIYV---EKQLHSQAIKF-GLASDS  157 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p-~~---------------~ty~~ll~~~~~~~~---a~~~~~~m~~~-g~~~~~  157 (323)
                      +.+.+.|++++|.+.|.+..+..-.. +.               ..+..+...|.+.|+   +.+.+....+. +-.++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            45678899999999999987643221 11               126777888888888   77777666543 222222


Q ss_pred             HH---HHHHHHH-HHhcCCCCChHHHHHHHHHHHH----cCCCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          158 FL---HNTLINM-YSSCWCLDQPDEAIKIFYRMEI----ENVKPN-AVTLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       158 ~~---~~~li~~-~~~~g~~~~~~~a~~~~~~m~~----~g~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                      .+   ...++.. +...|   +.+++.+++++...    .+..+. ..++..+...+...|++++|..++..+...-...
T Consensus        92 ~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~  168 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPD---SLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKL  168 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCS---CHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhc
Confidence            22   2222222 22334   67899999887754    233333 4577888999999999999999999986532111


Q ss_pred             -----ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC----CCchhhh--HHHhhhccCCCCCcchhh
Q 040801          229 -----HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP----WNNYGQW--AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       229 -----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~--~~~~~~~~~~~~~~~~~a  284 (323)
                           ....|..++..|...|++++|..++++....    +.++...  .+......+...++..+|
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A  235 (434)
T 4b4t_Q          169 DDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTA  235 (434)
T ss_dssp             SCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHH
Confidence                 2457888999999999999999999887532    2222221  333333344455666655

>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=96.61  E-value=0.051  Score=42.81  Aligned_cols=98  Identities=15%  Similarity=-0.028  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCC-CCC--------------hHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENV-KPN--------------AVTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~-~p~--------------~~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      ..+..+-..+.+.|   ++++|++.|++.....- .|+              ...|..+-.++...|++++|...++...
T Consensus        39 ~~~~~~g~~~~~~~---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al  115 (198)
T 2fbn_A           39 FDIKEEGNEFFKKN---EINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVL  115 (198)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            44566666777778   66899999988876321 111              2677788888888999999999999888


Q ss_pred             HhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          223 ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       223 ~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +.. +.+...+..+-.+|...|++++|...|++..+.
T Consensus       116 ~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  151 (198)
T 2fbn_A          116 KID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL  151 (198)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            763 335677888888899999999999999887643

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.59  E-value=0.029  Score=42.67  Aligned_cols=99  Identities=12%  Similarity=-0.083  Sum_probs=79.2

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc--------C---------CCCChHHHHHHHHHHhccCChHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE--------N---------VKPNAVTLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~--------g---------~~p~~~t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      ...+...=..+.+.|   ++++|++.|.+....        .         -.-+...|..+-.++.+.|++++|...++
T Consensus        11 a~~~~~~G~~~~~~~---~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~   87 (162)
T 3rkv_A           11 VEALRQKGNELFVQK---DYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSS   87 (162)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            345666677788888   679999999887664        0         01234688888999999999999999999


Q ss_pred             HHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          220 CVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       220 ~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...+.. +-+...|..+-.+|...|++++|...|++..+.
T Consensus        88 ~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           88 EVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            998874 335778888999999999999999999988764

>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=96.58  E-value=0.037  Score=43.64  Aligned_cols=148  Identities=14%  Similarity=0.000  Sum_probs=98.0

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      ...+..+=..+.+.|++++|.+.|++..+..  |+...+...     ....-.   ..       ....+|..+-.+|.+
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~-----~~~~~~---~~-------~~~~~~~~la~~~~~  100 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFF--IHTEEWDDQ-----ILLDKK---KN-------IEISCNLNLATCYNK  100 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--TTCTTCCCH-----HHHHHH---HH-------HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH--hcccccchh-----hHHHHH---HH-------HHHHHHHHHHHHHHH
Confidence            4567777788899999999999999987632  221111100     000000   00       024677888888999


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRA  249 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a  249 (323)
                      .|   ++++|++.+++..... ..+...|..+-.++...|++++|...++...+.. +-+...+..+...+.+.|+.+++
T Consensus       101 ~~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~  175 (198)
T 2fbn_A          101 NK---DYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKK  175 (198)
T ss_dssp             TT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC-
T ss_pred             hc---CHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHH
Confidence            89   7799999999988754 3467888889999999999999999999998763 22566777777788887777777


Q ss_pred             H-HHHHhccCC
Q 040801          250 W-DLFVKMLFP  259 (323)
Q Consensus       250 ~-~~~~~m~~~  259 (323)
                      . ..+..|...
T Consensus       176 ~~~~~~~~f~~  186 (198)
T 2fbn_A          176 DKLTFGGMFDK  186 (198)
T ss_dssp             -----------
T ss_pred             HHHHHHHHhcc
Confidence            6 555555443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.56  E-value=0.016  Score=41.22  Aligned_cols=79  Identities=8%  Similarity=-0.137  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      ++++.|++..... ..+...+..+-..+...|++++|...+++..+.. +.+...|..+-.+|.+.|+.++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4666666665533 2355677777777778888888888888877653 2245567777777888888888888887765


Q ss_pred             C
Q 040801          258 F  258 (323)
Q Consensus       258 ~  258 (323)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.54  E-value=0.0032  Score=44.28  Aligned_cols=62  Identities=11%  Similarity=-0.051  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ..|..+-..+.+.|   ++++|++.|++..... +.+...|..+-.++.+.|++++|...+++..+
T Consensus         5 ~~~~~~g~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            5 EKQKEQGNSLFKQG---LYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHHTTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcC---CHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34444555555555   4455555555554432 22344555555555555555555555555544

>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=96.46  E-value=0.0048  Score=56.65  Aligned_cols=117  Identities=15%  Similarity=-0.052  Sum_probs=78.2

Q ss_pred             hcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCCh
Q 040801          135 CADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDL  211 (323)
Q Consensus       135 ~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~  211 (323)
                      +.+.|+   |.+.++...+.. .-+...|..+-.+|.+.|   ++++|++.+++..+.. .-+...|..+-.++...|++
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g---~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~   90 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTE---CYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKF   90 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhc---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCH
Confidence            344455   778888777764 224777888888888888   6688888888887753 23567788888888888888


Q ss_pred             HHHHHHHHHHHHhCCccChhhHHHHHHH--HHhcCCHHHHHHHHHhcc
Q 040801          212 RTVKRVHKCVDESGFWSHVELKTTLMDA--YCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       212 ~~a~~~~~~m~~~g~~p~~~~~~~li~~--~~~~g~~~~a~~~~~~m~  257 (323)
                      ++|...+++..+.. +-+...+..+-.+  +.+.|++++|.+.+++-.
T Consensus        91 ~eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~~~  137 (477)
T 1wao_1           91 RAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  137 (477)
T ss_dssp             HHHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC------CC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            88888888887753 1133444444444  777888888888877643

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.45  E-value=0.26  Score=45.20  Aligned_cols=176  Identities=11%  Similarity=-0.051  Sum_probs=111.2

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcC---------CCC--
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFG---------LAS--  155 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g---------~~~--  155 (323)
                      +.+...|-..+.-+.+.|++++|.++|++-...   |+....-.....+.+.++   +++.+.+.-         ..+  
T Consensus       210 p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~---P~~~~l~~~y~~~~e~~~---~~~~l~~~~~~~~~~~~~~~~~~  283 (493)
T 2uy1_A          210 YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM---SDGMFLSLYYGLVMDEEA---VYGDLKRKYSMGEAESAEKVFSK  283 (493)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHTTCTH---HHHHHHHHTC----------CHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---CCcHHHHHHHHhhcchhH---HHHHHHHHHHhhccchhhhhccc
Confidence            445677888888889999999999999999887   655433222111111122   122322210         011  


Q ss_pred             -chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHH--HHHHHHhccCChHHHHHHHHHHHHhCCccChhh
Q 040801          156 -DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLV--NVLTARARARDLRTVKRVHKCVDESGFWSHVEL  232 (323)
Q Consensus       156 -~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~--~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  232 (323)
                       ...+|-..+..+.+.+   +.+.|.++|+.....+  .+...|.  +.+...+ .++.+.|..+|+...+.- .-+...
T Consensus       284 ~~~~lw~~y~~~~~r~~---~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~-~~~~~~  356 (493)
T 2uy1_A          284 ELDLLRINHLNYVLKKR---GLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH-PDSTLL  356 (493)
T ss_dssp             HHHHHHHHHHHHHHHHH---CHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC-TTCHHH
T ss_pred             ccHHHHHHHHHHHHHcC---CHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC-CCCHHH
Confidence             1345667777776777   5699999999882222  2334443  3333322 337999999999998753 223456


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccCCCCchhhh-HHHhhhccCCCC
Q 040801          233 KTTLMDAYCKCKFVSRAWDLFVKMLFPWNNYGQW-AMSATVGPQGLV  278 (323)
Q Consensus       233 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~~~~~~~~~  278 (323)
                      +...++...+.|+.++|..+|+...+   ....| .+...-..+|..
T Consensus       357 ~~~yid~e~~~~~~~~aR~l~er~~k---~~~lw~~~~~fE~~~G~~  400 (493)
T 2uy1_A          357 KEEFFLFLLRIGDEENARALFKRLEK---TSRMWDSMIEYEFMVGSM  400 (493)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHSCC---BHHHHHHHHHHHHHHSCH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCH
Confidence            67788888899999999999999854   35556 555555555543

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.37  E-value=0.03  Score=50.92  Aligned_cols=99  Identities=9%  Similarity=-0.103  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC--------------hHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN--------------AVTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--------------~~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      ...|..+-..|.+.|   ++++|++.|++.....-...              ...|..+-.++.+.|++++|...+++..
T Consensus       268 a~~~~~~G~~~~~~g---~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al  344 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGG---KYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKAL  344 (457)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCC---CHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            445666777778878   66888888887766321111              4777788888888888888888888887


Q ss_pred             HhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          223 ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       223 ~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +.. +-+...|..+-.+|.+.|++++|...|++..+.
T Consensus       345 ~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l  380 (457)
T 1kt0_A          345 GLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  380 (457)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            763 225667777788888888888888888887664

>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=96.34  E-value=0.021  Score=52.35  Aligned_cols=116  Identities=8%  Similarity=-0.025  Sum_probs=77.5

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCC
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCL  173 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~  173 (323)
                      ..+.+.|++++|.+.|++..+.  .| +..+|..+-.++.+.|+   |.+.++...+.. .-+...|..+-.+|.+.|  
T Consensus        14 ~~~~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g--   88 (477)
T 1wao_1           14 NDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALG--   88 (477)
T ss_dssp             SSTTTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHT--
T ss_pred             HHHHHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcC--
Confidence            3456778899999999887664  33 35677777777777777   888888877764 234677888888888888  


Q ss_pred             CChHHHHHHHHHHHHcCCCCChHHHHHHHHH--HhccCChHHHHHHHHH
Q 040801          174 DQPDEAIKIFYRMEIENVKPNAVTLVNVLTA--RARARDLRTVKRVHKC  220 (323)
Q Consensus       174 ~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~--~~~~~~~~~a~~~~~~  220 (323)
                       ++++|.+.|++..+..- -+...+..+-.+  +.+.|++++|...+++
T Consensus        89 -~~~eA~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~  135 (477)
T 1wao_1           89 -KFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEH  135 (477)
T ss_dssp             -CHHHHHHHHHHHHHHST-TCTTHHHHHHHHHHHHHHHHHCCC------
T ss_pred             -CHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence             66899999988876431 133344444444  6777888888777665

>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=96.34  E-value=0.071  Score=38.75  Aligned_cols=101  Identities=11%  Similarity=-0.026  Sum_probs=71.7

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      ..+...|..+-..+.+.|++++|.+.|++..+..  |+                               +...|..+-.+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~~-------------------------------~~~~~~~l~~~   52 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PL-------------------------------VAVYYTNRALC   52 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-------------------------------CHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC--cC-------------------------------cHHHHHHHHHH
Confidence            4456677777778888888888888887766531  21                               24456667777


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      |...|   ++++|...|++..... ..+...+..+-..+...|++++|...++...+.
T Consensus        53 ~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           53 YLKMQ---QPEQALADCRRALELD-GQSVKAHFFLGQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhc---CHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            77777   6688888888777654 235667777778888888888888888887654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=96.32  E-value=0.043  Score=41.68  Aligned_cols=66  Identities=12%  Similarity=0.020  Sum_probs=50.5

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG  225 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g  225 (323)
                      +...|..+-.+|...|   ++++|++.|++..... +-+...|..+-.++...|++++|...|+...+..
T Consensus        69 ~~~~~~~lg~~~~~~g---~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A           69 NVDYIMGLAAIYQIKE---QFQQAADLYAVAFALG-KNDYTPVFHTGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHc---cHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            4566777778888888   6688888888887754 2356777778888888888888888888887763

>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=96.32  E-value=0.078  Score=38.10  Aligned_cols=97  Identities=14%  Similarity=0.066  Sum_probs=64.7

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..|..+=..+.+.|++++|.+.|++..+.  .|+                               +...|..+-.+|.+.
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~-------------------------------~~~~~~~~a~~~~~~   51 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKR--APE-------------------------------DARGYSNRAAALAKL   51 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-------------------------------CHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCC-------------------------------ChHHHHHHHHHHHHh
Confidence            34555666777888888888888776553  122                               235566666667777


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      |   ++++|++.|++..... .-+...|..+-.++...|++++|...+++..+.
T Consensus        52 ~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           52 M---SFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLDAARTK  101 (126)
T ss_dssp             T---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             c---CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHHh
Confidence            7   5577777777776643 234566777777777777777777777777654

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.22  E-value=0.017  Score=53.15  Aligned_cols=100  Identities=12%  Similarity=-0.011  Sum_probs=77.8

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc-----C-CCCC-hHHHHHHHHHHhccCChHHHHHHHHHHHH-----h
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE-----N-VKPN-AVTLVNVLTARARARDLRTVKRVHKCVDE-----S  224 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~-----g-~~p~-~~t~~~li~~~~~~~~~~~a~~~~~~m~~-----~  224 (323)
                      ..+++.|...|...|   ++++|..++++...-     | -.|+ ..+++.|-..|...|++++|+.++++..+     .
T Consensus       351 a~~~~nLa~~y~~~g---~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~l  427 (490)
T 3n71_A          351 LRLLSIASEVLSYLQ---AYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTH  427 (490)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhc---CHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            567899999999999   669999998887541     2 1233 36899999999999999999999998864     2


Q ss_pred             CCc-c-ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          225 GFW-S-HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       225 g~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      |-. | ...+.+.|-.++...|.+++|+.+++.++++
T Consensus       428 G~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          428 GPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             CTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            322 2 2445567777888999999999999999764

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=96.16  E-value=0.072  Score=39.44  Aligned_cols=97  Identities=7%  Similarity=-0.071  Sum_probs=62.4

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhc
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSC  170 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~  170 (323)
                      ..+..+-..+.+.|++++|.+.|++....  .|                               .+...|..+-.+|.+.
T Consensus        19 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p-------------------------------~~~~~~~~lg~~~~~~   65 (142)
T 2xcb_A           19 EQLYALGFNQYQAGKWDDAQKIFQALCML--DH-------------------------------YDARYFLGLGACRQSL   65 (142)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT-------------------------------TCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHccHHHHHHHHHHHHHh--CC-------------------------------ccHHHHHHHHHHHHHH
Confidence            44455556677777777777777665542  12                               1334455566666677


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      |   ++++|++.|++..... +-+...+..+-.++...|++++|...++...+.
T Consensus        66 g---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           66 G---LYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             T---CHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             h---hHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7   5577777777776644 234556666777777777777777777777654

>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=96.16  E-value=0.058  Score=40.56  Aligned_cols=99  Identities=13%  Similarity=-0.005  Sum_probs=66.2

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYS  168 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~  168 (323)
                      +...+..+-..+.+.|++++|.+.|++....  .|                               .+...|..+-.+|.
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p-------------------------------~~~~~~~~lg~~~~   66 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVL--DH-------------------------------YDSRFFLGLGACRQ   66 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CT-------------------------------TCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHc--Cc-------------------------------ccHHHHHHHHHHHH
Confidence            3344555556666777777777766655432  11                               23455666666777


Q ss_pred             hcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          169 SCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       169 ~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ..|   ++++|++.|++..... +-+...|..+-.++...|++++|...++...+.
T Consensus        67 ~~g---~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           67 AMG---QYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HTT---CHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHh---hHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            777   6688888888877644 235567777778888888888888888887664

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.14  E-value=0.039  Score=47.98  Aligned_cols=96  Identities=10%  Similarity=-0.119  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChH------------------HHHHHHHHHhccCChHHHHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAV------------------TLVNVLTARARARDLRTVKRVHK  219 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~------------------t~~~li~~~~~~~~~~~a~~~~~  219 (323)
                      ..+..+-..+.+.|   ++++|...|++....  .|+..                  .|..+-.++.+.|++++|...++
T Consensus       180 ~~~~~~g~~~~~~g---~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~  254 (338)
T 2if4_A          180 DRRKMDGNSLFKEE---KLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCN  254 (338)
T ss_dssp             HHHHHHHHHTCSSS---CCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcC---CHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            33556666666777   558888888876653  34433                  78888899999999999999999


Q ss_pred             HHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          220 CVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       220 ~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...+.. +-+...|..+-.+|...|++++|...|++..+.
T Consensus       255 ~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l  293 (338)
T 2if4_A          255 IVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY  293 (338)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-
T ss_pred             HHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            998763 235778889999999999999999999998765

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.10  E-value=0.1  Score=34.66  Aligned_cols=63  Identities=21%  Similarity=0.037  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ..+..+-..|...|   ++++|.+.|++..... ..+...+..+-..+...|++++|...+++..+.
T Consensus        10 ~~~~~la~~~~~~~---~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A           10 EAWYNLGNAYYKQG---DYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcc---CHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            34455555555555   4466666666555432 223445555555556666666666666655544

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.09  E-value=0.073  Score=48.34  Aligned_cols=147  Identities=11%  Similarity=-0.028  Sum_probs=105.7

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      ....|..+=..|.+.|++++|.+.|++..+.  .|+...+         ..+ ..+    ...    .....|..+-.+|
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~---------~~~~~~~----~~~----~~~~~~~nla~~~  327 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSW--LEMEYGL---------SEKESKA----SES----FLLAAFLNLAMCY  327 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HTTCCSC---------CHHHHHH----HHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccC---------ChHHHHH----HHH----HHHHHHHHHHHHH
Confidence            3456778888999999999999999988662  2322111         011 111    111    1246788888999


Q ss_pred             HhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVS  247 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~  247 (323)
                      .+.|   ++++|++.|++..... .-+...|..+-.+|...|++++|...|++..+.. +-+...+..+-..+.+.|+.+
T Consensus       328 ~~~g---~~~~A~~~~~~al~~~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~  402 (457)
T 1kt0_A          328 LKLR---EYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN-PQNKAARLQISMCQKKAKEHN  402 (457)
T ss_dssp             HHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CHHHHHHHHHHHHHHHH
T ss_pred             HHhc---CHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHH
Confidence            9999   7799999999998764 3467889999999999999999999999998753 225677888888999999988


Q ss_pred             HHH-HHHHhccCC
Q 040801          248 RAW-DLFVKMLFP  259 (323)
Q Consensus       248 ~a~-~~~~~m~~~  259 (323)
                      ++. .++.+|..+
T Consensus       403 ~a~~~~~~~~f~k  415 (457)
T 1kt0_A          403 ERDRRIYANMFKK  415 (457)
T ss_dssp             HHHHHHHHHC---
T ss_pred             HHHHHHHHHHHhh
Confidence            876 456666544

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=96.07  E-value=0.033  Score=39.76  Aligned_cols=80  Identities=9%  Similarity=-0.130  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHcCC--CCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHH
Q 040801          141 EKQLHSQAIKFGL--ASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       141 a~~~~~~m~~~g~--~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                      |...++...+.+.  .-+...|..+-..|...|   ++++|++.|++..... +-+...+..+-.++...|+.++|...+
T Consensus         9 A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~   84 (117)
T 3k9i_A            9 AVPYYEKAIASGLQGKDLAECYLGLGSTFRTLG---EYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGVELL   84 (117)
T ss_dssp             CHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            5556666555431  224566788888899989   6799999999988765 235778888889999999999999999


Q ss_pred             HHHHHh
Q 040801          219 KCVDES  224 (323)
Q Consensus       219 ~~m~~~  224 (323)
                      ++..+.
T Consensus        85 ~~al~~   90 (117)
T 3k9i_A           85 LKIIAE   90 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            998765

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.05  E-value=0.017  Score=40.43  Aligned_cols=66  Identities=8%  Similarity=-0.195  Sum_probs=56.8

Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++...+..+-..+...|++++|...++...+.. +.+...|..+-.+|.+.|++++|.+.+++..+.
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   67 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY   67 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            356678888889999999999999999998863 335778888999999999999999999998765

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.02  E-value=0.02  Score=52.56  Aligned_cols=134  Identities=7%  Similarity=-0.052  Sum_probs=87.5

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCC---CC-ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCC
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQIS---NP-TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLI  122 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~---~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~  122 (323)
                      +...|++++|..++++..+..               ....   .| ...+++.|-..|...|++++|..++++..+    
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~---------------~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~----  379 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQ---------------EPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVD----  379 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHH---------------TTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH----
T ss_pred             HHhCCCHHHHHHHHHHHHHHH---------------HHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH----
Confidence            345566666666666555432               2222   12 346799999999999999999999987653    


Q ss_pred             CCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCc-hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH---cCCCCC---h
Q 040801          123 PDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASD-SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI---ENVKPN---A  195 (323)
Q Consensus       123 p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~---~g~~p~---~  195 (323)
                                           +++..... -.|+ ..+++.|-..|...|   ++++|..++++-..   .-..||   +
T Consensus       380 ---------------------i~~~~lG~-~Hp~~a~~l~nLa~~~~~~G---~~~eA~~~~~~Al~i~~~~lG~~Hp~~  434 (490)
T 3n71_A          380 ---------------------GYMKLYHH-NNAQLGMAVMRAGLTNWHAG---HIEVGHGMICKAYAILLVTHGPSHPIT  434 (490)
T ss_dssp             ---------------------HHHHHSCT-TCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHTCTTSHHH
T ss_pred             ---------------------HHHHHcCC-CCHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHHHHhCCCChHH
Confidence                                 22222221 2343 466888889999999   66888888877653   112233   3


Q ss_pred             -HHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          196 -VTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       196 -~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                       .+.+.+-.++...+.+++|+.++.++.+.
T Consensus       435 ~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          435 KDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             34455556666778899999999888653

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=95.95  E-value=0.088  Score=44.47  Aligned_cols=134  Identities=7%  Similarity=-0.099  Sum_probs=91.0

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCc----hHHHHHHHH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASD----SFLHNTLIN  165 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~----~~~~~~li~  165 (323)
                      +-.+...+...|++++|.++|+.+...+  |+....-.+-..+.+.++   |...++   +.+-.|+    ...+..+=.
T Consensus       105 ~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~---~a~~~~d~~~~~~a~~~LG~  179 (282)
T 4f3v_A          105 TMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVK---SAGKWPDKFLAGAAGVAHGV  179 (282)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHT---TGGGCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHH---HhhccCCcccHHHHHHHHHH
Confidence            3456778889999999999999887654  544333223334455555   666665   3332232    235667777


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCC--hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHH
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPN--AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTL  236 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  236 (323)
                      ++...|   ++++|++.|++.......|.  .......-.++.+.|+.++|..+|+++....  |+...+..|
T Consensus       180 al~~LG---~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~--P~~~~~~aL  247 (282)
T 4f3v_A          180 AAANLA---LFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH--PEPKVAAAL  247 (282)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--CCHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHHHHH
Confidence            889989   77999999998875443364  3355566677889999999999999998863  544444443

>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=95.77  E-value=0.2  Score=38.36  Aligned_cols=97  Identities=13%  Similarity=-0.092  Sum_probs=76.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC--------h-----HHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN--------A-----VTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~--------~-----~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ...+...-..+.+.|   ++++|++.|++-.+-  .|+        .     ..|+.+-.++.+.|++++|...+++..+
T Consensus        11 a~~~~~~G~~l~~~g---~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~   85 (159)
T 2hr2_A           11 AYLALSDAQRQLVAG---EYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   85 (159)
T ss_dssp             HHHHHHHHHHHHHHT---CHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCC---CHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344555666777888   779999999988763  233        2     3899999999999999999999999987


Q ss_pred             h-----CCccC-hhhH----HHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          224 S-----GFWSH-VELK----TTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       224 ~-----g~~p~-~~~~----~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .     .+.|+ ...|    ...=.++.+.|++++|...|++..+
T Consensus        86 l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           86 YFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            5     22564 4566    7777899999999999999998764

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.73  E-value=0.068  Score=37.00  Aligned_cols=62  Identities=11%  Similarity=0.037  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      ...+..+-..+...|++++|...|++..+.. +-+...|..+-.+|.+.|++++|.+.+++..
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444455555555555555555555555442 1134445555555555555555555555543

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=95.63  E-value=0.24  Score=36.61  Aligned_cols=80  Identities=11%  Similarity=-0.108  Sum_probs=45.2

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHh----cCCH
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCK----CKFV  246 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~g~~  246 (323)
                      ..++|++.|++-.+.|   +...+..|=..|..    .++.++|...+++..+.|   +...+..|-..|..    .++.
T Consensus        40 ~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~  113 (138)
T 1klx_A           40 NKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNE  113 (138)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             CHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCH
Confidence            3455666666555543   34444444444444    566666666666666554   34455555555555    5666


Q ss_pred             HHHHHHHHhccCCC
Q 040801          247 SRAWDLFVKMLFPW  260 (323)
Q Consensus       247 ~~a~~~~~~m~~~~  260 (323)
                      ++|.+.|++..+.|
T Consensus       114 ~~A~~~~~~Aa~~g  127 (138)
T 1klx_A          114 KQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHCC
Confidence            66666666665544

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.59  E-value=0.18  Score=35.48  Aligned_cols=79  Identities=13%  Similarity=-0.003  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      +...++...+.. ..+...+..+-..|...|   ++++|++.|++..... ..+...|..+-..+...|+.++|...++.
T Consensus         4 a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~   78 (115)
T 2kat_A            4 ITERLEAMLAQG-TDNMLLRFTLGKTYAEHE---QFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWES   78 (115)
T ss_dssp             HHHHHHHHHTTT-CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHcc---CHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            344555555543 235678888899999999   7799999999988754 33567888899999999999999999999


Q ss_pred             HHHh
Q 040801          221 VDES  224 (323)
Q Consensus       221 m~~~  224 (323)
                      ..+.
T Consensus        79 al~~   82 (115)
T 2kat_A           79 GLAA   82 (115)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8764

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=95.54  E-value=0.41  Score=34.05  Aligned_cols=94  Identities=11%  Similarity=0.013  Sum_probs=59.4

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~  175 (323)
                      +-..+.+.|++++|.+.|++..+..  |+...                            ....+..+-.+|.+.|   +
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~----------------------------~~~~~~~lg~~~~~~~---~   54 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELY--PNGVY----------------------------TPNALYWLGESYYATR---N   54 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--SSSTT----------------------------HHHHHHHHHHHHHHTT---C
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHC--CCCcc----------------------------cHHHHHHHHHHHHHhc---c
Confidence            4455667777777777777765431  22110                            0123444555666677   6


Q ss_pred             hHHHHHHHHHHHHcCCCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          176 PDEAIKIFYRMEIENVKPN----AVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +++|.+.|++.....  |+    ...+..+-.++...|+.++|...++.+.+.
T Consensus        55 ~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           55 FQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            678888887776643  22    455666777777888888888888887765

>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=95.39  E-value=0.12  Score=45.63  Aligned_cols=98  Identities=11%  Similarity=-0.054  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc--------------CCC-CChHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE--------------NVK-PNAVTLVNVLTARARARDLRTVKRVHKCVD  222 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~--------------g~~-p~~~t~~~li~~~~~~~~~~~a~~~~~~m~  222 (323)
                      ..+..+-..|.+.|   ++++|++.|++....              ... -+...|..+-.++.+.|++++|...+++..
T Consensus       224 ~~~~~~g~~~~~~g---~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al  300 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQ---NWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEAL  300 (370)
T ss_dssp             HHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc---CHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            34667777888888   668999988887651              012 245788888889999999999999999988


Q ss_pred             HhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          223 ESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       223 ~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +.. +-+...|..+-.+|.+.|++++|...|++..+.
T Consensus       301 ~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          301 EID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             TTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            753 225677888888999999999999999987654

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.35  E-value=0.14  Score=35.39  Aligned_cols=65  Identities=12%  Similarity=-0.013  Sum_probs=55.2

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +...+..+-..|.+.|   ++++|++.|++..+.. .-+...|..+-.++...|++++|...+++..+.
T Consensus         6 ~~~~~~~lg~~~~~~g---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHD---NASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            4667888889999999   7799999999998765 235678889999999999999999999998754

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=95.07  E-value=0.23  Score=35.61  Aligned_cols=63  Identities=5%  Similarity=-0.092  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      ...|..+-.++...|   ++++|+..|++..... .-+...+..+-..+...|+.++|...+++..+
T Consensus        51 ~~a~~~lg~~~~~~g---~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           51 EEAWRSLGLTQAENE---KDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344445555555555   4466666666655533 12445555566666666666666666666554

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=95.01  E-value=0.15  Score=44.27  Aligned_cols=148  Identities=12%  Similarity=0.032  Sum_probs=82.4

Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHh
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSS  169 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~  169 (323)
                      ...|..+=..+.+.|++++|.+.|++..+.  .|+...       +...++-.+....+.       ...|..+-.+|.+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~-------~~~~~nla~~~~~  242 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK-------NPCHLNIAACLIK  242 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH-------THHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH-------HHHHHHHHHHHHH
Confidence            344666777888899999999999987653  343221       122233111112221       2378888899999


Q ss_pred             cCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHH-HHhcCCHH
Q 040801          170 CWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDA-YCKCKFVS  247 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~-~~~~g~~~  247 (323)
                      .|   ++++|++.+++..... .-+...|..+-.++...|++++|...|++..+.  .| +...+..|... ....+..+
T Consensus       243 ~g---~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~~  316 (338)
T 2if4_A          243 LK---RYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALYQ  316 (338)
T ss_dssp             TT---CCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             cC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            99   5699999999988754 346789999999999999999999999998654  34 34445555444 33456778


Q ss_pred             HHHHHHHhccCC
Q 040801          248 RAWDLFVKMLFP  259 (323)
Q Consensus       248 ~a~~~~~~m~~~  259 (323)
                      ++..+|.+|...
T Consensus       317 ~a~~~~~~~l~~  328 (338)
T 2if4_A          317 KQKEMYKGIFKG  328 (338)
T ss_dssp             ------------
T ss_pred             HHHHHHHHhhCC
Confidence            888888888654

>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=94.93  E-value=0.21  Score=44.00  Aligned_cols=137  Identities=9%  Similarity=-0.069  Sum_probs=97.2

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCC-CchHHHHHHHHHHHhc
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLA-SDSFLHNTLINMYSSC  170 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~-~~~~~~~~li~~~~~~  170 (323)
                      .|..+=..+.+.|++++|.+.|++..+.-  ++.      -.      .  .-.+...  ... .+..+|..+-.+|.+.
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~--~~~------~~------~--~~~~~~~--~~~~~~~~~~~nla~~~~~~  286 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYV--EGS------RA------A--AEDADGA--KLQPVALSCVLNIGACKLKM  286 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHH------HH------H--SCHHHHG--GGHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHh--hcC------cc------c--cChHHHH--HHHHHHHHHHHHHHHHHHhc
Confidence            46777778889999999999998876520  000      00      0  0000110  011 2457788888999999


Q ss_pred             CCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHH
Q 040801          171 WCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAW  250 (323)
Q Consensus       171 g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~  250 (323)
                      |   ++++|++.+++..+.. .-+...|..+-.++...|++++|...+++..+.. +-+...+..+-..+.+.++.+++.
T Consensus       287 g---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~~~~~~~~~~~a~  361 (370)
T 1ihg_A          287 S---DWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIKAQKDKE  361 (370)
T ss_dssp             T---CHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             c---CHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9   7799999999988744 2367788889999999999999999999998763 225667777777787777777765


Q ss_pred             H
Q 040801          251 D  251 (323)
Q Consensus       251 ~  251 (323)
                      +
T Consensus       362 k  362 (370)
T 1ihg_A          362 K  362 (370)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=94.82  E-value=0.44  Score=34.40  Aligned_cols=104  Identities=13%  Similarity=0.082  Sum_probs=65.1

Q ss_pred             hHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcC
Q 040801           92 TCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCW  171 (323)
Q Consensus        92 ~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g  171 (323)
                      .+..+=..+.+.|++++|++.|++..+.  .|+                               +...|+.+-.+|.+.|
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~-------------------------------~~~~~~nlg~~~~~~~   56 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPS-------------------------------NITFYNNKAAVYFEEK   56 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT-------------------------------CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCC-------------------------------CHHHHHhHHHHHHHhh
Confidence            3445555677778888888888766542  221                               2455666777777777


Q ss_pred             CCCChHHHHHHHHHHHHcC--CCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhH
Q 040801          172 CLDQPDEAIKIFYRMEIEN--VKPN----AVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELK  233 (323)
Q Consensus       172 ~~~~~~~a~~~~~~m~~~g--~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  233 (323)
                         ++++|++.|++.....  ..++    ..+|..+=..+...|++++|...|++..+.  .||..+.
T Consensus        57 ---~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~  119 (127)
T 4gcn_A           57 ---KFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELV  119 (127)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHH
T ss_pred             ---hHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHH
Confidence               6678888887765421  1111    135555666677778888888888877664  3454433

>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=94.82  E-value=0.27  Score=44.26  Aligned_cols=91  Identities=8%  Similarity=0.000  Sum_probs=68.1

Q ss_pred             HhcCCCCChHHHHHHHHHHHHc---CCCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHh---CCc---cC-hhhH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIE---NVKPN----AVTLVNVLTARARARDLRTVKRVHKCVDES---GFW---SH-VELK  233 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~---g~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~---p~-~~~~  233 (323)
                      -+.....++++|+.++++..+.   -+.|+    ..+++.|...|...|++++|+.++++..+.   -+.   |+ ..+|
T Consensus       306 ~~~~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l  385 (433)
T 3qww_A          306 RRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMW  385 (433)
T ss_dssp             HHHTTTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHH
T ss_pred             HHhhhccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHH
Confidence            3333333778999999877652   22332    368999999999999999999999998642   122   22 4568


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          234 TTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       234 ~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +.|-..|...|++++|+.++++..+
T Consensus       386 ~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          386 LKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHH
Confidence            8999999999999999999988754

>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=94.74  E-value=0.42  Score=35.21  Aligned_cols=113  Identities=11%  Similarity=-0.033  Sum_probs=80.5

Q ss_pred             CCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhc-CCCCChHH
Q 040801          103 KNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSC-WCLDQPDE  178 (323)
Q Consensus       103 ~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~-g~~~~~~~  178 (323)
                      .+++++|++.|++-.+.|. |+  ..  |=..|..-+.   |.++++...+.|   +...+..|=..|..- |...+.++
T Consensus         8 ~~d~~~A~~~~~~aa~~g~-~~--a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~   79 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELNE-MF--GC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRK   79 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTTC-TT--HH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHH
T ss_pred             ccCHHHHHHHHHHHHcCCC-Hh--hh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHH
Confidence            3568999999999988873 32  22  3223322222   788888877765   456666676677661 11228899


Q ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHhc----cCChHHHHHHHHHHHHhCC
Q 040801          179 AIKIFYRMEIENVKPNAVTLVNVLTARAR----ARDLRTVKRVHKCVDESGF  226 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t~~~li~~~~~----~~~~~~a~~~~~~m~~~g~  226 (323)
                      |++.|++-.+.|   +...+..|-..|..    .++.++|...+++..+.|.
T Consensus        80 A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           80 AAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            999999998875   56667777777777    8999999999999988874

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=94.66  E-value=0.19  Score=33.21  Aligned_cols=65  Identities=20%  Similarity=0.038  Sum_probs=54.9

Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +...+..+-..+...|++++|...+++..+.. +.+...+..+-..|.+.|++++|...+++..+.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            35677778888999999999999999998764 235677888999999999999999999988654

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=94.46  E-value=1.5  Score=38.34  Aligned_cols=134  Identities=5%  Similarity=-0.035  Sum_probs=83.8

Q ss_pred             CCCCcccHHHHHHHhcchhh--------HHHHHHHHHHcCCCCc-hHHHHHHHHHHHh---cCCCCChHHHHHHHHHHHH
Q 040801          121 LIPDRFMFPSLFKSCADIYV--------EKQLHSQAIKFGLASD-SFLHNTLINMYSS---CWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       121 ~~p~~~ty~~ll~~~~~~~~--------a~~~~~~m~~~g~~~~-~~~~~~li~~~~~---~g~~~~~~~a~~~~~~m~~  188 (323)
                      .+.+...|...+++......        |..+|+...+..  |+ ...|..+--+|.-   .+.. .......+-..+..
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lD--P~~a~A~A~la~a~~~~~~~~~~-~~~~~~~l~~a~~a  266 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSS--PEFTYARAEKALVDIVRHSQHPL-DEKQLAALNTEIDN  266 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCC-CHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhccCCC-chhhHHHHHHHHHH
Confidence            45566777777766554322        777777776654  54 2333322222211   1111 11111111111111


Q ss_pred             ----cCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          189 ----ENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       189 ----~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                          ..-..+..+|..+-..+...|+++.|...++++.+.+  |+...|..+=..+.-.|+.++|.+.+++....
T Consensus       267 ~~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL  339 (372)
T 3ly7_A          267 IVTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL  339 (372)
T ss_dssp             HHTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence                2235677888887777777899999999999999886  77777777777888999999999999887654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=93.99  E-value=0.8  Score=41.94  Aligned_cols=76  Identities=8%  Similarity=0.065  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHh
Q 040801          176 PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  255 (323)
                      .+.|.++|+.....- .-+...+...++-..+.|+.+.|..+|+++.     .....|...++-=.+.|+.+.+..++++
T Consensus       336 ~~~ar~ife~al~~~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~  409 (493)
T 2uy1_A          336 RATPYNIFSSGLLKH-PDSTLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQ  409 (493)
T ss_dssp             SHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            477888887776542 1123344555666667778888888887762     2456677777766677888877777776


Q ss_pred             cc
Q 040801          256 ML  257 (323)
Q Consensus       256 m~  257 (323)
                      ..
T Consensus       410 ~~  411 (493)
T 2uy1_A          410 KM  411 (493)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=93.99  E-value=0.36  Score=43.46  Aligned_cols=92  Identities=10%  Similarity=-0.051  Sum_probs=71.2

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcC---CCCC----hHHHHHHHHHHhccCChHHHHHHHHHHHHh---CCc---c-C
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIEN---VKPN----AVTLVNVLTARARARDLRTVKRVHKCVDES---GFW---S-H  229 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g---~~p~----~~t~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~---p-~  229 (323)
                      +..+.+.|   ++++|++++++..+..   ..|+    ..+++.+...|...|++++|+.++++..+.   -+.   | .
T Consensus       294 ie~~~~~g---~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~  370 (429)
T 3qwp_A          294 IEELKAHW---KWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVR  370 (429)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHH
T ss_pred             HHHHHhhc---cHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHH
Confidence            45566677   6799999998887531   2332    468999999999999999999999988642   122   2 2


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..+++.|-..|...|++++|..++++..+
T Consensus       371 a~~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          371 GVQVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            45688899999999999999999998754

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=93.56  E-value=0.47  Score=32.03  Aligned_cols=56  Identities=7%  Similarity=-0.086  Sum_probs=38.5

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChH-HHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAV-TLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~-t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      ..+.+.|   ++++|++.|++..... ..+.. .|..+-..+...|++++|...+++..+.
T Consensus         8 ~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            8 KELINQG---DIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHT---CHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcC---CHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3455666   5678888887776643 22445 6777777777788888888888877765

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=93.38  E-value=3.3  Score=35.21  Aligned_cols=196  Identities=3%  Similarity=-0.106  Sum_probs=133.5

Q ss_pred             CchHHHHHHHHHHHhcCCCCCccch-hHHHhcccCC---CCChhhHHHHHHHHHhCC--ChHHHHHHHHHHHHCCCCCCc
Q 040801           52 TMRELKQIHAQMLRTSLFFDPCADY-HVRLVFSQIS---NPTIYTCNSIVRGYTNKN--LHHEAFLFYHEMIVQGLIPDR  125 (323)
Q Consensus        52 ~~~~a~~i~~~m~~~~~~~~~y~~~-~a~~lf~~m~---~~~~~~~~~li~~~~~~g--~~~~A~~~~~~m~~~g~~p~~  125 (323)
                      ++..+...+....+.|-      .. +|.++++.+.   +-+...||.-=..+...|  ++++++++++.+.... +-+.
T Consensus        31 ~y~~~~~~~~a~~~~~e------~s~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y  103 (306)
T 3dra_A           31 DYKQIMGLLLALMKAEE------YSERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNY  103 (306)
T ss_dssp             HHHHHHHHHHHHHHTTC------CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCC
T ss_pred             HHHHHHHHHHHHHHcCC------CCHHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccH
Confidence            45677777777777664      12 6777776655   445566887777777888  9999999999998742 2233


Q ss_pred             ccHHHHHHHh----cch---hh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh
Q 040801          126 FMFPSLFKSC----ADI---YV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA  195 (323)
Q Consensus       126 ~ty~~ll~~~----~~~---~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~  195 (323)
                      .+|+.--..+    .+.   ++   +.++++.+.+.. .-+-.+|+.---.+.+.|.. +.+++++.++++.+... -|.
T Consensus       104 ~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~-~~~~EL~~~~~~i~~d~-~N~  180 (306)
T 3dra_A          104 QIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLH-NDAKELSFVDKVIDTDL-KNN  180 (306)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHCT-TCH
T ss_pred             HHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccc-ChHHHHHHHHHHHHhCC-CCH
Confidence            3444332222    212   22   778888887754 34667777766667777744 12399999999998774 377


Q ss_pred             HHHHHHHHHHhccCC------hHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCH-HHHHHHHHhccC
Q 040801          196 VTLVNVLTARARARD------LRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFV-SRAWDLFVKMLF  258 (323)
Q Consensus       196 ~t~~~li~~~~~~~~------~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~  258 (323)
                      ..|+---..+.+.+.      ++++...++.+.+.. +-|...|+.+-..+.+.|+. +++.++.++..+
T Consensus       181 sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~  249 (306)
T 3dra_A          181 SAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVD  249 (306)
T ss_dssp             HHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEE
T ss_pred             HHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHh
Confidence            788766666666666      778888888887764 34788888888888888874 446667777654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=92.34  E-value=1.2  Score=30.26  Aligned_cols=65  Identities=12%  Similarity=-0.066  Sum_probs=39.1

Q ss_pred             CChHHHHHHHHHHhccCC---hHHHHHHHHHHHHhCCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          193 PNAVTLVNVLTARARARD---LRTVKRVHKCVDESGFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~---~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .|...+..+-.++...++   .++|..++++..+.  .|+ ......+-..+.+.|++++|...|+++.+.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            344555555555543333   56777777777665  343 444445555677777777777777777665

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=92.20  E-value=5.5  Score=34.79  Aligned_cols=139  Identities=7%  Similarity=-0.155  Sum_probs=92.9

Q ss_pred             CCChhhHHHHHHHHHh--CC---ChHHHHHHHHHHHHCCCCCCc-ccHHHHHHHhcc-------hhh-HHHHHHHHHH--
Q 040801           87 NPTIYTCNSIVRGYTN--KN---LHHEAFLFYHEMIVQGLIPDR-FMFPSLFKSCAD-------IYV-EKQLHSQAIK--  150 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~--~g---~~~~A~~~~~~m~~~g~~p~~-~ty~~ll~~~~~-------~~~-a~~~~~~m~~--  150 (323)
                      +.+...|...+++...  .+   ...+|.++|++-.+.  .|+- ..|..+--++.-       .+. ...+-..+..  
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~  268 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIV  268 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHH
Confidence            5577889998876553  23   358899999998773  5653 334433222210       111 2211112211  


Q ss_pred             -c-CCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          151 -F-GLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       151 -~-g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                       . .-..+..+|..+-..+...|   ++++|.+.+++....+  |+...|..+=..+...|+.++|...+++....  .|
T Consensus       269 a~~~~~~~a~~~~alal~~l~~g---d~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P  341 (372)
T 3ly7_A          269 TLPELNNLSIIYQIKAVSALVKG---KTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RP  341 (372)
T ss_dssp             TCGGGTTCHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SC
T ss_pred             hcccCCcCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CC
Confidence             1 22457788888777777778   7799999999999876  88888877777888999999999999998876  46


Q ss_pred             ChhhHH
Q 040801          229 HVELKT  234 (323)
Q Consensus       229 ~~~~~~  234 (323)
                      ...+|.
T Consensus       342 ~~~t~~  347 (372)
T 3ly7_A          342 GANTLY  347 (372)
T ss_dssp             SHHHHH
T ss_pred             CcChHH
Confidence            665553

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=92.14  E-value=0.38  Score=36.69  Aligned_cols=93  Identities=9%  Similarity=-0.129  Sum_probs=63.4

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCCh----------HHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhc
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDL----------RTVKRVHKCVDESGFWS-HVELKTTLMDAYCKC  243 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~----------~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~  243 (323)
                      .+++|.+.++.-.+.. .-+...|+.+=.++...+++          ++|...|++..+.  .| +...|..+=.+|.+.
T Consensus        17 ~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           17 LFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHh
Confidence            4578888887777654 33666777666677766554          5888888887776  34 456778888888776


Q ss_pred             C-----------CHHHHHHHHHhccCCCCchhhhHHHhhh
Q 040801          244 K-----------FVSRAWDLFVKMLFPWNNYGQWAMSATV  272 (323)
Q Consensus       244 g-----------~~~~a~~~~~~m~~~~~~~~~~~~~~~~  272 (323)
                      |           ++++|.+.|++..+-  +|....|..++
T Consensus        94 g~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al  131 (158)
T 1zu2_A           94 AFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSL  131 (158)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             cccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            4           899999999988764  44444443333

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=92.07  E-value=5.5  Score=34.52  Aligned_cols=218  Identities=8%  Similarity=-0.028  Sum_probs=129.5

Q ss_pred             hhcCCCchHHHHHHHHHHHhcCCCCC----ccc----------h-hHHHhcccCC---CCChhhHHHHHHHHHhC-C-Ch
Q 040801           47 LEKCSTMRELKQIHAQMLRTSLFFDP----CAD----------Y-HVRLVFSQIS---NPTIYTCNSIVRGYTNK-N-LH  106 (323)
Q Consensus        47 ~~~~~~~~~a~~i~~~m~~~~~~~~~----y~~----------~-~a~~lf~~m~---~~~~~~~~~li~~~~~~-g-~~  106 (323)
                      +.+....++|+.+.+.+....  |+.    +.|          . ++.++++.+.   +.+...|+.--..+.+. + ++
T Consensus        64 ~~~~e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~  141 (349)
T 3q7a_A           64 AAKEEKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDP  141 (349)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCC
T ss_pred             HHhCCCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCCh
Confidence            344445678999999988763  444    111          1 5555555543   55667787766666665 6 78


Q ss_pred             HHHHHHHHHHHHCCCCCCcccHHHH---HHHhcchh--------hHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC-
Q 040801          107 HEAFLFYHEMIVQGLIPDRFMFPSL---FKSCADIY--------VEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD-  174 (323)
Q Consensus       107 ~~A~~~~~~m~~~g~~p~~~ty~~l---l~~~~~~~--------~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~-  174 (323)
                      ++++++++.+.+.. +-|..+|+.-   +..+.+..        ++.+....+.+.. .-|...|+..-..+.+.++.. 
T Consensus       142 ~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~  219 (349)
T 3q7a_A          142 VSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAET  219 (349)
T ss_dssp             HHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcccccc
Confidence            88888888887642 2244444432   33334433        3566666666654 346677877777777776320 


Q ss_pred             ---ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCCh--------------------HHHHHHHHHHHHhC-----C
Q 040801          175 ---QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDL--------------------RTVKRVHKCVDESG-----F  226 (323)
Q Consensus       175 ---~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~--------------------~~a~~~~~~m~~~g-----~  226 (323)
                         .++++++.+++..... .-|...|+-+-..+.+.|..                    .........+...+     -
T Consensus       220 ~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  298 (349)
T 3q7a_A          220 SSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTP  298 (349)
T ss_dssp             CHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCC
T ss_pred             chHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccC
Confidence               1577888888777654 23666776555555444432                    12222222222211     0


Q ss_pred             ccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC--CCchhhhHHH
Q 040801          227 WSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP--WNNYGQWAMS  269 (323)
Q Consensus       227 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~~~~  269 (323)
                      .++......|.+.|...|+.++|.++++.+.++  ++....|.+.
T Consensus       299 ~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~~dpir~~yw~~~  343 (349)
T 3q7a_A          299 LPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEYDQMRAGYWEFR  343 (349)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhChHHHHHHHHH
Confidence            246677788888999999999999999988643  4555666443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=92.05  E-value=1.7  Score=41.95  Aligned_cols=86  Identities=16%  Similarity=0.112  Sum_probs=52.1

Q ss_pred             CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHH
Q 040801          155 SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKT  234 (323)
Q Consensus       155 ~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~  234 (323)
                      .+...|..|-..+.+.|   +++.|.+.|..+.+         |..+...+...|+.+...++-+.....|      .++
T Consensus       679 ~~~~~W~~la~~al~~~---~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~------~~~  740 (814)
T 3mkq_A          679 SAEMKWRALGDASLQRF---NFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTG------KFN  740 (814)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTT------CHH
T ss_pred             CcHhHHHHHHHHHHHcC---CHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcC------chH
Confidence            34567777777777777   55777777776642         2234444444556665555554444443      245


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccC
Q 040801          235 TLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       235 ~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      .-..+|.+.|++++|.+++.++.+
T Consensus       741 ~A~~~~~~~g~~~~a~~~~~~~~~  764 (814)
T 3mkq_A          741 LAFNAYWIAGDIQGAKDLLIKSQR  764 (814)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHcCC
Confidence            555566677777777777777654

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=91.96  E-value=1.6  Score=32.92  Aligned_cols=81  Identities=14%  Similarity=0.009  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccC---ChHHHHHHHHHHHHhCCcc--ChhhHHHHHHHHHhcCCHHHHHH
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARAR---DLRTVKRVHKCVDESGFWS--HVELKTTLMDAYCKCKFVSRAWD  251 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~---~~~~a~~~~~~m~~~g~~p--~~~~~~~li~~~~~~g~~~~a~~  251 (323)
                      ..+.+-|.+....|. ++..+--.+-.++++++   +++++..+++...+.. .|  ....+-.|--+|.+.|++++|.+
T Consensus        15 ~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHH
Confidence            455566666555554 67777667888888888   6778999999988765 24  23334445557799999999999


Q ss_pred             HHHhccCC
Q 040801          252 LFVKMLFP  259 (323)
Q Consensus       252 ~~~~m~~~  259 (323)
                      .++.+.+.
T Consensus        93 y~~~lL~i  100 (152)
T 1pc2_A           93 YVRGLLQT  100 (152)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            99988764

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=91.72  E-value=3.1  Score=30.88  Aligned_cols=109  Identities=14%  Similarity=0.018  Sum_probs=79.5

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHC------CCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHH
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQ------GLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~------g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      ..+...=..+.+.|++++|.+.|.+-.+.      .-.|+...+                 ..+.    ..+...|..+-
T Consensus        12 ~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~-----------------~~~~----~~~~~~~~nla   70 (162)
T 3rkv_A           12 EALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEW-----------------VELD----RKNIPLYANMS   70 (162)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHH-----------------HHHH----HTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHH-----------------HHHH----HHHHHHHHHHH
Confidence            34556667888999999999999886542      001111100                 1111    12356788888


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .+|.+.|   ++++|+..+++..... ..+...|..+-.++...|++++|...++...+.
T Consensus        71 ~~~~~~~---~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           71 QCYLNIG---DLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhcC---cHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            9999999   7799999999988754 346788889999999999999999999998876

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=91.59  E-value=3.2  Score=30.75  Aligned_cols=141  Identities=7%  Similarity=-0.032  Sum_probs=91.0

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHH
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEA  179 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a  179 (323)
                      +.-.|.+++..++..+....   -+..-||.+|-.....-+..-+++.+..-|--.|..          .+|   +...+
T Consensus        17 ~ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis----------~C~---NlKrV   80 (172)
T 1wy6_A           17 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLD----------KCQ---NLKSV   80 (172)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGG----------GCS---CTHHH
T ss_pred             HHHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhcCcH----------hhh---cHHHH
Confidence            34568888888888887653   234456666666555555666677776666444433          233   22333


Q ss_pred             HHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          180 IKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       180 ~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ..-+-.+     .-+..-+...|..+...|.-++-.++...+.. .-+|++...-.+-.+|.+.|+..+|.+++.+.-++
T Consensus        81 i~C~~~~-----n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~k  154 (172)
T 1wy6_A           81 VECGVIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKK  154 (172)
T ss_dssp             HHHHHHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHh-----cchHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Confidence            3333222     23445566677778888888888888887533 33667777778888888888888888888887777


Q ss_pred             CCc
Q 040801          260 WNN  262 (323)
Q Consensus       260 ~~~  262 (323)
                      |..
T Consensus       155 G~k  157 (172)
T 1wy6_A          155 GEK  157 (172)
T ss_dssp             TCH
T ss_pred             hhH
Confidence            644

>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=91.12  E-value=0.76  Score=41.35  Aligned_cols=69  Identities=9%  Similarity=-0.041  Sum_probs=50.4

Q ss_pred             hhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCc-hHHHHHHHHHHHh
Q 040801           91 YTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASD-SFLHNTLINMYSS  169 (323)
Q Consensus        91 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~-~~~~~~li~~~~~  169 (323)
                      .+++.|-..|...|++++|..++++..+                         +++..... -.|+ ..+++.|-..|..
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~-------------------------i~~~~lG~-~Hp~~a~~l~nLa~~~~~  394 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIK-------------------------PYSKHYPV-YSLNVASMWLKLGRLYMG  394 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-------------------------HHHHHSCS-SCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHH-------------------------HHHHHcCC-CChHHHHHHHHHHHHHHh
Confidence            6799999999999999999999988753                         11222111 2343 4568888888888


Q ss_pred             cCCCCChHHHHHHHHHHHH
Q 040801          170 CWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~  188 (323)
                      .|   ++++|..++++-.+
T Consensus       395 qg---~~~eA~~~~~~Al~  410 (433)
T 3qww_A          395 LE---NKAAGEKALKKAIA  410 (433)
T ss_dssp             TT---CHHHHHHHHHHHHH
T ss_pred             cc---CHHHHHHHHHHHHH
Confidence            88   66888888877643

>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=90.84  E-value=10  Score=35.23  Aligned_cols=130  Identities=8%  Similarity=-0.060  Sum_probs=78.8

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccC-ChHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARAR-DLRTVKRVHK  219 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~-~~~~a~~~~~  219 (323)
                      +.+.++.+.+.. .-+..+|+.---.+.+.|.. +++++++.++++.+... -|...|+---..+.+.| ..+++...++
T Consensus        92 eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~~-~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~~~~  168 (567)
T 1dce_A           92 ELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEP-NWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTD  168 (567)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSC-CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccc-cHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHHHHH
Confidence            555566655543 22344555554455555533 45788888888877653 36677776666666666 6777777777


Q ss_pred             HHHHhCCccChhhHHHHHHHHHhc--------------CCHHHHHHHHHhccC-CCCchhhhHHHhhhcc
Q 040801          220 CVDESGFWSHVELKTTLMDAYCKC--------------KFVSRAWDLFVKMLF-PWNNYGQWAMSATVGP  274 (323)
Q Consensus       220 ~m~~~g~~p~~~~~~~li~~~~~~--------------g~~~~a~~~~~~m~~-~~~~~~~~~~~~~~~~  274 (323)
                      ++.+.. .-|...|+..-..+.+.              +.++++.+.+++..+ .+.+...|.|...+-.
T Consensus       169 ~~I~~~-p~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~  237 (567)
T 1dce_A          169 SLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLG  237 (567)
T ss_dssp             TTTTTT-CCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHS
T ss_pred             HHHHHC-CCCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHh
Confidence            766543 22556666555555542              456778877776654 4567777865554433

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=90.72  E-value=0.98  Score=30.35  Aligned_cols=58  Identities=9%  Similarity=-0.024  Sum_probs=48.0

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHhCCccChh-hHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          201 VLTARARARDLRTVKRVHKCVDESGFWSHVE-LKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       201 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .-..+...|++++|...++...+.. +-+.. .|..+-.+|.+.|++++|.+.|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3456778899999999999998863 22456 7888889999999999999999998764

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=89.20  E-value=2.4  Score=29.21  Aligned_cols=65  Identities=14%  Similarity=-0.075  Sum_probs=49.2

Q ss_pred             ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC------CccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          194 NAVTLVNVLTARARARDLRTVKRVHKCVDESG------FWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       194 ~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      +..-+-.|=..+...|++..|...++...+.-      -.+....+..|-.+|.+.|++++|...+++..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            44445566677778888999888888876531      123456788899999999999999999998865

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=88.02  E-value=6.2  Score=29.66  Aligned_cols=85  Identities=5%  Similarity=-0.054  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCC--ChHHHHHHHHHHhccCChHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKP--NAVTLVNVLTARARARDLRTVKRVH  218 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p--~~~t~~~li~~~~~~~~~~~a~~~~  218 (323)
                      +++-|....+.|. ++..+.-.+--++++.+...+.++++.+|++..+.+ .|  +...+=.+--++.+.|++++|.+.+
T Consensus        17 ~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~   94 (152)
T 1pc2_A           17 FEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYV   94 (152)
T ss_dssp             HHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHHH
Confidence            4455555555554 677777777778888775545679999999988865 34  2344444666779999999999999


Q ss_pred             HHHHHhCCccC
Q 040801          219 KCVDESGFWSH  229 (323)
Q Consensus       219 ~~m~~~g~~p~  229 (323)
                      +.+.+.  +|+
T Consensus        95 ~~lL~i--eP~  103 (152)
T 1pc2_A           95 RGLLQT--EPQ  103 (152)
T ss_dssp             HHHHHH--CTT
T ss_pred             HHHHhc--CCC
Confidence            999886  564

>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=87.51  E-value=2  Score=38.55  Aligned_cols=89  Identities=6%  Similarity=-0.044  Sum_probs=49.5

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHC---CCCCCc----ccHHHHHHHhcchhh---HHHHHHHHHHc-----C-CCCc-hH
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQ---GLIPDR----FMFPSLFKSCADIYV---EKQLHSQAIKF-----G-LASD-SF  158 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~---g~~p~~----~ty~~ll~~~~~~~~---a~~~~~~m~~~-----g-~~~~-~~  158 (323)
                      .+..+.+.|++++|.+++++..+.   -+.|+.    .+++.|...|...|+   |+.+++...+.     | ..|+ ..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            355566777888888888777542   133333    355555556655555   55555544322     2 2332 34


Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHH
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRME  187 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~  187 (323)
                      +++.|-..|...|   ++++|+.++++..
T Consensus       373 ~l~nLa~~~~~~g---~~~eA~~~~~~Al  398 (429)
T 3qwp_A          373 QVMKVGKLQLHQG---MFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC---CHHHHHHHHHHHH
Confidence            4666666666666   4466666665543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=85.17  E-value=8.3  Score=37.19  Aligned_cols=114  Identities=13%  Similarity=0.043  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc------CCCCChH------HH-HHHH----H
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE------NVKPNAV------TL-VNVL----T  203 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~------g~~p~~~------t~-~~li----~  203 (323)
                      +..+++.+.+..-..+......+|..+.+.++  .--+|.++..+-.+.      ...+...      .+ ..|+    +
T Consensus       268 a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~--~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~LL~~Qa~  345 (754)
T 4gns_B          268 TIDYLKGLTKKDPIHDIYYKTAMITILDHIET--KELDMITILNETLDPLLSLLNDLPPRDADSARLMNCMSDLLNIQTN  345 (754)
T ss_dssp             HHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGG--GHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCchhHHHHHHHHHHHHHhhh--hhHHHHHHHHHHHHHhhhhhhhhcccccccccccCcchHHHHHHHH
Confidence            77888888776532233333344444444332  113456666554321      1222111      00 1122    3


Q ss_pred             HHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          204 ARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       204 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      -|...|+++.|..+-++....- +-+..+|..|..+|.+.|+++.|+-.++.+.
T Consensus       346 FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          346 FLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            4667899999999999987762 3357899999999999999999999999985

>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=84.59  E-value=6.2  Score=34.70  Aligned_cols=130  Identities=10%  Similarity=0.032  Sum_probs=83.2

Q ss_pred             ChhhHHHHHHHHH---hCCChHHHHHHHHHHHH--CC-CCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHH
Q 040801           89 TIYTCNSIVRGYT---NKNLHHEAFLFYHEMIV--QG-LIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNT  162 (323)
Q Consensus        89 ~~~~~~~li~~~~---~~g~~~~A~~~~~~m~~--~g-~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~  162 (323)
                      |...|..++....   ..|+.++|.+.+++...  +| .-++...+. .+..      ...-++++.       ..+...
T Consensus       111 D~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~-w~~~------~r~~l~~~~-------~~a~~~  176 (388)
T 2ff4_A          111 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQ-FVEP------FATALVEDK-------VLAHTA  176 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTST-THHH------HHHHHHHHH-------HHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCCchh-HHHH------HHHHHHHHH-------HHHHHH
Confidence            4445666665433   35888888888887755  23 222221110 0000      001111111       123455


Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH-----HhCCccChhhHHHH
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD-----ESGFWSHVELKTTL  236 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~-----~~g~~p~~~~~~~l  236 (323)
                      ++..+...|   +.++++..+....... ..+...|..+|.++.+.|+..+|.+.|+.+.     +.|+.|+..+-...
T Consensus       177 ~~~~~l~~g---~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          177 KAEAEIACG---RASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            778888888   6689999888887654 4578899999999999999999999998875     46999987764433

>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=84.54  E-value=2.7  Score=37.10  Aligned_cols=68  Identities=15%  Similarity=-0.021  Sum_probs=55.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-----CCchhhh
Q 040801          198 LVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-----WNNYGQW  266 (323)
Q Consensus       198 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~  266 (323)
                      ...++..+...|+.+++...+..+.... +.+...|..+|.+|.+.|+..+|.+.|+...+.     |.+|...
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~  246 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPT  246 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence            3456677788999999999888887653 447889999999999999999999999998654     7777665

>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=84.34  E-value=11  Score=28.40  Aligned_cols=108  Identities=13%  Similarity=-0.091  Sum_probs=75.1

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCC
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWC  172 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~  172 (323)
                      +...=..+.+.|++++|++.|++-.+-  .|+...=    .++    +..           ..+...|+.+-.++.+.| 
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~----~a~----~~~-----------~~~a~a~~n~g~al~~Lg-   71 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPE----EAF----DHA-----------GFDAFCHAGLAEALAGLR-   71 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTT----SCC----CHH-----------HHHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcch----hhh----hhc-----------cchHHHHHHHHHHHHHCC-
Confidence            444555678889999999999987652  2321100    000    000           012348899999999999 


Q ss_pred             CCChHHHHHHHHHHHHc-----CCCCC-hHHH----HHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          173 LDQPDEAIKIFYRMEIE-----NVKPN-AVTL----VNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~-----g~~p~-~~t~----~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                        ++++|+..+++-.+.     .+.|+ ...|    ...=.++...|++++|...|++..+.
T Consensus        72 --r~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel  131 (159)
T 2hr2_A           72 --SFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  131 (159)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             --CHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhc
Confidence              668999999888764     12564 4577    77888999999999999999999753

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=82.72  E-value=11  Score=30.49  Aligned_cols=143  Identities=11%  Similarity=-0.042  Sum_probs=74.8

Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCcc---cHHHHHHHhcchhhHHHHHHHHHHcCCCCchHH------------HHHH
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDRF---MFPSLFKSCADIYVEKQLHSQAIKFGLASDSFL------------HNTL  163 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~---ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~------------~~~l  163 (323)
                      ..+..|+.+    +++.+.+.|..++..   -++.|..++ ..|. .++.+.+.+.|..++...            ..+.
T Consensus        78 ~A~~~~~~~----~v~~Ll~~g~~~~~~~~~g~t~L~~A~-~~~~-~~~~~~Ll~~g~~~~~~~~~~~~~~~~~~~g~t~  151 (285)
T 1wdy_A           78 LAAIAGSVK----LLKLFLSKGADVNECDFYGFTAFMEAA-VYGK-VKALKFLYKRGANVNLRRKTKEDQERLRKGGATA  151 (285)
T ss_dssp             HHHHHTCHH----HHHHHHHTTCCTTCBCTTCCBHHHHHH-HTTC-HHHHHHHHHTTCCTTCCCCCCHHHHHTTCCCCCH
T ss_pred             HHHHcCCHH----HHHHHHHcCCCCCccCcccCCHHHHHH-HhCC-HHHHHHHHHhCCCcccccccHHHHHhhccCCCcH
Confidence            334455543    455555667655432   233443333 2332 345566667776654321            1234


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHc-CCCCCh---HHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhh--HHHHH
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIE-NVKPNA---VTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVEL--KTTLM  237 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~-g~~p~~---~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~--~~~li  237 (323)
                      +...++.|   +.+ .   ++.+.+. |..++.   .-.+. +...+..++......+.+.+.+.|..++...  -.+.+
T Consensus       152 L~~A~~~~---~~~-~---v~~Ll~~~~~~~~~~~~~g~t~-l~~a~~~~~~~~~~~i~~~Ll~~g~~~~~~~~~g~t~L  223 (285)
T 1wdy_A          152 LMDAAEKG---HVE-V---LKILLDEMGADVNACDNMGRNA-LIHALLSSDDSDVEAITHLLLDHGADVNVRGERGKTPL  223 (285)
T ss_dssp             HHHHHHHT---CHH-H---HHHHHHTSCCCTTCCCTTSCCH-HHHHHHCSCTTTHHHHHHHHHHTTCCSSCCCTTSCCHH
T ss_pred             HHHHHHcC---CHH-H---HHHHHHhcCCCCCccCCCCCCH-HHHHHHccccchHHHHHHHHHHcCCCCCCcCCCCCcHH
Confidence            44555555   222 2   3333333 444432   22333 3333445565556677888888888776542  23556


Q ss_pred             HHHHhcCCHHHHHHHHHh
Q 040801          238 DAYCKCKFVSRAWDLFVK  255 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~  255 (323)
                      ..-++.|+.+-+..+++.
T Consensus       224 ~~A~~~~~~~~v~~Ll~~  241 (285)
T 1wdy_A          224 ILAVEKKHLGLVQRLLEQ  241 (285)
T ss_dssp             HHHHHTTCHHHHHHHHHS
T ss_pred             HHHHHcCCHHHHHHHHhc
Confidence            666778888887777774

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=81.61  E-value=14  Score=27.94  Aligned_cols=59  Identities=10%  Similarity=0.059  Sum_probs=36.3

Q ss_pred             hHHHHHHHHHHHHcCCCC-ChHHHHHHHHHHhcc-----------CChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          176 PDEAIKIFYRMEIENVKP-NAVTLVNVLTARARA-----------RDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p-~~~t~~~li~~~~~~-----------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      +++|+..|++-..-.  | +..+|..+=.+|...           |++++|...|++..+.  .|+...|..-+.
T Consensus        62 ~~eAi~~le~AL~ld--P~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~  132 (158)
T 1zu2_A           62 IQEAITKFEEALLID--PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            357777776666533  3 445666666666655           3777788877777765  466555544333

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=80.75  E-value=26  Score=29.99  Aligned_cols=170  Identities=8%  Similarity=-0.030  Sum_probs=111.0

Q ss_pred             HhCCChH-HHHHHHHHHHHCCCCCCccc-HHH---HHHHhcch----------hhHHHHHHHHHHcCCCCchHHHHHHHH
Q 040801          101 TNKNLHH-EAFLFYHEMIVQGLIPDRFM-FPS---LFKSCADI----------YVEKQLHSQAIKFGLASDSFLHNTLIN  165 (323)
Q Consensus       101 ~~~g~~~-~A~~~~~~m~~~g~~p~~~t-y~~---ll~~~~~~----------~~a~~~~~~m~~~g~~~~~~~~~~li~  165 (323)
                      .+.|.++ +|+++++.+...  .|+..| |+.   ++....+.          .++..+++.+.+.. .-+..+|+.---
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~--nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~w  116 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCW  116 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            3455544 788888888763  344433 221   23333221          11666666666644 235667776666


Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC-hHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc-
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD-LRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC-  243 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~-~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~-  243 (323)
                      .+.+.|.. .+++++++++.+..... -|...|+---..+...|. .+++...++.+.+.. .-|...|+..-..+.+. 
T Consensus       117 lL~~l~~~-~~~~EL~~~~k~l~~dp-rNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~-p~N~SAW~~R~~ll~~l~  193 (331)
T 3dss_A          117 LLSRLPEP-NWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLH  193 (331)
T ss_dssp             HHHHCSSC-CHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHHS
T ss_pred             HHhccCcc-cHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhh
Confidence            66666643 46899999999988763 477788777777777777 588888899988765 33666776665555544 


Q ss_pred             -------------CCHHHHHHHHHhccC-CCCchhhhHHHhhhccCC
Q 040801          244 -------------KFVSRAWDLFVKMLF-PWNNYGQWAMSATVGPQG  276 (323)
Q Consensus       244 -------------g~~~~a~~~~~~m~~-~~~~~~~~~~~~~~~~~~  276 (323)
                                   +.++++.+.+++... .+.+...|.|...+-...
T Consensus       194 ~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~  240 (331)
T 3dss_A          194 PQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAG  240 (331)
T ss_dssp             CCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSS
T ss_pred             hccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence                         457888888887764 467889998776665444

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=80.59  E-value=11  Score=25.65  Aligned_cols=70  Identities=10%  Similarity=-0.187  Sum_probs=52.5

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc------CCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE------NVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH  229 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~------g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  229 (323)
                      +..-+-.|=..+.+.|   +++.|...|++....      +-.+....+..+-.++.+.|+++.|...++++.+.  .|+
T Consensus         4 sa~dc~~lG~~~~~~~---~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~   78 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEA---DYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPE   78 (104)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             CHHHHHHHHHHHHHcc---chHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCC
Confidence            3444556667777777   779999999887653      11346678888999999999999999999998875  455


Q ss_pred             h
Q 040801          230 V  230 (323)
Q Consensus       230 ~  230 (323)
                      .
T Consensus        79 ~   79 (104)
T 2v5f_A           79 H   79 (104)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=80.22  E-value=28  Score=30.04  Aligned_cols=96  Identities=7%  Similarity=-0.145  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChH--------HHHHHHHHHHHhCCccChhhHHHHHHHHHhcCC---
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLR--------TVKRVHKCVDESGFWSHVELKTTLMDAYCKCKF---  245 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~--------~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~---  245 (323)
                      ++++++++.+.... .-|...|+---..+.+.|..+        ++....+++.+.. .-|-..|+..-..+.+.|+   
T Consensus       142 ~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~  219 (349)
T 3q7a_A          142 VSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAET  219 (349)
T ss_dssp             HHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcccccc
Confidence            56666666666543 225555554433333333343        6666667766653 2255666666666666665   


Q ss_pred             ----HHHHHHHHHhccC-CCCchhhhHHHhhhcc
Q 040801          246 ----VSRAWDLFVKMLF-PWNNYGQWAMSATVGP  274 (323)
Q Consensus       246 ----~~~a~~~~~~m~~-~~~~~~~~~~~~~~~~  274 (323)
                          ++++.+.+++... .+.+...|.|...+-.
T Consensus       220 ~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~  253 (349)
T 3q7a_A          220 SSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLK  253 (349)
T ss_dssp             CHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence                6777777776653 3567777866444433

---

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	323
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.95
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.9
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.69
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.65
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.59
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.39
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.82
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.73
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.66
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.49
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.47
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.44
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.36
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.26
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.22
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.17
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.14
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.09
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.09
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	96.98
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.97
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	96.78
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	96.66
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.64
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	96.62
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.53
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	96.27
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.25
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.21
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.21
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.96
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	95.9
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	95.86
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	95.14
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	95.02
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.93
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	94.82
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	94.8
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	94.69
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	93.91
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	93.42
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	93.28
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	92.12
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	91.83
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	91.47
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	91.22
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	89.47
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	87.58
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	82.56
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	82.52
d1khda1	69	Anthranilate phosphoribosyltransferase (TrpD) {Pec	82.07
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	80.94
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	80.79

>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=98.95  E-value=1.2e-07  Score=81.23  Aligned_cols=164  Identities=10%  Similarity=-0.004  Sum_probs=105.4

Q ss_pred             CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHH
Q 040801           87 NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        87 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      +.+...|..+-..+...|++++|.+.|++...... .+...+..+-..+.+.|+   |...++...+.. .-+..+|..+
T Consensus       200 p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l  277 (388)
T d1w3ba_         200 PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNL  277 (388)
T ss_dssp             TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHH
T ss_pred             cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence            34556667777777777777777777777655422 233445555555555555   666666665543 1235566677


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHh
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCK  242 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~  242 (323)
                      ...|...|   ++++|.+.++...... +.+...+..+...+...|++++|...+++..+.  .| +...+..+-..|.+
T Consensus       278 ~~~~~~~~---~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~  351 (388)
T d1w3ba_         278 ANALKEKG---SVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQ  351 (388)
T ss_dssp             HHHHHHHS---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHcC---CHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence            77777777   5577777777665543 445666677777777777777777777776553  34 34556667777777


Q ss_pred             cCCHHHHHHHHHhccC
Q 040801          243 CKFVSRAWDLFVKMLF  258 (323)
Q Consensus       243 ~g~~~~a~~~~~~m~~  258 (323)
                      .|++++|...|++..+
T Consensus       352 ~g~~~~A~~~~~~al~  367 (388)
T d1w3ba_         352 QGKLQEALMHYKEAIR  367 (388)
T ss_dssp             TTCCHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            7777777777777654

>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=98.90  E-value=3e-07  Score=78.73  Aligned_cols=185  Identities=12%  Similarity=0.046  Sum_probs=143.3

Q ss_pred             ChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHH
Q 040801           89 TIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLI  164 (323)
Q Consensus        89 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li  164 (323)
                      +...+..+-..+...|++++|.+.+++..+.  .|+ ..+|..+-..+...|+   |...+....+.+. .+...+..+-
T Consensus       168 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~  244 (388)
T d1w3ba_         168 FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL--DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NHAVVHGNLA  244 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             hhHHHHhhcccccccCcHHHHHHHHHHHHHh--CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh-hHHHHHHHHH
Confidence            4566777788899999999999999988763  343 4567777777777777   8888888877653 4567788888


Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      ..|.+.|   ++++|.+.|++..+.. +-+..+|..+...+...|+.++|...++...+.. +.+...+..+...|.+.|
T Consensus       245 ~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  319 (388)
T d1w3ba_         245 CVYYEQG---LIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQG  319 (388)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHCC---CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCC
Confidence            9999999   7799999999987754 2356788999999999999999999999987753 456788889999999999


Q ss_pred             CHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhh
Q 040801          245 FVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a  284 (323)
                      ++++|.+.|++..+. +..+..| .+...+...   |+.++|
T Consensus       320 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~---g~~~~A  358 (388)
T d1w3ba_         320 NIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQ---GKLQEA  358 (388)
T ss_dssp             CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTT---TCCHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc---CCHHHH
Confidence            999999999998764 3334444 344444444   444444

>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=98.69  E-value=2.9e-06  Score=71.38  Aligned_cols=205  Identities=10%  Similarity=0.019  Sum_probs=150.6

Q ss_pred             HHHhhcCCCchHHHHHHHHHHHhcCCCCC----------ccch----hHHHhcccCC---CCChhhHHHHHHHHHhCCCh
Q 040801           44 LVSLEKCSTMRELKQIHAQMLRTSLFFDP----------CADY----HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLH  106 (323)
Q Consensus        44 i~~~~~~~~~~~a~~i~~~m~~~~~~~~~----------y~~~----~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~  106 (323)
                      -..+.+.|+++.|...|+...+.  .|+.          |...    .|.+.|++..   +.+...|..+...|...|++
T Consensus        26 g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~  103 (323)
T d1fcha_          26 GLRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQ  103 (323)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccc
Confidence            34567889999999999999875  4554          1111    7777776543   55678889999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCcccH----------HH------HHHHhcchhh---HHHHHHHHHHcC-CCCchHHHHHHHHH
Q 040801          107 HEAFLFYHEMIVQGLIPDRFMF----------PS------LFKSCADIYV---EKQLHSQAIKFG-LASDSFLHNTLINM  166 (323)
Q Consensus       107 ~~A~~~~~~m~~~g~~p~~~ty----------~~------ll~~~~~~~~---a~~~~~~m~~~g-~~~~~~~~~~li~~  166 (323)
                      ++|.+.+++.....  |+....          ..      .+..+...+.   +.+.+....+.. -..+..++..+-..
T Consensus       104 ~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~  181 (323)
T d1fcha_         104 RQACEILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL  181 (323)
T ss_dssp             HHHHHHHHHHHHTS--TTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH
T ss_pred             cccccchhhHHHhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHH
Confidence            99999999987632  221110          00      0111111122   556666655443 23467788888899


Q ss_pred             HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCC
Q 040801          167 YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKF  245 (323)
Q Consensus       167 ~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~  245 (323)
                      +...|   ++++|.+.|++..... +-+..+|..+-..+...|++++|...++...+.  .| +...|..+-.+|.+.|+
T Consensus       182 ~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~  255 (323)
T d1fcha_         182 FNLSG---EYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGA  255 (323)
T ss_dssp             HHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHH---HHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCC
Confidence            99999   7799999999987654 235778888999999999999999999999875  34 46678889999999999


Q ss_pred             HHHHHHHHHhccC
Q 040801          246 VSRAWDLFVKMLF  258 (323)
Q Consensus       246 ~~~a~~~~~~m~~  258 (323)
                      +++|.+.|++..+
T Consensus       256 ~~~A~~~~~~al~  268 (323)
T d1fcha_         256 HREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998754

>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=98.65  E-value=6.5e-07  Score=75.52  Aligned_cols=197  Identities=8%  Similarity=-0.033  Sum_probs=137.4

Q ss_pred             hHHHhcccCC---CCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC-CcccHHHHHHHhcchhh---HHHHHHHHH
Q 040801           77 HVRLVFSQIS---NPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP-DRFMFPSLFKSCADIYV---EKQLHSQAI  149 (323)
Q Consensus        77 ~a~~lf~~m~---~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~  149 (323)
                      +|.+.|++..   +.+...|..+-..|...|++++|.+.|.+..+.  .| +...+..+...+...|+   |.+.++...
T Consensus        37 ~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  114 (323)
T d1fcha_          37 NAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLEL--KPDNQTALMALAVSFTNESLQRQACEILRDWL  114 (323)
T ss_dssp             HHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcc--ccccccccccccccccccccccccccchhhHH
Confidence            7888887764   456788999999999999999999999988763  34 34566666677777777   777777776


Q ss_pred             HcCCCCchH----------------HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcC-CCCChHHHHHHHHHHhccCChH
Q 040801          150 KFGLASDSF----------------LHNTLINMYSSCWCLDQPDEAIKIFYRMEIEN-VKPNAVTLVNVLTARARARDLR  212 (323)
Q Consensus       150 ~~g~~~~~~----------------~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g-~~p~~~t~~~li~~~~~~~~~~  212 (323)
                      +..  |+..                .....+..+.+.+   ..+++.+.|.+..... -.++..++..+-..+...|+++
T Consensus       115 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~  189 (323)
T d1fcha_         115 RYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDS---LFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYD  189 (323)
T ss_dssp             HTS--TTTGGGCC---------------CTTHHHHHHH---HHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHH
T ss_pred             Hhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHhh---HHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHh
Confidence            543  2211                1111222223333   4577888887776533 2346678888888999999999


Q ss_pred             HHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHhhhccCCCCCcchhh
Q 040801          213 TVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSATVGPQGLVGRHSTA  284 (323)
Q Consensus       213 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~~~~~~~~~~~~~~a  284 (323)
                      +|...++...+.. +-+...|..+-..|.+.|++++|.+.|++..+. +..+..| .+...+...   |+.++|
T Consensus       190 ~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~---g~~~~A  259 (323)
T d1fcha_         190 KAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINL---GAHREA  259 (323)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH---TCHHHH
T ss_pred             hhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHC---CCHHHH
Confidence            9999999988763 224677888999999999999999999987653 3445555 444444444   444544

>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=98.59  E-value=4.7e-06  Score=70.02  Aligned_cols=177  Identities=8%  Similarity=0.007  Sum_probs=131.7

Q ss_pred             hHHHhcccC----CCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHH
Q 040801           77 HVRLVFSQI----SNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAI  149 (323)
Q Consensus        77 ~a~~lf~~m----~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~  149 (323)
                      .|.++|+.-    .+.+...|......+-+.|++++|..+|+++.+.........|...+..+.+.++   |.++++...
T Consensus        82 ~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al  161 (308)
T d2onda1          82 EAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAR  161 (308)
T ss_dssp             HHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            455555432    2556678888999999999999999999999875332223467788888777777   999999988


Q ss_pred             HcCCCCchHHHHHHHHH-HHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC-Cc
Q 040801          150 KFGLASDSFLHNTLINM-YSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG-FW  227 (323)
Q Consensus       150 ~~g~~~~~~~~~~li~~-~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~  227 (323)
                      +.+-. +...|-..... +...|   +.+.|.++|+...... .-+...|...+..+.+.|+++.|..+|++..+.. ..
T Consensus       162 ~~~~~-~~~~~~~~a~~e~~~~~---~~~~a~~i~e~~l~~~-p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~  236 (308)
T d2onda1         162 EDART-RHHVYVTAALMEYYCSK---DKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             TSTTC-CTHHHHHHHHHHHHTSC---CHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HhCCC-cHHHHHHHHHHHHHhcc---CHHHHHHHHHHHHHhh-hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCC
Confidence            76632 22233222222 23345   6689999999998753 4467889999999999999999999999987753 44


Q ss_pred             cC--hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          228 SH--VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       228 p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      |+  ...|...+.--.+.|+++.+..+++++.+
T Consensus       237 ~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            43  45788889888899999999999998754

>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=98.39  E-value=1.8e-05  Score=66.36  Aligned_cols=170  Identities=10%  Similarity=0.025  Sum_probs=120.0

Q ss_pred             CChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHH
Q 040801          104 NLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAI  180 (323)
Q Consensus       104 g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~  180 (323)
                      +..++|.++|++-.+...+-+...|........+.|+   +..+++.+.+........+|...+..+.+.|   +.++|.
T Consensus        78 ~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~---~~~~ar  154 (308)
T d2onda1          78 LFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAE---GIKSGR  154 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHH---CHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcC---ChHHHH
Confidence            3457888999888765443344445555555555555   9999999887654344567999999999999   669999


Q ss_pred             HHHHHHHHcCCCCChHHHHHHHH-HHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          181 KIFYRMEIENVKPNAVTLVNVLT-ARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       181 ~~~~~m~~~g~~p~~~t~~~li~-~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ++|+.....+. .+...|..... -+...|+.+.|..+|+.+.+. .+-+...|...++.+.+.|++++|..+|++..+.
T Consensus       155 ~i~~~al~~~~-~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~  232 (308)
T d2onda1         155 MIFKKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTS  232 (308)
T ss_dssp             HHHHHHHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHhCC-CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHh
Confidence            99999877552 23344433332 234568999999999999876 3445788999999999999999999999997554


Q ss_pred             -CCchh----hh-HHHhhhccCCCC
Q 040801          260 -WNNYG----QW-AMSATVGPQGLV  278 (323)
Q Consensus       260 -~~~~~----~~-~~~~~~~~~~~~  278 (323)
                       +..+.    .| .+...-..+|+.
T Consensus       233 ~~~~~~~~~~iw~~~~~fE~~~G~~  257 (308)
T d2onda1         233 GSLPPEKSGEIWARFLAFESNIGDL  257 (308)
T ss_dssp             SSSCGGGCHHHHHHHHHHHHHHSCH
T ss_pred             CCCChHHHHHHHHHHHHHHHHcCCH
Confidence             23332    35 555555555543

>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=97.82  E-value=0.00073  Score=56.39  Aligned_cols=191  Identities=8%  Similarity=-0.058  Sum_probs=101.6

Q ss_pred             CchHHHHHHHHHHHhcCCCCCccch-hHHHhcccCC---CCChhhHHHHHHHHHhCC-ChHHHHHHHHHHHHCCCCCCcc
Q 040801           52 TMRELKQIHAQMLRTSLFFDPCADY-HVRLVFSQIS---NPTIYTCNSIVRGYTNKN-LHHEAFLFYHEMIVQGLIPDRF  126 (323)
Q Consensus        52 ~~~~a~~i~~~m~~~~~~~~~y~~~-~a~~lf~~m~---~~~~~~~~~li~~~~~~g-~~~~A~~~~~~m~~~g~~p~~~  126 (323)
                      ++.+|...+......+=      +. +|.+++++..   +-+...|+..-..+.+.| ++++|++.++...+.. +-+..
T Consensus        41 ~~~~a~~~~~~~~~~~e------~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~  113 (315)
T d2h6fa1          41 KFRDVYDYFRAVLQRDE------RSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQ  113 (315)
T ss_dssp             HHHHHHHHHHHHHHHTC------CCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHHHHHHHHHHhCC------chHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-Hhhhh
Confidence            34555555554444321      12 5666665544   334455666666666655 3677777777665431 12345


Q ss_pred             cHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          127 MFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       127 ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      +|..+-..+.+.|+   |.+.+..+.+.. .-+...|+.+...+.+.|   ++++|++.|++..+.+. -+...|+.+-.
T Consensus       114 a~~~~~~~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~---~~~~Al~~~~~al~~~p-~n~~a~~~r~~  188 (315)
T d2h6fa1         114 VWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFK---LWDNELQYVDQLLKEDV-RNNSVWNQRYF  188 (315)
T ss_dssp             HHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHT---CCTTHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHhHHHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHH---hhHHHHHHHHHHHHHCC-ccHHHHHHHHH
Confidence            55555555555555   666666666643 224666777777777777   34677777777766442 24555655444


Q ss_pred             HHhccCC------hHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          204 ARARARD------LRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       204 ~~~~~~~------~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                      .+.+.+.      +++|...+....+.. +-+...|+-+-..+.. ...+++.+.++..
T Consensus       189 ~l~~~~~~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~  245 (315)
T d2h6fa1         189 VISNTTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQL  245 (315)
T ss_dssp             HHHHTTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHH
T ss_pred             HHHHccccchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHH
Confidence            4443333      445555555555542 1244455544444333 3345555555544

>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=97.73  E-value=0.0032  Score=52.31  Aligned_cols=211  Identities=9%  Similarity=-0.027  Sum_probs=147.0

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC-------------ccch--hHHHhcccCC---CCChhhHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP-------------CADY--HVRLVFSQIS---NPTIYTCNSIVRGYT  101 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~-------------y~~~--~a~~lf~~m~---~~~~~~~~~li~~~~  101 (323)
                      ++-+-..+.+.+.+++|.++++..++.  .|+.             ..+.  +|.+.++...   +.+..+|+.+-..+.
T Consensus        46 ~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~  123 (315)
T d2h6fa1          46 YDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVE  123 (315)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHH
Confidence            344555677778999999999999986  5666             1111  6777776553   667889999999999


Q ss_pred             hCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC---C
Q 040801          102 NKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD---Q  175 (323)
Q Consensus       102 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~---~  175 (323)
                      +.|++++|++.+++..+.. +-+...|..+-..+.+.++   |.+.++...+... -+...|+.+-..+.+.+...   .
T Consensus       124 ~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~~~~~~~~~~  201 (315)
T d2h6fa1         124 WLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYNDRAV  201 (315)
T ss_dssp             HHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSCSHHH
T ss_pred             hhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHHccccchhhh
Confidence            9999999999999998742 2356777777777777777   9999999988752 35667877776777766442   2


Q ss_pred             hHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhc--CCHHHHHHH
Q 040801          176 PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKC--KFVSRAWDL  252 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~--g~~~~a~~~  252 (323)
                      .++|++.+.+..... .-|...|+.+-..+ .....+++...++...+..-.+ +...+..+.+.|...  +..+.+...
T Consensus       202 ~~~ai~~~~~al~~~-P~~~~~~~~l~~ll-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~  279 (315)
T d2h6fa1         202 LEREVQYTLEMIKLV-PHNESAWNYLKGIL-QDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDI  279 (315)
T ss_dssp             HHHHHHHHHHHHHHS-TTCHHHHHHHHHHH-TTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHH
T ss_pred             hHHhHHHHHHHHHhC-CCchHHHHHHHHHH-HhcChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            578888888877654 23667777665544 4455678888888887654333 345566677766543  444555555


Q ss_pred             HHhc
Q 040801          253 FVKM  256 (323)
Q Consensus       253 ~~~m  256 (323)
                      +++.
T Consensus       280 ~~ka  283 (315)
T d2h6fa1         280 LNKA  283 (315)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=0.00051  Score=48.25  Aligned_cols=90  Identities=14%  Similarity=-0.078  Sum_probs=78.3

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      +.+.+.|   ++++|+..|++..... +-+...|..+-.++...|++++|...+....+.+ +.+...|..+-.+|...|
T Consensus        11 ~~~~~~g---~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~   85 (117)
T d1elwa_          11 NKALSVG---NIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLN   85 (117)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcC---CHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHcc
Confidence            4567778   7799999999998765 4467789999999999999999999999999875 447888999999999999


Q ss_pred             CHHHHHHHHHhccCC
Q 040801          245 FVSRAWDLFVKMLFP  259 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~  259 (323)
                      ++++|...|++..+.
T Consensus        86 ~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          86 RFEEAKRTYEEGLKH  100 (117)
T ss_dssp             CHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998865

>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=97.49  E-value=0.0024  Score=50.75  Aligned_cols=190  Identities=9%  Similarity=-0.094  Sum_probs=118.3

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIV  118 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  118 (323)
                      .+..+=..+.+.|+++.|...|+...+..                   +.+..+|+.+=.+|.+.|++++|++.|++..+
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l~-------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   99 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAIR-------------------PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLE   99 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhccC-------------------CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHH
Confidence            34445567777889999999998888764                   55778899999999999999999999999887


Q ss_pred             CCCCCC-cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCC
Q 040801          119 QGLIPD-RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPN  194 (323)
Q Consensus       119 ~g~~p~-~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~  194 (323)
                      .  .|+ ..++..+-..+...|+   |.+.++...+..- .+......+..++.+.+   ..+....+.......  .++
T Consensus       100 ~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~--~~~  171 (259)
T d1xnfa_         100 L--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP-NDPFRSLWLYLAEQKLD---EKQAKEVLKQHFEKS--DKE  171 (259)
T ss_dssp             H--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHC---HHHHHHHHHHHHHHS--CCC
T ss_pred             H--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-ccHHHHHHHHHHHHHhh---hHHHHHHHHHHhhcc--chh
Confidence            4  343 4567677777777777   8888888877652 23333333333444444   223444444444332  222


Q ss_pred             hHHHHHHHHHHhccCChHHHHHHHHHHHHh-----CCccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          195 AVTLVNVLTARARARDLRTVKRVHKCVDES-----GFWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       195 ~~t~~~li~~~~~~~~~~~a~~~~~~m~~~-----g~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...++ ++..+...  .... ..+......     ...|+ ..+|..+-..|...|+.++|...|++....
T Consensus       172 ~~~~~-~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  238 (259)
T d1xnfa_         172 QWGWN-IVEFYLGN--ISEQ-TLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN  238 (259)
T ss_dssp             STHHH-HHHHHTTS--SCHH-HHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hhhhh-HHHHHHHH--HHHH-HHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            22232 22222222  1111 112222111     11222 345667788999999999999999998765

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.47  E-value=0.00094  Score=51.15  Aligned_cols=97  Identities=12%  Similarity=-0.092  Sum_probs=57.0

Q ss_pred             CchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhH
Q 040801          155 SDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELK  233 (323)
Q Consensus       155 ~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~  233 (323)
                      |++......=..|.+.|   ++++|++.|++..... +-+...|+.+-.+|.+.|++++|...++...+.  .| +...|
T Consensus         2 ~~a~~l~~~Gn~~~~~g---~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~   75 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGR---KYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAH   75 (201)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHH
T ss_pred             hhHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHH
Confidence            33334444445566666   5566666666655543 235556666666666666666666666666543  34 34456


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          234 TTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       234 ~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      ..+-.+|.+.|++++|...|++..
T Consensus        76 ~~lg~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          76 FFLGQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHH
Confidence            666666666666666666666543

>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=97.44  E-value=0.0065  Score=49.85  Aligned_cols=216  Identities=9%  Similarity=-0.108  Sum_probs=134.7

Q ss_pred             hhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCC--------------cc---ch--------hHHHhcccCCCC----C
Q 040801           39 QAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDP--------------CA---DY--------HVRLVFSQISNP----T   89 (323)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~--------------y~---~~--------~a~~lf~~m~~~----~   89 (323)
                      .+..+-..+...|+++.|...+++..+..-..+.              |.   +.        .+.++......+    .
T Consensus        53 a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~  132 (366)
T d1hz4a_          53 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMH  132 (366)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHH
Confidence            3455666778889999999999988754322221              11   11        344444433311    1


Q ss_pred             hhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCC----CcccHHHHHHHhcchhh---HHHHHHHHHH----cCCCC--c
Q 040801           90 IYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIP----DRFMFPSLFKSCADIYV---EKQLHSQAIK----FGLAS--D  156 (323)
Q Consensus        90 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p----~~~ty~~ll~~~~~~~~---a~~~~~~m~~----~g~~~--~  156 (323)
                      ...+..+-..+...|+++.|...+.......-..    ...++......+...++   +...+.....    .+..+  .
T Consensus       133 ~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~  212 (366)
T d1hz4a_         133 EFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWI  212 (366)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHH
T ss_pred             HHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchH
Confidence            1345556678889999999999998876532211    12222233333333333   4444333322    22222  1


Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCC---CChHHHHHHHHHHhccCChHHHHHHHHHHHH----hCCccC
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVK---PNAVTLVNVLTARARARDLRTVKRVHKCVDE----SGFWSH  229 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~---p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p~  229 (323)
                      ...+..+...+...|   ++++|...+++.......   .....+..+-..+...|+.++|...++....    .+..|+
T Consensus       213 ~~~~~~~~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  289 (366)
T d1hz4a_         213 SNANKVRVIYWQMTG---DKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSD  289 (366)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhcc---cHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChH
Confidence            334566667777878   679999988876543222   2334566678889999999999999988753    355554


Q ss_pred             -hhhHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040801          230 -VELKTTLMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       230 -~~~~~~li~~~~~~g~~~~a~~~~~~m~  257 (323)
                       ...+..+-..|.+.|+.++|.+.+++..
T Consensus       290 ~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         290 LNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence             4567778889999999999999998764

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.0014  Score=48.49  Aligned_cols=90  Identities=14%  Similarity=-0.062  Sum_probs=74.6

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      ..|.+.|   ++++|+..|++..... +-+...|..+-..|...|++++|...|+.+.+.. +-+...|..+..+|...|
T Consensus        18 n~~~~~~---~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g   92 (159)
T d1a17a_          18 NDYFKAK---DYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALG   92 (159)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcC---CHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcC
Confidence            4566888   7799999999988765 3467788888889999999999999999998764 335578888999999999


Q ss_pred             CHHHHHHHHHhccCC
Q 040801          245 FVSRAWDLFVKMLFP  259 (323)
Q Consensus       245 ~~~~a~~~~~~m~~~  259 (323)
                      ++++|...+++..+.
T Consensus        93 ~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          93 KFRAALRDYETVVKV  107 (159)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHc
Confidence            999999999988764

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=0.00085  Score=47.58  Aligned_cols=95  Identities=14%  Similarity=-0.008  Sum_probs=69.3

Q ss_pred             HHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCC---hHHHHHHHHHHHHhCCccCh-hhHHHH
Q 040801          161 NTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARD---LRTVKRVHKCVDESGFWSHV-ELKTTL  236 (323)
Q Consensus       161 ~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~---~~~a~~~~~~m~~~g~~p~~-~~~~~l  236 (323)
                      ..|++.+...+   ++++|.+.|+.....+ +.+..++..+-.++.+.++   .++|..+++++.+.+-.|+. ..|..|
T Consensus         3 ~~l~n~~~~~~---~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~L   78 (122)
T d1nzna_           3 EAVLNELVSVE---DLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYL   78 (122)
T ss_dssp             HHHHHHHHHHH---HHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHhcCHH---HHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHH
Confidence            45677777777   6688888888887755 3466777778888876554   44688888887766544442 356677


Q ss_pred             HHHHHhcCCHHHHHHHHHhccCC
Q 040801          237 MDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       237 i~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      -.+|.+.|++++|.+.|++..+-
T Consensus        79 g~~y~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          79 AVGNYRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHh
Confidence            78888899999999999888753

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.22  E-value=0.0014  Score=45.43  Aligned_cols=88  Identities=7%  Similarity=-0.142  Sum_probs=74.2

Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhc
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKC  243 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  243 (323)
                      -..+.+.|   ++++|+..|++..... +-+..+|..+-..+.+.|++++|...++...+.. +-+...|..+-..|...
T Consensus        23 g~~~~~~g---~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~   97 (112)
T d1hxia_          23 GLSMLKLA---NLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNE   97 (112)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh---hhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHC
Confidence            44567778   7799999999998765 2267889999999999999999999999998864 33578888999999999


Q ss_pred             CCHHHHHHHHHhc
Q 040801          244 KFVSRAWDLFVKM  256 (323)
Q Consensus       244 g~~~~a~~~~~~m  256 (323)
                      |+.++|.+.+++.
T Consensus        98 g~~~~A~~~l~~~  110 (112)
T d1hxia_          98 HNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            9999999999874

>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=97.17  E-value=0.012  Score=44.92  Aligned_cols=79  Identities=11%  Similarity=-0.045  Sum_probs=36.5

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~  176 (323)
                      +...|++++|++.|.+.    ..|+..+|..+=..+.+.|+   |.+.|+...+.. .-+...|..+-.+|.+.|   ++
T Consensus        15 ~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g---~~   86 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTE---KY   86 (192)
T ss_dssp             HHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT---CH
T ss_pred             HHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhc---cH
Confidence            45667777777777543    22333334444334444444   444444444432 112334444444444444   33


Q ss_pred             HHHHHHHHHH
Q 040801          177 DEAIKIFYRM  186 (323)
Q Consensus       177 ~~a~~~~~~m  186 (323)
                      ++|++.|++-
T Consensus        87 ~~A~~~~~kA   96 (192)
T d1hh8a_          87 DLAIKDLKEA   96 (192)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>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=97.14  E-value=0.02  Score=46.73  Aligned_cols=196  Identities=8%  Similarity=-0.109  Sum_probs=94.3

Q ss_pred             HhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCC-CCC
Q 040801           46 SLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGL-IPD  124 (323)
Q Consensus        46 ~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~-~p~  124 (323)
                      .+...|+++.|..++++..+..  |+...            ......++.+-..|...|++++|.+.|++..+..- .++
T Consensus        21 ~~~~~g~~~~A~~~~~~aL~~~--~~~~~------------~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~   86 (366)
T d1hz4a_          21 VAINDGNPDEAERLAKLALEEL--PPGWF------------YSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDV   86 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTC--CTTCH------------HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHCCCHHHHHHHHHHHHhhC--cCCCc------------HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcc
Confidence            4567799999999999887653  21100            00012345555566666777777777666543210 011


Q ss_pred             ----cccHHHHHHHhcchhh---HHHHHHHHH----HcCCCCc---hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHc-
Q 040801          125 ----RFMFPSLFKSCADIYV---EKQLHSQAI----KFGLASD---SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIE-  189 (323)
Q Consensus       125 ----~~ty~~ll~~~~~~~~---a~~~~~~m~----~~g~~~~---~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~-  189 (323)
                          ..++..+...+...|+   +...+....    ..+....   ...+..+-..+...|   +++.+...+...... 
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~---~~~~a~~~~~~~~~~~  163 (366)
T d1hz4a_          87 WHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWA---RLDEAEASARSGIEVL  163 (366)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhc---chhhhHHHHHHHHHHh
Confidence                1122222233333333   333333322    1111111   123444445555656   446666666555442 


Q ss_pred             ---CCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC--Cc--c--ChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          190 ---NVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG--FW--S--HVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       190 ---g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~--p--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                         +......++......+...++...+...+.......  ..  +  ....+..+...+...|+.++|...+++..+
T Consensus       164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  241 (366)
T d1hz4a_         164 SSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAK  241 (366)
T ss_dssp             TTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCC
T ss_pred             hhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence               112223344444455556666666666655553311  01  0  122344445556666666666666665543

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.09  E-value=0.0019  Score=45.68  Aligned_cols=93  Identities=5%  Similarity=-0.009  Sum_probs=52.1

Q ss_pred             HHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCCh-HHHHHHHHHHh
Q 040801          131 LFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNA-VTLVNVLTARA  206 (323)
Q Consensus       131 ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~-~t~~~li~~~~  206 (323)
                      +++.+...++   |++.|+...+.+ ..+..++..+-.++.+.++.++.++|+++|++....+..|+. .+|..+-.+|.
T Consensus         5 l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y~   83 (122)
T d1nzna_           5 VLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNY   83 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH
Confidence            4444444444   555555555544 224455555555565555433445677777666554433332 35555666666


Q ss_pred             ccCChHHHHHHHHHHHHh
Q 040801          207 RARDLRTVKRVHKCVDES  224 (323)
Q Consensus       207 ~~~~~~~a~~~~~~m~~~  224 (323)
                      +.|++++|...|+++.+.
T Consensus        84 ~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          84 RLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHHh
Confidence            777777777777777664

>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=97.09  E-value=0.012  Score=47.78  Aligned_cols=200  Identities=10%  Similarity=-0.048  Sum_probs=96.6

Q ss_pred             hhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCC--ChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           40 AHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNP--TIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      |.-.-..+...+++++|...|....+...               +...+  -..+|+.+-.+|.+.|++++|.+.|++-.
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~---------------~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~  104 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQK---------------KAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAI  104 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHH---------------HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHH---------------HcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhh
Confidence            44455566666777777777776654321               11111  23567778888888999999988887654


Q ss_pred             HC----CC-CCCcccHHHHHHHhc-chhh---HHHHHHHHHHc----CCCC-chHHHHHHHHHHHhcCCCCChHHHHHHH
Q 040801          118 VQ----GL-IPDRFMFPSLFKSCA-DIYV---EKQLHSQAIKF----GLAS-DSFLHNTLINMYSSCWCLDQPDEAIKIF  183 (323)
Q Consensus       118 ~~----g~-~p~~~ty~~ll~~~~-~~~~---a~~~~~~m~~~----g~~~-~~~~~~~li~~~~~~g~~~~~~~a~~~~  183 (323)
                      +-    |- .....++..+...+- ..|+   |...++...+.    +..+ -..+|..+...|...|   ++++|++.|
T Consensus       105 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g---~y~~A~~~~  181 (290)
T d1qqea_         105 QIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDG---QYIEASDIY  181 (290)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             HHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcC---hHHHHHHHH
Confidence            31    10 011122333333331 1233   55555443321    1111 1234555666666666   556666666


Q ss_pred             HHHHHcCCCC-----Ch-HHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-cC---hhhHHHHHHHHHh--cCCHHHHHH
Q 040801          184 YRMEIENVKP-----NA-VTLVNVLTARARARDLRTVKRVHKCVDESGFW-SH---VELKTTLMDAYCK--CKFVSRAWD  251 (323)
Q Consensus       184 ~~m~~~g~~p-----~~-~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~---~~~~~~li~~~~~--~g~~~~a~~  251 (323)
                      ++........     +. ..|...+..+...|+.+.|...++...+.... ++   ......++.+|-.  .+.+++|..
T Consensus       182 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~  261 (290)
T d1qqea_         182 SKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCK  261 (290)
T ss_dssp             HHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHH
T ss_pred             HHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            6655422111     11 11222333444556666666666665443211 11   1233445555444  234556655


Q ss_pred             HHHhcc
Q 040801          252 LFVKML  257 (323)
Q Consensus       252 ~~~~m~  257 (323)
                      -|+++.
T Consensus       262 ~y~~~~  267 (290)
T d1qqea_         262 EFDNFM  267 (290)
T ss_dssp             HHTTSS
T ss_pred             HHHHHh
Confidence            555544

>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=96.98  E-value=0.0031  Score=52.55  Aligned_cols=202  Identities=6%  Similarity=-0.083  Sum_probs=109.7

Q ss_pred             CCchHHHHHHHHHHHhcCCCCCc----------------cch--------hHHHhcccCC---CCChhhHHHHHHHHHhC
Q 040801           51 STMRELKQIHAQMLRTSLFFDPC----------------ADY--------HVRLVFSQIS---NPTIYTCNSIVRGYTNK  103 (323)
Q Consensus        51 ~~~~~a~~i~~~m~~~~~~~~~y----------------~~~--------~a~~lf~~m~---~~~~~~~~~li~~~~~~  103 (323)
                      ...++|..+++...+.  .|+.+                ...        .|..+|+...   +.+...|..+-.++...
T Consensus        43 ~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~  120 (334)
T d1dcea1          43 ELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRL  120 (334)
T ss_dssp             CCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTC
T ss_pred             cccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHh
Confidence            3458999999988865  45541                100        5666666654   55777788777777776


Q ss_pred             CC--hHHHHHHHHHHHHCCCCCCcccHHHHH-HHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCC---
Q 040801          104 NL--HHEAFLFYHEMIVQGLIPDRFMFPSLF-KSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLD---  174 (323)
Q Consensus       104 g~--~~~A~~~~~~m~~~g~~p~~~ty~~ll-~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~---  174 (323)
                      ++  +++|...+++..+..- ++...+...+ ..+...+.   |...++...+... -+...|+.+-..+.+.|+.+   
T Consensus       121 ~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~~~~~~~A~  198 (334)
T d1dcea1         121 PEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHPQPDSG  198 (334)
T ss_dssp             SSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             ccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCHHHHH
Confidence            54  7899999999876421 2333333322 33333333   6666666555442 35677888888888888664   


Q ss_pred             ------------------------ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          175 ------------------------QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       175 ------------------------~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                                              ..+++...+....... .++...+..+...+...++..+|...+.+..+.. +-+.
T Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-p~~~  276 (334)
T d1dcea1         199 PQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQELEPEN-KWCL  276 (334)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHH
T ss_pred             HHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC-chHH
Confidence                                    1111111111111111 1122223333334444455555555555443332 1134


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          231 ELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       231 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      ..|..+...|.+.|+.++|.+.+++..+
T Consensus       277 ~~~~~l~~~~~~~~~~~eA~~~~~~ai~  304 (334)
T d1dcea1         277 LTIILLMRALDPLLYEKETLQYFSTLKA  304 (334)
T ss_dssp             HHHHHHHHHHCTGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4555555666666666666666666654

>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=96.97  E-value=0.0088  Score=48.70  Aligned_cols=164  Identities=9%  Similarity=-0.054  Sum_probs=112.0

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHC----CCCC-CcccHHHHHHHhcchhh---HHHHHHHHHHc----CC-CCchHH
Q 040801           93 CNSIVRGYTNKNLHHEAFLFYHEMIVQ----GLIP-DRFMFPSLFKSCADIYV---EKQLHSQAIKF----GL-ASDSFL  159 (323)
Q Consensus        93 ~~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p-~~~ty~~ll~~~~~~~~---a~~~~~~m~~~----g~-~~~~~~  159 (323)
                      |.-.-..|-..|++++|.+.|.+..+-    +-.+ -..+|..+-..|.+.|+   |...++...+.    |. .....+
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  119 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHH
Confidence            555667788899999999999887542    2211 12567777777777777   66666654432    21 112455


Q ss_pred             HHHHHHHHHh-cCCCCChHHHHHHHHHHHH----cCCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh---
Q 040801          160 HNTLINMYSS-CWCLDQPDEAIKIFYRMEI----ENVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV---  230 (323)
Q Consensus       160 ~~~li~~~~~-~g~~~~~~~a~~~~~~m~~----~g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~---  230 (323)
                      +..+...|-. .|   ++++|++.+++...    .+-.+ -..+|..+...+...|++++|...++++.+.......   
T Consensus       120 ~~~l~~~~~~~~~---~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~  196 (290)
T d1qqea_         120 KFELGEILENDLH---DYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (290)
T ss_dssp             HHHHHHHHHHTTC---CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHhHhhHHH---HHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhh
Confidence            6666666644 47   77999999988753    22222 2356888899999999999999999998765322111   


Q ss_pred             ---hhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          231 ---ELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       231 ---~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                         ..+......+...|+.+.|...+++..+.
T Consensus       197 ~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence               12344555677889999999999999875

>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=96.78  E-value=0.013  Score=46.29  Aligned_cols=148  Identities=10%  Similarity=-0.127  Sum_probs=99.2

Q ss_pred             ChHHHHHHHHHHHHCCC-CCC--cccHHHHHHHhcchhh---HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHH
Q 040801          105 LHHEAFLFYHEMIVQGL-IPD--RFMFPSLFKSCADIYV---EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDE  178 (323)
Q Consensus       105 ~~~~A~~~~~~m~~~g~-~p~--~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~  178 (323)
                      +.+.|+.-+++.....- .+.  ..+|-.+=..+.+.|+   |...|+...+.. .-+..+|+.+-.+|.+.|   ++++
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g---~~~~   89 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAG---NFDA   89 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHH---HHHH
Confidence            34566666777665422 221  1233333345555666   888888888764 235778888999999999   6799


Q ss_pred             HHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          179 AIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       179 a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      |++.|++..... +-+..++..+-..+...|+.++|...++...+.. +.+......+..++.+.+..+.+..+......
T Consensus        90 A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (259)
T d1xnfa_          90 AYEAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  167 (259)
T ss_dssp             HHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHH-hhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence            999999988754 2245678888888999999999999999988764 22344444444556666666666555555443

>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=96.66  E-value=0.027  Score=41.09  Aligned_cols=80  Identities=15%  Similarity=-0.012  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKC  220 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~  220 (323)
                      |...|+...+.. .-+...|..+-.+|...|   ++++|++.|+...+.. .-+...|..+..++...|++++|...+++
T Consensus        29 A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~---~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~eA~~~~~~  103 (159)
T d1a17a_          29 AIKFYSQAIELN-PSNAIYYGNRSLAYLRTE---CYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRDYET  103 (159)
T ss_dssp             HHHHHHHHHHHS-TTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHhhhccccc-hhhhhhhhhhHHHHHhcc---ccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            444444443333 234666777888888888   6688888888887654 33557888888888888888888888888


Q ss_pred             HHHhC
Q 040801          221 VDESG  225 (323)
Q Consensus       221 m~~~g  225 (323)
                      ..+..
T Consensus       104 a~~~~  108 (159)
T d1a17a_         104 VVKVK  108 (159)
T ss_dssp             HHHHS
T ss_pred             HHHcC
Confidence            87763

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.64  E-value=0.011  Score=41.80  Aligned_cols=92  Identities=16%  Similarity=0.082  Sum_probs=72.5

Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc-cC-----hhhHHH
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW-SH-----VELKTT  235 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~-----~~~~~~  235 (323)
                      .+=..|.+.|   ++++|++.|++..+.+ +.+...|..+-.+|.+.|++++|...++++.+..-. +.     ..+|..
T Consensus         9 ~~G~~~~~~~---~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           9 ELGNDAYKKK---DFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHcC---CHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            3445677888   7799999999998865 346889999999999999999999999998764211 11     236667


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcc
Q 040801          236 LMDAYCKCKFVSRAWDLFVKML  257 (323)
Q Consensus       236 li~~~~~~g~~~~a~~~~~~m~  257 (323)
                      +-..+...+++++|.+.|++-.
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH
Confidence            7778888899999999998764

>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=96.62  E-value=0.048  Score=41.25  Aligned_cols=101  Identities=16%  Similarity=-0.035  Sum_probs=58.7

Q ss_pred             CCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhC--------
Q 040801          154 ASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESG--------  225 (323)
Q Consensus       154 ~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g--------  225 (323)
                      .|+..+|..+=.+|.+.|   ++++|++.|++-.+.. +-+...|..+-.++.+.|+.++|...|+...+..        
T Consensus        33 ~~~~~~~~nlG~~~~~~g---~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~  108 (192)
T d1hh8a_          33 DPHSRICFNIGCMYTILK---NMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDY  108 (192)
T ss_dssp             SCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEEC
T ss_pred             CCCHHHHHHHHHHHHHcC---CchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCccCchHHH
Confidence            355566666666666666   5567777776666544 2345566666666667777777766666665321        


Q ss_pred             ----Cc--cC-hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          226 ----FW--SH-VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       226 ----~~--p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                          ..  ++ ..++..+-.+|.+.|++++|.+.++...+
T Consensus       109 ~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_         109 KILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             GGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence                00  00 12333445566667777777776666554

>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=96.53  E-value=0.026  Score=38.94  Aligned_cols=65  Identities=9%  Similarity=-0.121  Sum_probs=44.0

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      +...|..+-.+|.+.|   ++++|++.+++....+ +.+...|..+-.++...|++++|...++...+.
T Consensus        36 ~~~~~~~~a~~~~~~~---~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          36 NHVLYSNRSAAYAKKG---DYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  100 (117)
T ss_dssp             CHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             chhhhhcccccccccc---cccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3445666666666777   5577777777776654 346667777777777777777777777777654

>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=96.27  E-value=0.0093  Score=45.19  Aligned_cols=89  Identities=11%  Similarity=-0.120  Sum_probs=66.5

Q ss_pred             CChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC-CCchhhh-HHHh
Q 040801          193 PNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP-WNNYGQW-AMSA  270 (323)
Q Consensus       193 p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~-~~~~  270 (323)
                      |+...+...=..+.+.|++++|...|.+..+.. +-+...|..+-.+|.+.|++++|...|++..+- +..+..| ....
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~   80 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQ   80 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHH
Confidence            555566666678889999999999999998874 346778999999999999999999999999875 3334444 3444


Q ss_pred             hhccCCCCCcchhhh
Q 040801          271 TVGPQGLVGRHSTAH  285 (323)
Q Consensus       271 ~~~~~~~~~~~~~a~  285 (323)
                      ++..   .|+.++|.
T Consensus        81 ~~~~---l~~~~~A~   92 (201)
T d2c2la1          81 CQLE---MESYDEAI   92 (201)
T ss_dssp             HHHH---TTCHHHHH
T ss_pred             HHHH---CCCHHHHH
Confidence            4444   44555553

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.25  E-value=0.03  Score=41.47  Aligned_cols=93  Identities=10%  Similarity=-0.059  Sum_probs=72.5

Q ss_pred             HHHHHHhcCCCCChHHHHHHHHHHHHcC-CCC-------------ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc
Q 040801          163 LINMYSSCWCLDQPDEAIKIFYRMEIEN-VKP-------------NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS  228 (323)
Q Consensus       163 li~~~~~~g~~~~~~~a~~~~~~m~~~g-~~p-------------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  228 (323)
                      .=..+.+.|   ++++|++.|.+....- ..+             -..+|+.+-.+|.+.|++++|...++...+.. +-
T Consensus        19 ~G~~~~~~~---~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~   94 (170)
T d1p5qa1          19 RGTVYFKEG---KYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SN   94 (170)
T ss_dssp             HHHHHHHHT---CHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHcC---CHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-cc
Confidence            334677777   6689999888776521 111             13567778888999999999999999998874 23


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          229 HVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       229 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +...|..+-.+|...|++++|...|++..+-
T Consensus        95 ~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          95 NEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             chhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            6788888999999999999999999998764

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.21  E-value=0.018  Score=43.33  Aligned_cols=127  Identities=10%  Similarity=0.043  Sum_probs=87.9

Q ss_pred             ChhhHHHHH---HHHHhCCChHHHHHHHHHHHHC--CCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHH
Q 040801           89 TIYTCNSIV---RGYTNKNLHHEAFLFYHEMIVQ--GLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTL  163 (323)
Q Consensus        89 ~~~~~~~li---~~~~~~g~~~~A~~~~~~m~~~--g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~l  163 (323)
                      |+..|-.++   ......|++++|.+.|.+-..-  |-....         +.....+...-..+...    ....+..+
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~---------~~~~~w~~~~r~~l~~~----~~~a~~~l   73 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDD---------LRDFQFVEPFATALVED----KVLAHTAK   73 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGG---------GTTSTTHHHHHHHHHHH----HHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCccccccc---------CcchHHHHHHHHHHHHH----HHHHHHHH
Confidence            334444444   4678889999999999987652  221100         00000022222222221    24567889


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHH-----HhCCccChhh
Q 040801          164 INMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVD-----ESGFWSHVEL  232 (323)
Q Consensus       164 i~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~-----~~g~~p~~~~  232 (323)
                      ...+.+.|   ++++|++.++...... .-+...|..++.+|.+.|+..+|.+.|+++.     +.|+.|...+
T Consensus        74 a~~~~~~g---~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          74 AEAEIACG---RASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHCC---CchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999999   7799999999998865 4578899999999999999999999999984     4699998765

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.21  E-value=0.093  Score=38.64  Aligned_cols=124  Identities=15%  Similarity=0.008  Sum_probs=84.2

Q ss_pred             HHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChH
Q 040801           98 RGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPD  177 (323)
Q Consensus        98 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~  177 (323)
                      ..+.+.|++++|.+.|.+-.+.-  |....+         ..........+.       ..+|+.+-.+|.+.|   +++
T Consensus        21 ~~~~~~~~~~~Ai~~y~~al~~~--~~~~~~---------~~~~~~~~~~~~-------~~~~~nla~~y~k~~---~~~   79 (170)
T d1p5qa1          21 TVYFKEGKYKQALLQYKKIVSWL--EYESSF---------SNEEAQKAQALR-------LASHLNLAMCHLKLQ---AFS   79 (170)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHT--TTCCCC---------CSHHHHHHHHHH-------HHHHHHHHHHHHHTT---CHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHh--hhcccc---------chHHHhhhchhH-------HHHHHHHHHHHHhhh---hcc
Confidence            36788999999999998876531  111110         000111111111       236777888999999   779


Q ss_pred             HHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHHhcCC
Q 040801          178 EAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYCKCKF  245 (323)
Q Consensus       178 ~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~g~  245 (323)
                      +|++.+++..... +-+..+|..+-.++...|++++|...|+...+.  .| +......+-...-+.+.
T Consensus        80 ~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~~~~l~~~~~~~~~  145 (170)
T d1p5qa1          80 AAIESCNKALELD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRR  145 (170)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHH
T ss_pred             cccchhhhhhhcc-ccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHH
Confidence            9999999988754 337889999999999999999999999999886  45 44444444444433333

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=95.96  E-value=0.11  Score=37.47  Aligned_cols=91  Identities=15%  Similarity=-0.041  Sum_probs=72.0

Q ss_pred             HHHHhcCCCCChHHHHHHHHHHHHcC----CCC-----------ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccC
Q 040801          165 NMYSSCWCLDQPDEAIKIFYRMEIEN----VKP-----------NAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSH  229 (323)
Q Consensus       165 ~~~~~~g~~~~~~~a~~~~~~m~~~g----~~p-----------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  229 (323)
                      ..+.+.|   ++++|+..|.+....-    ..+           ...+|+.+-.+|.+.|++++|...+....+.. +-+
T Consensus        25 ~~~f~~~---~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~  100 (153)
T d2fbna1          25 NEFFKKN---EINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-KNN  100 (153)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTC
T ss_pred             HHHHHcC---CHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-chh
Confidence            4566777   6688888888766421    011           23577888889999999999999999998874 346


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          230 VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       230 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      ...|..+-.+|...|++++|...|++..+-
T Consensus       101 ~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1         101 VKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            789999999999999999999999998754

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=95.90  E-value=0.1  Score=37.65  Aligned_cols=112  Identities=15%  Similarity=-0.000  Sum_probs=80.2

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCC
Q 040801           96 IVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQ  175 (323)
Q Consensus        96 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~  175 (323)
                      -=..+.+.|++.+|+..|.+....-  +...           .............    ....+|+.+-.+|.+.|   +
T Consensus        23 ~G~~~f~~~~y~~A~~~Y~~al~~~--~~~~-----------~~~~~~~~~~~~~----~~~~~~~Nla~~~~~l~---~   82 (153)
T d2fbna1          23 EGNEFFKKNEINEAIVKYKEALDFF--IHTE-----------EWDDQILLDKKKN----IEISCNLNLATCYNKNK---D   82 (153)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTT--TTCT-----------TCCCHHHHHHHHH----HHHHHHHHHHHHHHHTT---C
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhC--cchh-----------hhhhHHHHHhhhh----HHHHHHhhHHHHHHHhc---c
Confidence            3356788999999999999876531  1100           0000011111111    12357888999999999   7


Q ss_pred             hHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh
Q 040801          176 PDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV  230 (323)
Q Consensus       176 ~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~  230 (323)
                      +++|++.+++....+ +.+..+|..+-.++...|++++|...|+...+..  |+-
T Consensus        83 ~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~--P~n  134 (153)
T d2fbna1          83 YPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN--PNN  134 (153)
T ss_dssp             HHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTC
T ss_pred             cchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC--CCC
Confidence            799999999988765 4478999999999999999999999999998873  543

>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=95.86  E-value=0.093  Score=39.17  Aligned_cols=89  Identities=12%  Similarity=-0.018  Sum_probs=69.2

Q ss_pred             HHHhcCCCCChHHHHHHHHHHHHc--CC-CC------------------ChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          166 MYSSCWCLDQPDEAIKIFYRMEIE--NV-KP------------------NAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       166 ~~~~~g~~~~~~~a~~~~~~m~~~--g~-~p------------------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .....|   ++++|.+.|.+-...  |- -+                  ....+..+...+.+.|++++|...++.+.+.
T Consensus        20 ~~~~~g---~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~al~~   96 (179)
T d2ff4a2          20 HAAAAG---RFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFE   96 (179)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHh
Confidence            445556   557777777666542  21 01                  1246778889999999999999999999886


Q ss_pred             CCccChhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          225 GFWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       225 g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                      . +-+...|..++.+|.+.|+.++|.+.|+++.+
T Consensus        97 ~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~  129 (179)
T d2ff4a2          97 H-PYREPLWTQLITAYYLSDRQSDALGAYRRVKT  129 (179)
T ss_dssp             S-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             C-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            4 44788999999999999999999999999854

>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=95.14  E-value=0.24  Score=40.32  Aligned_cols=151  Identities=7%  Similarity=-0.079  Sum_probs=83.9

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccH----HHHHHHhcchhh----------HHHHHHHHHHcCCCCchHH
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMF----PSLFKSCADIYV----------EKQLHSQAIKFGLASDSFL  159 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty----~~ll~~~~~~~~----------a~~~~~~m~~~g~~~~~~~  159 (323)
                      +.++...-+....++|+++++...+  ..|+..+.    ..++..+...+.          +..+++...+.. .-+...
T Consensus        33 ~~~~~~~~~~~~~~~al~~~~~~l~--~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~  109 (334)
T d1dcea1          33 QAVFQKRQAGELDESVLELTSQILG--ANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGT  109 (334)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHH--HCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHH
Confidence            3333333333445788888887765  34665432    122222222221          555666655543 224555


Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHH-HHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVL-TARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li-~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      |..+-.++...+.. +.++|+..+.+..... .++...+...+ ..+-..+..+.|...++.+.+.. +-+...|+.+-.
T Consensus       110 ~~~~~~~~~~~~~~-~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~  186 (334)
T d1dcea1         110 WHHRCWLLSRLPEP-NWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSC  186 (334)
T ss_dssp             HHHHHHHHHTCSSC-CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHH
T ss_pred             HHHhhHHHHHhccc-cHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHH
Confidence            66666666666644 5677777777776643 23444444333 45556677777777777666553 124556666666


Q ss_pred             HHHhcCCHHHHH
Q 040801          239 AYCKCKFVSRAW  250 (323)
Q Consensus       239 ~~~~~g~~~~a~  250 (323)
                      .|.+.|+.++|.
T Consensus       187 ~~~~~~~~~~A~  198 (334)
T d1dcea1         187 LLPQLHPQPDSG  198 (334)
T ss_dssp             HHHHHSCCCCSS
T ss_pred             HHHHhcCHHHHH
Confidence            777777665543

>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=95.02  E-value=0.1  Score=35.43  Aligned_cols=61  Identities=5%  Similarity=-0.058  Sum_probs=35.7

Q ss_pred             hHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHH
Q 040801          157 SFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCV  221 (323)
Q Consensus       157 ~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m  221 (323)
                      ...|..+-.+|.+.|   ++++|+..|++..+.. +-+...|..+-..+...|+.++|.+.+++.
T Consensus        50 ~~a~~~lg~~~~~~~---~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          50 EEAWRSLGLTQAENE---KDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhhhhhhhhhhhh---hHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            445555555666666   4466666666655533 224556666666666666666666666553

>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=94.93  E-value=0.43  Score=34.62  Aligned_cols=124  Identities=10%  Similarity=-0.057  Sum_probs=82.4

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCC-chHHHHHHHHHHHhcCC
Q 040801           94 NSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLAS-DSFLHNTLINMYSSCWC  172 (323)
Q Consensus        94 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~-~~~~~~~li~~~~~~g~  172 (323)
                      ...-..+.+.|++++|++.|.+..+.         ..........         .....+.| ....|+.+-.+|.+.| 
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~---------~~~~~~~~~~---------~~~~~~~~~~~~~~~nla~~~~~~~-   91 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRY---------VEGSRAAAED---------ADGAKLQPVALSCVLNIGACKLKMS-   91 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH---------HHHHHHHSCH---------HHHGGGHHHHHHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh---------hhhhhhhhhh---------HHHHHhChhhHHHHHHHHHHHHhhc-
Confidence            33455677899999999999876531         0000111110         00111112 3456777888899988 


Q ss_pred             CCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCcc-ChhhHHHHHHHHH
Q 040801          173 LDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWS-HVELKTTLMDAYC  241 (323)
Q Consensus       173 ~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~  241 (323)
                        ++++|+..+++..+.. +-+...|..+-.++.+.|++++|...|....+.  .| +...+..+-..+-
T Consensus        92 --~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~~~~  156 (169)
T d1ihga1          92 --DWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQ  156 (169)
T ss_dssp             --CHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             --ccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence              7799999999988754 346778989999999999999999999999886  34 3444554444443

>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=94.82  E-value=0.46  Score=34.48  Aligned_cols=125  Identities=12%  Similarity=-0.017  Sum_probs=82.2

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh-HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCC
Q 040801           95 SIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV-EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCL  173 (323)
Q Consensus        95 ~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~-a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~  173 (323)
                      -.=..+.+.|++++|.+.|.+-...  .+          ....... .......+       ...+|+.+-.+|.+.|  
T Consensus        20 e~G~~~~~~~~~~~A~~~Y~~al~~--~~----------~~~~~~~~~~~~~~~~-------~~~~~~Nla~~~~~l~--   78 (168)
T d1kt1a1          20 EKGTVYFKGGKYVQAVIQYGKIVSW--LE----------MEYGLSEKESKASESF-------LLAAFLNLAMCYLKLR--   78 (168)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--HT----------TCCSCCHHHHHHHHHH-------HHHHHHHHHHHHHHTT--
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH--HH----------Hhhccchhhhhhcchh-------HHHHHHhHHHHHHHhh--
Confidence            3345678899999999999875431  00          0000000 11111111       1345777888888988  


Q ss_pred             CChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccCh-hhHHHHHHHHHhcC
Q 040801          174 DQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHV-ELKTTLMDAYCKCK  244 (323)
Q Consensus       174 ~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~g  244 (323)
                       ++++|+..+++..... +.+...|..+-.++...|++++|...|+.+.+.  .|+- .....+-....+.+
T Consensus        79 -~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~~~~~~~~  146 (168)
T d1kt1a1          79 -EYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIFMCQKKAK  146 (168)
T ss_dssp             -CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHH
T ss_pred             -hcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHH
Confidence             7799999999988765 457789999999999999999999999998875  4543 33443333333333

>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=94.80  E-value=0.14  Score=37.40  Aligned_cols=94  Identities=13%  Similarity=0.009  Sum_probs=70.7

Q ss_pred             HHHHHHHhcCCCCChHHHHHHHHHHHHc--------------CCCC-ChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC
Q 040801          162 TLINMYSSCWCLDQPDEAIKIFYRMEIE--------------NVKP-NAVTLVNVLTARARARDLRTVKRVHKCVDESGF  226 (323)
Q Consensus       162 ~li~~~~~~g~~~~~~~a~~~~~~m~~~--------------g~~p-~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~  226 (323)
                      ..-..+.+.|   ++++|++.|.+....              .+.| +...|..+-.++.+.|++++|...++.+.+.. 
T Consensus        32 ~~~~~~~~~~---~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-  107 (169)
T d1ihga1          32 NIGNTFFKSQ---NWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  107 (169)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHcC---CHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-
Confidence            3445566667   667777777665321              0122 44567778888999999999999999998764 


Q ss_pred             ccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          227 WSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       227 ~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      +-+...|..+-.+|.+.|++++|.+.|++..+-
T Consensus       108 p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1         108 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            335778899999999999999999999988764

>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=94.69  E-value=0.46  Score=33.92  Aligned_cols=98  Identities=14%  Similarity=-0.077  Sum_probs=71.5

Q ss_pred             HHHHHH--HHHHHhcCCCCChHHHHHHHHHHHHcC-CCC----------ChHHHHHHHHHHhccCChHHHHHHHHHHHHh
Q 040801          158 FLHNTL--INMYSSCWCLDQPDEAIKIFYRMEIEN-VKP----------NAVTLVNVLTARARARDLRTVKRVHKCVDES  224 (323)
Q Consensus       158 ~~~~~l--i~~~~~~g~~~~~~~a~~~~~~m~~~g-~~p----------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~  224 (323)
                      .+|..+  -..+...|   ++++|++.|++-.+-. --|          ....|+.+-.+|...|++++|..-+++..+.
T Consensus         8 ~a~~~l~~g~~~~~~g---~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~   84 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAG---EYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHY   84 (156)
T ss_dssp             HHHHHHHHHHHHHHHT---CHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhc
Confidence            455555  44556668   6799999999887621 112          2468889999999999999999999888642


Q ss_pred             -----CCccC-----hhhHHHHHHHHHhcCCHHHHHHHHHhccC
Q 040801          225 -----GFWSH-----VELKTTLMDAYCKCKFVSRAWDLFVKMLF  258 (323)
Q Consensus       225 -----g~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  258 (323)
                           ...++     ...|..+-.+|.+.|++++|...|++..+
T Consensus        85 ~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          85 FNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                 12222     22466677899999999999999998653

>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=93.91  E-value=0.45  Score=34.50  Aligned_cols=96  Identities=9%  Similarity=-0.098  Sum_probs=73.1

Q ss_pred             HHHHHHHHHhcCCCCChHHHHHHHHHHHH---cCCCC-----------ChHHHHHHHHHHhccCChHHHHHHHHHHHHhC
Q 040801          160 HNTLINMYSSCWCLDQPDEAIKIFYRMEI---ENVKP-----------NAVTLVNVLTARARARDLRTVKRVHKCVDESG  225 (323)
Q Consensus       160 ~~~li~~~~~~g~~~~~~~a~~~~~~m~~---~g~~p-----------~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g  225 (323)
                      +...-..+.+.|   ++++|.+.|++-..   .....           ....|+.+-.++.+.|++++|...++...+..
T Consensus        18 ~~e~G~~~~~~~---~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          18 VKEKGTVYFKGG---KYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHTT---CHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcC---CHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            444455677778   66888888877553   11111           22456667778899999999999999998864


Q ss_pred             CccChhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          226 FWSHVELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       226 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                       +.+...|..+-.+|...|++++|...|++..+-
T Consensus        95 -p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          95 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             -cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             446788888999999999999999999998764

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.42  E-value=1.6  Score=35.60  Aligned_cols=172  Identities=9%  Similarity=-0.049  Sum_probs=102.4

Q ss_pred             hhhhhhHHHhhcCCCchHHHHHHHHHHHhcCCCCCccchhHHHhcccCCCCChhhHHHHHHHHHhCCChHHHHHHHHHHH
Q 040801           38 YQAHFCLVSLEKCSTMRELKQIHAQMLRTSLFFDPCADYHVRLVFSQISNPTIYTCNSIVRGYTNKNLHHEAFLFYHEMI  117 (323)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~i~~~m~~~~~~~~~y~~~~a~~lf~~m~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  117 (323)
                      .........|.+.|.++.|..++..+..                           |.-++..+.+.+++..|.++.....
T Consensus        15 ~d~~~i~~~c~~~~lye~A~~lY~~~~d---------------------------~~rl~~~~v~l~~~~~avd~~~k~~   67 (336)
T d1b89a_          15 AHIQQVGDRCYDEKMYDAAKLLYNNVSN---------------------------FGRLASTLVHLGEYQAAVDGARKAN   67 (336)
T ss_dssp             --------------CTTTHHHHHHHTTC---------------------------HHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHhCCC---------------------------HHHHHHHHHhhccHHHHHHHHHHcC
Confidence            3444556667777888888888764432                           4567888889999999988876442


Q ss_pred             HCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHH
Q 040801          118 VQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVT  197 (323)
Q Consensus       118 ~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t  197 (323)
                            +..+|..+...|.+.....-  ..+.......+......++..|-..|   .+++...++...... -.++...
T Consensus        68 ------~~~~~k~~~~~l~~~~e~~l--a~i~~~~~~~~~d~l~~~v~~ye~~~---~~e~Li~~Le~~~~~-~~~~~~~  135 (336)
T d1b89a_          68 ------STRTWKEVCFACVDGKEFRL--AQMCGLHIVVHADELEELINYYQDRG---YFEELITMLEAALGL-ERAHMGM  135 (336)
T ss_dssp             ------CHHHHHHHHHHHHHTTCHHH--HHHTTTTTTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHTTS-TTCCHHH
T ss_pred             ------CHHHHHHHHHHHHhCcHHHH--HHHHHHHhhcCHHHHHHHHHHHHHcC---ChHHHHHHHHHHHcC-CccchHH
Confidence                  44577777777776554111  12223344455566678999999988   668999999876543 2567778


Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHhC--Ccc--------ChhhHHHHHHHHHhcCCHHHHHHH
Q 040801          198 LVNVLTARARARDLRTVKRVHKCVDESG--FWS--------HVELKTTLMDAYCKCKFVSRAWDL  252 (323)
Q Consensus       198 ~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~p--------~~~~~~~li~~~~~~g~~~~a~~~  252 (323)
                      |+.++..|++.+.-    ++.+.+....  +.+        ....|.-++-.|.+.|++++|..+
T Consensus       136 ~~~L~~lyak~~~~----kl~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~  196 (336)
T d1b89a_         136 FTELAILYSKFKPQ----KMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT  196 (336)
T ss_dssp             HHHHHHHHHTTCHH----HHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhChH----HHHHHHHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHH
Confidence            88999999886532    3444444321  111        222356677777777777766544

>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=93.28  E-value=0.17  Score=35.08  Aligned_cols=87  Identities=14%  Similarity=0.051  Sum_probs=45.9

Q ss_pred             HHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcCC-CCc-----hHHHHHHHHHHHh
Q 040801           99 GYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFGL-ASD-----SFLHNTLINMYSS  169 (323)
Q Consensus        99 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g~-~~~-----~~~~~~li~~~~~  169 (323)
                      .|.+.|++++|++.|.+..+.. +-+...|..+-.++.+.|+   |.+.+....+..- .+.     ..+|..+-..+..
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            3555566666666665555431 1234445555555555555   5555554443210 001     2345556666666


Q ss_pred             cCCCCChHHHHHHHHHHHHc
Q 040801          170 CWCLDQPDEAIKIFYRMEIE  189 (323)
Q Consensus       170 ~g~~~~~~~a~~~~~~m~~~  189 (323)
                      .+   ++++|++.|+.-...
T Consensus        92 ~~---~~~~A~~~~~kal~~  108 (128)
T d1elra_          92 EE---KYKDAIHFYNKSLAE  108 (128)
T ss_dssp             TT---CHHHHHHHHHHHHHH
T ss_pred             hC---CHHHHHHHHHHHHhc
Confidence            66   668888888776554

>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=92.12  E-value=0.39  Score=34.01  Aligned_cols=98  Identities=12%  Similarity=-0.011  Sum_probs=46.0

Q ss_pred             HhCCChHHHHHHHHHHHHCCCCCCc-ccHHHHHHHhcchhh-------------HHHHHHHHHHcCCCCchHHHHHHHHH
Q 040801          101 TNKNLHHEAFLFYHEMIVQGLIPDR-FMFPSLFKSCADIYV-------------EKQLHSQAIKFGLASDSFLHNTLINM  166 (323)
Q Consensus       101 ~~~g~~~~A~~~~~~m~~~g~~p~~-~ty~~ll~~~~~~~~-------------a~~~~~~m~~~g~~~~~~~~~~li~~  166 (323)
                      -+.+.+++|.+.|+.-.+.  .|+. .++..+=.++...++             |...++...+.. .-+..+|..+-.+
T Consensus         8 ~r~~~fe~A~~~~e~al~~--~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~   84 (145)
T d1zu2a1           8 DRILLFEQIRQDAENTYKS--NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHhh--CCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHH
Confidence            3456678888888887663  3443 344444333332221             444444444432 1133445555555


Q ss_pred             HHhcCCCC--------ChHHHHHHHHHHHHcCCCCChHHHHHHHH
Q 040801          167 YSSCWCLD--------QPDEAIKIFYRMEIENVKPNAVTLVNVLT  203 (323)
Q Consensus       167 ~~~~g~~~--------~~~~a~~~~~~m~~~g~~p~~~t~~~li~  203 (323)
                      |...|++.        .+++|.+.|+...+  +.|+..+|..-|.
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~  127 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLE  127 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHH
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHH
Confidence            54443211        23445555544443  3455544444443

>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=91.83  E-value=2.7  Score=34.21  Aligned_cols=155  Identities=14%  Similarity=0.071  Sum_probs=102.6

Q ss_pred             CChhhHHHHHHHHHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCc----------h
Q 040801           88 PTIYTCNSIVRGYTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASD----------S  157 (323)
Q Consensus        88 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~----------~  157 (323)
                      .+...-..++..|-+.|.+++...+++..... -..+...++.++..+++.+. .++.+.+...+-..|          .
T Consensus        97 ~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~-~kl~e~l~~~s~~y~~~k~~~~c~~~  174 (336)
T d1b89a_          97 VHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP-QKMREHLELFWSRVNIPKVLRAAEQA  174 (336)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH-HHHHHHHHHHSTTSCHHHHHHHHHTT
T ss_pred             cCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh-HHHHHHHHhccccCCHHHHHHHHHHc
Confidence            34445577999999999999999999976532 34566778899999988764 455666655322222          1


Q ss_pred             HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHH
Q 040801          158 FLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLM  237 (323)
Q Consensus       158 ~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  237 (323)
                      ..|..++-.|.+.|   ++++|..+.   ...  .++..-....++.+.+..+.+...++.....+.    ++...+.|+
T Consensus       175 ~l~~elv~Ly~~~~---~~~~A~~~~---i~~--~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~----~p~~i~~lL  242 (336)
T d1b89a_         175 HLWAELVFLYDKYE---EYDNAIITM---MNH--PTDAWKEGQFKDIITKVANVELYYRAIQFYLEF----KPLLLNDLL  242 (336)
T ss_dssp             TCHHHHHHHHHHTT---CHHHHHHHH---HHS--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH----CGGGHHHHH
T ss_pred             CChHHHHHHHHhcC---CHHHHHHHH---HHc--chhhhhHHHHHHHHHccCChHHHHHHHHHHHHc----CHHHHHHHH
Confidence            12456666666666   446665543   221  344444556677788888888888888777654    245567777


Q ss_pred             HHHHhcCCHHHHHHHHHhc
Q 040801          238 DAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       238 ~~~~~~g~~~~a~~~~~~m  256 (323)
                      ......-+..+..+.+++-
T Consensus       243 ~~v~~~~d~~r~V~~~~k~  261 (336)
T d1b89a_         243 MVLSPRLDHTRAVNYFSKV  261 (336)
T ss_dssp             HHHGGGCCHHHHHHHHHHT
T ss_pred             HHhccCCCHHHHHHHHHhc
Confidence            7777777777777766543

>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=91.47  E-value=0.14  Score=40.81  Aligned_cols=44  Identities=18%  Similarity=0.121  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHHHhcCCCCChHHHHHHHHHHHH
Q 040801          141 EKQLHSQAIKFGLASDSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEI  188 (323)
Q Consensus       141 a~~~~~~m~~~g~~~~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~  188 (323)
                      |...++...+.. .-|...+..|...|+..|   ++++|.+.|+...+
T Consensus        15 Al~~l~~al~~~-P~d~~ar~~La~lL~~~G---~~e~A~~~l~~a~~   58 (264)
T d1zbpa1          15 ALELLIEAIKAS-PKDASLRSSFIELLCIDG---DFERADEQLMQSIK   58 (264)
T ss_dssp             HHHHHHHHHHTC-TTCHHHHHHHHHHHHHHT---CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHH
Confidence            444444443332 224455666666666666   44666666666554

>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=91.22  E-value=0.17  Score=40.33  Aligned_cols=52  Identities=15%  Similarity=-0.031  Sum_probs=35.7

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhh---HHHHHHHHHHcC
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYV---EKQLHSQAIKFG  152 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~---a~~~~~~m~~~g  152 (323)
                      ..+.|++++|++.+++-.+. -+-|...+..+...++..|+   |.+.++...+..
T Consensus         6 aL~~G~l~eAl~~l~~al~~-~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~   60 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKA-SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLF   60 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHT-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            34667888888888777664 23455777777777887777   666666666543

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=89.47  E-value=2.2  Score=29.33  Aligned_cols=137  Identities=7%  Similarity=-0.050  Sum_probs=78.6

Q ss_pred             HHhCCChHHHHHHHHHHHHCCCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHH---HHHHHHHHHhcCCCCCh
Q 040801          100 YTNKNLHHEAFLFYHEMIVQGLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFL---HNTLINMYSSCWCLDQP  176 (323)
Q Consensus       100 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~---~~~li~~~~~~g~~~~~  176 (323)
                      +...|.+++..++..+...+   -+..-||.+|-.....-+...+++.+..-|--.|..-   .-.++.+|.+.+     
T Consensus        12 ~ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n-----   83 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINN-----   83 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTT-----
T ss_pred             HHHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhc-----
Confidence            45568888889988887653   2334566666655555555566666665553333221   122333333322     


Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcCCHHHHHHHHHhc
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCKFVSRAWDLFVKM  256 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  256 (323)
                                      -+..-++..+..+...|.-++-..+.+.+.+.+ +|++...-.+-.+|-+.|...++.+++.+.
T Consensus        84 ----------------~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~A  146 (161)
T d1wy6a1          84 ----------------TLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEA  146 (161)
T ss_dssp             ----------------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ----------------chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence                            233444555666666666666666666654433 455566666666777777777777777666


Q ss_pred             cCCCC
Q 040801          257 LFPWN  261 (323)
Q Consensus       257 ~~~~~  261 (323)
                      -++|.
T Consensus       147 Ce~G~  151 (161)
T d1wy6a1         147 CKKGE  151 (161)
T ss_dssp             HHTTC
T ss_pred             HHHhH
Confidence            55553

>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=87.58  E-value=2.1  Score=27.37  Aligned_cols=60  Identities=13%  Similarity=-0.119  Sum_probs=45.7

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhC-----CccC-hhhHHHHHHHHHhcCCHHHHHHHHHhccCC
Q 040801          200 NVLTARARARDLRTVKRVHKCVDESG-----FWSH-VELKTTLMDAYCKCKFVSRAWDLFVKMLFP  259 (323)
Q Consensus       200 ~li~~~~~~~~~~~a~~~~~~m~~~g-----~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  259 (323)
                      .+=..+.+.|++++|...|++..+..     ..++ ..+++.|-.+|.+.|++++|...+++..+-
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            34556778899999999988886531     1122 456888999999999999999999998764

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=82.56  E-value=4.5  Score=26.21  Aligned_cols=61  Identities=18%  Similarity=0.159  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCccChhhHHHHHH
Q 040801          177 DEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFWSHVELKTTLMD  238 (323)
Q Consensus       177 ~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  238 (323)
                      -++.+-++.+.....-|+.....+.+++|-+.+|+..|.++++-.+.+ +.++...|..+++
T Consensus        23 we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilq   83 (105)
T d1v54e_          23 WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHH
Confidence            344444444444556677777777777777777777777777666533 2233445555544

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=82.52  E-value=2.4  Score=29.21  Aligned_cols=68  Identities=18%  Similarity=0.034  Sum_probs=43.5

Q ss_pred             chHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCCc
Q 040801          156 DSFLHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGFW  227 (323)
Q Consensus       156 ~~~~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~~  227 (323)
                      +.-..+.-++.+.+.|   .-+.-.++.+++...+ +|+....-.+-.+|-+.|+..++-.++.+..+.|++
T Consensus        85 ~se~vdlALd~lv~~~---kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          85 LNEHVNKALDILVIQG---KRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CCHHHHHHHHHHHHTT---CHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhc---cHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            4444566667777777   4466666666655433 566666666777777777777777777777776654

>d1khda1 a.46.2.1 (A:12-80) Anthranilate phosphoribosyltransferase (TrpD) {Pectobacterium carotovorum [TaxId: 554]}

class: All alpha proteins
fold: Methionine synthase domain-like
superfamily: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
family: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
domain: Anthranilate phosphoribosyltransferase (TrpD)
species: Pectobacterium carotovorum [TaxId: 554]

Probab=82.07  E-value=3.5  Score=24.68  Aligned_cols=66  Identities=6%  Similarity=0.128  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHhcCCCCChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhccCChHHHHHHHHHHHHhCC
Q 040801          159 LHNTLINMYSSCWCLDQPDEAIKIFYRMEIENVKPNAVTLVNVLTARARARDLRTVKRVHKCVDESGF  226 (323)
Q Consensus       159 ~~~~li~~~~~~g~~~~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~~~~~~a~~~~~~m~~~g~  226 (323)
                      ||..+|......+++ ..+++..+++.+.... -++...=..|+....+.-..++.....+.|.+++.
T Consensus         1 t~~~il~kl~~g~~L-s~ee~~~~~~~i~~g~-~~d~qiaafL~al~~kg~t~dEi~g~~~am~~~~~   66 (69)
T d1khda1           1 THQPILEKLFKSQSM-TQEESHQLFAAIVRGE-LEDSQLAAALISMKMRGERPEEIAGAASALLADAQ   66 (69)
T ss_dssp             CCHHHHHHHHTTCCC-CHHHHHHHHHHHTTTC-SCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTSC
T ss_pred             CHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCC
Confidence            467788888877777 7888888888877543 34555444444444555567777777777777664

>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=80.94  E-value=6.9  Score=27.20  Aligned_cols=108  Identities=14%  Similarity=-0.003  Sum_probs=69.3

Q ss_pred             hhHHHH--HHHHHhCCChHHHHHHHHHHHHC-CCCCCcccHHHHHHHhcchhhHHHHHHHHHHcCCCCchHHHHHHHHHH
Q 040801           91 YTCNSI--VRGYTNKNLHHEAFLFYHEMIVQ-GLIPDRFMFPSLFKSCADIYVEKQLHSQAIKFGLASDSFLHNTLINMY  167 (323)
Q Consensus        91 ~~~~~l--i~~~~~~g~~~~A~~~~~~m~~~-g~~p~~~ty~~ll~~~~~~~~a~~~~~~m~~~g~~~~~~~~~~li~~~  167 (323)
                      .+|..+  -..+.+.|++++|++.|++-.+- .-.|+......-         .             ....+|+.+-.+|
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~---------~-------------~~a~~~~nlg~~~   65 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHA---------G-------------FDAFCHAGLAEAL   65 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHH---------H-------------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccc---------h-------------hHHHHHHHHHHHH
Confidence            456666  44566779999999999987651 111332211000         0             0134677777888


Q ss_pred             HhcCCCCChHHHHHHHHHHHHc-----CCCCC-----hHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040801          168 SSCWCLDQPDEAIKIFYRMEIE-----NVKPN-----AVTLVNVLTARARARDLRTVKRVHKCVDE  223 (323)
Q Consensus       168 ~~~g~~~~~~~a~~~~~~m~~~-----g~~p~-----~~t~~~li~~~~~~~~~~~a~~~~~~m~~  223 (323)
                      .+.|   ++++|++-+++....     ...++     ...|+.+-.+|...|+.++|...|++..+
T Consensus        66 ~~lg---~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          66 AGLR---SFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHTT---CHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHcC---ccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888   567888777776531     12222     23678888889999999999999888764

>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=80.79  E-value=2.4  Score=29.56  Aligned_cols=82  Identities=11%  Similarity=-0.088  Sum_probs=51.1

Q ss_pred             ChHHHHHHHHHHHHcCCCCChHHHHHHHHHHhcc----------CChHHHHHHHHHHHHhCCccChhhHHHHHHHHHhcC
Q 040801          175 QPDEAIKIFYRMEIENVKPNAVTLVNVLTARARA----------RDLRTVKRVHKCVDESGFWSHVELKTTLMDAYCKCK  244 (323)
Q Consensus       175 ~~~~a~~~~~~m~~~g~~p~~~t~~~li~~~~~~----------~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~g  244 (323)
                      .+++|.+.|+.-.... +-|...+..+=.+|...          +.+++|...+++..+.. +-+...|..+-.+|...|
T Consensus        12 ~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~g   89 (145)
T d1zu2a1          12 LFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNAYTSFA   89 (145)
T ss_dssp             HHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHcc
Confidence            4578888888877644 23445555555555432          44567777777777653 224566776767776654


Q ss_pred             C-----------HHHHHHHHHhccC
Q 040801          245 F-----------VSRAWDLFVKMLF  258 (323)
Q Consensus       245 ~-----------~~~a~~~~~~m~~  258 (323)
                      +           +++|.+.|++..+
T Consensus        90 ~~~~~~~~~~~~~~~A~~~~~kal~  114 (145)
T d1zu2a1          90 FLTPDETEAKHNFDLATQFFQQAVD  114 (145)
T ss_dssp             HHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHhHHHhhhhhhcccc
Confidence            3           5777777777664