Citrus Sinensis ID: 045555

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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-----
Protein Sequence
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Secondary Structure (PSIPRED)
ccHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHcccccccccHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEHHHHHHHHccccHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEHHHHHHHHccc
Coil and Loop (DISEMBL)
MGFALEIfgnmknkdvISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQtsnirrdefTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Flexible Loop (DISEMBL)
MGFALEIFgnmknkdviSWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFremqtsnirrdefttvRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Low Complexity Region (SEG)
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Disordered region (IsUnstruct)
**FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC***
Disordered Region (DISOPRED)
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Disordered Region (DISEMBL)
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Disordered Region (DISPRO)
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN
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	175	2.2.26 [Sep-21-2011]
Q9LSB8	687	Putative pentatricopeptid	yes	no	1.0	0.254	0.515	5e-51
Q9C866	570	Pentatricopeptide repeat-	no	no	0.977	0.3	0.421	1e-39
Q9SJZ3	681	Pentatricopeptide repeat-	no	no	0.977	0.251	0.385	8e-38
Q9SJG6	559	Pentatricopeptide repeat-	no	no	0.982	0.307	0.367	7e-34
Q9MA50	500	Pentatricopeptide repeat-	no	no	0.96	0.336	0.359	4e-33
Q38959	455	Pentatricopeptide repeat-	no	no	0.965	0.371	0.387	8e-33
Q9FG16	622	Pentatricopeptide repeat-	no	no	0.977	0.274	0.354	3e-32
Q9FFG8	657	Pentatricopeptide repeat-	no	no	0.982	0.261	0.357	2e-31
Q683I9	573	Pentatricopeptide repeat-	no	no	0.977	0.298	0.361	4e-31
Q1PEU4	555	Pentatricopeptide repeat-	no	no	0.988	0.311	0.362	5e-31

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

 Score =  200 bits (508), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 101/196 (51%), Positives = 128/196 (65%), Gaps = 21/196 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A+ IF +MK +DVISWT+IV GY+ RG + +AR YF QMP RD + WT MIDGYLR 
Sbjct: 287 MDIAVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRA 346

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
             F E+L +FREMQ++ +  DEFT V +LT                        ND+ VG
Sbjct: 347 GCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVG 406

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG  EKAQ+VF  M ++DKFTWTAM+VGLA +G G  A+ +F QM   SI+
Sbjct: 407 NALIDMYFKCGCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQ 466

Query: 160 LDEVTYVGVLSACTHN 175
            D++TY+GVLSAC H+
Sbjct: 467 PDDITYLGVLSACNHS 482

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C866|PPR65_ARATH Pentatricopeptide repeat-containing protein At1g31430 OS=Arabidopsis thaliana GN=PCMP-E55 PE=2 SV=1

 Score =  162 bits (410), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 81/192 (42%), Positives = 118/192 (61%), Gaps = 21/192 (10%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A  +F +M++K+V  WT++V GY++ G++D AR  F + P +D VLWTAM++GY++ NRF
Sbjct: 201 ARAVFDSMRDKNVKCWTSMVFGYVSTGRIDEARVLFERSPVKDVVLWTAMMNGYVQFNRF 260

Query: 64  REALTLFREMQTSNIRRDEFTTVRILTTFNN---------------------DIFVGIAL 102
            EAL LFR MQT+ IR D F  V +LT                         D  VG AL
Sbjct: 261 DEALELFRCMQTAGIRPDNFVLVSLLTGCAQTGALEQGKWIHGYINENRVTVDKVVGTAL 320

Query: 103 IDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE 162
           +DMY KCG +E A  VF+++  +D  +WT++I GLA++G    ALD++ +M    +RLD 
Sbjct: 321 VDMYAKCGCIETALEVFYEIKERDTASWTSLIYGLAMNGMSGRALDLYYEMENVGVRLDA 380

Query: 163 VTYVGVLSACTH 174
           +T+V VL+AC H
Sbjct: 381 ITFVAVLTACNH 392

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 =  156 bits (394), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 74/192 (38%), Positives = 118/192 (61%), Gaps = 21/192 (10%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A  IF N++ + ++SWTT++SGY   G +D++R+ F  M E+D VLW AMI G ++  R 
Sbjct: 311 ARRIFDNLEKRTIVSWTTMISGYARCGLLDVSRKLFDDMEEKDVVLWNAMIGGSVQAKRG 370

Query: 64  REALTLFREMQTSNIRRDEFTTVRILT---------------------TFNNDIFVGIAL 102
           ++AL LF+EMQTSN + DE T +  L+                     + + ++ +G +L
Sbjct: 371 QDALALFQEMQTSNTKPDEITMIHCLSACSQLGALDVGIWIHRYIEKYSLSLNVALGTSL 430

Query: 103 IDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE 162
           +DMY KCG++ +A  VF  +  ++  T+TA+I GLA+ G   TA+  F++M+ A I  DE
Sbjct: 431 VDMYAKCGNISEALSVFHGIQTRNSLTYTAIIGGLALHGDASTAISYFNEMIDAGIAPDE 490

Query: 163 VTYVGVLSACTH 174
           +T++G+LSAC H
Sbjct: 491 ITFIGLLSACCH 502

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 =  142 bits (359), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 71/193 (36%), Positives = 111/193 (57%), Gaps = 21/193 (10%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A  IF  M   DV++W +++ G+   G +D A+  F +MP+R+ V W +MI G++R  RF
Sbjct: 180 AWRIFLGMIGFDVVAWNSMIMGFAKCGLIDQAQNLFDEMPQRNGVSWNSMISGFVRNGRF 239

Query: 64  REALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVGIAL 102
           ++AL +FREMQ  +++ D FT V +L                       F  +  V  AL
Sbjct: 240 KDALDMFREMQEKDVKPDGFTMVSLLNACAYLGASEQGRWIHEYIVRNRFELNSIVVTAL 299

Query: 103 IDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE 162
           IDMYCKCG +E+   VF    +K    W +MI+GLA +G  + A+D+FS++ R+ +  D 
Sbjct: 300 IDMYCKCGCIEEGLNVFECAPKKQLSCWNSMILGLANNGFEERAMDLFSELERSGLEPDS 359

Query: 163 VTYVGVLSACTHN 175
           V+++GVL+AC H+
Sbjct: 360 VSFIGVLTACAHS 372

Arabidopsis thaliana (taxid: 3702)

>sp|Q9MA50|PPR13_ARATH Pentatricopeptide repeat-containing protein At1g05750, chloroplastic OS=Arabidopsis thaliana GN=PDE247 PE=2 SV=1

 Score =  140 bits (353), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 68/189 (35%), Positives = 108/189 (57%), Gaps = 21/189 (11%)

Query: 7   IFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREA 66
           +F  M++K+ ++W T++ GY+  GQVD A + F +MPERD + WTAMI+G+++     EA
Sbjct: 131 VFDYMEDKNSVTWNTMIDGYMRSGQVDNAAKMFDKMPERDLISWTAMINGFVKKGYQEEA 190

Query: 67  LTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVGIALIDM 105
           L  FREMQ S ++ D    +  L                       F N++ V  +LID+
Sbjct: 191 LLWFREMQISGVKPDYVAIIAALNACTNLGALSFGLWVHRYVLSQDFKNNVRVSNSLIDL 250

Query: 106 YCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY 165
           YC+CG VE A++VF+ M ++   +W ++IVG A +G+   +L  F +M     + D VT+
Sbjct: 251 YCRCGCVEFARQVFYNMEKRTVVSWNSVIVGFAANGNAHESLVYFRKMQEKGFKPDAVTF 310

Query: 166 VGVLSACTH 174
            G L+AC+H
Sbjct: 311 TGALTACSH 319

Arabidopsis thaliana (taxid: 3702)

>sp|Q38959|PP257_ARATH Pentatricopeptide repeat-containing protein At3g26630, chloroplastic OS=Arabidopsis thaliana GN=PCMP-A6 PE=2 SV=1

 Score =  139 bits (351), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 74/191 (38%), Positives = 105/191 (54%), Gaps = 22/191 (11%)

Query: 6   EIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFRE 65
           ++F  M  + ++SWTT++ G ++  Q+D A   F QMP R+ V WTAMI  Y++  R  E
Sbjct: 175 KVFDKMPGRSIVSWTTMLYGLVSNSQLDSAEIVFNQMPMRNVVSWTAMITAYVKNRRPDE 234

Query: 66  ALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVGIALID 104
           A  LFR MQ  +++ +EFT V +L                       F  D F+G ALID
Sbjct: 235 AFQLFRRMQVDDVKPNEFTIVNLLQASTQLGSLSMGRWVHDYAHKNGFVLDCFLGTALID 294

Query: 105 MYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMF-SQMLRASIRLDEV 163
           MY KCG ++ A++VF  M  K   TW +MI  L + G G+ AL +F      AS+  D +
Sbjct: 295 MYSKCGSLQDARKVFDVMQGKSLATWNSMITSLGVHGCGEEALSLFEEMEEEASVEPDAI 354

Query: 164 TYVGVLSACTH 174
           T+VGVLSAC +
Sbjct: 355 TFVGVLSACAN 365

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FG16|PP367_ARATH Pentatricopeptide repeat-containing protein At5g06540 OS=Arabidopsis thaliana GN=PCMP-H88 PE=2 SV=1

 Score =  137 bits (346), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 68/192 (35%), Positives = 108/192 (56%), Gaps = 21/192 (10%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A  IFG M  +DV+SWT++V+GY   G V+ AR+ F +MP R+   W+ MI+GY + N F
Sbjct: 171 AGRIFGQMGFRDVVSWTSMVAGYCKCGMVENAREMFDEMPHRNLFTWSIMINGYAKNNCF 230

Query: 64  REALTLFREMQTSNIRRDEFTTVRILTTFNN---------------------DIFVGIAL 102
            +A+ LF  M+   +  +E   V ++++  +                     ++ +G AL
Sbjct: 231 EKAIDLFEFMKREGVVANETVMVSVISSCAHLGALEFGERAYEYVVKSHMTVNLILGTAL 290

Query: 103 IDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE 162
           +DM+ +CGD+EKA  VF  +   D  +W+++I GLA+ GH   A+  FSQM+       +
Sbjct: 291 VDMFWRCGDIEKAIHVFEGLPETDSLSWSSIIKGLAVHGHAHKAMHYFSQMISLGFIPRD 350

Query: 163 VTYVGVLSACTH 174
           VT+  VLSAC+H
Sbjct: 351 VTFTAVLSACSH 362

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FFG8|PP417_ARATH Pentatricopeptide repeat-containing protein At5g44230 OS=Arabidopsis thaliana GN=PCMP-H17 PE=2 SV=1

 Score =  134 bits (338), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 70/196 (35%), Positives = 109/196 (55%), Gaps = 24/196 (12%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A ++F  M  +DVISWT +++ Y   G ++ A + F  +P +D V WTAM+ G+ +  + 
Sbjct: 203 ARKVFDEMPERDVISWTELIAAYARVGNMECAAELFESLPTKDMVAWTAMVTGFAQNAKP 262

Query: 64  REALTLFREMQTSNIRRDEFTTVRILT-----------------------TFNNDIFVGI 100
           +EAL  F  M+ S IR DE T    ++                       + ++ + +G 
Sbjct: 263 QEALEYFDRMEKSGIRADEVTVAGYISACAQLGASKYADRAVQIAQKSGYSPSDHVVIGS 322

Query: 101 ALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQML-RASIR 159
           ALIDMY KCG+VE+A  VF  M  K+ FT+++MI+GLA  G    AL +F  M+ +  I+
Sbjct: 323 ALIDMYSKCGNVEEAVNVFMSMNNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIK 382

Query: 160 LDEVTYVGVLSACTHN 175
            + VT+VG L AC+H+
Sbjct: 383 PNTVTFVGALMACSHS 398

Arabidopsis thaliana (taxid: 3702)

>sp|Q683I9|PP295_ARATH Pentatricopeptide repeat-containing protein At3g62890 OS=Arabidopsis thaliana GN=PCMP-H82 PE=2 SV=1

 Score =  134 bits (336), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 72/199 (36%), Positives = 112/199 (56%), Gaps = 28/199 (14%)

Query: 4   ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
           A  +F +  +KD+ +W ++V+ Y   G +D AR+ F +MPER+ + W+ +I+GY+   ++
Sbjct: 116 AQRVFDDSGSKDLPAWNSVVNAYAKAGLIDDARKLFDEMPERNVISWSCLINGYVMCGKY 175

Query: 64  REALTLFREMQTSN-----IRRDEFTTVRILTTFNN---------------------DIF 97
           +EAL LFREMQ        +R +EFT   +L+                         DI 
Sbjct: 176 KEALDLFREMQLPKPNEAFVRPNEFTMSTVLSACGRLGALEQGKWVHAYIDKYHVEIDIV 235

Query: 98  VGIALIDMYCKCGDVEKAQRVFWKM-LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRA 156
           +G ALIDMY KCG +E+A+RVF  +  +KD   ++AMI  LA+ G  D    +FS+M  +
Sbjct: 236 LGTALIDMYAKCGSLERAKRVFNALGSKKDVKAYSAMICCLAMYGLTDECFQLFSEMTTS 295

Query: 157 -SIRLDEVTYVGVLSACTH 174
            +I  + VT+VG+L AC H
Sbjct: 296 DNINPNSVTFVGILGACVH 314

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PEU4|PP201_ARATH Pentatricopeptide repeat-containing protein At2g44880 OS=Arabidopsis thaliana GN=PCMP-E9 PE=2 SV=2

 Score =  133 bits (335), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 71/196 (36%), Positives = 111/196 (56%), Gaps = 23/196 (11%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A  +F  M +K VI+WTT++ GY N   +D AR+ F  MPER+ V W  MI GY + 
Sbjct: 192 MTSARRLFDEMTHKTVITWTTMIHGYCNIKDIDAARKLFDAMPERNLVSWNTMIGGYCQN 251

Query: 61  NRFREALTLFREMQ-TSNIRRDEFTTVRILTTFNN---------------------DIFV 98
            + +E + LF+EMQ T+++  D+ T + +L   ++                      + V
Sbjct: 252 KQPQEGIRLFQEMQATTSLDPDDVTILSVLPAISDTGALSLGEWCHCFVQRKKLDKKVKV 311

Query: 99  GIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASI 158
             A++DMY KCG++EKA+R+F +M  K   +W AMI G A++G+   ALD+F  M+    
Sbjct: 312 CTAILDMYSKCGEIEKAKRIFDEMPEKQVASWNAMIHGYALNGNARAALDLFVTMMIEE- 370

Query: 159 RLDEVTYVGVLSACTH 174
           + DE+T + V++AC H
Sbjct: 371 KPDEITMLAVITACNH 386

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	175
356528966	712	PREDICTED: putative pentatricopeptide re	0.994	0.244	0.620	2e-63
255553251	512	pentatricopeptide repeat-containing prot	0.994	0.339	0.625	3e-63
449491161	744	PREDICTED: LOW QUALITY PROTEIN: putative	0.994	0.233	0.594	2e-62
449436619	723	PREDICTED: putative pentatricopeptide re	0.994	0.240	0.594	2e-62
357468161	874	Pentatricopeptide repeat-containing prot	0.994	0.199	0.584	4e-60
225442904	724	PREDICTED: putative pentatricopeptide re	1.0	0.241	0.591	9e-59
224134923	635	predicted protein [Populus trichocarpa]	0.942	0.259	0.607	8e-58
9294596	695	unnamed protein product [Arabidopsis tha	1.0	0.251	0.515	2e-49
15233234	687	pentatricopeptide repeat-containing prot	1.0	0.254	0.515	2e-49
357127483	552	PREDICTED: putative pentatricopeptide re	0.994	0.315	0.492	7e-48

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

 Score =  246 bits (628), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 121/195 (62%), Positives = 143/195 (73%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A  +F NMKN+DVISWT+IV+G+ N GQ+D+AR+YF Q+PERDYV WTAMIDGYLR+
Sbjct: 259 MDEAQSVFDNMKNRDVISWTSIVTGFANIGQIDLARKYFDQIPERDYVSWTAMIDGYLRM 318

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILT---------------------TFNNDIFVG 99
           NRF EAL LFREMQ SN++ DEFT V ILT                     +  ND FVG
Sbjct: 319 NRFIEALALFREMQMSNVKPDEFTMVSILTACAHLGALELGEWVKTYIDKNSIKNDTFVG 378

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG+V KA++VF +M  KDKFTWTAMIVGLAI+GHG+ AL MFS M+ ASI 
Sbjct: 379 NALIDMYFKCGNVGKAKKVFKEMHHKDKFTWTAMIVGLAINGHGEEALAMFSNMIEASIT 438

Query: 160 LDEVTYVGVLSACTH 174
            DE+TY+GVL ACTH
Sbjct: 439 PDEITYIGVLCACTH 453

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  246 bits (627), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 122/195 (62%), Positives = 143/195 (73%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  AL IF +MK++DVISWT IV+G+ N GQ+DIAR+YF QMPERDYV WTAMIDGYL+V
Sbjct: 240 MSVALGIFESMKSRDVISWTAIVTGFANIGQLDIARKYFDQMPERDYVSWTAMIDGYLQV 299

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
           N F+EAL LF EMQTSN++ DEFT V ILT                        ND +VG
Sbjct: 300 NCFKEALVLFHEMQTSNVKPDEFTMVSILTACAQLGALELGEWVRTYIDKNKVKNDAYVG 359

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG+VEKA+ +F  M R DKFTWTAMIVGLAI+G+G+ ALDMF QML+AS+ 
Sbjct: 360 NALIDMYFKCGNVEKARSIFNSMPRPDKFTWTAMIVGLAINGYGEEALDMFVQMLKASVT 419

Query: 160 LDEVTYVGVLSACTH 174
            DE+TYVGVL ACTH
Sbjct: 420 PDEITYVGVLCACTH 434

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 116/195 (59%), Positives = 144/195 (73%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  AL IF +M N+D+ISWTTIVSG+ N G++D+AR YF +MPE+DYV WTAMIDGY+R 
Sbjct: 291 MDSALGIFRSMNNRDIISWTTIVSGFTNLGEIDVARNYFDKMPEKDYVSWTAMIDGYIRS 350

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
           NRF+EAL LFR MQ +N++ DEFT V +LT                        ND+FV 
Sbjct: 351 NRFKEALELFRNMQATNVKPDEFTMVSVLTACAHLGALELGEWIRTYIDRNKIKNDLFVR 410

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCGDV+KA+ +F +M ++DKFTWTAMIVGLA++GHG+ ALDMFS ML+ASI 
Sbjct: 411 NALIDMYFKCGDVDKAESIFREMSQRDKFTWTAMIVGLAVNGHGEKALDMFSNMLKASIL 470

Query: 160 LDEVTYVGVLSACTH 174
            DE+TY+GVLSACTH
Sbjct: 471 PDEITYIGVLSACTH 485

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 116/195 (59%), Positives = 144/195 (73%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  AL IF +M N+D+ISWTTIVSG+ N G++D+AR YF +MPE+DYV WTAMIDGY+R 
Sbjct: 270 MDSALGIFRSMNNRDIISWTTIVSGFTNLGEIDVARNYFDKMPEKDYVSWTAMIDGYIRS 329

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
           NRF+EAL LFR MQ +N++ DEFT V +LT                        ND+FV 
Sbjct: 330 NRFKEALELFRNMQATNVKPDEFTMVSVLTACAHLGALELGEWIRTYIDRNKIKNDLFVR 389

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCGDV+KA+ +F +M ++DKFTWTAMIVGLA++GHG+ ALDMFS ML+ASI 
Sbjct: 390 NALIDMYFKCGDVDKAESIFREMSQRDKFTWTAMIVGLAVNGHGEKALDMFSNMLKASIL 449

Query: 160 LDEVTYVGVLSACTH 174
            DE+TY+GVLSACTH
Sbjct: 450 PDEITYIGVLSACTH 464

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  235 bits (600), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 114/195 (58%), Positives = 141/195 (72%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A  +F  MK +DVISWT+IV+G+ N  ++D+AR+YF QMPERDYV WTAMIDGYLR+
Sbjct: 291 MDAARGVFDEMKTRDVISWTSIVTGFANTCRIDLARKYFDQMPERDYVSWTAMIDGYLRM 350

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
           NRF+E LTLFR+MQ SN++ DEFT V ILT                        ND F+G
Sbjct: 351 NRFKEVLTLFRDMQMSNVKPDEFTMVSILTACAHLGALELGEWAKTYIDKNKIKNDTFIG 410

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG+VEKA+++F +M +KDKFTWTAMIVGLA +GHG+ AL MFS ML AS+ 
Sbjct: 411 NALIDMYFKCGNVEKAKKIFNEMQKKDKFTWTAMIVGLANNGHGEEALTMFSYMLEASVT 470

Query: 160 LDEVTYVGVLSACTH 174
            DE+TY+GV+ ACTH
Sbjct: 471 PDEITYIGVMCACTH 485

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  231 bits (589), Expect = 9e-59,   Method: Compositional matrix adjust.
 Identities = 116/196 (59%), Positives = 140/196 (71%), Gaps = 21/196 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  AL IF NMK++DVISWT IV+G+ N GQV +AR YF +MPERD+V WTAMIDGYL+V
Sbjct: 271 MDTALGIFDNMKSRDVISWTAIVTGFTNLGQVGLARNYFDKMPERDFVSWTAMIDGYLQV 330

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTTFNN---------------------DIFVG 99
           NRF+E L+LFREMQ +NI+ DEFT V ILT   +                     D FVG
Sbjct: 331 NRFKEVLSLFREMQAANIKPDEFTMVSILTACAHLGALELGEWIKAYIDKNEIKIDSFVG 390

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY  CG+VEKA R+F  M  +DK +WTA+I GLAI+G+G+ ALDMFSQML+ASI 
Sbjct: 391 NALIDMYFNCGNVEKAIRIFNAMPHRDKISWTAVIFGLAINGYGEEALDMFSQMLKASIT 450

Query: 160 LDEVTYVGVLSACTHN 175
            DEVT +GVL ACTH+
Sbjct: 451 PDEVTCIGVLCACTHS 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  228 bits (581), Expect = 8e-58,   Method: Compositional matrix adjust.
 Identities = 113/186 (60%), Positives = 135/186 (72%), Gaps = 21/186 (11%)

Query: 10  NMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTL 69
           N   KDVISWT IV+G++N GQVD AR+YF +MPERD+V WTAMIDGYLR+N ++EAL L
Sbjct: 191 NRIKKDVISWTAIVTGFVNTGQVDAARKYFHKMPERDHVSWTAMIDGYLRLNCYKEALML 250

Query: 70  FREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVGIALIDMYCK 108
           FREMQTS I+ DEFT V +LT                        ND FVG ALIDMY K
Sbjct: 251 FREMQTSKIKPDEFTMVSVLTACAQLGALELGEWIRTYIDKNKVKNDTFVGNALIDMYFK 310

Query: 109 CGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGV 168
           CG+VE A  +F  + ++DKFTWTAM+VGLAI+G G+ AL+MFSQML+AS+  DEVTYVGV
Sbjct: 311 CGNVEMALSIFNTLPQRDKFTWTAMVVGLAINGCGEEALNMFSQMLKASVTPDEVTYVGV 370

Query: 169 LSACTH 174
           LSACTH
Sbjct: 371 LSACTH 376

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9294596|dbj|BAB02877.1| unnamed protein product [Arabidopsis thaliana]

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/196 (51%), Positives = 128/196 (65%), Gaps = 21/196 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A+ IF +MK +DVISWT+IV GY+ RG + +AR YF QMP RD + WT MIDGYLR 
Sbjct: 287 MDIAVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRA 346

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
             F E+L +FREMQ++ +  DEFT V +LT                        ND+ VG
Sbjct: 347 GCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVG 406

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG  EKAQ+VF  M ++DKFTWTAM+VGLA +G G  A+ +F QM   SI+
Sbjct: 407 NALIDMYFKCGCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQ 466

Query: 160 LDEVTYVGVLSACTHN 175
            D++TY+GVLSAC H+
Sbjct: 467 PDDITYLGVLSACNHS 482

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/196 (51%), Positives = 128/196 (65%), Gaps = 21/196 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A+ IF +MK +DVISWT+IV GY+ RG + +AR YF QMP RD + WT MIDGYLR 
Sbjct: 287 MDIAVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRA 346

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
             F E+L +FREMQ++ +  DEFT V +LT                        ND+ VG
Sbjct: 347 GCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVG 406

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            ALIDMY KCG  EKAQ+VF  M ++DKFTWTAM+VGLA +G G  A+ +F QM   SI+
Sbjct: 407 NALIDMYFKCGCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQ 466

Query: 160 LDEVTYVGVLSACTHN 175
            D++TY+GVLSAC H+
Sbjct: 467 PDDITYLGVLSACNHS 482

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357127483|ref|XP_003565409.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g15930-like [Brachypodium distachyon]

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 96/195 (49%), Positives = 130/195 (66%), Gaps = 21/195 (10%)

Query: 1   MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
           M  A E+F  M+ ++ +SWT+++SG++  GQVD AR  F  MPERD V WTAMIDGY++ 
Sbjct: 174 MDAAWELFEGMEVRNTVSWTSVISGFLRLGQVDQARTLFDCMPERDTVSWTAMIDGYVQA 233

Query: 61  NRFREALTLFREMQTSNIRRDEFTTVRILTT---------------------FNNDIFVG 99
            +FREAL +FREMQ S +R DEFT V ++T                         D FVG
Sbjct: 234 GQFREALEMFREMQFSKVRADEFTMVSVVTACAQLGALETGEWARIYMSRHGIKMDTFVG 293

Query: 100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR 159
            AL+DMY KCG +++A  VF +M  +DKFTWTA+I+GLA++GHG+ A++MF +MLR    
Sbjct: 294 NALVDMYSKCGSIQQALGVFKEMYIRDKFTWTAVILGLAVNGHGEEAINMFYRMLRVFEA 353

Query: 160 LDEVTYVGVLSACTH 174
            DEVT++GVL+ACTH
Sbjct: 354 PDEVTFIGVLTACTH 368

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	175
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.497	0.127	0.459	6.3e-35
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.428	0.101	0.493	6.2e-34
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.491	0.161	0.406	1.9e-28
TAIR|locus:2161018	530	AT5G56310 "AT5G56310" [Arabido	0.468	0.154	0.439	5.4e-28
TAIR|locus:2054966	555	AHG11 "ABA hypersensitive germ	0.817	0.257	0.331	3.8e-14
TAIR|locus:2006927	538	AT1G33350 [Arabidopsis thalian	0.462	0.150	0.395	1.9e-26
TAIR|locus:2027589	611	PGN "AT1G56570" [Arabidopsis t	0.474	0.135	0.404	3.3e-26
TAIR|locus:2129361	612	AT4G14050 [Arabidopsis thalian	0.474	0.135	0.409	4.2e-26
TAIR|locus:2018092	656	MEF9 "AT1G62260" [Arabidopsis	0.754	0.201	0.333	3.1e-14
TAIR|locus:2047017	597	AT2G21090 "AT2G21090" [Arabido	0.48	0.140	0.404	2.9e-12

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

 Score = 221 (82.9 bits), Expect = 6.3e-35, Sum P(2) = 6.3e-35
 Identities = 40/87 (45%), Positives = 60/87 (68%)

Query:     4 ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
             A  IF N++ + ++SWTT++SGY   G +D++R+ F  M E+D VLW AMI G ++  R 
Sbjct:   311 ARRIFDNLEKRTIVSWTTMISGYARCGLLDVSRKLFDDMEEKDVVLWNAMIGGSVQAKRG 370

Query:    64 REALTLFREMQTSNIRRDEFTTVRILT 90
             ++AL LF+EMQTSN + DE T +  L+
Sbjct:   371 QDALALFQEMQTSNTKPDEITMIHCLS 397

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 210 (79.0 bits), Expect = 6.2e-34, Sum P(2) = 6.2e-34
 Identities = 37/75 (49%), Positives = 54/75 (72%)

Query:   101 ALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL 160
             +LIDMY KCGD+E A +VF  +L K   +W AMI G A+ G  D + D+FS+M +  I+ 
Sbjct:   409 SLIDMYAKCGDIEAAHQVFNSILHKSLSSWNAMIFGFAMHGRADASFDLFSRMRKIGIQP 468

Query:   161 DEVTYVGVLSACTHN 175
             D++T+VG+LSAC+H+
Sbjct:   469 DDITFVGLLSACSHS 483

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

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

 Score = 178 (67.7 bits), Expect = 1.9e-28, Sum P(2) = 1.9e-28
 Identities = 35/86 (40%), Positives = 52/86 (60%)

Query:     4 ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRF 63
             A ++F  M  +DVISW +++SGY   GQ+  A+  F  M ++  V WTAMI GY  +  +
Sbjct:   163 AHKVFDEMYERDVISWNSLLSGYARLGQMKKAKGLFHLMLDKTIVSWTAMISGYTGIGCY 222

Query:    64 REALTLFREMQTSNIRRDEFTTVRIL 89
              EA+  FREMQ + I  DE + + +L
Sbjct:   223 VEAMDFFREMQLAGIEPDEISLISVL 248

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2161018 AT5G56310 "AT5G56310" [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 5.4e-28, Sum P(2) = 5.4e-28
 Identities = 36/82 (43%), Positives = 56/82 (68%)

Query:    93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ 152
             N  + +  A+IDMY K G++ KA  VF  +  ++  TWT +I GLA  GHG  AL MF++
Sbjct:   282 NRAVSLNNAVIDMYAKSGNITKALDVFECVNERNVVTWTTIIAGLATHGHGAEALAMFNR 341

Query:   153 MLRASIRLDEVTYVGVLSACTH 174
             M++A +R ++VT++ +LSAC+H
Sbjct:   342 MVKAGVRPNDVTFIAILSACSH 363

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2054966 AHG11 "ABA hypersensitive germination 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 51/154 (33%), Positives = 80/154 (51%)

Query:     1 MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
             M  A  +F  M +K VI+WTT++ GY N   +D AR+ F  MPER+ V W  MI GY + 
Sbjct:   192 MTSARRLFDEMTHKTVITWTTMIHGYCNIKDIDAARKLFDAMPERNLVSWNTMIGGYCQN 251

Query:    61 NRFREALTLFREMQ-TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVF 119
              + +E + LF+EMQ T+++  D+ T + +L   ++    G   +  +C C      QR  
Sbjct:   252 KQPQEGIRLFQEMQATTSLDPDDVTILSVLPAISD---TGALSLGEWCHCF----VQR-- 302

Query:   120 WKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQM 153
              K L K     TA++   +  G  + A  +F +M
Sbjct:   303 -KKLDKKVKVCTAILDMYSKCGEIEKAKRIFDEM 335

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2006927 AT1G33350 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 1.9e-26, Sum P(2) = 1.9e-26
 Identities = 34/86 (39%), Positives = 58/86 (67%)

Query:    93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFT-WTAMIVGLAISGHGDTALDMFS 151
             ++D+FV  +L+D+Y KCG++E+A  VF KM  K   T W +MI   A+ G  + A+ +F 
Sbjct:   292 SSDVFVSNSLVDLYGKCGNLEEASSVF-KMASKKSLTAWNSMINCFALHGRSEEAIAVFE 350

Query:   152 QMLRASI---RLDEVTYVGVLSACTH 174
             +M++ +I   + D +T++G+L+ACTH
Sbjct:   351 EMMKLNINDIKPDHITFIGLLNACTH 376

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 194 (73.4 bits), Expect = 3.3e-26, Sum P(2) = 3.3e-26
 Identities = 34/84 (40%), Positives = 59/84 (70%)

Query:    92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKML-RKDKFTWTAMIVGLAISGHGDTALDMF 150
             FN ++ +  ALIDMY KCG++  +QRVF +++ R++  +WT+M++G    G+G  A+++F
Sbjct:   344 FNKNVELANALIDMYAKCGNIPDSQRVFGEIVDRRNLVSWTSMMIGYGSHGYGAEAVELF 403

Query:   151 SQMLRASIRLDEVTYVGVLSACTH 174
              +M+ + IR D + ++ VLSAC H
Sbjct:   404 DKMVSSGIRPDRIVFMAVLSACRH 427

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

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

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

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

TAIR|locus:2129361 AT4G14050 [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 4.2e-26, Sum P(2) = 4.2e-26
 Identities = 34/83 (40%), Positives = 57/83 (68%)

Query:    92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFS 151
             F++ +F+  ALIDMY KC DV  A+ +F +M  +D  +WT++IVG+A  G  + AL ++ 
Sbjct:   269 FDSCVFISNALIDMYAKCSDVIAAKDIFSRMRHRDVVSWTSLIVGMAQHGQAEKALALYD 328

Query:   152 QMLRASIRLDEVTYVGVLSACTH 174
              M+   ++ +EVT+VG++ AC+H
Sbjct:   329 DMVSHGVKPNEVTFVGLIYACSH 351

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016020 "membrane" evidence=IDA

TAIR|locus:2018092 MEF9 "AT1G62260" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 3.1e-14, P = 3.1e-14
 Identities = 51/153 (33%), Positives = 83/153 (54%)

Query:     4 ALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVN-- 61
             A +IF  ++ ++ ++W T++SGY+ R +++ AR+ F  MP+RD V W  MI GY+     
Sbjct:    59 ARDIFEKLEARNTVTWNTMISGYVKRREMNQARKLFDVMPKRDVVTWNTMISGYVSCGGI 118

Query:    62 RF-REALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFW 120
             RF  EA  LF EM +    RD F+       +N        +I  Y K   + +A  +F 
Sbjct:   119 RFLEEARKLFDEMPS----RDSFS-------WNT-------MISGYAKNRRIGEALLLFE 160

Query:   121 KMLRKDKFTWTAMIVGLAISGHGDTALDMFSQM 153
             KM  ++  +W+AMI G   +G  D+A+ +F +M
Sbjct:   161 KMPERNAVSWSAMITGFCQNGEVDSAVVLFRKM 193

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0016554 "cytidine to uridine editing" evidence=IMP

TAIR|locus:2047017 AT2G21090 "AT2G21090" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 2.9e-12, P = 2.9e-12
 Identities = 34/84 (40%), Positives = 50/84 (59%)

Query:     1 MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV 60
             M  A   F  M  KD+  WTT++SGY   G ++ A + F +MPE++ V WTA+I GY+R 
Sbjct:   230 MESAKRCFDEMTVKDIHIWTTLISGYAKLGDMEAAEKLFCEMPEKNPVSWTALIAGYVRQ 289

Query:    61 NRFREALTLFREMQTSNIRRDEFT 84
                  AL LFR+M    ++ ++FT
Sbjct:   290 GSGNRALDLFRKMIALGVKPEQFT 313

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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: GSVIVG00000293001 SubName- Full=Chromosome chr9 scaffold_104, whole genome shotgun sequence; (724 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	175
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-29
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-26
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-25
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-23
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	5e-23
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-21
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	7e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	5e-06
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-06
pfam01535	31	pfam01535, PPR, PPR repeat	1e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002

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

 Score =  113 bits (283), Expect = 2e-29
 Identities = 57/164 (34%), Positives = 84/164 (51%), Gaps = 21/164 (12%)

Query: 30  GQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFT---TV 86
           G ++ AR  F  MPE+  V W +M+ GY       EAL L+ EM+ S +  D+FT    +
Sbjct: 273 GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMI 332

Query: 87  RILTT------------------FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKF 128
           RI +                   F  DI    AL+D+Y K G +E A+ VF +M RK+  
Sbjct: 333 RIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLI 392

Query: 129 TWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC 172
           +W A+I G    G G  A++MF +M+   +  + VT++ VLSAC
Sbjct: 393 SWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSAC 436

Length = 697

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

 Score =  103 bits (259), Expect = 3e-26
 Identities = 52/197 (26%), Positives = 89/197 (45%), Gaps = 25/197 (12%)

Query: 2   GFALEIFGNMKNK----DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGY 57
                ++ ++++     D      ++  ++  G +  AR+ F +MPER+   W  +I G 
Sbjct: 140 RCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGL 199

Query: 58  LRVNRFREALTLFREM--QTSNIRRDEFTT-VRILTTFN------------------NDI 96
           +    +REA  LFREM    S+     F   +R                         D 
Sbjct: 200 VDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDT 259

Query: 97  FVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRA 156
           FV  ALIDMY KCGD+E A+ VF  M  K    W +M+ G A+ G+ + AL ++ +M  +
Sbjct: 260 FVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDS 319

Query: 157 SIRLDEVTYVGVLSACT 173
            + +D+ T+  ++   +
Sbjct: 320 GVSIDQFTFSIMIRIFS 336

Length = 697

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

 Score =  100 bits (250), Expect = 6e-25
 Identities = 58/172 (33%), Positives = 84/172 (48%), Gaps = 21/172 (12%)

Query: 22  IVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRD 81
           ++S ++  G++  A   F +MPERD   W  ++ GY +   F EAL L+  M  + +R D
Sbjct: 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPD 186

Query: 82  EFTTVRILTT---------------------FNNDIFVGIALIDMYCKCGDVEKAQRVFW 120
            +T   +L T                     F  D+ V  ALI MY KCGDV  A+ VF 
Sbjct: 187 VYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFD 246

Query: 121 KMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC 172
           +M R+D  +W AMI G   +G     L++F  M   S+  D +T   V+SAC
Sbjct: 247 RMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAC 298

Length = 857

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

 Score = 96.1 bits (239), Expect = 1e-23
 Identities = 62/192 (32%), Positives = 92/192 (47%), Gaps = 30/192 (15%)

Query: 2   GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVN 61
           GF L++       DV++   +++ Y+  G V  AR  F +MP RD + W AMI GY    
Sbjct: 217 GFELDV-------DVVN--ALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENG 267

Query: 62  RFREALTLFREMQTSNIRRDEFTTVRIL---------------------TTFNNDIFVGI 100
              E L LF  M+  ++  D  T   ++                     T F  D+ V  
Sbjct: 268 ECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCN 327

Query: 101 ALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL 160
           +LI MY   G   +A++VF +M  KD  +WTAMI G   +G  D AL+ ++ M + ++  
Sbjct: 328 SLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSP 387

Query: 161 DEVTYVGVLSAC 172
           DE+T   VLSAC
Sbjct: 388 DEITIASVLSAC 399

Length = 857

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

 Score = 94.5 bits (235), Expect = 5e-23
 Identities = 56/180 (31%), Positives = 87/180 (48%), Gaps = 24/180 (13%)

Query: 15  DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFRE-ALTLFREM 73
           DV    +++  Y++ G    A + F++M  +D V WTAMI GY + N   + AL  +  M
Sbjct: 322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK-NGLPDKALETYALM 380

Query: 74  QTSNIRRDEFTTVRIL---------------------TTFNNDIFVGIALIDMYCKCGDV 112
           +  N+  DE T   +L                         + + V  ALI+MY KC  +
Sbjct: 381 EQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCI 440

Query: 113 EKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC 172
           +KA  VF  +  KD  +WT++I GL ++     AL  F QML  +++ + VT +  LSAC
Sbjct: 441 DKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSAC 499

Length = 857

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

 Score = 90.7 bits (225), Expect = 1e-21
 Identities = 49/179 (27%), Positives = 85/179 (47%), Gaps = 23/179 (12%)

Query: 16  VISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQT 75
           V+    ++  Y     +D A + F  +PE+D + WT++I G    NR  EAL  FR+M  
Sbjct: 424 VVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL 483

Query: 76  SNIRRDEFTTVRIL---------------------TTFNNDIFVGIALIDMYCKCGDVEK 114
           + ++ +  T +  L                     T    D F+  AL+D+Y +CG +  
Sbjct: 484 T-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNY 542

Query: 115 AQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT 173
           A   F     KD  +W  ++ G    G G  A+++F++M+ + +  DEVT++ +L AC+
Sbjct: 543 AWNQF-NSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACS 600

Length = 857

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

 Score = 60.6 bits (147), Expect = 3e-11
 Identities = 27/75 (36%), Positives = 45/75 (60%)

Query: 98  VGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRAS 157
           +G A++ M+ + G++  A  VF KM  +D F+W  ++ G A +G+ D AL ++ +ML A 
Sbjct: 123 LGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAG 182

Query: 158 IRLDEVTYVGVLSAC 172
           +R D  T+  VL  C
Sbjct: 183 VRPDVYTFPCVLRTC 197

Length = 857

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

 Score = 52.6 bits (126), Expect = 2e-08
 Identities = 40/174 (22%), Positives = 70/174 (40%), Gaps = 27/174 (15%)

Query: 2   GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVN 61
           GF L+I  N         T +V  Y   G+++ AR  F +MP ++ + W A+I GY    
Sbjct: 355 GFPLDIVAN---------TALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHG 405

Query: 62  RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK-CGDVEKAQRVFW 120
           R  +A+ +F  M    +  +  T + +L+                C+  G  E+   +F 
Sbjct: 406 RGTKAVEMFERMIAEGVAPNHVTFLAVLSA---------------CRYSGLSEQGWEIFQ 450

Query: 121 KMLRKDKFTWTAMIVGLAISGHGDTAL--DMFSQMLRASIRLDEVTYVGVLSAC 172
            M    +    AM     I   G   L  + ++ + RA  +     +  +L+AC
Sbjct: 451 SMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTAC 504

Length = 697

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

 Score = 46.6 bits (112), Expect = 7e-08
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 14/63 (22%)

Query: 46  DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM 105
           D V +  +IDGY +  +  EAL LF EM+   I+ + +       T++        LID 
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVY-------TYS-------ILIDG 47

Query: 106 YCK 108
            CK
Sbjct: 48  LCK 50

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

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

 Score = 41.6 bits (99), Expect = 5e-06
 Identities = 12/48 (25%), Positives = 23/48 (47%)

Query: 125 KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC 172
            D  T+  +I G    G  + AL +F++M +  I+ +  TY  ++   
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 40.9 bits (97), Expect = 9e-06
 Identities = 14/48 (29%), Positives = 29/48 (60%), Gaps = 4/48 (8%)

Query: 14 KDVISWTTIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGY 57
           DV+++ T++ GY  +G+V+ A + F +M +R    +   ++ +IDG 
Sbjct: 1  PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 40.1 bits (95), Expect = 1e-05
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 48 VLWTAMIDGYLRVNRFREALTLFREMQTSNI 78
          V + ++I GY +  +  EAL LF+EM+   +
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 40.1 bits (95), Expect = 2e-05
 Identities = 16/42 (38%), Positives = 27/42 (64%), Gaps = 4/42 (9%)

Query: 101 ALIDMYCKCGDVEKAQRVFWKMLRK----DKFTWTAMIVGLA 138
            LID YCK G VE+A ++F +M ++    + +T++ +I GL 
Sbjct: 8   TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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

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

 Score = 39.8 bits (94), Expect = 2e-05
 Identities = 14/35 (40%), Positives = 19/35 (54%)

Query: 48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE 82
          V +  +IDG  +  R  EAL LF+EM+   I  D 
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 40/169 (23%), Positives = 76/169 (44%), Gaps = 24/169 (14%)

Query: 15  DVISWTTIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLF 70
           D   +TT++S     G+VD   + F +M     E +   + A+IDG  R  +  +A   +
Sbjct: 471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAY 530

Query: 71  REMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM------LR 124
             M++ N++ D     R++  FN       ALI    + G V++A  V  +M      + 
Sbjct: 531 GIMRSKNVKPD-----RVV--FN-------ALISACGQSGAVDRAFDVLAEMKAETHPID 576

Query: 125 KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT 173
            D  T  A++   A +G  D A +++  +   +I+     Y   +++C+
Sbjct: 577 PDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCS 625

Length = 1060

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

 Score = 34.0 bits (79), Expect = 0.002
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 101 ALIDMYCKCGDVEKAQRVFWKMLRKD 126
           +LI  YCK G +E+A  +F +M  K 
Sbjct: 5   SLISGYCKAGKLEEALELFKEMKEKG 30

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

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

 Score = 34.0 bits (79), Expect = 0.002
 Identities = 11/35 (31%), Positives = 18/35 (51%)

Query: 128 FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE 162
            T+  +I GL  +G  + AL++F +M    I  D 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	175
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
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
PLN03077	857	Protein ECB2; Provisional	100.0
PF13041	50	PPR_2: PPR repeat family	99.74
PF13041	50	PPR_2: PPR repeat family	99.6
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.46
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.42
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.23
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.21
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.2
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.15
PF12854	34	PPR_1: PPR repeat	99.13
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.1
PF12854	34	PPR_1: PPR repeat	99.03
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	99.0
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.94
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.9
PRK12370	553	invasion protein regulator; Provisional	98.9
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.89
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.87
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.86
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.86
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.85
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.84
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.83
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.82
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.79
PRK12370	553	invasion protein regulator; Provisional	98.74
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.73
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.7
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.68
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.66
KOG1126	638	consensus DNA-binding cell division cycle control	98.65
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.65
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.64
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.63
KOG2003	840	consensus TPR repeat-containing protein [General f	98.63
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.63
PRK15359	144	type III secretion system chaperone protein SscB;	98.62
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.61
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.59
PRK14574	822	hmsH outer membrane protein; Provisional	98.59
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.58
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.56
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.55
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.54
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.5
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.49
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.48
KOG1126	638	consensus DNA-binding cell division cycle control	98.48
PRK11189	296	lipoprotein NlpI; Provisional	98.46
PRK15359	144	type III secretion system chaperone protein SscB;	98.45
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	98.45
PRK11189	296	lipoprotein NlpI; Provisional	98.44
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	98.42
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.41
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	98.41
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.4
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.39
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.39
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.38
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.37
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.35
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.35
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.34
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.33
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.32
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.3
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.29
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.28
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.26
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.18
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.18
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.17
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.17
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.15
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.14
PRK14574	822	hmsH outer membrane protein; Provisional	98.13
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.12
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.11
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.04
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.01
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.01
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.99
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.99
KOG1129	478	consensus TPR repeat-containing protein [General f	97.98
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.98
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.96
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.95
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.92
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.87
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.87
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.85
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.84
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.84
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.83
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.83
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.83
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.83
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.8
KOG1129	478	consensus TPR repeat-containing protein [General f	97.78
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.73
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.72
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.7
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.7
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.69
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.68
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.67
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.66
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.65
KOG2076	895	consensus RNA polymerase III transcription factor	97.63
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.63
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.62
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	97.62
KOG1125	579	consensus TPR repeat-containing protein [General f	97.61
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.61
KOG2003	840	consensus TPR repeat-containing protein [General f	97.6
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.6
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.59
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.56
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.54
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.54
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.54
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.53
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.51
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.49
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.46
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.46
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.46
PF12688	120	TPR_5: Tetratrico peptide repeat	97.46
KOG2076	895	consensus RNA polymerase III transcription factor	97.45
KOG0553	304	consensus TPR repeat-containing protein [General f	97.44
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.39
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.39
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.36
PLN02789	320	farnesyltranstransferase	97.35
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.34
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.33
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.33
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.32
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.28
KOG1125	579	consensus TPR repeat-containing protein [General f	97.24
PRK10803	263	tol-pal system protein YbgF; Provisional	97.24
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.23
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.23
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.22
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.22
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.18
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.17
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.15
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.15
PF13371	73	TPR_9: Tetratricopeptide repeat	97.13
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.12
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.11
PF12688	120	TPR_5: Tetratrico peptide repeat	97.11
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.09
KOG0553	304	consensus TPR repeat-containing protein [General f	97.09
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.07
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.06
PLN02789	320	farnesyltranstransferase	96.97
KOG0495	913	consensus HAT repeat protein [RNA processing and m	96.96
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.94
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.88
KOG2376	652	consensus Signal recognition particle, subunit Srp	96.86
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.84
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.83
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.76
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.74
PRK10803	263	tol-pal system protein YbgF; Provisional	96.73
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.72
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	96.7
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.64
PF13371	73	TPR_9: Tetratricopeptide repeat	96.6
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.6
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.58
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.57
PRK14720	906	transcript cleavage factor/unknown domain fusion p	96.56
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.55
KOG3941	406	consensus Intermediate in Toll signal transduction	96.55
PRK15331	165	chaperone protein SicA; Provisional	96.5
COG3629	280	DnrI DNA-binding transcriptional activator of the	96.48
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.47
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.45
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.45
KOG2376	652	consensus Signal recognition particle, subunit Srp	96.27
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.24
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	96.24
PRK15331	165	chaperone protein SicA; Provisional	96.15
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.07
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	96.05
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.03
KOG3941	406	consensus Intermediate in Toll signal transduction	96.02
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	95.95
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.75
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.73
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.72
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	95.71
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.69
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.69
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.48
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.45
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.44
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.37
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	95.32
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.28
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	95.2
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	95.08
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	95.06
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	94.91
PRK04841	903	transcriptional regulator MalT; Provisional	94.9
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	94.89
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	94.87
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.75
PF13512	142	TPR_18: Tetratricopeptide repeat	94.72
KOG1128	777	consensus Uncharacterized conserved protein, conta	94.72
KOG2041	1189	consensus WD40 repeat protein [General function pr	94.7
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	94.67
PF13428	44	TPR_14: Tetratricopeptide repeat	94.62
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.61
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	94.09
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.98
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.97
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	93.91
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.83
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	93.8
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	93.7
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.65
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	93.53
PF13428	44	TPR_14: Tetratricopeptide repeat	93.52
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	93.45
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.45
PRK04841	903	transcriptional regulator MalT; Provisional	93.44
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	93.07
PF13512	142	TPR_18: Tetratricopeptide repeat	93.02
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.93
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	92.88
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.69
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.68
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	92.55
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.52
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.48
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.43
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	92.33
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	92.31
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	92.29
KOG4555	175	consensus TPR repeat-containing protein [Function	92.06
COG4105	254	ComL DNA uptake lipoprotein [General function pred	91.96
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	91.87
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	91.81
PF13762	145	MNE1: Mitochondrial splicing apparatus component	91.62
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	91.37
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	90.94
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	90.88
COG3118	304	Thioredoxin domain-containing protein [Posttransla	90.76
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	90.69
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	90.51
PRK10564	303	maltose regulon periplasmic protein; Provisional	90.27
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	90.18
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	89.91
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	89.89
KOG4555	175	consensus TPR repeat-containing protein [Function	89.63
COG4455	273	ImpE Protein of avirulence locus involved in tempe	89.61
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	89.36
PF13431	34	TPR_17: Tetratricopeptide repeat	89.35
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	89.35
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.33
COG4455	273	ImpE Protein of avirulence locus involved in tempe	89.01
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	88.85
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	88.75
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	88.68
KOG2041	1189	consensus WD40 repeat protein [General function pr	88.35
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	88.33
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	88.26
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	88.23
COG4700	251	Uncharacterized protein conserved in bacteria cont	88.04
COG3118	304	Thioredoxin domain-containing protein [Posttransla	88.01
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	87.44
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	87.38
KOG4648	536	consensus Uncharacterized conserved protein, conta	87.1
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	86.76
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	86.66
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	86.28
KOG1585	308	consensus Protein required for fusion of vesicles	85.98
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	85.67
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	84.83
COG4105	254	ComL DNA uptake lipoprotein [General function pred	84.65
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	84.56
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	84.06
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	83.76
PRK09687	280	putative lyase; Provisional	83.39
KOG4234	271	consensus TPR repeat-containing protein [General f	83.13
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	83.02
KOG2796	366	consensus Uncharacterized conserved protein [Funct	82.97
PRK11906	458	transcriptional regulator; Provisional	82.91
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	82.72
COG3898	531	Uncharacterized membrane-bound protein [Function u	82.44
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.31
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	81.99
PF10366	108	Vps39_1: Vacuolar sorting protein 39 domain 1; Int	81.82
KOG2610	491	consensus Uncharacterized conserved protein [Funct	81.72
KOG2908	380	consensus 26S proteasome regulatory complex, subun	81.69
PF10475	291	DUF2450: Protein of unknown function N-terminal do	81.06
PF13762	145	MNE1: Mitochondrial splicing apparatus component	80.91
PRK10564	303	maltose regulon periplasmic protein; Provisional	80.88
KOG4234	271	consensus TPR repeat-containing protein [General f	80.7
PF14669	233	Asp_Glu_race_2: Putative aspartate racemase	80.69
KOG4570	418	consensus Uncharacterized conserved protein [Funct	80.57
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	80.49
PF14669	233	Asp_Glu_race_2: Putative aspartate racemase	80.28
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	80.14

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

Probab=100.00  E-value=4.1e-37  Score=244.97  Aligned_cols=162  Identities=35%  Similarity=0.616  Sum_probs=156.8

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---   90 (175)
                      ||..+||+||.+|++.|++++|.++|+.|.++|.++||+||.+|++.|++++|.++|++|.+.|+.||..||+.++.   
T Consensus       257 ~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~  336 (697)
T PLN03081        257 GDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFS  336 (697)
T ss_pred             ccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            46667789999999999999999999999999999999999999999999999999999999999999999999998   


Q ss_pred             ------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           91 ------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        91 ------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                                        ++.||..++|+||++|++.|++++|.++|++|.+||..+||+||.+|+++|+.++|.++|++
T Consensus       337 ~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~  416 (697)
T PLN03081        337 RLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFER  416 (697)
T ss_pred             hccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHH
Confidence                              67999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHCCCCCcHHHHHHHHhhhcCC
Q 045555          153 MLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       153 m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      |.+.|+.||..||+.+|.+|+++
T Consensus       417 M~~~g~~Pd~~T~~~ll~a~~~~  439 (697)
T PLN03081        417 MIAEGVAPNHVTFLAVLSACRYS  439 (697)
T ss_pred             HHHhCCCCCHHHHHHHHHHHhcC
Confidence            99999999999999999999874

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

Probab=100.00  E-value=1.7e-35  Score=235.69  Aligned_cols=174  Identities=30%  Similarity=0.519  Sum_probs=166.4

Q ss_pred             chHHHHhhccCC----CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            2 GFALEIFGNMKN----KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         2 ~~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +.|.+++..|.+    ||..+||.++.+|++.|+++.|.++|++|.+||.++||++|.+|++.|++++|+++|++|.+.|
T Consensus       140 ~~a~~l~~~m~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g  219 (697)
T PLN03081        140 RCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDG  219 (697)
T ss_pred             HHHHHHHHHHHHhCCCcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhC
Confidence            457778888764    8999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHhhh---------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHH
Q 045555           78 IRRDEFTTVRILT---------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVG  136 (175)
Q Consensus        78 ~~p~~~~~~~l~~---------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~  136 (175)
                      +.|+..||+.++.                     ++.||..++|+||++|++.|++++|.++|++|.++|+.+||++|.+
T Consensus       220 ~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~  299 (697)
T PLN03081        220 SDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAG  299 (697)
T ss_pred             CCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHH
Confidence            9999999999876                     6789999999999999999999999999999999999999999999


Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcCC
Q 045555          137 LAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       137 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      |++.|++++|.++|++|.+.|+.||..||+.++.+|++.
T Consensus       300 y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~  338 (697)
T PLN03081        300 YALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRL  338 (697)
T ss_pred             HHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999863

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=7.2e-35  Score=236.92  Aligned_cols=174  Identities=21%  Similarity=0.313  Sum_probs=156.3

Q ss_pred             chHHHHhhccC------CCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC----CChhHHHHHHHHHhccCChHHHHHHHH
Q 045555            2 GFALEIFGNMK------NKDVISWTTIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~   71 (175)
                      ++|.++|++|.      .||..+|+++|.+|++.|++++|.++|+.|.+    |+..+|+.+|.+|++.|++++|.++|+
T Consensus       559 deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~  638 (1060)
T PLN03218        559 DRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYD  638 (1060)
T ss_pred             HHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            57888888884      37888888888888888888888888888874    577889999999999999999999999


Q ss_pred             HhHhCCCCCChHHHHHhhh---------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh----cCCC
Q 045555           72 EMQTSNIRRDEFTTVRILT---------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM----LRKD  126 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~---------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~----~~~~  126 (175)
                      +|.+.|+.||..+|+.++.                     ++.|+..+|+++|.+|++.|++++|.++|++|    ..||
T Consensus       639 eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~Pd  718 (1060)
T PLN03218        639 DMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPT  718 (1060)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence            9999999999999998888                     78899999999999999999999999999999    4689


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcCC
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      ..+||.+|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.
T Consensus       719 vvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~  767 (1060)
T PLN03218        719 VSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERK  767 (1060)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHC
Confidence            9999999999999999999999999999999999999999999999863

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.2e-34  Score=235.56  Aligned_cols=173  Identities=22%  Similarity=0.362  Sum_probs=129.5

Q ss_pred             chHHHHhhccCC----CcHHHHHHHHHHHHhcCChhHHHHHhhcCC----CCChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN----KDVISWTTIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|.++|++|.+    ||..+|+++|.+|++.|++++|.++|++|.    .||..+|+.||.+|++.|++++|.++|++|
T Consensus       454 e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M  533 (1060)
T PLN03218        454 DGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIM  533 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            456777777764    677777777777777777777777777776    367777777777777777777777777777


Q ss_pred             HhCCCCCChHHHHHhhh-----------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----CC
Q 045555           74 QTSNIRRDEFTTVRILT-----------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----KD  126 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~-----------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~  126 (175)
                      .+.|+.||..+|+.++.                       ++.||..+|+++|.+|++.|++++|.++|+.|.+    |+
T Consensus       534 ~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~  613 (1060)
T PLN03218        534 RSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGT  613 (1060)
T ss_pred             HHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            77777777777777777                       3567777777777777777777777777777743    45


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      ..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.++++|++
T Consensus       614 ~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k  661 (1060)
T PLN03218        614 PEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGH  661 (1060)
T ss_pred             hHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence            677777777777777777777777777777777777777777777765

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=7.8e-35  Score=236.38  Aligned_cols=162  Identities=36%  Similarity=0.568  Sum_probs=155.5

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---   90 (175)
                      ||..+||++|.+|++.|++++|..+|+.|.+||.++||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.   
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            45556688889999999999999999999999999999999999999999999999999999999999999999997   


Q ss_pred             ------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           91 ------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        91 ------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                                        |+.||..+||+||.+|++.|++++|.++|++|..||..+||.+|.+|++.|++++|.++|++
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                              78899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHCCCCCcHHHHHHHHhhhcCC
Q 045555          153 MLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       153 m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      |.+.|+.||..||+.++.+|++.
T Consensus       380 M~~~g~~Pd~~t~~~ll~a~~~~  402 (857)
T PLN03077        380 MEQDNVSPDEITIASVLSACACL  402 (857)
T ss_pred             HHHhCCCCCceeHHHHHHHHhcc
Confidence            99999999999999999999863

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.1e-33  Score=229.77  Aligned_cols=161  Identities=36%  Similarity=0.554  Sum_probs=155.7

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---   90 (175)
                      ++...+|+++.+|++.|+++.|.++|++|.+||..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.+++   
T Consensus       119 ~~~~~~n~li~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~  198 (857)
T PLN03077        119 LGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCG  198 (857)
T ss_pred             CCchHHHHHHHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhC
Confidence            56677899999999999999999999999999999999999999999999999999999999999999999999987   


Q ss_pred             ------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           91 ------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        91 ------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                                        |+.||..++|++|.+|++.|++++|.++|++|.+||..+||++|.+|++.|++++|.++|++
T Consensus       199 ~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~  278 (857)
T PLN03077        199 GIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFT  278 (857)
T ss_pred             CccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHH
Confidence                              67899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHCCCCCcHHHHHHHHhhhcC
Q 045555          153 MLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       153 m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      |.+.|+.||..||+.+|.+|++
T Consensus       279 M~~~g~~Pd~~ty~~ll~a~~~  300 (857)
T PLN03077        279 MRELSVDPDLMTITSVISACEL  300 (857)
T ss_pred             HHHcCCCCChhHHHHHHHHHHh
Confidence            9999999999999999999986

>PF13041 PPR_2: PPR repeat family

Probab=99.74  E-value=9.2e-18  Score=89.59  Aligned_cols=50  Identities=26%  Similarity=0.443  Sum_probs=48.9

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          125 KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       125 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      ||+.+||++|++|++.|++++|.++|++|.++|++||..||+.+|++|||
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            78999999999999999999999999999999999999999999999986

>PF13041 PPR_2: PPR repeat family

Probab=99.60  E-value=4.5e-15  Score=79.09  Aligned_cols=50  Identities=40%  Similarity=0.741  Sum_probs=44.5

Q ss_pred             CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh
Q 045555           45 RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK  108 (175)
Q Consensus        45 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~  108 (175)
                      ||+++||++|++|++.|++++|.++|++|.+.|+.||..||              +.+|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty--------------~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTY--------------NILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHH--------------HHHHHHHcC
Confidence            78999999999999999999999999999999998888888              567777654

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.46  E-value=7.9e-12  Score=93.93  Aligned_cols=61  Identities=13%  Similarity=0.290  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ..+..+...|.+.|++++|..+|+++.+   .+..+++.++..+.+.|++++|.+.++.+.+.+
T Consensus       108 ~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  171 (389)
T PRK11788        108 LALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLG  171 (389)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhc
Confidence            3455555566666666666666665543   244455555556666666666666666555543

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.42  E-value=1.9e-11  Score=91.92  Aligned_cols=170  Identities=15%  Similarity=0.132  Sum_probs=104.2

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CC------hhHHHHHHHHHhccCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE-RD------YVLWTAMIDGYLRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~------~~~~~~li~~~~~~~~~~~a~~~~~   71 (175)
                      ++|.+.|+++.+  | +..++..+...+.+.|++++|..+++.+.. ++      ...+..+...|.+.|++++|..+|+
T Consensus        52 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~  131 (389)
T PRK11788         52 DKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFL  131 (389)
T ss_pred             HHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            567788887765  4 556788888888888888888888887664 21      2457777888888888888888888


Q ss_pred             HhHhCCCCCChHHHHHhhh-------------------ccCcc------hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           72 EMQTSNIRRDEFTTVRILT-------------------TFNND------IFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~-------------------~~~~~------~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ++.+.. .++..++..+..                   ...|+      ...+..+...+.+.|++++|.+.|+++.+  
T Consensus       132 ~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~  210 (389)
T PRK11788        132 QLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD  210 (389)
T ss_pred             HHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC
Confidence            887652 223334433332                   01111      12344555666667777777777776643  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      | +...+..+...+.+.|++++|.+.|+++.+.+-.+...++..+..+|
T Consensus       211 p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~  259 (389)
T PRK11788        211 PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECY  259 (389)
T ss_pred             cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHH
Confidence            2 34455556666666666666666666666542222233344444443

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

Probab=99.23  E-value=5.3e-10  Score=91.40  Aligned_cols=169  Identities=14%  Similarity=0.063  Sum_probs=116.6

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|.++++.+.+   ++...+..+...+.+.|++++|...|+.+.+  |+..++..+..++.+.|++++|.+.++++.+.
T Consensus       686 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  765 (899)
T TIGR02917       686 ESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKT  765 (899)
T ss_pred             HHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            567777777765   3566777777888888888888888887653  55566667777777778888887777777765


Q ss_pred             CCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHH
Q 045555           77 NIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAM  133 (175)
Q Consensus        77 ~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l  133 (175)
                      .. .+...+..+..                    ..+++..+++.+...+.+.|+ ++|...++....  | +...+..+
T Consensus       766 ~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~  843 (899)
T TIGR02917       766 HP-NDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTL  843 (899)
T ss_pred             CC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHH
Confidence            32 22222222111                    234456667777778888887 778777777633  2 55667778


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          134 IVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      ...+...|++++|.+.|+++.+.+.. +..++..+..++.
T Consensus       844 ~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~  882 (899)
T TIGR02917       844 GWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLALALL  882 (899)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHH
Confidence            88888889999999999988886543 7777777766654

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=99.21  E-value=1.3e-09  Score=89.11  Aligned_cols=73  Identities=12%  Similarity=0.251  Sum_probs=34.7

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|..+|+++.+   .+...+..+...|.+.|++++|..+++.+.+   .+...|..+..++.+.|++++|...|+++.+
T Consensus       551 ~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  629 (899)
T TIGR02917       551 EAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLA  629 (899)
T ss_pred             HHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44444444432   2333444455555555555555555554432   2334455555555555555555555555544

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

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.20  E-value=2.1e-09  Score=79.51  Aligned_cols=166  Identities=14%  Similarity=0.197  Sum_probs=130.9

Q ss_pred             HhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCC-----------------------------------CCChhHHH
Q 045555            7 IFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMP-----------------------------------ERDYVLWT   51 (175)
Q Consensus         7 ~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----------------------------------~~~~~~~~   51 (175)
                      +|+..+ ++..++..||.++|+-...+.|.++|++..                                   .||..|||
T Consensus       199 ~~E~~P-KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqkm~Pnl~TfN  277 (625)
T KOG4422|consen  199 LFETLP-KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVGKKLVAEMISQKMTPNLFTFN  277 (625)
T ss_pred             HHhhcC-CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhccHHHHHHHHHhhcCCchHhHH
Confidence            333333 456688888888888888888888777653                                   26999999


Q ss_pred             HHHHHHhccCChHH----HHHHHHHhHhCCCCCChHHHHHhhh------------------------------ccCcchh
Q 045555           52 AMIDGYLRVNRFRE----ALTLFREMQTSNIRRDEFTTVRILT------------------------------TFNNDIF   97 (175)
Q Consensus        52 ~li~~~~~~~~~~~----a~~~~~~m~~~~~~p~~~~~~~l~~------------------------------~~~~~~~   97 (175)
                      +++.+..+.|+++.    |.+++.+|++.|+.|...+|..++.                              ..+.|..
T Consensus       278 alL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~  357 (625)
T KOG4422|consen  278 ALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNK  357 (625)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhH
Confidence            99999999998755    4678889999999999999998888                              1233556


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC--------C---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR--------K---DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~--------~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      .+...++.|.+..+.+.|.++..-...        +   ...-|..+....|+....+.-.+.|..|.-.-+-|+..+..
T Consensus       358 FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~  437 (625)
T KOG4422|consen  358 FFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMI  437 (625)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHH
Confidence            777888888899999999888776632        1   23356778888888889999999999999888899999999


Q ss_pred             HHHhhhc
Q 045555          167 GVLSACT  173 (175)
Q Consensus       167 ~ll~~~~  173 (175)
                      .+++|..
T Consensus       438 ~~lrA~~  444 (625)
T KOG4422|consen  438 HLLRALD  444 (625)
T ss_pred             HHHHHHh
Confidence            9988764

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.15  E-value=1.7e-09  Score=80.06  Aligned_cols=123  Identities=14%  Similarity=0.159  Sum_probs=86.1

Q ss_pred             HhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHH
Q 045555           38 YFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQR  117 (175)
Q Consensus        38 ~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~  117 (175)
                      ++.+....+..++.+||.++|+-...+.|.+++.+-.....+.+..+|              |.+|.+-+-..+-+..-+
T Consensus       198 L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aF--------------N~lI~~~S~~~~K~Lv~E  263 (625)
T KOG4422|consen  198 LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAF--------------NGLIGASSYSVGKKLVAE  263 (625)
T ss_pred             HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhh--------------hhhhhHHHhhccHHHHHH
Confidence            444444456678999999999999999999999999988777676666              455544443333333333


Q ss_pred             HHHhhcCCChhhHHHHHHHHHhcCChhHH----HHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          118 VFWKMLRKDKFTWTAMIVGLAISGHGDTA----LDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       118 ~~~~~~~~~~~~~~~li~~~~~~g~~~~a----~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      +...-..||..|+|+++.+.++.|+++.|    .+++.+|++-|+.|...+|..+|...+|
T Consensus       264 Misqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~r  324 (625)
T KOG4422|consen  264 MISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKR  324 (625)
T ss_pred             HHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcc
Confidence            33333567788888888887777777654    5566777777888887777777765544

>PF12854 PPR_1: PPR repeat

Probab=99.13  E-value=1e-10  Score=56.68  Aligned_cols=32  Identities=38%  Similarity=0.573  Sum_probs=22.5

Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      |+.||..+||+||++|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            34555556677777777777777777777776

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.10  E-value=2.2e-08  Score=69.39  Aligned_cols=142  Identities=12%  Similarity=0.096  Sum_probs=100.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.+++..+  | +...+..+...+.+.|++++|.+.+++..+   .+...+..+...+...|++++|...+++..+
T Consensus        48 ~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  127 (234)
T TIGR02521        48 EVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIE  127 (234)
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            345555555443  3 455666777777777777777777776543   3445566667777777777777777777765


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      ....|             .....+..+...+.+.|++++|...+.+...  | +...+..+...+...|++++|.+.+++
T Consensus       128 ~~~~~-------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  194 (234)
T TIGR02521       128 DPLYP-------------QPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLER  194 (234)
T ss_pred             ccccc-------------cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            42111             1223445678888999999999999998854  2 456788888999999999999999999


Q ss_pred             HHHC
Q 045555          153 MLRA  156 (175)
Q Consensus       153 m~~~  156 (175)
                      ..+.
T Consensus       195 ~~~~  198 (234)
T TIGR02521       195 YQQT  198 (234)
T ss_pred             HHHh
Confidence            8876

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

>PF12854 PPR_1: PPR repeat

Probab=99.03  E-value=4e-10  Score=54.59  Aligned_cols=32  Identities=28%  Similarity=0.510  Sum_probs=30.1

Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          123 LRKDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       123 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      ..||..+||++|.+||+.|++++|.++|++|.
T Consensus         3 ~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    3 CEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            46899999999999999999999999999984

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=99.00  E-value=9.4e-10  Score=53.61  Aligned_cols=35  Identities=34%  Similarity=0.595  Sum_probs=33.0

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999983

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.

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

Probab=98.94  E-value=3e-08  Score=71.58  Aligned_cols=153  Identities=19%  Similarity=0.241  Sum_probs=87.8

Q ss_pred             hHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCC-----CCChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMP-----ERDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|.++++..-+  ++...+...+..+.+.++++++.++++...     +++...|..+...+.+.|++++|++.+++.++
T Consensus        95 ~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~  174 (280)
T PF13429_consen   95 EALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALE  174 (280)
T ss_dssp             -----------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44555544432  455666677777777788877777777643     23566677777777788888888888888777


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc---CCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML---RKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      ..  |             .+..+.+.++..+...|+.+++.++++...   ..|...|..+..+|...|+.++|...|++
T Consensus       175 ~~--P-------------~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~  239 (280)
T PF13429_consen  175 LD--P-------------DDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEK  239 (280)
T ss_dssp             H---T-------------T-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             cC--C-------------CCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccc
Confidence            43  2             235556678888888888888776666653   34667778888888888888888888888


Q ss_pred             HHHCCCCC-cHHHHHHHHhhh
Q 045555          153 MLRASIRL-DEVTYVGVLSAC  172 (175)
Q Consensus       153 m~~~g~~p-~~~t~~~ll~~~  172 (175)
                      ....  .| |+.+...+-+++
T Consensus       240 ~~~~--~p~d~~~~~~~a~~l  258 (280)
T PF13429_consen  240 ALKL--NPDDPLWLLAYADAL  258 (280)
T ss_dssp             HHHH--STT-HHHHHHHHHHH
T ss_pred             cccc--ccccccccccccccc
Confidence            7763  34 455544444443

>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=98.90  E-value=8.2e-08  Score=76.61  Aligned_cols=153  Identities=14%  Similarity=0.014  Sum_probs=103.5

Q ss_pred             chHHHHhhccCC-----C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN-----K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~-----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      ++|.+.|+...+     | +...++.+...+...|++++|...|++..+  | +...|..+...+...|++++|+..|++
T Consensus       311 ~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~  390 (615)
T TIGR00990       311 EEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDK  390 (615)
T ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            456666665542     2 345677777777778888888888877653  3 344667777777777778888877777


Q ss_pred             hHhCCCCCC-hHHHHHhhh-------------------ccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-Chh
Q 045555           73 MQTSNIRRD-EFTTVRILT-------------------TFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKF  128 (175)
Q Consensus        73 m~~~~~~p~-~~~~~~l~~-------------------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~  128 (175)
                      ..+..  |+ ...+..+-.                   ...| +...+..+...+.+.|++++|...|+...+  | +..
T Consensus       391 al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~  468 (615)
T TIGR00990       391 ALKLN--SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPD  468 (615)
T ss_pred             HHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChH
Confidence            76643  22 222221111                   1223 355666778888888888888888888743  3 567


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .|+.+...+...|++++|.+.|++..+.
T Consensus       469 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l  496 (615)
T TIGR00990       469 VYNYYGELLLDQNKFDEAIEKFDTAIEL  496 (615)
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            7888888888888999998888887764

>PRK12370 invasion protein regulator; Provisional

Probab=98.90  E-value=1.9e-07  Score=73.66  Aligned_cols=140  Identities=11%  Similarity=-0.016  Sum_probs=104.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|...+++..+  | +..++..+...+...|++++|...|++..+  | +...+..+...+...|++++|+..+++..+
T Consensus       321 ~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~  400 (553)
T PRK12370        321 IKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLK  400 (553)
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            356666766654  4 677888888899999999999999998764  4 456788889999999999999999999998


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---C-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---K-DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~-~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      ....+....               ..+...+...|++++|...+++...   | +...+..+..++...|+.++|...++
T Consensus       401 l~P~~~~~~---------------~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~  465 (553)
T PRK12370        401 LDPTRAAAG---------------ITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTK  465 (553)
T ss_pred             cCCCChhhH---------------HHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            653211111               1233345557888888888887742   3 34456667777888888888888888


Q ss_pred             HHHHC
Q 045555          152 QMLRA  156 (175)
Q Consensus       152 ~m~~~  156 (175)
                      ++...
T Consensus       466 ~~~~~  470 (553)
T PRK12370        466 EISTQ  470 (553)
T ss_pred             Hhhhc
Confidence            86543

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.89  E-value=3.8e-09  Score=51.16  Aligned_cols=34  Identities=26%  Similarity=0.471  Sum_probs=32.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCC
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL  160 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  160 (175)
                      +.+|+.+|.+|++.|+++.|.++|++|.+.|++|
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            3689999999999999999999999999999998

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.87  E-value=4.4e-09  Score=51.15  Aligned_cols=35  Identities=40%  Similarity=0.654  Sum_probs=32.7

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE   82 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   82 (175)
                      .+||++|++|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999873

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

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

Probab=98.86  E-value=7.7e-08  Score=76.79  Aligned_cols=156  Identities=12%  Similarity=0.144  Sum_probs=96.1

Q ss_pred             CCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------------------------CChhHHHHHHHHHhccCChH
Q 045555           13 NKDVISWTTIVSGYINRGQVDIARQYFAQMPE----------------------------RDYVLWTAMIDGYLRVNRFR   64 (175)
Q Consensus        13 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------------------------~~~~~~~~li~~~~~~~~~~   64 (175)
                      .||.++|..+|.-||..|+++.|- +|..|+-                            |...||..|..+|.+.|+..
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll~ayr~hGDli  100 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLLKAYRIHGDLI  100 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHHHHHHhccchH
Confidence            499999999999999999999998 7777651                            35578999999999999965


Q ss_pred             H---HHHHHHHhHh----CCCCCChHHHHHhhh-----------------------------------------------
Q 045555           65 E---ALTLFREMQT----SNIRRDEFTTVRILT-----------------------------------------------   90 (175)
Q Consensus        65 ~---a~~~~~~m~~----~~~~p~~~~~~~l~~-----------------------------------------------   90 (175)
                      .   +.+.+..+..    .|+.....-+..-++                                               
T Consensus       101 ~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~~~p~~vfLrq  180 (1088)
T KOG4318|consen  101 LFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQ  180 (1088)
T ss_pred             HHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccccchHHHHHHH
Confidence            4   2222222211    233222222222222                                               


Q ss_pred             -----------------cc-CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC----hhhHHHHHHHHHhcCChhHHHH
Q 045555           91 -----------------TF-NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKD----KFTWTAMIVGLAISGHGDTALD  148 (175)
Q Consensus        91 -----------------~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~li~~~~~~g~~~~a~~  148 (175)
                                       .. .|+..++.+++++-...|+.+.|..+..+|.+.+    .+-|-.++-+   .++...+..
T Consensus       181 nv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~  257 (1088)
T KOG4318|consen  181 NVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEF  257 (1088)
T ss_pred             hccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHH
Confidence                             11 3566666666666666666666666666665542    2222223322   566666666


Q ss_pred             HHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          149 MFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       149 ~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      +++-|.+.|+.|++.|+..-+..|
T Consensus       258 vlrgmqe~gv~p~seT~adyvip~  281 (1088)
T KOG4318|consen  258 VLRGMQEKGVQPGSETQADYVIPQ  281 (1088)
T ss_pred             HHHHHHHhcCCCCcchhHHHHHhh
Confidence            666666666667666666554444

>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=98.86  E-value=2.4e-07  Score=73.95  Aligned_cols=128  Identities=10%  Similarity=0.016  Sum_probs=93.6

Q ss_pred             HhcCChhHHHHHhhcCCC-----C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChH-HHHHhhh---------
Q 045555           27 INRGQVDIARQYFAQMPE-----R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEF-TTVRILT---------   90 (175)
Q Consensus        27 ~~~~~~~~a~~~~~~m~~-----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~~~l~~---------   90 (175)
                      ...+++++|...|+...+     | +...|+.+...+...|++++|+..|++.....  |+.. .|..+-.         
T Consensus       305 ~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~  382 (615)
T TIGR00990       305 KADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD--PRVTQSYIKRASMNLELGDPD  382 (615)
T ss_pred             hhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHCCCHH
Confidence            446789999999998763     2 44568888888999999999999999998853  4322 2211111         


Q ss_pred             -----------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           91 -----------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        91 -----------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                                 ..+.+..++..+...+...|++++|...|++..+  | +...|..+...+.+.|++++|...|++.++.
T Consensus       383 eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  462 (615)
T TIGR00990       383 KAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN  462 (615)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence                       2233466777888888888888888888888744  3 4556777777888888888888888887753

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.85  E-value=2.3e-07  Score=74.50  Aligned_cols=153  Identities=15%  Similarity=0.063  Sum_probs=79.9

Q ss_pred             chHHHHhhccCC----CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHH----HHHHH
Q 045555            2 GFALEIFGNMKN----KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFRE----ALTLF   70 (175)
Q Consensus         2 ~~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~----a~~~~   70 (175)
                      ++|...++.+.+    ++......+...+.+.|++++|...|+...+   .+...+..+...+.+.|++++    |...|
T Consensus       194 ~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~  273 (656)
T PRK15174        194 PEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHW  273 (656)
T ss_pred             HHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHH
Confidence            345555555433    1222333444556666666666666665443   234455556666666666554    56666


Q ss_pred             HHhHhCCCCCChH-HHHHhhh-------------------ccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CCh
Q 045555           71 REMQTSNIRRDEF-TTVRILT-------------------TFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDK  127 (175)
Q Consensus        71 ~~m~~~~~~p~~~-~~~~l~~-------------------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~  127 (175)
                      ++..+.  .|+.. .+..+-.                   ...| +...+..+..+|.+.|++++|.+.|+.+..  |+.
T Consensus       274 ~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~  351 (656)
T PRK15174        274 RHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVT  351 (656)
T ss_pred             HHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc
Confidence            666553  22211 1111000                   0111 233445566777777777777777777643  332


Q ss_pred             hh-HHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          128 FT-WTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       128 ~~-~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .. +..+..++...|+.++|.+.|++..+.
T Consensus       352 ~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        352 SKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            22 233445666777777777777776654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.84  E-value=6.3e-07  Score=67.95  Aligned_cols=169  Identities=17%  Similarity=0.225  Sum_probs=120.9

Q ss_pred             chHHHHhhccCC--CcHHHHH--HHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--KDVISWT--TIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|.+.+.++.+  |+....-  .....+...|+++.|...++...+  | +......+...|.+.|+|++|.+++.++.
T Consensus       135 ~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~  214 (398)
T PRK10747        135 ARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMA  214 (398)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            467788887776  5543333  336688899999999999999875  3 66778899999999999999999999999


Q ss_pred             hCCCCCChH-------HHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---
Q 045555           75 TSNIRRDEF-------TTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---  124 (175)
Q Consensus        75 ~~~~~p~~~-------~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---  124 (175)
                      +.+..++..       .|..++.                    ..+.+......+...+...|+.++|.+.+.+..+   
T Consensus       215 k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~  294 (398)
T PRK10747        215 KAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQY  294 (398)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            987653221       2222121                    1223455666677777777777777777666511   


Q ss_pred             ------------------------------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          125 ------------------------------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       125 ------------------------------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                                                    | |...+.++...+.+.|++++|.+.|+...+.  .|+..++..+-..+
T Consensus       295 ~~~l~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~  371 (398)
T PRK10747        295 DERLVLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADAL  371 (398)
T ss_pred             CHHHHHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHH
Confidence                                          1 4455677888888999999999999998874  68888776665554

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

Probab=98.83  E-value=1.6e-08  Score=72.97  Aligned_cols=138  Identities=22%  Similarity=0.223  Sum_probs=96.5

Q ss_pred             hHHHHhhccC-----CCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            3 FALEIFGNMK-----NKDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         3 ~A~~~~~~m~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++.++++...     .++...|..+...+.+.|++++|...|++..+  | |....+.++..+...|+.+++.+++....
T Consensus       128 ~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~  207 (280)
T PF13429_consen  128 EAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLL  207 (280)
T ss_dssp             HHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            4455555533     25788899999999999999999999999874  5 57788999999999999999999999988


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      +..               +.+...+..+..+|...|+.++|...|+...+  | |......+..++...|+.++|.++.+
T Consensus       208 ~~~---------------~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~~~~A~~~~~  272 (280)
T PF13429_consen  208 KAA---------------PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGRKDEALRLRR  272 (280)
T ss_dssp             HH----------------HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT-------------
T ss_pred             HHC---------------cCHHHHHHHHHHHhcccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            864               23344557899999999999999999999854  4 78888889999999999999999988


Q ss_pred             HHHH
Q 045555          152 QMLR  155 (175)
Q Consensus       152 ~m~~  155 (175)
                      +..+
T Consensus       273 ~~~~  276 (280)
T PF13429_consen  273 QALR  276 (280)
T ss_dssp             ----
T ss_pred             cccc
Confidence            7654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.82  E-value=4.4e-07  Score=62.76  Aligned_cols=139  Identities=14%  Similarity=0.016  Sum_probs=111.3

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|.+.++...+   .+...+..+...+...|++++|...|+....     .....+..+...+...|++++|...+++.
T Consensus        82 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  161 (234)
T TIGR02521        82 EKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRA  161 (234)
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            457777776654   4567888899999999999999999998764     13456777888899999999999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHH
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                      .+..  |+             +...+..+...+...|++++|.+.+++..+   .+...+..+...+...|+.++|..+.
T Consensus       162 ~~~~--~~-------------~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~  226 (234)
T TIGR02521       162 LQID--PQ-------------RPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYG  226 (234)
T ss_pred             HHhC--cC-------------ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            8854  22             233456788999999999999999998743   35667777888888999999999998


Q ss_pred             HHHHH
Q 045555          151 SQMLR  155 (175)
Q Consensus       151 ~~m~~  155 (175)
                      +.+..
T Consensus       227 ~~~~~  231 (234)
T TIGR02521       227 AQLQK  231 (234)
T ss_pred             HHHHh
Confidence            88765

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.79  E-value=1.2e-08  Score=49.37  Aligned_cols=33  Identities=21%  Similarity=0.390  Sum_probs=31.5

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCC
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRR   80 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   80 (175)
                      .+|+.+|.+|++.|+++.|.++|++|++.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            589999999999999999999999999999887

>PRK12370 invasion protein regulator; Provisional

Probab=98.74  E-value=1.1e-06  Score=69.48  Aligned_cols=140  Identities=10%  Similarity=0.019  Sum_probs=106.1

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHH---------hcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYI---------NRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREA   66 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~---------~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a   66 (175)
                      ++|+.+|++..+  | +...|..+..++.         ..+++++|...+++..+  | +...+..+...+...|++++|
T Consensus       278 ~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~~A  357 (553)
T PRK12370        278 QQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYIVG  357 (553)
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHHHH
Confidence            467888887776  4 4456666655544         23457899999998775  3 667788888889999999999


Q ss_pred             HHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CCh-hhHHHHHHHHHhcCCh
Q 045555           67 LTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDK-FTWTAMIVGLAISGHG  143 (175)
Q Consensus        67 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~-~~~~~li~~~~~~g~~  143 (175)
                      ...|++..+.+  |+             +...+..+...+...|++++|...++...+  |+. ..+..+...+...|++
T Consensus       358 ~~~~~~Al~l~--P~-------------~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~  422 (553)
T PRK12370        358 SLLFKQANLLS--PI-------------SADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGI  422 (553)
T ss_pred             HHHHHHHHHhC--CC-------------CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCH
Confidence            99999999864  32             334456788999999999999999999855  432 2334455567778999


Q ss_pred             hHHHHHHHHHHHC
Q 045555          144 DTALDMFSQMLRA  156 (175)
Q Consensus       144 ~~a~~~~~~m~~~  156 (175)
                      ++|.+.+++..+.
T Consensus       423 eeA~~~~~~~l~~  435 (553)
T PRK12370        423 DDAIRLGDELRSQ  435 (553)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999998765

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.73  E-value=1.2e-06  Score=70.39  Aligned_cols=52  Identities=10%  Similarity=0.030  Sum_probs=33.4

Q ss_pred             HHHhcCCHHHHHHHHHhhcCC----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          105 MYCKCGDVEKAQRVFWKMLRK----DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       105 ~~~~~~~~~~a~~~~~~~~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+.+.|++++|...++.+...    +...+..+...+...|++++|.+.+++..+.
T Consensus       186 ~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~  241 (656)
T PRK15174        186 SFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALAR  241 (656)
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            356677777777777776432    2233344456677777777777777777754

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

Probab=98.70  E-value=2.5e-08  Score=47.10  Aligned_cols=31  Identities=29%  Similarity=0.529  Sum_probs=26.9

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHCCC
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLRASI  158 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  158 (175)
                      ++|+.+|++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4789999999999999999999999988774

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.

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.68  E-value=7.7e-07  Score=74.05  Aligned_cols=152  Identities=11%  Similarity=0.013  Sum_probs=91.9

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|...|+.+..  |+...+..+...+.+.|++++|...|++..+.   +...+..+...+.+.|++++|...+++..+.
T Consensus       526 eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l  605 (987)
T PRK09782        526 ATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRSLNI  605 (987)
T ss_pred             HHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence            466777775553  44445566667777788888888887766542   2222222333344457777777777777764


Q ss_pred             CCCCChHHHHHhhh-------------------cc-CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHH
Q 045555           77 NIRRDEFTTVRILT-------------------TF-NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAM  133 (175)
Q Consensus        77 ~~~p~~~~~~~l~~-------------------~~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l  133 (175)
                      .  |+...+..+-.                   .. +.+...++.+...+...|++++|.+.++...+  | +...+..+
T Consensus       606 ~--P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nL  683 (987)
T PRK09782        606 A--PSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQL  683 (987)
T ss_pred             C--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            3  33333322111                   11 22345556666677777777777777777643  3 55667777


Q ss_pred             HHHHHhcCChhHHHHHHHHHHH
Q 045555          134 IVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..++...|++++|...|++..+
T Consensus       684 A~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        684 AYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHh
Confidence            7777777777777777777765

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

Probab=98.66  E-value=2.9e-06  Score=63.73  Aligned_cols=139  Identities=17%  Similarity=0.196  Sum_probs=91.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      |+|+..|+...+  | ...+|+.|.+-|...++...|.+-|+...+   .|-..|..|..+|.-.+...=|+-.|++..+
T Consensus       347 EKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~  426 (559)
T KOG1155|consen  347 EKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALE  426 (559)
T ss_pred             HHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHh
Confidence            344444544443  2 233455555555555555555555554332   3444555555555555555555555555444


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      -               -+.|..+|.+|.++|.+.++.++|...|+....-   +...+..+.+.|-+.++..+|...|.+
T Consensus       427 ~---------------kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek  491 (559)
T KOG1155|consen  427 L---------------KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEK  491 (559)
T ss_pred             c---------------CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            2               1347889999999999999999999999998553   347899999999999999999998877


Q ss_pred             HHH
Q 045555          153 MLR  155 (175)
Q Consensus       153 m~~  155 (175)
                      -++
T Consensus       492 ~v~  494 (559)
T KOG1155|consen  492 YVE  494 (559)
T ss_pred             HHH
Confidence            664

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

Probab=98.65  E-value=1.2e-06  Score=68.09  Aligned_cols=148  Identities=15%  Similarity=0.115  Sum_probs=106.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh-
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT-   90 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~-   90 (175)
                      .+.+|.++.++|+-+++.+.|+..|++..+   ...++|+.+-+-+.....++.|...|+..+    ..|+..|++... 
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al----~~~~rhYnAwYGl  495 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKAL----GVDPRHYNAWYGL  495 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhh----cCCchhhHHHHhh
Confidence            578899999999999999999999998775   256677777777777777777777777663    345555655444 


Q ss_pred             ---------------------ccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhH
Q 045555           91 ---------------------TFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDT  145 (175)
Q Consensus        91 ---------------------~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~  145 (175)
                                           .++|. ......+...+.+.|+.|+|.+++++...   .|+-.--.....+...++.++
T Consensus       496 G~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~e  575 (638)
T KOG1126|consen  496 GTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVE  575 (638)
T ss_pred             hhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHH
Confidence                                 33443 44455677788899999999999998843   255555556666777888899


Q ss_pred             HHHHHHHHHHCCCCCcHHHHHHH
Q 045555          146 ALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       146 a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                      |+..++++++  +.|+..+--.+
T Consensus       576 al~~LEeLk~--~vP~es~v~~l  596 (638)
T KOG1126|consen  576 ALQELEELKE--LVPQESSVFAL  596 (638)
T ss_pred             HHHHHHHHHH--hCcchHHHHHH
Confidence            9998888876  46665444333

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

Probab=98.65  E-value=1.5e-06  Score=65.22  Aligned_cols=123  Identities=19%  Similarity=0.102  Sum_probs=103.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDI   96 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~   96 (175)
                      ....+++..+...++++.|.++|+++.+.+......+...+...++-.+|++++++.++..               +.+.
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~---------------p~d~  234 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKEN---------------PQDS  234 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHhC---------------CCCH
Confidence            4456778888889999999999999998776677788899999999999999999999753               2234


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      .+...-.+.+.+.++++.|..+.++..+  | +..+|..|..+|...|+++.|+-.++.+-
T Consensus       235 ~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  235 ELLNLQAEFLLSKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            4455677778999999999999999965  4 67799999999999999999999988774

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

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

Probab=98.64  E-value=8.8e-07  Score=66.41  Aligned_cols=139  Identities=18%  Similarity=0.167  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      .|+..+.+.|+-.++.++|...|+...+   .....|+.+.+-|...++...|++-++...+-+               +
T Consensus       331 ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~---------------p  395 (559)
T KOG1155|consen  331 ETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN---------------P  395 (559)
T ss_pred             cceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC---------------c
Confidence            3444555666667888888888887664   345678888888999999999998888887742               4


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHh
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKML--RK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLS  170 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  170 (175)
                      .|-..|=.|.++|.-.+...=|.-.|++..  +| |...|.+|..+|.+.++.++|.+.|.....-|-. +...+..|-+
T Consensus       396 ~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~Lak  474 (559)
T KOG1155|consen  396 RDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAK  474 (559)
T ss_pred             hhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHH
Confidence            466677889999999999999999999984  34 8999999999999999999999999999876533 4445554444


Q ss_pred             h
Q 045555          171 A  171 (175)
Q Consensus       171 ~  171 (175)
                      .
T Consensus       475 L  475 (559)
T KOG1155|consen  475 L  475 (559)
T ss_pred             H
Confidence            3

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

Probab=98.63  E-value=5.2e-08  Score=45.97  Aligned_cols=31  Identities=39%  Similarity=0.790  Sum_probs=27.1

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++|+++|++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4789999999999999999999999988774

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.

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

Probab=98.63  E-value=6.6e-06  Score=62.04  Aligned_cols=169  Identities=18%  Similarity=0.184  Sum_probs=120.6

Q ss_pred             chHHHHhhccCCCcHHHHHHHHH---HHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKNKDVISWTTIVS---GYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~---~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.+++....|...-.+|.+   .+-..|+.++|++.|-++..   .+..+...+.+.|-...+...|++++.+...
T Consensus       507 dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~s  586 (840)
T KOG2003|consen  507 DKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANS  586 (840)
T ss_pred             HHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcc
Confidence            56777777777655544333332   35567888888888876543   4666666777777777778888887766544


Q ss_pred             CCCCC-ChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCCChhhHHH
Q 045555           76 SNIRR-DEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRKDKFTWTA  132 (175)
Q Consensus        76 ~~~~p-~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~~~~~~~~  132 (175)
                        +.| |+...+.+-.                    .++-+..+...|..-|....-++++...|++.  .+|+..-|..
T Consensus       587 --lip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwql  664 (840)
T KOG2003|consen  587 --LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQL  664 (840)
T ss_pred             --cCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHH
Confidence              444 4444443333                    23445667777888888899999999999986  7899999999


Q ss_pred             HHHHHH-hcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          133 MIVGLA-ISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       133 li~~~~-~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      ||..|. +.|++.+|+++|++... .++-|......|+..|.
T Consensus       665 miasc~rrsgnyqka~d~yk~~hr-kfpedldclkflvri~~  705 (840)
T KOG2003|consen  665 MIASCFRRSGNYQKAFDLYKDIHR-KFPEDLDCLKFLVRIAG  705 (840)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHH-hCccchHHHHHHHHHhc
Confidence            986655 79999999999999875 46777777777776653

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.63  E-value=2.3e-06  Score=71.29  Aligned_cols=153  Identities=10%  Similarity=-0.005  Sum_probs=113.5

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ++|+..+.....  |+......+...+.+.|++++|...|+++..  |+...+..+...+.+.|++++|...+++..+.+
T Consensus       493 ~eAi~a~~~Al~~~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~  572 (987)
T PRK09782        493 GVALYAWLQAEQRQPDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG  572 (987)
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            457775555443  6544433445555689999999999997664  455556777888999999999999999998865


Q ss_pred             CCCChH-HHHHhh------h-------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHH
Q 045555           78 IRRDEF-TTVRIL------T-------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMI  134 (175)
Q Consensus        78 ~~p~~~-~~~~l~------~-------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li  134 (175)
                        |+.. .+..+.      .             ...|+...+..+...+.+.|++++|...++....  | +...++.+.
T Consensus       573 --P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG  650 (987)
T PRK09782        573 --LGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALG  650 (987)
T ss_pred             --CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence              3322 121111      1             3456778888889999999999999999998854  4 566778888


Q ss_pred             HHHHhcCChhHHHHHHHHHHHC
Q 045555          135 VGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       135 ~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ..+...|++++|.+.|++..+.
T Consensus       651 ~aL~~~G~~eeAi~~l~~AL~l  672 (987)
T PRK09782        651 YALWDSGDIAQSREMLERAHKG  672 (987)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh
Confidence            8899999999999999988864

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.62  E-value=3e-06  Score=55.17  Aligned_cols=104  Identities=14%  Similarity=0.037  Sum_probs=68.5

Q ss_pred             HhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHH
Q 045555           38 YFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQR  117 (175)
Q Consensus        38 ~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~  117 (175)
                      +|++..+-+...+..+...+.+.|++++|...|+......               +.+...+..+..++.+.|++++|..
T Consensus        15 ~~~~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~---------------P~~~~a~~~lg~~~~~~g~~~~A~~   79 (144)
T PRK15359         15 ILKQLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVMAQ---------------PWSWRAHIALAGTWMMLKEYTTAIN   79 (144)
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC---------------CCcHHHHHHHHHHHHHHhhHHHHHH
Confidence            3444333333334556666777777777777777776643               2234445667777777777777777


Q ss_pred             HHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          118 VFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       118 ~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .|+....  | +...+..+..++...|+.++|...|+...+.
T Consensus        80 ~y~~Al~l~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~  121 (144)
T PRK15359         80 FYGHALMLDASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKM  121 (144)
T ss_pred             HHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7777744  2 5566777777777777888887777777653

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.61  E-value=5.2e-06  Score=68.04  Aligned_cols=75  Identities=12%  Similarity=0.095  Sum_probs=54.7

Q ss_pred             chHHHHhhccCCC---cHH-HHHHHHHHHHhcCChhHHHHHhhcCCC--CC-----hhHHHHHHHHHhccCChHHHHHHH
Q 045555            2 GFALEIFGNMKNK---DVI-SWTTIVSGYINRGQVDIARQYFAQMPE--RD-----YVLWTAMIDGYLRVNRFREALTLF   70 (175)
Q Consensus         2 ~~A~~~~~~m~~~---~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-----~~~~~~li~~~~~~~~~~~a~~~~   70 (175)
                      ++|+..|+.+.+.   ++. .--.+...|...|++++|...|+++.+  |.     ......|..++.+.|++++|.+.+
T Consensus       254 ~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l  333 (765)
T PRK10049        254 KDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVT  333 (765)
T ss_pred             HHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHH
Confidence            5688888888751   121 222357788999999999999998654  21     234566777888999999999999


Q ss_pred             HHhHhC
Q 045555           71 REMQTS   76 (175)
Q Consensus        71 ~~m~~~   76 (175)
                      +++...
T Consensus       334 ~~~~~~  339 (765)
T PRK10049        334 AHTINN  339 (765)
T ss_pred             HHHhhc
Confidence            998875

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.59  E-value=3.5e-06  Score=71.92  Aligned_cols=143  Identities=14%  Similarity=0.144  Sum_probs=107.7

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++|.++++.-+ ++...+..+...+.+.|++++|...|+...+  | +...+..+...+...|++++|.+.++...+.. 
T Consensus       590 ~eA~~~l~~~p-~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~-  667 (1157)
T PRK11447        590 AEAEALLRQQP-PSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATA-  667 (1157)
T ss_pred             HHHHHHHHhCC-CCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccC-
Confidence            45666666322 3556677888889999999999999998764  3 66788888999999999999999999887642 


Q ss_pred             CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---------ChhhHHHHHHHHHhcCChhHHHHH
Q 045555           79 RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---------DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        79 ~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                       |+             +...+..+..++.+.|++++|.++++.+...         +...+..+...+...|+.++|.+.
T Consensus       668 -p~-------------~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~  733 (1157)
T PRK11447        668 -ND-------------SLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALET  733 (1157)
T ss_pred             -CC-------------ChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence             22             2233456778888999999999999998542         123566667888899999999999


Q ss_pred             HHHHHH-CCCCC
Q 045555          150 FSQMLR-ASIRL  160 (175)
Q Consensus       150 ~~~m~~-~g~~p  160 (175)
                      |++... .|+.|
T Consensus       734 y~~Al~~~~~~~  745 (1157)
T PRK11447        734 YKDAMVASGITP  745 (1157)
T ss_pred             HHHHHhhcCCCC
Confidence            998864 35544

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.59  E-value=5.3e-06  Score=67.97  Aligned_cols=153  Identities=10%  Similarity=-0.003  Sum_probs=109.3

Q ss_pred             chHHHHhhccCC--CcH--HHHHHHHHHHHhcCChhHHHHHhhcCCCCChh-HHHHH--HHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--KDV--ISWTTIVSGYINRGQVDIARQYFAQMPERDYV-LWTAM--IDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-~~~~l--i~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +.|+..|++..+  |+.  ..+ .++..+...|+.++|+.++++...|+.. .+..+  ...+...|++++|+++|+++.
T Consensus        51 ~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~kaL  129 (822)
T PRK14574         51 APVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSSL  129 (822)
T ss_pred             HHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            467888887776  543  234 8889999999999999999999876433 33333  457888899999999999999


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--DKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      +..  |+             +...+..++..|...++.++|.+.++.+...  +...+..++..+...++..+|.+.+++
T Consensus       130 ~~d--P~-------------n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ek  194 (822)
T PRK14574        130 KKD--PT-------------NPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSE  194 (822)
T ss_pred             hhC--CC-------------CHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHH
Confidence            864  22             2334457788999999999999999999664  444443333334345666679999999


Q ss_pred             HHHCCCCCc-HHHHHHHHhhh
Q 045555          153 MLRASIRLD-EVTYVGVLSAC  172 (175)
Q Consensus       153 m~~~g~~p~-~~t~~~ll~~~  172 (175)
                      +.+.  .|+ ...+..+..+.
T Consensus       195 ll~~--~P~n~e~~~~~~~~l  213 (822)
T PRK14574        195 AVRL--APTSEEVLKNHLEIL  213 (822)
T ss_pred             HHHh--CCCCHHHHHHHHHHH
Confidence            9986  354 44444444443

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

Probab=98.58  E-value=1.8e-06  Score=62.07  Aligned_cols=76  Identities=20%  Similarity=0.274  Sum_probs=59.2

Q ss_pred             chHHHHhhccCCCcHH---HHHHHHHHHHhcCChhHHHHHhhcCCC-CChh------HHHHHHHHHhccCChHHHHHHHH
Q 045555            2 GFALEIFGNMKNKDVI---SWTTIVSGYINRGQVDIARQYFAQMPE-RDYV------LWTAMIDGYLRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~------~~~~li~~~~~~~~~~~a~~~~~   71 (175)
                      |+|+.+|-+|.+-|+.   +.-+|.+.|-+.|..+.|+.+.+.+.+ ||..      ..-.|..-|...|-++.|..+|.
T Consensus        52 dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~  131 (389)
T COG2956          52 DKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFN  131 (389)
T ss_pred             chHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            7899999999874444   455888999999999999999998765 5432      23445556778888999999999


Q ss_pred             HhHhCC
Q 045555           72 EMQTSN   77 (175)
Q Consensus        72 ~m~~~~   77 (175)
                      .+.+.|
T Consensus       132 ~L~de~  137 (389)
T COG2956         132 QLVDEG  137 (389)
T ss_pred             HHhcch
Confidence            988855

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.56  E-value=6.3e-06  Score=62.56  Aligned_cols=127  Identities=17%  Similarity=0.152  Sum_probs=98.0

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      .++.....+...+.+.|+.++|..++++..+.....--.++.+.+..++.+++++..++..+..               +
T Consensus       261 ~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~---------------P  325 (398)
T PRK10747        261 HQVALQVAMAEHLIECDDHDTAQQIILDGLKRQYDERLVLLIPRLKTNNPEQLEKVLRQQIKQH---------------G  325 (398)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHhhccCCChHHHHHHHHHHHhhC---------------C
Confidence            3666777788888888888888888876654222222334455556688888888888887753               2


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      -|......+...+.+.+++++|.+.|+..  ..|+...|..+...+.+.|+.++|.+++++-..
T Consensus       326 ~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        326 DTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            34555678999999999999999999999  458888899999999999999999999998754

>TIGR00540 hemY_coli hemY protein

Probab=98.55  E-value=2e-05  Score=60.12  Aligned_cols=171  Identities=16%  Similarity=0.168  Sum_probs=119.7

Q ss_pred             chHHHHhhccCC--CcH--HHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--KDV--ISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|.+.+.+..+  |+.  ..--.....+.+.|+++.|...++.+.+  | +..+...+...+.+.|+|++|.+.+.++.
T Consensus       135 ~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~  214 (409)
T TIGR00540       135 ARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMA  214 (409)
T ss_pred             HHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            356666666533  443  2334457788889999999999998875  4 66678899999999999999999999999


Q ss_pred             hCCCCCChHH-------HHHhhh---------------ccC-----cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           75 TSNIRRDEFT-------TVRILT---------------TFN-----NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        75 ~~~~~p~~~~-------~~~l~~---------------~~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      +.++.++...       +...+.               .-.     .+...+..+...+...|+.++|.+.+++..+  |
T Consensus       215 k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~p  294 (409)
T TIGR00540       215 KAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLG  294 (409)
T ss_pred             HcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCC
Confidence            9875433322       211121               112     2667778888888888888888888877622  1


Q ss_pred             -------------------------------------Ch--hhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          126 -------------------------------------DK--FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       126 -------------------------------------~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                                                           |.  ....++...+.+.|++++|.+.|+........||..++.
T Consensus       295 d~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~  374 (409)
T TIGR00540       295 DDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLA  374 (409)
T ss_pred             CcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHH
Confidence                                                 22  334466777788889999999888544444578887777


Q ss_pred             HHHhhh
Q 045555          167 GVLSAC  172 (175)
Q Consensus       167 ~ll~~~  172 (175)
                      .+-..+
T Consensus       375 ~La~ll  380 (409)
T TIGR00540       375 MAADAF  380 (409)
T ss_pred             HHHHHH
Confidence            665443

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.

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

Probab=98.54  E-value=1.1e-05  Score=59.50  Aligned_cols=148  Identities=14%  Similarity=0.099  Sum_probs=117.4

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC---------------------------------------------Chh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPER---------------------------------------------DYV   48 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---------------------------------------------~~~   48 (175)
                      .++..-.....+|.+.|++.....+...+.+.                                             +..
T Consensus       185 r~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~  264 (400)
T COG3071         185 RHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPE  264 (400)
T ss_pred             CChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChh
Confidence            46667777788888888888888777776531                                             233


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh----------------ccCcchhHHHHHHHHHHhcCCH
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT----------------TFNNDIFVGIALIDMYCKCGDV  112 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~----------------~~~~~~~~~~~li~~~~~~~~~  112 (175)
                      .-..++.-+.+.|+.++|.++..+-.+.+-.|+...+..-+.                ..+.+...+.+|...|.+++.|
T Consensus       265 l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w  344 (400)
T COG3071         265 LVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLW  344 (400)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCchHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHH
Confidence            445677778999999999999999999988887555544333                3344567888999999999999


Q ss_pred             HHHHHHHHhh--cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          113 EKAQRVFWKM--LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       113 ~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      .+|...|+..  ..|+..+|+.+.+++.+.|+..+|.+++++-...-.+|+
T Consensus       345 ~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         345 GKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             HHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence            9999999987  457999999999999999999999999999775444554

>TIGR00540 hemY_coli hemY protein

Probab=98.50  E-value=1.9e-05  Score=60.19  Aligned_cols=154  Identities=13%  Similarity=0.069  Sum_probs=109.1

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------------------------------
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE----------------------------------   44 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------------------------------   44 (175)
                      ++|...++.+.+  | +..+...+...+.+.|++++|.+.+..+.+                                  
T Consensus       170 ~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~  249 (409)
T TIGR00540       170 HAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLL  249 (409)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            345566666554  3 555677777777777777776666665441                                  


Q ss_pred             -----------CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChH---HHHHhhh-----------------ccC
Q 045555           45 -----------RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEF---TTVRILT-----------------TFN   93 (175)
Q Consensus        45 -----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~---~~~~l~~-----------------~~~   93 (175)
                                 .+...+..+...+...|+.++|.+++++..+........   .+.....                 .-.
T Consensus       250 ~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~  329 (409)
T TIGR00540       250 NWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNV  329 (409)
T ss_pred             HHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhC
Confidence                       134456666777888899999999999998864332211   1111111                 223


Q ss_pred             c-ch--hHHHHHHHHHHhcCCHHHHHHHHHh--h--cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           94 N-DI--FVGIALIDMYCKCGDVEKAQRVFWK--M--LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        94 ~-~~--~~~~~li~~~~~~~~~~~a~~~~~~--~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      | |.  ....++...+.+.|++++|.+.|+.  .  ..|+...+..+...+.+.|+.++|.+++++-..
T Consensus       330 p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       330 DDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             CCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3 34  5667899999999999999999993  5  468888899999999999999999999998653

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.

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

Probab=98.49  E-value=1.1e-06  Score=68.33  Aligned_cols=121  Identities=17%  Similarity=0.207  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      +..+...|-..|.++.|...|++..+  | -...|+.|.+++-..|+..+|.+.|.+.+...  |             ..
T Consensus       289 ~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~--p-------------~h  353 (966)
T KOG4626|consen  289 HGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLC--P-------------NH  353 (966)
T ss_pred             ccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhC--C-------------cc
Confidence            33333333344444444444444332  2 23456666666666666666666666665532  1             12


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC-hhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD-KFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      ....+.|...|.+.|.+++|.++|....+  |+ ....|.+...|-+.|++++|...|++.+
T Consensus       354 adam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal  415 (966)
T KOG4626|consen  354 ADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEAL  415 (966)
T ss_pred             HHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHH
Confidence            22233444455555555555555544422  21 1234444455555555555555555444

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

Probab=98.48  E-value=4.1e-06  Score=60.76  Aligned_cols=57  Identities=25%  Similarity=0.186  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCCh-hHHHHHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHG-DTALDMFSQML  154 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~-~~a~~~~~~m~  154 (175)
                      +.|.+..++...|++++|++++.+....   +..+...++......|+. +.+.+.+.++.
T Consensus       203 ~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~  263 (290)
T PF04733_consen  203 LLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQLK  263 (290)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHHHH
Confidence            3345555555555555555555554332   333444444444444444 33444444444

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.

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

Probab=98.48  E-value=7.8e-06  Score=63.65  Aligned_cols=147  Identities=14%  Similarity=0.113  Sum_probs=113.9

Q ss_pred             CchHHHHhhccCCCcHHHH---HHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            1 MGFALEIFGNMKNKDVISW---TTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         1 ~~~A~~~~~~m~~~~~~~~---~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +|.|...|+.....|+..|   .-+...|.+.++++.|+-.|+...+   .+.+....+...+-+.|+.++|+.++++..
T Consensus       471 ~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~  550 (638)
T KOG1126|consen  471 FDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAI  550 (638)
T ss_pred             HHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHH
Confidence            3667777777776555544   4567778899999999999988775   367777888888889999999999999988


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      ....+-...-|               ..+..+...+++++|...++++++  | +..+|-.+...|.+.|+.+.|..-|-
T Consensus       551 ~ld~kn~l~~~---------------~~~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~  615 (638)
T KOG1126|consen  551 HLDPKNPLCKY---------------HRASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFS  615 (638)
T ss_pred             hcCCCCchhHH---------------HHHHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhH
Confidence            76543222222               366777889999999999999954  4 67788999999999999999999998


Q ss_pred             HHHHCCCCCcH
Q 045555          152 QMLRASIRLDE  162 (175)
Q Consensus       152 ~m~~~g~~p~~  162 (175)
                      -+.+-.-++..
T Consensus       616 ~A~~ldpkg~~  626 (638)
T KOG1126|consen  616 WALDLDPKGAQ  626 (638)
T ss_pred             HHhcCCCccch
Confidence            88775444444

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.46  E-value=3.5e-05  Score=56.26  Aligned_cols=158  Identities=11%  Similarity=0.036  Sum_probs=97.9

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|...|+...+  | +..+|+.+...+.+.|++++|...|+...+  | +..+|..+...+...|++++|++.|++..+.
T Consensus        82 ~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~  161 (296)
T PRK11189         82 LARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD  161 (296)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            45555665543  3 567888888888999999999988888754  3 4567788888888889999999999888875


Q ss_pred             CCCCChH---HHHHhhh-----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc---C-------CC
Q 045555           77 NIRRDEF---TTVRILT-----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML---R-------KD  126 (175)
Q Consensus        77 ~~~p~~~---~~~~l~~-----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~-------~~  126 (175)
                      .  |+..   .+..+..                 ...|+...+ .+..  ...|++..+ ..+..+.   +       ..
T Consensus       162 ~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~~~~~~~~-~~~~--~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~  235 (296)
T PRK11189        162 D--PNDPYRALWLYLAESKLDPKQAKENLKQRYEKLDKEQWGW-NIVE--FYLGKISEE-TLMERLKAGATDNTELAERL  235 (296)
T ss_pred             C--CCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhCCccccHH-HHHH--HHccCCCHH-HHHHHHHhcCCCcHHHHHHH
Confidence            4  3221   1111111                 111111111 1222  223333322 1222221   1       12


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHH
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVG  167 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  167 (175)
                      ...|..+...+.+.|++++|...|++..+.+ .||..-+..
T Consensus       236 ~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~-~~~~~e~~~  275 (296)
T PRK11189        236 CETYFYLAKYYLSLGDLDEAAALFKLALANN-VYNFVEHRY  275 (296)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CchHHHHHH
Confidence            3568888899999999999999999998654 345444433

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.45  E-value=9.4e-06  Score=52.83  Aligned_cols=103  Identities=10%  Similarity=0.050  Sum_probs=83.8

Q ss_pred             HhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChH
Q 045555            7 IFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEF   83 (175)
Q Consensus         7 ~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~   83 (175)
                      +|+...+-++..+......+.+.|++++|...|+....   .+...|..+...+.+.|++++|+..|++.....  |   
T Consensus        15 ~~~~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~--p---   89 (144)
T PRK15359         15 ILKQLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD--A---   89 (144)
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--C---
Confidence            34444443454566778889999999999999998764   477789999999999999999999999999854  2   


Q ss_pred             HHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           84 TTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        84 ~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                                .+...+..+..++.+.|++++|...|+...+
T Consensus        90 ----------~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359         90 ----------SHPEPVYQTGVCLKMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             ----------CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                      2445557899999999999999999999854

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=98.45  E-value=7.9e-06  Score=69.81  Aligned_cols=73  Identities=16%  Similarity=0.019  Sum_probs=47.3

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|++.|++..+  | +...+..+...|.+.|++++|...+++..+  | +...+..+...+.+.+++++|+..++++.
T Consensus       478 ~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~  556 (1157)
T PRK11447        478 AQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLP  556 (1157)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            466777776654  4 556677788888888888888888887643  3 33334444444555666666666666543

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.44  E-value=4.7e-05  Score=55.54  Aligned_cols=125  Identities=12%  Similarity=-0.043  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      ...|..+...|.+.|+.++|...|++..+   .+...|+.+...+...|++++|.+.|++..+..  |+           
T Consensus        64 a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~-----------  130 (296)
T PRK11189         64 AQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLELD--PT-----------  130 (296)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CC-----------
Confidence            45688888899999999999999998764   367789999999999999999999999999843  33           


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                        +...+..+..++...|++++|.+.|+...+  |+..............++.++|.+.|.+...
T Consensus       131 --~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~  193 (296)
T PRK11189        131 --YNYAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLYLAESKLDPKQAKENLKQRYE  193 (296)
T ss_pred             --CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence              234456788888899999999999999854  3322122222233456789999999977554

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

Probab=98.42  E-value=7.8e-06  Score=63.77  Aligned_cols=157  Identities=12%  Similarity=0.131  Sum_probs=101.7

Q ss_pred             chHHHHhhccCC--Cc-HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--KD-VISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      |-|+..+++..+  |+ +.+|+.|..++-..|+..+|.+.|++...  | ...+.+.|.+.+.+.|.+++|..+|.....
T Consensus       303 dlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~  382 (966)
T KOG4626|consen  303 DLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALE  382 (966)
T ss_pred             HHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHh
Confidence            456677776664  54 46899999999999999999999998764  3 455788899999999999999999888876


Q ss_pred             CCCCCChH-HHH---Hhhh----------------ccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHH
Q 045555           76 SNIRRDEF-TTV---RILT----------------TFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWT  131 (175)
Q Consensus        76 ~~~~p~~~-~~~---~l~~----------------~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~  131 (175)
                      -  -|.-. .++   ++.+                .+.|. ...++.+...|-..|+++.|.+.+...+.  | -....+
T Consensus       383 v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhs  460 (966)
T KOG4626|consen  383 V--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHS  460 (966)
T ss_pred             h--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHh
Confidence            3  22211 010   0000                22222 33444444445555555555555544432  2 123566


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          132 AMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       132 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      .+...|-.+|++.+|..-|++.++  ++||.
T Consensus       461 NLasi~kDsGni~~AI~sY~~aLk--lkPDf  489 (966)
T KOG4626|consen  461 NLASIYKDSGNIPEAIQSYRTALK--LKPDF  489 (966)
T ss_pred             hHHHHhhccCCcHHHHHHHHHHHc--cCCCC
Confidence            777788888888888888888764  46664

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

Probab=98.41  E-value=3.4e-05  Score=55.78  Aligned_cols=161  Identities=14%  Similarity=0.197  Sum_probs=112.4

Q ss_pred             CchHHHHhhccCC-CcH------HHHHHHHHHHHhcCChhHHHHHhhcCCC-C--ChhHHHHHHHHHhccCChHHHHHHH
Q 045555            1 MGFALEIFGNMKN-KDV------ISWTTIVSGYINRGQVDIARQYFAQMPE-R--DYVLWTAMIDGYLRVNRFREALTLF   70 (175)
Q Consensus         1 ~~~A~~~~~~m~~-~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~-~--~~~~~~~li~~~~~~~~~~~a~~~~   70 (175)
                      +|.|+++...+.+ ||.      .+--.|..-|...|-+|.|.++|..+.+ +  -....-.|+..|-...+|++|+++-
T Consensus        85 vDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A  164 (389)
T COG2956          85 VDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVA  164 (389)
T ss_pred             HHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            4678888876665 653      3445666778889999999999999887 3  2345778899999999999999999


Q ss_pred             HHhHhCCCCCChHHHHH----hhh-------------------ccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC
Q 045555           71 REMQTSNIRRDEFTTVR----ILT-------------------TFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLRKD  126 (175)
Q Consensus        71 ~~m~~~~~~p~~~~~~~----l~~-------------------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  126 (175)
                      +++.+.+..+..+-...    +-.                   ...| .+..-..+.+.+...|+++.|.+.++...+.|
T Consensus       165 ~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn  244 (389)
T COG2956         165 ERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQN  244 (389)
T ss_pred             HHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhC
Confidence            99988765544322111    111                   1112 22333456667778888888888888886655


Q ss_pred             h----hhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          127 K----FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       127 ~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      .    .+...+..+|.+.|+.++....+.++.+..-.++
T Consensus       245 ~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~  283 (389)
T COG2956         245 PEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGAD  283 (389)
T ss_pred             hHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCcc
Confidence            4    3566778888888998888888888776543333

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=98.41  E-value=2e-05  Score=64.72  Aligned_cols=137  Identities=13%  Similarity=0.119  Sum_probs=93.1

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++++.....   .+...+..+...+.+.|++++|..+|++..   ..+...+..+...+...|++++|+..+++..+
T Consensus        32 ~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~  111 (765)
T PRK10049         32 AEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAKQLVS  111 (765)
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            356666666553   344457777777788888888888888743   23455566777777778888888888888776


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      ..  |+             +.. +..+..++...|+.++|...+++..+  | +...+..+...+...|+.++|.+.++.
T Consensus       112 ~~--P~-------------~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~  175 (765)
T PRK10049        112 GA--PD-------------KAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDD  175 (765)
T ss_pred             hC--CC-------------CHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHh
Confidence            52  21             233 45677778888888888888888744  3 445556667777777788878777765


Q ss_pred             HH
Q 045555          153 ML  154 (175)
Q Consensus       153 m~  154 (175)
                      ..
T Consensus       176 ~~  177 (765)
T PRK10049        176 AN  177 (765)
T ss_pred             CC
Confidence            43

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

Probab=98.40  E-value=2.2e-05  Score=54.89  Aligned_cols=124  Identities=17%  Similarity=0.167  Sum_probs=93.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      |...-+..+....+.|++..|...+++...   +|...|+.+--+|.+.|++++|..-|.+..+--  |+          
T Consensus        99 d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~--~~----------  166 (257)
T COG5010          99 DRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELA--PN----------  166 (257)
T ss_pred             cHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhc--cC----------
Confidence            445556677788888888888888887664   578888888888888888888888888887742  22          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                         +....|.+.-.|.-.|+.++|..++.....   .|..+-..+.-.....|++++|.++...-
T Consensus       167 ---~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~~e  228 (257)
T COG5010         167 ---EPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAVQE  228 (257)
T ss_pred             ---CchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhcccc
Confidence               233446677777788888888888887732   26777777888888888888888776543

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

Probab=98.39  E-value=2.1e-05  Score=54.02  Aligned_cols=104  Identities=14%  Similarity=0.210  Sum_probs=83.0

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHH-HHhcCC--HHHHHHHHHhh
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM-YCKCGD--VEKAQRVFWKM  122 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~-~~~~~~--~~~a~~~~~~~  122 (175)
                      |...|..|...|...|++++|...|++..+..  |+             +...+..+..+ +...|+  .++|.+++++.
T Consensus        72 ~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~--P~-------------~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~a  136 (198)
T PRK10370         72 NSEQWALLGEYYLWRNDYDNALLAYRQALQLR--GE-------------NAELYAALATVLYYQAGQHMTPQTREMIDKA  136 (198)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CC-------------CHHHHHHHHHHHHHhcCCCCcHHHHHHHHHH
Confidence            77789999999999999999999999999854  32             34445667765 467777  59999999999


Q ss_pred             cC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHH
Q 045555          123 LR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY  165 (175)
Q Consensus       123 ~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  165 (175)
                      .+  | +...+..+...+...|++++|...++++.+. ..|+..-.
T Consensus       137 l~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l-~~~~~~r~  181 (198)
T PRK10370        137 LALDANEVTALMLLASDAFMQADYAQAIELWQKVLDL-NSPRVNRT  181 (198)
T ss_pred             HHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CCCCccHH
Confidence            55  3 6778888999999999999999999999874 34444333

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.39  E-value=3.2e-05  Score=62.38  Aligned_cols=127  Identities=12%  Similarity=0.057  Sum_probs=109.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +..++-.|.....+.|..++|..+++...+  | +......+...+.+.+++++|+..+++.....  |+          
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~--p~----------  152 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG--SS----------  152 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC--CC----------
Confidence            578888999999999999999999999875  5 56678889999999999999999999999854  33          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                         +......+..++.+.|++++|..+|++...+   +...+..+-.++-..|+.++|...|++..+.
T Consensus       153 ---~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        153 ---SAREILLEAKSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             ---CHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence               2334467889999999999999999999754   3678888889999999999999999999864

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

Probab=98.38  E-value=4.7e-05  Score=49.55  Aligned_cols=125  Identities=10%  Similarity=0.077  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--RDY----VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      ...|..++..+ ..++...+...++.+.+  |+.    ...-.+...+...|++++|...|+......  |+....    
T Consensus        12 ~~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~----   84 (145)
T PF09976_consen   12 SALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANA--PDPELK----   84 (145)
T ss_pred             HHHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCHHHH----
Confidence            34577777777 48899999888888875  322    223345577889999999999999999976  332211    


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                            ....-.|...+...|++++|...++....+  ....+....+.|.+.|++++|...|+..
T Consensus        85 ------~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   85 ------PLARLRLARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             ------HHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence                  112235888999999999999999886543  4456777888999999999999999864

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

Probab=98.37  E-value=1.3e-05  Score=57.91  Aligned_cols=139  Identities=14%  Similarity=0.157  Sum_probs=104.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCCCh---hHHHHHHHH-HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPERDY---VLWTAMIDG-YLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      .+|..+|+..-+.+..+.|+.+|.+.++...   .+|-..... +...++.+.|..+|+..++.               +
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~---------------f   66 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK---------------F   66 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH---------------H
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH---------------C
Confidence            5789999999999999999999999886433   333333333 33457788899999999885               2


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK------DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      ..+...|..-++.+.+.++.+.|..+|+.....      ....|...+..-.+.|+++.+.++.+++.+.  -|+..++.
T Consensus        67 ~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~  144 (280)
T PF05843_consen   67 PSDPDFWLEYLDFLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLE  144 (280)
T ss_dssp             TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHH
T ss_pred             CCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHH
Confidence            456667788889999999999999999999653      3458999999999999999999999999874  45555555


Q ss_pred             HHHhhh
Q 045555          167 GVLSAC  172 (175)
Q Consensus       167 ~ll~~~  172 (175)
                      .+++-|
T Consensus       145 ~f~~ry  150 (280)
T PF05843_consen  145 LFSDRY  150 (280)
T ss_dssp             HHHCCT
T ss_pred             HHHHHh
Confidence            555433

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.

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

Probab=98.35  E-value=3e-05  Score=49.58  Aligned_cols=108  Identities=15%  Similarity=0.114  Sum_probs=84.6

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +......+...+.+.|++++|.+.|++....+               +.+...+..+...+.+.|++++|...++.... 
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~---------------p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~   80 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD---------------PYNSRYWLGLAACCQMLKEYEEAIDAYALAAAL   80 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC---------------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44556677788889999999999999988754               22445556889999999999999999998844 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHh
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLS  170 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  170 (175)
                       | +...+..+...+...|++++|.+.|++..+.  .|+...+..+..
T Consensus        81 ~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~  126 (135)
T TIGR02552        81 DPDDPRPYFHAAECLLALGEPESALKALDLAIEI--CGENPEYSELKE  126 (135)
T ss_pred             CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--ccccchHHHHHH
Confidence             3 5677888888999999999999999998874  566666554444

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

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

Probab=98.35  E-value=8.5e-06  Score=65.59  Aligned_cols=127  Identities=15%  Similarity=0.116  Sum_probs=104.0

Q ss_pred             CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc----------CcchhHHHHHHHHHHhcCCHH
Q 045555           44 ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF----------NNDIFVGIALIDMYCKCGDVE  113 (175)
Q Consensus        44 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~----------~~~~~~~~~li~~~~~~~~~~  113 (175)
                      .||.+||..+|..||..|+.+.|- +|.-|+-.....+...++.++.+.          .|...+|+.|..+|.+.||+.
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt~Ll~ayr~hGDli  100 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYTNLLKAYRIHGDLI  100 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHHHHHHHHHhccchH
Confidence            588899999999999999999998 999998888888888898888842          567889999999999999976


Q ss_pred             HHHHHHHhh------------------------------------------------------cC---------------
Q 045555          114 KAQRVFWKM------------------------------------------------------LR---------------  124 (175)
Q Consensus       114 ~a~~~~~~~------------------------------------------------------~~---------------  124 (175)
                      .-+.+=+.+                                                      ..               
T Consensus       101 ~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa~~~p~~vfLrq  180 (1088)
T KOG4318|consen  101 LFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQ  180 (1088)
T ss_pred             HHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCcccccchHHHHHHH
Confidence            533332222                                                      00               


Q ss_pred             ---------------------CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          125 ---------------------KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       125 ---------------------~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                                           ++..+|...++.-..+|+++.|..++.+|.++|+.-++.-|..||-+
T Consensus       181 nv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g  248 (1088)
T KOG4318|consen  181 NVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG  248 (1088)
T ss_pred             hccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc
Confidence                                 13346777888888899999999999999999999999988888766

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

Probab=98.34  E-value=3.6e-05  Score=55.90  Aligned_cols=136  Identities=15%  Similarity=0.135  Sum_probs=97.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhH
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFV   98 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~   98 (175)
                      .-.....+...|++++|+++++.-  .+.-.....+..|.+.++++.|.+.++.|.+.+  .|....           .+
T Consensus       105 ~~~~A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~~l~-----------qL  169 (290)
T PF04733_consen  105 QLLAATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQID--EDSILT-----------QL  169 (290)
T ss_dssp             HHHHHHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCHHHH-----------HH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHHH-----------HH
Confidence            333445567789999999988876  455556778889999999999999999998753  332222           12


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHh
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLS  170 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  170 (175)
                      ..+.+..+.-.+.+.+|.-+|+++..   +++.+.|.+..+....|++++|.+++.+..+.. +-|+.|...++-
T Consensus       170 a~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv  243 (290)
T PF04733_consen  170 AEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIV  243 (290)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHH
T ss_pred             HHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHH
Confidence            34555555555689999999999954   467788888899999999999999999987643 234555555443

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.

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

Probab=98.33  E-value=1.4e-05  Score=67.05  Aligned_cols=133  Identities=17%  Similarity=0.239  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      ..|..|...|.+.+..++|.++++.|.+   ....+|...+..+.+..+-++|.+++.+.++.=.+...           
T Consensus      1531 ~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eH----------- 1599 (1710)
T KOG1070|consen 1531 TVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEH----------- 1599 (1710)
T ss_pred             HHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhh-----------
Confidence            3456666666666666666666666654   24555666666666666666666666666653221111           


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                        .....-.+..-.+.|+.+.+..+|+.....   -...|+.+|+.-.++|+.+.+.++|++..+.++.|-.
T Consensus      1600 --v~~IskfAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kk 1669 (1710)
T KOG1070|consen 1600 --VEFISKFAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKK 1669 (1710)
T ss_pred             --HHHHHHHHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhH
Confidence              223345666667999999999999998542   6789999999999999999999999999999988853

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.32  E-value=1.2e-05  Score=62.21  Aligned_cols=143  Identities=15%  Similarity=0.167  Sum_probs=105.3

Q ss_pred             hHHHHhhccCCC----cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------CChh-HHHHHHHHHhccCChHHHH
Q 045555            3 FALEIFGNMKNK----DVISWTTIVSGYINRGQVDIARQYFAQMPE----------RDYV-LWTAMIDGYLRVNRFREAL   67 (175)
Q Consensus         3 ~A~~~~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------~~~~-~~~~li~~~~~~~~~~~a~   67 (175)
                      +|+.+++....+    -..+++.|...|.+.|++++|...++...+          +.+. .++.+...|...+++++|.
T Consensus       266 ~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~  345 (508)
T KOG1840|consen  266 EALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAK  345 (508)
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHH
Confidence            344444443332    345688888889999999999988887552          2332 3677788889999999999


Q ss_pred             HHHHHhHhCC---CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----------ChhhHHHH
Q 045555           68 TLFREMQTSN---IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----------DKFTWTAM  133 (175)
Q Consensus        68 ~~~~~m~~~~---~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----------~~~~~~~l  133 (175)
                      .++.+..+.-   +.++.+          .-..+++.|...|-..|++++|+++|++.+..           ....++.+
T Consensus       346 ~l~q~al~i~~~~~g~~~~----------~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~l  415 (508)
T KOG1840|consen  346 KLLQKALKIYLDAPGEDNV----------NLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQL  415 (508)
T ss_pred             HHHHHHHHHHHhhccccch----------HHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHH
Confidence            9999776531   222211          12457789999999999999999999998431           23467889


Q ss_pred             HHHHHhcCChhHHHHHHHHHHH
Q 045555          134 IVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ...|.+.++..+|.++|.+-..
T Consensus       416 a~~~~~~k~~~~a~~l~~~~~~  437 (508)
T KOG1840|consen  416 AEAYEELKKYEEAEQLFEEAKD  437 (508)
T ss_pred             HHHHHHhcccchHHHHHHHHHH
Confidence            9999999999999999988543

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

Probab=98.30  E-value=5.5e-05  Score=52.21  Aligned_cols=122  Identities=18%  Similarity=0.166  Sum_probs=68.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      ..-+...|.+.|+...|..-+++..+  | +..+|..+...|.+.|+.+.|.+.|++.....  |             -+
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~--p-------------~~  102 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSLA--P-------------NN  102 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC--C-------------Cc
Confidence            44455556666666666666666554  2 33455666666666666666666666665532  1             12


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC-C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR-K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..+.|.-.--+|..|++++|...|+.... |    -..+|..+.-+-.++|+.+.|.+.|++-++
T Consensus       103 GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~  167 (250)
T COG3063         103 GDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALE  167 (250)
T ss_pred             cchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHH
Confidence            33344555555666666666666666533 2    234555555555566666666666665554

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

Probab=98.29  E-value=0.00011  Score=50.77  Aligned_cols=151  Identities=11%  Similarity=-0.046  Sum_probs=119.4

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      .|.+-+++..+  | +..+|..+...|.+.|..+.|.+.|++..+   .+-.+.|..-.-+|..|.+++|..-|++....
T Consensus        53 ~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~  132 (250)
T COG3063          53 QAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALAD  132 (250)
T ss_pred             HHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhC
Confidence            35555555554  3 567899999999999999999999998664   45667888888999999999999999999886


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                      .--|             .-..+|..+.-+..+.|+.+.|++.|+.-.+.   ...+.-.+.....+.|++-.|...++..
T Consensus       133 P~Y~-------------~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~  199 (250)
T COG3063         133 PAYG-------------EPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERY  199 (250)
T ss_pred             CCCC-------------CcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHH
Confidence            4211             22345567888889999999999999998553   4557778888899999999999999998


Q ss_pred             HHCCCCCcHHHHHH
Q 045555          154 LRASIRLDEVTYVG  167 (175)
Q Consensus       154 ~~~g~~p~~~t~~~  167 (175)
                      ...|. ++..+.-.
T Consensus       200 ~~~~~-~~A~sL~L  212 (250)
T COG3063         200 QQRGG-AQAESLLL  212 (250)
T ss_pred             Hhccc-ccHHHHHH
Confidence            87655 66655443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.28  E-value=2.9e-05  Score=54.51  Aligned_cols=56  Identities=16%  Similarity=0.109  Sum_probs=47.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcC--C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLR--K----DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~--~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+...|.+.|++++|...+....+  |    ....+..+..++...|++++|.+.++.+...
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            456778899999999999999854  2    2468889999999999999999999988764

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).

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

Probab=98.26  E-value=0.00027  Score=52.38  Aligned_cols=157  Identities=17%  Similarity=0.219  Sum_probs=121.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh-------HH
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE-------FT   84 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-------~~   84 (175)
                      +....-+........|+...|..-..++.   ..+.........+|.+.|+|.+...++.+|.+.|+--++       .+
T Consensus       152 ~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a  231 (400)
T COG3071         152 TLAVELTRARLLLNRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQA  231 (400)
T ss_pred             hHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHH
Confidence            44556666677777777777777666544   346777899999999999999999999999999864433       25


Q ss_pred             HHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-------------------
Q 045555           85 TVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-------------------  125 (175)
Q Consensus        85 ~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------------------  125 (175)
                      |..++.                    ....++..-.+++.-+.++|+.++|.++.++..+.                   
T Consensus       232 ~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~~~~~~l~~~d~~  311 (400)
T COG3071         232 WEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLCRLIPRLRPGDPE  311 (400)
T ss_pred             HHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHHHHHhhcCCCCch
Confidence            555555                    23345566678899999999999999998886210                   


Q ss_pred             ---------------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          126 ---------------DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       126 ---------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                                     +...+.++...|.+.+.|.+|.+.|+....  ..|+..++..+-+++.
T Consensus       312 ~l~k~~e~~l~~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~  372 (400)
T COG3071         312 PLIKAAEKWLKQHPEDPLLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALD  372 (400)
T ss_pred             HHHHHHHHHHHhCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHH
Confidence                           455788899999999999999999997665  5899999998877654

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

Probab=98.18  E-value=0.00034  Score=49.13  Aligned_cols=131  Identities=16%  Similarity=0.167  Sum_probs=104.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      |... ..+-..+...|+-+.+..+......   .|......++....+.|++.+|+..+++.....              
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~--------------  130 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA--------------  130 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC--------------
Confidence            3344 5566666677777777777666442   255556678999999999999999999998853              


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                       ++|...|+.+.-+|-+.|+.++|..-|.+..+   .+....|.+...|.-.|+.+.|..++......+-.+.
T Consensus       131 -p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~  202 (257)
T COG5010         131 -PTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADS  202 (257)
T ss_pred             -CCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCch
Confidence             56778889999999999999999999999854   3778899999999999999999999999877654433

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

Probab=98.18  E-value=8.3e-05  Score=51.06  Aligned_cols=96  Identities=15%  Similarity=0.184  Sum_probs=80.5

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHH-hccCC--hHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGY-LRVNR--FREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~-~~~~~--~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .|...|..+...|...|++++|...|++..+   .+...+..+..++ ...|+  .++|.+++++..+.+.         
T Consensus        71 ~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP---------  141 (198)
T PRK10370         71 QNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDA---------  141 (198)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC---------
Confidence            4888999999999999999999999998764   3677788887764 67777  5999999999999652         


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                            .+...+..+...+.+.|++++|...|+.+.+
T Consensus       142 ------~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~  172 (198)
T PRK10370        142 ------NEVTALMLLASDAFMQADYAQAIELWQKVLD  172 (198)
T ss_pred             ------CChhHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                  2445557889999999999999999999854

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

Probab=98.17  E-value=8.9e-05  Score=47.37  Aligned_cols=95  Identities=12%  Similarity=0.161  Sum_probs=78.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +......+...+.+.|++++|.+.|+...+   .+...|..+...+.+.|++++|...+++..+.+  |           
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--p-----------   82 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD--P-----------   82 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--C-----------
Confidence            456677888889999999999999998754   366788899999999999999999999988864  2           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        .+...+..+...|...|++++|...|+...+
T Consensus        83 --~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        83 --DDPRPYFHAAECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             --CChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              2333445688899999999999999998854

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

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

Probab=98.17  E-value=0.00019  Score=54.43  Aligned_cols=124  Identities=13%  Similarity=0.110  Sum_probs=60.2

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC-hhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|+..++.+.+  | |+..+......+.+.++.++|.+.++.+..  |+ ...+-.+-.+|.+.|++.+|+.++++....
T Consensus       324 ~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~  403 (484)
T COG4783         324 EALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN  403 (484)
T ss_pred             hHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc
Confidence            34444444432  3 333344444455555555555555555443  32 233444445555555555555555555544


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .               +.|...|..|..+|.+.|+..++..-              .-++|...|+++.|...+....+
T Consensus       404 ~---------------p~dp~~w~~LAqay~~~g~~~~a~~A--------------~AE~~~~~G~~~~A~~~l~~A~~  453 (484)
T COG4783         404 D---------------PEDPNGWDLLAQAYAELGNRAEALLA--------------RAEGYALAGRLEQAIIFLMRASQ  453 (484)
T ss_pred             C---------------CCCchHHHHHHHHHHHhCchHHHHHH--------------HHHHHHhCCCHHHHHHHHHHHHH
Confidence            2               22333445555555555555554322              23344455666666666655554

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

Probab=98.15  E-value=8.2e-05  Score=43.40  Aligned_cols=93  Identities=18%  Similarity=0.238  Sum_probs=74.8

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-  125 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-  125 (175)
                      ++..+...+...|++++|...+++..+..  |+             +...+..+...+...+++++|.+.|+....  | 
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~-------------~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~   66 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD--PD-------------NADAYYNLAAAYYKLGKYEEALEDYEKALELDPD   66 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC--Cc-------------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            35667778888999999999999998753  22             223446788899999999999999998743  2 


Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          126 DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       126 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +..++..+...+...|++++|.+.+.+..+.
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          67 NAKAYYNLGLAYYKLGKYEEALEAYEKALEL   97 (100)
T ss_pred             chhHHHHHHHHHHHHHhHHHHHHHHHHHHcc
Confidence            4567888889999999999999999887653

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

Probab=98.14  E-value=0.00011  Score=55.89  Aligned_cols=116  Identities=12%  Similarity=0.116  Sum_probs=81.3

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +.....++++.+....+.+++..++.+.+...-.-.          ..|  .+..++|..|.+.|..+.+..+++.-.. 
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~----------~~~--~t~ha~vR~~l~~~~~~~~l~~L~n~~~y  132 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSY----------LLP--STHHALVRQCLELGAEDELLELLKNRLQY  132 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCccccc----------ccC--ccHHHHHHHHHhcCCHHHHHHHHhChhhc
Confidence            455566677777777777777777777776521110          011  1224788888888888888888777543 


Q ss_pred             ---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          125 ---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       125 ---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                         ||..++|.+|+.+.+.|++..|.++..+|..++...++.|+..-+.+|.
T Consensus       133 GiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~  184 (429)
T PF10037_consen  133 GIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCY  184 (429)
T ss_pred             ccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHH
Confidence               6778888888888888888888888888887777777777777776664

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=98.13  E-value=0.00016  Score=59.48  Aligned_cols=157  Identities=11%  Similarity=-0.005  Sum_probs=113.9

Q ss_pred             chHHHHhhccCCC----cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC---------ChhHHHHHHHHHhccCChHHHHH
Q 045555            2 GFALEIFGNMKNK----DVISWTTIVSGYINRGQVDIARQYFAQMPER---------DYVLWTAMIDGYLRVNRFREALT   68 (175)
Q Consensus         2 ~~A~~~~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~~~~~~a~~   68 (175)
                      .+|++-|+.++.+    -..+--++..+|...+.+++|..+|..+..+         +......|..++...+++++|..
T Consensus       309 ~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~  388 (822)
T PRK14574        309 ADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQ  388 (822)
T ss_pred             HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHH
Confidence            4677777877741    2346778999999999999999999987431         33335789999999999999999


Q ss_pred             HHHHhHhCCCCC-ChHHHHHhhhccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCCh
Q 045555           69 LFREMQTSNIRR-DEFTTVRILTTFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHG  143 (175)
Q Consensus        69 ~~~~m~~~~~~p-~~~~~~~l~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~  143 (175)
                      +++++.+.  .| -...+..-....+|| ......++..+...|++.+|++.++++..  | |......+.+.+...|.+
T Consensus       389 ~l~~~~~~--~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p  466 (822)
T PRK14574        389 FAVNYSEQ--TPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLP  466 (822)
T ss_pred             HHHHHHhc--CCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCH
Confidence            99999874  23 111121111223344 23445667778899999999999999844  4 777888888889999999


Q ss_pred             hHHHHHHHHHHHCCCCCcH
Q 045555          144 DTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       144 ~~a~~~~~~m~~~g~~p~~  162 (175)
                      .+|.+.++..+..  .|+.
T Consensus       467 ~~A~~~~k~a~~l--~P~~  483 (822)
T PRK14574        467 RKAEQELKAVESL--APRS  483 (822)
T ss_pred             HHHHHHHHHHhhh--CCcc
Confidence            9999999666543  5553

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

Probab=98.12  E-value=7.4e-05  Score=45.87  Aligned_cols=88  Identities=14%  Similarity=0.152  Sum_probs=63.8

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCC-CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCCh
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNI-RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDK  127 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  127 (175)
                      |-...|..+...+++.....+|..+++.|+ .|+..+|              +.++.+.+++..              |.
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Y--------------n~VL~Si~~R~l--------------D~   78 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELY--------------NKVLKSIAKREL--------------DS   78 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHH--------------HHHHHHHHHccc--------------cc
Confidence            345567777777999999999999999998 6666666              556666554321              10


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                               ..-.+++-..+.+|++|+..+++|+..||+.++..+-
T Consensus        79 ---------~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Ll  115 (120)
T PF08579_consen   79 ---------EDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLL  115 (120)
T ss_pred             ---------hhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHH
Confidence                     1123356677889999999999999999999988764

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 [, , ].

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

Probab=98.11  E-value=0.00055  Score=52.98  Aligned_cols=156  Identities=19%  Similarity=0.212  Sum_probs=107.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhC--C------------
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTS--N------------   77 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~------------   77 (175)
                      .+.+|-++.-.|.-.|+.++|++.|.+...  | -...|-...++|+-.|..+.|+..+...-+.  |            
T Consensus       311 ~a~sW~aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey  390 (611)
T KOG1173|consen  311 KALSWFAVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGMEY  390 (611)
T ss_pred             CCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHHHH
Confidence            567888888888888999999999987653  2 2234555555555555555555544444332  1            


Q ss_pred             ------------------CCCCh-HHHHHh--hh-------------------------ccCcchhHHHHHHHHHHhcCC
Q 045555           78 ------------------IRRDE-FTTVRI--LT-------------------------TFNNDIFVGIALIDMYCKCGD  111 (175)
Q Consensus        78 ------------------~~p~~-~~~~~l--~~-------------------------~~~~~~~~~~~li~~~~~~~~  111 (175)
                                        +.|+. ...+-+  +.                         ...-...+++.|..+|.+.++
T Consensus       391 ~~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~  470 (611)
T KOG1173|consen  391 MRTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNK  470 (611)
T ss_pred             HHhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhh
Confidence                              22211 111000  00                         001133468899999999999


Q ss_pred             HHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          112 VEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       112 ~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      +++|...|+....   .+..++.++.-.|...|+++.|.+.|++.+  .+.||..+...+|+.+
T Consensus       471 ~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  471 YEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHH
Confidence            9999999999743   488899999999999999999999999977  5789998888888754

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

Probab=98.04  E-value=0.00038  Score=51.85  Aligned_cols=113  Identities=13%  Similarity=0.130  Sum_probs=81.4

Q ss_pred             cCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHH
Q 045555           29 RGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM  105 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~  105 (175)
                      .+....+.+.+....+  | .......+...+...|++++|...+++..+..  |+             +...+..+...
T Consensus        93 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~--p~-------------~~~~~~~la~i  157 (355)
T cd05804          93 SGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN--PD-------------DAWAVHAVAHV  157 (355)
T ss_pred             ccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CC-------------CcHHHHHHHHH
Confidence            4555566666554222  2 23344555667788899999999999988854  22             23445678899


Q ss_pred             HHhcCCHHHHHHHHHhhcCC-----C--hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          106 YCKCGDVEKAQRVFWKMLRK-----D--KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       106 ~~~~~~~~~a~~~~~~~~~~-----~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      |...|++++|.+.+++..+.     +  ...|-.+...+...|++++|.+.+++....
T Consensus       158 ~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~  215 (355)
T cd05804         158 LEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAP  215 (355)
T ss_pred             HHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            99999999999999987542     2  234567888899999999999999998643

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=98.01  E-value=7.7e-05  Score=56.27  Aligned_cols=106  Identities=15%  Similarity=0.161  Sum_probs=89.4

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++|+.+|+++.+.++.....+++.+...++-.+|.++.++...   .+......-...|.+.++.+.|+.+.++..+.. 
T Consensus       186 ~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~ls-  264 (395)
T PF09295_consen  186 DEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKAVELS-  264 (395)
T ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-
Confidence            6799999999987777788899999999999999999998764   355556666777899999999999999999852 


Q ss_pred             CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           79 RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        79 ~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                       |+             +-.+|..|..+|.+.|+++.|...++.+
T Consensus       265 -P~-------------~f~~W~~La~~Yi~~~d~e~ALlaLNs~  294 (395)
T PF09295_consen  265 -PS-------------EFETWYQLAECYIQLGDFENALLALNSC  294 (395)
T ss_pred             -ch-------------hHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence             22             3457889999999999999999999887

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

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

Probab=98.01  E-value=0.00021  Score=53.54  Aligned_cols=102  Identities=10%  Similarity=0.042  Sum_probs=82.9

Q ss_pred             HHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhH
Q 045555           54 IDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTW  130 (175)
Q Consensus        54 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~  130 (175)
                      ...+...|++++|++.|++.++..  |+             +...|..+..+|.+.|++++|...++....  | +...|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~--P~-------------~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~   73 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD--PN-------------NAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAY   73 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC--CC-------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHH
Confidence            456778899999999999999854  22             344556788999999999999999999954  3 56688


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          131 TAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       131 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      ..+..+|...|++++|.+.|++.++  +.|+...+...+..|
T Consensus        74 ~~lg~~~~~lg~~~eA~~~~~~al~--l~P~~~~~~~~l~~~  113 (356)
T PLN03088         74 LRKGTACMKLEEYQTAKAALEKGAS--LAPGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHH
Confidence            8889999999999999999999986  457766666666555

>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=97.99  E-value=0.00011  Score=42.85  Aligned_cols=92  Identities=20%  Similarity=0.258  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      ++..+...+.+.|++++|...++...+  | +...+..+...+...+++++|...+++..+....               
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~---------------   66 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD---------------   66 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc---------------
Confidence            456777888899999999999998754  3 4467888888999999999999999999886421               


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      +..++..+...+...|++++|...+....+
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          67 NAKAYYNLGLAYYKLGKYEEALEAYEKALE   96 (100)
T ss_pred             chhHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence            223446788899999999999999987643

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.99  E-value=0.0013  Score=46.12  Aligned_cols=131  Identities=10%  Similarity=0.031  Sum_probs=95.2

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC-h---hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RD-Y---VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .....+-.+...+.+.|+++.|...|++..+  |+ .   .++..+..++.+.|++++|+..++++.+.........+  
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~--  108 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADY--  108 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHH--
Confidence            3567788888899999999999999998764  32 2   46788889999999999999999999985432111101  


Q ss_pred             hhhccCcchhHHHHHHHHHHhc--------CCHHHHHHHHHhhcC--CCh-hhH-----------------HHHHHHHHh
Q 045555           88 ILTTFNNDIFVGIALIDMYCKC--------GDVEKAQRVFWKMLR--KDK-FTW-----------------TAMIVGLAI  139 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~--------~~~~~a~~~~~~~~~--~~~-~~~-----------------~~li~~~~~  139 (175)
                                .+..+..++.+.        |++++|.+.|+....  |+. ..+                 ..+...+.+
T Consensus       109 ----------a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~  178 (235)
T TIGR03302       109 ----------AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLK  178 (235)
T ss_pred             ----------HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                      122344444433        789999999999854  322 121                 134566788


Q ss_pred             cCChhHHHHHHHHHHHC
Q 045555          140 SGHGDTALDMFSQMLRA  156 (175)
Q Consensus       140 ~g~~~~a~~~~~~m~~~  156 (175)
                      .|++.+|...+++..+.
T Consensus       179 ~g~~~~A~~~~~~al~~  195 (235)
T TIGR03302       179 RGAYVAAINRFETVVEN  195 (235)
T ss_pred             cCChHHHHHHHHHHHHH
Confidence            99999999999999875

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).

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

Probab=97.98  E-value=0.00018  Score=52.37  Aligned_cols=131  Identities=15%  Similarity=0.107  Sum_probs=104.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      |...-+-+.++|.+.|.+.+|...++.-.+  |-+.||-.|-..|.+..++..|+.+|.+-++.  -|..+||       
T Consensus       222 dwwWk~Q~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~-------  292 (478)
T KOG1129|consen  222 DWWWKQQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTY-------  292 (478)
T ss_pred             hHHHHHHHHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhh-------
Confidence            455557889999999999999999987654  67889999999999999999999999988874  4555555       


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL  160 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  160 (175)
                            ..-+...+...++.++|.++++...+.   ++....++..+|.-.++.+-|.+.|+++++-|+..
T Consensus       293 ------l~g~ARi~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~s  357 (478)
T KOG1129|consen  293 ------LLGQARIHEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQS  357 (478)
T ss_pred             ------hhhhHHHHHHHHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCC
Confidence                  245667778888999999999988553   55566667777888888888898888888887653

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.98  E-value=0.00041  Score=46.45  Aligned_cols=83  Identities=13%  Similarity=0.076  Sum_probs=64.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      +...+..+...+.+.|++++|...|++..+  |+    ...+..+...+.+.|++++|...+.+..+..  |+       
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~-------  104 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN--PK-------  104 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cc-------
Confidence            556788888899999999999999998763  22    3578889999999999999999999998853  32       


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCH
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDV  112 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~  112 (175)
                            +...+..+..+|...|+.
T Consensus       105 ------~~~~~~~lg~~~~~~g~~  122 (172)
T PRK02603        105 ------QPSALNNIAVIYHKRGEK  122 (172)
T ss_pred             ------cHHHHHHHHHHHHHcCCh
Confidence                  223344566677776663

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.96  E-value=0.00014  Score=56.47  Aligned_cols=142  Identities=15%  Similarity=0.205  Sum_probs=107.2

Q ss_pred             chHHHHhhccCC---CcH-HHHHHHHHHHHhcCChhHHHHHhhcCCC-------C-C---hhHHHHHHHHHhccCChHHH
Q 045555            2 GFALEIFGNMKN---KDV-ISWTTIVSGYINRGQVDIARQYFAQMPE-------R-D---YVLWTAMIDGYLRVNRFREA   66 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~-~---~~~~~~li~~~~~~~~~~~a   66 (175)
                      ++|.++++....   |.+ ...+.+...++..+++++|..+++...+       + +   ..+++.|-..|.+.|++++|
T Consensus       307 e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~~~~a~~~~nl~~l~~~~gk~~ea  386 (508)
T KOG1840|consen  307 ERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDNVNLAKIYANLAELYLKMGKYKEA  386 (508)
T ss_pred             HHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHhcchhHH
Confidence            456666666332   332 3477888889999999999999986542       2 2   35799999999999999999


Q ss_pred             HHHHHHhHhCC----CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc------CC----ChhhHHH
Q 045555           67 LTLFREMQTSN----IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML------RK----DKFTWTA  132 (175)
Q Consensus        67 ~~~~~~m~~~~----~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~------~~----~~~~~~~  132 (175)
                      .+++++..+..    -.-+..           .....+.+...|.+.+++++|.++|.+-.      .|    ...+|..
T Consensus       387 ~~~~k~ai~~~~~~~~~~~~~-----------~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~n  455 (508)
T KOG1840|consen  387 EELYKKAIQILRELLGKKDYG-----------VGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLN  455 (508)
T ss_pred             HHHHHHHHHHHHhcccCcChh-----------hhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHH
Confidence            99999987642    111111           12344679999999999999999998862      22    3468999


Q ss_pred             HHHHHHhcCChhHHHHHHHHHH
Q 045555          133 MIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      |...|.+.|++++|.++.+...
T Consensus       456 L~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  456 LAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHHcccHHHHHHHHHHHH
Confidence            9999999999999999988775

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.95  E-value=0.00073  Score=41.84  Aligned_cols=97  Identities=12%  Similarity=0.146  Sum_probs=76.5

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      .++..+...+.+.|++++|...|.++.+..  |+.          ......+..+..++.+.|+++.|...|+....  |
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~----------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p   70 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKY--PKS----------TYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYP   70 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCc----------cccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCC
Confidence            356677788899999999999999998753  221          00122334689999999999999999999853  4


Q ss_pred             C----hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          126 D----KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       126 ~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +    ...+..+..++.+.|+.++|.+.++++.+.
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        71 KSPKAPDALLKLGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             CCCcccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            3    356778888899999999999999999986

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

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

Probab=97.92  E-value=0.00012  Score=42.95  Aligned_cols=80  Identities=13%  Similarity=0.159  Sum_probs=58.8

Q ss_pred             cCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhHHHHHHHH
Q 045555           60 VNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTWTAMIVGL  137 (175)
Q Consensus        60 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~  137 (175)
                      .|+++.|+.+++++.+.... +            ++...+-.+..+|.+.|++++|..+++...  ..+....-.+..++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~-~------------~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~   68 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPT-N------------PNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCL   68 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCG-T------------HHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCC-C------------hhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            58899999999999986431 1            122233458999999999999999998831  12334455567889


Q ss_pred             HhcCChhHHHHHHHH
Q 045555          138 AISGHGDTALDMFSQ  152 (175)
Q Consensus       138 ~~~g~~~~a~~~~~~  152 (175)
                      .+.|++++|.+.|++
T Consensus        69 ~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   69 LKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHTT-HHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHhc
Confidence            999999999999976

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

Probab=97.87  E-value=0.00042  Score=43.96  Aligned_cols=77  Identities=13%  Similarity=0.119  Sum_probs=66.9

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhh-------------------cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKM-------------------LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~-------------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ..++.++|.++++.|+++....+.+..                   ..|+..+..+++.+|+..|++..|.++.+...+.
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~   81 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRK   81 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            456678999999999999999999876                   1257789999999999999999999999999886


Q ss_pred             -CCCCcHHHHHHHHhhh
Q 045555          157 -SIRLDEVTYVGVLSAC  172 (175)
Q Consensus       157 -g~~p~~~t~~~ll~~~  172 (175)
                       +++-+..++..|++=+
T Consensus        82 Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   82 YPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             cCCCCCHHHHHHHHHHH
Confidence             7888899999888643

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

>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=97.87  E-value=0.0018  Score=50.85  Aligned_cols=154  Identities=16%  Similarity=0.114  Sum_probs=98.1

Q ss_pred             chHHHHhhccCC--Cc-HHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhH-HHHHHHHHhcc-----CChHHHHHHH
Q 045555            2 GFALEIFGNMKN--KD-VISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVL-WTAMIDGYLRV-----NRFREALTLF   70 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~-~~~li~~~~~~-----~~~~~a~~~~   70 (175)
                      ++|++.++.-.+  .| ..........+.+.|+.++|..+|..+.+  |+... |..+..+....     .+.+...++|
T Consensus        21 ~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y  100 (517)
T PF12569_consen   21 EEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELY  100 (517)
T ss_pred             HHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHH
Confidence            467777766554  44 44566888889999999999999999875  55444 44444444222     2466667777


Q ss_pred             HHhHhCCCCCChHHHHH-----------hhh----------------------------------------------c--
Q 045555           71 REMQTSNIRRDEFTTVR-----------ILT----------------------------------------------T--   91 (175)
Q Consensus        71 ~~m~~~~~~p~~~~~~~-----------l~~----------------------------------------------~--   91 (175)
                      +++...-...+..-...           .+.                                              .  
T Consensus       101 ~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~  180 (517)
T PF12569_consen  101 DELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFS  180 (517)
T ss_pred             HHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCC
Confidence            77755432211111111           110                                              0  


Q ss_pred             -------cCcchh--HHHHHHHHHHhcCCHHHHHHHHHhhcC--CC-hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           92 -------FNNDIF--VGIALIDMYCKCGDVEKAQRVFWKMLR--KD-KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        92 -------~~~~~~--~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                             -+|++.  ++..+...|-..|++++|.+.++..++  |+ +..|..-.+.+-+.|++.+|.+.+++..+
T Consensus       181 ~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~  256 (517)
T PF12569_consen  181 NGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARE  256 (517)
T ss_pred             CccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence                   123443  445667788889999999999988755  32 45666777778888888888887777654

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 [], [].

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.85  E-value=0.0013  Score=43.16  Aligned_cols=110  Identities=9%  Similarity=-0.042  Sum_probs=80.5

Q ss_pred             HHhhcCC-CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHH
Q 045555           37 QYFAQMP-ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKA  115 (175)
Q Consensus        37 ~~~~~m~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a  115 (175)
                      ..+..+. +.+......+-.-+...|++++|..+|+-+....  |.             +..-|-.|.-++...|++++|
T Consensus        24 ~~l~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D--p~-------------~~~y~~gLG~~~Q~~g~~~~A   88 (157)
T PRK15363         24 RMLLDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYD--AW-------------SFDYWFRLGECCQAQKHWGEA   88 (157)
T ss_pred             HHHHCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cc-------------cHHHHHHHHHHHHHHhhHHHH
Confidence            3344455 4455556666777788899999999999888743  32             333456788888899999999


Q ss_pred             HHHHHhhc--C-CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCCc
Q 045555          116 QRVFWKML--R-KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA-SIRLD  161 (175)
Q Consensus       116 ~~~~~~~~--~-~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~  161 (175)
                      ...|....  . .|...+-.+..++...|+.+.|.+.|+..+.. +-.|.
T Consensus        89 I~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~~~A~~aF~~Ai~~~~~~~~  138 (157)
T PRK15363         89 IYAYGRAAQIKIDAPQAPWAAAECYLACDNVCYAIKALKAVVRICGEVSE  138 (157)
T ss_pred             HHHHHHHHhcCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHHhccChh
Confidence            99998873  2 36778888888888999999999999887764 44443

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

Probab=97.84  E-value=0.00011  Score=59.86  Aligned_cols=139  Identities=13%  Similarity=0.202  Sum_probs=91.6

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CChhHHHHHHHHHhcc------------CC
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRV------------NR   62 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~------------~~   62 (175)
                      +|..+++....   .|+.+++.+...+.+...+..|..-|..+.+     +|.++.-.|.+.|.+.            +.
T Consensus       548 ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~  627 (1018)
T KOG2002|consen  548 EASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKH  627 (1018)
T ss_pred             HHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHH
Confidence            45555555443   5667777777777777777777775554432     3555555555544332            34


Q ss_pred             hHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHh
Q 045555           63 FREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAI  139 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~  139 (175)
                      .++|+++|.+.++..               +-+...-|-+.-.++..|++.+|..+|..+.+.   ...+|-.+.++|..
T Consensus       628 ~~KAlq~y~kvL~~d---------------pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e  692 (1018)
T KOG2002|consen  628 QEKALQLYGKVLRND---------------PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVE  692 (1018)
T ss_pred             HHHHHHHHHHHHhcC---------------cchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHH
Confidence            677788887777753               234445566777777888888888888877653   44677777788888


Q ss_pred             cCChhHHHHHHHHHHHC
Q 045555          140 SGHGDTALDMFSQMLRA  156 (175)
Q Consensus       140 ~g~~~~a~~~~~~m~~~  156 (175)
                      .|++..|.++|..-...
T Consensus       693 ~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  693 QGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            88888888887766554

>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=97.84  E-value=0.00023  Score=48.91  Aligned_cols=103  Identities=21%  Similarity=0.400  Sum_probs=77.1

Q ss_pred             HHhhcc--CCCcHHHHHHHHHHHHhc-----CChhHHHHHhhcCCC----CChhHHHHHHHHHhccC-------------
Q 045555            6 EIFGNM--KNKDVISWTTIVSGYINR-----GQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVN-------------   61 (175)
Q Consensus         6 ~~~~~m--~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~-------------   61 (175)
                      ..|+..  ..+|-.+|..++..|.+.     |..+-....+..|.+    .|..+|+.|++.+-+..             
T Consensus        35 ~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~h  114 (228)
T PF06239_consen   35 ELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMH  114 (228)
T ss_pred             HHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhcc
Confidence            445554  447889999999999864     566666666666664    79999999999987643             


Q ss_pred             ---ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCH-HHHHHHHHhh
Q 045555           62 ---RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDV-EKAQRVFWKM  122 (175)
Q Consensus        62 ---~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~  122 (175)
                         +.+-|++++++|...|+.||..++              ..+++.+++.+.. .+..++.-.|
T Consensus       115 yp~Qq~c~i~lL~qME~~gV~Pd~Et~--------------~~ll~iFG~~s~p~~K~~rmmYWm  165 (228)
T PF06239_consen  115 YPRQQECAIDLLEQMENNGVMPDKETE--------------QMLLNIFGRKSHPMKKYRRMMYWM  165 (228)
T ss_pred             CcHHHHHHHHHHHHHHHcCCCCcHHHH--------------HHHHHHhccccHHHHHHHHHHHHH
Confidence               357789999999999998877777              6888888877664 4555555555

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=97.83  E-value=0.00022  Score=54.25  Aligned_cols=112  Identities=16%  Similarity=0.139  Sum_probs=89.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-C-----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE-R-----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      +......+++.+....+.+++..++...+. |     -..|..++++.|.+.|..+.++.++..=...|+          
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGi----------  134 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGI----------  134 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhccc----------
Confidence            666778888888888899999998888774 2     223567999999999999999999999999886          


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC----ChhhHHHHHHHHHhc
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK----DKFTWTAMIVGLAIS  140 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~li~~~~~~  140 (175)
                          .||..++|.|++.+.+.|++..|.++...|...    +..|+..-+.+|.+-
T Consensus       135 ----F~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  135 ----FPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             ----CCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence                455555589999999999999999999998543    455666555555554

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 [].

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

Probab=97.83  E-value=8.8e-05  Score=60.40  Aligned_cols=139  Identities=14%  Similarity=0.129  Sum_probs=105.1

Q ss_pred             CcHHHHHHHHHHHHh------------cCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555           14 KDVISWTTIVSGYIN------------RGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus        14 ~~~~~~~~li~~~~~------------~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      +|+.+--+|.+.|.+            .+..++|+++|.+...   .|...-|.+.-.++..|++.+|..+|.+.+....
T Consensus       598 ~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~  677 (1018)
T KOG2002|consen  598 TDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS  677 (1018)
T ss_pred             CchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHh
Confidence            355555556665543            3556788999887664   3778888888899999999999999999998753


Q ss_pred             CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           79 RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KDKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        79 ~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                                     -...+|-.+.++|...|++-.|.++|+...+     .+..+.+.|.+++.+.|++.+|.+.....
T Consensus       678 ---------------~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a  742 (1018)
T KOG2002|consen  678 ---------------DFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKA  742 (1018)
T ss_pred             ---------------hCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence                           1233556799999999999999999998733     37888999999999999999999998877


Q ss_pred             HHCCCCCcHHHHHH
Q 045555          154 LRASIRLDEVTYVG  167 (175)
Q Consensus       154 ~~~g~~p~~~t~~~  167 (175)
                      ......-...-|+.
T Consensus       743 ~~~~p~~~~v~FN~  756 (1018)
T KOG2002|consen  743 RHLAPSNTSVKFNL  756 (1018)
T ss_pred             HHhCCccchHHhHH
Confidence            76533333334443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.83  E-value=0.00088  Score=44.63  Aligned_cols=62  Identities=10%  Similarity=-0.020  Sum_probs=52.3

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ....|..+...+...|++++|...|+....  ++    ..+|..+...+...|++++|+..+++..+.
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            356678888889999999999999998742  22    347889999999999999999999999875

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.83  E-value=0.00091  Score=54.27  Aligned_cols=119  Identities=8%  Similarity=0.047  Sum_probs=95.5

Q ss_pred             CchHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            1 MGFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         1 ~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      .++|..+++...+  | +......+...+.+.+++++|+..+++...  | +....+.+-.++.+.|++++|+++|++..
T Consensus       102 ~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~  181 (694)
T PRK15179        102 SDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEIGQSEQADACFERLS  181 (694)
T ss_pred             cHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHH
Confidence            3678888888876  6 455788999999999999999999999875  4 55667888888999999999999999999


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMI  134 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li  134 (175)
                      ..+.  +             +...+..+..++-+.|+.++|...|+...+   +...-|+.++
T Consensus       182 ~~~p--~-------------~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~  229 (694)
T PRK15179        182 RQHP--E-------------FENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRRL  229 (694)
T ss_pred             hcCC--C-------------cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHHH
Confidence            8442  1             244556799999999999999999999844   4555555443

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

Probab=97.80  E-value=2.5e-05  Score=45.89  Aligned_cols=77  Identities=18%  Similarity=0.310  Sum_probs=48.5

Q ss_pred             cCChhHHHHHhhcCCC--C---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHH
Q 045555           29 RGQVDIARQYFAQMPE--R---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALI  103 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~--~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li  103 (175)
                      .|+++.|..+|+++.+  |   +...+..+..++.+.|++++|+.++++ .+.+  |+             +....-.+.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~--~~-------------~~~~~~l~a   65 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD--PS-------------NPDIHYLLA   65 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH--HC-------------HHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC--CC-------------CHHHHHHHH
Confidence            4677788888887763  3   233455577888888888888888877 2221  11             111222457


Q ss_pred             HHHHhcCCHHHHHHHHHh
Q 045555          104 DMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus       104 ~~~~~~~~~~~a~~~~~~  121 (175)
                      .+|.+.|++++|.+++++
T Consensus        66 ~~~~~l~~y~eAi~~l~~   83 (84)
T PF12895_consen   66 RCLLKLGKYEEAIKALEK   83 (84)
T ss_dssp             HHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHhc
Confidence            778888888888887764

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

Probab=97.78  E-value=0.00034  Score=51.00  Aligned_cols=138  Identities=12%  Similarity=0.025  Sum_probs=84.4

Q ss_pred             hHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhH-HHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            3 FALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVL-WTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         3 ~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +|.+-|+.-.+  |-+.+|-.|-+.|.+..++..|+.+|.+-.+  |..+| ...+.+.+-..++.++|.++|+...+..
T Consensus       241 ~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~  320 (478)
T KOG1129|consen  241 RAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLH  320 (478)
T ss_pred             hhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcC
Confidence            45555554432  7888999999999999999999999998775  54444 3455556666788888888888887753


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      .               .++.....+...|.-.++.+.|.+.+..+..   .+...|+.+.-+|...++++-++.-|.+.+
T Consensus       321 ~---------------~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~sf~RAl  385 (478)
T KOG1129|consen  321 P---------------INVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPSFQRAL  385 (478)
T ss_pred             C---------------ccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHHHHHHH
Confidence            1               1111122334444555555555555555432   244455555555555555555555554444


Q ss_pred             H
Q 045555          155 R  155 (175)
Q Consensus       155 ~  155 (175)
                      .
T Consensus       386 s  386 (478)
T KOG1129|consen  386 S  386 (478)
T ss_pred             h
Confidence            3

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.73  E-value=0.00093  Score=43.76  Aligned_cols=96  Identities=13%  Similarity=0.167  Sum_probs=77.9

Q ss_pred             CCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           13 NKDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        13 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      ..+....-.+...+.+.|++++|..+|+.+..  | +..-|..|-.++-..|++++|+..|.......+  |        
T Consensus        32 ~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~--d--------  101 (157)
T PRK15363         32 TQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI--D--------  101 (157)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC--C--------
Confidence            34555666777788899999999999998764  4 666788999999999999999999999988653  2        


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                           |...+-.+..++...|+.+.|.+.|+..+
T Consensus       102 -----dp~~~~~ag~c~L~lG~~~~A~~aF~~Ai  130 (157)
T PRK15363        102 -----APQAPWAAAECYLACDNVCYAIKALKAVV  130 (157)
T ss_pred             -----CchHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                 23333468999999999999999998764

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

Probab=97.72  E-value=0.00066  Score=54.04  Aligned_cols=148  Identities=18%  Similarity=0.174  Sum_probs=105.1

Q ss_pred             hHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhC----
Q 045555            3 FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTS----   76 (175)
Q Consensus         3 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----   76 (175)
                      +|..+|+..     ..|..+|.+|...|+..+|..+..+..+  ||..-|..+.+......-+++|.+++++.-..    
T Consensus       416 sAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawElsn~~sarA~r~  490 (777)
T KOG1128|consen  416 SALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWELSNYISARAQRS  490 (777)
T ss_pred             HHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHHhhhhhHHHHHh
Confidence            344444443     3788889999999988888888776654  67778888888887777788888888776332    


Q ss_pred             -CCCC-ChHHHHHhhh----------------------------------------ccCcc-hhHHHHHHHHHHhcCCHH
Q 045555           77 -NIRR-DEFTTVRILT----------------------------------------TFNND-IFVGIALIDMYCKCGDVE  113 (175)
Q Consensus        77 -~~~p-~~~~~~~l~~----------------------------------------~~~~~-~~~~~~li~~~~~~~~~~  113 (175)
                       |..+ +...|....+                                        ...|| ...||.+-.+|.+.|+-.
T Consensus       491 ~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~  570 (777)
T KOG1128|consen  491 LALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKK  570 (777)
T ss_pred             hccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhH
Confidence             1101 1111222222                                        23344 567899999999999999


Q ss_pred             HHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          114 KAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       114 ~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +|...+++..+-   +...|...+....+-|.+++|.+.+.++.+
T Consensus       571 ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  571 RAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             HHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            999999888653   556777888888889999999999888765

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

Probab=97.70  E-value=0.0015  Score=46.31  Aligned_cols=121  Identities=15%  Similarity=0.160  Sum_probs=64.1

Q ss_pred             HHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHH
Q 045555           21 TIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGI  100 (175)
Q Consensus        21 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  100 (175)
                      .-...|+..|++++|.........-+...  .=...+.+..+++-|...+++|.+-.   +..|.+.          .-+
T Consensus       113 ~aa~i~~~~~~~deAl~~~~~~~~lE~~A--l~VqI~lk~~r~d~A~~~lk~mq~id---ed~tLtQ----------LA~  177 (299)
T KOG3081|consen  113 LAAIIYMHDGDFDEALKALHLGENLEAAA--LNVQILLKMHRFDLAEKELKKMQQID---EDATLTQ----------LAQ  177 (299)
T ss_pred             HhhHHhhcCCChHHHHHHHhccchHHHHH--HHHHHHHHHHHHHHHHHHHHHHHccc---hHHHHHH----------HHH
Confidence            33445677777777777777622222222  22333455666666776667766532   1111211          112


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +.+......+.+.+|.-+|++|.+   |+.-+.+-...++...|++++|..++++.+++
T Consensus       178 awv~la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  178 AWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             HHHHHhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            344444445556666666666644   34444445555555666666666666666654

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

Probab=97.70  E-value=0.0021  Score=49.25  Aligned_cols=138  Identities=14%  Similarity=0.194  Sum_probs=96.5

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ..|+++|+....   .+...|-.-+.+=.+...+.+|+.+|+....  | =...|...+..=-..|+...|..+|+....
T Consensus        90 ~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqiferW~~  169 (677)
T KOG1915|consen   90 QRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFERWME  169 (677)
T ss_pred             HHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHHHHHc
Confidence            357777776654   5666777777777888888899998887654  2 223466666666677889999999998887


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRKDKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                      -                .|+...|++.|+--.+-+.++.|..+++..  ..|++.+|--...---++|+...|..+|...
T Consensus       170 w----------------~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerA  233 (677)
T KOG1915|consen  170 W----------------EPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERA  233 (677)
T ss_pred             C----------------CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3                455555566777777777777777777765  4567777766666666777777777766665


Q ss_pred             HH
Q 045555          154 LR  155 (175)
Q Consensus       154 ~~  155 (175)
                      .+
T Consensus       234 ie  235 (677)
T KOG1915|consen  234 IE  235 (677)
T ss_pred             HH
Confidence            54

>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=97.69  E-value=0.0012  Score=45.53  Aligned_cols=111  Identities=17%  Similarity=0.260  Sum_probs=73.7

Q ss_pred             HHHHhhcC--CCCChhHHHHHHHHHhcc-----CChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHH
Q 045555           35 ARQYFAQM--PERDYVLWTAMIDGYLRV-----NRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYC  107 (175)
Q Consensus        35 a~~~~~~m--~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~  107 (175)
                      ....|+..  ..+|..+|..++..|.+.     |..+=....+..|.+-|+.-|..+|              +.|++.+=
T Consensus        33 ~~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y--------------~~LLDvFP   98 (228)
T PF06239_consen   33 HEELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVY--------------KALLDVFP   98 (228)
T ss_pred             hHHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHH--------------HHHHHhCC
Confidence            34555555  456888888888888655     6788888888999999986666666              56666665


Q ss_pred             hcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          108 KCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       108 ~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      + |.+- -..+|           .++.-.|  -.+.+-|.+++++|.+.|+-||..|+..|++.+.+
T Consensus        99 K-g~fv-p~n~f-----------Q~~F~hy--p~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~  150 (228)
T PF06239_consen   99 K-GKFV-PRNFF-----------QAEFMHY--PRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGR  150 (228)
T ss_pred             C-CCcc-cccHH-----------HHHhccC--cHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcc
Confidence            4 2221 11111           1222222  22456788888888888888888888888887654

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

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

Probab=97.68  E-value=0.00048  Score=38.41  Aligned_cols=50  Identities=20%  Similarity=0.360  Sum_probs=27.8

Q ss_pred             ccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           59 RVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        59 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                      +.|++++|++.|+++.....               .+...+..+..+|.+.|++++|.++++.+.
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p---------------~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNP---------------DNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTT---------------TSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             hccCHHHHHHHHHHHHHHCC---------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45666666666666665431               123333456666666666666666666663

...

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

Probab=97.67  E-value=0.0034  Score=46.32  Aligned_cols=109  Identities=15%  Similarity=0.124  Sum_probs=87.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF   97 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~   97 (175)
                      +.+..|.-+...|....|..+-.+.+-|+..-|-..+.+++..++|++-..+... +++     +..|            
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s-kKs-----PIGy------------  240 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS-KKS-----PIGY------------  240 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC-CCC-----CCCh------------
Confidence            4566677788899999999999999999999999999999999999887776432 221     2223            


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                        -..+++|.+.|...+|..+...      ..+..-+..|.+.|++.+|.+.-.+
T Consensus       241 --epFv~~~~~~~~~~eA~~yI~k------~~~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  241 --EPFVEACLKYGNKKEASKYIPK------IPDEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             --HHHHHHHHHCCCHHHHHHHHHh------CChHHHHHHHHHCCCHHHHHHHHHH
Confidence              5688999999999999998887      3357888999999999999766433

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

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

Probab=97.66  E-value=0.002  Score=49.17  Aligned_cols=116  Identities=18%  Similarity=0.171  Sum_probs=91.3

Q ss_pred             HHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHH
Q 045555           25 GYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIA  101 (175)
Q Consensus        25 ~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~  101 (175)
                      .+.+.|.++.|+..++.+..  | |..-+......+.+.++.++|.+.++.+....  |+.             ....-.
T Consensus       315 ~~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~--P~~-------------~~l~~~  379 (484)
T COG4783         315 QTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALALD--PNS-------------PLLQLN  379 (484)
T ss_pred             HHHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CCc-------------cHHHHH
Confidence            34467888888888887653  4 55666677778899999999999999998853  321             333457


Q ss_pred             HHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          102 LIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +..+|.+.|++.+|.+.++....  | |...|..+-.+|...|+..++.....|...
T Consensus       380 ~a~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~  436 (484)
T COG4783         380 LAQALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARAEGYA  436 (484)
T ss_pred             HHHHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHHHHHH
Confidence            88999999999999999998844  2 788999999999999999999988887764

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

Probab=97.65  E-value=0.00032  Score=39.18  Aligned_cols=61  Identities=21%  Similarity=0.272  Sum_probs=50.0

Q ss_pred             HhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHH
Q 045555          107 CKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVL  169 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll  169 (175)
                      .+.|++++|.+.|+.+..  | +...+-.+..+|.+.|++++|.++++++...  .|+...+..++
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~l~   65 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ--DPDNPEYQQLL   65 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG--GTTHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCHHHHHHHH
Confidence            468999999999999943  4 7778888999999999999999999999875  67766665554

...

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

Probab=97.63  E-value=0.0076  Score=49.25  Aligned_cols=153  Identities=18%  Similarity=0.227  Sum_probs=99.1

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+++.+..+   .+...|..|...|-+.|+.+++...+-...   +.|..-|..+-.-..+.|+++.|.-.|.+..+
T Consensus       156 eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~  235 (895)
T KOG2076|consen  156 EEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQARYCYSRAIQ  235 (895)
T ss_pred             HHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHHHHHHHHHh
Confidence            567778877776   356678888888888888888877665433   34666777777777888888888888888877


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCCh--------hhHHHHHHHHHhcCChhHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDK--------FTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~li~~~~~~g~~~~a~  147 (175)
                      ...               ++....--=++.|-+.|+...|.+.|..+...+.        ..--.+++.+...++-+.|.
T Consensus       236 ~~p---------------~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~  300 (895)
T KOG2076|consen  236 ANP---------------SNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAA  300 (895)
T ss_pred             cCC---------------cchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            642               2222223456677788888888888877744322        11222445566666667777


Q ss_pred             HHHHHHHHCC----CCCcHHHHHHHH
Q 045555          148 DMFSQMLRAS----IRLDEVTYVGVL  169 (175)
Q Consensus       148 ~~~~~m~~~g----~~p~~~t~~~ll  169 (175)
                      +.+......+    --||..++..|+
T Consensus       301 ~~le~~~s~~~~~~~~ed~ni~ael~  326 (895)
T KOG2076|consen  301 KALEGALSKEKDEASLEDLNILAELF  326 (895)
T ss_pred             HHHHHHHhhccccccccHHHHHHHHH
Confidence            7776665521    224555554444

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

Probab=97.63  E-value=0.0015  Score=49.00  Aligned_cols=87  Identities=10%  Similarity=0.055  Sum_probs=72.6

Q ss_pred             HHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHH
Q 045555           23 VSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVG   99 (175)
Q Consensus        23 i~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~   99 (175)
                      ...+...|++++|.+.|.+..+   .+...|..+..+|.+.|++++|+..+++.++..  |             .+...|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~--P-------------~~~~a~   73 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELD--P-------------SLAKAY   73 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--c-------------CCHHHH
Confidence            4556688999999999998874   366788899999999999999999999998854  2             234455


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      ..+..+|...|++++|...|+...+
T Consensus        74 ~~lg~~~~~lg~~~eA~~~~~~al~   98 (356)
T PLN03088         74 LRKGTACMKLEEYQTAKAALEKGAS   98 (356)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            6788999999999999999999854

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.62  E-value=0.0012  Score=40.76  Aligned_cols=96  Identities=14%  Similarity=0.086  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      .++......+.+.|++++|.+.|..+.+  |+    ...+..+...+.+.|++++|...|+++........         
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~---------   73 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSP---------   73 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCC---------
Confidence            4566778888999999999999999864  33    34577789999999999999999999987532110         


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                         .....+..+..++.+.|+.++|.+.++...+
T Consensus        74 ---~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        74 ---KAPDALLKLGMSLQELGDKEKAKATLQQVIK  104 (119)
T ss_pred             ---cccHHHHHHHHHHHHhCChHHHHHHHHHHHH
Confidence               0122345688889999999999999999854

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.

>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=97.62  E-value=0.0058  Score=48.05  Aligned_cols=123  Identities=18%  Similarity=0.225  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--CC-hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      ++.-+...|-..|++++|+++.+...+  |+ +-.|..-...+-+.|++.+|.+..++.+...               .-
T Consensus       196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD---------------~~  260 (517)
T PF12569_consen  196 TLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELD---------------LA  260 (517)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCC---------------hh
Confidence            345556778899999999999998775  54 3467788888999999999999999998865               23


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChh----------hH--HHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKF----------TW--TAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~----------~~--~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      |..+-+-.+..+.|.|++++|.+++..-.+++..          .|  .-...+|.+.|++..|++-|....+
T Consensus       261 DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  261 DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            5566678889999999999999999988665421          22  3456789999999999887776654

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 [], [].

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.61  E-value=0.0053  Score=47.80  Aligned_cols=157  Identities=15%  Similarity=0.163  Sum_probs=118.5

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|.-.|+.-.+  | +..+|..|...-...++=..|+.-+++..+   .|....-.|.-+|...|.-..|+..+++..+.
T Consensus       303 ~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al~~L~~Wi~~  382 (579)
T KOG1125|consen  303 EAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQALKMLDKWIRN  382 (579)
T ss_pred             HHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence            44555554443  3 567888888888888887888888887665   36777888888999999999999999999554


Q ss_pred             CC------C-------------CChHHHHHhhh---------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCC-
Q 045555           77 NI------R-------------RDEFTTVRILT---------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRK-  125 (175)
Q Consensus        77 ~~------~-------------p~~~~~~~l~~---------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~-  125 (175)
                      ..      .             ++...+..+..         +-.+|..+...|.-.|--.|+++.|..+|+..  ++| 
T Consensus       383 ~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pn  462 (579)
T KOG1125|consen  383 KPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPN  462 (579)
T ss_pred             CccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCc
Confidence            31      0             12222222222         33467888888999999999999999999998  445 


Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          126 DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       126 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      |...||-|...++...+.++|+..|++.++  ++|+
T Consensus       463 d~~lWNRLGAtLAN~~~s~EAIsAY~rALq--LqP~  496 (579)
T KOG1125|consen  463 DYLLWNRLGATLANGNRSEEAISAYNRALQ--LQPG  496 (579)
T ss_pred             hHHHHHHhhHHhcCCcccHHHHHHHHHHHh--cCCC
Confidence            788999999999999999999999999886  3554

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

Probab=97.61  E-value=0.00071  Score=43.95  Aligned_cols=70  Identities=21%  Similarity=0.255  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHH-----HCCCCCcHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQML-----RASIRLDEVTYVG  167 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t~~~  167 (175)
                      ....++..+...|++++|.+.......  | +...|..+|.+|...|+...|.+.|+++.     +-|+.|+..|-..
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~l  141 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRAL  141 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHHH
Confidence            445678888899999999999999954  4 77899999999999999999999998874     3499999877543

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

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

Probab=97.60  E-value=0.004  Score=47.58  Aligned_cols=143  Identities=17%  Similarity=0.237  Sum_probs=104.3

Q ss_pred             cCChhHHHHHhhcCCCCChhHHHHHHHH---HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---------------
Q 045555           29 RGQVDIARQYFAQMPERDYVLWTAMIDG---YLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---------------   90 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~~~~~~~~~li~~---~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---------------   90 (175)
                      .|++++|.+.|.+....|...-..|.+.   +-..|++++|++.|-++..- +.-+......+-.               
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            5788888888888777666544444332   55678899999888776431 0111111111111               


Q ss_pred             -----ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555           91 -----TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus        91 -----~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                           -++.|+.+.+-|.+.|-+.|+-..|.+++-+--+   -++.+..++...|....-+++|...|++..  -+.|++
T Consensus       582 ~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaa--liqp~~  659 (840)
T KOG2003|consen  582 MQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--LIQPNQ  659 (840)
T ss_pred             HHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--hcCccH
Confidence                 4566788899999999999999999998877532   388888999999998889999999998865  478999


Q ss_pred             HHHHHHHhhhcC
Q 045555          163 VTYVGVLSACTH  174 (175)
Q Consensus       163 ~t~~~ll~~~~~  174 (175)
                      .-|..++..|-|
T Consensus       660 ~kwqlmiasc~r  671 (840)
T KOG2003|consen  660 SKWQLMIASCFR  671 (840)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988854

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

Probab=97.60  E-value=0.00076  Score=43.86  Aligned_cols=87  Identities=17%  Similarity=0.234  Sum_probs=66.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--RDY----VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      .-.+...+...|++++|...|+....  |+.    .....|...+...|++++|+..++......               
T Consensus        51 ~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~---------------  115 (145)
T PF09976_consen   51 ALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEA---------------  115 (145)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcc---------------
Confidence            33455778889999999999998775  332    245567788899999999999997743322               


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                       .....+....+.|.+.|++++|...|+.
T Consensus       116 -~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  116 -FKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             -hHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence             1233446799999999999999999975

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

Probab=97.59  E-value=0.00044  Score=38.25  Aligned_cols=55  Identities=24%  Similarity=0.310  Sum_probs=47.3

Q ss_pred             HHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          102 LIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +...+.+.|++++|.+.|+...+.   +...|..+..++...|++++|...|+++++.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            556788999999999999999664   5667888999999999999999999999864

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

Probab=97.56  E-value=0.00091  Score=51.17  Aligned_cols=122  Identities=10%  Similarity=0.151  Sum_probs=96.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      |--+...|....+.++....|+....   .|..+|..-...+.-.+++++|+.=|++.....  |+             +
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~--pe-------------~  427 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD--PE-------------N  427 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC--hh-------------h
Confidence            77777788888888888888887664   366677777777777888899998888887743  22             2


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ...|.-+.-+.-|.+++++++..|++.++  | -+.+|+-....+...+++++|.+.|+..++
T Consensus       428 ~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~  490 (606)
T KOG0547|consen  428 AYAYIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIE  490 (606)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHh
Confidence            33444556666688899999999999966  3 577999999999999999999999998765

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

Probab=97.54  E-value=0.0013  Score=41.80  Aligned_cols=89  Identities=15%  Similarity=0.128  Sum_probs=67.3

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC---------CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHH
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSN---------IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQ  116 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---------~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~  116 (175)
                      |..++.++|.++++.|+.+....+++..-.-+         +.|+.        ...|+..+..+++.+|+.+|++..|.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~s--------pl~Pt~~lL~AIv~sf~~n~~i~~al   72 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSS--------PLYPTSRLLIAIVHSFGYNGDIFSAL   72 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCC--------CCCCCHHHHHHHHHHHHhcccHHHHH
Confidence            45678888889999999888888887664322         22222        23589999999999999999999999


Q ss_pred             HHHHhhcCC-----ChhhHHHHHHHHHhcCC
Q 045555          117 RVFWKMLRK-----DKFTWTAMIVGLAISGH  142 (175)
Q Consensus       117 ~~~~~~~~~-----~~~~~~~li~~~~~~g~  142 (175)
                      ++.+...+.     +..+|..|+......-+
T Consensus        73 ~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   73 KLVDFFSRKYPIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHhcC
Confidence            999998442     56789999886654433

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

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.54  E-value=0.0066  Score=40.63  Aligned_cols=98  Identities=15%  Similarity=0.174  Sum_probs=72.9

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      ....+..+...+...|++++|...|++..+.+..+..            ....+..+...+.+.|++++|...+.+... 
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~------------~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  101 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPND------------RSYILYNMGIIYASNGEHDKALEYYHQALEL  101 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccch------------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4556888888899999999999999999875432221            123456899999999999999999999854 


Q ss_pred             -C-ChhhHHHHHHHHHhcCC--------------hhHHHHHHHHHHH
Q 045555          125 -K-DKFTWTAMIVGLAISGH--------------GDTALDMFSQMLR  155 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~--------------~~~a~~~~~~m~~  155 (175)
                       | +...+..+...+...|+              +++|.+.+++...
T Consensus       102 ~p~~~~~~~~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~  148 (172)
T PRK02603        102 NPKQPSALNNIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIR  148 (172)
T ss_pred             CcccHHHHHHHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHh
Confidence             3 55667777777777776              4556666666554

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

Probab=97.54  E-value=0.0008  Score=41.41  Aligned_cols=72  Identities=8%  Similarity=0.271  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-----CChhHHHHHHHHHhccC--------ChHHHHHHHHHhHhCCCCCChHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVN--------RFREALTLFREMQTSNIRRDEFT   84 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~~--------~~~~a~~~~~~m~~~~~~p~~~~   84 (175)
                      +-...|..+...+++...-.+|+.+++     |++.+|+.++.+.++..        ...+.+.+|.+|+..+++|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            344566667777999999999998875     78889999999987763        35678899999999999888888


Q ss_pred             HHHhh
Q 045555           85 TVRIL   89 (175)
Q Consensus        85 ~~~l~   89 (175)
                      |+.++
T Consensus       107 Ynivl  111 (120)
T PF08579_consen  107 YNIVL  111 (120)
T ss_pred             HHHHH
Confidence            85544

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 [, , ].

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.53  E-value=0.0078  Score=40.06  Aligned_cols=95  Identities=16%  Similarity=0.092  Sum_probs=69.8

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...|..+...+...|++++|+..|++.......|..            ...++..+...|...|++++|...++....  
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~------------~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~  102 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYD------------RSYILYNIGLIHTSNGEHTKALEYYFQALERN  102 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchh------------hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            456788888888999999999999999875322211            123557899999999999999999999854  


Q ss_pred             C-ChhhHHHHHHHHH-------hcCChhHHHHHHHHH
Q 045555          125 K-DKFTWTAMIVGLA-------ISGHGDTALDMFSQM  153 (175)
Q Consensus       125 ~-~~~~~~~li~~~~-------~~g~~~~a~~~~~~m  153 (175)
                      | ....+..+...+.       ..|+++.|...+++.
T Consensus       103 ~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        103 PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            2 3455666666666       788888666555543

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

Probab=97.51  E-value=0.016  Score=41.20  Aligned_cols=137  Identities=16%  Similarity=0.134  Sum_probs=96.7

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-ChhHHHHHHHHHh----ccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYL----RVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~----~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|++..+..  -+..+...-...+.+..+++.|.+.+++|.+- +..|.+-|..++.    ..+...+|.-+|++|-+.
T Consensus       125 deAl~~~~~~--~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~tLtQLA~awv~la~ggek~qdAfyifeE~s~k  202 (299)
T KOG3081|consen  125 DEALKALHLG--ENLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK  202 (299)
T ss_pred             HHHHHHHhcc--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc
Confidence            4555555552  34555555566778899999999999999984 4455665655554    446799999999999875


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhH-HHHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDT-ALDMFSQ  152 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~-a~~~~~~  152 (175)
                                     +.|++.+.|-...++...|++++|+.+++....+   +..+...+|.+--..|+-.+ -.+.+.+
T Consensus       203 ---------------~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~Nliv~a~~~Gkd~~~~~r~l~Q  267 (299)
T KOG3081|consen  203 ---------------TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLANLIVLALHLGKDAEVTERNLSQ  267 (299)
T ss_pred             ---------------cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCChHHHHHHHHH
Confidence                           2455555578888999999999999999999654   55566556655556665544 4555666


Q ss_pred             HHH
Q 045555          153 MLR  155 (175)
Q Consensus       153 m~~  155 (175)
                      +..
T Consensus       268 Lk~  270 (299)
T KOG3081|consen  268 LKL  270 (299)
T ss_pred             HHh
Confidence            654

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

Probab=97.49  E-value=0.0019  Score=46.83  Aligned_cols=95  Identities=19%  Similarity=0.379  Sum_probs=72.1

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---  124 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---  124 (175)
                      .+|..+++..-+.+..+.|..+|.+.++.+. .+            .+..+..++++.++ .++.+.|.++|+...+   
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~-~~------------~~vy~~~A~~E~~~-~~d~~~A~~Ife~glk~f~   67 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKR-CT------------YHVYVAYALMEYYC-NKDPKRARKIFERGLKKFP   67 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-S-------------THHHHHHHHHHHHT-CS-HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCC-CC------------HHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHCC
Confidence            4688999999999999999999999986542 11            22223334444333 6778889999999855   


Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+...|...++.+...|+.+.|..+|++....
T Consensus        68 ~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~   99 (280)
T PF05843_consen   68 SDPDFWLEYLDFLIKLNDINNARALFERAISS   99 (280)
T ss_dssp             T-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCT
T ss_pred             CCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHh
Confidence            48889999999999999999999999999865

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.

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.46  E-value=0.0016  Score=47.13  Aligned_cols=169  Identities=13%  Similarity=0.134  Sum_probs=101.4

Q ss_pred             HHHHhhccC-CCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC----CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            4 ALEIFGNMK-NKDVISWTTIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         4 A~~~~~~m~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++.+.++.+ +.+..+-+...-...+.|+++.|.+-|+...+    .....||.-+..| +.|+...|++...++...|+
T Consensus       131 ~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~  209 (459)
T KOG4340|consen  131 SRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGI  209 (459)
T ss_pred             hHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhh
Confidence            344555555 24455555555556678888888888887665    3556677776554 55788888888888887775


Q ss_pred             CCChHHHH-Hhhhc-----c-Ccch-------hHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----ChhhHHHHHHHHHh
Q 045555           79 RRDEFTTV-RILTT-----F-NNDI-------FVGIALIDMYCKCGDVEKAQRVFWKMLRK-----DKFTWTAMIVGLAI  139 (175)
Q Consensus        79 ~p~~~~~~-~l~~~-----~-~~~~-------~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~li~~~~~  139 (175)
                      +--+..-. ....+     + +|-.       ..+|.-...+-+.|+++.|.+.+-+|+.+     |++|...+.-.= .
T Consensus       210 r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~  288 (459)
T KOG4340|consen  210 RQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-M  288 (459)
T ss_pred             hcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-c
Confidence            42111000 00000     0 1111       22333334456899999999999999653     666665544332 2


Q ss_pred             cCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcCC
Q 045555          140 SGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       140 ~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      .+++.+..+-+.-+++.+- --+.||..++-.||+|
T Consensus       289 ~~~p~~g~~KLqFLL~~nP-fP~ETFANlLllyCKN  323 (459)
T KOG4340|consen  289 DARPTEGFEKLQFLLQQNP-FPPETFANLLLLYCKN  323 (459)
T ss_pred             cCCccccHHHHHHHHhcCC-CChHHHHHHHHHHhhh
Confidence            4556666666666665533 3456888888888875

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

Probab=97.46  E-value=0.0056  Score=48.57  Aligned_cols=137  Identities=13%  Similarity=0.248  Sum_probs=85.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC-----CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ..|-.-+....+.|++...+..|+....     ....+|...+.-....+-++-++++++..++-.  |..         
T Consensus       103 RIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~~--P~~---------  171 (835)
T KOG2047|consen  103 RIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKVA--PEA---------  171 (835)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhcC--HHH---------
Confidence            3555566666677777777777776442     233456666666666677777777777776632  221         


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--------------------------------------------C--
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--------------------------------------------K--  125 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--------------------------------------------~--  125 (175)
                             -+--|..+++.+++++|.+.+...+.                                            +  
T Consensus       172 -------~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rft  244 (835)
T KOG2047|consen  172 -------REEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFT  244 (835)
T ss_pred             -------HHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCc
Confidence                   23345555566666665555554421                                            1  


Q ss_pred             --ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          126 --DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       126 --~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                        =...|++|.+-|.+.|++++|.++|++-...-.  ...-|..++++|+
T Consensus       245 Dq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~--tvrDFt~ifd~Ya  292 (835)
T KOG2047|consen  245 DQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTVM--TVRDFTQIFDAYA  292 (835)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhe--ehhhHHHHHHHHH
Confidence              123688899999999999999999988876533  3344555555554

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

Probab=97.46  E-value=0.0034  Score=48.19  Aligned_cols=120  Identities=13%  Similarity=0.199  Sum_probs=70.3

Q ss_pred             HhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCC-hHHHHHhhhccCcchhHHHHH
Q 045555           27 INRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRD-EFTTVRILTTFNNDIFVGIAL  102 (175)
Q Consensus        27 ~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~~~~~~~l  102 (175)
                      -+.++++++...|++.++  | -.-.|+.....+.-.++++.|.+-|+......  |+ ..+      .+.+.+.+...+
T Consensus       439 Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE--~~~~~~------~v~~~plV~Ka~  510 (606)
T KOG0547|consen  439 YRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELE--PREHLI------IVNAAPLVHKAL  510 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhc--cccccc------cccchhhhhhhH
Confidence            344444555555544443  2 12234444444445555555555555444421  11 000      112333344444


Q ss_pred             HHHHHhcCCHHHHHHHHHhhcCCC---hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          103 IDMYCKCGDVEKAQRVFWKMLRKD---KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +-.-.+ +++..|..++.+..+-|   ...|..|...-.+.|+.++|+++|++-..
T Consensus       511 l~~qwk-~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  511 LVLQWK-EDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             hhhchh-hhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            444444 99999999999997654   45788899999999999999999988643

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.46  E-value=0.0098  Score=37.40  Aligned_cols=105  Identities=16%  Similarity=0.134  Sum_probs=75.5

Q ss_pred             HHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC----
Q 045555           53 MIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD----  126 (175)
Q Consensus        53 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----  126 (175)
                      +-.++-..|+.++|+.+|++....|.......            ..+-.+.+++...|++++|..++++...  |+    
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~------------~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~   74 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRR------------RALIQLASTLRNLGRYDEALALLEEALEEFPDDELN   74 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHH------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcccc
Confidence            44567788999999999999999886543222            2334689999999999999999999854  43    


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      ......+..++...|+.++|.+.+-...-    ++...|.--|..|+
T Consensus        75 ~~l~~f~Al~L~~~gr~~eAl~~~l~~la----~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   75 AALRVFLALALYNLGRPKEALEWLLEALA----ETLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence            12222344577889999999999877653    34446665555554

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

Probab=97.45  E-value=0.0087  Score=48.94  Aligned_cols=121  Identities=15%  Similarity=0.204  Sum_probs=96.4

Q ss_pred             HHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh
Q 045555           21 TIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF   97 (175)
Q Consensus        21 ~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~   97 (175)
                      ...+...-.|+.++|..++.+..+   .+...|.+|...|-+.|+.+++...+--.-...               +.|..
T Consensus       144 ~eAN~lfarg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~---------------p~d~e  208 (895)
T KOG2076|consen  144 GEANNLFARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN---------------PKDYE  208 (895)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC---------------CCChH
Confidence            333444445999999999999875   367789999999999999999988765554432               33557


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcCCChh---hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLRKDKF---TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .|..+-+...+.|.++.|.-+|.+.+..++.   .+---...|-+.|+...|.+.|.++.+.
T Consensus       209 ~W~~ladls~~~~~i~qA~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~  270 (895)
T KOG2076|consen  209 LWKRLADLSEQLGNINQARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQL  270 (895)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhh
Confidence            7889999999999999999999999764443   3444566788999999999999999875

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.44  E-value=0.0041  Score=44.75  Aligned_cols=99  Identities=15%  Similarity=0.194  Sum_probs=79.9

Q ss_pred             HHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHH
Q 045555           56 GYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTA  132 (175)
Q Consensus        56 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~  132 (175)
                      -+.+.+++.+|+..|.+.++.  .|+             |.+.|-.-..+|.+.|.++.|.+-.+..+.-   ....|..
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l--~P~-------------nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~R  154 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIEL--DPT-------------NAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGR  154 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhc--CCC-------------cchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHH
Confidence            366778899999999999884  343             4444667888999999999999888887553   4568899


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      |-.+|...|++++|.+.|++.++  +.|+..+|-.=|+.
T Consensus       155 LG~A~~~~gk~~~A~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  155 LGLAYLALGKYEEAIEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHccCcHHHHHHHHHhhhc--cCCCcHHHHHHHHH
Confidence            99999999999999999999886  68988888765543

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=97.39  E-value=0.00077  Score=38.74  Aligned_cols=60  Identities=18%  Similarity=0.137  Sum_probs=49.9

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC---------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR---------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..+++.+...|.+.|++++|...|++..+         + -..+++.+...+...|++++|.+.+++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            35678899999999999999999999832         1 256788899999999999999999988654

...

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

Probab=97.39  E-value=0.024  Score=45.31  Aligned_cols=150  Identities=18%  Similarity=0.185  Sum_probs=113.8

Q ss_pred             HHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            4 ALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         4 A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      |+.++...-+  | +...|-+-+..-+....++.|+.+|.+.+.  ++...|..-++.---.++.++|++++++.++.- 
T Consensus       603 ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~f-  681 (913)
T KOG0495|consen  603 ARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALRLLEEALKSF-  681 (913)
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhC-
Confidence            4444444433  3 556788888888889999999999998774  677788877777777888999999888887743 


Q ss_pred             CCChHHHHHhhh---------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CC-ChhhHHHHH
Q 045555           79 RRDEFTTVRILT---------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RK-DKFTWTAMI  134 (175)
Q Consensus        79 ~p~~~~~~~l~~---------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li  134 (175)
                       |+-.-+-.++.                     .|+.....|-.|...-.+.|.+-.|..+++.-.  .| +...|-..|
T Consensus       682 -p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~I  760 (913)
T KOG0495|consen  682 -PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESI  760 (913)
T ss_pred             -CchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHH
Confidence             33332222222                     566777888888888889999999999999873  34 778899999


Q ss_pred             HHHHhcCChhHHHHHHHHHHH
Q 045555          135 VGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       135 ~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..-.+.|..+.|..+..+.++
T Consensus       761 r~ElR~gn~~~a~~lmakALQ  781 (913)
T KOG0495|consen  761 RMELRAGNKEQAELLMAKALQ  781 (913)
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            999999999999888877664

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

Probab=97.36  E-value=0.012  Score=45.34  Aligned_cols=140  Identities=14%  Similarity=0.230  Sum_probs=109.4

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHH----HhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGY----INRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~----~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      +.+.++|+...+   ...+||..+=..|    .++.+...|+.++.....  |-..+|-..|..=.+.++++.+..++++
T Consensus       383 ertr~vyq~~l~lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEk  462 (677)
T KOG1915|consen  383 ERTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEK  462 (677)
T ss_pred             HHHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            345555554444   2445555554444    467889999999988765  7777888888888899999999999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-C----ChhhHHHHHHHHHhcCChhHHH
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-K----DKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~----~~~~~~~li~~~~~~g~~~~a~  147 (175)
                      .+.-+               +.++.+|.-....-...|+.+.|..+|.-.+. |    -...|.+.|+--...|.+++|.
T Consensus       463 fle~~---------------Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR  527 (677)
T KOG1915|consen  463 FLEFS---------------PENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKAR  527 (677)
T ss_pred             HHhcC---------------hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHH
Confidence            99865               34667777788888899999999999998854 3    3457888898888999999999


Q ss_pred             HHHHHHHHC
Q 045555          148 DMFSQMLRA  156 (175)
Q Consensus       148 ~~~~~m~~~  156 (175)
                      .+|+++++.
T Consensus       528 ~LYerlL~r  536 (677)
T KOG1915|consen  528 ALYERLLDR  536 (677)
T ss_pred             HHHHHHHHh
Confidence            999999875

>PLN02789 farnesyltranstransferase

Probab=97.35  E-value=0.012  Score=43.56  Aligned_cols=129  Identities=16%  Similarity=0.160  Sum_probs=89.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccC-ChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVN-RFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      .++..+-..+...++.++|+.++.++.+  | +..+|+..-..+...| +++++++.++++.+.+.              
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~np--------------  103 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNP--------------  103 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCC--------------
Confidence            3555666667778899999999998774  3 4456776666666667 57899999999887642              


Q ss_pred             CcchhHHHHHHHHHHhcCC--HHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCC
Q 045555           93 NNDIFVGIALIDMYCKCGD--VEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL  160 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~--~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p  160 (175)
                       .+..+|+..-..+.+.|+  .+++..+++.+.+   .+..+|+...-.+.+.|+++++++.+.++++.+...
T Consensus       104 -knyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N  175 (320)
T PLN02789        104 -KNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRN  175 (320)
T ss_pred             -cchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCc
Confidence             122334444444445554  2567777777744   367788888888888888999999998888765443

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.34  E-value=0.00048  Score=38.56  Aligned_cols=62  Identities=18%  Similarity=0.360  Sum_probs=54.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccC-ChHHHHHHHHHhHhC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVN-RFREALTLFREMQTS   76 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~   76 (175)
                      ++.+|..+...+.+.|++++|...|.+..+  | +...|..+..++.+.| ++++|++.+++.++.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            567899999999999999999999998774  3 6678999999999999 799999999998763

...

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.33  E-value=0.015  Score=45.89  Aligned_cols=137  Identities=12%  Similarity=0.014  Sum_probs=89.2

Q ss_pred             CcHHHHHHHHHHHHh--c---CChhHHHHHhhcCCC--CC-hhHHHHHHHHHhccC--------ChHHHHHHHHHhHhCC
Q 045555           14 KDVISWTTIVSGYIN--R---GQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVN--------RFREALTLFREMQTSN   77 (175)
Q Consensus        14 ~~~~~~~~li~~~~~--~---~~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~--------~~~~a~~~~~~m~~~~   77 (175)
                      .|..+|...+.+...  .   +....|.++|++..+  |+ ...|..+..++....        ++..+.+...+.....
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al~  414 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVALP  414 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhcc
Confidence            578899999988553  2   337789999999875  53 344554433332221        1223333333322221


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..             ..+...+.++.-.....|++++|.+.+++..  .|+...|..+...+...|+.++|.+.|++...
T Consensus       415 ~~-------------~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        415 EL-------------NVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             cC-------------cCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            11             1122344555555666899999999999994  46788889999999999999999999999875


Q ss_pred             CCCCCcHHHH
Q 045555          156 ASIRLDEVTY  165 (175)
Q Consensus       156 ~g~~p~~~t~  165 (175)
                      .  .|...||
T Consensus       482 L--~P~~pt~  489 (517)
T PRK10153        482 L--RPGENTL  489 (517)
T ss_pred             c--CCCCchH
Confidence            3  5554444

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.33  E-value=0.0043  Score=45.97  Aligned_cols=53  Identities=15%  Similarity=0.211  Sum_probs=31.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHH-HHHHHHhcCChhHHHHHHHHH
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTA-MIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~-li~~~~~~g~~~~a~~~~~~m  153 (175)
                      .+.++++-.|.+.+|+++|-.+..|   |-.+|.+ +.++|.+.++++.|++++-++
T Consensus       398 N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  398 NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence            3566666666666777666666443   3444544 335566666666666666554

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.32  E-value=0.0013  Score=36.74  Aligned_cols=56  Identities=21%  Similarity=0.271  Sum_probs=26.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcC-ChhHHHHHHHHHH
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISG-HGDTALDMFSQML  154 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g-~~~~a~~~~~~m~  154 (175)
                      |..+...+.+.|++++|...|++..+  | +...|..+..++.+.| ++++|.+.+++.+
T Consensus         6 ~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    6 WYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            34444444555555555555554422  2 3334444445555555 4555555554443

...

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

Probab=97.28  E-value=0.0079  Score=51.58  Aligned_cols=127  Identities=14%  Similarity=0.246  Sum_probs=102.9

Q ss_pred             Cc-HHHHHHHHHHHHhcCChhHHHHHhhcCCCC--------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHH
Q 045555           14 KD-VISWTTIVSGYINRGQVDIARQYFAQMPER--------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFT   84 (175)
Q Consensus        14 ~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~   84 (175)
                      || ...|-..|....+.++.+.|++++++....        -.-.|.++++.--..|.-+...++|++..+..       
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc------- 1527 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC------- 1527 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc-------
Confidence            53 456888888999999999999999987641        23467788877777788888899999998852       


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                               ..-.+|..|...|.+.+.+++|.++++.|.+   ....+|-..+..+.+.++-+.|.+++.+.++.
T Consensus      1528 ---------d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~ 1593 (1710)
T KOG1070|consen 1528 ---------DAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKS 1593 (1710)
T ss_pred             ---------chHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh
Confidence                     2234567899999999999999999999965   36778999999999999999999998887653

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.24  E-value=0.0046  Score=48.15  Aligned_cols=121  Identities=18%  Similarity=0.210  Sum_probs=96.3

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      +|+.+.+.|.-.|--.|.+++|.+.|+....  | |...||-|-..++...+.++|+..|++.++.  +|+         
T Consensus       428 ~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~---------  496 (579)
T KOG1125|consen  428 IDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPG---------  496 (579)
T ss_pred             CChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCC---------
Confidence            5888999999999999999999999998763  4 7788999999999999999999999999984  332         


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------------CChhhHHHHHHHHHhcCChhHHHHH
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-------------KDKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------------~~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                          -+.+.-.|.-+|...|.+++|...|-....             ++...|..|=.++...++.+.+.+.
T Consensus       497 ----yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  497 ----YVRVRYNLGISCMNLGAYKEAVKHLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             ----eeeeehhhhhhhhhhhhHHHHHHHHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence                133334578889999999999988887621             1235788877777777777655443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.24  E-value=0.009  Score=42.92  Aligned_cols=100  Identities=13%  Similarity=0.077  Sum_probs=73.3

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD  126 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~  126 (175)
                      .|..-+..+.+.|++++|+..|+.+.+......   |       .  ...+-.+..+|...|++++|...|+.+..  |+
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~---~-------a--~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~  212 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDST---Y-------Q--PNANYWLGQLNYNKGKKDDAAYYFASVVKNYPK  212 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCc---c-------h--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence            455555555678999999999999998642211   0       0  11223599999999999999999999964  32


Q ss_pred             ----hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          127 ----KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       127 ----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                          ...+-.+...+...|+.++|.+.|+++.+.  .|+.
T Consensus       213 s~~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~~--yP~s  250 (263)
T PRK10803        213 SPKAADAMFKVGVIMQDKGDTAKAKAVYQQVIKK--YPGT  250 (263)
T ss_pred             CcchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCC
Confidence                344555666788899999999999999875  4544

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

Probab=97.23  E-value=0.0032  Score=34.72  Aligned_cols=57  Identities=14%  Similarity=0.201  Sum_probs=47.0

Q ss_pred             HHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           53 MIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        53 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      +...+.+.|++++|.+.|++.++..  |+             +...+..+..++.+.|++++|...|+...+
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~--P~-------------~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQD--PD-------------NPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCS--TT-------------HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC--CC-------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            4567889999999999999999975  32             455567899999999999999999998843

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

Probab=97.23  E-value=0.025  Score=47.46  Aligned_cols=135  Identities=15%  Similarity=0.158  Sum_probs=96.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .+..|+.+..+=.+.|...+|.+-|-+  ..|...|..++....+.|.|++-++.+.-.++..-+|...           
T Consensus      1103 ~p~vWsqlakAQL~~~~v~dAieSyik--adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id----------- 1169 (1666)
T KOG0985|consen 1103 EPAVWSQLAKAQLQGGLVKDAIESYIK--ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID----------- 1169 (1666)
T ss_pred             ChHHHHHHHHHHHhcCchHHHHHHHHh--cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch-----------
Confidence            456788888888888888888887754  3466678999999999999999999887777765555433           


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----------------------CChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----------------------KDKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----------------------~~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                           +.||-+|++.+++.+.+++...--.                       .++..|..+...++..|++..|.+.-+
T Consensus      1170 -----~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aR 1244 (1666)
T KOG0985|consen 1170 -----SELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAAR 1244 (1666)
T ss_pred             -----HHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                 3588888888888887776654210                       144566777777888888888877766


Q ss_pred             HHHHCCCCCcHHHHHHHHhhhc
Q 045555          152 QMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       152 ~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      +.-      +..||..+-.+|.
T Consensus      1245 KAn------s~ktWK~VcfaCv 1260 (1666)
T KOG0985|consen 1245 KAN------STKTWKEVCFACV 1260 (1666)
T ss_pred             hcc------chhHHHHHHHHHh
Confidence            643      4456666555553

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.22  E-value=0.0073  Score=43.84  Aligned_cols=145  Identities=12%  Similarity=0.137  Sum_probs=87.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-------CC--hhHHHHHHHHHhcc-CChHHHHHHHHHhHhCCCCC-ChHHHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-------RD--YVLWTAMIDGYLRV-NRFREALTLFREMQTSNIRR-DEFTTV   86 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-------~~--~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p-~~~~~~   86 (175)
                      .|.....+|.+. ++++|.+.+++..+       ++  ...+..+...|-.. |++++|++.|.+....--.- ....  
T Consensus        77 ~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~--  153 (282)
T PF14938_consen   77 AYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHS--  153 (282)
T ss_dssp             HHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHH--
T ss_pred             HHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhh--
Confidence            344444455333 77676666665542       22  23466667777777 78888888888876531111 1111  


Q ss_pred             HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---------Chh-hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           87 RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---------DKF-TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        87 ~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                              -..++..+...+.+.|++++|.++|++....         ++. .|-..+-++...||...|.+.+++..+.
T Consensus       154 --------a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  154 --------AAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             --------HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             --------HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence                    1344567889999999999999999988321         111 2223344555689999999999998754


Q ss_pred             --CCCC--cHHHHHHHHhhhc
Q 045555          157 --SIRL--DEVTYVGVLSACT  173 (175)
Q Consensus       157 --g~~p--~~~t~~~ll~~~~  173 (175)
                        ++..  .......||.+|-
T Consensus       226 ~~~F~~s~E~~~~~~l~~A~~  246 (282)
T PF14938_consen  226 DPSFASSREYKFLEDLLEAYE  246 (282)
T ss_dssp             STTSTTSHHHHHHHHHHHHHH
T ss_pred             CCCCCCcHHHHHHHHHHHHHH
Confidence              3332  3556666777664

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

Probab=97.22  E-value=0.012  Score=43.85  Aligned_cols=96  Identities=18%  Similarity=0.068  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHHhhhc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVRILTT   91 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~   91 (175)
                      ......+...+...|++++|...+++..+   .+...+..+...+.+.|++++|...+++....... |+..        
T Consensus       114 ~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~--------  185 (355)
T cd05804         114 WYLLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLR--------  185 (355)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchh--------
Confidence            34445666778899999999999998764   35667888889999999999999999998875321 1111        


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                          ...|-.+...+...|++++|.++++...
T Consensus       186 ----~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         186 ----GHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             ----HHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence                1233467888999999999999999975

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.

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

Probab=97.18  E-value=0.0015  Score=42.38  Aligned_cols=69  Identities=13%  Similarity=0.168  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh-----CCCCCChHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT-----SNIRRDEFTT   85 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~   85 (175)
                      .+...++..+...|++++|..+.+.+..  | |...|..+|.+|...|+..+|.+.|+++.+     .|+.|++.+-
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            3556677778889999999999998874  4 778999999999999999999999999855     4888876654

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

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.17  E-value=0.0023  Score=51.64  Aligned_cols=101  Identities=20%  Similarity=0.185  Sum_probs=64.5

Q ss_pred             hcCChhHHHHHhhcCCCCChh--HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHH
Q 045555           28 NRGQVDIARQYFAQMPERDYV--LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM  105 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~~~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~  105 (175)
                      ....|.+|+.+++.+..++..  -|..+...|+..|+++-|.++|.+.-.                       ++-.|.+
T Consensus       744 ~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~~-----------------------~~dai~m  800 (1636)
T KOG3616|consen  744 GAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEADL-----------------------FKDAIDM  800 (1636)
T ss_pred             hhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcch-----------------------hHHHHHH
Confidence            455566666666655544332  256666777777777777777765422                       2457888


Q ss_pred             HHhcCCHHHHHHHHHhhcCC--ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555          106 YCKCGDVEKAQRVFWKMLRK--DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus       106 ~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      |.+.|+|++|.++-.+-..|  ....|-+-..-+-.+|++.+|.++|-
T Consensus       801 y~k~~kw~da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyi  848 (1636)
T KOG3616|consen  801 YGKAGKWEDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYI  848 (1636)
T ss_pred             HhccccHHHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeE
Confidence            88888888888887776555  34455555555666666666665553

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=97.15  E-value=0.00098  Score=38.29  Aligned_cols=60  Identities=18%  Similarity=0.352  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---------CC-hhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---------RD-YVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---------~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ..+++.+...|...|++++|+..|++..+         ++ ..+++.+...+...|++++|+..+++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            35789999999999999999999997652         22 45789999999999999999999998764

...

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

Probab=97.15  E-value=0.023  Score=47.45  Aligned_cols=140  Identities=9%  Similarity=0.095  Sum_probs=99.7

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CCh-hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCC---ChHHHHH
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDY-VLWTAMIDGYLRVNRFREALTLFREMQTSNIRR---DEFTTVR   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p---~~~~~~~   87 (175)
                      .+...+..|+..|...+++++|.++.+...+  |+. ..|..+...+.+.++.+++..+  .+...-...   +.+.|..
T Consensus        29 ~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~~~~~~~~~ve~~~  106 (906)
T PRK14720         29 SKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL--NLIDSFSQNLKWAIVEHIC  106 (906)
T ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh--hhhhhcccccchhHHHHHH
Confidence            4678899999999999999999999996654  433 3344444467777777777777  444431111   1122111


Q ss_pred             -hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           88 -ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        88 -l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       .+..+.-+...+-.+..+|-+.|+.++|..+|+++.+-   |+.+.|.+...|... ++++|.+++.+.+..
T Consensus       107 ~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~  178 (906)
T PRK14720        107 DKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYR  178 (906)
T ss_pred             HHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHH
Confidence             11123334456667999999999999999999999653   778889999999988 999999998887653

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.13  E-value=0.0058  Score=34.46  Aligned_cols=62  Identities=23%  Similarity=0.229  Sum_probs=51.2

Q ss_pred             HHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          103 IDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      -..|.+.+++++|.++++.+..  | +...|......+.+.|++++|.+.|+...+.  .|+..+..
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~--~p~~~~~~   66 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALEL--SPDDPDAR   66 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHH--CCCcHHHH
Confidence            3578899999999999999954  3 6677888889999999999999999999975  45554433

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

Probab=97.12  E-value=0.038  Score=44.13  Aligned_cols=58  Identities=17%  Similarity=0.229  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcCCC-------hhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLRKD-------KFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      ..|..+.+.|..+|+++.|..+|++..+-+       ..+|....+.-.++.+++.|+++.++..
T Consensus       388 ~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~  452 (835)
T KOG2047|consen  388 TLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRAT  452 (835)
T ss_pred             hHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhh
Confidence            467788999999999999999999985532       2456666677777888888888887764

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

Probab=97.11  E-value=0.04  Score=41.85  Aligned_cols=141  Identities=13%  Similarity=0.059  Sum_probs=104.8

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCC--CC-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh---
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI---   88 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l---   88 (175)
                      +...+-.=.+.+.+.|++++|.-.|+...  .| +...|..|+.+|.-.|.+.+|.-.-+...+. +..+..+...+   
T Consensus       333 ~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~  411 (564)
T KOG1174|consen  333 NHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTL  411 (564)
T ss_pred             cchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcce
Confidence            44445444566788999999999998755  34 7889999999999999999998776665543 11122222111   


Q ss_pred             hh------------------ccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhHHHHHHHHHhcCChhHHH
Q 045555           89 LT------------------TFNND-IFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        89 ~~------------------~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~  147 (175)
                      +.                  ..+|+ ....+.+.+.+...|+.+++..+++...  .+|...-+.+.+.+...+.+.+|.
T Consensus       412 V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am  491 (564)
T KOG1174|consen  412 VLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAM  491 (564)
T ss_pred             eeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHH
Confidence            11                  23444 4566789999999999999999999874  478889999999999999999999


Q ss_pred             HHHHHHHHC
Q 045555          148 DMFSQMLRA  156 (175)
Q Consensus       148 ~~~~~m~~~  156 (175)
                      +.|...+..
T Consensus       492 ~~y~~ALr~  500 (564)
T KOG1174|consen  492 EYYYKALRQ  500 (564)
T ss_pred             HHHHHHHhc
Confidence            999887653

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.11  E-value=0.019  Score=36.07  Aligned_cols=105  Identities=13%  Similarity=0.082  Sum_probs=75.4

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCCC---C---hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           22 IVSGYINRGQVDIARQYFAQMPER---D---YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~~---~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      ...++-..|+.++|..+|++....   +   ...+-.+-+.+...|++++|..++++.......++  .          +
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~--~----------~   74 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDE--L----------N   74 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcc--c----------c
Confidence            445667889999999999986642   1   23566788889999999999999999987642211  0          1


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLA  138 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~  138 (175)
                      ..+...+.-++...|+.++|.+.+-....++..-|.--|..|.
T Consensus        75 ~~l~~f~Al~L~~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   75 AALRVFLALALYNLGRPKEALEWLLEALAETLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            1112234557788999999999998877776666666666654

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

Probab=97.09  E-value=0.0064  Score=47.37  Aligned_cols=119  Identities=17%  Similarity=0.188  Sum_probs=87.4

Q ss_pred             HHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC----------ChhHHHHHHHHHhccCChHHHHHHH
Q 045555            4 ALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPER----------DYVLWTAMIDGYLRVNRFREALTLF   70 (175)
Q Consensus         4 A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----------~~~~~~~li~~~~~~~~~~~a~~~~   70 (175)
                      |.++|.+...  | |+...+-+.-..-..+.+.+|...|+...++          -..+++.|.++|.+.+.+++|+..+
T Consensus       399 Ae~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~  478 (611)
T KOG1173|consen  399 AEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYY  478 (611)
T ss_pred             HHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHH
Confidence            4455554443  3 6666676666666777888888888765521          2345888999999999999999999


Q ss_pred             HHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCCChhhHHHHHHHH
Q 045555           71 REMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRKDKFTWTAMIVGL  137 (175)
Q Consensus        71 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~~~~~~~~li~~~  137 (175)
                      ++.+...               +-+..++.++.-.|...|+++.|.+.|.+.  .+|+-.+-..++..+
T Consensus       479 q~aL~l~---------------~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  479 QKALLLS---------------PKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHcC---------------CCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHH
Confidence            9988753               335566689999999999999999999998  567666655555543

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.09  E-value=0.0079  Score=43.35  Aligned_cols=96  Identities=14%  Similarity=0.135  Sum_probs=76.3

Q ss_pred             HHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHH
Q 045555           25 GYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIA  101 (175)
Q Consensus        25 ~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~  101 (175)
                      -..+.+++.+|++.|.+..+   .|.+-|..-..+|++.|.++.|++=.+..++.+               +.....|..
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD---------------p~yskay~R  154 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID---------------PHYSKAYGR  154 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC---------------hHHHHHHHH
Confidence            35678999999999998775   478889999999999999999998877776643               224667889


Q ss_pred             HHHHHHhcCCHHHHHHHHHhhc--CCChhhHHHHHH
Q 045555          102 LIDMYCKCGDVEKAQRVFWKML--RKDKFTWTAMIV  135 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~  135 (175)
                      |--+|...|++++|.+.|++..  +|+-.+|-.=++
T Consensus       155 LG~A~~~~gk~~~A~~aykKaLeldP~Ne~~K~nL~  190 (304)
T KOG0553|consen  155 LGLAYLALGKYEEAIEAYKKALELDPDNESYKSNLK  190 (304)
T ss_pred             HHHHHHccCcHHHHHHHHHhhhccCCCcHHHHHHHH
Confidence            9999999999999999999984  465555544433

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.07  E-value=0.0057  Score=44.39  Aligned_cols=131  Identities=12%  Similarity=0.123  Sum_probs=89.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC-------C--ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ..|..-...|-..|++++|.+.|.+...       +  -...|......|.+. ++++|+..+++....-...+.     
T Consensus        36 ~~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~-----  109 (282)
T PF14938_consen   36 DLYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGR-----  109 (282)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT------
T ss_pred             HHHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCc-----
Confidence            4578888888889999999988887642       2  122455555555444 999999998888653111110     


Q ss_pred             hhhccCcchhHHHHHHHHHHhc-CCHHHHHHHHHhhcC-----C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKC-GDVEKAQRVFWKMLR-----K----DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                          +..-...+..+...|... |++++|.+.|++..+     .    -..++..+...+.+.|++++|.++|++....-
T Consensus       110 ----~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~  185 (282)
T PF14938_consen  110 ----FSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKC  185 (282)
T ss_dssp             ----HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTC
T ss_pred             ----HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHh
Confidence                011134567888899888 999999999999833     1    23467778889999999999999999987643

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

Probab=97.06  E-value=0.034  Score=41.16  Aligned_cols=107  Identities=17%  Similarity=0.257  Sum_probs=81.9

Q ss_pred             hHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh
Q 045555            3 FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE   82 (175)
Q Consensus         3 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   82 (175)
                      .|.++-++..=|+...|-..+.+|++.++|++-..+-..  +.+++.|.-.+.+|.+.|+..+|......+..       
T Consensus       195 ~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s--kKsPIGyepFv~~~~~~~~~~eA~~yI~k~~~-------  265 (319)
T PF04840_consen  195 QAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS--KKSPIGYEPFVEACLKYGNKKEASKYIPKIPD-------  265 (319)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC--CCCCCChHHHHHHHHHCCCHHHHHHHHHhCCh-------
Confidence            455666666669999999999999999999998886554  44668899999999999999999999888432       


Q ss_pred             HHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHH
Q 045555           83 FTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGL  137 (175)
Q Consensus        83 ~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  137 (175)
                                       ..-+..|.+.|++.+|.+.--+  ..|......+...+
T Consensus       266 -----------------~~rv~~y~~~~~~~~A~~~A~~--~kd~~~L~~i~~~~  301 (319)
T PF04840_consen  266 -----------------EERVEMYLKCGDYKEAAQEAFK--EKDIDLLKQILKRC  301 (319)
T ss_pred             -----------------HHHHHHHHHCCCHHHHHHHHHH--cCCHHHHHHHHHHC
Confidence                             3578899999999998766443  34554444444443

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

>PLN02789 farnesyltranstransferase

Probab=96.97  E-value=0.052  Score=40.22  Aligned_cols=155  Identities=8%  Similarity=0.087  Sum_probs=90.0

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCCh--hHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQV--DIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~--~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +|+.+++.+.+   .+..+|+..--.+.+.|+.  +++.++++.+.+   .|..+|+.....+.+.|+++++++.+++++
T Consensus        90 eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I  169 (320)
T PLN02789         90 EELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLL  169 (320)
T ss_pred             HHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            45555555543   3445566544444455542  556666766553   467778888888888888888888888888


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhc---CCH----HHHHHHHHhhc--CC-ChhhHHHHHHHHHhc----
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKC---GDV----EKAQRVFWKML--RK-DKFTWTAMIVGLAIS----  140 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~---~~~----~~a~~~~~~~~--~~-~~~~~~~li~~~~~~----  140 (175)
                      +.++.               +...|+.....+.+.   |+.    ++......+.+  .| +...|+-+...+...    
T Consensus       170 ~~d~~---------------N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l  234 (320)
T PLN02789        170 EEDVR---------------NNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEAL  234 (320)
T ss_pred             HHCCC---------------chhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCccc
Confidence            86532               222333333333332   222    45555555553  33 667888777777763    


Q ss_pred             CChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          141 GHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       141 g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      ++..+|.+.+.+..+.+ ..+......|++.|+
T Consensus       235 ~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~  266 (320)
T PLN02789        235 VSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLC  266 (320)
T ss_pred             ccchhHHHHHHHhhccc-CCcHHHHHHHHHHHH
Confidence            34466777777766532 223444555555543

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

Probab=96.96  E-value=0.1  Score=42.03  Aligned_cols=63  Identities=16%  Similarity=0.231  Sum_probs=28.5

Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      |.-|..+.-.+...|-...++++|.+-|...++.   ...+|..+...+.++|.-+.-.+++....
T Consensus       813 ce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~  878 (913)
T KOG0495|consen  813 CEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCE  878 (913)
T ss_pred             ccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHh
Confidence            3344444444444444444445555544444331   23344444455555554444444444433

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.94  E-value=0.014  Score=43.32  Aligned_cols=141  Identities=15%  Similarity=0.191  Sum_probs=91.1

Q ss_pred             chHHHHhhccCC--C-----cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--------C----------------ChhHH
Q 045555            2 GFALEIFGNMKN--K-----DVISWTTIVSGYINRGQVDIARQYFAQMPE--------R----------------DYVLW   50 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--------~----------------~~~~~   50 (175)
                      ++|..+.+++..  |     ..+++.++..-.......+-|.+.|+..-+        |                |+.+|
T Consensus       302 qeA~~L~Kdl~PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~Y  381 (557)
T KOG3785|consen  302 QEAISLCKDLDPTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTY  381 (557)
T ss_pred             HHHHHHHhhcCCCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHH
Confidence            466666666664  2     234455555555555666667776664432        0                22222


Q ss_pred             H---------------HHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHH
Q 045555           51 T---------------AMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKA  115 (175)
Q Consensus        51 ~---------------~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a  115 (175)
                      -               .+..+.+..|++.+|.++|-++....+ .+..+|             .+.|..+|.+++..+.|
T Consensus       382 lnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~i-kn~~~Y-------------~s~LArCyi~nkkP~lA  447 (557)
T KOG3785|consen  382 LNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEI-KNKILY-------------KSMLARCYIRNKKPQLA  447 (557)
T ss_pred             HHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhh-hhhHHH-------------HHHHHHHHHhcCCchHH
Confidence            2               345566777888888888866644322 233444             25678899999999999


Q ss_pred             HHHHHhhcCC-Chhh-HHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          116 QRVFWKMLRK-DKFT-WTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       116 ~~~~~~~~~~-~~~~-~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +.++-++..| +..+ ...+..-|.+++++--|.+.|+++...
T Consensus       448 W~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l  490 (557)
T KOG3785|consen  448 WDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEIL  490 (557)
T ss_pred             HHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc
Confidence            9999988776 3333 444456677999999999999988754

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.88  E-value=0.0097  Score=48.25  Aligned_cols=146  Identities=21%  Similarity=0.214  Sum_probs=83.9

Q ss_pred             chHHHHhhccCCCcHH--HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC
Q 045555            2 GFALEIFGNMKNKDVI--SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR   79 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   79 (175)
                      .+|+.+++.++..+..  -|-.+..-|+..|+++.|.++|-+.-     .++--|..|.+.|+|+.|.++-++...  ..
T Consensus       749 ~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~~~dai~my~k~~kw~da~kla~e~~~--~e  821 (1636)
T KOG3616|consen  749 KKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD-----LFKDAIDMYGKAGKWEDAFKLAEECHG--PE  821 (1636)
T ss_pred             hhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc-----hhHHHHHHHhccccHHHHHHHHHHhcC--ch
Confidence            3567777777654332  36677788999999999999997642     367778899999999999998777643  33


Q ss_pred             CChHHHHHhhh-----c-------cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-CChhhHHHHHHHHHhcCChhHH
Q 045555           80 RDEFTTVRILT-----T-------FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-KDKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        80 p~~~~~~~l~~-----~-------~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~a  146 (175)
                      .....|..--.     |       .......=...|.+|-+.|..++..++..+-.. .=..|--.+..-|-..|++..|
T Consensus       822 ~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv~k~h~d~l~dt~~~f~~e~e~~g~lkaa  901 (1636)
T KOG3616|consen  822 ATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLVEKHHGDHLHDTHKHFAKELEAEGDLKAA  901 (1636)
T ss_pred             hHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHHHHhChhhhhHHHHHHHHHHHhccChhHH
Confidence            33333321111     0       000000001234444444444444444433211 1123444555666667777777


Q ss_pred             HHHHHHHH
Q 045555          147 LDMFSQML  154 (175)
Q Consensus       147 ~~~~~~m~  154 (175)
                      .+-|-+..
T Consensus       902 e~~flea~  909 (1636)
T KOG3616|consen  902 EEHFLEAG  909 (1636)
T ss_pred             HHHHHhhh
Confidence            77765543

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

Probab=96.86  E-value=0.11  Score=40.99  Aligned_cols=154  Identities=11%  Similarity=0.079  Sum_probs=95.5

Q ss_pred             HHHHhhccCC--CcHHHHHHHHHHHH-hcCChhHHHHHhhcCCC--C--ChhHHHHHHHHHhccCChHHHHHHHH-----
Q 045555            4 ALEIFGNMKN--KDVISWTTIVSGYI-NRGQVDIARQYFAQMPE--R--DYVLWTAMIDGYLRVNRFREALTLFR-----   71 (175)
Q Consensus         4 A~~~~~~m~~--~~~~~~~~li~~~~-~~~~~~~a~~~~~~m~~--~--~~~~~~~li~~~~~~~~~~~a~~~~~-----   71 (175)
                      ++++....+.  |....=+.+..++- +.....+|.+++....+  |  ...+--+++......|+++.|++++.     
T Consensus       326 ~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~  405 (652)
T KOG2376|consen  326 VRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLES  405 (652)
T ss_pred             HHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh
Confidence            4444444444  44333333333332 22346677777776654  2  34456667777888999999999999     


Q ss_pred             ---HhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------CCh----hhHHHHHHHHH
Q 045555           72 ---EMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------KDK----FTWTAMIVGLA  138 (175)
Q Consensus        72 ---~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~----~~~~~li~~~~  138 (175)
                         .+...+-.|..+                .++...|.+-++-+.|..+++....      +..    .++......-.
T Consensus       406 ~~ss~~~~~~~P~~V----------------~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~l  469 (652)
T KOG2376|consen  406 WKSSILEAKHLPGTV----------------GAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKL  469 (652)
T ss_pred             hhhhhhhhccChhHH----------------HHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHH
Confidence               444444444443                3477777877877777777777632      111    23333444455


Q ss_pred             hcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          139 ISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       139 ~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      +.|+-++|..+++++.+. -.+|..+..-++.+|++
T Consensus       470 r~G~~~ea~s~leel~k~-n~~d~~~l~~lV~a~~~  504 (652)
T KOG2376|consen  470 RHGNEEEASSLLEELVKF-NPNDTDLLVQLVTAYAR  504 (652)
T ss_pred             hcCchHHHHHHHHHHHHh-CCchHHHHHHHHHHHHh
Confidence            678888888888888763 25677777777777764

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.84  E-value=0.032  Score=39.92  Aligned_cols=142  Identities=11%  Similarity=0.107  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCCC----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ..+-+.++.++.-.|.+.-....+++..+.    +...-+.|.+.-.+.|+.+.|...|++..+..-..+..+.+.++. 
T Consensus       177 ~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~-  255 (366)
T KOG2796|consen  177 GRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVL-  255 (366)
T ss_pred             HHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHH-
Confidence            345567777777788888888888877653    566678888888899999999999998887655555555533322 


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                              ......|.-.+++..|.+.|.+....   +++.-|.-.-+..-.|+..+|.+....|.+.  -|...+-.++
T Consensus       256 --------~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~  325 (366)
T KOG2796|consen  256 --------MNSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESV  325 (366)
T ss_pred             --------hhhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhH
Confidence                    34445566778888999999887553   4555555555555678999999999999875  4555444443

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.83  E-value=0.089  Score=37.37  Aligned_cols=139  Identities=17%  Similarity=0.264  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHH-HHhccCChHHHHHHHHHhHhCCCCCChHHHHH---hhh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMID-GYLRVNRFREALTLFREMQTSNIRRDEFTTVR---ILT   90 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~-~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~---l~~   90 (175)
                      ..|--++.+..-.|+.+.|..++++++.  |...--..|=. -+--.|++++|+++++.++..+ +-|.+++..   +++
T Consensus        53 ~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilk  131 (289)
T KOG3060|consen   53 TLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILK  131 (289)
T ss_pred             HHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHHHH
Confidence            3466677777788999999999998764  32221122211 2334588999999999998876 233333321   111


Q ss_pred             -----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--cCC-ChhhHHHHHHHHHhcC---ChhHHH
Q 045555           91 -----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--LRK-DKFTWTAMIVGLAISG---HGDTAL  147 (175)
Q Consensus        91 -----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--~~~-~~~~~~~li~~~~~~g---~~~~a~  147 (175)
                                       .+..|...|--+.+.|...|+++.|.-+++++  ..| +.-.+..+.+.+.-.|   +.+.|.
T Consensus       132 a~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~ar  211 (289)
T KOG3060|consen  132 AQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELAR  211 (289)
T ss_pred             HcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHH
Confidence                             56778888888888998899999988888888  445 3334444555544333   566677


Q ss_pred             HHHHHHHHC
Q 045555          148 DMFSQMLRA  156 (175)
Q Consensus       148 ~~~~~m~~~  156 (175)
                      +.|.+.++.
T Consensus       212 kyy~~alkl  220 (289)
T KOG3060|consen  212 KYYERALKL  220 (289)
T ss_pred             HHHHHHHHh
Confidence            788777754

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.76  E-value=0.047  Score=41.93  Aligned_cols=68  Identities=13%  Similarity=-0.027  Sum_probs=46.6

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                      +...|+.+..+|.+.|++++|+..|++.++..  |+....          ...|..+..+|...|+.++|.+.++...+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd~aeA----------~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELN--PNPDEA----------QAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCchHH----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            45567888888888888888888888877743  331100          023456888888888888888888877553

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.74  E-value=0.019  Score=41.75  Aligned_cols=146  Identities=14%  Similarity=0.162  Sum_probs=90.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHH-HHHHhccCChHHHHHHHHHhHhCC-CCCChHHHHHhhh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAM-IDGYLRVNRFREALTLFREMQTSN-IRRDEFTTVRILT   90 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~l-i~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~l~~   90 (175)
                      +....+.+..+|-...++..|...|+++..  |...-|... ..++.+.+.+-+|+++...|.... +.......-+.|.
T Consensus        43 ~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIk  122 (459)
T KOG4340|consen   43 SRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKACIYADALRVAFLLLDNPALHSRVLQLQAAIK  122 (459)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence            556677777777777778888888877764  333222211 344566677777777777775531 1111111111111


Q ss_pred             --------------cc--CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC----ChhhHHHHHHHHHhcCChhHHHHHH
Q 045555           91 --------------TF--NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK----DKFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        91 --------------~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                                    ..  +.+..+.+......-+.|+++.|.+-|+...+-    ....||.-+..| +.|+++.|.+..
T Consensus       123 Yse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~i  201 (459)
T KOG4340|consen  123 YSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHI  201 (459)
T ss_pred             cccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHH
Confidence                          11  123334444444556889999999999988552    455677666555 568999999999


Q ss_pred             HHHHHCCCCCc
Q 045555          151 SQMLRASIRLD  161 (175)
Q Consensus       151 ~~m~~~g~~p~  161 (175)
                      .+++++|++..
T Consensus       202 SEIieRG~r~H  212 (459)
T KOG4340|consen  202 SEIIERGIRQH  212 (459)
T ss_pred             HHHHHhhhhcC
Confidence            99999988743

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.73  E-value=0.03  Score=40.28  Aligned_cols=96  Identities=11%  Similarity=0.045  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--RDY----VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      ..|..-+..+.+.|++++|...|+.+.+  |+.    ..+..+...|...|++++|...|+.+.+...  +..       
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP--~s~-------  214 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYP--KSP-------  214 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC--CCc-------
Confidence            4566666666778999999999999874  543    4678888999999999999999999987532  110       


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                         .....+-.+...+...|+.++|.+.|+.+.+
T Consensus       215 ---~~~dAl~klg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        215 ---KAADAMFKVGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             ---chhHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               0112223467778899999999999998855

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.72  E-value=0.097  Score=35.62  Aligned_cols=128  Identities=13%  Similarity=0.095  Sum_probs=95.3

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC----CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      |+.-.--.|...+.+.|+..+|...|++...    .|....-.+.++....+++-+|...++++.+...  ..       
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~p--a~-------  157 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNP--AF-------  157 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCC--cc-------
Confidence            5666666788889999999999999998765    4777788888899999999999999999988642  10       


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                        -.||..  -.+...|...|+.++|+.-|+....  |+...-.-.-..+.+.|+..++..-+.++.
T Consensus       158 --r~pd~~--Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v~  220 (251)
T COG4700         158 --RSPDGH--LLFARTLAAQGKYADAESAFEVAISYYPGPQARIYYAEMLAKQGRLREANAQYVAVV  220 (251)
T ss_pred             --CCCCch--HHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence              112222  2478889999999999999998854  555544445556677887777755554443

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

Probab=96.70  E-value=0.14  Score=40.94  Aligned_cols=159  Identities=13%  Similarity=0.127  Sum_probs=98.4

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C--------------------------------
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R--------------------------------   45 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~--------------------------------   45 (175)
                      +|.+..+...+   .+.+.|..+.-.+-...++++|...|.....  |                                
T Consensus        59 ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql  138 (700)
T KOG1156|consen   59 EAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQL  138 (700)
T ss_pred             HHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence            45555555544   4677888888888888888888888886542  1                                


Q ss_pred             ---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC-CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           46 ---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNI-RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        46 ---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                         ....|..+.-++.-.|+...|..+.++..+... .|+...+....        ..-.-.....+.|.+++|.+...+
T Consensus       139 ~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se--------~~Ly~n~i~~E~g~~q~ale~L~~  210 (700)
T KOG1156|consen  139 RPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSE--------LLLYQNQILIEAGSLQKALEHLLD  210 (700)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHH--------HHHHHHHHHHHcccHHHHHHHHHh
Confidence               223466666667777888888888888877642 44544442111        111223344567777777776665


Q ss_pred             hcCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          122 MLRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       122 ~~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      ....   ..-.-..-...+.+.+++++|..+++.++..  .||..-|...+..
T Consensus       211 ~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~  261 (700)
T KOG1156|consen  211 NEKQIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEK  261 (700)
T ss_pred             hhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHH
Confidence            5332   2222334556677788888888888888775  4666655554443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.64  E-value=0.14  Score=36.45  Aligned_cols=65  Identities=9%  Similarity=-0.037  Sum_probs=46.3

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CCh-hH---HHHHHHHHhccCChHHHHHHHHHhHhCCCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDY-VL---WTAMIDGYLRVNRFREALTLFREMQTSNIR   79 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~-~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   79 (175)
                      +....-.....+.+.|++++|.+.|+.+..  |+. ..   .-.+..++.+.+++++|...+++..+....
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~  101 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT  101 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcC
Confidence            344444455556678999999999998875  322 22   245667788999999999999999886543

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.60  E-value=0.0066  Score=34.22  Aligned_cols=55  Identities=18%  Similarity=0.259  Sum_probs=48.2

Q ss_pred             HHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           23 VSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        23 i~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      -..|.+.+++++|.++++.+.+  | +...|.....++.+.|++++|.+.|++..+.+
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            3568899999999999999874  3 66778888999999999999999999999854

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.60  E-value=0.038  Score=39.45  Aligned_cols=91  Identities=19%  Similarity=0.269  Sum_probs=74.6

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCC----CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSN----IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .|+.-+ .+.+.|++.+|...|....+..    ..|+..-|                |.+++...|++++|..+|..+.+
T Consensus       144 ~Y~~A~-~~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW----------------LGe~~y~qg~y~~Aa~~f~~~~k  206 (262)
T COG1729         144 LYNAAL-DLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW----------------LGESLYAQGDYEDAAYIFARVVK  206 (262)
T ss_pred             HHHHHH-HHHHcCCHHHHHHHHHHHHHcCCCCcccchhHHH----------------HHHHHHhcccchHHHHHHHHHHH
Confidence            366666 4567788999999999999974    34454444                99999999999999999999954


Q ss_pred             --C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 --K----DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 --~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                        |    -...+--+..+..+.|+.++|-.+|+++.++
T Consensus       207 ~~P~s~KApdallKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         207 DYPKSPKAPDALLKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             hCCCCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence              2    3467778888999999999999999999876

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.58  E-value=0.13  Score=35.40  Aligned_cols=136  Identities=9%  Similarity=0.034  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      ...-.....+.+.|++++|...|+.+..  |    -....-.+..++.+.|++++|...++++.+.-.......+...+.
T Consensus         6 ~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~   85 (203)
T PF13525_consen    6 EALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYML   85 (203)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHH
Confidence            3444455667789999999999998874  3    223456778889999999999999999988654333322322111


Q ss_pred             ccCcchhHHHHHHHH---HHhcCCHHHHHHHHHhhcC--CCh------------------hhHHHHHHHHHhcCChhHHH
Q 045555           91 TFNNDIFVGIALIDM---YCKCGDVEKAQRVFWKMLR--KDK------------------FTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        91 ~~~~~~~~~~~li~~---~~~~~~~~~a~~~~~~~~~--~~~------------------~~~~~li~~~~~~g~~~~a~  147 (175)
                      +.    ..+...=..   ....+...+|...|+.+++  |+.                  ..--.+.+-|.+.|.+..|.
T Consensus        86 g~----~~~~~~~~~~~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~la~~e~~ia~~Y~~~~~y~aA~  161 (203)
T PF13525_consen   86 GL----SYYKQIPGILRSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRLAEHELYIARFYYKRGKYKAAI  161 (203)
T ss_dssp             HH----HHHHHHHHHH-TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHH
T ss_pred             HH----HHHHhCccchhcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHH
Confidence            10    000000000   1112223445555555532  211                  11123566788899999999


Q ss_pred             HHHHHHHHC
Q 045555          148 DMFSQMLRA  156 (175)
Q Consensus       148 ~~~~~m~~~  156 (175)
                      .-++.+++.
T Consensus       162 ~r~~~v~~~  170 (203)
T PF13525_consen  162 IRFQYVIEN  170 (203)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998875

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

Probab=96.57  E-value=0.045  Score=45.80  Aligned_cols=139  Identities=17%  Similarity=0.137  Sum_probs=91.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhH-------------hCCC-C
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQ-------------TSNI-R   79 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~-------------~~~~-~   79 (175)
                      ..|+.|...|....+...|...|+...+-   +...+-.....|++..+|++|..+.-..-             +.|+ .
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yy  572 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYY  572 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccc
Confidence            47888888888888888888888887763   44556777777888888888877732221             1111 1


Q ss_pred             CChHHHHHhhh-------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCCh-hhHHHHH--HHHHhcCChhHHHHH
Q 045555           80 RDEFTTVRILT-------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDK-FTWTAMI--VGLAISGHGDTALDM  149 (175)
Q Consensus        80 p~~~~~~~l~~-------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~li--~~~~~~g~~~~a~~~  149 (175)
                      |....+...+.       --+.|...|..+.++|.++|++..|.++|.+...-++ ..|....  ...|..|++.+|++.
T Consensus       573 Lea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYkeald~  652 (1238)
T KOG1127|consen  573 LEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKEALDA  652 (1238)
T ss_pred             cCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHHHHHH
Confidence            11111111111       2244678899999999999999999999988744322 2333332  235667888888888


Q ss_pred             HHHHHH
Q 045555          150 FSQMLR  155 (175)
Q Consensus       150 ~~~m~~  155 (175)
                      +.....
T Consensus       653 l~~ii~  658 (1238)
T KOG1127|consen  653 LGLIIY  658 (1238)
T ss_pred             HHHHHH
Confidence            877653

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

Probab=96.56  E-value=0.1  Score=43.76  Aligned_cols=121  Identities=12%  Similarity=0.124  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC---CC--hHHHHHh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR---RD--EFTTVRI   88 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---p~--~~~~~~l   88 (175)
                      .+.-.+..+|-+.|+.++|..+|++..+   .|..+.|.+...|+.. ++++|.+++.+....-+.   ++  ...|..+
T Consensus       117 ~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~~i~~kq~~~~~e~W~k~  195 (906)
T PRK14720        117 LALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAIYRFIKKKQYVGIEEIWSKL  195 (906)
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHhhhcchHHHHHHHHH
Confidence            4566677777777888888888887765   3566677777777777 777777766666443210   00  0001111


Q ss_pred             hh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHH
Q 045555           89 LT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLA  138 (175)
Q Consensus        89 ~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~  138 (175)
                      +.                    +..--..++--+-..|.+.++|+++..+++.+.+-   |.....-++.+|.
T Consensus       196 ~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        196 VHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             HhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            11                    11222334445556666777777777777776442   4445555666655

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

Probab=96.55  E-value=0.26  Score=38.83  Aligned_cols=122  Identities=16%  Similarity=0.224  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC----C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE----R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      +|...|+.--+...++.|+.+|.+.++    + ++.+++++|.-+| .++..-|.++|+--++.               +
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk---------------f  431 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKK---------------F  431 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHh---------------c
Confidence            344444444444445555555554443    1 3344444443332 23444444444443332               1


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK------DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..+...-..-++-+...++=..+..+|+.....      ....|..+++--..-|++..+.++-+++..
T Consensus       432 ~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  432 GDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             CCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            222223345566666777777777777777443      345788888887788888887777766654

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

Probab=96.55  E-value=0.092  Score=38.05  Aligned_cols=112  Identities=13%  Similarity=0.140  Sum_probs=71.9

Q ss_pred             HHHHHhhcCC--CCChhHHHHHHHHHhcc-----CChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHH
Q 045555           34 IARQYFAQMP--ERDYVLWTAMIDGYLRV-----NRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        34 ~a~~~~~~m~--~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      ..+..|....  ++|-.+|-..+.-+...     ++.+-....++.|.+.|+.-|..+|              +.|++.+
T Consensus        52 ~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vY--------------k~Llnvf  117 (406)
T KOG3941|consen   52 HVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVY--------------KGLLNVF  117 (406)
T ss_pred             chhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHH--------------HHHHHhC
Confidence            3455566655  46777788777776544     5677778888888888876666665              5565555


Q ss_pred             HhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          107 CKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      -+-.-.            | ...+......|=+  +-+=+.+++++|...|+.||..+-..|++++.+
T Consensus       118 PKgkfi------------P-~nvfQ~~F~HYP~--QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr  170 (406)
T KOG3941|consen  118 PKGKFI------------P-QNVFQKVFLHYPQ--QQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGR  170 (406)
T ss_pred             cccccc------------c-HHHHHHHHhhCch--hhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcc
Confidence            432211            1 1122233333333  234578888999999999999998888887754

>PRK15331 chaperone protein SicA; Provisional

Probab=96.50  E-value=0.056  Score=35.79  Aligned_cols=92  Identities=15%  Similarity=0.046  Sum_probs=74.7

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh---cCCC
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM---LRKD  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~---~~~~  126 (175)
                      ......-+-+.|++++|..+|.-+...+.               .+...+..|..++...+++++|...|...   ...|
T Consensus        40 iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~---------------~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~d  104 (165)
T PRK15331         40 LYAHAYEFYNQGRLDEAETFFRFLCIYDF---------------YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKND  104 (165)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCc---------------CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence            44455567789999999999999988552               33445678999999999999999999886   2346


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +..+-....+|...|+.+.|.+.|....++
T Consensus       105 p~p~f~agqC~l~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        105 YRPVFFTGQCQLLMRKAAKARQCFELVNER  134 (165)
T ss_pred             CCccchHHHHHHHhCCHHHHHHHHHHHHhC
Confidence            667777888999999999999999998873

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

Probab=96.48  E-value=0.054  Score=39.16  Aligned_cols=76  Identities=12%  Similarity=0.185  Sum_probs=65.1

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH-----CCCCCcHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR-----ASIRLDEVTYVG  167 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~  167 (175)
                      ..++..+++.+...|+++.+.+.++.+..  | +...|..+|.+|.+.|+...|.+.|+++.+     .|+.|-..+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            35677899999999999999999999965  3 778999999999999999999999998764     589998877766


Q ss_pred             HHhh
Q 045555          168 VLSA  171 (175)
Q Consensus       168 ll~~  171 (175)
                      ..+.
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            5544

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.47  E-value=0.081  Score=41.88  Aligned_cols=113  Identities=12%  Similarity=0.044  Sum_probs=76.4

Q ss_pred             chHHHHhhccCC--Cc-HHHHHHHHHHHHhc--------CChhHHHHHhhcCC-----CCChhHHHHHHHHHhccCChHH
Q 045555            2 GFALEIFGNMKN--KD-VISWTTIVSGYINR--------GQVDIARQYFAQMP-----ERDYVLWTAMIDGYLRVNRFRE   65 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~-~~~~~~li~~~~~~--------~~~~~a~~~~~~m~-----~~~~~~~~~li~~~~~~~~~~~   65 (175)
                      ++|..+|++..+  |+ ...|..+..++...        ++...+.+......     ..+...|.++.-.....|++++
T Consensus       359 ~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~  438 (517)
T PRK10153        359 NKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVALPELNVLPRIYEILAVQALVKGKTDE  438 (517)
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHH
Confidence            468888888876  54 34555544444322        12334444444422     2245677777666667899999


Q ss_pred             HHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhH
Q 045555           66 ALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTW  130 (175)
Q Consensus        66 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~  130 (175)
                      |...+++....+                |+...|..+...+...|+.++|.+.++....  |...+|
T Consensus       439 A~~~l~rAl~L~----------------ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt~  489 (517)
T PRK10153        439 AYQAINKAIDLE----------------MSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENTL  489 (517)
T ss_pred             HHHHHHHHHHcC----------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCchH
Confidence            999999999864                3344557899999999999999999999844  544444

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

Probab=96.45  E-value=0.12  Score=39.92  Aligned_cols=122  Identities=13%  Similarity=0.117  Sum_probs=84.7

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCC-CCCChHHHHHhhh------------------ccCcchh-HHHHHHHHHH
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSN-IRRDEFTTVRILT------------------TFNNDIF-VGIALIDMYC  107 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~l~~------------------~~~~~~~-~~~~li~~~~  107 (175)
                      .+|+..|+.-.+..-.+.|..+|-+..+.| +.++...+++++.                  ...||.. .-+--+.-+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d~~ta~~ifelGl~~f~d~~~y~~kyl~fLi  477 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYNIFELGLLKFPDSTLYKEKYLLFLI  477 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHHHHHHHHHhCCCchHHHHHHHHHHH
Confidence            456777777777777777777777777777 4667777766666                  1223332 2345566667


Q ss_pred             hcCCHHHHHHHHHhhcCC---C--hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          108 KCGDVEKAQRVFWKMLRK---D--KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       108 ~~~~~~~a~~~~~~~~~~---~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      +-++=+.|..+|+..+++   +  -..|..+|+--..-|++..+..+-+.|.+.  -|...+...+...
T Consensus       478 ~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sr  544 (660)
T COG5107         478 RINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSR  544 (660)
T ss_pred             HhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHH
Confidence            888999999999977543   2  457999999999999999998888888763  5555555444443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.45  E-value=0.029  Score=43.03  Aligned_cols=63  Identities=19%  Similarity=0.116  Sum_probs=55.0

Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CCh----hhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDK----FTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+...++.+..+|.+.|++++|...|+...+  |+.    ..|..+..+|...|+.++|.+.+++.++.
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3567889999999999999999999999744  543    35999999999999999999999999875

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

Probab=96.27  E-value=0.081  Score=41.78  Aligned_cols=119  Identities=14%  Similarity=0.139  Sum_probs=86.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      .-+=++-+.+.|++++|....+++..  | +...+..=+-++++.+.+++|+.+.+.-....                  
T Consensus        15 l~t~ln~~~~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~------------------   76 (652)
T KOG2376|consen   15 LLTDLNRHGKNGEYEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKKNGALL------------------   76 (652)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhh------------------
Confidence            33456667788999999999988764  3 55556666668999999999995544332110                  


Q ss_pred             hhHHHH--HHHHH--HhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           96 IFVGIA--LIDMY--CKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        96 ~~~~~~--li~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                        +++.  +=.+|  -+.++.|+|...++...+.+..+...-...+.+.|++++|+++|+.+.+.+
T Consensus        77 --~~~~~~fEKAYc~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~  140 (652)
T KOG2376|consen   77 --VINSFFFEKAYCEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNN  140 (652)
T ss_pred             --hcchhhHHHHHHHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence              0111  23344  488999999999997766676677777788889999999999999997654

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.24  E-value=0.26  Score=35.13  Aligned_cols=123  Identities=14%  Similarity=0.140  Sum_probs=79.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.++++.+.+  | |.+++--=+...--.|+..+|++-++...+   .|.-.|.-+-..|...|++++|.-.++++.-
T Consensus       103 ~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  103 KEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             hhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            456667766665  3 444555455555556666666666665554   4778888999999999999999999999876


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHH---HhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHh
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMY---CKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAI  139 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~---~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~  139 (175)
                      ..               +-+...+..+.+.+   +...+++.|.+.|....+-+......+...|..
T Consensus       183 ~~---------------P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~~~~ral~GI~lc  234 (289)
T KOG3060|consen  183 IQ---------------PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNPKNLRALFGIYLC  234 (289)
T ss_pred             cC---------------CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhChHhHHHHHHHHHH
Confidence            43               12333444444444   344556778888888877666544555554443

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

Probab=96.24  E-value=0.36  Score=38.76  Aligned_cols=64  Identities=16%  Similarity=0.015  Sum_probs=49.0

Q ss_pred             CcchhHHH--HHHHHHHhcCCHHHHHHHHHhhcCCChhhH---HHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           93 NNDIFVGI--ALIDMYCKCGDVEKAQRVFWKMLRKDKFTW---TAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        93 ~~~~~~~~--~li~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +|.+..|+  .++..|=+.|+++.|....+.....++..+   -.-.+.+..+|++++|...+.+..+-
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~el  434 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQEL  434 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhc
Confidence            45544443  678888999999999999999987654443   34457889999999999999887653

>PRK15331 chaperone protein SicA; Provisional

Probab=96.15  E-value=0.1  Score=34.60  Aligned_cols=93  Identities=13%  Similarity=0.024  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC-CCChHHHHHhhhcc
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI-RRDEFTTVRILTTF   92 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~   92 (175)
                      ...-.....+-+.|++++|..+|..+.-   -|..-|..|..++-..+++++|+..|...-..+. .|.+..+       
T Consensus        38 e~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~-------  110 (165)
T PRK15331         38 DGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFF-------  110 (165)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccch-------
Confidence            3344455556689999999999998663   3556678888888888999999999988866543 3333333       


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                               ...+|...|+.+.|...|....+.
T Consensus       111 ---------agqC~l~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        111 ---------TGQCQLLMRKAAKARQCFELVNER  134 (165)
T ss_pred             ---------HHHHHHHhCCHHHHHHHHHHHHhC
Confidence                     888999999999999999988653

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

Probab=96.07  E-value=0.16  Score=41.98  Aligned_cols=103  Identities=12%  Similarity=0.157  Sum_probs=54.8

Q ss_pred             hcCChhHHHHHhhcCCC--CChhHHHHHHHH--HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHH
Q 045555           28 NRGQVDIARQYFAQMPE--RDYVLWTAMIDG--YLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALI  103 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~--~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li  103 (175)
                      ..+++..|.....++.+  ||.. |...+.+  ..+.|..++|..+++.....+..               |..+...+-
T Consensus        21 d~~qfkkal~~~~kllkk~Pn~~-~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~---------------D~~tLq~l~   84 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKHPNAL-YAKVLKALSLFRLGKGDEALKLLEALYGLKGT---------------DDLTLQFLQ   84 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHCCCcH-HHHHHHHHHHHHhcCchhHHHHHhhhccCCCC---------------chHHHHHHH
Confidence            34555556555555442  3332 3334444  34556666666665555443321               333445666


Q ss_pred             HHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCChhHH
Q 045555          104 DMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus       104 ~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a  146 (175)
                      ..|.+.+..++|..+|+....  |+......+..+|+|.+.+.+-
T Consensus        85 ~~y~d~~~~d~~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~q  129 (932)
T KOG2053|consen   85 NVYRDLGKLDEAVHLYERANQKYPSEELLYHLFMAYVREKSYKKQ  129 (932)
T ss_pred             HHHHHHhhhhHHHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666666633  4545555556666665555443

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

Probab=96.05  E-value=0.47  Score=36.35  Aligned_cols=140  Identities=6%  Similarity=-0.146  Sum_probs=87.3

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhH---HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVL---WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR---   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~---   87 (175)
                      -|.+....+..++...|+.++|...|++.+.-|..+   .....-.+.+.|+.+....+.+.+....- -....|..   
T Consensus       230 ~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~-~ta~~wfV~~~  308 (564)
T KOG1174|consen  230 CNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVK-YTASHWFVHAQ  308 (564)
T ss_pred             ccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhh-cchhhhhhhhh
Confidence            366778888888888999999999998766433222   11222223466777666666666644320 11111110   


Q ss_pred             ----------hhh------ccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHH
Q 045555           88 ----------ILT------TFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        88 ----------l~~------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~  147 (175)
                                .+.      ...| +...+..=...+...|+.++|.-.|.....  | +..+|.-++++|...|++.+|.
T Consensus       309 ~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~  388 (564)
T KOG1174|consen  309 LLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEAN  388 (564)
T ss_pred             hhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHH
Confidence                      000      1111 222333334566788999999999988743  4 7899999999999999999987


Q ss_pred             HHHHHHH
Q 045555          148 DMFSQML  154 (175)
Q Consensus       148 ~~~~~m~  154 (175)
                      -+-++..
T Consensus       389 ~~An~~~  395 (564)
T KOG1174|consen  389 ALANWTI  395 (564)
T ss_pred             HHHHHHH
Confidence            6655543

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.03  E-value=0.25  Score=35.86  Aligned_cols=30  Identities=23%  Similarity=0.411  Sum_probs=16.6

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      |...|-.|-..|...|+.+.|..-|.+..+
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~r  184 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALR  184 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence            444555555555555555555555555554

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

Probab=96.02  E-value=0.064  Score=38.80  Aligned_cols=103  Identities=16%  Similarity=0.283  Sum_probs=71.6

Q ss_pred             HHhhccC--CCcHHHHHHHHHHHHhc-----CChhHHHHHhhcCC----CCChhHHHHHHHHHhccC-------------
Q 045555            6 EIFGNMK--NKDVISWTTIVSGYINR-----GQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVN-------------   61 (175)
Q Consensus         6 ~~~~~m~--~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~-------------   61 (175)
                      ..|+..+  ++|-.+|-+.+..+...     +.++-....++.|+    ++|..+|+.||+.+-+..             
T Consensus        55 ~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~H  134 (406)
T KOG3941|consen   55 KQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLH  134 (406)
T ss_pred             hhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhh
Confidence            4555555  46788888888888654     33443333344444    479999999999987764             


Q ss_pred             ---ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCH-HHHHHHHHhh
Q 045555           62 ---RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDV-EKAQRVFWKM  122 (175)
Q Consensus        62 ---~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~  122 (175)
                         +-+=+++++++|...|+.||..+-              -.+++++++-+-. .+..++.-.|
T Consensus       135 YP~QQ~C~I~vLeqME~hGVmPdkE~e--------------~~lvn~FGr~~~p~~K~~Rm~yWm  185 (406)
T KOG3941|consen  135 YPQQQNCAIKVLEQMEWHGVMPDKEIE--------------DILVNAFGRWNFPTKKVKRMLYWM  185 (406)
T ss_pred             CchhhhHHHHHHHHHHHcCCCCchHHH--------------HHHHHHhccccccHHHHHHHHHhh
Confidence               235578999999999998887777              5677788766653 4455555555

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

Probab=95.95  E-value=0.14  Score=43.00  Aligned_cols=116  Identities=17%  Similarity=0.160  Sum_probs=85.4

Q ss_pred             CChhHHHHHhhcCCCCC---hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHH
Q 045555           30 GQVDIARQYFAQMPERD---YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      ++...|...|-+..+.|   ...|..|..-|+..-+...|...|+......               ..+...+..+.+.|
T Consensus       472 K~~~~al~ali~alrld~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD---------------atdaeaaaa~adty  536 (1238)
T KOG1127|consen  472 KNSALALHALIRALRLDVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD---------------ATDAEAAAASADTY  536 (1238)
T ss_pred             hhHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---------------chhhhhHHHHHHHh
Confidence            33666777776655533   3469999999988889999999999887743               23444556788888


Q ss_pred             HhcCCHHHHHHHHHhh------------------------------------c--CC-ChhhHHHHHHHHHhcCChhHHH
Q 045555          107 CKCGDVEKAQRVFWKM------------------------------------L--RK-DKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~------------------------------------~--~~-~~~~~~~li~~~~~~g~~~~a~  147 (175)
                      ++..+++.|..+.-..                                    .  .| |...|..+..+|...|++..|.
T Consensus       537 ae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~Al  616 (1238)
T KOG1127|consen  537 AEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHAL  616 (1238)
T ss_pred             hccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHH
Confidence            8888888887764332                                    0  11 6678999999999999999999


Q ss_pred             HHHHHHHHCCCCCcH
Q 045555          148 DMFSQMLRASIRLDE  162 (175)
Q Consensus       148 ~~~~~m~~~g~~p~~  162 (175)
                      ++|.+...  +.|+.
T Consensus       617 KvF~kAs~--LrP~s  629 (1238)
T KOG1127|consen  617 KVFTKASL--LRPLS  629 (1238)
T ss_pred             HhhhhhHh--cCcHh
Confidence            99988764  45654

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

Probab=95.75  E-value=0.69  Score=35.90  Aligned_cols=73  Identities=16%  Similarity=0.343  Sum_probs=52.8

Q ss_pred             HHhhccCC-C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCCh---hHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            6 EIFGNMKN-K-DVISWTTIVSGYINRGQVDIARQYFAQMPERDY---VLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         6 ~~~~~m~~-~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++-+.++. | |..+|-.|+..|...|..++.++++++|..|..   .+|..-|++=....+++.+..+|.+.+....
T Consensus        30 rLRerIkdNPtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~pfp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~l  107 (660)
T COG5107          30 RLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKSL  107 (660)
T ss_pred             HHHHHhhcCchhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCCccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhhc
Confidence            44445554 4 778999999999999999999999999998743   3466666655555666666666666655443

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.73  E-value=0.63  Score=35.28  Aligned_cols=144  Identities=11%  Similarity=0.094  Sum_probs=88.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCC-------ChhHHHHHHHHHhc---cCChHHHHHHHHHhHhCCCCCChHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLR---VNRFREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~-------~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      .+.-.++-+|-...+++...++++.+...       ...+--...-++-+   .|+.++|++++.++....-.+++.++.
T Consensus       142 div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~g  221 (374)
T PF13281_consen  142 DIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLG  221 (374)
T ss_pred             hHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHH
Confidence            33446666788889999999999998863       22222233445556   799999999999977766667777776


Q ss_pred             Hhhh----------------------------ccCcchhHHHHHHHHHHhcCC-HH---HHHHHH---Hhh--------c
Q 045555           87 RILT----------------------------TFNNDIFVGIALIDMYCKCGD-VE---KAQRVF---WKM--------L  123 (175)
Q Consensus        87 ~l~~----------------------------~~~~~~~~~~~li~~~~~~~~-~~---~a~~~~---~~~--------~  123 (175)
                      .+-.                            ...|+...--.+...+...|. .+   +..++-   ..+        .
T Consensus       222 L~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~  301 (374)
T PF13281_consen  222 LLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEK  301 (374)
T ss_pred             HHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccc
Confidence            5544                            112222221122222222222 11   112221   111        1


Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          124 RKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       124 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      ..+...+.+++.++.-.|+.++|.+..++|.... +|.
T Consensus       302 ~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~-~~~  338 (374)
T PF13281_consen  302 MQDYWDVATLLEASVLAGDYEKAIQAAEKAFKLK-PPA  338 (374)
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcC-Ccc
Confidence            1366678889999999999999999999998653 444

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.72  E-value=0.52  Score=34.26  Aligned_cols=106  Identities=14%  Similarity=0.134  Sum_probs=81.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccC---ChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVN---RFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      |...|-.|...|.+.|+.+.|..-|....+   +|...+..+..++....   ...++..+|++.++..           
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D-----------  223 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALD-----------  223 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-----------
Confidence            778899999999999999999999987653   67777777777665543   3678889999998854           


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHH
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIV  135 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~  135 (175)
                          +.+......|.-.+...|++.+|...|+.|.+  |....+..+|.
T Consensus       224 ----~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie  268 (287)
T COG4235         224 ----PANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIE  268 (287)
T ss_pred             ----CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence                34677777888888999999999999999854  33444544443

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=95.71  E-value=0.45  Score=38.93  Aligned_cols=123  Identities=16%  Similarity=0.159  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .|......+.+.+..++|...+.+...-   ....|......+...|.+.+|.+.|......  .|+             
T Consensus       652 lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~l--dP~-------------  716 (799)
T KOG4162|consen  652 LWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALAL--DPD-------------  716 (799)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhc--CCC-------------
Confidence            4666777788889999998888877753   4556777777788889999999999988874  344             


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHH--HHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQR--VFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~--~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ++..-+++..++.+.|+-..|..  +..++.+  | +...|-.+...+-+.|+.+.|.+.|....+
T Consensus       717 hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~q  782 (799)
T KOG4162|consen  717 HVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQ  782 (799)
T ss_pred             CcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHh
Confidence            33445789999999999888877  8888855  3 678999999999999999999999988765

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.69  E-value=0.77  Score=36.05  Aligned_cols=137  Identities=13%  Similarity=0.132  Sum_probs=90.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC-C---------ChhHHHHHHHHHhc----cCChHHHHHHHHHhHhCCCCCChHH
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE-R---------DYVLWTAMIDGYLR----VNRFREALTLFREMQTSNIRRDEFT   84 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~-~---------~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~   84 (175)
                      ...++...+-.|+-+.+++.+.+..+ +         -...|+..+..++-    ..+.+.|.+++..+.+.-  |+...
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~y--P~s~l  268 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRY--PNSAL  268 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhC--CCcHH
Confidence            44566666778888888888887554 2         22346666665554    456888999999998852  33333


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-------DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                      |             .-.-...+...|++++|.+.|+.....       ....+--+.-.+.-.++|++|.+.|.++.+..
T Consensus       269 f-------------l~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s  335 (468)
T PF10300_consen  269 F-------------LFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES  335 (468)
T ss_pred             H-------------HHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc
Confidence            3             123446678899999999999976431       22334445555777899999999999999853


Q ss_pred             CCCcHHHHHHHHhh
Q 045555          158 IRLDEVTYVGVLSA  171 (175)
Q Consensus       158 ~~p~~~t~~~ll~~  171 (175)
                       ..+.-+|..+..+
T Consensus       336 -~WSka~Y~Y~~a~  348 (468)
T PF10300_consen  336 -KWSKAFYAYLAAA  348 (468)
T ss_pred             -ccHHHHHHHHHHH
Confidence             2334444444333

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.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=95.69  E-value=0.035  Score=26.67  Aligned_cols=26  Identities=15%  Similarity=0.187  Sum_probs=19.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      +|+.|...|.+.|++++|.++|++.+
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            46778888888888888888888854

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=95.48  E-value=0.37  Score=30.94  Aligned_cols=131  Identities=8%  Similarity=0.051  Sum_probs=75.5

Q ss_pred             HHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh------ccCcchhH
Q 045555           26 YINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT------TFNNDIFV   98 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~------~~~~~~~~   98 (175)
                      +.-.|..++..++..+... .+..-+|-+|--....-+=+-..++++.+=+   -.|......+-+      ....+...
T Consensus        12 ~ildG~V~qGveii~k~v~Ssni~E~NWvICNiiDaa~C~yvv~~LdsIGk---iFDis~C~NlKrVi~C~~~~n~~se~   88 (161)
T PF09205_consen   12 RILDGDVKQGVEIIEKTVNSSNIKEYNWVICNIIDAADCDYVVETLDSIGK---IFDISKCGNLKRVIECYAKRNKLSEY   88 (161)
T ss_dssp             HHHTT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHHHHHGG---GS-GGG-S-THHHHHHHHHTT---HH
T ss_pred             HHHhchHHHHHHHHHHHcCcCCccccceeeeecchhhchhHHHHHHHHHhh---hcCchhhcchHHHHHHHHHhcchHHH
Confidence            3446777777787777654 3333444444333333333333333333321   111111100000      12334556


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhc---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKML---RKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  159 (175)
                      ....++.....|+-|.-.++..++.   ++++...-.+..+|.+.|+..++-+++++.-++|++
T Consensus        89 vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   89 VDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            6788899999999999999999986   467888888999999999999999999999999875

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.45  E-value=0.23  Score=38.86  Aligned_cols=106  Identities=13%  Similarity=0.065  Sum_probs=75.0

Q ss_pred             chHHHHhhccCC--CcHHHHHHH-HHHHHhcCChhHHHHHhhcCCCC-------ChhHHHHHHHHHhccCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN--KDVISWTTI-VSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~l-i~~~~~~~~~~~a~~~~~~m~~~-------~~~~~~~li~~~~~~~~~~~a~~~~~   71 (175)
                      ++|.++++.+.+  |+...|... .+.+...|++++|.+.|+.....       ....+--+.-.+.-..+|++|.+.|.
T Consensus       250 ~~a~~lL~~~~~~yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~  329 (468)
T PF10300_consen  250 EEAEELLEEMLKRYPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFL  329 (468)
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHH
Confidence            457788888876  877666533 35567789999999999975531       33345556667888899999999999


Q ss_pred             HhHhCCCCCChHHHHHhhhccCcchhHHHH-HHHHHHhcCCH-------HHHHHHHHhh
Q 045555           72 EMQTSNIRRDEFTTVRILTTFNNDIFVGIA-LIDMYCKCGDV-------EKAQRVFWKM  122 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~-li~~~~~~~~~-------~~a~~~~~~~  122 (175)
                      .+.+.+               .++..+|.. ...++...++.       ++|.++|.+.
T Consensus       330 ~L~~~s---------------~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~v  373 (468)
T PF10300_consen  330 RLLKES---------------KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKV  373 (468)
T ss_pred             HHHhcc---------------ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHH
Confidence            999864               223333333 33444667777       8899999887

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.44  E-value=0.34  Score=36.64  Aligned_cols=119  Identities=12%  Similarity=0.135  Sum_probs=85.0

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCC------------------CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChH
Q 045555           22 IVSGYINRGQVDIARQYFAQMPE------------------RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEF   83 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~   83 (175)
                      -.+.|.+.|++..|..-|+....                  .-...++.|..++.+.+++.+|+..-++.+..+..--..
T Consensus       214 ~Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KA  293 (397)
T KOG0543|consen  214 RGNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKA  293 (397)
T ss_pred             hhhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhH
Confidence            34567899999999999887432                  123468888899999999999999999998865322222


Q ss_pred             HHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChh-hHHHHHHHHHhcCCh-hHHHHHHHHHHH
Q 045555           84 TTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKF-TWTAMIVGLAISGHG-DTALDMFSQMLR  155 (175)
Q Consensus        84 ~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~-~~~~li~~~~~~g~~-~~a~~~~~~m~~  155 (175)
                      .|               .-..+|...|+++.|+..|+++.  +|+-. .-+.++..--+..+. ++..++|..|..
T Consensus       294 Ly---------------RrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  294 LY---------------RRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HH---------------HHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            23               57788999999999999999995  45333 334444444444433 445788888865

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.37  E-value=0.4  Score=30.71  Aligned_cols=122  Identities=16%  Similarity=0.192  Sum_probs=76.6

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      ...++..+.+.+.+.....+++.+...   +....+.++..|++.. .++.++.+..  .    ++...           
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~----~~~yd-----------   71 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN--K----SNHYD-----------   71 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh--c----cccCC-----------
Confidence            456778888888888888888876543   4557888888888764 3444454442  1    11111           


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhc-CChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAIS-GHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                         ...++..|.+.+.++++.-++..+..     |...+..+... ++++.|.+.+.+-      .+...|..++..|
T Consensus        72 ---~~~~~~~c~~~~l~~~~~~l~~k~~~-----~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~  135 (140)
T smart00299       72 ---IEKVGKLCEKAKLYEEAVELYKKDGN-----FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKAL  135 (140)
T ss_pred             ---HHHHHHHHHHcCcHHHHHHHHHhhcC-----HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHH
Confidence               13467777777777777777776532     33344444444 7788888777752      2555666666655

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=95.32  E-value=1.5  Score=36.86  Aligned_cols=144  Identities=12%  Similarity=0.020  Sum_probs=88.0

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC---
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLRVNRFREALTLFREMQTSN---   77 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---   77 (175)
                      ++|..+|++.+     -|..|-..|-..|.+++|.++-+.--+- -..||..-..-+-..++.+.|++.|++--..-   
T Consensus       817 EeA~~lYr~ck-----R~DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev  891 (1416)
T KOG3617|consen  817 EEALILYRQCK-----RYDLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEV  891 (1416)
T ss_pred             HHHHHHHHHHH-----HHHHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHH
Confidence            45555555554     3555666677777777777765543221 23456666666777788888888887653211   


Q ss_pred             ------CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------------------------CCh
Q 045555           78 ------IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------------------------KDK  127 (175)
Q Consensus        78 ------~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------------------------~~~  127 (175)
                            -.|...-|.    .-..|...|.-...-+...|+.|.|..++.....                        .|.
T Consensus       892 ~rmL~e~p~~~e~Yv----~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~C~qGk~~kAa~iA~esgd~  967 (1416)
T KOG3617|consen  892 FRMLKEYPKQIEQYV----RRKRDESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIKCIQGKTDKAARIAEESGDK  967 (1416)
T ss_pred             HHHHHhChHHHHHHH----HhccchHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeEeeccCchHHHHHHHhcccH
Confidence                  011111111    1223455677777777888999999888887521                        133


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      -..-.+.+.|-..|++.+|...|.+..
T Consensus       968 AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  968 AACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            445567777777778877777776653

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

Probab=95.28  E-value=1.5  Score=36.72  Aligned_cols=73  Identities=15%  Similarity=0.269  Sum_probs=41.0

Q ss_pred             hHHHHhhccCC--CcHHHHHHHHHHH--HhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN--KDVISWTTIVSGY--INRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~--~~~~~~~~li~~~--~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|....+.+.+  ||. .|...+.++  .|.|+.++|..+++....   .|..|..++-.+|...++.++|..+|++..+
T Consensus        27 kal~~~~kllkk~Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~  105 (932)
T KOG2053|consen   27 KALAKLGKLLKKHPNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQ  105 (932)
T ss_pred             HHHHHHHHHHHHCCCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence            34444444433  443 233333333  356666666666665543   2556666666666666777777776666655


Q ss_pred             C
Q 045555           76 S   76 (175)
Q Consensus        76 ~   76 (175)
                      .
T Consensus       106 ~  106 (932)
T KOG2053|consen  106 K  106 (932)
T ss_pred             h
Confidence            4

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=95.20  E-value=0.057  Score=25.93  Aligned_cols=26  Identities=8%  Similarity=0.184  Sum_probs=20.1

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhH
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +|+.|...|.+.|++++|+++|++.+
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            46778888888888888888888854

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=95.08  E-value=1.3  Score=36.46  Aligned_cols=140  Identities=15%  Similarity=0.200  Sum_probs=90.9

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      .|...|..+--++...|+++.+.+.|++...   .....|+.+-.++.-.|.-..|+.+.++-......|+..+-..+..
T Consensus       321 nd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmas  400 (799)
T KOG4162|consen  321 NDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMAS  400 (799)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHH
Confidence            3667777888888888888888888887654   2344577777777777777777777776655443343333222222


Q ss_pred             --------------------------------------------------------------------------ccCcch
Q 045555           91 --------------------------------------------------------------------------TFNNDI   96 (175)
Q Consensus        91 --------------------------------------------------------------------------~~~~~~   96 (175)
                                                                                                .-.|+.
T Consensus       401 klc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~  480 (799)
T KOG4162|consen  401 KLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLV  480 (799)
T ss_pred             HHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchH
Confidence                                                                                      223333


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcC----CChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLR----KDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..|  +---|+..++++.|.+..++..+    .+...|..+.-.+...+++.+|.++.+...+
T Consensus       481 if~--lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~  541 (799)
T KOG4162|consen  481 IFY--LALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALE  541 (799)
T ss_pred             HHH--HHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            333  33345667778888777777632    3677888888888888888888888776654

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

Probab=95.06  E-value=2  Score=36.96  Aligned_cols=152  Identities=11%  Similarity=0.116  Sum_probs=105.3

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCC-CCChh-----H------------------HH---------HHHHHHhcc
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMP-ERDYV-----L------------------WT---------AMIDGYLRV   60 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~-~~~~~-----~------------------~~---------~li~~~~~~   60 (175)
                      .|+...+..+.++.-.+-+.+-.++++++. +++..     .                  |-         .+...+...
T Consensus       982 ~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAikad~trVm~YI~rLdnyDa~~ia~iai~~ 1061 (1666)
T KOG0985|consen  982 QDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIAEIAIEN 1061 (1666)
T ss_pred             CChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhhcChHHHHHHHHHhccCCchhHHHHHhhh
Confidence            477778888888989999999999998865 21110     0                  11         122234455


Q ss_pred             CChHHHHHHHHHhHhCCCCCChHHHHHhhh------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChh
Q 045555           61 NRFREALTLFREMQTSNIRRDEFTTVRILT------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKF  128 (175)
Q Consensus        61 ~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~  128 (175)
                      +-+++|.++|++.--.     ......++.            .-.....+|+.+..+-.+.|.+.+|.+-|-+.  .|+.
T Consensus      1062 ~LyEEAF~ifkkf~~n-----~~A~~VLie~i~~ldRA~efAe~~n~p~vWsqlakAQL~~~~v~dAieSyika--dDps 1134 (1666)
T KOG0985|consen 1062 QLYEEAFAIFKKFDMN-----VSAIQVLIENIGSLDRAYEFAERCNEPAVWSQLAKAQLQGGLVKDAIESYIKA--DDPS 1134 (1666)
T ss_pred             hHHHHHHHHHHHhccc-----HHHHHHHHHHhhhHHHHHHHHHhhCChHHHHHHHHHHHhcCchHHHHHHHHhc--CCcH
Confidence            6678888888776332     233333333            11234678999999999999999998887653  4667


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      .|..++....+.|.+++-.+.+.-..++.-+|...+  .||-||++
T Consensus      1135 ~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~AyAk 1178 (1666)
T KOG0985|consen 1135 NYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFAYAK 1178 (1666)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHHHHH
Confidence            899999999999999999999888887777776543  45555543

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=94.91  E-value=1.2  Score=33.52  Aligned_cols=141  Identities=13%  Similarity=0.014  Sum_probs=91.6

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHH----H
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTT----V   86 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~----~   86 (175)
                      .|+..+..-..+|...|.+..|+.=+....   ..+.-++..+-..+...|+.+.++...++.++.  .||.-..    -
T Consensus       187 Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~~YK  264 (504)
T KOG0624|consen  187 WDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFPFYK  264 (504)
T ss_pred             chhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHHHHH
Confidence            367777778888888899888877666544   345556666677777888888888888888774  4544322    1


Q ss_pred             Hhhh----------------------------ccCcc-----hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhH
Q 045555           87 RILT----------------------------TFNND-----IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTW  130 (175)
Q Consensus        87 ~l~~----------------------------~~~~~-----~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~  130 (175)
                      .+-+                            ...|.     ...+-.+-.+|...+.+.+|.+...+..+  | |+.++
T Consensus       265 klkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l  344 (504)
T KOG0624|consen  265 KLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVL  344 (504)
T ss_pred             HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcCchHHHHH
Confidence            1111                            12222     12233455666777777777777777643  3 46667


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          131 TAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       131 ~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .--..+|.....++.|..-|+...+.
T Consensus       345 ~dRAeA~l~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  345 CDRAEAYLGDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHHhc
Confidence            66777777777777777777776653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.90  E-value=0.46  Score=40.20  Aligned_cols=127  Identities=9%  Similarity=-0.022  Sum_probs=87.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-------C--ChhHHHHHHHHHhccCChHHHHHHHHHhHhC----CCCCChHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFREMQTS----NIRRDEFT   84 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~   84 (175)
                      +.+.+...+...|++++|...+.+...       +  -..+...+...+...|++++|...+++....    +. ++.. 
T Consensus       493 a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~-~~~~-  570 (903)
T PRK04841        493 ATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHL-EQLP-  570 (903)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc-cccc-
Confidence            456666777889999999999887652       1  1234556667788899999999998887663    11 1100 


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------C--ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------K--DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                               .....+..+...+...|++++|...+.+...      +  ....+..+...+...|+.++|.+.+.+...
T Consensus       571 ---------~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~  640 (903)
T PRK04841        571 ---------MHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLEN  640 (903)
T ss_pred             ---------HHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                     0112234566667778999999999888632      1  133444566678889999999999888754

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

Probab=94.89  E-value=1.5  Score=34.87  Aligned_cols=136  Identities=15%  Similarity=0.122  Sum_probs=98.5

Q ss_pred             chHHHHhhccCC----C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhH-HHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN----K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVL-WTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~-~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      .-|+.+|.+..+    + ++.+.+++|..||. ++.+-|..+|+--.+  +|... -...+.-++..++-..+..+|+..
T Consensus       383 kaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrIFeLGLkkf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~  461 (656)
T KOG1914|consen  383 KAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRIFELGLKKFGDSPEYVLKYLDFLSHLNDDNNARALFERV  461 (656)
T ss_pred             HHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHHHHHHHHhcCCChHHHHHHHHHHHHhCcchhHHHHHHHH
Confidence            457888888876    3 77889999999974 667899999996443  45444 356777888999999999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------CChhhHHHHHHHHHhcCChhHH
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-------KDKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~~~~~~~~li~~~~~~g~~~~a  146 (175)
                      +..++.|+.            +..+|..+++--+..|++..+.++-+.+..       +....-..+++-|.-.+.+.--
T Consensus       462 l~s~l~~~k------------s~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~~c~  529 (656)
T KOG1914|consen  462 LTSVLSADK------------SKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLYPCS  529 (656)
T ss_pred             HhccCChhh------------hHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhccccccc
Confidence            998665552            345789999999999999999888887732       2223444555666555555444


Q ss_pred             HHHH
Q 045555          147 LDMF  150 (175)
Q Consensus       147 ~~~~  150 (175)
                      ..-+
T Consensus       530 ~~el  533 (656)
T KOG1914|consen  530 LDEL  533 (656)
T ss_pred             HHHH
Confidence            3333

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=94.87  E-value=0.94  Score=32.25  Aligned_cols=82  Identities=18%  Similarity=0.195  Sum_probs=55.6

Q ss_pred             CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           45 RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        45 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .+...+......+.+.|++++|++.|+++......+.....            ..-.+..+|-+.+++++|...|+...+
T Consensus        30 ~~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~------------a~l~la~ayy~~~~y~~A~~~~e~fi~   97 (243)
T PRK10866         30 NPPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQ------------VQLDLIYAYYKNADLPLAQAAIDRFIR   97 (243)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHH------------HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            35554555666778899999999999999986543322211            112588899999999999999999854


Q ss_pred             --CC--hhhHHHHHHHHH
Q 045555          125 --KD--KFTWTAMIVGLA  138 (175)
Q Consensus       125 --~~--~~~~~~li~~~~  138 (175)
                        |+  -.-|...+.+.+
T Consensus        98 ~~P~~~~~~~a~Y~~g~~  115 (243)
T PRK10866         98 LNPTHPNIDYVLYMRGLT  115 (243)
T ss_pred             hCcCCCchHHHHHHHHHh
Confidence              32  223444455443

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

Probab=94.75  E-value=0.3  Score=35.39  Aligned_cols=70  Identities=17%  Similarity=0.283  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh-----CCCCCChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT-----SNIRRDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~   85 (175)
                      ..++..++..+...|+.+.+.+.++.+.+  | +...|..+|.+|.+.|+...|+..|+++.+     .|+.|...+.
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~  230 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELR  230 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHH
Confidence            34677788888899999999999998875  3 777899999999999999999999999977     4666665544

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.72  E-value=0.61  Score=30.23  Aligned_cols=61  Identities=10%  Similarity=0.084  Sum_probs=46.6

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRK------DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ....|+.-..+ .+.|++++|.+.|+.+..+      ....--.++.+|.+.|++++|...+++.++.
T Consensus        10 ~~~ly~~a~~~-l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL   76 (142)
T PF13512_consen   10 PQELYQEAQEA-LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL   76 (142)
T ss_pred             HHHHHHHHHHH-HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            34445544444 4589999999999999553      4456677889999999999999999998875

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

Probab=94.72  E-value=0.75  Score=37.56  Aligned_cols=63  Identities=16%  Similarity=0.174  Sum_probs=50.7

Q ss_pred             HHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           21 TIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        21 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      .+...+.+.|-...|..+|++.     ..|.-+|.+|+..|+..+|..+..+-.+  -.|++.-|..+-.
T Consensus       403 ~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGD  465 (777)
T KOG1128|consen  403 LLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGD  465 (777)
T ss_pred             HHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhh
Confidence            4566677888889999998875     4688888999999999999999988887  4677777766555

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=94.70  E-value=0.61  Score=38.15  Aligned_cols=143  Identities=10%  Similarity=0.090  Sum_probs=79.5

Q ss_pred             CchHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-----ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            1 MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPER-----DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         1 ~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      |+||.+++-++.++|.     -|..+.+.|++-...++++.-...     -...|+.+...+.....|++|.+.|..-..
T Consensus       750 feeaek~yld~drrDL-----Aielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~  824 (1189)
T KOG2041|consen  750 FEEAEKLYLDADRRDL-----AIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD  824 (1189)
T ss_pred             hhHhhhhhhccchhhh-----hHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            4677777777776544     356667778887777777654432     123566666666666666666666655432


Q ss_pred             CCCCCChHHHH-------HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHH
Q 045555           76 SNIRRDEFTTV-------RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALD  148 (175)
Q Consensus        76 ~~~~p~~~~~~-------~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~  148 (175)
                      ..-..+..-..       .+....+.+....-.+.+++.+.|.-++|.+.|-.-..|.     .-+..|...++|.+|.+
T Consensus       825 ~e~~~ecly~le~f~~LE~la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~pk-----aAv~tCv~LnQW~~ave  899 (1189)
T KOG2041|consen  825 TENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRSLPK-----AAVHTCVELNQWGEAVE  899 (1189)
T ss_pred             hHhHHHHHHHHHhhhhHHHHHHhcCcccchHHHHHHHHHhhchHHHHHHHHHhccCcH-----HHHHHHHHHHHHHHHHH
Confidence            21100000000       0111223344555567777777777777777666544442     23455666667777776


Q ss_pred             HHHHH
Q 045555          149 MFSQM  153 (175)
Q Consensus       149 ~~~~m  153 (175)
                      +-+..
T Consensus       900 laq~~  904 (1189)
T KOG2041|consen  900 LAQRF  904 (1189)
T ss_pred             HHHhc
Confidence            65554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=94.67  E-value=0.63  Score=38.84  Aligned_cols=117  Identities=17%  Similarity=0.177  Sum_probs=78.0

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-----------Ch-hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCC
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPER-----------DY-VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRD   81 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----------~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~   81 (175)
                      ++-..|..|...|.+..+.+-|.-.+..|...           |. -+-....-.-.+.|.+++|..+|++.++..    
T Consensus       755 kS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~e~eakvAvLAieLgMlEeA~~lYr~ckR~D----  830 (1416)
T KOG3617|consen  755 KSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGEEDEAKVAVLAIELGMLEEALILYRQCKRYD----  830 (1416)
T ss_pred             hhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCcchhhHHHHHHHHHhhHHHHHHHHHHHHHHH----
Confidence            35568899999999998888888888877631           11 111122222356788899999999888854    


Q ss_pred             hHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           82 EFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        82 ~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                                         .|=+.|...|+|++|.++-+.-.+- =-.||......+-..++.+.|++.|++-
T Consensus       831 -------------------LlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~  884 (1416)
T KOG3617|consen  831 -------------------LLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKA  884 (1416)
T ss_pred             -------------------HHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhc
Confidence                               4566677888888888877654221 1235555556666667777777777653

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=94.62  E-value=0.18  Score=25.33  Aligned_cols=28  Identities=21%  Similarity=0.347  Sum_probs=18.2

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +|..+...|.+.|++++|.++|++.++.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4555666666677777777777666653

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=94.61  E-value=0.88  Score=30.71  Aligned_cols=93  Identities=14%  Similarity=0.150  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---  124 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---  124 (175)
                      ..+..+...|++.|+.++|++.|.++......|....            .++-.+|......+++..+.....+...   
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~i------------d~~l~~irv~i~~~d~~~v~~~i~ka~~~~~  104 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKI------------DMCLNVIRVAIFFGDWSHVEKYIEKAESLIE  104 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHH------------HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHh
Confidence            3577888888888888888888888877654433222            2344678888888888888777777632   


Q ss_pred             -C-Ch------hhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          125 -K-DK------FTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       125 -~-~~------~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                       . |.      .+|..+  .+...|++.+|.+.|-+..
T Consensus       105 ~~~d~~~~nrlk~~~gL--~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  105 KGGDWERRNRLKVYEGL--ANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             ccchHHHHHHHHHHHHH--HHHHhchHHHHHHHHHccC
Confidence             1 11      122222  2234678999988887765

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.

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=94.09  E-value=2.2  Score=33.55  Aligned_cols=75  Identities=17%  Similarity=0.215  Sum_probs=54.7

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---C
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---K  125 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~  125 (175)
                      +-..|..++-+.|+.++|++.+++|.+....-|             ...+.-.|++++...++++++..++.+..+   |
T Consensus       261 ~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~-------------~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lp  327 (539)
T PF04184_consen  261 AKRRLAMCARKLGRLREAIKMFRDLLKEFPNLD-------------NLNIRENLIEALLELQAYADVQALLAKYDDISLP  327 (539)
T ss_pred             hHHHHHHHHHHhCChHHHHHHHHHHHhhCCccc-------------hhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCC
Confidence            334566677888999999999999988642111             122446799999999999999999998753   2


Q ss_pred             --ChhhHHHHHHH
Q 045555          126 --DKFTWTAMIVG  136 (175)
Q Consensus       126 --~~~~~~~li~~  136 (175)
                        -..+|+..+--
T Consensus       328 kSAti~YTaALLk  340 (539)
T PF04184_consen  328 KSATICYTAALLK  340 (539)
T ss_pred             chHHHHHHHHHHH
Confidence              35677775543

The molecular function of this protein is uncertain.

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=93.98  E-value=0.98  Score=30.50  Aligned_cols=99  Identities=11%  Similarity=0.165  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCCC------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      ...+..+...|.+.|+.+.|.+.|.++++.      -...+-.+|......++|..+.....+....--.+.....    
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~----  111 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWER----  111 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHH----
Confidence            357889999999999999999999999874      2235678888899999999999988888765333221111    


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                         .+-..+|..|..  ...+++..|-+.|-+..
T Consensus       112 ---~nrlk~~~gL~~--l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  112 ---RNRLKVYEGLAN--LAQRDFKEAAELFLDSL  140 (177)
T ss_pred             ---HHHHHHHHHHHH--HHhchHHHHHHHHHccC
Confidence               111223333332  34679999998888873

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.97  E-value=0.66  Score=35.94  Aligned_cols=135  Identities=9%  Similarity=0.209  Sum_probs=80.5

Q ss_pred             chHHHHhhccCC---Cc------HHHHHHHHHHHHhcCChhHHHHHhhcCCCC-ChhHHHHHHHH--HhccCChHHHHHH
Q 045555            2 GFALEIFGNMKN---KD------VISWTTIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDG--YLRVNRFREALTL   69 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~li~~--~~~~~~~~~a~~~   69 (175)
                      ++|.++|.+..+   .+      .+.-+-++++|.. .+.+..........+. ....|-.|..+  +.+.+++++|++.
T Consensus        23 ~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~Y~~k~~~kal~~  101 (549)
T PF07079_consen   23 QESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQFGKSAYLPLFKALVAYKQKEYRKALQA  101 (549)
T ss_pred             hHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhhhHHHHHHH
Confidence            456666666653   12      2334566677654 3344444444444331 13334455444  3567888999888


Q ss_pred             HHHhHhC--CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--------ChhhHHHHHHHHHh
Q 045555           70 FREMQTS--NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--------DKFTWTAMIVGLAI  139 (175)
Q Consensus        70 ~~~m~~~--~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~li~~~~~  139 (175)
                      +......  +-.|.....  =+....+|-..-+..++++.+.|++.++..+++.+.+.        +..+||-.+-.+++
T Consensus       102 ls~w~~~~~~~~~~~Ld~--ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsr  179 (549)
T PF07079_consen  102 LSVWKEQIKGTESPWLDT--NIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSR  179 (549)
T ss_pred             HHHHHhhhcccccchhhh--hHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhH
Confidence            8887765  333322211  12223445556678899999999999999999998542        77788875555544

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.91  E-value=0.84  Score=32.77  Aligned_cols=94  Identities=11%  Similarity=0.123  Sum_probs=72.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      .|+.-+..| +.|++..|...|....+  |    ..-.+.-|..++...|++++|..+|..+.+.-....          
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~----------  212 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSP----------  212 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCC----------
Confidence            577766665 78889999999998775  3    333577899999999999999999999988643211          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        ..+...--|..+..+.|+.++|..+|.++.+
T Consensus       213 --KApdallKlg~~~~~l~~~d~A~atl~qv~k  243 (262)
T COG1729         213 --KAPDALLKLGVSLGRLGNTDEACATLQQVIK  243 (262)
T ss_pred             --CChHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence              1112223588888999999999999999865

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.83  E-value=1.1  Score=38.66  Aligned_cols=104  Identities=16%  Similarity=0.174  Sum_probs=62.4

Q ss_pred             hcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHH
Q 045555           28 NRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYC  107 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~  107 (175)
                      +.|.+.+|+.+|.-=.+.-...|.+....+.+...+++|--.|+..-+.                       .-.+.+|.
T Consensus       920 kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl-----------------------ekAl~a~~  976 (1265)
T KOG1920|consen  920 KHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL-----------------------EKALKAYK  976 (1265)
T ss_pred             hcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH-----------------------HHHHHHHH
Confidence            3344444444333322223344556666666777788877777666443                       24677888


Q ss_pred             hcCCHHHHHHHHHhhcCCChhhH---HHHHHHHHhcCChhHHHHHHHHHH
Q 045555          108 KCGDVEKAQRVFWKMLRKDKFTW---TAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       108 ~~~~~~~a~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      .+|+|.+|..+-..+..+-...-   ..|+.-+...++.-+|-++..+..
T Consensus       977 ~~~dWr~~l~~a~ql~~~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~ 1026 (1265)
T KOG1920|consen  977 ECGDWREALSLAAQLSEGKDELVILAEELVSRLVEQRKHYEAAKILLEYL 1026 (1265)
T ss_pred             HhccHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHcccchhHHHHHHHHh
Confidence            88888888888887755432222   556666666666666666666554

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=93.80  E-value=1.3  Score=34.93  Aligned_cols=134  Identities=16%  Similarity=0.172  Sum_probs=88.1

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCC----CChh-------------------------HHHHHHHHHhccCChHHHHHHHHH
Q 045555           22 IVSGYINRGQVDIARQYFAQMPE----RDYV-------------------------LWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~----~~~~-------------------------~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      +...|.+.++++.+...|++...    |+..                         -.-.=.+.+.+.|++..|+..|.+
T Consensus       304 ~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~Yte  383 (539)
T KOG0548|consen  304 LGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTE  383 (539)
T ss_pred             hhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHH
Confidence            44466777888888888887542    1110                         011114557788999999999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChh---hHHHHHHHHHhcCChhHHHHH
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKF---TWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~li~~~~~~g~~~~a~~~  149 (175)
                      +++..  |             .|...|....-+|.+.|.+..|.+--+.-.+.+..   -|.-=..++....++++|.+.
T Consensus       384 AIkr~--P-------------~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAlea  448 (539)
T KOG0548|consen  384 AIKRD--P-------------EDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEA  448 (539)
T ss_pred             HHhcC--C-------------chhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            98865  3             35566788889999999999988877766554333   232223344456678888888


Q ss_pred             HHHHHHCCCCCcHHHHHHHHhhh
Q 045555          150 FSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       150 ~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      |.+-++.  .|+..-+..-+.-|
T Consensus       449 y~eale~--dp~~~e~~~~~~rc  469 (539)
T KOG0548|consen  449 YQEALEL--DPSNAEAIDGYRRC  469 (539)
T ss_pred             HHHHHhc--CchhHHHHHHHHHH
Confidence            8887765  36554444444333

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=93.70  E-value=1.7  Score=33.86  Aligned_cols=111  Identities=16%  Similarity=0.188  Sum_probs=56.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---------------------CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---------------------RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      .-.+.++..+-+.|.++.|+++-..-..                     ++...|..|.....+.|+++-|.+.|.+...
T Consensus       296 ~~~~~i~~fL~~~G~~e~AL~~~~D~~~rFeLAl~lg~L~~A~~~a~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d  375 (443)
T PF04053_consen  296 DQGQSIARFLEKKGYPELALQFVTDPDHRFELALQLGNLDIALEIAKELDDPEKWKQLGDEALRQGNIELAEECYQKAKD  375 (443)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHSS-HHHHHHHHHHCT-HHHHHHHCCCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT-
T ss_pred             hHHHHHHHHHHHCCCHHHHHhhcCChHHHhHHHHhcCCHHHHHHHHHhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC
Confidence            3478888888888888888887654210                     1334455555555555555555555555443


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      .                       ..|+-.|.-.|+.+.-.++-+.....  .-+|.-..++...|+.++..+++.+
T Consensus       376 ~-----------------------~~L~lLy~~~g~~~~L~kl~~~a~~~--~~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  376 F-----------------------SGLLLLYSSTGDREKLSKLAKIAEER--GDINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             H-----------------------HHHHHHHHHCT-HHHHHHHHHHHHHT--T-HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             c-----------------------cccHHHHHHhCCHHHHHHHHHHHHHc--cCHHHHHHHHHHcCCHHHHHHHHHH
Confidence            2                       23444444444444444443333221  1245555555555666666655544

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=93.65  E-value=1.4  Score=29.47  Aligned_cols=125  Identities=14%  Similarity=0.073  Sum_probs=82.6

Q ss_pred             CCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhC-CCCCChHHHHHhhh
Q 045555           12 KNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTS-NIRRDEFTTVRILT   90 (175)
Q Consensus        12 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~   90 (175)
                      ..|+...+..++..+.+.|.+..-..+.+--.=+|...-...+-.+.  +....+..+--+|.+. +.            
T Consensus        25 i~~~~~L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkRL~~------------   90 (167)
T PF07035_consen   25 IPVQHELYELLIDLLIRNGQFSQLHQLLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKRLGT------------   90 (167)
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHHhhh------------
Confidence            34778889999999999999888888777655444333232222222  2233444444444332 10            


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                             .+..+++.+-..|++-+|.++.+....-+...-..++++-.+.+|...-..+|+-..+++
T Consensus        91 -------~~~~iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~n  150 (167)
T PF07035_consen   91 -------AYEEIIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQLFYAVFRFFEERN  150 (167)
T ss_pred             -------hHHHHHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence                   124688899999999999999988755555556778888888888877777777766644

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=93.53  E-value=0.23  Score=24.16  Aligned_cols=28  Identities=14%  Similarity=0.260  Sum_probs=20.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .+++.+...|...|++++|.+++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4677778888888888888888877654

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.52  E-value=0.23  Score=24.88  Aligned_cols=36  Identities=28%  Similarity=0.517  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAM  133 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l  133 (175)
                      ++..+...|.+.|++++|.++|+...+  | |...|..+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~L   41 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHh
Confidence            456789999999999999999999965  3 44444443

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=93.45  E-value=0.76  Score=36.08  Aligned_cols=99  Identities=16%  Similarity=0.118  Sum_probs=76.1

Q ss_pred             HHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHH
Q 045555           24 SGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGI  100 (175)
Q Consensus        24 ~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  100 (175)
                      +..+..|+++.|..+|-...   ++|.+.|+.-..+|...|++++|+.=-.+-++.  .|+             ...-|+
T Consensus        10 naa~s~~d~~~ai~~~t~ai~l~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l--~p~-------------w~kgy~   74 (539)
T KOG0548|consen   10 NAAFSSGDFETAIRLFTEAIMLSPTNHVLYSNRSAAYASLGSYEKALKDATKTRRL--NPD-------------WAKGYS   74 (539)
T ss_pred             HhhcccccHHHHHHHHHHHHccCCCccchhcchHHHHHHHhhHHHHHHHHHHHHhc--CCc-------------hhhHHH
Confidence            45568899999999998754   358888999999999999999998877777763  333             234567


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHH
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGL  137 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~  137 (175)
                      ....++.-.|++++|..-|.+=.+  | +...++-+..++
T Consensus        75 r~Gaa~~~lg~~~eA~~ay~~GL~~d~~n~~L~~gl~~a~  114 (539)
T KOG0548|consen   75 RKGAALFGLGDYEEAILAYSEGLEKDPSNKQLKTGLAQAY  114 (539)
T ss_pred             HhHHHHHhcccHHHHHHHHHHHhhcCCchHHHHHhHHHhh
Confidence            888888889999999999988754  3 455666666665

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.45  E-value=1.5  Score=34.07  Aligned_cols=131  Identities=10%  Similarity=0.117  Sum_probs=83.9

Q ss_pred             HHhcCChhHHHHHhhcCCCC---C------hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch
Q 045555           26 YINRGQVDIARQYFAQMPER---D------YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDI   96 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~~---~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~   96 (175)
                      +-+.+++.+|..+|.++-..   +      .+.-+-++++|... +.+.....+.++.+..  | ...|.          
T Consensus        16 Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~~--~-~s~~l----------   81 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQF--G-KSAYL----------   81 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHhc--C-CchHH----------
Confidence            34789999999999987641   1      33456777777654 4555555555555532  1 11221          


Q ss_pred             hHHHHHHHHH--HhcCCHHHHHHHHHhhcCC------------------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           97 FVGIALIDMY--CKCGDVEKAQRVFWKMLRK------------------DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        97 ~~~~~li~~~--~~~~~~~~a~~~~~~~~~~------------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                          .+..+.  -+.+.+.+|.+.+..-.+.                  |...=+..++++...|++.++..++++|.++
T Consensus        82 ----~LF~~L~~Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~  157 (549)
T PF07079_consen   82 ----PLFKALVAYKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIER  157 (549)
T ss_pred             ----HHHHHHHHHHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHH
Confidence                222222  3567777777666554221                  2233356778888999999999999998876


Q ss_pred             CCC----CcHHHHHHHHhhhcC
Q 045555          157 SIR----LDEVTYVGVLSACTH  174 (175)
Q Consensus       157 g~~----p~~~t~~~ll~~~~~  174 (175)
                      =++    .|..+|+-++-.++|
T Consensus       158 llkrE~~w~~d~yd~~vlmlsr  179 (549)
T PF07079_consen  158 LLKRECEWNSDMYDRAVLMLSR  179 (549)
T ss_pred             HhhhhhcccHHHHHHHHHHHhH
Confidence            555    899999886666555

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=93.44  E-value=4.4  Score=34.49  Aligned_cols=125  Identities=14%  Similarity=0.055  Sum_probs=84.7

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCC----CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           22 IVSGYINRGQVDIARQYFAQMPE----RDY----VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      +...+...|++++|...++...+    .+.    ...+.+...+...|++++|...+++.....-.....         .
T Consensus       458 ~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~---------~  528 (903)
T PRK04841        458 RAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVY---------H  528 (903)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcch---------H
Confidence            34456689999999998887542    222    245666667788999999999999987632111100         0


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-------K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +.......+...+...|+++.|.+.+.+...       +    ....+..+...+...|++++|...+.+...
T Consensus       529 ~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~  601 (903)
T PRK04841        529 YALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLE  601 (903)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHH
Confidence            1122345677788899999999999887632       1    122344455667778999999999988765

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=93.07  E-value=2.9  Score=31.49  Aligned_cols=122  Identities=13%  Similarity=0.133  Sum_probs=89.2

Q ss_pred             HHHHhcCChhHHHHHhhcCCC--CCh----------------hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHH
Q 045555           24 SGYINRGQVDIARQYFAQMPE--RDY----------------VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTT   85 (175)
Q Consensus        24 ~~~~~~~~~~~a~~~~~~m~~--~~~----------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~   85 (175)
                      ..+.+.|.+++|..=|+....  |+.                ......+..+.-.|+...|++...+++.-         
T Consensus       114 ~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi---------  184 (504)
T KOG0624|consen  114 VVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI---------  184 (504)
T ss_pred             hhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc---------
Confidence            346688999999888887663  210                11223344566677778888877777764         


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                            .++|...+..-.++|...|++..|..=++...+   .++...--+-..+..-|+.+.++...++-++  +.||.
T Consensus       185 ------~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpdH  256 (504)
T KOG0624|consen  185 ------QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPDH  256 (504)
T ss_pred             ------CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcch
Confidence                  356788888999999999999999887777643   4666777777788889999999998888775  45654

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=93.02  E-value=1.6  Score=28.32  Aligned_cols=66  Identities=9%  Similarity=0.133  Sum_probs=51.1

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCCC------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHH
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTT   85 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~   85 (175)
                      -.-.....+.|++++|.+.|+.+..+      ....--.|+.+|.+.+++++|...+++.++......-+.|
T Consensus        14 y~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdY   85 (142)
T PF13512_consen   14 YQEAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDY   85 (142)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccH
Confidence            33344455899999999999998852      3455678899999999999999999999997654333333

>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=92.93  E-value=0.055  Score=34.87  Aligned_cols=108  Identities=16%  Similarity=0.189  Sum_probs=67.0

Q ss_pred             HHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC------
Q 045555           52 AMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK------  125 (175)
Q Consensus        52 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------  125 (175)
                      .++..+.+.+.++.....++.+...+...              +....+.++..|++.++.++..++++....=      
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~--------------~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~yd~~~~~   77 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKEN--------------NPDLHTLLLELYIKYDPYEKLLEFLKTSNNYDLDKAL   77 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC---------------SHHHHHHHHHHHHCTTTCCHHHHTTTSSSSS-CTHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhccccc--------------CHHHHHHHHHHHHhcCCchHHHHHcccccccCHHHHH
Confidence            35667777888888888888888765332              3445588999999999889998888854221      


Q ss_pred             ----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH-------CCCCCcHHHHHHHHhhhc
Q 045555          126 ----DKFTWTAMIVGLAISGHGDTALDMFSQMLR-------ASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       126 ----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-------~g~~p~~~t~~~ll~~~~  173 (175)
                          ....|...+-.|.+.|++++|.+++.++..       ..-.+|...|..+++.|-
T Consensus        78 ~~c~~~~l~~~a~~Ly~~~~~~~~al~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l  136 (143)
T PF00637_consen   78 RLCEKHGLYEEAVYLYSKLGNHDEALEILHKLKDYEEAIEYAKKVDDPELWEQLLKYCL  136 (143)
T ss_dssp             HHHHTTTSHHHHHHHHHCCTTHTTCSSTSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHC
T ss_pred             HHHHhcchHHHHHHHHHHcccHHHHHHHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence                223455555566666666666554322211       011245667777766654

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.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.88  E-value=1.4  Score=36.27  Aligned_cols=109  Identities=16%  Similarity=0.185  Sum_probs=86.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF   97 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~   97 (175)
                      +.+-.+.-++..|+..+|.++-.+.+-||-..|-.=+.+++..++|++-.++-..++.      +..             
T Consensus       686 Sl~dTv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskks------PIG-------------  746 (829)
T KOG2280|consen  686 SLHDTVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKKS------PIG-------------  746 (829)
T ss_pred             cHHHHHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccCC------CCC-------------
Confidence            4566677788899999999999999999999999999999999999887666554432      112             


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                       |.-.+.+|.+.|+.++|.+.+-....-     .-.+.+|.+.|++.+|.++--
T Consensus       747 -y~PFVe~c~~~~n~~EA~KYiprv~~l-----~ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  747 -YLPFVEACLKQGNKDEAKKYIPRVGGL-----QEKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             -chhHHHHHHhcccHHHHhhhhhccCCh-----HHHHHHHHHhccHHHHHHHHH
Confidence             245788999999999999988765322     267889999999999877643

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.69  E-value=1.7  Score=27.76  Aligned_cols=96  Identities=15%  Similarity=0.152  Sum_probs=55.3

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      +...+|.++..|++.+. ....+.+..  ..+.+.....++.|.+.+.++++.-++.++...                  
T Consensus        40 ~~~~~~~li~ly~~~~~-~~ll~~l~~--~~~~yd~~~~~~~c~~~~l~~~~~~l~~k~~~~------------------   98 (140)
T smart00299       40 NPALQTKLIELYAKYDP-QKEIERLDN--KSNHYDIEKVGKLCEKAKLYEEAVELYKKDGNF------------------   98 (140)
T ss_pred             chhHHHHHHHHHHHHCH-HHHHHHHHh--ccccCCHHHHHHHHHHcCcHHHHHHHHHhhcCH------------------
Confidence            45567777777776533 344444442  233444555677777777777777777666432                  


Q ss_pred             chhHHHHHHHHHHhc-CCHHHHHHHHHhhcCCChhhHHHHHHHHH
Q 045555           95 DIFVGIALIDMYCKC-GDVEKAQRVFWKMLRKDKFTWTAMIVGLA  138 (175)
Q Consensus        95 ~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~li~~~~  138 (175)
                           ...++.+... ++++.|.+.+..-  .+...|..++..+.
T Consensus        99 -----~~Al~~~l~~~~d~~~a~~~~~~~--~~~~lw~~~~~~~l  136 (140)
T smart00299       99 -----KDAIVTLIEHLGNYEKAIEYFVKQ--NNPELWAEVLKALL  136 (140)
T ss_pred             -----HHHHHHHHHcccCHHHHHHHHHhC--CCHHHHHHHHHHHH
Confidence                 2344444444 6777777776652  34556666665554

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=92.68  E-value=0.37  Score=23.36  Aligned_cols=29  Identities=24%  Similarity=0.362  Sum_probs=22.5

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ..+++.|...|...|++++|..++++...
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            35678888888888888888888888765

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.55  E-value=2.3  Score=28.85  Aligned_cols=133  Identities=10%  Similarity=0.077  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHH-----HHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMI-----DGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li-----~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      .|..-+. +.+.+..++|+.-|..+.+.+...|-.|.     ....+.|+..+|+..|++.-.....|...--..     
T Consensus        61 ~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~A-----  134 (221)
T COG4649          61 AFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLA-----  134 (221)
T ss_pred             HHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHH-----
Confidence            3444333 45778889999988888876555544442     336788999999999999988765554331100     


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK----DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                            --.-.-.+..+|.+++...-.+-+..+    ....-..|--+-.+.|++.+|.+.|..+.+....|..
T Consensus       135 ------Rlraa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~aprn  202 (221)
T COG4649         135 ------RLRAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPRN  202 (221)
T ss_pred             ------HHHHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCcHH
Confidence                  011223456788888887777766433    2233456666777999999999999999876666644

>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=92.52  E-value=0.023  Score=36.68  Aligned_cols=56  Identities=11%  Similarity=0.122  Sum_probs=26.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      +....+.++..|++.+..+...++++....   +-...++..|.+.|.++++.-++.++
T Consensus        41 ~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~a~~Ly~~~   96 (143)
T PF00637_consen   41 NPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEEAVYLYSKL   96 (143)
T ss_dssp             SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHHHHHHHHHc
Confidence            344555555555555555555554442221   22234444444555554444444443

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.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.48  E-value=0.48  Score=21.94  Aligned_cols=28  Identities=14%  Similarity=0.167  Sum_probs=21.2

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .+|..+...|...|++++|.+.|++.++
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            3577777888888888888888888775

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.43  E-value=0.4  Score=22.23  Aligned_cols=27  Identities=15%  Similarity=0.432  Sum_probs=19.3

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|..+...+...|++++|+..|++.++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            566777777777777777777777766

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=92.33  E-value=0.51  Score=23.91  Aligned_cols=28  Identities=7%  Similarity=0.121  Sum_probs=19.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCC
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRASIRL  160 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~g~~p  160 (175)
                      +..+|...|+.+.|.+++++....|-.|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~~~~   32 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEGDEA   32 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcCCHH
Confidence            5567777777777877777777654333

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=92.31  E-value=1.6  Score=33.21  Aligned_cols=94  Identities=11%  Similarity=0.113  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      .-+++.+..+|.+.+++..|.+.-+...   ++|+....---.+|...|+++.|...|.++++.  .|+           
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~--~P~-----------  323 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKL--EPS-----------  323 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh--CCC-----------
Confidence            3468899999999999999999988755   468888888888999999999999999999994  333           


Q ss_pred             CcchhHHHHHHHHHHhcCCHHH-HHHHHHhhcC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEK-AQRVFWKMLR  124 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~-a~~~~~~~~~  124 (175)
                        +...-+-|+.+-.+..+..+ ..++|..|..
T Consensus       324 --Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  324 --NKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             --cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence              33344566666666666654 4778888843

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=92.29  E-value=0.72  Score=37.42  Aligned_cols=113  Identities=12%  Similarity=0.047  Sum_probs=72.7

Q ss_pred             HHHHHHhcCChhHHHHHhhcC-------------CCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           22 IVSGYINRGQVDIARQYFAQM-------------PERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m-------------~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      -...+..+|+..+|..+...-             ...+..+.-.+..-+.+...+.-|-++|..|-..            
T Consensus       709 AAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~------------  776 (1081)
T KOG1538|consen  709 AAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGDL------------  776 (1081)
T ss_pred             HHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhccH------------
Confidence            344455666666666554322             1123333444444444556677777777777543            


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--Ch-----------hhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--DK-----------FTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~-----------~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                                 .++++.....++|.+|.++-+..++-  |+           .-|.---.+|-++|+..+|..+++++.+
T Consensus       777 -----------ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  777 -----------KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             -----------HHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhh
Confidence                       36889999999999999999988653  22           2234455678888888999988888865


Q ss_pred             CC
Q 045555          156 AS  157 (175)
Q Consensus       156 ~g  157 (175)
                      ..
T Consensus       846 na  847 (1081)
T KOG1538|consen  846 NA  847 (1081)
T ss_pred             hh
Confidence            43

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=92.06  E-value=2.2  Score=27.53  Aligned_cols=89  Identities=16%  Similarity=0.032  Sum_probs=67.7

Q ss_pred             HHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---C----h
Q 045555           55 DGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---D----K  127 (175)
Q Consensus        55 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~----~  127 (175)
                      -+++..|+.++|++.|.+.+..  .|             -....||.-..++.-.|+.++|..-+++..+.   .    -
T Consensus        51 valaE~g~Ld~AlE~F~qal~l--~P-------------~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtac  115 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCL--AP-------------ERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTAC  115 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHh--cc-------------cchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHH
Confidence            3578899999999999999874  22             23445688999999999999999988887542   1    2


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHCCC
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQMLRASI  158 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  158 (175)
                      ..|..-...|...|+-+.|..-|...-+-|-
T Consensus       116 qa~vQRg~lyRl~g~dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  116 QAFVQRGLLYRLLGNDDAARADFEAAAQLGS  146 (175)
T ss_pred             HHHHHHHHHHHHhCchHHHHHhHHHHHHhCC
Confidence            3444555667788999999988888776553

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=91.96  E-value=3.4  Score=29.58  Aligned_cols=137  Identities=15%  Similarity=0.133  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCC------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChH---HHHHh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEF---TTVRI   88 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~---~~~~l   88 (175)
                      .|+.-+ .-.+.|++++|.+.|+.+.++      ...+--.++-++-+.+++++|+..+++..+......-.   .|...
T Consensus        37 LY~~g~-~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~Ylkg  115 (254)
T COG4105          37 LYNEGL-TELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKG  115 (254)
T ss_pred             HHHHHH-HHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHH
Confidence            444444 445899999999999998752      34456677888899999999999999998875433333   33333


Q ss_pred             hh--------------------------------ccCcchh------------HHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           89 LT--------------------------------TFNNDIF------------VGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        89 ~~--------------------------------~~~~~~~------------~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      +.                                .+.||..            .=..+..-|.++|.+..|..=+++|.+
T Consensus       116 Ls~~~~i~~~~rDq~~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~~v~e  195 (254)
T COG4105         116 LSYFFQIDDVTRDQSAARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFEEVLE  195 (254)
T ss_pred             HHHhccCCccccCHHHHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHh
Confidence            32                                1111211            011455666777777777777777755


Q ss_pred             C------ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 K------DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 ~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .      .....-.+..+|-+.|-.++|.+.-+-+..
T Consensus       196 ~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~  232 (254)
T COG4105         196 NYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGA  232 (254)
T ss_pred             ccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHh
Confidence            3      122344566777777777777666555543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=91.87  E-value=1.6  Score=35.61  Aligned_cols=98  Identities=13%  Similarity=0.142  Sum_probs=60.8

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHH-HHHhhhcc
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFT-TVRILTTF   92 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~-~~~l~~~~   92 (175)
                      .+..+...+...+.+...+-.|-++|..|-..     -.++......++|++|.++-+...+  ..||... |...+   
T Consensus       745 ~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~-----ksiVqlHve~~~W~eAFalAe~hPe--~~~dVy~pyaqwL---  814 (1081)
T KOG1538|consen  745 AEREPLLLCATYLKKLDSPGLAAEIFLKMGDL-----KSLVQLHVETQRWDEAFALAEKHPE--FKDDVYMPYAQWL---  814 (1081)
T ss_pred             hhhhHHHHHHHHHhhccccchHHHHHHHhccH-----HHHhhheeecccchHhHhhhhhCcc--ccccccchHHHHh---
Confidence            45556666666777778888888988887642     3345667788999999999887765  3333221 10000   


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                       ....-+.-.=++|.+.|+-.+|.++++++
T Consensus       815 -AE~DrFeEAqkAfhkAGr~~EA~~vLeQL  843 (1081)
T KOG1538|consen  815 -AENDRFEEAQKAFHKAGRQREAVQVLEQL  843 (1081)
T ss_pred             -hhhhhHHHHHHHHHHhcchHHHHHHHHHh
Confidence             01111223445666777777777777666

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=91.81  E-value=4.1  Score=31.86  Aligned_cols=83  Identities=12%  Similarity=0.215  Sum_probs=62.7

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      ++...|..|.....+.|+++.|.+.|++...     |..|+--|.-.|+.+.-.++.+.....|-               
T Consensus       345 ~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d-----~~~L~lLy~~~g~~~~L~kl~~~a~~~~~---------------  404 (443)
T PF04053_consen  345 DDPEKWKQLGDEALRQGNIELAEECYQKAKD-----FSGLLLLYSSTGDREKLSKLAKIAEERGD---------------  404 (443)
T ss_dssp             STHHHHHHHHHHHHHTTBHHHHHHHHHHCT------HHHHHHHHHHCT-HHHHHHHHHHHHHTT----------------
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC-----ccccHHHHHHhCCHHHHHHHHHHHHHccC---------------
Confidence            4677999999999999999999999999875     66677777888888887777777776652               


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                           +|....++...|++++..+++.+
T Consensus       405 -----~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  405 -----INIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             -----HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             -----HHHHHHHHHHcCCHHHHHHHHHH
Confidence                 24566666677777777766664

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=91.62  E-value=2.6  Score=27.49  Aligned_cols=77  Identities=12%  Similarity=0.176  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC---------CChhhHHHHHHHHHhcCC-hhHHHHHHHHHHHCCCCCcHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR---------KDKFTWTAMIVGLAISGH-GDTALDMFSQMLRASIRLDEVTYVG  167 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~g~-~~~a~~~~~~m~~~g~~p~~~t~~~  167 (175)
                      ..|.++.-....+++....++++.+..         .+-.+|.+++.+.++..- ---+..+|.-|.+.+.+++..-|..
T Consensus        41 fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~  120 (145)
T PF13762_consen   41 FINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSC  120 (145)
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            457788888888888888888888722         366789999999977665 3456778888988899999999999


Q ss_pred             HHhhhcC
Q 045555          168 VLSACTH  174 (175)
Q Consensus       168 ll~~~~~  174 (175)
                      ++++|-+
T Consensus       121 li~~~l~  127 (145)
T PF13762_consen  121 LIKAALR  127 (145)
T ss_pred             HHHHHHc
Confidence            9999864

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=91.37  E-value=2.1  Score=26.04  Aligned_cols=62  Identities=18%  Similarity=0.166  Sum_probs=46.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          102 LIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      -+..+...|++++|..+.+.+.-||...|-++-.  .+.|..+++..-+.+|..+| .|...+|.
T Consensus        45 RlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~sg-~p~lq~Fa  106 (115)
T TIGR02508        45 RLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAASG-DPRLQTFV  106 (115)
T ss_pred             HHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhCC-CHHHHHHH
Confidence            4456678999999999999998899998877754  36777778888888887766 44444443

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.94  E-value=0.88  Score=20.85  Aligned_cols=27  Identities=19%  Similarity=0.351  Sum_probs=19.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .|..+-..+...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            456677778888888888888887765

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=90.88  E-value=3.9  Score=28.15  Aligned_cols=95  Identities=18%  Similarity=0.285  Sum_probs=59.2

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC-
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD-  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-  126 (175)
                      .-.....+.+.|++.+|+..|+++..........            ....-.++.++-+.|++++|...++...+  |+ 
T Consensus         8 lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a------------~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~   75 (203)
T PF13525_consen    8 LYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYA------------PQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNS   75 (203)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTH------------HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHH------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC
Confidence            3445566788999999999999999864321111            11223689999999999999999999844  32 


Q ss_pred             -hhhHHHHHHHHHh-------------cCChhHHHHHHHHHHHC
Q 045555          127 -KFTWTAMIVGLAI-------------SGHGDTALDMFSQMLRA  156 (175)
Q Consensus       127 -~~~~~~li~~~~~-------------~g~~~~a~~~~~~m~~~  156 (175)
                       ..-+...+.+.+.             .+...+|...|++++++
T Consensus        76 ~~~~~A~Y~~g~~~~~~~~~~~~~~~D~~~~~~A~~~~~~li~~  119 (203)
T PF13525_consen   76 PKADYALYMLGLSYYKQIPGILRSDRDQTSTRKAIEEFEELIKR  119 (203)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHH-TT---HHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHHhCccchhcccChHHHHHHHHHHHHHHHH
Confidence             1223333333221             22345678888887764

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=90.76  E-value=5.2  Score=29.39  Aligned_cols=52  Identities=21%  Similarity=0.249  Sum_probs=27.1

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----ChhhHHHHHHHHHhcCChhHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----DKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~li~~~~~~g~~~~a~  147 (175)
                      ...--.+...+...|+.+.|.+.+-.+.++     |...-..+++.+---|..+.+.
T Consensus       236 ~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~~  292 (304)
T COG3118         236 VEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPLV  292 (304)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHHH
Confidence            333445666666666666666655555433     3344445555555555443333

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=90.69  E-value=6.1  Score=30.14  Aligned_cols=69  Identities=14%  Similarity=0.070  Sum_probs=53.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcCC-------ChhhHHHHHHHHHh---cCChhHHHHHHHHHHHCCCCCcHHHHHHHH
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLRK-------DKFTWTAMIVGLAI---SGHGDTALDMFSQMLRASIRLDEVTYVGVL  169 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~li~~~~~---~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll  169 (175)
                      .++-+|....+++...++.+.+...       ...+-....-++.+   .|+-++|.+++..+....-.+++.|+..+=
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~G  224 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLG  224 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHH
Confidence            4666799999999999999999654       22233345556667   999999999999977777778888877653

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=90.51  E-value=3.5  Score=27.03  Aligned_cols=89  Identities=15%  Similarity=0.250  Sum_probs=46.9

Q ss_pred             hccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC-hhhHHHHHHH
Q 045555           58 LRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKD-KFTWTAMIVG  136 (175)
Q Consensus        58 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~li~~  136 (175)
                      ...++++++..+++.|.-.  .|+.           +...+  .-.-.+..+|+|++|.++|.+..+.. ...|..-+.+
T Consensus        21 L~~~d~~D~e~lLdALrvL--rP~~-----------~e~d~--~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A   85 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVL--RPNL-----------KELDM--FDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLA   85 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHh--CCCc-----------cccch--hHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHH
Confidence            3467777887777777663  3321           11111  23334567888888888888876543 2345544444


Q ss_pred             HHhcCChhHHHHHH-HHHHHCCCCCc
Q 045555          137 LAISGHGDTALDMF-SQMLRASIRLD  161 (175)
Q Consensus       137 ~~~~g~~~~a~~~~-~~m~~~g~~p~  161 (175)
                      +|-.-.-+-.++.+ .++++.|-.|+
T Consensus        86 ~CL~al~Dp~Wr~~A~~~le~~~~~~  111 (153)
T TIGR02561        86 LCLNAKGDAEWHVHADEVLARDADAD  111 (153)
T ss_pred             HHHHhcCChHHHHHHHHHHHhCCCHh
Confidence            44433333344333 33333333333

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=90.27  E-value=0.89  Score=33.27  Aligned_cols=43  Identities=16%  Similarity=0.233  Sum_probs=37.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      -|+.-|+.-.+.||+++|+++++|.+..|++--..||..-+++
T Consensus       259 Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~~  301 (303)
T PRK10564        259 YFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVKG  301 (303)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhhc
Confidence            4678999999999999999999999999999888888776653

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=90.18  E-value=2.7  Score=25.38  Aligned_cols=60  Identities=12%  Similarity=0.041  Sum_probs=39.2

Q ss_pred             ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHH
Q 045555           62 RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIV  135 (175)
Q Consensus        62 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~  135 (175)
                      +.-++.+-++.+....+.|++...              .+.+.+|.|.+++..|.++|+..+.+   +...|..++.
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii--------------~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVI--------------EAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHH--------------HHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHHH
Confidence            344556666666666665554444              78888999999999999998877432   2334555443

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=89.91  E-value=5.6  Score=28.47  Aligned_cols=140  Identities=13%  Similarity=0.082  Sum_probs=74.7

Q ss_pred             HHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch-hHH
Q 045555           21 TIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDI-FVG   99 (175)
Q Consensus        21 ~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~~   99 (175)
                      -.+..|++.-++..|-..++++.+|=..- .++ -.|.+..+..---++.+-....++.-+......++---.-|. ...
T Consensus       135 RtMEiyS~ttRFalaCN~s~KIiEPIQSR-CAi-LRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~GDMRQal  212 (333)
T KOG0991|consen  135 RTMEIYSNTTRFALACNQSEKIIEPIQSR-CAI-LRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQGDMRQAL  212 (333)
T ss_pred             HHHHHHcccchhhhhhcchhhhhhhHHhh-hHh-hhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccchHHHHH
Confidence            34556666666666666666666652221 122 234444444333344443344444333222222222112221 122


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHH
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVT  164 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  164 (175)
                      |.|=+.....|. -.++.+|+-..+|.+.....++..|. .+++++|.++++++-+.|+.|....
T Consensus       213 NnLQst~~g~g~-Vn~enVfKv~d~PhP~~v~~ml~~~~-~~~~~~A~~il~~lw~lgysp~Dii  275 (333)
T KOG0991|consen  213 NNLQSTVNGFGL-VNQENVFKVCDEPHPLLVKKMLQACL-KRNIDEALKILAELWKLGYSPEDII  275 (333)
T ss_pred             HHHHHHhccccc-cchhhhhhccCCCChHHHHHHHHHHH-hccHHHHHHHHHHHHHcCCCHHHHH
Confidence            333333333332 23456666666788877778887765 5789999999999999999997643

>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=89.89  E-value=3.5  Score=26.64  Aligned_cols=64  Identities=14%  Similarity=0.202  Sum_probs=48.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      +....+.-+..+.+.|+-++-.++++.+.   +++....-.+.++|.+.|+..++-+++.+..+.|+
T Consensus        85 ~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   85 LSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             --HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            44556677778888888888888888865   46777788899999999999999999999998885

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=89.63  E-value=4  Score=26.36  Aligned_cols=88  Identities=15%  Similarity=0.024  Sum_probs=66.9

Q ss_pred             HHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC-CCCCChHHHHHhhhccCcchhHH
Q 045555           24 SGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS-NIRRDEFTTVRILTTFNNDIFVG   99 (175)
Q Consensus        24 ~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~   99 (175)
                      -+++..|+.+.|++.|.+...   .....||.-..++.-.|+.++|++=+++.+.. |.+ +. |          -+..|
T Consensus        51 valaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-tr-t----------acqa~  118 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TR-T----------ACQAF  118 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-ch-H----------HHHHH
Confidence            356789999999999998653   57888999999999999999999999888774 321 11 1          12223


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhc
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                      ---...|...|+-+.|..-|...-
T Consensus       119 vQRg~lyRl~g~dd~AR~DFe~AA  142 (175)
T KOG4555|consen  119 VQRGLLYRLLGNDDAARADFEAAA  142 (175)
T ss_pred             HHHHHHHHHhCchHHHHHhHHHHH
Confidence            344556788899999999888763

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=89.61  E-value=3.7  Score=28.95  Aligned_cols=72  Identities=11%  Similarity=0.076  Sum_probs=52.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH--CCCCCcHHHHHHHHhh
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR--ASIRLDEVTYVGVLSA  171 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~g~~p~~~t~~~ll~~  171 (175)
                      +..++.+.+.+.+.++.....+-++  | |..+-..++..||-.|++++|..-++-.-.  ....+-..+|..+|.+
T Consensus         5 ~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           5 RDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            4566777788888888887777643  3 666777888999999999999766655543  3456677778777764

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=89.36  E-value=0.85  Score=19.95  Aligned_cols=21  Identities=14%  Similarity=0.317  Sum_probs=10.9

Q ss_pred             HHHHHHHHhcCChhHHHHHhh
Q 045555           20 TTIVSGYINRGQVDIARQYFA   40 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~   40 (175)
                      ..+...+...|++++|..+++
T Consensus         5 ~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    5 LALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHcCCHHHHHHHHh
Confidence            344455555555555555543

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=89.35  E-value=0.66  Score=21.87  Aligned_cols=20  Identities=30%  Similarity=0.311  Sum_probs=10.3

Q ss_pred             hhHHHHHHHHHHhcCCHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKA  115 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a  115 (175)
                      ...|+.+...|...|++++|
T Consensus        13 ~~a~~nla~~~~~~g~~~~A   32 (34)
T PF13431_consen   13 AEAYNNLANLYLNQGDYEEA   32 (34)
T ss_pred             HHHHHHHHHHHHHCcCHHhh
Confidence            44445555555555555554

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=89.35  E-value=3.4  Score=25.21  Aligned_cols=57  Identities=12%  Similarity=0.076  Sum_probs=34.5

Q ss_pred             HHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHH
Q 045555           65 EALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIV  135 (175)
Q Consensus        65 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~  135 (175)
                      +..+-++.+....+.|++.              +..+.+.+|.|.+++..|.++|+.++.+   ....|..++.
T Consensus        28 e~rrglN~l~~~DlVP~P~--------------ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPK--------------IIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HH--------------HHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChH--------------HHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHH
Confidence            4455555555555544444              4478888999999999999998887432   2225666554

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.33  E-value=4.7  Score=26.77  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=22.6

Q ss_pred             HhcCCHHHHHHHHHhh--cCCCh---hhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          107 CKCGDVEKAQRVFWKM--LRKDK---FTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~--~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+.++.++++.++..+  .+|..   .++...  .+.+.|++.+|.++|+++.+.
T Consensus        21 l~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~--l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLRPEFPELDLFDGW--LHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HccCChHHHHHHHHHHHHhCCCchHHHHHHHH--HHHHhCCHHHHHHHHHHHhcc
Confidence            3455555555555555  22322   222222  233455566666666655443

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=89.01  E-value=4.2  Score=28.69  Aligned_cols=59  Identities=24%  Similarity=0.240  Sum_probs=45.3

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      |.+.-++.+.+.+.+.+++...++=.+..               +.+...-..+++.||-.|+|++|..=++-.
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak---------------Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~   61 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK---------------PTDAGGRHFLFQLLCVAGDWEKALAQLNLA   61 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC---------------CccccchhHHHHHHhhcchHHHHHHHHHHH
Confidence            34556778889999999999998888864               224444567999999999999997666554

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=88.85  E-value=0.93  Score=20.55  Aligned_cols=25  Identities=16%  Similarity=0.304  Sum_probs=16.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          132 AMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       132 ~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+..++.+.|++++|.+.|+++++.
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~~   29 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIKR   29 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHH
Confidence            3445566677777777777776653

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=88.75  E-value=1.5  Score=20.16  Aligned_cols=27  Identities=19%  Similarity=0.218  Sum_probs=18.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +|..+...|...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            455666667777777777777776654

...

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=88.68  E-value=5.1  Score=26.31  Aligned_cols=49  Identities=20%  Similarity=0.298  Sum_probs=38.0

Q ss_pred             HhcCCHHHHHHHHHhh--cCC---ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555          107 CKCGDVEKAQRVFWKM--LRK---DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~--~~~---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                      .+.++.++++.+++.|  .+|   ...++...+  +...|++.+|.++|+++.+.+
T Consensus        21 L~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l--~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVLRPNLKELDMFDGWL--LIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHhCCCccccchhHHHH--HHHcCCHHHHHHHHHhhhccC
Confidence            4589999999999999  345   344544444  456899999999999999875

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=88.35  E-value=8.7  Score=31.97  Aligned_cols=83  Identities=17%  Similarity=0.184  Sum_probs=52.2

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CCh---------hH---HHHHHHHHhccCChHHHHHHHHHhHhCCCCC
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE-RDY---------VL---WTAMIDGYLRVNRFREALTLFREMQTSNIRR   80 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~---------~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   80 (175)
                      |.+..|..+...-.+.-.++-|...|-+... +.+         .+   -.+=+.  .--|++++|.++|-+|-+..   
T Consensus       690 PHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~--~~~g~feeaek~yld~drrD---  764 (1189)
T KOG2041|consen  690 PHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEIS--AFYGEFEEAEKLYLDADRRD---  764 (1189)
T ss_pred             CchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHh--hhhcchhHhhhhhhccchhh---
Confidence            6677888888887777788888888876653 211         11   111122  23478889988888887764   


Q ss_pred             ChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           81 DEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        81 ~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                                          ..|..+-+.|+|-.+.++++.
T Consensus       765 --------------------LAielr~klgDwfrV~qL~r~  785 (1189)
T KOG2041|consen  765 --------------------LAIELRKKLGDWFRVYQLIRN  785 (1189)
T ss_pred             --------------------hhHHHHHhhhhHHHHHHHHHc
Confidence                                355555556666555555544

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=88.33  E-value=8.6  Score=28.53  Aligned_cols=138  Identities=12%  Similarity=0.192  Sum_probs=89.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC--------C----hhHHHHHHHHHhccCChHHHHHHH------------
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPER--------D----YVLWTAMIDGYLRVNRFREALTLF------------   70 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--------~----~~~~~~li~~~~~~~~~~~a~~~~------------   70 (175)
                      +...+.++...  +.++++++....+..+..        .    ...|..|+. +.....++++..+.            
T Consensus        30 ~~~~~~al~~l--~~~~~~~~~~~i~~~r~~~~~~l~~~~~~s~~~~y~~l~~-lq~L~Elee~~~~~~~~~~~~~~~~~  106 (352)
T PF02259_consen   30 EYSFYRALLAL--RQGDYDEAKKYIEKARQLLLDELSALSSESYQRAYPSLVK-LQQLVELEEIIELKSNLSQNPQDLKS  106 (352)
T ss_pred             hHHHHHHHHHH--hCccHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHH-HhHHHHHHHHHHHHHhhcccHHHHHH
Confidence            34445555444  889999998888877641        1    112322221 22222333333333            


Q ss_pred             --HHhHh--CCCCCChHHHHHhhh------c----cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-------Chhh
Q 045555           71 --REMQT--SNIRRDEFTTVRILT------T----FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-------DKFT  129 (175)
Q Consensus        71 --~~m~~--~~~~p~~~~~~~l~~------~----~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~  129 (175)
                        +....  .++.++..++..++.      .    ......+|..+.+.+.+.|.++.|...+..+...       ...+
T Consensus       107 l~~~W~~Rl~~~~~~~~~~~~il~~R~~~l~~~~~~~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v  186 (352)
T PF02259_consen  107 LLKRWRSRLPNMQDDFSVWEPILSLRRLVLSLILLPEELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRV  186 (352)
T ss_pred             HHHHHHHHHHHhccchHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcch
Confidence              22222  234566666666666      2    3345678899999999999999999999998652       3556


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          130 WTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       130 ~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .-.-.+.+...|+-.+|...+++..+
T Consensus       187 ~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  187 FLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66677888899999999999988887

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.26  E-value=3.7  Score=33.93  Aligned_cols=93  Identities=13%  Similarity=0.155  Sum_probs=73.1

Q ss_pred             hHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh
Q 045555            3 FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE   82 (175)
Q Consensus         3 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   82 (175)
                      +|.++-.+.+=||-..|-.-+.+++..+++++-.++-+.+++  ..-|.=...+|.+.|+.++|...+-..-..      
T Consensus       702 ~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskks--PIGy~PFVe~c~~~~n~~EA~KYiprv~~l------  773 (829)
T KOG2280|consen  702 RAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKKS--PIGYLPFVEACLKQGNKDEAKKYIPRVGGL------  773 (829)
T ss_pred             HHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccCC--CCCchhHHHHHHhcccHHHHhhhhhccCCh------
Confidence            455666666669999999999999999999998887777666  455677788999999999999988766432      


Q ss_pred             HHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHH
Q 045555           83 FTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFW  120 (175)
Q Consensus        83 ~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~  120 (175)
                                       .-...+|.+.|++.+|.++=-
T Consensus       774 -----------------~ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  774 -----------------QEKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             -----------------HHHHHHHHHhccHHHHHHHHH
Confidence                             137888999999988866543

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=88.23  E-value=1.1  Score=22.68  Aligned_cols=26  Identities=15%  Similarity=0.341  Sum_probs=22.6

Q ss_pred             HHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           52 AMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        52 ~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      .|..+|...|+.+.|.+++++....|
T Consensus         4 dLA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         4 DLARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHcC
Confidence            46788999999999999999998755

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=88.04  E-value=6.8  Score=27.02  Aligned_cols=103  Identities=12%  Similarity=0.101  Sum_probs=81.0

Q ss_pred             CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           45 RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        45 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      |++..-..|..++.+.|+..+|...|.+...--.              .-|..+.-.+..+....+++..|...++++.+
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~f--------------A~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e  152 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIF--------------AHDAAMLLGLAQAQFAIQEFAAAQQTLEDLME  152 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhcccc--------------CCCHHHHHHHHHHHHhhccHHHHHHHHHHHhh
Confidence            4555566788999999999999999999876432              33444556788999999999999999999854


Q ss_pred             -----CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          125 -----KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       125 -----~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                           ++..+--.+.+.|...|+...|..-|+.....--.|.
T Consensus       153 ~~pa~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~  194 (251)
T COG4700         153 YNPAFRSPDGHLLFARTLAAQGKYADAESAFEVAISYYPGPQ  194 (251)
T ss_pred             cCCccCCCCchHHHHHHHHhcCCchhHHHHHHHHHHhCCCHH
Confidence                 2556667788899999999999999998887533333

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=88.01  E-value=8.7  Score=28.24  Aligned_cols=121  Identities=13%  Similarity=0.122  Sum_probs=78.9

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhH
Q 045555           22 IVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFV   98 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~   98 (175)
                      -.......|++.+|...|.....   .+.-.--.+..+|...|+.+.|..++..+...--......              
T Consensus       140 ~~~~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~--------------  205 (304)
T COG3118         140 EAKELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHG--------------  205 (304)
T ss_pred             HhhhhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHH--------------
Confidence            33456678888888888887663   3445567788889999999999999988855421111111              


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhh-cCC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKM-LRK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~-~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...-|+.+.+.....+...+-... ..| |...--.+...+...|+.+.|.+.+-.+..+
T Consensus       206 l~a~i~ll~qaa~~~~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~  265 (304)
T COG3118         206 LQAQIELLEQAAATPEIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRR  265 (304)
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            122344444444444444433333 234 5666667888899999999999988877765

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=87.44  E-value=2.7  Score=21.66  Aligned_cols=35  Identities=11%  Similarity=0.139  Sum_probs=30.0

Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          137 LAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       137 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      ..+.|-.+++..++++|.+.|+.-+...+..+++-
T Consensus        12 Ak~~GlI~~~~~~l~~l~~~g~~is~~l~~~~L~~   46 (48)
T PF11848_consen   12 AKRRGLISEVKPLLDRLQQAGFRISPKLIEEILRR   46 (48)
T ss_pred             HHHcCChhhHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence            34678888999999999999999999998888764

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.38  E-value=8.5  Score=32.11  Aligned_cols=46  Identities=13%  Similarity=0.198  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNR   62 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~   62 (175)
                      ..+...|..+.-.|++++|-+..-.|-..+..-|.-.+.-+...++
T Consensus       393 kv~~~yI~HLl~~~~y~~Aas~~p~m~gn~~~eWe~~V~~f~e~~~  438 (846)
T KOG2066|consen  393 KVGKTYIDHLLFEGKYDEAASLCPKMLGNNAAEWELWVFKFAELDQ  438 (846)
T ss_pred             HHHHHHHHHHHhcchHHHHHhhhHHHhcchHHHHHHHHHHhccccc
Confidence            3556666666677777777766666665555555555444444444

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=87.10  E-value=2.2  Score=32.13  Aligned_cols=52  Identities=15%  Similarity=0.151  Sum_probs=38.9

Q ss_pred             HHHHHhcCChhHHHHHhhcCC--CC-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555           23 VSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus        23 i~~~~~~~~~~~a~~~~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      .+-|.+.|.+++|.+.|..-.  .| |.+++..-..+|.+...+-.|..=-+...
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~Ai  158 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAVYPHNPVYHINRALAYLKQKSFAQAEEDCEAAI  158 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhccCCCCccchhhHHHHHHHHHHHHHHHHhHHHHH
Confidence            456788999999999998755  35 78888888888988888776655444443

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=86.76  E-value=0.99  Score=28.91  Aligned_cols=34  Identities=21%  Similarity=0.316  Sum_probs=27.2

Q ss_pred             HhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          138 AISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       138 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      -..|.-.+|..+|++|++.|-.||.  +..|+..+.
T Consensus       106 R~ygsk~DaY~VF~kML~~G~pPdd--W~~Ll~~a~  139 (140)
T PF11663_consen  106 RAYGSKTDAYAVFRKMLERGNPPDD--WDALLKEAK  139 (140)
T ss_pred             hhhccCCcHHHHHHHHHhCCCCCcc--HHHHHHHhc
Confidence            3446677899999999999999984  777877664

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=86.66  E-value=7.3  Score=25.89  Aligned_cols=53  Identities=17%  Similarity=0.069  Sum_probs=30.6

Q ss_pred             HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           57 YLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        57 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      -.+.++.+++..++.-+...  .|.....           .+  .-...+.++|+|.+|.++|+++.+
T Consensus        20 al~~~~~~D~e~lL~ALrvL--RP~~~e~-----------~~--~~~~l~i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   20 ALRLGDPDDAEALLDALRVL--RPEFPEL-----------DL--FDGWLHIVRGDWDDALRLLRELEE   72 (160)
T ss_pred             HHccCChHHHHHHHHHHHHh--CCCchHH-----------HH--HHHHHHHHhCCHHHHHHHHHHHhc
Confidence            34556777777777777663  3332211           11  233345677777777777777754

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=86.28  E-value=11  Score=27.76  Aligned_cols=23  Identities=22%  Similarity=0.681  Sum_probs=12.1

Q ss_pred             hHHHHHHHHHhHhCCCCCChHHH
Q 045555           63 FREALTLFREMQTSNIRRDEFTT   85 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~p~~~~~   85 (175)
                      +++.+.+++.|.+.|..-+..+|
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~  100 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLY  100 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHH
Confidence            34445555555555555554444

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.98  E-value=11  Score=27.21  Aligned_cols=52  Identities=13%  Similarity=0.201  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhh---cC----CChhhHHHHHHHHHhcCChhHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKM---LR----KDKFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~---~~----~~~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                      .+-+.|-.|.-..++..|+++++.-   ..    .+..+...|+.+|- .|+.+++.+++
T Consensus       192 ~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd-~gD~E~~~kvl  250 (308)
T KOG1585|consen  192 AYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD-EGDIEEIKKVL  250 (308)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc-cCCHHHHHHHH
Confidence            3455666666778899999999884   11    26678888888884 67877776654

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=85.67  E-value=2.4  Score=23.14  Aligned_cols=45  Identities=16%  Similarity=0.246  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          111 DVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       111 ~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .++...++.+.+..  .|...--.+|.+|...|++++|.+.++++.+
T Consensus         5 ~~~~~~~~~~~lR~~RHD~~NhLqvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen    5 QLEELEELIDSLRAQRHDFLNHLQVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34555566666543  2555555688999999999999999988875

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=84.83  E-value=6.8  Score=23.93  Aligned_cols=81  Identities=17%  Similarity=0.099  Sum_probs=56.4

Q ss_pred             chHHHHhhccCC-CcHHHHHHHH--HHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            2 GFALEIFGNMKN-KDVISWTTIV--SGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li--~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      +||..+=+++.. ++..-.-.||  ..+.+.|++++|..+.+.+..||...|-.|..  -+.|..++...-+..|..+| 
T Consensus        22 qEA~tIAdwL~~~~~~~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~sg-   98 (115)
T TIGR02508        22 QEANTIADWLHLKGESEEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAASG-   98 (115)
T ss_pred             HHHHHHHHHHhcCCchHHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhCC-
Confidence            455556565554 4323333444  45778999999999999999999999988755  36777777877788887776 


Q ss_pred             CCChHHH
Q 045555           79 RRDEFTT   85 (175)
Q Consensus        79 ~p~~~~~   85 (175)
                      .|....|
T Consensus        99 ~p~lq~F  105 (115)
T TIGR02508        99 DPRLQTF  105 (115)
T ss_pred             CHHHHHH
Confidence            3443333

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=84.65  E-value=13  Score=26.81  Aligned_cols=75  Identities=15%  Similarity=0.108  Sum_probs=52.1

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcCC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCCcHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLRK------DKFTWTAMIVGLAISGHGDTALDMFSQMLRA-SIRLDEVTYVGV  168 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~l  168 (175)
                      ...|+-.+.- .+.|++++|.+.|+.+...      ...+--.++-++.+.++++.|...+++.... +-.||. -|..-
T Consensus        35 ~~LY~~g~~~-L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~-dY~~Y  112 (254)
T COG4105          35 SELYNEGLTE-LQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNA-DYAYY  112 (254)
T ss_pred             HHHHHHHHHH-HhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCCh-hHHHH
Confidence            3445544443 4689999999999999543      3345556677888999999999999998875 445554 44444


Q ss_pred             Hhhh
Q 045555          169 LSAC  172 (175)
Q Consensus       169 l~~~  172 (175)
                      |.|.
T Consensus       113 lkgL  116 (254)
T COG4105         113 LKGL  116 (254)
T ss_pred             HHHH
Confidence            4443

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=84.56  E-value=11  Score=26.10  Aligned_cols=40  Identities=13%  Similarity=0.029  Sum_probs=26.2

Q ss_pred             hcCCHHHHHHHHHhhc-------CCChhhHHHHHHHHHhcCChhHHH
Q 045555          108 KCGDVEKAQRVFWKML-------RKDKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus       108 ~~~~~~~a~~~~~~~~-------~~~~~~~~~li~~~~~~g~~~~a~  147 (175)
                      -..+.+++..++....       +.|+..+.+|...+-+.|+++.|.
T Consensus       152 ~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  152 TKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             HccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            3566677776666652       236667777777777777777664

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=84.06  E-value=13  Score=28.82  Aligned_cols=118  Identities=12%  Similarity=0.045  Sum_probs=82.4

Q ss_pred             hcCChhHHHHHhhcCCC--CChh-------------HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           28 NRGQVDIARQYFAQMPE--RDYV-------------LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~--~~~~-------------~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      -.++.+.|...|++...  |+..             .|..=-+-..+.|++..|.+.|.+.+.  +.|+         ..
T Consensus       215 y~~~~~ka~~hf~qal~ldpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~--idP~---------n~  283 (486)
T KOG0550|consen  215 YNDNADKAINHFQQALRLDPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALN--IDPS---------NK  283 (486)
T ss_pred             cccchHHHHHHHhhhhccChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhc--CCcc---------cc
Confidence            45677777777877664  3221             122223446788999999999999887  4444         24


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChh-hHHHHH--HHHHhcCChhHHHHHHHHHHHC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKF-TWTAMI--VGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~li--~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .|+...|-.......+.|+..+|..--+....-|.. .+..+.  .++...++|++|++-|++..+.
T Consensus       284 ~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  284 KTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             chhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            566677778888899999999999999888766543 233333  3455678999999998887654

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=83.76  E-value=26  Score=31.00  Aligned_cols=21  Identities=33%  Similarity=0.464  Sum_probs=11.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHhh
Q 045555          102 LIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~  122 (175)
                      .+..|++...|++|.++-..-
T Consensus      1032 av~ll~ka~~~~eAlrva~~~ 1052 (1265)
T KOG1920|consen 1032 AVALLCKAKEWEEALRVASKA 1052 (1265)
T ss_pred             HHHHHhhHhHHHHHHHHHHhc
Confidence            444555555555555554443

>PRK09687 putative lyase; Provisional

Probab=83.39  E-value=15  Score=26.81  Aligned_cols=166  Identities=11%  Similarity=0.040  Sum_probs=96.5

Q ss_pred             hHHHHhhcc--CCCcHHHHHHHHHHHHhcCCh-----hHHHHHhhc-CCCCChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            3 FALEIFGNM--KNKDVISWTTIVSGYINRGQV-----DIARQYFAQ-MPERDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         3 ~A~~~~~~m--~~~~~~~~~~li~~~~~~~~~-----~~a~~~~~~-m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++...+..+  ..|+..+-...+.+++..+..     ..+.+.+.. +..++..+=...+.++.+.++ ++++..+-.+.
T Consensus        90 ~a~~~L~~l~~~D~d~~VR~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L  168 (280)
T PRK09687         90 NVFNILNNLALEDKSACVRASAINATGHRCKKNPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVIND-EAAIPLLINLL  168 (280)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHhcccccccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccCC-HHHHHHHHHHh
Confidence            566666655  346666666666666655421     223333332 334455555566666666665 34555555555


Q ss_pred             hCCCCCCh----------------HHHHHhhh-ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHH
Q 045555           75 TSNIRRDE----------------FTTVRILT-TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGL  137 (175)
Q Consensus        75 ~~~~~p~~----------------~~~~~l~~-~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  137 (175)
                      +.. .++.                .....++. -..++..+-...+.++++.|+..-...+.+.+..++  ..-..+.++
T Consensus       169 ~d~-~~~VR~~A~~aLg~~~~~~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~~~av~~Li~~L~~~~--~~~~a~~AL  245 (280)
T PRK09687        169 KDP-NGDVRNWAAFALNSNKYDNPDIREAFVAMLQDKNEEIRIEAIIGLALRKDKRVLSVLIKELKKGT--VGDLIIEAA  245 (280)
T ss_pred             cCC-CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHccCChhHHHHHHHHHcCCc--hHHHHHHHH
Confidence            431 1111                11111111 112355666778888888888554444555444444  345688889


Q ss_pred             HhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcCC
Q 045555          138 AISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       138 ~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      ...|.. +|...+.++.+.  .||...-...+.+|.++
T Consensus       246 g~ig~~-~a~p~L~~l~~~--~~d~~v~~~a~~a~~~~  280 (280)
T PRK09687        246 GELGDK-TLLPVLDTLLYK--FDDNEIITKAIDKLKRS  280 (280)
T ss_pred             HhcCCH-hHHHHHHHHHhh--CCChhHHHHHHHHHhcC
Confidence            998885 789999888864  46888888888888753

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=83.13  E-value=13  Score=25.96  Aligned_cols=93  Identities=14%  Similarity=0.055  Sum_probs=63.8

Q ss_pred             HHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHH
Q 045555           54 IDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAM  133 (175)
Q Consensus        54 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l  133 (175)
                      -+-+.+.|++++|..-|.+.+..  .|...+-        .-...|..-..++.+.+.++.|..-..+.++.+..---++
T Consensus       102 GN~~F~ngdyeeA~skY~~Ale~--cp~~~~e--------~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl  171 (271)
T KOG4234|consen  102 GNELFKNGDYEEANSKYQEALES--CPSTSTE--------ERSILYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKAL  171 (271)
T ss_pred             HHHhhhcccHHHHHHHHHHHHHh--CccccHH--------HHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHH
Confidence            34467889999999999888874  3332221        1234556667788888999888887777766544333333


Q ss_pred             H---HHHHhcCChhHHHHHHHHHHHC
Q 045555          134 I---VGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       134 i---~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .   .+|-+..++++|++-|+.+++.
T Consensus       172 ~RRAeayek~ek~eealeDyKki~E~  197 (271)
T KOG4234|consen  172 ERRAEAYEKMEKYEEALEDYKKILES  197 (271)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHh
Confidence            3   4677788899999999888765

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=83.02  E-value=0.88  Score=34.98  Aligned_cols=129  Identities=14%  Similarity=0.084  Sum_probs=88.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---------CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---------RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .+|-.|-+.|--.|+++.|....+.-.+         .....++.|-++++-.|+++.|.+.|..-...-++....    
T Consensus       196 Ra~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r----  271 (639)
T KOG1130|consen  196 RAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNR----  271 (639)
T ss_pred             chhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcch----
Confidence            3566666666678899999886654321         134568899999999999999999988764432211111    


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---------CChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---------KDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                           .....++-+|..+|.-..++++|...+..-..         -....|-++..+|...|.-++|......-+
T Consensus       272 -----~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  272 -----TVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             -----hHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence                 11233445788899989999999998887521         144566778888888888888876655443

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.97  E-value=16  Score=26.73  Aligned_cols=124  Identities=12%  Similarity=0.056  Sum_probs=83.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCCC----------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPER----------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~~----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      ++.+++.+.-....++-...++.=..|          -..+.+.+++.+...|.+.-....+++..+...+.+       
T Consensus       139 qesLdRl~~L~~~V~~ii~~~e~~~~~ESsv~lW~KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~-------  211 (366)
T KOG2796|consen  139 QESLDRLHKLKTVVSKILANLEQGLAEESSIRLWRKRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQE-------  211 (366)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCccc-------
Confidence            555666655544444444444443332          234567788888888888888889998888654333       


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----CChhhHHHHH-----HHHHhcCChhHHHHHHHHHHHC
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----KDKFTWTAMI-----VGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~li-----~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                             +.....|...--+.||.+.|...|+...+    .|..+.+.++     ..|..++++.+|...|.+....
T Consensus       212 -------p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~  281 (366)
T KOG2796|consen  212 -------PQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRM  281 (366)
T ss_pred             -------HHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhcccc
Confidence                   33346788888899999999999997632    2444444433     3466678999999999887754

>PRK11906 transcriptional regulator; Provisional

Probab=82.91  E-value=21  Score=28.07  Aligned_cols=97  Identities=14%  Similarity=0.067  Sum_probs=67.0

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC-hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      -|+.+...+.....-.++++.|...|++...  || ..+|...--.+.-.|+.++|.+.+++..+..  |....-     
T Consensus       336 ~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLs--P~~~~~-----  408 (458)
T PRK11906        336 VDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLE--PRRRKA-----  408 (458)
T ss_pred             CCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC--chhhHH-----
Confidence            4777777777777888889999999998764  53 4456555556677899999999999977643  332222     


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                            .+....++.|+ ...+++|.+++.+-.+
T Consensus       409 ------~~~~~~~~~~~-~~~~~~~~~~~~~~~~  435 (458)
T PRK11906        409 ------VVIKECVDMYV-PNPLKNNIKLYYKETE  435 (458)
T ss_pred             ------HHHHHHHHHHc-CCchhhhHHHHhhccc
Confidence                  22245666777 4567888888776543

>smart00028 TPR Tetratricopeptide repeats

Probab=82.72  E-value=2.8  Score=17.85  Aligned_cols=27  Identities=19%  Similarity=0.198  Sum_probs=20.3

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .|..+...+...|++++|...|++.++
T Consensus         3 ~~~~~a~~~~~~~~~~~a~~~~~~~~~   29 (34)
T smart00028        3 ALYNLGNAYLKLGDYDEALEYYEKALE   29 (34)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            466677777788888888888877664

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=82.44  E-value=21  Score=27.69  Aligned_cols=83  Identities=13%  Similarity=0.173  Sum_probs=53.1

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCC-CCCChHHHH--Hhhh----------------------ccCcchh-HHHHH
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSN-IRRDEFTTV--RILT----------------------TFNNDIF-VGIAL  102 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~--~l~~----------------------~~~~~~~-~~~~l  102 (175)
                      .+...+...|..|+|++|+++.+.-+... +.++..--.  .++.                      ...||.. .--..
T Consensus       190 A~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvPaav~A  269 (531)
T COG3898         190 AARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPAAVVA  269 (531)
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccchHHHHH
Confidence            46788999999999999999999887654 345443221  1222                      2333321 12235


Q ss_pred             HHHHHhcCCHHHHHHHHHhh--cCCChhhHH
Q 045555          103 IDMYCKCGDVEKAQRVFWKM--LRKDKFTWT  131 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~--~~~~~~~~~  131 (175)
                      ..++.+.|++.++-.+++.+  .+|....+.
T Consensus       270 Aralf~d~~~rKg~~ilE~aWK~ePHP~ia~  300 (531)
T COG3898         270 ARALFRDGNLRKGSKILETAWKAEPHPDIAL  300 (531)
T ss_pred             HHHHHhccchhhhhhHHHHHHhcCCChHHHH
Confidence            56778888888888888887  334444443

>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=82.31  E-value=14  Score=25.61  Aligned_cols=79  Identities=15%  Similarity=0.097  Sum_probs=52.6

Q ss_pred             HHhcCChhHHHHHhhcCCC-C--ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHH
Q 045555           26 YINRGQVDIARQYFAQMPE-R--DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIAL  102 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~-~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~l  102 (175)
                      +.+.|+ +.|+..|-.+.. |  +....-.-+..|--..+.++++.++.+.+...-.-           -.+++..+.+|
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~krD~~Kt~~ll~~~L~l~~~~-----------~~~n~eil~sL  184 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYYTKRDPEKTIQLLLRALELSNPD-----------DNFNPEILKSL  184 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHccCHHHHHHHHHHHHHhcCCC-----------CCCCHHHHHHH
Confidence            344555 566666666654 2  22333344445555789999999999988753211           14556677899


Q ss_pred             HHHHHhcCCHHHHH
Q 045555          103 IDMYCKCGDVEKAQ  116 (175)
Q Consensus       103 i~~~~~~~~~~~a~  116 (175)
                      .+.|-+.|+++.|.
T Consensus       185 as~~~~~~~~e~AY  198 (203)
T PF11207_consen  185 ASIYQKLKNYEQAY  198 (203)
T ss_pred             HHHHHHhcchhhhh
Confidence            99999999999885

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=81.99  E-value=16  Score=29.90  Aligned_cols=59  Identities=15%  Similarity=0.110  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCC---------------------CCChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMP---------------------ERDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~---------------------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      .-+.+.+.+-+.|..++|+++--.--                     ..+..-|..|-.+....|++..|.+.|......
T Consensus       616 ~rt~va~Fle~~g~~e~AL~~s~D~d~rFelal~lgrl~iA~~la~e~~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d~  695 (794)
T KOG0276|consen  616 IRTKVAHFLESQGMKEQALELSTDPDQRFELALKLGRLDIAFDLAVEANSEVKWRQLGDAALSAGELPLASECFLRARDL  695 (794)
T ss_pred             hhhhHHhHhhhccchHhhhhcCCChhhhhhhhhhcCcHHHHHHHHHhhcchHHHHHHHHHHhhcccchhHHHHHHhhcch
Confidence            44566666666666666665432111                     013444666666666666666666666665553

>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=81.82  E-value=8.6  Score=23.67  Aligned_cols=55  Identities=15%  Similarity=0.275  Sum_probs=40.5

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCC----------CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPE----------RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++++.+|... +......+++.=..          ....-|..|+.-|...|..++|++++.++..
T Consensus         3 TaLlk~Yl~~-~~~~l~~llr~~N~C~~~~~e~~L~~~~~~~eL~~lY~~kg~h~~AL~ll~~l~~   67 (108)
T PF10366_consen    3 TALLKCYLET-NPSLLGPLLRLPNYCDLEEVEEVLKEHGKYQELVDLYQGKGLHRKALELLKKLAD   67 (108)
T ss_pred             HHHHHHHHHh-CHHHHHHHHccCCcCCHHHHHHHHHHcCCHHHHHHHHHccCccHHHHHHHHHHhc
Confidence            4677777777 66666665553211          1233589999999999999999999999988

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.72  E-value=21  Score=27.15  Aligned_cols=126  Identities=10%  Similarity=0.079  Sum_probs=84.6

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChh--HH--HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYV--LW--TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~--~~--~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      |..+++-.-.++.-.|+.+.....++++..   +|..  +|  ..+.-++...|-+++|.+.-++..+.+          
T Consensus       136 Dlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dAEk~A~ralqiN----------  205 (491)
T KOG2610|consen  136 DLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDAEKQADRALQIN----------  205 (491)
T ss_pred             hhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhHHHHHHhhccCC----------
Confidence            666777777788888888888888887764   3432  22  333445667788999988888877754          


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-------ChhhHHHHHHHHHhcCChhHHHHHHHH-HHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-------DKFTWTAMIVGLAISGHGDTALDMFSQ-MLR  155 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~li~~~~~~g~~~~a~~~~~~-m~~  155 (175)
                           +.|+-.-.+....+.-.|+..++.++..+-...       -...|=...-.+...+.++.|+++|+. |..
T Consensus       206 -----~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~ei~k  276 (491)
T KOG2610|consen  206 -----RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDREIWK  276 (491)
T ss_pred             -----CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHHHHHH
Confidence                 334555567888888899999998888765321       112233333344556899999999954 443

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]

Probab=81.69  E-value=20  Score=27.03  Aligned_cols=65  Identities=8%  Similarity=0.041  Sum_probs=50.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhc-------CCChhhHHH--HHHHHHhcCChhHHHHHHHHHHH-----CCCCCcHHH
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKML-------RKDKFTWTA--MIVGLAISGHGDTALDMFSQMLR-----ASIRLDEVT  164 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~-------~~~~~~~~~--li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t  164 (175)
                      ..++....+.++.++|.+..+++.       +|+.+.|-.  +...+...|+..++.+.+.+..+     -|++|+..+
T Consensus        79 ei~l~~~~~~~D~~~al~~Le~i~~~~~~~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~  157 (380)
T KOG2908|consen   79 EILLVVSEQISDKDEALEFLEKIIEKLKEYKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHS  157 (380)
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhh
Confidence            356667777889999999999983       466666644  55667789999999999988877     688886554

>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known

Probab=81.06  E-value=19  Score=26.40  Aligned_cols=52  Identities=15%  Similarity=0.111  Sum_probs=31.7

Q ss_pred             HHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           23 VSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        23 i~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +...-+.++.....+.+..++  ....-...+..+...|++.+|+++..+..+.
T Consensus       105 l~~~rkr~~l~~ll~~L~~i~--~v~~~~~~l~~ll~~~dy~~Al~li~~~~~~  156 (291)
T PF10475_consen  105 LRLQRKRQNLKKLLEKLEQIK--TVQQTQSRLQELLEEGDYPGALDLIEECQQL  156 (291)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            333334444444444444332  3344456677788899999999999888763

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=80.91  E-value=13  Score=24.30  Aligned_cols=72  Identities=11%  Similarity=0.061  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---------CChhHHHHHHHHHhccCC-hHHHHHHHHHhHhCCCCCChHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---------RDYVLWTAMIDGYLRVNR-FREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---------~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      ...|.++.-....+++.-..++++.+..         .+..+|.+++.+.++... ---+..+|+-|++.+.++++..|.
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            3567888887888888888888887752         366689999999988877 556788999999988888777774


Q ss_pred             Hh
Q 045555           87 RI   88 (175)
Q Consensus        87 ~l   88 (175)
                      .+
T Consensus       120 ~l  121 (145)
T PF13762_consen  120 CL  121 (145)
T ss_pred             HH
Confidence            33

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=80.88  E-value=4.5  Score=29.77  Aligned_cols=40  Identities=15%  Similarity=0.153  Sum_probs=34.0

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHH
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      ..-|+.-|..-.+.||+++|+.+++|.++.|+.--..+|.
T Consensus       257 e~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFi  296 (303)
T PRK10564        257 ESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFI  296 (303)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHH
Confidence            3448899999999999999999999999999866555554

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=80.70  E-value=9.1  Score=26.74  Aligned_cols=90  Identities=17%  Similarity=0.215  Sum_probs=66.5

Q ss_pred             HHHHHhcCChhHHHHHhhcCCC--C------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           23 VSGYINRGQVDIARQYFAQMPE--R------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        23 i~~~~~~~~~~~a~~~~~~m~~--~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .+-+.+.|++++|.+-|....+  |      -.+.|..-..++.+.+.++.|+.--.+..+.+.     ||...+     
T Consensus       102 GN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~p-----ty~kAl-----  171 (271)
T KOG4234|consen  102 GNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNP-----TYEKAL-----  171 (271)
T ss_pred             HHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCc-----hhHHHH-----
Confidence            3456788999999999997654  2      234577777889999999999998888877553     222111     


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCCCh
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDK  127 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  127 (175)
                           -.-..+|.+...+++|..=++.+.+.|+
T Consensus       172 -----~RRAeayek~ek~eealeDyKki~E~dP  199 (271)
T KOG4234|consen  172 -----ERRAEAYEKMEKYEEALEDYKKILESDP  199 (271)
T ss_pred             -----HHHHHHHHhhhhHHHHHHHHHHHHHhCc
Confidence                 2345689999999999999999966443

>PF14669 Asp_Glu_race_2: Putative aspartate racemase

Probab=80.69  E-value=3.6  Score=28.31  Aligned_cols=71  Identities=8%  Similarity=0.185  Sum_probs=46.2

Q ss_pred             HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           51 TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        51 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      -.++..|.+.-+|.++..+++.|.+..+.-+..--..=-....+-..+.|...+.|.+.|.+|.|..++++
T Consensus       136 iS~m~~Yhk~~qW~KGrkvLd~l~el~i~ft~LKGL~g~e~~asrCqivn~AaEiFL~sgsidGA~~vLre  206 (233)
T PF14669_consen  136 ISLMYSYHKTLQWSKGRKVLDKLHELQIHFTSLKGLTGPEKLASRCQIVNIAAEIFLKSGSIDGALWVLRE  206 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCccCccccCchhhhHHHHHHHHHHcCCchHHHHHHhc
Confidence            35667788888999999999999775442211000000002234456677888888888888888888775

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.57  E-value=12  Score=27.94  Aligned_cols=94  Identities=17%  Similarity=0.180  Sum_probs=61.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-C------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE-R------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ...+....+..-.+..+++.+...+-+++. |      +... .++++- +-.-++++++.++..=.+.|+         
T Consensus        63 s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~-~~~irl-llky~pq~~i~~l~npIqYGi---------  131 (418)
T KOG4570|consen   63 SSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTI-HTWIRL-LLKYDPQKAIYTLVNPIQYGI---------  131 (418)
T ss_pred             ceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccH-HHHHHH-HHccChHHHHHHHhCcchhcc---------
Confidence            344555566666667777887777776663 2      2221 222222 233456677777776666665         


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                           .||..++..+|+.+.+.+++.+|.++--.|..
T Consensus       132 -----F~dqf~~c~l~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  132 -----FPDQFTFCLLMDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             -----ccchhhHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence                 56666668999999999999998888777744

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=80.49  E-value=12  Score=23.68  Aligned_cols=57  Identities=12%  Similarity=0.211  Sum_probs=40.8

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      |-.+--.|+..-+  ++.++|..|...|+.-..             ...|......+...|++++|.++|..
T Consensus        68 ylkiWi~ya~~~~--~~~~if~~l~~~~IG~~~-------------A~fY~~wA~~le~~~~~~~A~~I~~~  124 (126)
T PF08311_consen   68 YLKIWIKYADLSS--DPREIFKFLYSKGIGTKL-------------ALFYEEWAEFLEKRGNFKKADEIYQL  124 (126)
T ss_dssp             HHHHHHHHHTTBS--HHHHHHHHHHHHTTSTTB-------------HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHcc--CHHHHHHHHHHcCccHHH-------------HHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence            3333334444333  999999999999985443             34467888899999999999999874

This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.

>PF14669 Asp_Glu_race_2: Putative aspartate racemase

Probab=80.28  E-value=17  Score=25.19  Aligned_cols=55  Identities=24%  Similarity=0.176  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC------------------CChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR------------------KDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~------------------~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      +--+++..|-+..+|.+..++++.|.+                  +.-+.-|.-...+.+.|.++.|..++++
T Consensus       134 iGiS~m~~Yhk~~qW~KGrkvLd~l~el~i~ft~LKGL~g~e~~asrCqivn~AaEiFL~sgsidGA~~vLre  206 (233)
T PF14669_consen  134 IGISLMYSYHKTLQWSKGRKVLDKLHELQIHFTSLKGLTGPEKLASRCQIVNIAAEIFLKSGSIDGALWVLRE  206 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCccCccccCchhhhHHHHHHHHHHcCCchHHHHHHhc
Confidence            445788899999999999999999832                  1335678888999999999999999985

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.14  E-value=36  Score=28.98  Aligned_cols=81  Identities=19%  Similarity=0.277  Sum_probs=49.1

Q ss_pred             HHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHH
Q 045555           26 YINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM  105 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~  105 (175)
                      +-+.|++++|..-|-+-..--..  .-+|.-|.......+-...++.+.+.|+.-...+               +.|+.+
T Consensus       378 Ly~Kgdf~~A~~qYI~tI~~le~--s~Vi~kfLdaq~IknLt~YLe~L~~~gla~~dht---------------tlLLnc  440 (933)
T KOG2114|consen  378 LYGKGDFDEATDQYIETIGFLEP--SEVIKKFLDAQRIKNLTSYLEALHKKGLANSDHT---------------TLLLNC  440 (933)
T ss_pred             HHhcCCHHHHHHHHHHHcccCCh--HHHHHHhcCHHHHHHHHHHHHHHHHcccccchhH---------------HHHHHH
Confidence            34678888887777664431111  1234455566666666667777777765433222               368888


Q ss_pred             HHhcCCHHHHHHHHHhhc
Q 045555          106 YCKCGDVEKAQRVFWKML  123 (175)
Q Consensus       106 ~~~~~~~~~a~~~~~~~~  123 (175)
                      |.+.++.++-.++.+.-.
T Consensus       441 YiKlkd~~kL~efI~~~~  458 (933)
T KOG2114|consen  441 YIKLKDVEKLTEFISKCD  458 (933)
T ss_pred             HHHhcchHHHHHHHhcCC
Confidence            888888777766666543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	175
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-07
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	2e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 49.0 bits (115), Expect = 2e-07
 Identities = 13/154 (8%), Positives = 44/154 (28%), Gaps = 21/154 (13%)

Query: 15  DVISWTTIVSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLRVNRFREAL 67
                       +   Q+ +A         +          ++ A++ G+ R   F+E +
Sbjct: 126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELV 185

Query: 68  TLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDK 127
            +   ++ + +  D       L ++        A +    +            + + ++ 
Sbjct: 186 YVLFMVKDAGLTPD-------LLSYA-------AALQCMGRQDQDAGTIERCLEQMSQEG 231

Query: 128 FTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD 161
               A+   + +S      +      ++ +  L 
Sbjct: 232 LKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus} Length = 291

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 25/150 (16%), Positives = 51/150 (34%), Gaps = 20/150 (13%)

Query: 10  NMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTL 69
           ++   +        S Y      D A +   Q    + +  T  I   L+++R   A   
Sbjct: 95  SVDVTNTTFLLMAASIYFYDQNPDAALRTLHQGDSLECMAMTVQI--LLKLDRLDLARKE 152

Query: 70  FREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFT 129
            ++MQ  +   ++ T  ++ T          A + +      ++ A  +F +M  K   T
Sbjct: 153 LKKMQDQD---EDATLTQLAT----------AWVSLAAGGEKLQDAYYIFQEMADKCSPT 199

Query: 130 WTAMIVGLAIS----GHGDTALDMFSQMLR 155
              +  G A      G  + A  +  + L 
Sbjct: 200 LLLL-NGQAACHMAQGRWEAAEGVLQEALD 228

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	175
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	99.89
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.87
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.73
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.7
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.42
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.41
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.4
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.39
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.37
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.37
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.35
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.34
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.34
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.33
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.31
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.31
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.3
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.3
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.28
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.27
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.25
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.25
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.25
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.24
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.23
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.23
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.22
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.22
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.21
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.2
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.2
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.19
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.17
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.16
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.16
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.15
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.15
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.14
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.12
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.12
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.12
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.1
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.08
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.08
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.07
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.06
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.06
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.04
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.03
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.03
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.02
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.99
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.98
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.94
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.94
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.93
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.93
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.91
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.9
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.89
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.88
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.87
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.87
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.86
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.86
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.86
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.85
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.84
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.82
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.82
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.8
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.8
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.79
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.79
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.79
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.78
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.75
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.75
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.75
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.74
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.74
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.73
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.73
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.71
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.71
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.69
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.67
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.67
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.66
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.66
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.66
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.65
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.64
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.63
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.63
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.63
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.62
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.61
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.61
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.6
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.6
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.59
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.59
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.59
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.59
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.59
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.58
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.57
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.57
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.56
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.56
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.55
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.55
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.55
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.55
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.53
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.52
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.52
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.5
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.5
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.49
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.49
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.49
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.49
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.48
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.48
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.47
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.47
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.47
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.47
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.46
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.46
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.45
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.44
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.44
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.44
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.44
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.42
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.42
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.42
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.41
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.4
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.39
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	98.38
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.38
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.36
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.36
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.35
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.35
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.33
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.33
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.33
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.31
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.3
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.28
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.27
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.27
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.26
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.26
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.24
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.21
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.2
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.2
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.14
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.1
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.1
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.08
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.08
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.07
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.04
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.04
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.01
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.98
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.96
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.96
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.95
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	97.93
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.92
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.87
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.87
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.86
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.83
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.82
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.81
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.8
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.79
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.77
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.76
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.7
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.69
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.69
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.67
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.66
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.63
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.58
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.48
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.44
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.41
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.33
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.29
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.24
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.13
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.11
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.03
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.99
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.95
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	96.86
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.79
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	96.77
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.7
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.53
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.48
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.32
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	96.2
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.19
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.07
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.03
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.0
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.93
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	95.75
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.69
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.4
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.36
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.98
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.97
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.05
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.71
1pc2_A	152	Mitochondria fission protein; unknown function; NM	93.15
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	93.08
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	92.93
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.37
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	91.34
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	90.75
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	90.43
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	89.38
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	89.05
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	88.35
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	88.35
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	87.65
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	87.6
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	87.51
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	87.28
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	86.82
2p58_C	116	Putative type III secretion protein YSCG; type III	86.53
3ltj_A	201	Alpharep-4; protein engineering, heat-like repeat,	85.77
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	85.55
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	85.43
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	85.42
2ion_A	152	PDCD4, programmed cell death 4, PDCD4; alpha-helic	85.04
2p58_C	116	Putative type III secretion protein YSCG; type III	84.96
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	84.41
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	83.71
2nsz_A	129	Programmed cell death protein 4; PDCD4, tumor supp	82.64
3ygs_P	97	Procaspase 9; apoptosis, caspase activation, caspa	82.54
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	81.99
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	81.6

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=9.6e-34  Score=216.94  Aligned_cols=171  Identities=11%  Similarity=0.090  Sum_probs=141.0

Q ss_pred             HHHHhhccCC----Cc-HHHHHHHHHHHHhcCChhHHHHHhhcCC----CCChhHHHHHHHHHhccCC---------hHH
Q 045555            4 ALEIFGNMKN----KD-VISWTTIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNR---------FRE   65 (175)
Q Consensus         4 A~~~~~~m~~----~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~~---------~~~   65 (175)
                      +..+.+.+.+    +. ...++.+|.+|++.|++++|.++|++|.    +||.+|||+||++|++.+.         ++.
T Consensus         9 ~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~   88 (501)
T 4g26_A            9 SENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSR   88 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHH
T ss_pred             HHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHH
Confidence            4455555554    22 2357778888888888888888888887    3788888888888877654         577


Q ss_pred             HHHHHHHhHhCCCCCChHHHHHhhh---------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh--
Q 045555           66 ALTLFREMQTSNIRRDEFTTVRILT---------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM--  122 (175)
Q Consensus        66 a~~~~~~m~~~~~~p~~~~~~~l~~---------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~--  122 (175)
                      |.++|++|...|+.||..||++++.                     |+.||..+||++|.+|++.|++++|.++|++|  
T Consensus        89 A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~  168 (501)
T 4g26_A           89 GFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVE  168 (501)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            8888888888888888888888887                     77888999999999999999999999999999  


Q ss_pred             --cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          123 --LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       123 --~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                        ..||..+|++||.+|++.|++++|.++|++|.+.|..|+..||..|+..+++
T Consensus       169 ~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          169 SEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             TTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             cCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence              4589999999999999999999999999999999999999999999998764

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=6.6e-32  Score=206.78  Aligned_cols=142  Identities=13%  Similarity=0.148  Sum_probs=123.5

Q ss_pred             HHHHHhhcCCCC-----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh------------------
Q 045555           34 IARQYFAQMPER-----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT------------------   90 (175)
Q Consensus        34 ~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~------------------   90 (175)
                      .+..+.+.+++.     ....++.+|++|++.|++++|+++|++|.+.|+.||..||++++.                  
T Consensus         8 ~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~   87 (501)
T 4g26_A            8 PSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLS   87 (501)
T ss_dssp             ----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHH
T ss_pred             hHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHH
Confidence            345555566542     345689999999999999999999999999999999999999985                  


Q ss_pred             ------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc----CCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           91 ------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML----RKDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        91 ------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                                  |+.||..+||++|.+|++.|++++|.++|++|.    .||..+||++|.+|++.|++++|.++|++|.
T Consensus        88 ~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~  167 (501)
T 4g26_A           88 RGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMV  167 (501)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHH
Confidence                        788999999999999999999999999999994    5799999999999999999999999999999


Q ss_pred             HCCCCCcHHHHHHHHhhhcCC
Q 045555          155 RASIRLDEVTYVGVLSACTHN  175 (175)
Q Consensus       155 ~~g~~p~~~t~~~ll~~~~~~  175 (175)
                      +.|+.||..||+.||++|+++
T Consensus       168 ~~G~~Pd~~ty~~Li~~~~~~  188 (501)
T 4g26_A          168 ESEVVPEEPELAALLKVSMDT  188 (501)
T ss_dssp             HTTCCCCHHHHHHHHHHHHHT
T ss_pred             hcCCCCCHHHHHHHHHHHhhC
Confidence            999999999999999999864

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.89  E-value=1.8e-23  Score=167.32  Aligned_cols=114  Identities=14%  Similarity=0.102  Sum_probs=100.9

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHh---CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh-
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQT---SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM-  122 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~-  122 (175)
                      ..|||+||++||+.|++++|.++|++|.+   .|+.||.+||              |+||++||+.|++++|.++|++| 
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTY--------------NtLI~Glck~G~~~eA~~Lf~eM~  192 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMY--------------NAVMLGWARQGAFKELVYVLFMVK  192 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHH--------------HHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHH--------------HHHHHHHHhCCCHHHHHHHHHHHH
Confidence            35899999999999999999999988764   4666665555              89999999999999999999999 


Q ss_pred             ---cCCChhhHHHHHHHHHhcCCh-hHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          123 ---LRKDKFTWTAMIVGLAISGHG-DTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       123 ---~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                         ..||.+|||++|.++|+.|+. ++|.++|++|.++|+.||..||+.++.++.+
T Consensus       193 ~~G~~PDvvTYntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR  248 (1134)
T 3spa_A          193 DAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR  248 (1134)
T ss_dssp             HTTCCCCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH
T ss_pred             HcCCCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH
Confidence               458999999999999999985 7899999999999999999999987776643

>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=1.2e-22  Score=162.76  Aligned_cols=127  Identities=12%  Similarity=0.172  Sum_probs=110.4

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCC-------CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMP-------ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      ..+||++|++||+.|++++|.++|..|.       .||++|||+||++||+.|++++|.++|++|...|+.||.+||   
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY---  203 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY---  203 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH---
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH---
Confidence            4589999999999999999999997754       589999999999999999999999999999999988887777   


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCH-HHHHHHHHhh----cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDV-EKAQRVFWKM----LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                                 |++|+++++.|+. ++|.++|++|    ..||..+|++++.++.+.    .+++..+++ ..+++|+
T Consensus       204 -----------ntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~----~vL~~Vrkv-~P~f~p~  265 (1134)
T 3spa_A          204 -----------AAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA----TVLKAVHKV-KPTFSLP  265 (1134)
T ss_dssp             -----------HHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH----HHHHHHGGG-CCCCCCC
T ss_pred             -----------HHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH----HHHHHHHHh-CcccCCC
Confidence                       7999999999985 7899999999    458999999999877654    555555555 4466665

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.73  E-value=8.1e-17  Score=124.96  Aligned_cols=145  Identities=13%  Similarity=0.153  Sum_probs=103.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +..+++.++..|.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|+++|+++.+.+              
T Consensus       372 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--------------  437 (597)
T 2xpi_A          372 KAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF--------------  437 (597)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT--------------
T ss_pred             cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--------------
Confidence            344555555555555555555555554431   234455555555555555555555555554432              


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC----CCCCc--H
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA----SIRLD--E  162 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----g~~p~--~  162 (175)
                       +.+..+++.++.+|.+.|++++|.++|+.+.+   .+..+|+.++..|.+.|++++|.++|+++.+.    +..|+  .
T Consensus       438 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~  516 (597)
T 2xpi_A          438 -QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWA  516 (597)
T ss_dssp             -TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGH
T ss_pred             -ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHH
Confidence             33567778999999999999999999999854   47889999999999999999999999999876    77888  7


Q ss_pred             HHHHHHHhhhcC
Q 045555          163 VTYVGVLSACTH  174 (175)
Q Consensus       163 ~t~~~ll~~~~~  174 (175)
                      .++..+..+|.+
T Consensus       517 ~~~~~l~~~~~~  528 (597)
T 2xpi_A          517 ATWANLGHAYRK  528 (597)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            788888887753

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.70  E-value=3.6e-16  Score=121.33  Aligned_cols=171  Identities=8%  Similarity=-0.019  Sum_probs=132.8

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|.++|+++.+  ++..+++.++..|.+.|++++|.++|+++.+   .+..+|+.++.++.+.|++++|..+++++.+.
T Consensus       289 ~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  368 (597)
T 2xpi_A          289 RRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDR  368 (597)
T ss_dssp             HHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhh
Confidence            578999999987  7999999999999999999999999998863   46778999999999999999999999999864


Q ss_pred             CCCCChHHHHHhhh-------------------c-cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHH
Q 045555           77 NIRRDEFTTVRILT-------------------T-FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAM  133 (175)
Q Consensus        77 ~~~p~~~~~~~l~~-------------------~-~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~l  133 (175)
                      . ..+..++..+..                   . .+.+..+|+.++.+|.+.|++++|.++|+++.+   .+..+|+.+
T Consensus       369 ~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l  447 (597)
T 2xpi_A          369 H-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFL  447 (597)
T ss_dssp             C-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHH
T ss_pred             C-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHH
Confidence            3 234555555433                   1 233466788888888888888888888887743   367788888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          134 IVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      +.+|.+.|++++|.+.|+++.+.. +.+..++..+...|.+
T Consensus       448 ~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~  487 (597)
T 2xpi_A          448 GMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFN  487 (597)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHH
Confidence            888888888888888888887642 3356777777766643

>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=99.42  E-value=1.6e-13  Score=102.58  Aligned_cols=157  Identities=12%  Similarity=0.154  Sum_probs=48.1

Q ss_pred             CchHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCC
Q 045555            1 MGFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRR   80 (175)
Q Consensus         1 ~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   80 (175)
                      +++|.++++++..|  .+|..+..++.+.|++++|.+.|.+.  +|..+|..++.++...|++++|+..+...++.  .+
T Consensus        19 ld~A~~fae~~~~~--~vWs~La~A~l~~g~~~eAIdsfika--~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~   92 (449)
T 1b89_A           19 LDRAYEFAERCNEP--AVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--AR   92 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHhCCCh--HHHHHHHHHHHHcCCHHHHHHHHHcC--CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--Cc
Confidence            36788888888655  49999999999999999999999764  67779999999999999999999977766664  33


Q ss_pred             ChHHHHHhhh--------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHH
Q 045555           81 DEFTTVRILT--------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        81 ~~~~~~~l~~--------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  146 (175)
                      ++.+.+.++.              --.|+...|+.+.+.|...|++++|...|..+     ..|..++.++++.|++++|
T Consensus        93 ~~~i~~~Li~~Y~Klg~l~e~e~f~~~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-----~n~~~LA~~L~~Lg~yq~A  167 (449)
T 1b89_A           93 ESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAA  167 (449)
T ss_dssp             ----------------CHHHHTTTTTCC----------------CTTTHHHHHHHT-----TCHHHHHHHHHTTTCHHHH
T ss_pred             cchhHHHHHHHHHHhCCHHHHHHHHcCCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-----hhHHHHHHHHHHhccHHHH
Confidence            3444444443              12466678899999999999999999999977     4899999999999999999


Q ss_pred             HHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          147 LDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       147 ~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                      .+.++++      .+..||..++.+|..
T Consensus       168 Vea~~KA------~~~~~Wk~v~~aCv~  189 (449)
T 1b89_A          168 VDGARKA------NSTRTWKEVCFACVD  189 (449)
T ss_dssp             HHHHHHH------TCHHHHHHHHHHHHH
T ss_pred             HHHHHHc------CCchhHHHHHHHHHH
Confidence            9999988      378889998888863

>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=99.41  E-value=7.7e-12  Score=92.34  Aligned_cols=153  Identities=13%  Similarity=0.078  Sum_probs=95.3

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|++.|+++.+  | +...+..+...+...|++++|...|++..+  | +..++..+...+.+.|++++|+..|+++.+.
T Consensus       187 ~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  266 (388)
T 1w3b_A          187 LAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL  266 (388)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            45555555543  2 344555555666666666666666554432  2 3455555556666666666666666665553


Q ss_pred             CCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHH
Q 045555           77 NIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAM  133 (175)
Q Consensus        77 ~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l  133 (175)
                      +.. +...+..+..                    ..+.+..++..+...+.+.|++++|.+.|+++.+  | +..+|..+
T Consensus       267 ~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l  345 (388)
T 1w3b_A          267 QPH-FPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNL  345 (388)
T ss_dssp             CSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHH
Confidence            211 1112221111                    2244566778888888888999999888888854  3 46678888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHC
Q 045555          134 IVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...|.+.|++++|.+.|+++.+.
T Consensus       346 ~~~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          346 ASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhh
Confidence            88888899999999999888763

>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=2.3e-11  Score=89.82  Aligned_cols=169  Identities=10%  Similarity=0.068  Sum_probs=129.7

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.|+.+.+  | +..+|..+...+.+.|++++|...|+++.+  | +...|..+...+...|++++|+..|++..+
T Consensus       152 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  231 (388)
T 1w3b_A          152 EEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALS  231 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            578889988875  4 578999999999999999999999998864  3 567899999999999999999999999988


Q ss_pred             CCCCCC-hHHHHHhhh-------------------ccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHH
Q 045555           76 SNIRRD-EFTTVRILT-------------------TFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWT  131 (175)
Q Consensus        76 ~~~~p~-~~~~~~l~~-------------------~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~  131 (175)
                      ..  |+ ...+..+..                   ...| +..++..+...+.+.|++++|.+.|+.+.+   .+..+|+
T Consensus       232 ~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~  309 (388)
T 1w3b_A          232 LS--PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLN  309 (388)
T ss_dssp             HC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             hC--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHH
Confidence            53  43 333333222                   2223 466788888888888888888888888743   3677888


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          132 AMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       132 ~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      .+...+...|++++|.+.++++.+. .+.+..++..+...+.
T Consensus       310 ~l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~  350 (388)
T 1w3b_A          310 NLANIKREQGNIEEAVRLYRKALEV-FPEFAAAHSNLASVLQ  350 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTS-CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhc-CCCcHHHHHHHHHHHH
Confidence            8888888888888888888888764 2334556666655543

>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=99.39  E-value=7.3e-11  Score=81.89  Aligned_cols=154  Identities=12%  Similarity=0.035  Sum_probs=93.6

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.|+...+   .+..++..+...|.+.|++++|.+.|++..+   .+...+..+...+.+.|++++|.+.++++.+
T Consensus        54 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  133 (252)
T 2ho1_A           54 EQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLLEASQ  133 (252)
T ss_dssp             GGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Confidence            567777776654   3667888888888888888888888887653   3666788888888888888888888888877


Q ss_pred             CCCCCChH-HHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHH
Q 045555           76 SNIRRDEF-TTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWT  131 (175)
Q Consensus        76 ~~~~p~~~-~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~  131 (175)
                      .+..|+.. .+..+..                    ..+.+...+..+...|.+.|++++|...++...+   .+...+.
T Consensus       134 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~  213 (252)
T 2ho1_A          134 DTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLL  213 (252)
T ss_dssp             CTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             CccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHH
Confidence            33334322 1111110                    1112234444555555555555555555555432   1334444


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHH
Q 045555          132 AMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       132 ~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .+...+...|++++|.+.++++.+
T Consensus       214 ~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          214 LGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHH
Confidence            555555555555555555555544

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.37  E-value=5.4e-11  Score=80.81  Aligned_cols=142  Identities=13%  Similarity=0.029  Sum_probs=107.0

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhcc-CChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRV-NRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~   74 (175)
                      ++|.+.|+...+   .+...+..+...|.+.|++++|...|++..+   .+..++..+...+... |++++|...++++.
T Consensus        25 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~  104 (225)
T 2vq2_A           25 RQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKAL  104 (225)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            467777776654   3577888999999999999999999998753   4677888899999999 99999999999998


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      +.+..|+             +...+..+..++.+.|++++|...|+...+  | +...+..+...+...|++++|.+.++
T Consensus       105 ~~~~~~~-------------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  171 (225)
T 2vq2_A          105 ADPTYPT-------------PYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFK  171 (225)
T ss_dssp             TSTTCSC-------------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             cCcCCcc-------------hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHH
Confidence            8332232             233445677777777888888777777633  2 46667777777777778888877777


Q ss_pred             HHHHC
Q 045555          152 QMLRA  156 (175)
Q Consensus       152 ~m~~~  156 (175)
                      +..+.
T Consensus       172 ~~~~~  176 (225)
T 2vq2_A          172 KYQSR  176 (225)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            77664

>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=99.37  E-value=1.9e-11  Score=91.67  Aligned_cols=159  Identities=14%  Similarity=0.096  Sum_probs=126.0

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|+++|+.+.+   .+..++..+..+|.+.|++++|...|+++.+   .+..++..+...|.+.|++++|...|+++.+
T Consensus        43 ~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  122 (450)
T 2y4t_A           43 ADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLK  122 (450)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            578888887764   4788899999999999999999999998764   3677899999999999999999999999988


Q ss_pred             CCCCCCh----HHHHHhh--------------------------------hccCcchhHHHHHHHHHHhcCCHHHHHHHH
Q 045555           76 SNIRRDE----FTTVRIL--------------------------------TTFNNDIFVGIALIDMYCKCGDVEKAQRVF  119 (175)
Q Consensus        76 ~~~~p~~----~~~~~l~--------------------------------~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  119 (175)
                      ..  |+.    ..+..+.                                ...+.+...+..+..+|.+.|++++|.+.|
T Consensus       123 ~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  200 (450)
T 2y4t_A          123 SN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDL  200 (450)
T ss_dssp             SC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHH
T ss_pred             cC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHH
Confidence            54  433    2222221                                123446778888999999999999999999


Q ss_pred             HhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHH
Q 045555          120 WKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVT  164 (175)
Q Consensus       120 ~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t  164 (175)
                      +.+.+   .+..+|..+...|...|++++|.+.|+++.+.  .|+...
T Consensus       201 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~  246 (450)
T 2y4t_A          201 KAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKR  246 (450)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHH
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHH
Confidence            98843   46788999999999999999999999999864  454433

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.35  E-value=1.1e-10  Score=76.86  Aligned_cols=139  Identities=17%  Similarity=0.182  Sum_probs=89.7

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.|+...+   .+..++..+...+.+.|++++|...+++..+   .+...+..+...+...|++++|...+++..+
T Consensus        25 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  104 (186)
T 3as5_A           25 SQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAE  104 (186)
T ss_dssp             HHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            355666665554   2455666666666666666666666665442   3455566666666666666666666666665


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                      ..               +.+...+..+...+.+.|++++|.+.++...+   .+...+..+...+...|++++|.+.+++
T Consensus       105 ~~---------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  169 (186)
T 3as5_A          105 AN---------------PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKK  169 (186)
T ss_dssp             HC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cC---------------cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            42               22334456677777777788887777777633   2556777777777777788888777777


Q ss_pred             HHH
Q 045555          153 MLR  155 (175)
Q Consensus       153 m~~  155 (175)
                      ..+
T Consensus       170 ~~~  172 (186)
T 3as5_A          170 ANE  172 (186)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            665

>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=99.34  E-value=5.5e-11  Score=89.09  Aligned_cols=157  Identities=11%  Similarity=0.066  Sum_probs=121.6

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+.+.+   .+..++..+...|.+.|++++|...|+++.+   .+..+|..+...+.+.|++++|+..|+++.+
T Consensus       160 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  239 (450)
T 2y4t_A          160 TAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLK  239 (450)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467788887764   4788999999999999999999999999864   5788999999999999999999999999987


Q ss_pred             CCCCCChHHHHHhh-------------h-------------------ccCcc-----hhHHHHHHHHHHhcCCHHHHHHH
Q 045555           76 SNIRRDEFTTVRIL-------------T-------------------TFNND-----IFVGIALIDMYCKCGDVEKAQRV  118 (175)
Q Consensus        76 ~~~~p~~~~~~~l~-------------~-------------------~~~~~-----~~~~~~li~~~~~~~~~~~a~~~  118 (175)
                      .  .|+.......+             .                   ...|+     ...+..+..++.+.|++++|...
T Consensus       240 ~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  317 (450)
T 2y4t_A          240 L--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRV  317 (450)
T ss_dssp             H--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             h--CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            5  34433322111             0                   22343     34677788888888888888888


Q ss_pred             HHhhc--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          119 FWKML--RK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       119 ~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      ++.+.  .| +...|..+..+|...|++++|.+.|+++.+  +.|+.
T Consensus       318 ~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~--~~p~~  362 (450)
T 2y4t_A          318 CSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQE--HNEND  362 (450)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TSSSC
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--hCcch
Confidence            88874  34 577888888888888888888888888876  34543

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.34  E-value=1.6e-10  Score=76.72  Aligned_cols=146  Identities=12%  Similarity=0.083  Sum_probs=107.6

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh-
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT-   90 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~-   90 (175)
                      +...|..+...|.+.|++++|...|++..+   .+..+|..+...+.+.|++++|+..+.+.................. 
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~   83 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSAN   83 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHH
Confidence            456777788888888888888888887653   3566777777778888888888888877776543222111111000 


Q ss_pred             ------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHH
Q 045555           91 ------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        91 ------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                                        ..+.+...+..+...|.+.|++++|.+.|++..+  | +...|..+...|.+.|++++|.+.
T Consensus        84 ~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A~~~  163 (184)
T 3vtx_A           84 FMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEAVKY  163 (184)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHHHHH
Confidence                              2234567788899999999999999999999843  4 677899999999999999999999


Q ss_pred             HHHHHHCCCCCcH
Q 045555          150 FSQMLRASIRLDE  162 (175)
Q Consensus       150 ~~~m~~~g~~p~~  162 (175)
                      |++.++.  .|+.
T Consensus       164 ~~~al~~--~p~~  174 (184)
T 3vtx_A          164 FKKALEK--EEKK  174 (184)
T ss_dssp             HHHHHHT--THHH
T ss_pred             HHHHHhC--CccC
Confidence            9999874  4554

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.33  E-value=2.3e-10  Score=81.87  Aligned_cols=150  Identities=15%  Similarity=0.084  Sum_probs=104.4

Q ss_pred             chHHHHhhccC----CC-cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMK----NK-DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|++.++++.    .| +...+..+...+.+.|++++|...+++  ..+...+..+...+.+.|++++|...|+++.+.
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~  159 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQ  159 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence            46788888763    24 566777888999999999999999998  567788999999999999999999999999986


Q ss_pred             CCCCChHH------HHHhhh-----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhH
Q 045555           77 NIRRDEFT------TVRILT-----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTW  130 (175)
Q Consensus        77 ~~~p~~~~------~~~l~~-----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~  130 (175)
                      .  |+...      |..+..                 ..+.+...++.+..++.+.|++++|.+.|++..+  | +..++
T Consensus       160 ~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l  237 (291)
T 3mkr_A          160 D--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETL  237 (291)
T ss_dssp             C--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             C--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHH
Confidence            4  44321      111110                 2344555666666666666666666666666532  3 45566


Q ss_pred             HHHHHHHHhcCChhH-HHHHHHHHHH
Q 045555          131 TAMIVGLAISGHGDT-ALDMFSQMLR  155 (175)
Q Consensus       131 ~~li~~~~~~g~~~~-a~~~~~~m~~  155 (175)
                      ..++..+...|+.++ +.++++++.+
T Consensus       238 ~~l~~~~~~~g~~~eaa~~~~~~~~~  263 (291)
T 3mkr_A          238 INLVVLSQHLGKPPEVTNRYLSQLKD  263 (291)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            666666666666654 3456666554

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.31  E-value=1.5e-10  Score=72.07  Aligned_cols=125  Identities=20%  Similarity=0.366  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      .+|..+...+.+.|++++|..+|+++.+   .+...+..+...+...|++++|...++++.+.+.               
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~---------------   66 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP---------------   66 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT---------------
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCC---------------
Confidence            3678889999999999999999998753   4677888999999999999999999999987542               


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+...+..+...+.+.|++++|.+.++.+..   .+...+..+...+.+.|++++|.+.++++.+.
T Consensus        67 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           67 RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHcc
Confidence            2334556789999999999999999999843   36778889999999999999999999998864

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.31  E-value=1.2e-10  Score=80.18  Aligned_cols=153  Identities=14%  Similarity=0.144  Sum_probs=91.5

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|...|+...+   .+...+..+...+.+.|++++|...|++..+   .+...+..+...+...|++++|...+++..+
T Consensus        40 ~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  119 (243)
T 2q7f_A           40 EKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALR  119 (243)
T ss_dssp             --CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            345555555543   3567778888888888888888888887653   3566777788888888888888888888877


Q ss_pred             CCCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHH
Q 045555           76 SNIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTA  132 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~  132 (175)
                      .... +...+..+..                    ..+.+...+..+...|.+.|++++|...|+...+   .+..+|..
T Consensus       120 ~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  198 (243)
T 2q7f_A          120 AGME-NGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYN  198 (243)
T ss_dssp             HTCC-SHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             hCCC-CHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHH
Confidence            5421 2222211111                    1122344555555555566666666666555522   23445555


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHH
Q 045555          133 MIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +...|...|++++|.+.++++.+
T Consensus       199 la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          199 AGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             HHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHc
Confidence            55666666666666666666554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.30  E-value=2e-10  Score=78.62  Aligned_cols=152  Identities=16%  Similarity=0.131  Sum_probs=119.1

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhcc-----------CChH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRV-----------NRFR   64 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~-----------~~~~   64 (175)
                      ++|+..|+...+  | +...+..+...+.+.|++++|...|++..+  | +...+..+...+.+.           |+++
T Consensus        22 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~  101 (217)
T 2pl2_A           22 DAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAEDRERGKGYLE  101 (217)
T ss_dssp             HHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhhhcccccCHH
Confidence            467777776654  3 677888888888889999999988887653  3 566788888888888           8899


Q ss_pred             HHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCC
Q 045555           65 EALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGH  142 (175)
Q Consensus        65 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~  142 (175)
                      +|+..|++..+..  |             .+...+..+...|...|++++|...|++..+  .+...+..+...|...|+
T Consensus       102 ~A~~~~~~al~~~--P-------------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~  166 (217)
T 2pl2_A          102 QALSVLKDAERVN--P-------------RYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGR  166 (217)
T ss_dssp             HHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhC--c-------------ccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCC
Confidence            9999888888753  2             2345567899999999999999999999843  677788999999999999


Q ss_pred             hhHHHHHHHHHHHCCCCC-cHHHHHHHHh
Q 045555          143 GDTALDMFSQMLRASIRL-DEVTYVGVLS  170 (175)
Q Consensus       143 ~~~a~~~~~~m~~~g~~p-~~~t~~~ll~  170 (175)
                      +++|...|++..+.  .| +...+..+-.
T Consensus       167 ~~~A~~~~~~al~~--~P~~~~~~~~la~  193 (217)
T 2pl2_A          167 LDEALAQYAKALEQ--APKDLDLRVRYAS  193 (217)
T ss_dssp             HHHHHHHHHHHHHH--STTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh--CCCChHHHHHHHH
Confidence            99999999999874  34 3444444433

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.30  E-value=5.9e-11  Score=86.82  Aligned_cols=166  Identities=13%  Similarity=0.136  Sum_probs=129.1

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+.+.+   .+..++..+...|.+.|++++|...|++..+   .+..+|..+...|.+.|++++|+..|+++.+
T Consensus        82 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  161 (365)
T 4eqf_A           82 PVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIK  161 (365)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHH
Confidence            568888887765   4778999999999999999999999998763   4678899999999999999999999999987


Q ss_pred             CCCCCChHH-H------------------------------HHhhhccCc---chhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           76 SNIRRDEFT-T------------------------------VRILTTFNN---DIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        76 ~~~~p~~~~-~------------------------------~~l~~~~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      ..  |+... +                              ...+ ...|   +..++..+...|.+.|++++|.+.|++
T Consensus       162 ~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al-~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  238 (365)
T 4eqf_A          162 QN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAA-HQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNA  238 (365)
T ss_dssp             HC--HHHHCC-------------------CCHHHHHHHHHHHHHH-HHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHH-HhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            43  22111 0                              0011 1223   577888999999999999999999999


Q ss_pred             hcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc-HHHHHHHHhhh
Q 045555          122 MLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD-EVTYVGVLSAC  172 (175)
Q Consensus       122 ~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~  172 (175)
                      ..+  | +..+|..+...|...|++++|.+.|++..+.  .|+ ..++..+-..|
T Consensus       239 al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~  291 (365)
T 4eqf_A          239 ALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEI--QPGFIRSRYNLGISC  291 (365)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHH
Confidence            843  3 6788999999999999999999999998875  343 55555554443

>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=99.28  E-value=5.4e-10  Score=81.50  Aligned_cols=168  Identities=15%  Similarity=0.142  Sum_probs=128.3

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|+..|+.+.+   .+..++..+...|.+.|++++|...|++..+   .+..++..+...+...|++++|...++++.+
T Consensus        81 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  160 (368)
T 1fch_A           81 PNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLR  160 (368)
T ss_dssp             HHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467788887764   4677899999999999999999999998663   4777899999999999999999999999988


Q ss_pred             CCCCCChHH----------------------------------HHHhhhccCc---chhHHHHHHHHHHhcCCHHHHHHH
Q 045555           76 SNIRRDEFT----------------------------------TVRILTTFNN---DIFVGIALIDMYCKCGDVEKAQRV  118 (175)
Q Consensus        76 ~~~~p~~~~----------------------------------~~~l~~~~~~---~~~~~~~li~~~~~~~~~~~a~~~  118 (175)
                      .........                                  +..++ ...|   +..++..+...|.+.|++++|...
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~-~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~  239 (368)
T 1fch_A          161 YTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAV-RLDPTSIDPDVQCGLGVLFNLSGEYDKAVDC  239 (368)
T ss_dssp             TSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHH-HHSTTSCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHH-HhCcCcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            643221111                                  11111 1233   477888999999999999999999


Q ss_pred             HHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          119 FWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       119 ~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      |++...  | +...|..+...+...|++++|.+.|+++.+.. +.+...+..+-..
T Consensus       240 ~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~  294 (368)
T 1fch_A          240 FTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGIS  294 (368)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            999843  3 57789999999999999999999999988742 2234455444443

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.27  E-value=2.4e-10  Score=78.60  Aligned_cols=122  Identities=12%  Similarity=0.046  Sum_probs=88.7

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+   .+..++..+...|.+.|++++|...|++..+   .+...+..+...+.+.|++++|...+++..+
T Consensus        74 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  153 (243)
T 2q7f_A           74 ERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVE  153 (243)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            456666666553   3667788888888888888888888887653   4666778888888888888888888888877


Q ss_pred             CCCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           76 SNIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .... +...+..+..                    ..+.+..++..+...|.+.|++++|...++...+
T Consensus       154 ~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          154 LNEN-DTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             HCTT-CHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             hCCc-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHc
Confidence            5321 2223322221                    2234577888999999999999999999999854

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.25  E-value=4.7e-10  Score=76.79  Aligned_cols=141  Identities=15%  Similarity=0.022  Sum_probs=118.1

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      ++...+..+...+.+.|++++|...|++..+   .+...+..+...+.+.|++++|+..|++..+..  |+         
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~---------   71 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVART--PR---------   71 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT---------
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC---------
Confidence            4667888999999999999999999998654   367789999999999999999999999999854  22         


Q ss_pred             ccCcchhHHHHHHHHHHhc-----------CCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           91 TFNNDIFVGIALIDMYCKC-----------GDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~-----------~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                          +...+..+...+.+.           |++++|...|++..+  | +...|..+...+...|++++|.+.|++..+.
T Consensus        72 ----~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  147 (217)
T 2pl2_A           72 ----YLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALAL  147 (217)
T ss_dssp             ----CHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ----cHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhc
Confidence                345567888899999           999999999999854  4 5778999999999999999999999999987


Q ss_pred             CCCCcHHHHHHHHhh
Q 045555          157 SIRLDEVTYVGVLSA  171 (175)
Q Consensus       157 g~~p~~~t~~~ll~~  171 (175)
                      .  .+...+..+-..
T Consensus       148 ~--~~~~~~~~la~~  160 (217)
T 2pl2_A          148 E--DTPEIRSALAEL  160 (217)
T ss_dssp             C--CCHHHHHHHHHH
T ss_pred             c--cchHHHHHHHHH
Confidence            6  566666555443

>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=6.3e-10  Score=75.46  Aligned_cols=152  Identities=13%  Similarity=-0.047  Sum_probs=123.4

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhc-CChhHHHHHhhcCCC----C-ChhHHHHHHHHHhccCChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINR-GQVDIARQYFAQMPE----R-DYVLWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~----~-~~~~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      ++|.+.|+...+   .+..++..+...+... |++++|...|+.+.+    | +...+..+...+.+.|++++|...+++
T Consensus        59 ~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  138 (225)
T 2vq2_A           59 DKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKR  138 (225)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            467777777654   4678899999999999 999999999998765    2 356788999999999999999999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----CChhhHHHHHHHHHhcCChhHHHH
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----KDKFTWTAMIVGLAISGHGDTALD  148 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~a~~  148 (175)
                      ..+..  |             .+...+..+...|.+.|++++|.+.++...+    .+...+..+...+...|+.++|..
T Consensus       139 ~~~~~--~-------------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  203 (225)
T 2vq2_A          139 SLAAQ--P-------------QFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYE  203 (225)
T ss_dssp             HHHHS--T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHhC--C-------------CCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHH
Confidence            98853  2             2344567899999999999999999999843    466778888888899999999999


Q ss_pred             HHHHHHHCCCCCcHHHHHHHHh
Q 045555          149 MFSQMLRASIRLDEVTYVGVLS  170 (175)
Q Consensus       149 ~~~~m~~~g~~p~~~t~~~ll~  170 (175)
                      .++.+.+.  .|+......++.
T Consensus       204 ~~~~~~~~--~p~~~~~~~~l~  223 (225)
T 2vq2_A          204 YEAQLQAN--FPYSEELQTVLT  223 (225)
T ss_dssp             HHHHHHHH--CTTCHHHHHHHC
T ss_pred             HHHHHHHh--CCCCHHHHHHhc
Confidence            99998764  466655555543

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.25  E-value=3.3e-09  Score=69.56  Aligned_cols=140  Identities=14%  Similarity=0.073  Sum_probs=114.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      ...+..+...+.+.|++++|...|+.+.+   .+...+..+...+...|++++|...+++..+..               
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~---------------   72 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA---------------   72 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---------------
Confidence            45678888999999999999999999875   367789999999999999999999999998863               


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHH
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVL  169 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll  169 (175)
                      +.+...+..+...+...|++++|.+.++....   .+...+..+...+...|++++|.+.+++..+.. +.+...+..+.
T Consensus        73 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la  151 (186)
T 3as5_A           73 PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIA  151 (186)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHH
Confidence            22345567889999999999999999999843   367788889999999999999999999998753 22344554444


Q ss_pred             hh
Q 045555          170 SA  171 (175)
Q Consensus       170 ~~  171 (175)
                      ..
T Consensus       152 ~~  153 (186)
T 3as5_A          152 FS  153 (186)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.24  E-value=1.2e-09  Score=78.14  Aligned_cols=169  Identities=10%  Similarity=0.034  Sum_probs=114.0

Q ss_pred             chHHHHhhccCC--Cc--HHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            2 GFALEIFGNMKN--KD--VISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~--~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ++|+..++....  |+  ......+.++|...|+++.|...++....|+..++..+...+...++.++|++.++++...+
T Consensus        16 ~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~   95 (291)
T 3mkr_A           16 QQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRS   95 (291)
T ss_dssp             HHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcc
Confidence            356666665544  33  24556778999999999999998888666777888999999999999999999999999887


Q ss_pred             CCCChHHHHHhhh----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhH---HHHHHH
Q 045555           78 IRRDEFTTVRILT----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTW---TAMIVG  136 (175)
Q Consensus        78 ~~p~~~~~~~l~~----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~---~~li~~  136 (175)
                      ..|+...+...+.                .-+.+...+..+...|.+.|++++|.+.|+.+.+  |+....   ..++..
T Consensus        96 ~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~l~~a~~~l  175 (291)
T 3mkr_A           96 VDVTNTTFLLMAASIYFYDQNPDAALRTLHQGDSLECMAMTVQILLKLDRLDLARKELKKMQDQDEDATLTQLATAWVSL  175 (291)
T ss_dssp             CCCSCHHHHHHHHHHHHHTTCHHHHHHHHTTCCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHCCCHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCcHHHHHHHHHHHH
Confidence            6676554433322                1134566677777777777777777777777743  332211   122233


Q ss_pred             HHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          137 LAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       137 ~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      +...|++++|..+|+++.+. .+.+...+..+-.+
T Consensus       176 ~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~  209 (291)
T 3mkr_A          176 AAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAAC  209 (291)
T ss_dssp             HHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHH
T ss_pred             HhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHH
Confidence            34457777787777777765 33455555544333

>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=99.23  E-value=1.3e-09  Score=77.97  Aligned_cols=169  Identities=14%  Similarity=0.115  Sum_probs=129.3

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.++|+.+.+   .+..++..+...+.+.|++++|...|++..+   .+..++..+...+...|++++|...+++..+
T Consensus        38 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  117 (327)
T 3cv0_A           38 AEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLL  117 (327)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            568888887764   3677899999999999999999999998763   4677899999999999999999999999987


Q ss_pred             CCCCCChHH----------------------------------HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           76 SNIRRDEFT----------------------------------TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        76 ~~~~p~~~~----------------------------------~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      .........                                  +..++...+.+...+..+...|.+.|++++|.+.++.
T Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  197 (327)
T 3cv0_A          118 SQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRR  197 (327)
T ss_dssp             TSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence            642211111                                  1111113344677888999999999999999999998


Q ss_pred             hcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          122 MLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       122 ~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      ..+  | +...|..+...+...|++++|.+.|++..+.. +.+..++..+-..
T Consensus       198 ~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~  249 (327)
T 3cv0_A          198 AVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVS  249 (327)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHH
Confidence            843  3 57788999999999999999999999988753 2234555554443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.23  E-value=2.5e-10  Score=83.45  Aligned_cols=155  Identities=12%  Similarity=0.005  Sum_probs=109.2

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC-----------hhHHHHHHHHHhccCChHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RD-----------YVLWTAMIDGYLRVNRFRE   65 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~-----------~~~~~~li~~~~~~~~~~~   65 (175)
                      ++|++.|+...+   .+..++..+...|.+.|++++|...|+++.+  |+           ...+..+...+.+.|++++
T Consensus       116 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  195 (365)
T 4eqf_A          116 QAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEG  195 (365)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHH
Confidence            467788887764   3678899999999999999999999988753  21           1122334556666677777


Q ss_pred             HHHHHHHhHhCCCC-CChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           66 ALTLFREMQTSNIR-RDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        66 a~~~~~~m~~~~~~-p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      |+..|+++.+.... ++...+..+-.                    ..+.+..++..+..+|.+.|++++|.+.|++..+
T Consensus       196 A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  275 (365)
T 4eqf_A          196 VKELYLEAAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALE  275 (365)
T ss_dssp             HHHHHHHHHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            77777777664322 12333333222                    2234577889999999999999999999999843


Q ss_pred             --C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 --K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 --~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                        | +..+|..+...|.+.|++++|.+.|++..+.
T Consensus       276 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  310 (365)
T 4eqf_A          276 IQPGFIRSRYNLGISCINLGAYREAVSNFLTALSL  310 (365)
T ss_dssp             HCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence              4 5788999999999999999999999998863

>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=99.22  E-value=8e-10  Score=79.18  Aligned_cols=58  Identities=19%  Similarity=0.115  Sum_probs=28.1

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      .++..+...|.+.|++++|...|+...+   .+...|..+...+.+.|++++|.+.|++..
T Consensus       237 ~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  297 (330)
T 3hym_B          237 PLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTAL  297 (330)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            3444455555555555555555554421   134444455555555555555555555544

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=99.22  E-value=3.4e-09  Score=71.68  Aligned_cols=127  Identities=10%  Similarity=-0.017  Sum_probs=109.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      ...+..+...+.+.|++++|...|++...++...|..+...+.+.|++++|+..|++..+..  |             .+
T Consensus         6 ~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~-------------~~   70 (213)
T 1hh8_A            6 AISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD--K-------------HL   70 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TC
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--c-------------cc
Confidence            34566778888999999999999999998899999999999999999999999999998854  2             23


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-Ch----------------hhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DK----------------FTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~----------------~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...+..+..+|.+.|++++|.+.|+...+  | +.                ..|..+...|...|++++|.+.|++..+.
T Consensus        71 ~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           71 AVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            45567899999999999999999999854  2 22                67888999999999999999999999875


Q ss_pred             C
Q 045555          157 S  157 (175)
Q Consensus       157 g  157 (175)
                      .
T Consensus       151 ~  151 (213)
T 1hh8_A          151 K  151 (213)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.21  E-value=4.4e-10  Score=77.78  Aligned_cols=155  Identities=10%  Similarity=0.020  Sum_probs=122.5

Q ss_pred             chHHHHhhccCC--Cc--------HHHHHHHHHHHHhcCChhHHHHHhhcCCC--------------------------C
Q 045555            2 GFALEIFGNMKN--KD--------VISWTTIVSGYINRGQVDIARQYFAQMPE--------------------------R   45 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~--------~~~~~~li~~~~~~~~~~~a~~~~~~m~~--------------------------~   45 (175)
                      ++|.+.|+...+  |+        ..++..+...|.+.|++++|...|++..+                          .
T Consensus        55 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  134 (258)
T 3uq3_A           55 ETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYV  134 (258)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHc
Confidence            456677776654  22        57899999999999999999999998654                          1


Q ss_pred             ---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           46 ---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        46 ---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                         +...+..+...+...|++++|+..+++..+..               +.+...+..+...|.+.|++++|.+.|+..
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~---------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  199 (258)
T 3uq3_A          135 NPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA---------------PEDARGYSNRAAALAKLMSFPEAIADCNKA  199 (258)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC---------------cccHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence               34568888889999999999999999998854               223456678999999999999999999998


Q ss_pred             cC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC----CCCcHHHHHHHHhh
Q 045555          123 LR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS----IRLDEVTYVGVLSA  171 (175)
Q Consensus       123 ~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~t~~~ll~~  171 (175)
                      .+  | +...|..+...+...|++++|.+.|++..+..    ..|+.......+.-
T Consensus       200 l~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~p~~~~~~~~l~~  255 (258)
T 3uq3_A          200 IEKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYK  255 (258)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhChhhcCCCchHHHHHHHHH
Confidence            43  3 57789999999999999999999999987642    22665555444443

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.20  E-value=9.2e-10  Score=76.16  Aligned_cols=167  Identities=13%  Similarity=0.124  Sum_probs=129.0

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-C-------hhHHHHHHHHHhccCChHHHHHH
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-D-------YVLWTAMIDGYLRVNRFREALTL   69 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~-------~~~~~~li~~~~~~~~~~~a~~~   69 (175)
                      ++|++.|+...+  ++..++..+...|.+.|++++|...|+...+  | +       ..+|..+...+.+.|++++|+..
T Consensus        22 ~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  101 (258)
T 3uq3_A           22 DEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEY  101 (258)
T ss_dssp             HHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHH
Confidence            456666665543  6788999999999999999999999998764  2 1       57899999999999999999999


Q ss_pred             HHHhHhCCCCCChHHHHHhhh-------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHH
Q 045555           70 FREMQTSNIRRDEFTTVRILT-------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAM  133 (175)
Q Consensus        70 ~~~m~~~~~~p~~~~~~~l~~-------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~l  133 (175)
                      |++..+..  |+...+..+-.             ..+.+...+..+...+...|++++|...|+...+   .+...|..+
T Consensus       102 ~~~a~~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l  179 (258)
T 3uq3_A          102 YQKSLTEH--RTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNR  179 (258)
T ss_dssp             HHHHHHHC--CCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHhcC--chhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHH
Confidence            99999854  43332222111             2233466788999999999999999999999843   367889999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhh
Q 045555          134 IVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSA  171 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~  171 (175)
                      ...+...|++++|.+.|++..+.. +.+...+..+-..
T Consensus       180 ~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~  216 (258)
T 3uq3_A          180 AAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATA  216 (258)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHH
Confidence            999999999999999999998753 2234455444333

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.20  E-value=2.8e-10  Score=90.85  Aligned_cols=137  Identities=10%  Similarity=0.060  Sum_probs=71.0

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|++.|++..+  | +..+|+.+...|.+.|++++|...|++..+   .+...|+.+...|.+.|++++|++.|++..+.
T Consensus        27 eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l  106 (723)
T 4gyw_A           27 EAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI  106 (723)
T ss_dssp             HHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            44444444432  2 344555555555555555555555554432   23444555555555555555555555555442


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                      .  |             -+...++.+..+|.+.|++++|.+.|++..+  | +...|..+...|...|++++|.+.+++.
T Consensus       107 ~--P-------------~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~~~~ka  171 (723)
T 4gyw_A          107 N--P-------------AFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKL  171 (723)
T ss_dssp             C--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHHHHHHH
T ss_pred             C--C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHHHHHHH
Confidence            1  1             1233445566666666666666666665532  2 4455566666666666666666555554


Q ss_pred             H
Q 045555          154 L  154 (175)
Q Consensus       154 ~  154 (175)
                      .
T Consensus       172 l  172 (723)
T 4gyw_A          172 V  172 (723)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=99.19  E-value=9.6e-10  Score=78.78  Aligned_cols=153  Identities=14%  Similarity=0.071  Sum_probs=89.2

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccC-ChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVN-RFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~   75 (175)
                      +|+++|+.+.+  | +...+..++..+.+.|++++|..+++++.+   .+...|..+...+...| ++++|...|++..+
T Consensus        40 ~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~  119 (330)
T 3hym_B           40 MCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFAVGCYYLMVGHKNEHARRYLSKATT  119 (330)
T ss_dssp             HHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            44555554432  1 233344444555555555555555554432   23444555555555555 55555555555544


Q ss_pred             CCCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHH
Q 045555           76 SNIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTA  132 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~  132 (175)
                      .... +...+..+-.                    ..+.+...+..+...|...|++++|.+.++...+   .+...+..
T Consensus       120 ~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  198 (330)
T 3hym_B          120 LEKT-YGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIAPEDPFVMHE  198 (330)
T ss_dssp             TCTT-CTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHH
T ss_pred             hCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCCCChHHHHH
Confidence            3211 1111111111                    1122345556788889999999999999998854   25678888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHC
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +...+...|++++|.+.+++..+.
T Consensus       199 l~~~~~~~~~~~~A~~~~~~a~~~  222 (330)
T 3hym_B          199 VGVVAFQNGEWKTAEKWFLDALEK  222 (330)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHH
Confidence            999999999999999999888763

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.17  E-value=7.1e-10  Score=77.62  Aligned_cols=140  Identities=11%  Similarity=-0.011  Sum_probs=112.9

Q ss_pred             chHHHHhhccCC-------CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN-------KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~-------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~   71 (175)
                      ++|++.|+.+.+       .+..++..+...+.+.|++++|...|++..+   .+..+|..+...+.+.|++++|+..|+
T Consensus        22 ~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  101 (275)
T 1xnf_A           22 EVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFD  101 (275)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            567888887765       1567899999999999999999999998763   467889999999999999999999999


Q ss_pred             HhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhcCChhHHHHH
Q 045555           72 EMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                      +..+..  |             .+...+..+...|.+.|++++|.+.|+...+  |+.......+..+...|++++|...
T Consensus       102 ~al~~~--~-------------~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~  166 (275)
T 1xnf_A          102 SVLELD--P-------------TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEV  166 (275)
T ss_dssp             HHHHHC--T-------------TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             HHHhcC--c-------------cccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHH
Confidence            999853  2             2345567899999999999999999999843  5544445555555677899999999


Q ss_pred             HHHHHHC
Q 045555          150 FSQMLRA  156 (175)
Q Consensus       150 ~~~m~~~  156 (175)
                      +++....
T Consensus       167 ~~~~~~~  173 (275)
T 1xnf_A          167 LKQHFEK  173 (275)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhc
Confidence            9777654

>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=99.16  E-value=2.8e-09  Score=73.79  Aligned_cols=139  Identities=15%  Similarity=0.028  Sum_probs=98.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh--
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT--   90 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~--   90 (175)
                      ...+..+...+...|++++|...|+++.+   .+...+..+...+.+.|++++|.+.+++..+.... +...+..+..  
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~  115 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASDSR-NARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHHH
Confidence            67789999999999999999999998763   46778999999999999999999999999886422 2222222211  


Q ss_pred             -----------------c--cCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHH
Q 045555           91 -----------------T--FNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        91 -----------------~--~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~  147 (175)
                                       .  ..| +...+..+...|.+.|++++|.+.|++..+  | +...+..+...+...|++++|.
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  195 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPAR  195 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHH
Confidence                             1  222 345556666666666667666666666532  2 4556666666666777777777


Q ss_pred             HHHHHHHH
Q 045555          148 DMFSQMLR  155 (175)
Q Consensus       148 ~~~~~m~~  155 (175)
                      +.++++.+
T Consensus       196 ~~~~~~~~  203 (252)
T 2ho1_A          196 QYYDLFAQ  203 (252)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHH
Confidence            77766654

>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=99.16  E-value=1.7e-10  Score=86.44  Aligned_cols=104  Identities=11%  Similarity=0.050  Sum_probs=36.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      ++.+.+.++.+|.+.|+++++.++++   .|+..+|+.+...|...|.+++|...|..+.                    
T Consensus        93 ~~~i~~~Li~~Y~Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~--------------------  149 (449)
T 1b89_A           93 ESYVETELIFALAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS--------------------  149 (449)
T ss_dssp             ----------------CHHHHTTTTT---CC----------------CTTTHHHHHHHTT--------------------
T ss_pred             cchhHHHHHHHHHHhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCCHHHHHHHHHHhh--------------------
Confidence            34455555556666666555555543   2444455555555555555555555555441                    


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  146 (175)
                         .|..+++++.+.|++++|.+.+.++.  ++.+|..++.+|+..|+++.|
T Consensus       150 ---n~~~LA~~L~~Lg~yq~AVea~~KA~--~~~~Wk~v~~aCv~~~ef~lA  196 (449)
T 1b89_A          150 ---NFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFRLA  196 (449)
T ss_dssp             ---CHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTCHHHH
T ss_pred             ---hHHHHHHHHHHhccHHHHHHHHHHcC--CchhHHHHHHHHHHcCcHHHH
Confidence               23455555555555555555555552  445555555554444444444

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.15  E-value=2.1e-09  Score=85.80  Aligned_cols=139  Identities=12%  Similarity=0.090  Sum_probs=118.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +..+++.+...|.+.|++++|...|++..+   .+..+|+.|...|.+.|++++|++.|++.++..  |+          
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~--P~----------   75 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS--PT----------   75 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT----------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC----------
Confidence            567899999999999999999999998764   467889999999999999999999999998853  32          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc-HHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD-EVTYVG  167 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~  167 (175)
                         +...|..+..+|.+.|++++|.+.|++..+  | +...|+.+...|...|++++|.+.|++.++.  .|+ ...+..
T Consensus        76 ---~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~  150 (723)
T 4gyw_A           76 ---FADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCN  150 (723)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHH
T ss_pred             ---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhh
Confidence               355678899999999999999999999844  4 6789999999999999999999999999874  454 344444


Q ss_pred             HHh
Q 045555          168 VLS  170 (175)
Q Consensus       168 ll~  170 (175)
                      +..
T Consensus       151 L~~  153 (723)
T 4gyw_A          151 LAH  153 (723)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            433

>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=99.15  E-value=5.1e-10  Score=81.63  Aligned_cols=137  Identities=18%  Similarity=0.170  Sum_probs=108.3

Q ss_pred             chHHHHhhccCC--C---cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN--K---DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~--~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|++.|+.+.+  |   +..++..+...|.+.|++++|...|++..+   .+..+|..+...+.+.|++++|+..|++.
T Consensus       198 ~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  277 (368)
T 1fch_A          198 LEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRA  277 (368)
T ss_dssp             HHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            467777776654  4   477888899999999999999999988653   35678888899999999999999999998


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-C-----------hhhHHHHHHHHHh
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-D-----------KFTWTAMIVGLAI  139 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~-----------~~~~~~li~~~~~  139 (175)
                      .+..  |             .+...+..+..+|.+.|++++|...|+...+  | +           ..+|..+..+|..
T Consensus       278 l~~~--~-------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  342 (368)
T 1fch_A          278 LELQ--P-------------GYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSM  342 (368)
T ss_dssp             HHHC--T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHH
T ss_pred             HHhC--C-------------CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHH
Confidence            8753  2             2345567888899999999999999988743  2 2           5788889999999


Q ss_pred             cCChhHHHHHHHHH
Q 045555          140 SGHGDTALDMFSQM  153 (175)
Q Consensus       140 ~g~~~~a~~~~~~m  153 (175)
                      .|+.++|..++++-
T Consensus       343 ~g~~~~A~~~~~~~  356 (368)
T 1fch_A          343 LGQSDAYGAADARD  356 (368)
T ss_dssp             HTCGGGHHHHHTTC
T ss_pred             hCChHhHHHhHHHH
Confidence            99999998887643

>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=99.14  E-value=5.2e-10  Score=80.06  Aligned_cols=138  Identities=15%  Similarity=0.136  Sum_probs=110.0

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.+++..+   .+..++..+...|.+.|++++|...+++..+   .+..++..+...+.+.|++++|...+++..+
T Consensus       155 ~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  234 (327)
T 3cv0_A          155 RECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALD  234 (327)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            456677776654   3677888999999999999999999988653   3567888999999999999999999999887


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC-------------hhhHHHHHHHHHhc
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD-------------KFTWTAMIVGLAIS  140 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-------------~~~~~~li~~~~~~  140 (175)
                      ..  |             .+...+..+...|.+.|++++|.+.|+....  |+             ...|..+..++.+.
T Consensus       235 ~~--~-------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  299 (327)
T 3cv0_A          235 IN--P-------------GYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVM  299 (327)
T ss_dssp             HC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHT
T ss_pred             cC--C-------------CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhc
Confidence            53  2             2344557888899999999999999988733  33             56888889999999


Q ss_pred             CChhHHHHHHHHHH
Q 045555          141 GHGDTALDMFSQML  154 (175)
Q Consensus       141 g~~~~a~~~~~~m~  154 (175)
                      |++++|.+++++..
T Consensus       300 g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          300 NRPDLVELTYAQNV  313 (327)
T ss_dssp             TCHHHHHHHTTCCS
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999998887644

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.12  E-value=3.7e-09  Score=76.41  Aligned_cols=155  Identities=14%  Similarity=0.088  Sum_probs=113.5

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+   .+..++..+...+.+.|++++|...|+...+  | +...+..+...+.+.|++++|...|++..+
T Consensus        20 ~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   99 (359)
T 3ieg_A           20 ADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLK   99 (359)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHh
Confidence            578888887764   3678999999999999999999999998763  3 667899999999999999999999999988


Q ss_pred             CCCC--CChHHHHHh--------------------------------hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           76 SNIR--RDEFTTVRI--------------------------------LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        76 ~~~~--p~~~~~~~l--------------------------------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      ....  .+...+..+                                +...+.+...+..+...+.+.|++++|...++.
T Consensus       100 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~  179 (359)
T 3ieg_A          100 SNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKA  179 (359)
T ss_dssp             SCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             cCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            5420  122222111                                002233456667777777777777777777777


Q ss_pred             hcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          122 MLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       122 ~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ..+   .+...|..+...+...|++++|.+.|++..+.
T Consensus       180 ~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  217 (359)
T 3ieg_A          180 ASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL  217 (359)
T ss_dssp             HHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            643   25667777777777777777777777777653

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.12  E-value=2.4e-09  Score=81.27  Aligned_cols=76  Identities=9%  Similarity=0.137  Sum_probs=68.3

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|++.|+++.+  ||..+|..+..+|.+.|++++|...|+++.+  | +..+|..+..++.+.|++++|...|+++.+.
T Consensus        23 ~~A~~~~~~al~~~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  102 (514)
T 2gw1_A           23 DDAIKYYNWALELKEDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKFADAMFDLSVLSLN  102 (514)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhcCccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            578888888875  8999999999999999999999999998763  3 6678999999999999999999999999876


Q ss_pred             C
Q 045555           77 N   77 (175)
Q Consensus        77 ~   77 (175)
                      +
T Consensus       103 ~  103 (514)
T 2gw1_A          103 G  103 (514)
T ss_dssp             S
T ss_pred             C
Confidence            5

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.12  E-value=7.7e-10  Score=84.32  Aligned_cols=140  Identities=13%  Similarity=0.038  Sum_probs=95.5

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhcc---------CChHHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRV---------NRFREAL   67 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~---------~~~~~a~   67 (175)
                      ++|++.|++..+  | +..+|..+...|.+.|++++|...|++..+  |+...+..+...+...         |++++|+
T Consensus       120 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~  199 (474)
T 4abn_A          120 PEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSV  199 (474)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHH
Confidence            345555554433  2 345555566666666666666666555432  4445555555555555         5666666


Q ss_pred             HHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhc--------CCHHHHHHHHHhhcC--C----ChhhHHHH
Q 045555           68 TLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKC--------GDVEKAQRVFWKMLR--K----DKFTWTAM  133 (175)
Q Consensus        68 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~--------~~~~~a~~~~~~~~~--~----~~~~~~~l  133 (175)
                      ..|++..+..               +.+...|..+..+|...        |++++|.+.|+...+  |    +...|..+
T Consensus       200 ~~~~~al~~~---------------p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~l  264 (474)
T 4abn_A          200 RQAKLAVQMD---------------VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNR  264 (474)
T ss_dssp             HHHHHHHHHC---------------TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHH
T ss_pred             HHHHHHHHhC---------------CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHH
Confidence            6666555532               23456677888999888        999999999999843  4    67789999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHC
Q 045555          134 IVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...|...|++++|.+.|++..+.
T Consensus       265 g~~~~~~g~~~~A~~~~~~al~l  287 (474)
T 4abn_A          265 ATLHKYEESYGEALEGFSQAAAL  287 (474)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999999999998874

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.10  E-value=4.1e-09  Score=80.55  Aligned_cols=139  Identities=9%  Similarity=0.007  Sum_probs=87.1

Q ss_pred             chHHHHhhccCC--Cc--------HHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHH
Q 045555            2 GFALEIFGNMKN--KD--------VISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTL   69 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~--------~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~   69 (175)
                      ++|..+|+.+.+  |+        ..++..+...+...|++++|...|+...+  |+...|..+...+...|++++|...
T Consensus       219 ~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  298 (537)
T 3fp2_A          219 TKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKF  298 (537)
T ss_dssp             HHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHH
Confidence            356667776655  33        33566777778888888888888887763  5667788888888888888888888


Q ss_pred             HHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHH
Q 045555           70 FREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        70 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a  146 (175)
                      +++..+...  +             +..++..+...|...|++++|...|+...+  | +...|..+...+...|++++|
T Consensus       299 ~~~~~~~~~--~-------------~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A  363 (537)
T 3fp2_A          299 FQKAVDLNP--E-------------YPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTES  363 (537)
T ss_dssp             HHHHHHHCT--T-------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhccCC--C-------------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence            888877542  1             223334455555555555555555555422  2 344455555555555555555


Q ss_pred             HHHHHHHHH
Q 045555          147 LDMFSQMLR  155 (175)
Q Consensus       147 ~~~~~~m~~  155 (175)
                      .+.++++.+
T Consensus       364 ~~~~~~~~~  372 (537)
T 3fp2_A          364 EAFFNETKL  372 (537)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.08  E-value=2.3e-09  Score=81.93  Aligned_cols=140  Identities=15%  Similarity=0.093  Sum_probs=120.1

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++|.+.|+...+  |+..++..+...+.+.|++++|...|++..+   .+..+|..+...+...|++++|+..|++..+.
T Consensus       260 ~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  339 (537)
T 3fp2_A          260 LDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSL  339 (537)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            467777777764  7788899999999999999999999998763   46778999999999999999999999999885


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                      .  |             .+...+..+...|.+.|++++|...++...+  | +...|..+...+...|++++|.+.|+++
T Consensus       340 ~--~-------------~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  404 (537)
T 3fp2_A          340 N--P-------------ENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIA  404 (537)
T ss_dssp             C--T-------------TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             C--C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            4  2             2344567899999999999999999999843  3 6778999999999999999999999998


Q ss_pred             HHC
Q 045555          154 LRA  156 (175)
Q Consensus       154 ~~~  156 (175)
                      .+.
T Consensus       405 ~~~  407 (537)
T 3fp2_A          405 KRL  407 (537)
T ss_dssp             HHH
T ss_pred             HHc
Confidence            764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.08  E-value=9e-09  Score=73.94  Aligned_cols=153  Identities=11%  Similarity=0.149  Sum_probs=96.7

Q ss_pred             chHHHHhhccCC---C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-Chh-HHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN---K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYV-LWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~-~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|+.+|+...+   | +...|..++..+.+.|++++|..+|++..+  | +.. .|..+...+.+.|++++|..+|++.
T Consensus        81 ~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a  160 (308)
T 2ond_A           81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKA  160 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            578888887654   4 566899999999999999999999998764  4 343 7999999999999999999999999


Q ss_pred             HhCCCCCChHHHHHh---------------------hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----C---
Q 045555           74 QTSNIRRDEFTTVRI---------------------LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----K---  125 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l---------------------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~---  125 (175)
                      .+.+. ++...|...                     +...+.+...|..++..+.+.|++++|..+|+....    +   
T Consensus       161 ~~~~p-~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~  239 (308)
T 2ond_A          161 REDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEK  239 (308)
T ss_dssp             HTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGG
T ss_pred             HhcCC-CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHH
Confidence            88642 122222110                     001122334444455555555555555555555432    1   


Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          126 DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       126 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ....|..++..+.+.|+.++|..+++++.+
T Consensus       240 ~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~  269 (308)
T 2ond_A          240 SGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             CHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            223444555555555555555555555444

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.07  E-value=1.7e-08  Score=70.53  Aligned_cols=152  Identities=10%  Similarity=-0.035  Sum_probs=117.8

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.+.|+...+   .+..++..+...|.+.|++++|...|++..+   .+...+..+...+.+.|++++|...|+++.+
T Consensus        60 ~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  139 (275)
T 1xnf_A           60 ALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  139 (275)
T ss_dssp             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            467788887764   3688999999999999999999999998764   3678899999999999999999999999998


Q ss_pred             CCCCCChHHHH--------------------HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC-------hh
Q 045555           76 SNIRRDEFTTV--------------------RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKD-------KF  128 (175)
Q Consensus        76 ~~~~p~~~~~~--------------------~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-------~~  128 (175)
                      ..  |+.....                    ..+...+++...+ .+...+...++.++|...+......+       ..
T Consensus       140 ~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  216 (275)
T 1xnf_A          140 DD--PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSE  216 (275)
T ss_dssp             HC--TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHH
T ss_pred             hC--CCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccH
Confidence            54  3332111                    1111233333444 36666777778888888888875542       47


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .|..+...|.+.|++++|.+.|++..+.
T Consensus       217 ~~~~la~~~~~~g~~~~A~~~~~~al~~  244 (275)
T 1xnf_A          217 TNFYLGKYYLSLGDLDSATALFKLAVAN  244 (275)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            8888999999999999999999999875

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.06  E-value=3.5e-09  Score=74.06  Aligned_cols=140  Identities=11%  Similarity=0.074  Sum_probs=105.2

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      ++|++.|+...+  | +..++..+...|.+.|++++|...|++..+  ++    ...|..+...+.+.|++++|+..|++
T Consensus        20 ~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~   99 (272)
T 3u4t_A           20 AEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILMKKGQDSLAIQQYQA   99 (272)
T ss_dssp             HHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            467777777654  3 455788888899999999999999887654  22    22478888889999999999999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHH
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                      ..+..               +.+...+..+...|.+.|++++|...|++..+  | +...|..+...+...+++++|.+.
T Consensus       100 a~~~~---------------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  164 (272)
T 3u4t_A          100 AVDRD---------------TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSS  164 (272)
T ss_dssp             HHHHS---------------TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhcC---------------cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88853               22344567888888999999999999988854  3 556666666344445688888888


Q ss_pred             HHHHHHC
Q 045555          150 FSQMLRA  156 (175)
Q Consensus       150 ~~~m~~~  156 (175)
                      |++..+.
T Consensus       165 ~~~a~~~  171 (272)
T 3u4t_A          165 FVKVLEL  171 (272)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            8888764

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.06  E-value=6.7e-09  Score=80.63  Aligned_cols=142  Identities=9%  Similarity=0.028  Sum_probs=111.4

Q ss_pred             CchHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            1 MGFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         1 ~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      .++|.+.|++..+  | +...+..+...|.+.|++++|.+.|++..+   .+...+..+...+.+.|++++|.+.+++..
T Consensus         5 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al   84 (568)
T 2vsy_A            5 GPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQAS   84 (568)
T ss_dssp             ----------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3678888888765  3 678899999999999999999999998764   367789999999999999999999999998


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhc---CChhHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAIS---GHGDTALD  148 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~---g~~~~a~~  148 (175)
                      +..  |             .+...+..+..+|.+.|++++|.+.|++..+  | +...+..+...+...   |+.++|.+
T Consensus        85 ~~~--p-------------~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~  149 (568)
T 2vsy_A           85 DAA--P-------------EHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSA  149 (568)
T ss_dssp             HHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHH
T ss_pred             hcC--C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHH
Confidence            854  2             2345667899999999999999999999843  3 677889999999999   99999999


Q ss_pred             HHHHHHHCC
Q 045555          149 MFSQMLRAS  157 (175)
Q Consensus       149 ~~~~m~~~g  157 (175)
                      .+++..+.+
T Consensus       150 ~~~~al~~~  158 (568)
T 2vsy_A          150 QVRAAVAQG  158 (568)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHhcC
Confidence            999998754

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.04  E-value=8.1e-09  Score=74.60  Aligned_cols=122  Identities=11%  Similarity=0.051  Sum_probs=93.4

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C----ChhHHHHH------------HHHHhcc
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAM------------IDGYLRV   60 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~----~~~~~~~l------------i~~~~~~   60 (175)
                      ++|.+.|+...+  | +...+..+...+.+.|++++|...|+...+  |    +...+..+            ...+...
T Consensus        54 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  133 (359)
T 3ieg_A           54 KAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDG  133 (359)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            467778877664  4 678899999999999999999999998764  4    33344444            5788999


Q ss_pred             CChHHHHHHHHHhHhCCCCCChHHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHH
Q 045555           61 NRFREALTLFREMQTSNIRRDEFTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFW  120 (175)
Q Consensus        61 ~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~  120 (175)
                      |++++|+..++++.+.... +...+..+-.                    ..+.+...+..+...|.+.|++++|...|+
T Consensus       134 ~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  212 (359)
T 3ieg_A          134 ADYTAAITFLDKILEVCVW-DAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVR  212 (359)
T ss_dssp             TCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999999886432 2233322222                    334467889999999999999999999999


Q ss_pred             hhcC
Q 045555          121 KMLR  124 (175)
Q Consensus       121 ~~~~  124 (175)
                      ...+
T Consensus       213 ~a~~  216 (359)
T 3ieg_A          213 ECLK  216 (359)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9854

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.03  E-value=4.5e-09  Score=79.74  Aligned_cols=74  Identities=15%  Similarity=0.109  Sum_probs=40.1

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|.+.|+...+   .+..++..+...|.+.|++++|...|+...   ..+...+..+...+.+.|++++|...++++.+.
T Consensus       288 ~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  367 (514)
T 2gw1_A          288 EYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRK  367 (514)
T ss_dssp             TGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            44444444433   244455555666666666666666665543   124445555556666666666666666665553

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.03  E-value=4.1e-08  Score=67.16  Aligned_cols=131  Identities=10%  Similarity=0.028  Sum_probs=110.4

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC----CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      .|+..+......+.+.|++++|...|++..+    ++...+..+..++.+.|++++|+..|++..+..  |+        
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~--------   74 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN--YN--------   74 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--CS--------
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC--cc--------
Confidence            4667888999999999999999999997653    677777779999999999999999999999854  22        


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-Ch-------hhHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DK-------FTWTAMIVGLAISGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~-------~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  159 (175)
                           +...+..+...|.+.|++++|...|++..+  | +.       ..|..+...+...|++++|.+.|++..+.  .
T Consensus        75 -----~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~  147 (228)
T 4i17_A           75 -----LANAYIGKSAAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--T  147 (228)
T ss_dssp             -----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--S
T ss_pred             -----hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--C
Confidence                 345567899999999999999999999844  4 34       45788888899999999999999999864  5


Q ss_pred             Cc
Q 045555          160 LD  161 (175)
Q Consensus       160 p~  161 (175)
                      |+
T Consensus       148 p~  149 (228)
T 4i17_A          148 SK  149 (228)
T ss_dssp             CH
T ss_pred             CC
Confidence            65

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.02  E-value=2.4e-09  Score=74.84  Aligned_cols=145  Identities=12%  Similarity=0.045  Sum_probs=112.7

Q ss_pred             chHHHHhhccCCC----cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------C-ChhHHHHHHHHHhccCChHHH
Q 045555            2 GFALEIFGNMKNK----DVISWTTIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREA   66 (175)
Q Consensus         2 ~~A~~~~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a   66 (175)
                      ++|+++++....+    ...++..+...|...|++++|...|++..+          | ...++..+...+...|++++|
T Consensus        25 ~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  104 (283)
T 3edt_B           25 KQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEA  104 (283)
T ss_dssp             HHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHH
Confidence            3455555555422    466889999999999999999999998652          1 345789999999999999999


Q ss_pred             HHHHHHhHhCCC---CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----------ChhhHHH
Q 045555           67 LTLFREMQTSNI---RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----------DKFTWTA  132 (175)
Q Consensus        67 ~~~~~~m~~~~~---~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----------~~~~~~~  132 (175)
                      ...+++..+...   .|+          .+.....+..+...|...|++++|.+.|++..+.           ...++..
T Consensus       105 ~~~~~~al~~~~~~~~~~----------~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~  174 (283)
T 3edt_B          105 EPLCKRALEIREKVLGKF----------HPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNN  174 (283)
T ss_dssp             HHHHHHHHHHHHHHHCTT----------CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCC----------ChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            999999977410   011          0112456678999999999999999999998431           3457888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHC
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +...|...|++++|.+.+++..+.
T Consensus       175 la~~~~~~g~~~~A~~~~~~~l~~  198 (283)
T 3edt_B          175 LASCYLKQGKYQDAETLYKEILTR  198 (283)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999998763

>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=98.99  E-value=1.5e-08  Score=69.41  Aligned_cols=157  Identities=12%  Similarity=0.063  Sum_probs=119.9

Q ss_pred             chHHHHhhccCC----CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN----KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|++.|+...+    ++...+..+..++.+.|++++|...|++..+  | +...|..+...+.+.|++++|+..+++..
T Consensus        24 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  103 (228)
T 4i17_A           24 AVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSAAYRDMKNNQEYIATLTEGI  103 (228)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            467777776653    5777888899999999999999999998763  3 56789999999999999999999999999


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC---hhhHHHHHHHHHhcCCh------
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD---KFTWTAMIVGLAISGHG------  143 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~---~~~~~~li~~~~~~g~~------  143 (175)
                      +..  |+...+.      ..-...|..+...+.+.|++++|.+.|++..+  |+   ...|..+...|...|+.      
T Consensus       104 ~~~--p~~~~~~------~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~~~a~  175 (228)
T 4i17_A          104 KAV--PGNATIE------KLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGVLFYNNGADVLRKAT  175 (228)
T ss_dssp             HHS--TTCHHHH------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHG
T ss_pred             HHC--CCcHHHH------HHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            853  3321110      00013567888999999999999999999965  33   45677788888888877      


Q ss_pred             ---------------------hHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555          144 ---------------------DTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       144 ---------------------~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                                           ++|.+.|++..+.  .|+......+
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~l--~p~~~~~~~~  219 (228)
T 4i17_A          176 PLASSNKEKYASEKAKADAAFKKAVDYLGEAVTL--SPNRTEIKQM  219 (228)
T ss_dssp             GGTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             hcccCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc--CCCCHHHHHH
Confidence                                 8899999998874  5654444333

>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=98.98  E-value=3.5e-08  Score=65.09  Aligned_cols=137  Identities=15%  Similarity=0.239  Sum_probs=80.3

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHH--HhccCChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDG--YLRVNRFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|...|+...+   .+...+..+...+.+.|++++|...|+...+  |+.. +..+...  +.+.+...+|+..+++..+
T Consensus        24 ~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~-~~~~~~~~~~~~~~~~~~a~~~~~~al~  102 (176)
T 2r5s_A           24 QALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNS-YKSLIAKLELHQQAAESPELKRLEQELA  102 (176)
T ss_dssp             HHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHH-HHHHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChH-HHHHHHHHHHHhhcccchHHHHHHHHHH
Confidence            44455554443   2444555555555555555555555555543  2221 1111111  1111122234444444444


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC---hhhHHHHHHHHHhcCChhHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD---KFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~---~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                      ..               +.+...+..+...+.+.|++++|...|++..+  |+   ...+..+...+...|+.++|...|
T Consensus       103 ~~---------------P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y  167 (176)
T 2r5s_A          103 AN---------------PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKY  167 (176)
T ss_dssp             HS---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             hC---------------CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHH
Confidence            22               22456667888889999999999999998854  32   447888888999999999999998


Q ss_pred             HHHHH
Q 045555          151 SQMLR  155 (175)
Q Consensus       151 ~~m~~  155 (175)
                      ++.+.
T Consensus       168 ~~al~  172 (176)
T 2r5s_A          168 RRQLY  172 (176)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87654

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.94  E-value=3.2e-08  Score=69.16  Aligned_cols=129  Identities=8%  Similarity=-0.049  Sum_probs=106.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      ..........+.+.|++++|...|++..+  | +...+..+...+.+.|++++|+..+++..+.+..|+.          
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~----------   72 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKA----------   72 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTC----------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhH----------
Confidence            34456677889999999999999998753  3 5568999999999999999999999999984322221          


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                        ....|..+...|.+.|++++|.+.|+...+  | +...|..+...|...|++++|.+.|++..+.
T Consensus        73 --~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  137 (272)
T 3u4t_A           73 --KSADFEYYGKILMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP  137 (272)
T ss_dssp             --CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS
T ss_pred             --HHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc
Confidence              123456899999999999999999999844  3 6789999999999999999999999998865

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.94  E-value=1.2e-08  Score=77.70  Aligned_cols=150  Identities=11%  Similarity=0.021  Sum_probs=121.6

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCCh-hHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQV-DIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~-~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +|++.++...+   .+...+..+...|...|++ ++|...|++..+  | +...|..+...|.+.|++++|...|++..+
T Consensus        86 ~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  165 (474)
T 4abn_A           86 KTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALT  165 (474)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44555554443   3788999999999999999 999999998763  3 677899999999999999999999999998


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhc---------CCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhc---
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKC---------GDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAIS---  140 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~---------~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~---  140 (175)
                      ..  |+              ...+..+...|...         |++++|.+.|++..+  | +...|..+..+|...   
T Consensus       166 ~~--p~--------------~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~  229 (474)
T 4abn_A          166 HC--KN--------------KVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFN  229 (474)
T ss_dssp             TC--CC--------------HHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             hC--CC--------------HHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence            54  44              33446788899999         999999999999843  3 678899999999998   


Q ss_pred             -----CChhHHHHHHHHHHHCCCCC----cHHHHHHHHh
Q 045555          141 -----GHGDTALDMFSQMLRASIRL----DEVTYVGVLS  170 (175)
Q Consensus       141 -----g~~~~a~~~~~~m~~~g~~p----~~~t~~~ll~  170 (175)
                           |++++|.+.|++..+.  .|    +...+..+-.
T Consensus       230 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~lg~  266 (474)
T 4abn_A          230 TGQNPKISQQALSAYAQAEKV--DRKASSNPDLHLNRAT  266 (474)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHH--CGGGGGCHHHHHHHHH
T ss_pred             hccccchHHHHHHHHHHHHHh--CCCcccCHHHHHHHHH
Confidence                 9999999999999875  34    4555544433

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=98.93  E-value=2e-08  Score=74.54  Aligned_cols=139  Identities=9%  Similarity=0.120  Sum_probs=83.1

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCC-hhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQ-VDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|++.|+...+  | +..+|+.+...+.+.|+ +++|+..|++..+   .+...|+.+...+.+.|++++|+..|++.+
T Consensus       114 ~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal  193 (382)
T 2h6f_A          114 ERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADIL  193 (382)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            345555555443  2 45556666666666664 6666666665542   244556666666666666666666666665


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHh-cCChhHH----
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAI-SGHGDTA----  146 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~-~g~~~~a----  146 (175)
                      +..               +.+...|..+..++.+.|++++|...|+++.+  | +...|+.+...+.+ .|..++|    
T Consensus       194 ~ld---------------P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~  258 (382)
T 2h6f_A          194 NQD---------------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLER  258 (382)
T ss_dssp             HHC---------------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHH
T ss_pred             HhC---------------ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHH
Confidence            532               22345556677777777777777777777743  2 55667777777776 5554666    


Q ss_pred             -HHHHHHHHH
Q 045555          147 -LDMFSQMLR  155 (175)
Q Consensus       147 -~~~~~~m~~  155 (175)
                       .+.|++.++
T Consensus       259 el~~~~~Al~  268 (382)
T 2h6f_A          259 EVQYTLEMIK  268 (382)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence             366666654

>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=98.93  E-value=1.2e-07  Score=66.48  Aligned_cols=152  Identities=13%  Similarity=-0.026  Sum_probs=86.1

Q ss_pred             chHHHHhhccCCC-cHHHHHHHHHHHHh----cCChhHHHHHhhcCCC-CChhHHHHHHHHHhc----cCChHHHHHHHH
Q 045555            2 GFALEIFGNMKNK-DVISWTTIVSGYIN----RGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~   71 (175)
                      ++|.+.|+...+| +..++..+...|.+    .+++++|...|++..+ .+...+..+...|..    .+++++|+..|+
T Consensus        23 ~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~  102 (273)
T 1ouv_A           23 TQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYS  102 (273)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCcccCHHHHHHHHH
Confidence            4566666655543 45667777777777    7777777777776553 355667777777777    777777777777


Q ss_pred             HhHhCCCCCChHHHHHhhh---c-------------------cCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCC
Q 045555           72 EMQTSNIRRDEFTTVRILT---T-------------------FNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~---~-------------------~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~  125 (175)
                      +..+.+   +...+..+-.   .                   -..+...+..+...|..    .+++++|...|+...+.
T Consensus       103 ~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~  179 (273)
T 1ouv_A          103 KACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDL  179 (273)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence            777654   1111111000   0                   00022334444455554    55555555555555332


Q ss_pred             -ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHC
Q 045555          126 -DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRA  156 (175)
Q Consensus       126 -~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~  156 (175)
                       +...+..+...|..    .+++++|.+.|++..+.
T Consensus       180 ~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~  215 (273)
T 1ouv_A          180 KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACEL  215 (273)
T ss_dssp             TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhC
Confidence             34445555555555    55666666666555554

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.91  E-value=6.6e-09  Score=73.75  Aligned_cols=131  Identities=14%  Similarity=0.091  Sum_probs=104.8

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC---CCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSN---IRR   80 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~p   80 (175)
                      ...++..+...|...|++++|...|++..+          + ....+..+...+...|++++|+..+++..+..   ..+
T Consensus       110 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  189 (311)
T 3nf1_A          110 VAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGP  189 (311)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCT
T ss_pred             HHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCC
Confidence            456788999999999999999999998653          1 34568889999999999999999999997741   001


Q ss_pred             ChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------------------------------------
Q 045555           81 DEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------------------------------------  124 (175)
Q Consensus        81 ~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------------------------------------  124 (175)
                      +.          +....++..+...|.+.|++++|.+.|++..+                                    
T Consensus       190 ~~----------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (311)
T 3nf1_A          190 DD----------PNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTS  259 (311)
T ss_dssp             TC----------HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CC
T ss_pred             CC----------HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHH
Confidence            10          11234567899999999999999999998752                                    


Q ss_pred             ---------------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 ---------------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 ---------------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                                     | ...+|..+...|.+.|++++|.+.|++..+
T Consensus       260 ~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          260 FGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             SCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                           1 345688899999999999999999998875

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.90  E-value=3.4e-08  Score=70.91  Aligned_cols=122  Identities=9%  Similarity=0.008  Sum_probs=80.3

Q ss_pred             chHHHHhhccCC--C-cHH-HHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHH-hccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN--K-DVI-SWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGY-LRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~-~~~~~~~~a~~~~~~m   73 (175)
                      ++|.++|+...+  | +.. +|..+...+.+.|++++|..+|++..+  | +...|....... ...|++++|..+|++.
T Consensus       116 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~a  195 (308)
T 2ond_A          116 EKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELG  195 (308)
T ss_dssp             HHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            467777777665  4 343 788888888888888888888887654  2 333343332221 1257777787777777


Q ss_pred             HhCCCCCChHHHHHhhh--------------------c--cCc--chhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           74 QTSNIRRDEFTTVRILT--------------------T--FNN--DIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~--------------------~--~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .+... -+...+..+..                    .  ..|  ...+|..++..+.+.|+.+.|..+++.+.+
T Consensus       196 l~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~  269 (308)
T 2ond_A          196 LKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66421 12333332222                    1  244  356899999999999999999999999865

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.89  E-value=8e-09  Score=75.36  Aligned_cols=125  Identities=14%  Similarity=0.078  Sum_probs=105.8

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-C---------------hhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-D---------------YVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +...+..+...|.+.|++++|...|++..+  | +               ...|..+..++.+.|++++|+..+++.++.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            567889999999999999999999998663  3 3               478999999999999999999999999985


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHH-HHHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTA-LDMFSQ  152 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a-~~~~~~  152 (175)
                      .  |             .+...+..+..+|...|++++|...|++..+  | +...+..+...+.+.|+.++| .+.|+.
T Consensus       226 ~--p-------------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~  290 (336)
T 1p5q_A          226 D--S-------------NNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYAN  290 (336)
T ss_dssp             C--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C--C-------------CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4  2             2445567899999999999999999999843  4 677888999999999999998 556777


Q ss_pred             HH
Q 045555          153 ML  154 (175)
Q Consensus       153 m~  154 (175)
                      |.
T Consensus       291 ~~  292 (336)
T 1p5q_A          291 MF  292 (336)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>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=98.88  E-value=5.7e-08  Score=72.14  Aligned_cols=127  Identities=10%  Similarity=0.045  Sum_probs=111.8

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCC-hHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNR-FREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      +..+|+.+...+.+.|++++|+..|++..+   .+...|+.+...+.+.|+ +++|+..|++.++..             
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-------------  162 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-------------  162 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-------------
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-------------
Confidence            456889999999999999999999998764   467789999999999997 999999999999854             


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                        +.+...|..+..++.+.|++++|...|++..+  | +...|..+..++.+.|++++|.+.|+++++.
T Consensus       163 --P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l  229 (382)
T 2h6f_A          163 --PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE  229 (382)
T ss_dssp             --TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH
T ss_pred             --CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh
Confidence              22456678899999999999999999999954  3 7789999999999999999999999999975

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.87  E-value=3.1e-08  Score=63.83  Aligned_cols=124  Identities=10%  Similarity=-0.030  Sum_probs=95.8

Q ss_pred             HHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhH
Q 045555           22 IVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFV   98 (175)
Q Consensus        22 li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~   98 (175)
                      |...+...|++++|...++...+.   +...+..+...|.+.|++++|++.|++..+..  |             .+...
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~--p-------------~~~~a   67 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ--E-------------RDPKA   67 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHH
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-------------CCHHH
Confidence            344566778899999999887753   44567788889999999999999999998853  2             24566


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHH-HHHHHCCCCCcH
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMF-SQMLRASIRLDE  162 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~-~~m~~~g~~p~~  162 (175)
                      |..+..+|.+.|++++|...|+...+  | +...|..+...|.+.|++++|.+.| ++..+.  .|+.
T Consensus        68 ~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~  133 (150)
T 4ga2_A           68 HRFLGLLYELEENTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGS  133 (150)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTC
T ss_pred             HHHHHHHHHHcCchHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCC
Confidence            78899999999999999999999843  4 6778899999999999998877664 776653  4543

>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=98.87  E-value=3.2e-07  Score=64.39  Aligned_cols=126  Identities=11%  Similarity=0.041  Sum_probs=91.3

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-ChhHHHHHHHHHhc----cCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLR----VNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      ++.++..+...|.+.|++++|...|++..++ +...+..+...|..    .+++++|+..|++..+.+   +..      
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~------   75 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSN------   75 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHH------
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHH------
Confidence            6678888999999999999999999987765 56778888889999    999999999999998875   222      


Q ss_pred             hccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHCC
Q 045555           90 TTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  157 (175)
                              .+..+...|..    .+++++|.+.|+...+. +...+..+...|..    .+++++|.+.|++..+.+
T Consensus        76 --------a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~  144 (273)
T 1ouv_A           76 --------GCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN  144 (273)
T ss_dssp             --------HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT
T ss_pred             --------HHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC
Confidence                    22345555655    66666666666665433 44555555566665    666666666666665544

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.86  E-value=1.9e-08  Score=70.33  Aligned_cols=154  Identities=10%  Similarity=0.067  Sum_probs=103.3

Q ss_pred             chHHHHhhccCC--C-c---HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C----ChhHHHHHHHHHhc--------cC
Q 045555            2 GFALEIFGNMKN--K-D---VISWTTIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLR--------VN   61 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~----~~~~~~~li~~~~~--------~~   61 (175)
                      ++|+..|+...+  | +   ..++..+..+|.+.|++++|...|+...+  |    ....+..+..++.+        .|
T Consensus        32 ~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~  111 (261)
T 3qky_A           32 DRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQT  111 (261)
T ss_dssp             HHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCH
T ss_pred             HHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccch
Confidence            467777777664  4 2   56777788888888888888888887653  3    13356666777777        78


Q ss_pred             ChHHHHHHHHHhHhCCCCCChHHHHHh--hhccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC----hhhHHH
Q 045555           62 RFREALTLFREMQTSNIRRDEFTTVRI--LTTFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD----KFTWTA  132 (175)
Q Consensus        62 ~~~~a~~~~~~m~~~~~~p~~~~~~~l--~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~----~~~~~~  132 (175)
                      ++++|+..|++..+........ ....  +....+ -...+..+...|.+.|++++|...|+...+  |+    ...+..
T Consensus       112 ~~~~A~~~~~~~l~~~p~~~~~-~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~  190 (261)
T 3qky_A          112 DTRKAIEAFQLFIDRYPNHELV-DDATQKIRELRAKLARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVG  190 (261)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTH-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCcCchhH-HHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHH
Confidence            8888888888887753211100 0000  000000 000114578899999999999999999854  43    346777


Q ss_pred             HHHHHHhc----------CChhHHHHHHHHHHHC
Q 045555          133 MIVGLAIS----------GHGDTALDMFSQMLRA  156 (175)
Q Consensus       133 li~~~~~~----------g~~~~a~~~~~~m~~~  156 (175)
                      +..+|...          |++++|.+.|+++.+.
T Consensus       191 l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          191 AMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            78888766          8999999999999875

>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=98.86  E-value=3.9e-08  Score=60.84  Aligned_cols=108  Identities=20%  Similarity=0.368  Sum_probs=89.7

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|.++|+.+.+   .+...+..+...+.+.|++++|...|+++.+   .+...+..+...+.+.|++++|...++++.+
T Consensus        18 ~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~   97 (136)
T 2fo7_A           18 DEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE   97 (136)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            567888887654   4677889999999999999999999998753   4667888999999999999999999999988


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      ...               .+...+..+...+.+.|++++|.+.++.+..
T Consensus        98 ~~~---------------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           98 LDP---------------RSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             HCT---------------TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             hCC---------------CChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            542               2334556789999999999999999998743

>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=98.86  E-value=1.4e-08  Score=70.98  Aligned_cols=131  Identities=15%  Similarity=0.076  Sum_probs=104.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC---CCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSN---IRR   80 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~p   80 (175)
                      ...++..+...|...|++++|...|++..+          | ...++..+...+...|++++|...+++..+..   ..+
T Consensus        84 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  163 (283)
T 3edt_B           84 VAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGP  163 (283)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCC
Confidence            456899999999999999999999998653          1 34578899999999999999999999998751   011


Q ss_pred             ChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----------------------------------
Q 045555           81 DEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----------------------------------  125 (175)
Q Consensus        81 ~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----------------------------------  125 (175)
                      +.          +....++..+...|.+.|++++|...+++..+.                                   
T Consensus       164 ~~----------~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (283)
T 3edt_B          164 DD----------PNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP  233 (283)
T ss_dssp             TC----------HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC---
T ss_pred             CC----------HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH
Confidence            10          112445678999999999999999999887321                                   


Q ss_pred             -----------------ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          126 -----------------DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       126 -----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                                       ...++..+...|...|++++|.+.|++..+
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          234 YGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             ---------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                             223677888999999999999999998775

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.85  E-value=1.3e-07  Score=60.97  Aligned_cols=126  Identities=13%  Similarity=0.053  Sum_probs=101.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ....+..+...+.+.|++++|...|+...+   .+...+..+...+.+.|++++|+..+++..+..  |           
T Consensus        12 ~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~-----------   78 (166)
T 1a17_A           12 RAEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--K-----------   78 (166)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--c-----------
Confidence            356788889999999999999999998653   467789999999999999999999999998854  2           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHH--HHHhcCChhHHHHHHHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIV--GLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~--~~~~~g~~~~a~~~~~~m~~  155 (175)
                        .+...+..+..++.+.|++++|.+.|++..+  | +...+..+..  .+...|++++|.+.+.+...
T Consensus        79 --~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           79 --KYIKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence              2344567889999999999999999999844  3 4455544433  47788999999999887653

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.84  E-value=2.3e-08  Score=64.40  Aligned_cols=126  Identities=12%  Similarity=0.080  Sum_probs=99.3

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|+..+.....  | +...+-.+...|.+.|++++|.+.|++..+   .+..+|..+...+.+.|++++|+..|++..+
T Consensus        14 e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~   93 (150)
T 4ga2_A           14 ERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKAVECYRRSVE   93 (150)
T ss_dssp             HHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHH
Confidence            567777777665  2 455677889999999999999999998763   4778899999999999999999999999998


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHH-Hhhc--CC-ChhhHHHHHHHHHhcCC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVF-WKML--RK-DKFTWTAMIVGLAISGH  142 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~-~~~~--~~-~~~~~~~li~~~~~~g~  142 (175)
                      ..  |             .+...+..+...|.+.|++++|.+.| +...  .| +..+|......+...|+
T Consensus        94 ~~--p-------------~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           94 LN--P-------------TQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HC--T-------------TCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             hC--C-------------CCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            53  2             24556678999999999998776654 6553  35 66777777777766664

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.82  E-value=1.8e-07  Score=66.58  Aligned_cols=139  Identities=14%  Similarity=0.093  Sum_probs=92.6

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR---   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~---   87 (175)
                      .+...+..+...+.+.|++++|...|++..+  | +...+..+...+.+.|++++|...+++.....  |+......   
T Consensus       115 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~  192 (287)
T 3qou_A          115 REEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQ  192 (287)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHH
Confidence            3455667777778888888888888887653  3 56677888888888888888888888876643  33221111   


Q ss_pred             ------------------hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC---hhhHHHHHHHHHhcCChh
Q 045555           88 ------------------ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD---KFTWTAMIVGLAISGHGD  144 (175)
Q Consensus        88 ------------------l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~---~~~~~~li~~~~~~g~~~  144 (175)
                                        .+..-+.+...+..+...|...|++++|.+.|....+  |+   ...+..+...+...|+.+
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence                              0111233455666777777777777777777777743  32   456777777777777777


Q ss_pred             HHHHHHHHHH
Q 045555          145 TALDMFSQML  154 (175)
Q Consensus       145 ~a~~~~~~m~  154 (175)
                      +|...|++..
T Consensus       273 ~a~~~~r~al  282 (287)
T 3qou_A          273 ALASXYRRQL  282 (287)
T ss_dssp             HHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            7777776654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.82  E-value=8.1e-08  Score=65.13  Aligned_cols=150  Identities=11%  Similarity=0.109  Sum_probs=110.9

Q ss_pred             chHHHHhhccCC--C-cHHHHHH----------------HHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhc
Q 045555            2 GFALEIFGNMKN--K-DVISWTT----------------IVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLR   59 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~----------------li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~   59 (175)
                      ++|+..|+...+  | +...|..                +...|.+.|++++|...|++..+   .+...+..+...+..
T Consensus        21 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~  100 (208)
T 3urz_A           21 GQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVC  100 (208)
T ss_dssp             HHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence            467778877765  4 4456666                89999999999999999998763   377889999999999


Q ss_pred             cCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCC--HHHHHHHHHhhcCCChhh--HHHHHH
Q 045555           60 VNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGD--VEKAQRVFWKMLRKDKFT--WTAMIV  135 (175)
Q Consensus        60 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~--~~~a~~~~~~~~~~~~~~--~~~li~  135 (175)
                      .|++++|+..|++..+..  |+             +...+..+...|...|+  .+.+...++....++...  +.....
T Consensus       101 ~g~~~~A~~~~~~al~~~--P~-------------~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~g~  165 (208)
T 3urz_A          101 RGQEKDALRMYEKILQLE--AD-------------NLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARYRDGL  165 (208)
T ss_dssp             HTCHHHHHHHHHHHHHHC--TT-------------CHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHcC--CC-------------CHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHHHHHH
Confidence            999999999999999854  32             34455677777765543  556777888877776543  333455


Q ss_pred             HHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555          136 GLAISGHGDTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       136 ~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                      ++...|++++|...|++.++  +.|+......+
T Consensus       166 ~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l  196 (208)
T 3urz_A          166 SKLFTTRYEKARNSLQKVIL--RFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHH--hCCCHHHHHHH
Confidence            66678999999999999986  46776554443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.80  E-value=1.6e-07  Score=60.71  Aligned_cols=125  Identities=13%  Similarity=0.049  Sum_probs=96.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF   97 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~   97 (175)
                      ....+...+..-+.+.++.+    +.+.+...+..+...+.+.|++++|+..|++..+..  |             .+..
T Consensus        11 ~~~~l~~~~~~~~~l~~al~----l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~--P-------------~~~~   71 (151)
T 3gyz_A           11 ISTAVIDAINSGATLKDINA----IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD--F-------------YNVD   71 (151)
T ss_dssp             HHHHHHHHHHTSCCTGGGCC----SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHH
T ss_pred             HHHHHHHHHHCCCCHHHHhC----CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-------------CCHH
Confidence            34455555544444333322    111255678888999999999999999999999854  2             3456


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHH
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEV  163 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  163 (175)
                      .|..+..+|.+.|++++|...|++...  | +...|..+..+|...|++++|.+.|++.++.  .||..
T Consensus        72 ~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A           72 YIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCHH
Confidence            678899999999999999999999843  4 6788999999999999999999999999875  45543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.80  E-value=4.9e-07  Score=56.43  Aligned_cols=102  Identities=9%  Similarity=0.003  Sum_probs=85.6

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      ..+......|.+.|++++|+..|++.++..               +.+...|..+..+|.+.|++++|...|+...+  |
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~---------------p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p   78 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD---------------PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS   78 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC---------------CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh
Confidence            457788899999999999999999998854               23455667899999999999999999999844  3


Q ss_pred             -ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          126 -DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       126 -~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                       +...|..+..+|...|++++|.+.|++.++.  .|+.....
T Consensus        79 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~l--~P~~~~a~  118 (126)
T 4gco_A           79 KFIKGYIRKAACLVAMREWSKAQRAYEDALQV--DPSNEEAR  118 (126)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             hhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcCCHHHH
Confidence             6788999999999999999999999999874  56544433

>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=98.79  E-value=1.7e-08  Score=80.20  Aligned_cols=138  Identities=12%  Similarity=0.086  Sum_probs=108.8

Q ss_pred             chHHHHhhccC--------C---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHH
Q 045555            2 GFALEIFGNMK--------N---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREAL   67 (175)
Q Consensus         2 ~~A~~~~~~m~--------~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~   67 (175)
                      ++|++.++...        +   .+...+..+...|.+.|++++|...|++..+   .+...|..+...+.+.|++++|+
T Consensus       408 ~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~  487 (681)
T 2pzi_A          408 VQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSAT  487 (681)
T ss_dssp             HHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHHHH
Confidence            46777777665        2   4677899999999999999999999998774   47778999999999999999999


Q ss_pred             HHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChh
Q 045555           68 TLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGD  144 (175)
Q Consensus        68 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~  144 (175)
                      +.|++..+..  |+             +...+..+..+|.+.|++++ .+.|++..+  | +...|..+..++.+.|+++
T Consensus       488 ~~~~~al~l~--P~-------------~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~  551 (681)
T 2pzi_A          488 KHFTEVLDTF--PG-------------ELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRV  551 (681)
T ss_dssp             HHHHHHHHHS--TT-------------CSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHhC--CC-------------ChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHH
Confidence            9999998854  22             34445677777888888888 778877643  3 5667777788888888888


Q ss_pred             HHHHHHHHHHH
Q 045555          145 TALDMFSQMLR  155 (175)
Q Consensus       145 ~a~~~~~~m~~  155 (175)
                      +|.+.|++..+
T Consensus       552 ~A~~~~~~al~  562 (681)
T 2pzi_A          552 GAVRTLDEVPP  562 (681)
T ss_dssp             HHHHHHHTSCT
T ss_pred             HHHHHHHhhcc
Confidence            88888877764

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.79  E-value=2.5e-07  Score=56.43  Aligned_cols=95  Identities=19%  Similarity=0.324  Sum_probs=58.2

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...|..+...+.+.|++++|...++++.+..  |             .+...+..+...+.+.|++++|...|+.+..  
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~-------------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~   73 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD--P-------------NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--c-------------CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence            3455566666666666666666666666542  1             1233345566666667777777766666632  


Q ss_pred             -CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 -KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       .+..++..+...+...|++++|.+.|+++.+.
T Consensus        74 ~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           74 PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence             24556666666677777777777777766653

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.79  E-value=5.2e-07  Score=61.32  Aligned_cols=137  Identities=12%  Similarity=0.043  Sum_probs=105.0

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhccC----ChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLRVN----RFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~   75 (175)
                      .+|.++|+...+ -++.++..+...|.+.+++++|...|++..+ .+...+..|-..|.. +    ++++|+..|++..+
T Consensus         3 ~eA~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~   81 (212)
T 3rjv_A            3 TEPGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVE   81 (212)
T ss_dssp             -CTTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHH
Confidence            367778877665 5888999999999999999999999998765 466778888888887 6    89999999999987


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCCC-----hhhHHHHHHHHHh----cCC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRKD-----KFTWTAMIVGLAI----SGH  142 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~-----~~~~~~li~~~~~----~g~  142 (175)
                      .|.                 ...+..|...|..    .+++++|.+.|+...+.+     ...+..+-..|..    .++
T Consensus        82 ~g~-----------------~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d  144 (212)
T 3rjv_A           82 AGS-----------------KSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPED  144 (212)
T ss_dssp             TTC-----------------HHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCC
T ss_pred             CCC-----------------HHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCC
Confidence            652                 2233456666665    778888888888876543     4677777777777    677


Q ss_pred             hhHHHHHHHHHHHC
Q 045555          143 GDTALDMFSQMLRA  156 (175)
Q Consensus       143 ~~~a~~~~~~m~~~  156 (175)
                      +++|.+.|++..+.
T Consensus       145 ~~~A~~~~~~A~~~  158 (212)
T 3rjv_A          145 DVKASEYFKGSSSL  158 (212)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHc
Confidence            88888888887765

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.78  E-value=1.2e-07  Score=63.91  Aligned_cols=124  Identities=15%  Similarity=0.030  Sum_probs=96.6

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++|++.|+....|+..++..+...|.+.|++++|...|++..+   .+...|..+...+.+.|++++|+..|++..+...
T Consensus        23 ~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~  102 (213)
T 1hh8_A           23 KGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLR  102 (213)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCC
Confidence            5788999988888999999999999999999999999998763   4677899999999999999999999999988542


Q ss_pred             CCChHHHHHhhhccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           79 RRDEFTTVRILTTFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        79 ~p~~~~~~~l~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                      ......+..+-....| ....+..+..+|.+.|++++|.+.|+...+.
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A          103 GNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             TCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             CccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            2110000000000111 2356678999999999999999999998653

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.75  E-value=3.6e-07  Score=56.54  Aligned_cols=93  Identities=16%  Similarity=0.078  Sum_probs=51.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|++..+   .+...+..+...+...|++++|+..+++..+..  |           
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~-----------   81 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE--P-----------   81 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--C-----------
Confidence            445555666666666666666666665432   244555556666666666666666666665532  1           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                        .+...+..+..+|.+.|++++|.+.|+..
T Consensus        82 --~~~~~~~~la~~~~~~~~~~~A~~~~~~~  110 (133)
T 2lni_A           82 --TFIKGYTRKAAALEAMKDYTKAMDVYQKA  110 (133)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             --CchHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence              12233345555556666666666666555

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.75  E-value=2e-07  Score=63.92  Aligned_cols=154  Identities=12%  Similarity=0.037  Sum_probs=102.3

Q ss_pred             chHHHHhhccCC--Cc----HHHHHHHHHHHHhcCChhHHHHHhhcCCC--CCh----hHHHHHHHHHhc----------
Q 045555            2 GFALEIFGNMKN--KD----VISWTTIVSGYINRGQVDIARQYFAQMPE--RDY----VLWTAMIDGYLR----------   59 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~----~~~~~li~~~~~----------   59 (175)
                      ++|+..|+.+.+  |+    ..++..+..+|.+.|++++|...|++..+  |+.    ..+..+..++.+          
T Consensus        21 ~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~g~~~~~~~~~~~~~~~  100 (225)
T 2yhc_A           21 RQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFF  100 (225)
T ss_dssp             HHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHHHHHHHHhhhhhhhhhhh
Confidence            467777777664  42    35677788888888888888888888653  321    134444444433          


Q ss_pred             --------cCChHHHHHHHHHhHhCCCCCChHH-HHHh--hhccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           60 --------VNRFREALTLFREMQTSNIRRDEFT-TVRI--LTTFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        60 --------~~~~~~a~~~~~~m~~~~~~p~~~~-~~~l--~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                              .|++++|+..|+++.+..  |+... ....  +..+... ....-.+...|.+.|++++|...|+.+.+  |
T Consensus       101 ~~~~~~~~~~~~~~A~~~~~~~l~~~--P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p  178 (225)
T 2yhc_A          101 GVDRSDRDPQQARAAFSDFSKLVRGY--PNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYP  178 (225)
T ss_dssp             -------CCHHHHHHHHHHHHHHTTC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST
T ss_pred             ccchhhcCcHHHHHHHHHHHHHHHHC--cCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCc
Confidence                    567888888888888753  22111 1000  0000000 01112467788999999999999999854  4


Q ss_pred             Ch----hhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555          126 DK----FTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus       126 ~~----~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                      +.    ..+..+..+|.+.|+.++|.+.++.+...+
T Consensus       179 ~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          179 DTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             TSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             CCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            32    468889999999999999999999988763

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.75  E-value=3.3e-07  Score=56.36  Aligned_cols=113  Identities=8%  Similarity=-0.001  Sum_probs=64.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+...|++++|...|++..+   .+...+..+...+...|++++|...+++..+..  |           
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~-----------   77 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID--P-----------   77 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC--c-----------
Confidence            344566666666666666666666665442   245556666666666666666666666666532  1           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGH  142 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~  142 (175)
                        .+...+..+...|.+.|++++|...|+...+  | +...+..+...+.+.|+
T Consensus        78 --~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           78 --AYSKAYGRMGLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTT
T ss_pred             --cCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhc
Confidence              1223334566666666666666666666532  2 44455555555555544

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.74  E-value=8.9e-08  Score=68.28  Aligned_cols=131  Identities=7%  Similarity=-0.017  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhcc-CChHHHHHHHHHhHhCCCCCChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRV-NRFREALTLFREMQTSNIRRDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p~~~~~   85 (175)
                      ..+|+.+..+|.+.|++++|...|++..+     .+    ..+++.+...|... |++++|+..|++..+.....+... 
T Consensus        77 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~-  155 (292)
T 1qqe_A           77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVA-  155 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH-
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChH-
Confidence            56899999999999999999999987664     12    35788899999996 999999999999987421100000 


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CCh-h-------hHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDK-F-------TWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~-~-------~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                              ....+++.+...|.+.|++++|...|+...+  |+. .       .|..+..++...|++++|...|++..+
T Consensus       156 --------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          156 --------LSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             --------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             --------HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence                    0134567899999999999999999999844  221 1       567788889999999999999999875

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.74  E-value=2.7e-07  Score=57.65  Aligned_cols=95  Identities=15%  Similarity=0.113  Sum_probs=82.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ....+......|.+.|++++|.+.|++..+   .+...|..+..++.+.|++++|+..|++.++.+              
T Consensus        12 ~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--------------   77 (126)
T 4gco_A           12 LAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD--------------   77 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh--------------
Confidence            346788899999999999999999998663   477889999999999999999999999998854              


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                       +.+...|..+..+|...|++++|.+.|++..+
T Consensus        78 -p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           78 -SKFIKGYIRKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -hhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             22455667899999999999999999999854

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.73  E-value=2.3e-07  Score=65.74  Aligned_cols=132  Identities=15%  Similarity=0.160  Sum_probs=106.6

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--------C---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC---CC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--------R---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNI---RR   80 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--------~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~p   80 (175)
                      +..++..+...+...|++++|..+|+++.+        .   ....+..+...+...|++++|...+++..+...   .+
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            567899999999999999999999998764        1   345688899999999999999999999976410   01


Q ss_pred             ChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------C----ChhhHHHHHHHHHhcCChhHHHHH
Q 045555           81 DEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-------K----DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        81 ~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~----~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                      +          .+.....+..+...|...|++++|.+.|++..+       +    ....+..+...+...|++++|.+.
T Consensus       106 ~----------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  175 (311)
T 3nf1_A          106 D----------HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYY  175 (311)
T ss_dssp             T----------CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             C----------ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            1          011245667899999999999999999999843       1    345688889999999999999999


Q ss_pred             HHHHHHC
Q 045555          150 FSQMLRA  156 (175)
Q Consensus       150 ~~~m~~~  156 (175)
                      +++..+.
T Consensus       176 ~~~a~~~  182 (311)
T 3nf1_A          176 YQRALEI  182 (311)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998764

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.73  E-value=8.4e-08  Score=64.05  Aligned_cols=144  Identities=12%  Similarity=-0.015  Sum_probs=109.6

Q ss_pred             chHHH---HhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC------C---ChhHHHHHHHHHhccCChHHHHHH
Q 045555            2 GFALE---IFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE------R---DYVLWTAMIDGYLRVNRFREALTL   69 (175)
Q Consensus         2 ~~A~~---~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~------~---~~~~~~~li~~~~~~~~~~~a~~~   69 (175)
                      ++|.+   ++..-+.....++..+...+...|++++|...+++..+      .   ...++..+...+...|++++|...
T Consensus         9 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~   88 (203)
T 3gw4_A            9 ALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRC   88 (203)
T ss_dssp             HHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            45666   55443334677899999999999999999999988654      1   345688888999999999999999


Q ss_pred             HHHhHhCCC-CC-ChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHHHHHHHH
Q 045555           70 FREMQTSNI-RR-DEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTAMIVGLA  138 (175)
Q Consensus        70 ~~~m~~~~~-~p-~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~  138 (175)
                      +++..+..- .+ +...          ....+..+...+...|++++|.+.+++..+     .+    ..++..+...+.
T Consensus        89 ~~~al~~~~~~~~~~~~----------~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  158 (203)
T 3gw4_A           89 FLEERELLASLPEDPLA----------ASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQ  158 (203)
T ss_dssp             HHHHHHHHHHSCCCHHH----------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCccHHH----------HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence            999877410 11 1101          133457889999999999999999998742     12    234677888999


Q ss_pred             hcCChhHHHHHHHHHHH
Q 045555          139 ISGHGDTALDMFSQMLR  155 (175)
Q Consensus       139 ~~g~~~~a~~~~~~m~~  155 (175)
                      ..|++++|.+.+++..+
T Consensus       159 ~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          159 QEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            99999999999988765

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.71  E-value=4.9e-07  Score=56.43  Aligned_cols=104  Identities=10%  Similarity=0.035  Sum_probs=83.3

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      ..+..+...+.+.|++++|+..|++.++..  |+             +...|..+..+|.+.|++++|.+.|+...+  |
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~--p~-------------~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~   73 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELD--PS-------------NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGR   73 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC-------------CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCc
Confidence            457788899999999999999999998843  32             355668899999999999999999998843  2


Q ss_pred             C--------hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555          126 D--------KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       126 ~--------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                      +        ..+|..+..++...|++++|.+.|++.++.  .||+.+...|
T Consensus        74 ~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~~l  122 (127)
T 4gcn_A           74 ETRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVKKV  122 (127)
T ss_dssp             HTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHHHH
Confidence            1        236777888899999999999999998864  5676665544

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.71  E-value=6.7e-07  Score=54.46  Aligned_cols=110  Identities=19%  Similarity=0.300  Sum_probs=89.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCCh---hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDY---VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|+++.+.+.   .++..+...+.+.|++++|...++++.+..              
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--------------   73 (125)
T 1na0_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD--------------   73 (125)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--------------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--------------
Confidence            367888999999999999999999999887664   357788889999999999999999998753              


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHh
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAI  139 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~  139 (175)
                       +.+...+..+...|.+.|++++|...|+...+  | +...+..+...+..
T Consensus        74 -~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           74 -PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             -CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh
Confidence             23456788899999999999999999999843  3 44555555554443

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.69  E-value=1.2e-06  Score=67.44  Aligned_cols=140  Identities=14%  Similarity=0.141  Sum_probs=97.1

Q ss_pred             hHHHHhhccCC---C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-Ch-hHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            3 FALEIFGNMKN---K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DY-VLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         3 ~A~~~~~~m~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~-~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +|+.+|+...+   | +...|..++..+.+.|++++|..+|++..+  | +. ..|..++..+.+.|++++|.++|++..
T Consensus       304 ~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al  383 (530)
T 2ooe_A          304 EAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAR  383 (530)
T ss_dssp             HHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            78888987764   4 578899999999999999999999998763  4 33 479999999999999999999999998


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      +.... +...+            ....++ .+...|++++|..+|+...+  | +...|..++..+.+.|+.++|..+|+
T Consensus       384 ~~~~~-~~~~~------------~~~a~~-~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~  449 (530)
T 2ooe_A          384 EDART-RHHVY------------VTAALM-EYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFE  449 (530)
T ss_dssp             TCTTC-CTHHH------------HHHHHH-HHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             hccCC-chHHH------------HHHHHH-HHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHH
Confidence            85321 11111            111111 12245666666666665532  2 45566666666666666666666666


Q ss_pred             HHHHC
Q 045555          152 QMLRA  156 (175)
Q Consensus       152 ~m~~~  156 (175)
                      +....
T Consensus       450 ~al~~  454 (530)
T 2ooe_A          450 RVLTS  454 (530)
T ss_dssp             HHHHS
T ss_pred             HHHhc
Confidence            66654

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.67  E-value=3.4e-06  Score=58.75  Aligned_cols=131  Identities=13%  Similarity=0.046  Sum_probs=104.8

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-C---hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-D---YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .+...+-.+...+.+.|++++|...|+.+.+  | +   ...+..+..++.+.|++++|+..|++..+...  +.     
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p--~~-----   85 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQ--ID-----   85 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TC-----
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCC--CC-----
Confidence            4677888888999999999999999999874  4 3   56788899999999999999999999998642  11     


Q ss_pred             hhhccCcchhHHHHHHHHHHh--------cCCHHHHHHHHHhhcC--C-ChhhH-----------------HHHHHHHHh
Q 045555           88 ILTTFNNDIFVGIALIDMYCK--------CGDVEKAQRVFWKMLR--K-DKFTW-----------------TAMIVGLAI  139 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~--------~~~~~~a~~~~~~~~~--~-~~~~~-----------------~~li~~~~~  139 (175)
                           +.....+..+..++.+        .|++++|...|++..+  | +...+                 ..+...|.+
T Consensus        86 -----~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~  160 (261)
T 3qky_A           86 -----PRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYER  160 (261)
T ss_dssp             -----TTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -----chhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 0112334567888888        9999999999999854  4 33334                 455778999


Q ss_pred             cCChhHHHHHHHHHHHC
Q 045555          140 SGHGDTALDMFSQMLRA  156 (175)
Q Consensus       140 ~g~~~~a~~~~~~m~~~  156 (175)
                      .|++++|...|+++++.
T Consensus       161 ~g~~~~A~~~~~~~l~~  177 (261)
T 3qky_A          161 RELYEAAAVTYEAVFDA  177 (261)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHH
Confidence            99999999999999875

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.67  E-value=4.6e-07  Score=66.72  Aligned_cols=144  Identities=13%  Similarity=0.053  Sum_probs=110.0

Q ss_pred             chHHHHhhccCC-----C----cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-----C-----ChhHHHHHHHHHhccCC
Q 045555            2 GFALEIFGNMKN-----K----DVISWTTIVSGYINRGQVDIARQYFAQMPE-----R-----DYVLWTAMIDGYLRVNR   62 (175)
Q Consensus         2 ~~A~~~~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~-----~~~~~~~li~~~~~~~~   62 (175)
                      ++|.+.|+...+     +    ...++..+...|...|++++|...+++..+     +     ...+++.+...|...|+
T Consensus       120 ~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~  199 (383)
T 3ulq_A          120 LSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQ  199 (383)
T ss_dssp             HHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcC
Confidence            355566655433     2    456788999999999999999998887653     2     23468888899999999


Q ss_pred             hHHHHHHHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHH
Q 045555           63 FREALTLFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTA  132 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~  132 (175)
                      +++|...|++..+.... ++...          ...++..+...|...|++++|.+.|++..+     .+    ..++..
T Consensus       200 ~~~A~~~~~~al~~~~~~~~~~~----------~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  269 (383)
T 3ulq_A          200 YEDAISHFQKAYSMAEAEKQPQL----------MGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFL  269 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHH----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCChHH----------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHH
Confidence            99999999998764211 11111          134567899999999999999999999854     22    456888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHH
Q 045555          133 MIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +...|.+.|++++|.+.+++..+
T Consensus       270 l~~~~~~~g~~~~A~~~~~~al~  292 (383)
T 3ulq_A          270 ITQIHYKLGKIDKAHEYHSKGMA  292 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999999999998875

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.66  E-value=1.9e-06  Score=53.23  Aligned_cols=108  Identities=9%  Similarity=-0.076  Sum_probs=85.6

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      ..|..+...+.+.|++++|+..|++..+..  |             .+...+..+..+|.+.|++++|...|+...+  |
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p-------------~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p   69 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA--P-------------EDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP   69 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--C-------------CChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC
Confidence            457778888999999999999999998854  2             2455667899999999999999999999843  4


Q ss_pred             -ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC----CCCcHHHHHHHHh
Q 045555          126 -DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS----IRLDEVTYVGVLS  170 (175)
Q Consensus       126 -~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g----~~p~~~t~~~ll~  170 (175)
                       +...|..+..++...|++++|.+.|++..+..    -.|+.......+.
T Consensus        70 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~p~~~~~~~~l~  119 (126)
T 3upv_A           70 NFVRAYIRKATAQIAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYY  119 (126)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhCcccCCchhHHHHHHHHH
Confidence             67788999999999999999999999988642    1165554444443

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.66  E-value=8.2e-08  Score=63.10  Aligned_cols=115  Identities=11%  Similarity=0.188  Sum_probs=83.0

Q ss_pred             HhcCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHH
Q 045555           27 INRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALI  103 (175)
Q Consensus        27 ~~~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li  103 (175)
                      ...|++++|...++...   ..+...|..+...+...|++++|+..|++..+..  |             .+...+..+.
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p-------------~~~~~~~~la   85 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR--G-------------ENAELYAALA   85 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--C-------------SCHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--C-------------CCHHHHHHHH
Confidence            45677777777777654   2366778888888888899999999888887743  1             2334445677


Q ss_pred             HH-HHhcCCH--HHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          104 DM-YCKCGDV--EKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       104 ~~-~~~~~~~--~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+ |...|++  ++|...|+...+  | +...|..+...|...|++++|.+.|++..+.
T Consensus        86 ~~l~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           86 TVLYYQASQHMTAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCcchHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            77 7788888  888888888743  3 5667778888888889999999999888775

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.66  E-value=3.7e-07  Score=58.96  Aligned_cols=95  Identities=13%  Similarity=0.109  Sum_probs=82.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|++..+  | +...|..+..+|.+.|++++|+..|++..+..  |+          
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~----------  102 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KN----------  102 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SS----------
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CC----------
Confidence            566888999999999999999999998773  4 77889999999999999999999999999854  22          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                         +...|..+..+|.+.|++++|.+.|+...+
T Consensus       103 ---~~~~~~~lg~~~~~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          103 ---DYTPVFHTGQCQLRLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             ---CCHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---CcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               345567899999999999999999999844

>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=98.65  E-value=3.7e-06  Score=70.95  Aligned_cols=142  Identities=11%  Similarity=0.091  Sum_probs=107.6

Q ss_pred             hHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh
Q 045555            3 FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE   82 (175)
Q Consensus         3 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   82 (175)
                      +|.++.++.  .+..+|..+..++.+.|++++|.+.|.+.  .|...|..++.+|.+.|++++|++.+...++..-.|..
T Consensus      1094 rAiE~Aerv--n~p~vWsqLAKAql~~G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~I 1169 (1630)
T 1xi4_A         1094 RAYEFAERC--NEPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYV 1169 (1630)
T ss_pred             HHHHHHHhc--CCHHHHHHHHHHHHhCCCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccc
Confidence            344444433  35678899999999999999999999764  67778889999999999999999999887765422211


Q ss_pred             HHH-----HHh-----hh--ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHH
Q 045555           83 FTT-----VRI-----LT--TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        83 ~~~-----~~l-----~~--~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                      .+.     ..+     +.  --.++..-+..+.+.|...|++++|..+|...     ..|..+...|++.|++++|.+.+
T Consensus      1170 dt~LafaYAKl~rleele~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q~AIEaa 1244 (1630)
T 1xi4_A         1170 ETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGA 1244 (1630)
T ss_pred             cHHHHHHHHhhcCHHHHHHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHHHHHHHH
Confidence            111     111     00  11334455667899999999999999999974     58999999999999999999999


Q ss_pred             HHH
Q 045555          151 SQM  153 (175)
Q Consensus       151 ~~m  153 (175)
                      ++.
T Consensus      1245 rKA 1247 (1630)
T 1xi4_A         1245 RKA 1247 (1630)
T ss_pred             HHh
Confidence            886

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.64  E-value=5.2e-07  Score=64.21  Aligned_cols=109  Identities=17%  Similarity=0.210  Sum_probs=80.1

Q ss_pred             HHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHH
Q 045555           34 IARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVE  113 (175)
Q Consensus        34 ~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~  113 (175)
                      ...+.+......+...+..+...+.+.|++++|...|++..+..  |+..             ..+..+...+.+.|+++
T Consensus       104 ~l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~-------------~a~~~la~~~~~~g~~~  168 (287)
T 3qou_A          104 AIRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQLS--NQNG-------------EIGLLLAETLIALNRSE  168 (287)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TSCH-------------HHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC--Ccch-------------hHHHHHHHHHHHCCCHH
Confidence            34444444444556667888888999999999999999999854  4421             12245777777777777


Q ss_pred             HHHHHHHhhcC------------------------------------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          114 KAQRVFWKMLR------------------------------------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       114 ~a~~~~~~~~~------------------------------------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +|.+.++....                                    | +...+..+...+...|++++|.+.|++++..
T Consensus       169 ~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~  248 (287)
T 3qou_A          169 DAEAVLXTIPLQDQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRX  248 (287)
T ss_dssp             HHHHHHTTSCGGGCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCchhhcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhc
Confidence            77777776521                                    2 4567788888999999999999999999875


Q ss_pred             C
Q 045555          157 S  157 (175)
Q Consensus       157 g  157 (175)
                      .
T Consensus       249 ~  249 (287)
T 3qou_A          249 D  249 (287)
T ss_dssp             C
T ss_pred             c
Confidence            3

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.63  E-value=2.6e-06  Score=54.55  Aligned_cols=96  Identities=9%  Similarity=-0.086  Sum_probs=79.4

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...+..+...+.+.|++++|+..|++.....               +.+...|..+..+|.+.|++++|...|+.... 
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~---------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l   84 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD---------------HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVM   84 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC---------------cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            45567778888999999999999999988753               22455567888999999999999999999843 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       | +...|..+..+|...|++++|.+.|++..+.
T Consensus        85 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           85 DIXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             STTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             4 6778888999999999999999999998764

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.63  E-value=1.3e-06  Score=52.18  Aligned_cols=96  Identities=11%  Similarity=0.013  Sum_probs=73.8

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...+..+...+.+.|++++|...|++..+...               .+...+..+...+.+.|++++|...|++..+ 
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~---------------~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~   69 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDP---------------EESKYWLMKGKALYNLERYEEAVDCYNYVINV   69 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCC---------------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCc---------------CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            445667777788888888888888888877531               2334456788888888999999888888743 


Q ss_pred             -C---ChhhHHHHHHHHHhc-CChhHHHHHHHHHHHC
Q 045555          125 -K---DKFTWTAMIVGLAIS-GHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~---~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~  156 (175)
                       |   +...|..+...+... |++++|.+.+++..+.
T Consensus        70 ~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           70 IEDEYNKDVWAAKADALRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             SCCTTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGGG
T ss_pred             CcccchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhhc
Confidence             3   466788888888888 9999999999888765

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.63  E-value=1.3e-07  Score=63.32  Aligned_cols=128  Identities=9%  Similarity=0.051  Sum_probs=84.2

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CCh----------------hHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDY----------------VLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~----------------~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ....+..+...+.+.|++++|...|++..+   .+.                ..|..+..++.+.|++++|+..+++..+
T Consensus        37 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~  116 (198)
T 2fbn_A           37 SAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLK  116 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            345677777788888888888888887542   222                5677788888888888888888888877


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHH-HHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTAL-DMFS  151 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~-~~~~  151 (175)
                      ..  |             .+...+..+..+|...|++++|...|+...+  | +...+..+...+...++..++. ..|.
T Consensus       117 ~~--p-------------~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~  181 (198)
T 2fbn_A          117 ID--K-------------NNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEARKKDKLTFG  181 (198)
T ss_dssp             HS--T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHC-------
T ss_pred             hC--c-------------ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            53  2             2344456788888888888888888888733  3 5567777777777777777666 5566


Q ss_pred             HHHHCC
Q 045555          152 QMLRAS  157 (175)
Q Consensus       152 ~m~~~g  157 (175)
                      .|...|
T Consensus       182 ~~f~~~  187 (198)
T 2fbn_A          182 GMFDKG  187 (198)
T ss_dssp             ------
T ss_pred             HHhccc
Confidence            665543

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.62  E-value=3.1e-07  Score=67.60  Aligned_cols=145  Identities=12%  Similarity=0.103  Sum_probs=110.7

Q ss_pred             chHHHHhhccCC-----C----cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-----C-----ChhHHHHHHHHHhccCC
Q 045555            2 GFALEIFGNMKN-----K----DVISWTTIVSGYINRGQVDIARQYFAQMPE-----R-----DYVLWTAMIDGYLRVNR   62 (175)
Q Consensus         2 ~~A~~~~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~-----~~~~~~~li~~~~~~~~   62 (175)
                      ++|+..|+...+     +    ...++..+...|...|+++.|...+++..+     +     ...+++.+...|...|+
T Consensus       118 ~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~  197 (378)
T 3q15_A          118 VEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKH  197 (378)
T ss_dssp             HHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCC
Confidence            355666655432     2    356788999999999999999998887552     1     23468889999999999


Q ss_pred             hHHHHHHHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----C---ChhhHHHH
Q 045555           63 FREALTLFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----K---DKFTWTAM  133 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~---~~~~~~~l  133 (175)
                      +++|.+.|++..+.... ++..          ....++..+..+|...|++++|.+.|++..+     .   ...++..+
T Consensus       198 ~~~A~~~~~~al~~~~~~~~~~----------~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  267 (378)
T 3q15_A          198 YDKALPHLEAALELAMDIQNDR----------FIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGL  267 (378)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHH----------HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHH----------HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHH
Confidence            99999999998763210 1111          1134567899999999999999999999854     2   34577888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHC
Q 045555          134 IVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       134 i~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...+.+.|++++|.+.+++..+.
T Consensus       268 a~~~~~~g~~~~A~~~~~~al~~  290 (378)
T 3q15_A          268 SWTLCKAGQTQKAFQFIEEGLDH  290 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHH
Confidence            89999999999999999998864

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.61  E-value=2e-06  Score=61.82  Aligned_cols=141  Identities=12%  Similarity=0.038  Sum_probs=101.2

Q ss_pred             HHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-----ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            4 ALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPER-----DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         4 A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      |+..|++...   ++..+...+...+...|++++|++.+.+...+     +...+..++..+.+.|+.+.|.+.+++|.+
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            3455554442   56666678889999999999999999987432     455678889999999999999999999988


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHH----HHhcCCHHHHHHHHHhhcCC--ChhhHHHHHHHHHhcCChhHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDM----YCKCGDVEKAQRVFWKMLRK--DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~----~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                      .  .||....         +..+...+..+    ....+++.+|..+|+++...  +..+-..++.++.+.|++++|.+.
T Consensus       165 ~--~~d~~~~---------~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~  233 (310)
T 3mv2_B          165 A--IEDTVSG---------DNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGI  233 (310)
T ss_dssp             H--SCHHHHH---------HHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             c--Ccccccc---------chHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHH
Confidence            4  2310000         12222345545    33344999999999999653  323444555588999999999999


Q ss_pred             HHHHHH
Q 045555          150 FSQMLR  155 (175)
Q Consensus       150 ~~~m~~  155 (175)
                      ++.+.+
T Consensus       234 L~~l~~  239 (310)
T 3mv2_B          234 VELLLS  239 (310)
T ss_dssp             HHHHHS
T ss_pred             HHHHHH
Confidence            997764

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.61  E-value=2.3e-07  Score=68.57  Aligned_cols=131  Identities=12%  Similarity=0.059  Sum_probs=104.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      ..++..+...|...|++++|...|++..+     ++    ...+..+...+...|++++|...+++..+.......    
T Consensus       223 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~----  298 (411)
T 4a1s_A          223 GRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGE----  298 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTC----
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCC----
Confidence            45788899999999999999999998764     12    237889999999999999999999998774211000    


Q ss_pred             HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---------ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           87 RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---------DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        87 ~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                           ......++..+...|.+.|++++|.+.+++...-         ...++..+...|...|++++|.+.|++..+
T Consensus       299 -----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          299 -----REVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             -----HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence                 0012456678999999999999999999988431         244788899999999999999999999865

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.60  E-value=4.1e-07  Score=57.97  Aligned_cols=130  Identities=16%  Similarity=0.121  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~   85 (175)
                      ..++..+...|...|++++|...+++..+     ++    ..++..+...+...|++++|...+++..+.... ++..  
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~--   86 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRA--   86 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH--
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcH--
Confidence            45788889999999999999999998764     12    246888999999999999999999998764211 1111  


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                              .....+..+...+...|++++|.+.+++...     .    ....+..+...+...|++++|.+.+++..+
T Consensus        87 --------~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           87 --------VEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             --------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --------HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence                    1134567889999999999999999998742     1    235677888899999999999999998765

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.60  E-value=7.1e-07  Score=64.15  Aligned_cols=141  Identities=11%  Similarity=0.114  Sum_probs=102.6

Q ss_pred             chHHHHhhccCC-----CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-----ChhHHHHHHHHH--hc--cCChHH
Q 045555            2 GFALEIFGNMKN-----KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-----DYVLWTAMIDGY--LR--VNRFRE   65 (175)
Q Consensus         2 ~~A~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-----~~~~~~~li~~~--~~--~~~~~~   65 (175)
                      ++|++++.....     -+...+..++..+.+.|+.+.|.+.++.|.+  |     +..+...|..++  ..  .++..+
T Consensus       117 eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~  196 (310)
T 3mv2_B          117 DKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATS  196 (310)
T ss_dssp             HHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTH
T ss_pred             HHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHH
Confidence            578888888743     2667888999999999999999999999875  4     244555555552  22  348999


Q ss_pred             HHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------------C-ChhhHHH
Q 045555           66 ALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------------K-DKFTWTA  132 (175)
Q Consensus        66 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------------~-~~~~~~~  132 (175)
                      |..+|+++.+..  |+..              ....++.++.+.|++++|++.++.+.+            | +..+.-.
T Consensus       197 A~~~f~El~~~~--p~~~--------------~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN  260 (310)
T 3mv2_B          197 NFYYYEELSQTF--PTWK--------------TQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLAN  260 (310)
T ss_dssp             HHHHHHHHHTTS--CSHH--------------HHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHH
T ss_pred             HHHHHHHHHHhC--CCcc--------------cHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHH
Confidence            999999997753  3211              112344489999999999999987633            3 5667756


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      +|......|+  +|.+++.++.+.  .|+.
T Consensus       261 ~i~l~~~lgk--~a~~l~~qL~~~--~P~h  286 (310)
T 3mv2_B          261 QITLALMQGL--DTEDLTNQLVKL--DHEH  286 (310)
T ss_dssp             HHHHHHHTTC--TTHHHHHHHHHT--TCCC
T ss_pred             HHHHHHHhCh--HHHHHHHHHHHh--CCCC
Confidence            6666666776  899999999874  4543

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.59  E-value=2.8e-06  Score=52.10  Aligned_cols=104  Identities=10%  Similarity=0.116  Sum_probs=83.0

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      ..|..+...+...|++++|...|++..+..  |             .+...+..+...|.+.|++++|...++....  |
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~-------------~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~   69 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD--P-------------TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR   69 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--C-------------ccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc
Confidence            457788888999999999999999998854  2             2344557889999999999999999999843  2


Q ss_pred             -C-------hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555          126 -D-------KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       126 -~-------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                       +       ..+|..+...+...|++++|.+.|++..+.  .|+......+
T Consensus        70 ~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l  118 (131)
T 1elr_A           70 ENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVLKKC  118 (131)
T ss_dssp             HSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHH
T ss_pred             ccchhHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCHHHHHHH
Confidence             2       678888999999999999999999999875  3555444433

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.59  E-value=2.1e-06  Score=54.43  Aligned_cols=104  Identities=13%  Similarity=-0.062  Sum_probs=79.6

Q ss_pred             HhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHH
Q 045555           38 YFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEK  114 (175)
Q Consensus        38 ~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~  114 (175)
                      .|++..+.   +...+..+...+.+.|++++|+..|++.....  |             .+...|..+..+|.+.|++++
T Consensus         6 ~l~~al~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--p-------------~~~~~~~~lg~~~~~~g~~~~   70 (142)
T 2xcb_A            6 TLAMLRGLSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLD--H-------------YDARYFLGLGACRQSLGLYEQ   70 (142)
T ss_dssp             ---CCTTCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHH
T ss_pred             hHHHHHcCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhC--C-------------ccHHHHHHHHHHHHHHhhHHH
Confidence            34444432   44456677788889999999999999988754  2             244556778889999999999


Q ss_pred             HHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          115 AQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       115 a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      |...|+....  | +...|..+..+|...|++++|.+.|++..+.
T Consensus        71 A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           71 ALQSYSYGALMDINEPRFPFHAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            9999998843  3 6677888889999999999999999988764

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.59  E-value=2.2e-06  Score=66.48  Aligned_cols=126  Identities=9%  Similarity=-0.011  Sum_probs=89.0

Q ss_pred             cCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHH
Q 045555           29 RGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDM  105 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~  105 (175)
                      .|++++|...|++..+   .+...|..+...+.+.|++++|.+.|++..+..  |             .+...+..+..+
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p-------------~~~~~~~~lg~~   66 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH--P-------------GHPEAVARLGRV   66 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS--T-------------TCHHHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-------------CCHHHHHHHHHH
Confidence            4788999999998775   357789999999999999999999999999853  2             234556789999


Q ss_pred             HHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHh
Q 045555          106 YCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLS  170 (175)
Q Consensus       106 ~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~  170 (175)
                      |.+.|++++|.+.+++..+  | +...|..+...|.+.|++++|.+.|++..+.. ..+...+..+..
T Consensus        67 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  133 (568)
T 2vsy_A           67 RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLN  133 (568)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            9999999999999999843  3 67789999999999999999999999998752 123444444433

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.59  E-value=5.8e-07  Score=58.96  Aligned_cols=108  Identities=10%  Similarity=0.166  Sum_probs=88.0

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHH-HhccCCh--HHHHHHHHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDG-YLRVNRF--REALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~-~~~~~~~--~~a~~~~~~   72 (175)
                      ++|...++...+   .+...|..+...|...|++++|...|++..+   .+...+..+... +.+.|++  ++|...+++
T Consensus        27 ~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~  106 (177)
T 2e2e_A           27 EAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAMIDK  106 (177)
T ss_dssp             CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHHHHHH
Confidence            456666665543   4778999999999999999999999998764   467778888888 7789998  999999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      ..+..  |+             +...+..+...|.+.|++++|...|+...+
T Consensus       107 al~~~--p~-------------~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          107 ALALD--SN-------------EITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHC--TT-------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhC--CC-------------cHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            98864  22             344556789999999999999999999854

>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=98.59  E-value=2.8e-06  Score=55.76  Aligned_cols=137  Identities=13%  Similarity=0.116  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      ....+...+.+.|++++|...|++..+   .+...+..+...+.+.|++++|+..+++......  ++..+         
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~---------   76 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYK---------   76 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHH---------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHH---------
Confidence            345667788999999999999999885   3677899999999999999999999999877532  32222         


Q ss_pred             chhHHHHHHHH-HHhcCCHHHHHHHHHhhc--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCC-cHHHHHHHH
Q 045555           95 DIFVGIALIDM-YCKCGDVEKAQRVFWKML--RK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL-DEVTYVGVL  169 (175)
Q Consensus        95 ~~~~~~~li~~-~~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll  169 (175)
                           ...... +.+.+...+|...++...  .| +...+..+...+...|++++|.+.|+++.+..-.+ +...+..+.
T Consensus        77 -----~~~~~~~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~  151 (176)
T 2r5s_A           77 -----SLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFM  151 (176)
T ss_dssp             -----HHHHHHHHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHH
T ss_pred             -----HHHHHHHHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHH
Confidence                 111111 122223334677777774  34 67889999999999999999999999998764332 233444444


Q ss_pred             h
Q 045555          170 S  170 (175)
Q Consensus       170 ~  170 (175)
                      .
T Consensus       152 ~  152 (176)
T 2r5s_A          152 D  152 (176)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.58  E-value=3.7e-06  Score=52.41  Aligned_cols=95  Identities=12%  Similarity=-0.070  Sum_probs=52.7

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...|..+...+...|++++|+..|++.....  |             .+...+..+..+|...|++++|...++...+ 
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~-------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~   72 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN--P-------------LVAVYYTNRALCYLKMQQPEQALADCRRALEL   72 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC--c-------------CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            44455555555666666666666666655532  1             1233344555566666666666666665532 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                       | +...|..+..++...|++++|.+.|++..+
T Consensus        73 ~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           73 DGQSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence             2 445555666666666666666666666553

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.57  E-value=1.8e-07  Score=70.94  Aligned_cols=126  Identities=10%  Similarity=0.090  Sum_probs=102.0

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-C---------------hhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-D---------------YVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +...+..+...|.+.|++++|...|++..+  | +               ...|..+..+|.+.|++++|+..+++.++.
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            456788999999999999999999998764  3 3               578999999999999999999999999985


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHH-HHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTAL-DMFSQ  152 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~-~~~~~  152 (175)
                      .  |             .+...+..+..+|.+.|++++|...|+...+  | +...+..+..++.+.|+.+++. ..++.
T Consensus       347 ~--p-------------~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~  411 (457)
T 1kt0_A          347 D--S-------------ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRIYAN  411 (457)
T ss_dssp             S--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C--C-------------ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4  2             2345567899999999999999999999855  3 5678888999999999888875 45666


Q ss_pred             HHH
Q 045555          153 MLR  155 (175)
Q Consensus       153 m~~  155 (175)
                      |..
T Consensus       412 ~f~  414 (457)
T 1kt0_A          412 MFK  414 (457)
T ss_dssp             C--
T ss_pred             HHh
Confidence            643

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.57  E-value=2.5e-06  Score=52.61  Aligned_cols=96  Identities=13%  Similarity=0.074  Sum_probs=82.5

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...|..+...+.+.|++++|+..|++..+..  |             .+...+..+...|...|++++|...+++..+ 
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--~-------------~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~   79 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN--P-------------KDAKLYSNRAACYTKLLEFQLALKDCEECIQL   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC--T-------------TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--C-------------CcHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            55678899999999999999999999998853  2             2345567899999999999999999999843 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       | +...|..+...+.+.|++++|.+.|++..+.
T Consensus        80 ~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~  113 (133)
T 2lni_A           80 EPTFIKGYTRKAAALEAMKDYTKAMDVYQKALDL  113 (133)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence             3 6778899999999999999999999998874

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.56  E-value=6.1e-07  Score=65.89  Aligned_cols=130  Identities=16%  Similarity=0.107  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~   85 (175)
                      ..++..+...|...|++++|...+++..+     ++    ..++..+...+...|++++|...+++..+.... ++..  
T Consensus       187 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~--  264 (406)
T 3sf4_A          187 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRA--  264 (406)
T ss_dssp             HHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH--
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCch--
Confidence            45788999999999999999999998763     22    337889999999999999999999998764211 1110  


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                              ....++..+...|.+.|++++|.+.++....     .+    ..++..+...|...|++++|.+.+++..+
T Consensus       265 --------~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          265 --------VEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             --------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --------HHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                    1144667899999999999999999998843     12    55788899999999999999999998764

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.56  E-value=5.3e-07  Score=64.20  Aligned_cols=131  Identities=17%  Similarity=0.111  Sum_probs=103.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~   85 (175)
                      ..++..+...+...|++++|...+++..+     ++    ..++..+...+...|++++|...+++..+.... ++..  
T Consensus       183 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~--  260 (338)
T 3ro2_A          183 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRA--  260 (338)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHH--
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchh--
Confidence            45788899999999999999999998763     12    337888999999999999999999998763211 1110  


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                              ....++..+...|...|++++|...+++...     .+    ..++..+...|.+.|++++|.+.+++..+.
T Consensus       261 --------~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          261 --------VEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             --------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             --------HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence                    1144567899999999999999999998743     12    447888999999999999999999998864

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.55  E-value=2.7e-06  Score=55.12  Aligned_cols=94  Identities=10%  Similarity=0.030  Sum_probs=57.1

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...+..+...+.+.|++++|+..|++..+..  |             .+...+..+..+|.+.|++++|...|+...+  
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p-------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~   75 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIA--P-------------ANPIYLSNRAAAYSASGQHEKAAEDAELATVVD   75 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-------------cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            3445566666666666666666666666532  1             1333445666666666666666666666632  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      | +...|..+..+|...|++++|.+.|++.++
T Consensus        76 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           76 PKYSKAWSRLGLARFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            2 455666666666666666666666666654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.55  E-value=1.2e-06  Score=62.31  Aligned_cols=131  Identities=13%  Similarity=0.096  Sum_probs=102.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-------C--ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      .|......|...|++++|...|.+..+       +  ...+|+.+...|.+.|++++|+..|++..+.......      
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~------  112 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQ------  112 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCC------
Confidence            577778888899999999999987653       1  2457999999999999999999999998773210000      


Q ss_pred             hhccCcchhHHHHHHHHHHhc-CCHHHHHHHHHhhcC--C---C----hhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           89 LTTFNNDIFVGIALIDMYCKC-GDVEKAQRVFWKMLR--K---D----KFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~--~---~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                         ......+++.+...|... |++++|...|++..+  |   +    ..+|+.+...+.+.|++++|.+.|++..+..
T Consensus       113 ---~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  188 (292)
T 1qqe_A          113 ---FRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS  188 (292)
T ss_dssp             ---HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             ---HHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence               000134667899999996 999999999999843  2   1    3578889999999999999999999998854

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.55  E-value=2.7e-06  Score=57.74  Aligned_cols=149  Identities=12%  Similarity=-0.026  Sum_probs=117.4

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHhcC----ChhHHHHHhhcCCCC-ChhHHHHHHHHHhc----cCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYINRG----QVDIARQYFAQMPER-DYVLWTAMIDGYLR----VNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~   71 (175)
                      ++|+++|+...+ .++.++..+...|.+ +    ++++|...|++..++ +...+..|-..|..    .+++++|+..|+
T Consensus        35 ~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~  113 (212)
T 3rjv_A           35 QKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQ  113 (212)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHH
Confidence            568888887765 477888899999988 7    899999999988754 67778888888887    889999999999


Q ss_pred             HhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcC--CChhhHHHHHHHHHhc-C---
Q 045555           72 EMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLR--KDKFTWTAMIVGLAIS-G---  141 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~-g---  141 (175)
                      +..+.|...             .....+..|...|..    .+++++|...|+...+  .+...+..+-..|... |   
T Consensus       114 ~A~~~~~~~-------------~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~a~~~Lg~~y~~g~gg~~  180 (212)
T 3rjv_A          114 DAARDSESD-------------AAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSRTGYAEYWAGMMFQQGEKGFI  180 (212)
T ss_dssp             HHTSSTTSH-------------HHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSCTTHHHHHHHHHHHHCBTTTB
T ss_pred             HHHHcCCCc-------------chHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCC
Confidence            999876310             013444678888888    8899999999999854  4677788888887653 3   


Q ss_pred             --ChhHHHHHHHHHHHCCCCCcHHH
Q 045555          142 --HGDTALDMFSQMLRASIRLDEVT  164 (175)
Q Consensus       142 --~~~~a~~~~~~m~~~g~~p~~~t  164 (175)
                        +.++|.+.|++..+.|...-...
T Consensus       181 ~~d~~~A~~~~~~A~~~g~~~A~~~  205 (212)
T 3rjv_A          181 EPNKQKALHWLNVSCLEGFDTGCEE  205 (212)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence              89999999999998875544433

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.55  E-value=7e-06  Score=49.30  Aligned_cols=95  Identities=16%  Similarity=0.079  Sum_probs=72.1

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...+..+...+...|++++|...|++.....  |             .+...+..+...+.+.|++++|...++....  
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~-------------~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~   68 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLD--P-------------HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK   68 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHC--C-------------CcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC
Confidence            3456777778888888888888888887743  1             2344456778888888888888888888743  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      | +...|..+...+...|++++|.+.+++..+.
T Consensus        69 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           69 PDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence            3 5667888888888889999999888888754

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.53  E-value=1.3e-06  Score=57.56  Aligned_cols=111  Identities=14%  Similarity=0.082  Sum_probs=76.6

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---C------------------------------
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---R------------------------------   45 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~------------------------------   45 (175)
                      ++|++.|++..+  | +..++..+...|.+.|++++|...+.....   .                              
T Consensus        22 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~  101 (184)
T 3vtx_A           22 DGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAAIDALQRAIA  101 (184)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            567777777654  3 667788888888888888888887776542   2                              


Q ss_pred             ----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           46 ----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        46 ----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                          +...+..+...+.+.|++++|++.|++..+..               +.+...+..+..+|.+.|++++|.+.|++
T Consensus       102 ~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~---------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~  166 (184)
T 3vtx_A          102 LNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK---------------PGFIRAYQSIGLAYEGKGLRDEAVKYFKK  166 (184)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc---------------chhhhHHHHHHHHHHHCCCHHHHHHHHHH
Confidence                23344445555555555555555555555432               33466778999999999999999999999


Q ss_pred             hcCCCh
Q 045555          122 MLRKDK  127 (175)
Q Consensus       122 ~~~~~~  127 (175)
                      ..+.+.
T Consensus       167 al~~~p  172 (184)
T 3vtx_A          167 ALEKEE  172 (184)
T ss_dssp             HHHTTH
T ss_pred             HHhCCc
Confidence            866544

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.52  E-value=1.1e-05  Score=49.35  Aligned_cols=107  Identities=12%  Similarity=0.085  Sum_probs=85.9

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...+..+...+...|++++|+..+++.....  |             .+...+..+...+...|++++|...++.... 
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~-------------~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   75 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELN--P-------------ANAVYFCNRAAAYSKLGNYAGAVQDCERAICI   75 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC--C-------------CCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc
Confidence            45578888899999999999999999998753  2             2344567889999999999999999999843 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCC-cHHHHHHHH
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRL-DEVTYVGVL  169 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p-~~~t~~~ll  169 (175)
                       | +...|..+...+...|++++|.+.|++..+.  .| +...+..+-
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~l~  121 (131)
T 2vyi_A           76 DPAYSKAYGRMGLALSSLNKHVEAVAYYKKALEL--DPDNETYKSNLK  121 (131)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CccchHHHHHHH
Confidence             3 5778889999999999999999999998875  33 344444433

>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=98.52  E-value=1.1e-06  Score=62.56  Aligned_cols=144  Identities=9%  Similarity=-0.024  Sum_probs=105.2

Q ss_pred             chHHHHhhccCC-----Cc----HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCCh
Q 045555            2 GFALEIFGNMKN-----KD----VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRF   63 (175)
Q Consensus         2 ~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~   63 (175)
                      ++|.++++...+     |+    ...+..+...+...|++++|...|++..+     ++    ..+++.+...|...|++
T Consensus        92 ~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~  171 (293)
T 3u3w_A           92 KEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYL  171 (293)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCH
Confidence            456666666543     22    22444577778888899999999987542     23    23688999999999999


Q ss_pred             HHHHHHHHHhHhCC--CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---------ChhhHHH
Q 045555           64 REALTLFREMQTSN--IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---------DKFTWTA  132 (175)
Q Consensus        64 ~~a~~~~~~m~~~~--~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~  132 (175)
                      ++|+..|++..+.-  ...+..          ....++..+...|.+.|++++|...+++..+-         -..+|..
T Consensus       172 ~~A~~~~~~al~~~~~~~~~~~----------~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~  241 (293)
T 3u3w_A          172 KKGIDLFEQILKQLEALHDNEE----------FDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQ  241 (293)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCHH----------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccchh----------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            99999999998521  101111          11336678999999999999999999987431         1567888


Q ss_pred             HHHHHHhcCC-hhHHHHHHHHHHH
Q 045555          133 MIVGLAISGH-GDTALDMFSQMLR  155 (175)
Q Consensus       133 li~~~~~~g~-~~~a~~~~~~m~~  155 (175)
                      +..+|.+.|+ +++|.+.|++...
T Consensus       242 lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          242 RGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHH
Confidence            9999999995 6999999988764

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.50  E-value=1.5e-06  Score=62.36  Aligned_cols=129  Identities=7%  Similarity=-0.054  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-------C--ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      ..+|+.+...|.+.|++++|...|++..+       +  -..+++.+...|.. |++++|+..|++........+...  
T Consensus        76 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~--  152 (307)
T 2ifu_A           76 AKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLR--  152 (307)
T ss_dssp             HHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHH--
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChh--
Confidence            45788999999999999999998887542       1  13568888888888 999999999999876321110000  


Q ss_pred             HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           87 RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        87 ~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                             ....+++.+...|.+.|++++|.+.|++...     ++    ...+..+...+...|++++|.+.|++..
T Consensus       153 -------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          153 -------QAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             -------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             -------HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence                   0134667899999999999999999999854     11    2356667777888899999999999987

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.50  E-value=6.1e-06  Score=49.58  Aligned_cols=96  Identities=14%  Similarity=0.054  Sum_probs=81.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+...|++++|...|+...+   .+...+..+...+.+.|++++|...+++..+..  |           
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~-----------   69 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK--P-----------   69 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC--c-----------
Confidence            456788889999999999999999998753   467788999999999999999999999998854  2           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                        .+...+..+..++.+.|++++|.+.++...+.
T Consensus        70 --~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           70 --DWGKGYSRKAAALEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             --ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHc
Confidence              23445578899999999999999999998553

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.49  E-value=4.3e-06  Score=56.51  Aligned_cols=123  Identities=16%  Similarity=0.141  Sum_probs=93.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHH----------------HHHHHhccCChHHHHHHHHHhHhCC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTA----------------MIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ...-.....+.+.|++++|...|++..+  | +...|..                +...+.+.|++++|+..|++..+..
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   84 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA   84 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            3444556677899999999999998774  3 3445666                8889999999999999999999854


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCC--hhHHHHHHHH
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGH--GDTALDMFSQ  152 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~--~~~a~~~~~~  152 (175)
                        |             .+...+..+...|...|++++|...|++..+  | +...|..+...|...|+  ...+...++.
T Consensus        85 --p-------------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~  149 (208)
T 3urz_A           85 --P-------------NNVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKK  149 (208)
T ss_dssp             --T-------------TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             --C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence              2             2455667899999999999999999999844  4 67788888888876553  3445555555


Q ss_pred             HH
Q 045555          153 ML  154 (175)
Q Consensus       153 m~  154 (175)
                      ..
T Consensus       150 ~~  151 (208)
T 3urz_A          150 LS  151 (208)
T ss_dssp             --
T ss_pred             Hh
Confidence            43

>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=98.49  E-value=1.6e-05  Score=56.48  Aligned_cols=127  Identities=9%  Similarity=0.139  Sum_probs=96.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHHh
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVRI   88 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l   88 (175)
                      +...+..+.+.|++++|..++++..+     ++    ...+..+...+...|++++|+..|++..+.... ++..     
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~-----  152 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVY-----  152 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTT-----
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHH-----
Confidence            33457788899999999999998654     12    113445777778888999999999999984322 2211     


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                           ....+++.+...|...|++++|...|++..+      .    ...+|..+...|.+.|++++|.+.+++.++
T Consensus       153 -----~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~  224 (293)
T 3u3w_A          153 -----QNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIE  224 (293)
T ss_dssp             -----HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence                 0133568899999999999999999999852      1    234788899999999999999999998764

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.49  E-value=2e-06  Score=55.07  Aligned_cols=95  Identities=7%  Similarity=0.065  Sum_probs=80.8

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|+....   .+...|..+..++.+.|++++|+..|++.....  |           
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p-----------   86 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD--I-----------   86 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--T-----------
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--C-----------
Confidence            566788889999999999999999998753   477889999999999999999999999998854  2           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        .+...+..+..+|...|++++|.+.|+...+
T Consensus        87 --~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           87 --XEPRFPFHAAECLLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             --TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --CCchHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              2344556799999999999999999998843

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.49  E-value=1.7e-06  Score=63.65  Aligned_cols=107  Identities=14%  Similarity=0.116  Sum_probs=71.8

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHH
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLF   70 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~   70 (175)
                      +|++++.....   ....+++.+...|...|++++|...|++..+     ++    ..++..+...|...|++++|+..+
T Consensus       168 ~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~  247 (383)
T 3ulq_A          168 QAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYF  247 (383)
T ss_dssp             HHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            44555555432   1345788888889999999999998887653     11    246888888899999999999999


Q ss_pred             HHhHhC----CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           71 REMQTS----NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        71 ~~m~~~----~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      ++..+.    +..|+             ...++..+...|.+.|++++|...+++.
T Consensus       248 ~~al~~~~~~~~~~~-------------~~~~~~~l~~~~~~~g~~~~A~~~~~~a  290 (383)
T 3ulq_A          248 KRAIAVFEESNILPS-------------LPQAYFLITQIHYKLGKIDKAHEYHSKG  290 (383)
T ss_dssp             HHHHHHHHHTTCGGG-------------HHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhccchh-------------HHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            888773    11121             1233455666666666666666666655

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.48  E-value=2.2e-06  Score=52.97  Aligned_cols=95  Identities=11%  Similarity=0.009  Sum_probs=80.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|++..+   .+...|..+..++.+.|++++|+..+++..+..  |           
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--p-----------   69 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD--P-----------   69 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-----------
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--C-----------
Confidence            345788888999999999999999998763   467889999999999999999999999999854  2           


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        .+...+..+..++...|++++|...|++..+
T Consensus        70 --~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           70 --NFVRAYIRKATAQIAVKEYASALETLDAART  100 (126)
T ss_dssp             --TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --CcHHHHHHHHHHHHHHhCHHHHHHHHHHHHH
Confidence              2344567899999999999999999998743

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.48  E-value=3.7e-07  Score=65.03  Aligned_cols=75  Identities=11%  Similarity=0.082  Sum_probs=60.1

Q ss_pred             chHHHHhhccCC--C-c----HHHHHHHHHHHHhcCChhHHHHHhhcCCC---------CChhHHHHHHHHHhccCChHH
Q 045555            2 GFALEIFGNMKN--K-D----VISWTTIVSGYINRGQVDIARQYFAQMPE---------RDYVLWTAMIDGYLRVNRFRE   65 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~---------~~~~~~~~li~~~~~~~~~~~   65 (175)
                      ++|...|++..+  | +    ...+..+...|...|++++|.+.+++..+         ....++..+...+...|++++
T Consensus        22 ~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  101 (338)
T 3ro2_A           22 RAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTLKVLGNFDE  101 (338)
T ss_dssp             HHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHHccCHHH
Confidence            467777777654  3 2    46788999999999999999999987653         134578888999999999999


Q ss_pred             HHHHHHHhHhC
Q 045555           66 ALTLFREMQTS   76 (175)
Q Consensus        66 a~~~~~~m~~~   76 (175)
                      |...+++..+.
T Consensus       102 A~~~~~~al~~  112 (338)
T 3ro2_A          102 AIVCCQRHLDI  112 (338)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999998664

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.47  E-value=2.5e-06  Score=54.04  Aligned_cols=104  Identities=12%  Similarity=0.108  Sum_probs=82.4

Q ss_pred             HHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC
Q 045555            6 EIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR   79 (175)
Q Consensus         6 ~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   79 (175)
                      ..|+...+  | +...+..+...+.+.|++++|...|+....   .+...|..+..++.+.|++++|+..|++..+..  
T Consensus         5 ~~l~~al~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--   82 (142)
T 2xcb_A            5 GTLAMLRGLSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD--   82 (142)
T ss_dssp             ----CCTTCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             hhHHHHHcCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--
Confidence            34555554  3 455677788889999999999999998763   477789999999999999999999999999864  


Q ss_pred             CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           80 RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        80 p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      |             .+...+..+..+|...|++++|.+.|+...+
T Consensus        83 p-------------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           83 I-------------NEPRFPFHAAECHLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             T-------------TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             C-------------CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2             2334456799999999999999999998844

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.47  E-value=2.2e-06  Score=65.95  Aligned_cols=140  Identities=13%  Similarity=0.119  Sum_probs=108.5

Q ss_pred             chHHHHhhccCC--C-cH-HHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHH-HHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN--K-DV-ISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMID-GYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~-~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|..+|+...+  | +. ..|...+..+.+.|++++|+.+|++..+  | +...|..... .+...|+.++|..+|++.
T Consensus       338 ~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~a  417 (530)
T 2ooe_A          338 EKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELG  417 (530)
T ss_dssp             HHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHHH
Confidence            567888887664  4 33 5899999999999999999999998765  2 2222322221 233689999999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-C----hhhHHHHHHHHHhcCChhHH
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-D----KFTWTAMIVGLAISGHGDTA  146 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~----~~~~~~li~~~~~~g~~~~a  146 (175)
                      .+..               +.+..+|..++..+.+.|+.++|..+|+....  | +    ...|...+......|+.+.+
T Consensus       418 l~~~---------------p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~  482 (530)
T 2ooe_A          418 LKKY---------------GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASI  482 (530)
T ss_dssp             HHHH---------------TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHC---------------CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            8853               22456678899999999999999999999854  2 2    33898999999999999999


Q ss_pred             HHHHHHHHHC
Q 045555          147 LDMFSQMLRA  156 (175)
Q Consensus       147 ~~~~~~m~~~  156 (175)
                      .++++++.+.
T Consensus       483 ~~~~~r~~~~  492 (530)
T 2ooe_A          483 LKVEKRRFTA  492 (530)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999998764

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.47  E-value=1.8e-06  Score=53.04  Aligned_cols=111  Identities=11%  Similarity=0.047  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC--CChHHHHHhhh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR--RDEFTTVRILT   90 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p~~~~~~~l~~   90 (175)
                      ...+..+...+.+.|++++|...|+...+   .+...+..+...+...|++++|...+++..+....  ++...      
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~------   77 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQ------   77 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHH------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHH------
Confidence            45788899999999999999999998653   46778899999999999999999999999875321  11000      


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CChhhHHHHHHH
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KDKFTWTAMIVG  136 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~li~~  136 (175)
                          ....+..+..+|.+.|++++|.+.|+...+  |+...+..+...
T Consensus        78 ----~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~  121 (131)
T 1elr_A           78 ----IAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQA  121 (131)
T ss_dssp             ----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence                044567899999999999999999999843  555554444433

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.47  E-value=3.4e-06  Score=59.96  Aligned_cols=128  Identities=9%  Similarity=-0.003  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCC-CCCChHHHHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSN-IRRDEFTTVR   87 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~   87 (175)
                      .+..+...+...|++++|...|++..+     .+    ..+|+.+...|...|++++|+..|++..+.- ..|+...   
T Consensus       117 ~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~---  193 (293)
T 2qfc_A          117 WQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEE---  193 (293)
T ss_dssp             HHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHH---
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCcccc---
Confidence            345566777888999999999886532     11    3478899999999999999999999987421 1111110   


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-------ChhhHHHHHHHHHhcCChhHH-HHHHHHHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-------DKFTWTAMIVGLAISGHGDTA-LDMFSQML  154 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-------~~~~~~~li~~~~~~g~~~~a-~~~~~~m~  154 (175)
                            ....++..+...|.+.|++++|...+++..+  +       -..+|..+...|.+.|++++| ...+++..
T Consensus       194 ------~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          194 ------FDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             ------chHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence                  0124667899999999999999999998743  1       156788899999999999999 77777754

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.46  E-value=2.6e-05  Score=48.94  Aligned_cols=99  Identities=12%  Similarity=0.018  Sum_probs=75.8

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +...+..+...+.+.|++++|+..|++..+..  |+...          ....+..+..+|.+.|++++|...++...+ 
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~----------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~   94 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQD----------QAVLHRNRAACHLKLEDYDKAETEASKAIEK   94 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHH----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchH----------HHHHHHHHHHHHHHHccHHHHHHHHHHHHhh
Confidence            56678888888888899999999998888743  33100          034456788888889999999988888743 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       | +...|..+..++...|++++|.+.|++..+.
T Consensus        95 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           95 DGGDVKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             TSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence             3 5677888888888999999999999888764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.46  E-value=4e-06  Score=54.30  Aligned_cols=96  Identities=9%  Similarity=-0.023  Sum_probs=83.1

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      .+...+..+...+.+.|++++|...|++..+   .+...|..+..+|.+.|++++|+..|++.++..  |+         
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~---------   77 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVD--PK---------   77 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT---------
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CC---------
Confidence            3567889999999999999999999998763   477889999999999999999999999999864  22         


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                          +...|..+..+|.+.|++++|...|++..+
T Consensus        78 ----~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           78 ----YSKAWSRLGLARFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             ----CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----CHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence                355567899999999999999999999844

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.45  E-value=7.6e-06  Score=50.93  Aligned_cols=105  Identities=13%  Similarity=0.098  Sum_probs=82.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC--CCChHHHHHhhh
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI--RRDEFTTVRILT   90 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~--~p~~~~~~~l~~   90 (175)
                      ..++..+...+.+.|++++|++.|++..+   .+...|+.+..+|.+.|++++|++.+++.++...  .++...      
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~------   81 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKL------   81 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHH------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHH------
Confidence            45788899999999999999999998663   4677899999999999999999999999987431  111111      


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhH
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTW  130 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~  130 (175)
                          -..+|..+..++...|++++|.+.|++..  .|+..+.
T Consensus        82 ----~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~~~~~~~~  119 (127)
T 4gcn_A           82 ----IAKAMSRAGNAFQKQNDLSLAVQWFHRSLSEFRDPELV  119 (127)
T ss_dssp             ----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCHHHH
T ss_pred             ----HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCHHHH
Confidence                12356778899999999999999999874  3555443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.44  E-value=2.4e-05  Score=55.53  Aligned_cols=129  Identities=10%  Similarity=0.033  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      ..-.....+...|++++|.++|..+..  |+......+...+.+.++|++|+..|+...+.   |+...          .
T Consensus       104 l~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~---~d~~~----------~  170 (282)
T 4f3v_A          104 ITMGFAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW---PDKFL----------A  170 (282)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC---SCHHH----------H
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc---CCccc----------H
Confidence            445677888999999999999999874  54436667777899999999999999855442   11110          1


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC------hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLRKD------KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      ...+..+-.++.+.|++++|.+.|++....+      .........++.+.|+.++|...|+++...  .|+
T Consensus       171 ~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~  240 (282)
T 4f3v_A          171 GAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPE  240 (282)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCc
Confidence            2234578999999999999999999985322      235666777888999999999999999975  455

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.44  E-value=3.7e-06  Score=52.44  Aligned_cols=96  Identities=10%  Similarity=0.008  Sum_probs=82.8

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      .+...+..+...+.+.|++++|...|+...+   .+...|..+..++.+.|++++|+..+++..+..  |          
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--p----------   74 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD--G----------   74 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T----------
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--c----------
Confidence            5778899999999999999999999998653   467789999999999999999999999998854  2          


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                         .+...+..+..+|...|++++|...|+...+
T Consensus        75 ---~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           75 ---QSVKAHFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             ---TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---hhHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence               2345567899999999999999999998843

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.44  E-value=3.2e-06  Score=52.20  Aligned_cols=93  Identities=13%  Similarity=-0.056  Sum_probs=78.7

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-  125 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-  125 (175)
                      .+..+...+.+.|++++|+..|++..+..  |             .+...|..+..++.+.|++++|...|+...+  | 
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--P-------------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~   83 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE--P-------------EREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK   83 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC--C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            45667778899999999999999999854  2             2455667899999999999999999999844  4 


Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          126 DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       126 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +...|..+..++...|++++|.+.|++.++.
T Consensus        84 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           84 DIAVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            6778899999999999999999999998853

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.44  E-value=1.9e-05  Score=60.16  Aligned_cols=137  Identities=10%  Similarity=0.012  Sum_probs=73.4

Q ss_pred             hHHHHhhccCC-CcHHHHHHHHHHHHh----cCChhHHHHHhhcCCC-CChhHHHHHHHHHhc----cCChHHHHHHHHH
Q 045555            3 FALEIFGNMKN-KDVISWTTIVSGYIN----RGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFRE   72 (175)
Q Consensus         3 ~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~   72 (175)
                      +|..+|+...+ .++.++..+...|..    .+++++|...|++..+ .+...+..|-..|..    .+++++|+..|++
T Consensus        61 ~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~  140 (490)
T 2xm6_A           61 QAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRL  140 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            45555554433 355666666666666    6777777777776554 345555666666665    5677777777777


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHh----cCCh
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAI----SGHG  143 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~  143 (175)
                      ..+.|.                 ...+..+...|..    .+++++|.+.|+...+. +...+..+...|..    .++.
T Consensus       141 a~~~~~-----------------~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~  203 (490)
T 2xm6_A          141 AAEQGR-----------------DSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERND  203 (490)
T ss_dssp             HHHTTC-----------------HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCH
T ss_pred             HHHCCC-----------------HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCH
Confidence            666542                 1122234444443    44555555555544322 33444444444444    4455


Q ss_pred             hHHHHHHHHHHHC
Q 045555          144 DTALDMFSQMLRA  156 (175)
Q Consensus       144 ~~a~~~~~~m~~~  156 (175)
                      ++|.+.|++..+.
T Consensus       204 ~~A~~~~~~a~~~  216 (490)
T 2xm6_A          204 AISAQWYRKSATS  216 (490)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHC
Confidence            5555555544443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.42  E-value=6.2e-06  Score=56.33  Aligned_cols=130  Identities=12%  Similarity=0.013  Sum_probs=95.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      +...+..+...+.+.|++++|...|+.+.+  |+    ...+..+..++.+.|++++|+..|++..+.........+   
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~---   79 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDY---   79 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHH---
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHH---
Confidence            455667778889999999999999999774  42    246788899999999999999999999986432111100   


Q ss_pred             hhccCcchhHHHHHHHHHH------------------hcCCHHHHHHHHHhhcC--CC-hhhH-----------------
Q 045555           89 LTTFNNDIFVGIALIDMYC------------------KCGDVEKAQRVFWKMLR--KD-KFTW-----------------  130 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~------------------~~~~~~~a~~~~~~~~~--~~-~~~~-----------------  130 (175)
                               .+-.+..++.                  ..|++++|...|+...+  |+ ...+                 
T Consensus        80 ---------a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~  150 (225)
T 2yhc_A           80 ---------VMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYE  150 (225)
T ss_dssp             ---------HHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------HHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHH
Confidence                     1112333333                  46789999999999965  32 2222                 


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          131 TAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       131 ~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      -.+...|.+.|++++|...|+++++.
T Consensus       151 ~~~a~~~~~~~~~~~A~~~~~~~l~~  176 (225)
T 2yhc_A          151 YSVAEYYTERGAWVAVVNRVEGMLRD  176 (225)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHH
Confidence            23456788999999999999999875

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.42  E-value=1.2e-06  Score=52.37  Aligned_cols=97  Identities=12%  Similarity=0.055  Sum_probs=80.6

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|++..+   .+...|..+...+.+.|++++|...+++..+..  |+          
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~----------   72 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI--ED----------   72 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--CC----------
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--cc----------
Confidence            455677888899999999999999998653   467788999999999999999999999999864  22          


Q ss_pred             cCcchhHHHHHHHHHHhc-CCHHHHHHHHHhhcC
Q 045555           92 FNNDIFVGIALIDMYCKC-GDVEKAQRVFWKMLR  124 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~  124 (175)
                       ..+...+..+..++.+. |++++|.+.++....
T Consensus        73 -~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           73 -EYNKDVWAAKADALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             -TTCHHHHHHHHHHHTTCSSCSHHHHHHHHHHGG
T ss_pred             -cchHHHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Confidence             00344567899999999 999999999999854

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.42  E-value=2.9e-06  Score=56.73  Aligned_cols=135  Identities=16%  Similarity=0.072  Sum_probs=89.5

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCCC---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CCh--HHHHHhhhccC
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDE--FTTVRILTTFN   93 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~--~~~~~l~~~~~   93 (175)
                      +..+......|+++.+.+.|..-.+.   ....+..+...+.+.|++++|+..|++..+.... |+.  .....-  ...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~--~~~   85 (198)
T 2fbn_A            8 HHHSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDK--KKN   85 (198)
T ss_dssp             --------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHH--HHH
T ss_pred             cchhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHH--HHH
Confidence            44555566677888888877754432   4456888888999999999999999999885321 100  000000  000


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ....++..+..+|.+.|++++|...++...+   .+...|..+..+|...|++++|.+.|++..+.
T Consensus        86 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~  151 (198)
T 2fbn_A           86 IEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASL  151 (198)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            0125667899999999999999999999843   36778999999999999999999999998874

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.41  E-value=1.2e-05  Score=50.47  Aligned_cols=96  Identities=14%  Similarity=0.043  Sum_probs=81.4

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC----hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .+...+..+...+.+.|++++|...|+...+  |+    ...|..+...+.+.|++++|+..+++..+..  |       
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~-------   96 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD--G-------   96 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--S-------
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--c-------
Confidence            4678899999999999999999999998764  54    6778889999999999999999999998853  2       


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                            .+...+..+..+|...|++++|...|++..+
T Consensus        97 ------~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A           97 ------GDVKALYRRSQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             ------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             ------cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                  2344556789999999999999999998843

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.40  E-value=7e-07  Score=66.00  Aligned_cols=131  Identities=15%  Similarity=0.063  Sum_probs=98.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC---------ChhHHHHHHHHHhccCC-----------------hHHHHH
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPER---------DYVLWTAMIDGYLRVNR-----------------FREALT   68 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~~~-----------------~~~a~~   68 (175)
                      ...++..+...|...|++++|...|++..+-         ...++..+...|...|+                 +++|+.
T Consensus       125 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~  204 (411)
T 4a1s_A          125 EAKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVE  204 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHH
Confidence            4567888888899999999999998876531         34467888888889999                 888888


Q ss_pred             HHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----C----hhhHHHHHHHHH
Q 045555           69 LFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----D----KFTWTAMIVGLA  138 (175)
Q Consensus        69 ~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~----~~~~~~li~~~~  138 (175)
                      .+++..+.... .+.          ......+..+...|...|++++|.+.+++..+-     +    ...+..+...|.
T Consensus       205 ~~~~al~~~~~~~~~----------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  274 (411)
T 4a1s_A          205 FYQENLKLMRDLGDR----------GAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHI  274 (411)
T ss_dssp             HHHHHHHHHHHHTCH----------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCH----------HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHH
Confidence            88887552100 010          112345678889999999999999999988431     2    237888889999


Q ss_pred             hcCChhHHHHHHHHHHH
Q 045555          139 ISGHGDTALDMFSQMLR  155 (175)
Q Consensus       139 ~~g~~~~a~~~~~~m~~  155 (175)
                      ..|++++|.+.+++..+
T Consensus       275 ~~g~~~~A~~~~~~al~  291 (411)
T 4a1s_A          275 FLGQFEDAAEHYKRTLA  291 (411)
T ss_dssp             TTTCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            99999999999988765

>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=98.39  E-value=6.1e-07  Score=71.33  Aligned_cols=125  Identities=13%  Similarity=0.028  Sum_probs=100.5

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+  | +...|..+...|.+.|++++|...|++..+  | +...|..+..++.+.|++++ ++.|++..+
T Consensus       450 ~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~  528 (681)
T 2pzi_A          450 AKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWS  528 (681)
T ss_dssp             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHH
T ss_pred             HHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHH
Confidence            567888887765  4 778999999999999999999999998763  3 67789999999999999999 999999988


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGH  142 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~  142 (175)
                      .+  |             .+...+..+..+|.+.|++++|.+.|++..+  | +...|..+..++...|+
T Consensus       529 ~~--P-------------~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          529 TN--D-------------GVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             hC--C-------------chHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            54  2             2345567899999999999999999999965  3 34567777777766554

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=98.38  E-value=1.7e-05  Score=60.41  Aligned_cols=153  Identities=12%  Similarity=0.080  Sum_probs=92.0

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHh----cCChhHHHHHhhcCCCC-ChhHHHHHHHHHhc----cCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYIN----RGQVDIARQYFAQMPER-DYVLWTAMIDGYLR----VNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~   71 (175)
                      ++|.++|+...+ .+..++..|...|..    .+++++|...|++..++ +...+..|...|..    .+++++|+..|+
T Consensus        96 ~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~  175 (490)
T 2xm6_A           96 AQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYS  175 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            456677776554 466677777777877    77888888888876543 55667777777766    678888888888


Q ss_pred             HhHhCCCCCChHHHHHhhh------cc----------------CcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCC
Q 045555           72 EMQTSNIRRDEFTTVRILT------TF----------------NNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~------~~----------------~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~  125 (175)
                      +..+.|.   ...+..+-.      ++                ..+...+..+...|..    .+++++|.+.|+...+.
T Consensus       176 ~a~~~~~---~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~  252 (490)
T 2xm6_A          176 KAAEQGN---VWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQ  252 (490)
T ss_dssp             HHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTT
T ss_pred             HHHHCCC---HHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence            8777641   111111100      00                1122334445555554    56666666666665443


Q ss_pred             -ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHCC
Q 045555          126 -DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRAS  157 (175)
Q Consensus       126 -~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g  157 (175)
                       +...+..+...|..    .++.++|.+.|++..+.|
T Consensus       253 ~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~  289 (490)
T 2xm6_A          253 GNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG  289 (490)
T ss_dssp             TCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC
Confidence             44455555555555    666666666666666543

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.38  E-value=2.2e-06  Score=61.45  Aligned_cols=129  Identities=12%  Similarity=0.020  Sum_probs=100.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC-----C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ..|+.....|...|++++|...|.+..+     .    -..+|+.+...|.+.|++++|+..|++..+.-......    
T Consensus        37 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~----  112 (307)
T 2ifu_A           37 SEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTP----  112 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCH----
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCH----
Confidence            3677888889999999999999987653     1    13478899999999999999999999887631111100    


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC---------ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK---------DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                           .....+++.+...|.+ |++++|...|++..+-         ...+++.+...|.+.|++++|.+.|++..+
T Consensus       113 -----~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          113 -----DTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             -----HHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                 0113456788899988 9999999999987431         146788899999999999999999999876

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.36  E-value=2.1e-05  Score=50.35  Aligned_cols=95  Identities=9%  Similarity=0.039  Sum_probs=80.9

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...+..+...+...|++++|...|++..+..               +.+..++..+..++...|++++|...++...+  
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~---------------~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~   77 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN---------------PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD   77 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC---------------CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            3457888889999999999999999998853               22345567899999999999999999999843  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      | +...|..+...+...|++++|.+.|++..+.
T Consensus        78 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~  110 (166)
T 1a17_A           78 KKYIKGYYRRAASNMALGKFRAALRDYETVVKV  110 (166)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            3 6778899999999999999999999999875

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.36  E-value=1e-05  Score=53.73  Aligned_cols=120  Identities=14%  Similarity=0.076  Sum_probs=89.4

Q ss_pred             HhcCChhHHHH---HhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHH
Q 045555           27 INRGQVDIARQ---YFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALI  103 (175)
Q Consensus        27 ~~~~~~~~a~~---~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li  103 (175)
                      ...|++++|.+   .+..-......++..+...+...|++++|...+++........+.         .......+..+.
T Consensus         3 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~---------~~~~~~~~~~l~   73 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGD---------HTAEHRALHQVG   73 (203)
T ss_dssp             ----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCC---------HHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCC---------cHHHHHHHHHHH
Confidence            46899999999   665544446678899999999999999999999998773211100         011244567899


Q ss_pred             HHHHhcCCHHHHHHHHHhhcC-----C-C----hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          104 DMYCKCGDVEKAQRVFWKMLR-----K-D----KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       104 ~~~~~~~~~~~a~~~~~~~~~-----~-~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..|...|++++|.+.+++...     + +    ...+..+...+...|++++|.+.+++..+
T Consensus        74 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  135 (203)
T 3gw4_A           74 MVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLV  135 (203)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            999999999999999998733     2 2    34577888899999999999999998874

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.35  E-value=1.8e-05  Score=56.15  Aligned_cols=130  Identities=8%  Similarity=0.088  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CC------hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RD------YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ..+...+..+...|++++|.+.+....+   ..      ...+..+...+...|++++|+..+++...........    
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~----  151 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDV----  151 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCT----
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCch----
Confidence            3455677888999999999999975432   11      1234456666788899999999999988643221100    


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc-----CCC-----hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML-----RKD-----KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~-----~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                           .....+++.+...|...|++++|...|++..     .++     ..+|+.+...|...|++++|.+.+++..+
T Consensus       152 -----~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~  224 (293)
T 2qfc_A          152 -----YQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIE  224 (293)
T ss_dssp             -----THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHH
Confidence                 0013466889999999999999999999874     122     25888999999999999999999998765

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.35  E-value=2.1e-06  Score=62.96  Aligned_cols=130  Identities=13%  Similarity=0.037  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----CC----hhHHHHHHHHHhccCC--------------------hHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNR--------------------FREA   66 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~----~~~~~~li~~~~~~~~--------------------~~~a   66 (175)
                      ..++..+...|...|++++|...+++..+     ++    ..++..+...+...|+                    +++|
T Consensus        87 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A  166 (406)
T 3sf4_A           87 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAA  166 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHH
Confidence            55788888889999999999998887653     12    3468888888888899                    8888


Q ss_pred             HHHHHHhHhCCC-CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC----hhhHHHHHHH
Q 045555           67 LTLFREMQTSNI-RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD----KFTWTAMIVG  136 (175)
Q Consensus        67 ~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~----~~~~~~li~~  136 (175)
                      ...+++..+... .++.          .....++..+...|...|++++|...+++..+     ++    ..+|..+...
T Consensus       167 ~~~~~~al~~~~~~~~~----------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  236 (406)
T 3sf4_A          167 VDFYEENLSLVTALGDR----------AAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNA  236 (406)
T ss_dssp             HHHHHHHHHHHHHTTCH----------HHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCc----------HHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence            888887765310 0111          11234567888999999999999999988743     12    2378888888


Q ss_pred             HHhcCChhHHHHHHHHHHH
Q 045555          137 LAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       137 ~~~~g~~~~a~~~~~~m~~  155 (175)
                      |...|++++|.+.+++..+
T Consensus       237 ~~~~g~~~~A~~~~~~al~  255 (406)
T 3sf4_A          237 YIFLGEFETASEYYKKTLL  255 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHH
Confidence            9999999999999988764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.33  E-value=6.6e-06  Score=60.48  Aligned_cols=130  Identities=15%  Similarity=0.075  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-------C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-------R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ..+++.+...|.+.|++++|...|++..+       | ...++..+...+.+.|++++|...+++..+.....+..    
T Consensus       222 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~----  297 (378)
T 3q15_A          222 AISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHK----  297 (378)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCS----
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCH----
Confidence            45788888999999999999999987654       2 34567888888999999999999999988753221111    


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCC---HHHHHHHHHhhcCC--ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGD---VEKAQRVFWKMLRK--DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                            .....+..+...|...++   +++|...++.....  ....+..+...|...|++++|.+.|++..+
T Consensus       298 ------~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          298 ------FYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             ------CHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  112234667778888888   88898888875332  234667788999999999999999998865

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.33  E-value=2.1e-05  Score=62.57  Aligned_cols=169  Identities=7%  Similarity=0.061  Sum_probs=117.1

Q ss_pred             chHH-HHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-------------CC------------hhHHHH
Q 045555            2 GFAL-EIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE-------------RD------------YVLWTA   52 (175)
Q Consensus         2 ~~A~-~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------------~~------------~~~~~~   52 (175)
                      ++|. ++|+....  | +...|-..+...-+.|+++.|.++|+.+.+             |+            ..+|..
T Consensus       360 ~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~  439 (679)
T 4e6h_A          360 STVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCV  439 (679)
T ss_dssp             TTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHH
Confidence            4564 77776654  4 555677778888888999999999887653             21            235777


Q ss_pred             HHHHHhccCChHHHHHHHHHhHhC-C-CCCChHHHHHhhh-------------------ccCcchhHHHHHHHHHHhcCC
Q 045555           53 MIDGYLRVNRFREALTLFREMQTS-N-IRRDEFTTVRILT-------------------TFNNDIFVGIALIDMYCKCGD  111 (175)
Q Consensus        53 li~~~~~~~~~~~a~~~~~~m~~~-~-~~p~~~~~~~l~~-------------------~~~~~~~~~~~li~~~~~~~~  111 (175)
                      .+....+.|..+.|..+|.+.++. + ..+......+.+.                   .++.+...+...++.....|+
T Consensus       440 y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~  519 (679)
T 4e6h_A          440 YMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNE  519 (679)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCC
Confidence            777777888899999999998876 2 2222222222222                   334455667777777778889


Q ss_pred             HHHHHHHHHhhcCC------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          112 VEKAQRVFWKMLRK------DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       112 ~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      .+.|..+|+.....      ....|...+..-.+.|+.+.+.++.+++.+.  .|+......+.+-|
T Consensus       520 ~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~--~P~~~~~~~f~~ry  584 (679)
T 4e6h_A          520 ESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK--FPEVNKLEEFTNKY  584 (679)
T ss_dssp             HHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--STTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCcHHHHHHHHh
Confidence            99999999987553      2357888888888889999999999988875  45544555555444

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.33  E-value=4e-05  Score=47.05  Aligned_cols=95  Identities=12%  Similarity=0.016  Sum_probs=75.3

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--CC-
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--KD-  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~~-  126 (175)
                      +..+...+.+.|++++|...|++..+......            .....+..+..++.+.|++++|...|+....  |+ 
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~------------~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~   72 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELYPNGV------------YTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTH   72 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSSST------------THHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTS
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHCCCCc------------ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCC
Confidence            34566778899999999999999988542111            0013445788999999999999999999854  43 


Q ss_pred             ---hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          127 ---KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       127 ---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                         ...+..+..++...|++++|.+.|+++.+.
T Consensus        73 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           73 DKAAGGLLKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             TTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence               566888889999999999999999999875

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.31  E-value=1.8e-06  Score=65.89  Aligned_cols=118  Identities=14%  Similarity=0.068  Sum_probs=91.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND   95 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~   95 (175)
                      +..+...+.+.|++++|.+.|++..+   .+...|..+..++.+.|++++|++.+++..+..  |             .+
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p-------------~~   73 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--K-------------KY   73 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC--T-------------TC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--C-------------CC
Confidence            33444567789999999999998763   467889999999999999999999999999863  2             23


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHH--HHhcCChhHHHHHHH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVG--LAISGHGDTALDMFS  151 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~--~~~~g~~~~a~~~~~  151 (175)
                      ...+..+..+|.+.|++++|.+.|++..+  | +...+..+..+  +.+.|++++|.+.++
T Consensus        74 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           74 IKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            45567899999999999999999999843  3 45566666666  888899999999988

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.30  E-value=3.2e-05  Score=49.81  Aligned_cols=117  Identities=14%  Similarity=0.102  Sum_probs=84.0

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCC------CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHh
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSN------IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWK  121 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  121 (175)
                      ..+......+.+.|++++|+..|.+.+..-      -.|+...+..   .-+.+...|..+..+|.+.|++++|...++.
T Consensus        12 ~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~   88 (162)
T 3rkv_A           12 EALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVE---LDRKNIPLYANMSQCYLNIGDLHEAEETSSE   88 (162)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHH---HHHTHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHH---HHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            356677777888888888888888877640      0111111100   0122345678899999999999999999999


Q ss_pred             hcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHH-HHHHHH
Q 045555          122 MLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEV-TYVGVL  169 (175)
Q Consensus       122 ~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~-t~~~ll  169 (175)
                      ..+  | +...|..+..+|...|++++|.+.|++.++.  .|+.. .....+
T Consensus        89 al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~l  138 (162)
T 3rkv_A           89 VLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN--HPAAASVVAREM  138 (162)
T ss_dssp             HHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CGGGHHHHHHHH
T ss_pred             HHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc--CCCCHHHHHHHH
Confidence            843  4 6778999999999999999999999998875  56544 444333

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.28  E-value=2.9e-05  Score=55.02  Aligned_cols=91  Identities=12%  Similarity=-0.061  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-  125 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-  125 (175)
                      .+..+...+.+.|++++|+..|++..+..  |             .+...+..+..+|.+.|++++|.+.++...+  | 
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p-------------~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~   70 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRN--P-------------LVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ   70 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--S-------------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC--C-------------ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC
Confidence            34444444555555555555555554431  1             1223334455555555555555555555433  1 


Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          126 DKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       126 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      +...|..+..+|...|++++|.+.|++..
T Consensus        71 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           71 SVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33444445555555555555555555443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.27  E-value=4.8e-06  Score=50.87  Aligned_cols=102  Identities=11%  Similarity=0.094  Sum_probs=74.1

Q ss_pred             ccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHH
Q 045555           59 RVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIV  135 (175)
Q Consensus        59 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~  135 (175)
                      ..|++++|+..|++..+.+.. +           +.+...+..+..+|.+.|++++|.+.|++..+  | +...+..+..
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~-~-----------p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   69 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQ-G-----------KDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAM   69 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCC-H-----------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCC-C-----------ccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHH
Confidence            468899999999999886421 1           11345567899999999999999999999854  4 6778899999


Q ss_pred             HHHhcCChhHHHHHHHHHHHC-CCCCcHHHHHHHHhhh
Q 045555          136 GLAISGHGDTALDMFSQMLRA-SIRLDEVTYVGVLSAC  172 (175)
Q Consensus       136 ~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~~~  172 (175)
                      ++...|++++|.+.+++..+. .-.|+...|...+..+
T Consensus        70 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~ai~~~  107 (117)
T 3k9i_A           70 VLYNLGRYEQGVELLLKIIAETSDDETIQSYKQAILFY  107 (117)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHCCCHHHHHTHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            999999999999999998875 2334444444444444

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.27  E-value=5.3e-06  Score=51.22  Aligned_cols=93  Identities=12%  Similarity=-0.008  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .+..+...+.+.|++++|...|++..+  | +...|..+..++.+.|++++|+..|++..+..  |+             
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~-------------   83 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PK-------------   83 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-------------
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC-------------
Confidence            455677888999999999999998764  4 77789999999999999999999999998854  22             


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                      +...+..+..+|.+.|++++|...|+...+.
T Consensus        84 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           84 DIAVHAALAVSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3445578999999999999999999988653

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.26  E-value=4e-06  Score=64.18  Aligned_cols=124  Identities=12%  Similarity=-0.008  Sum_probs=94.3

Q ss_pred             HHHhcCChhHHHHHhhcCCC-------C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           25 GYINRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        25 ~~~~~~~~~~a~~~~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      .+...|++++|..++++..+       +    ...+++.|...|...|++++|..++++.+..-        ...+..-.
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~--------~~~lG~~H  389 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGY--------MKLYHHNN  389 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--------HHHSCTTC
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH--------HHHcCCCC
Confidence            35578999999999886542       2    34579999999999999999999999986631        11111113


Q ss_pred             cc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------CC----hhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           94 ND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR-------KD----KFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        94 ~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      |+ ..+++.|...|...|++++|+.++++..+       |+    ..+.+.+-.++...|++++|..+|+++.++
T Consensus       390 p~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          390 AQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33 35678999999999999999999998732       32    235566778888899999999999999863

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.26  E-value=4e-06  Score=61.09  Aligned_cols=127  Identities=11%  Similarity=0.074  Sum_probs=78.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChh------------------HHHHHHHHHhccCChHHHHHHHHHhH
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYV------------------LWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~------------------~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ....+..+...+.+.|++++|...|++...  |+..                  .|..+..+|.+.|++++|+..+++.+
T Consensus       178 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al  257 (338)
T 2if4_A          178 AADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVL  257 (338)
T ss_dssp             HHHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            455678888899999999999999998653  4322                  78889999999999999999999998


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHH-HHhcCChhHHHHHH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVG-LAISGHGDTALDMF  150 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~-~~~~g~~~~a~~~~  150 (175)
                      +..  |             .+...+..+..+|...|++++|...|+...+  | +...+..+... ....+..+++.+.|
T Consensus       258 ~~~--p-------------~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~~  322 (338)
T 2if4_A          258 TEE--E-------------KNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEMY  322 (338)
T ss_dssp             HHC--T-------------TCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------------------
T ss_pred             HhC--C-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            853  2             2345567899999999999999999999855  3 44455555555 33456778888999


Q ss_pred             HHHHHC
Q 045555          151 SQMLRA  156 (175)
Q Consensus       151 ~~m~~~  156 (175)
                      +.|...
T Consensus       323 ~~~l~~  328 (338)
T 2if4_A          323 KGIFKG  328 (338)
T ss_dssp             ------
T ss_pred             HHhhCC
Confidence            988754

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.24  E-value=1.5e-05  Score=58.84  Aligned_cols=118  Identities=8%  Similarity=-0.025  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-------------------CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-------------------RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ...+..+...+.+.|++++|...|++..+                   .+...|..+..+|.+.|++++|+..+++.++.
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  302 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI  302 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh
Confidence            34577888888899999999999987654                   14456888888888889999999988888874


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHH
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALD  148 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~  148 (175)
                      .  |+             +...+..+..+|.+.|++++|.+.|++..+  | +...+..+...+...++.+++.+
T Consensus       303 ~--p~-------------~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          303 D--PS-------------NTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             C--TT-------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C--ch-------------hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3  22             344456788888888999999888888743  3 55566666677766666666543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.21  E-value=7.8e-05  Score=52.90  Aligned_cols=111  Identities=12%  Similarity=-0.099  Sum_probs=86.5

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC-C----hhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPER-D----YVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~----~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|.++|+.+..  |+......+...+.+.+++++|+..|+...+. +    ...+..+-.++.+.|++++|++.|++..
T Consensus       119 ~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~  198 (282)
T 4f3v_A          119 ADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLTEAN  198 (282)
T ss_dssp             HHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            678999998875  64446677777899999999999999976642 2    3467888999999999999999999998


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .....|...            .........++.+.|+.++|..+|+++..
T Consensus       199 ~g~~~P~~~------------~da~~~~glaL~~lGr~deA~~~l~~a~a  236 (282)
T 4f3v_A          199 DSPAGEACA------------RAIAWYLAMARRSQGNESAAVALLEWLQT  236 (282)
T ss_dssp             TSTTTTTTH------------HHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCCCCcccc------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            543324311            11223688899999999999999999843

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.20  E-value=8.4e-05  Score=55.84  Aligned_cols=140  Identities=11%  Similarity=0.102  Sum_probs=96.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-------C----ChhHHHHHHHHHhcc--CChHHHHHHHHHhHhCCCCCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRV--NRFREALTLFREMQTSNIRRD   81 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~----~~~~~~~li~~~~~~--~~~~~a~~~~~~m~~~~~~p~   81 (175)
                      ...+|+.+...|...|++++|...+++..+       +    ...+++.+..++.+.  +++++|+..|++..+..  |+
T Consensus        93 ~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~--p~  170 (472)
T 4g1t_A           93 SLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK--PK  170 (472)
T ss_dssp             THHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS--TT
T ss_pred             HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC--CC
Confidence            467899999999999999999998886542       1    334566666566554  57999999999998853  44


Q ss_pred             hHHHH-Hh--h----h----------------ccCc-chhHHHHHHHHHH----hcCCHHHHHHHHHhhcC---CChhhH
Q 045555           82 EFTTV-RI--L----T----------------TFNN-DIFVGIALIDMYC----KCGDVEKAQRVFWKMLR---KDKFTW  130 (175)
Q Consensus        82 ~~~~~-~l--~----~----------------~~~~-~~~~~~~li~~~~----~~~~~~~a~~~~~~~~~---~~~~~~  130 (175)
                      ..... .+  +    .                ...| +...+..+...+.    ..+++++|.+.+++...   .+..++
T Consensus       171 ~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~  250 (472)
T 4g1t_A          171 NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVL  250 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHH
T ss_pred             CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHH
Confidence            32211 11  0    0                1223 3445555544444    45678889999988733   367788


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          131 TAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       131 ~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ..+...|...|++++|.+.+++..+.
T Consensus       251 ~~lg~~~~~~~~~~~A~~~~~~al~~  276 (472)
T 4g1t_A          251 RSAAKFYRRKDEPDKAIELLKKALEY  276 (472)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCchHHHHHHHHHHHHh
Confidence            99999999999999999999998874

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.20  E-value=5.2e-05  Score=55.34  Aligned_cols=131  Identities=9%  Similarity=0.002  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh-HHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--R------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE-FTTV   86 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~   86 (175)
                      ...+..+...+...|++++|...+++..+  +      ...++..+...+...|++++|...+++.......++. ..+.
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~  214 (373)
T 1hz4_A          135 EFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWI  214 (373)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHH
Confidence            34567788889999999999999987542  1      2346778888899999999999999998764222211 1110


Q ss_pred             HhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCC-------hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           87 RILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKD-------KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        87 ~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                               .......+..+...|++++|.+.+.....++       ...+..+...+...|++++|.+.+++...
T Consensus       215 ---------~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~  281 (373)
T 1hz4_A          215 ---------SNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNE  281 (373)
T ss_dssp             ---------HHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---------HHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                     0001134455789999999999999986542       12456777889999999999999988764

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.14  E-value=2.6e-05  Score=47.89  Aligned_cols=94  Identities=17%  Similarity=0.116  Sum_probs=73.8

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--CC-h---hHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--RD-Y---VLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~~-~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      +..+...+.+.|++++|...|+...+  |+ .   ..+..+..++.+.|++++|+..|++..+.......          
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~----------   74 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDK----------   74 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTT----------
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcc----------
Confidence            34566778899999999999998763  43 3   47888889999999999999999999886421100          


Q ss_pred             CcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           93 NNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        ....+..+..+|.+.|++++|...|+....
T Consensus        75 --~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           75 --AAGGLLKLGLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             --HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              023445788999999999999999999854

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.10  E-value=3.8e-05  Score=54.37  Aligned_cols=94  Identities=11%  Similarity=0.017  Sum_probs=77.9

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      +...+..+...+.+.|++++|...|++..+  | +...|..+..++.+.|++++|+..+++..+..  |+          
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~----------   70 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD--GQ----------   70 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC--TT----------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CC----------
Confidence            456788888899999999999999998653  4 67788999999999999999999999998753  22          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                         +...+..+..+|.+.|++++|...|....
T Consensus        71 ---~~~~~~~lg~~~~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           71 ---SVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (281)
T ss_dssp             ---CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ---CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence               34455788999999999999999998873

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.10  E-value=0.00011  Score=53.35  Aligned_cols=127  Identities=11%  Similarity=0.052  Sum_probs=91.3

Q ss_pred             CChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHH
Q 045555           30 GQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      +++++|...|+...+  | +...+..+...+.+.|++++|+..|++..+................-......|..+..+|
T Consensus       127 ~~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~  206 (336)
T 1p5q_A          127 KSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCH  206 (336)
T ss_dssp             EEEECCCCGGGCCHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eecccccchhcCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHH
Confidence            344455555554432  2 4567889999999999999999999999885421110000000000000135678899999


Q ss_pred             HhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          107 CKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+.|++++|...|+...+  | +...|..+..+|...|++++|.+.|++.++.
T Consensus       207 ~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l  259 (336)
T 1p5q_A          207 LKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  259 (336)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            999999999999999854  3 6788999999999999999999999999874

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.08  E-value=0.00013  Score=47.33  Aligned_cols=113  Identities=16%  Similarity=0.133  Sum_probs=82.0

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc----
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML----  123 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----  123 (175)
                      .+......+.+.|++++|+..|++.++.... |+..    .+...+.+...|+.+..++.+.|++++|...++...    
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~----a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n   88 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEE----AFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFN   88 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTS----CCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchh----hhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhh
Confidence            4566677788899999999999999885432 1100    000001123478899999999999999999999984    


Q ss_pred             -----CC-ChhhH----HHHHHHHHhcCChhHHHHHHHHHHH-----CCCCCcHHHH
Q 045555          124 -----RK-DKFTW----TAMIVGLAISGHGDTALDMFSQMLR-----ASIRLDEVTY  165 (175)
Q Consensus       124 -----~~-~~~~~----~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~  165 (175)
                           .| +...|    .....++...|++++|...|++.++     .|+.+.....
T Consensus        89 ~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~  145 (159)
T 2hr2_A           89 RRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERM  145 (159)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHH
T ss_pred             ccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence                 55 34577    8889999999999999999999864     3555554433

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.08  E-value=0.00011  Score=55.21  Aligned_cols=139  Identities=12%  Similarity=0.020  Sum_probs=78.8

Q ss_pred             cHHHHHHHHHHHHh----cCChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh-HHHH
Q 045555           15 DVISWTTIVSGYIN----RGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE-FTTV   86 (175)
Q Consensus        15 ~~~~~~~li~~~~~----~~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~   86 (175)
                      +..++..+...+.+    .|++++|...+++..   ..+..++..+...|.+.|++++|+..+++..+..  |+. ..+.
T Consensus       208 ~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~  285 (472)
T 4g1t_A          208 NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI--PNNAYLHC  285 (472)
T ss_dssp             CHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHH
T ss_pred             chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC--CChHHHHH
Confidence            44455544444433    456677777777654   2466678888888999999999999999988753  332 1221


Q ss_pred             Hhhh---------------------------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C
Q 045555           87 RILT---------------------------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K  125 (175)
Q Consensus        87 ~l~~---------------------------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~  125 (175)
                      .+-.                                       .-+.+...+..+...|.+.|++++|...|++...  +
T Consensus       286 ~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~  365 (472)
T 4g1t_A          286 QIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSKEL  365 (472)
T ss_dssp             HHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCC
Confidence            1100                                       1122234455666777777777777777776632  2


Q ss_pred             Chh----hHHHHHH-HHHhcCChhHHHHHHHHHHH
Q 045555          126 DKF----TWTAMIV-GLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       126 ~~~----~~~~li~-~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +..    .+..+.. .+...|+.++|.+.|++.++
T Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~  400 (472)
T 4g1t_A          366 TPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK  400 (472)
T ss_dssp             CHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            221    1222222 23356677777777777665

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.07  E-value=4.6e-05  Score=49.05  Aligned_cols=95  Identities=14%  Similarity=0.101  Sum_probs=79.2

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCC---------------------ChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPER---------------------DYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ....+......+.+.|++++|...|.+..+-                     +...|..+..+|.+.|++++|+..+++.
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~a   89 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEV   89 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3557888899999999999999999975431                     2357889999999999999999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      ++..  |             .+...|..+..+|...|++++|...|+....
T Consensus        90 l~~~--p-------------~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           90 LKRE--E-------------TNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHS--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhcC--C-------------cchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            9854  2             2345567899999999999999999999854

>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=98.04  E-value=0.00023  Score=60.54  Aligned_cols=127  Identities=9%  Similarity=0.045  Sum_probs=64.9

Q ss_pred             chHHHHhhccCC--CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC
Q 045555            2 GFALEIFGNMKN--KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIR   79 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   79 (175)
                      ++|.+.+....+  ++....+.++.+|++.+++++...+.   ..++...|..+...|...|++++|...|....     
T Consensus      1151 EEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI---~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA~----- 1222 (1630)
T 1xi4_A         1151 EELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS----- 1222 (1630)
T ss_pred             HHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHH---hCCCHHHHHHHHHHHHhcCCHHHHHHHHHhhh-----
Confidence            345555543322  23333334666666666655433332   33444444555555555566666655555531     


Q ss_pred             CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC----------------------------ChhhHH
Q 045555           80 RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK----------------------------DKFTWT  131 (175)
Q Consensus        80 p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----------------------------~~~~~~  131 (175)
                          .              |..+..+|.+.|++++|.+.+++...+                            +...+.
T Consensus      1223 ----n--------------y~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLe 1284 (1630)
T 1xi4_A         1223 ----N--------------FGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELE 1284 (1630)
T ss_pred             ----H--------------HHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHH
Confidence                1              234444555555555555444443222                            233455


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHH
Q 045555          132 AMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       132 ~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      .++..|-+.|.+++|.++++..+
T Consensus      1285 eli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1285 ELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHh
Confidence            66667777777777777776554

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.04  E-value=1.9e-05  Score=60.27  Aligned_cols=104  Identities=13%  Similarity=0.070  Sum_probs=79.3

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|++..+  | +..+|..+..+|.+.|++++|...|++..+   .+...|..+..+|.+.|++++|.+.|++..+
T Consensus        23 ~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~  102 (477)
T 1wao_1           23 ENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAALRDYETVVK  102 (477)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            567888887664  4 688999999999999999999999998653   4677899999999999999999999999988


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHH--HHhcCCHHHHHHHHH
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDM--YCKCGDVEKAQRVFW  120 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~--~~~~~~~~~a~~~~~  120 (175)
                      ..  |+             +...+..+..+  +.+.|++++|.+.++
T Consensus       103 ~~--p~-------------~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1          103 VK--PH-------------DKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HS--TT-------------CTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             hC--CC-------------CHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            54  22             12222334444  888899999999999

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.01  E-value=3.8e-05  Score=49.79  Aligned_cols=96  Identities=14%  Similarity=0.042  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--CC--------hh-----HHHHHHHHHhccCChHHHHHHHHHhHhC----
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--RD--------YV-----LWTAMIDGYLRVNRFREALTLFREMQTS----   76 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~--------~~-----~~~~li~~~~~~~~~~~a~~~~~~m~~~----   76 (175)
                      ...+......+.+.|++++|...|++..+  |+        ..     .|+.+..++.+.|++++|+..+++.++.    
T Consensus        11 a~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~   90 (159)
T 2hr2_A           11 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   90 (159)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcc
Confidence            34566777888899999999999998764  33        22     8999999999999999999999999884    


Q ss_pred             -CCCCChHHHHHhhhccCcchhHH----HHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           77 -NIRRDEFTTVRILTTFNNDIFVG----IALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        77 -~~~p~~~~~~~l~~~~~~~~~~~----~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                       .+.|+             +...|    .....++...|++++|...|++..+
T Consensus        91 ~e~~pd-------------~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           91 GELNQD-------------EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             CCTTST-------------HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCCCc-------------hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence             11333             34556    7899999999999999999999843

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.98  E-value=1.9e-05  Score=48.16  Aligned_cols=82  Identities=10%  Similarity=0.117  Sum_probs=60.1

Q ss_pred             hcCChhHHHHHhhcCCCC------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHH
Q 045555           28 NRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIA  101 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~  101 (175)
                      ..|++++|...|++..+.      +...+..+...+.+.|++++|+..|++..+..  |+             +...+..
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~-------------~~~~~~~   66 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF--PN-------------HQALRVF   66 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT-------------CHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC-------------chHHHHH
Confidence            457888888888876542      34568888888999999999999999988854  22             3445567


Q ss_pred             HHHHHHhcCCHHHHHHHHHhhcC
Q 045555          102 LIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      +..++.+.|++++|...|++...
T Consensus        67 l~~~~~~~g~~~~A~~~~~~al~   89 (117)
T 3k9i_A           67 YAMVLYNLGRYEQGVELLLKIIA   89 (117)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            88899999999999999988743

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.96  E-value=0.00082  Score=50.79  Aligned_cols=139  Identities=11%  Similarity=0.055  Sum_probs=91.1

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhc----CChhHHHHHhhcCCCCChhHHHHHHHH-H--hccCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINR----GQVDIARQYFAQMPERDYVLWTAMIDG-Y--LRVNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~~~~~li~~-~--~~~~~~~~a~~~~~   71 (175)
                      ++|+++|+...+   ++...+..+...|.+-    +++++|...|++....+...+..|-.. +  ...+++++|+..|+
T Consensus       196 ~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~  275 (452)
T 3e4b_A          196 AELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLD  275 (452)
T ss_dssp             HHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Confidence            356666665543   3455556677777554    688899999998773356667777666 4  56788999999999


Q ss_pred             HhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcC-----CHHHHHHHHHhhcCCChhhHHHHHHHHHh----cCC
Q 045555           72 EMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCG-----DVEKAQRVFWKMLRKDKFTWTAMIVGLAI----SGH  142 (175)
Q Consensus        72 ~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~li~~~~~----~g~  142 (175)
                      +..+.|.                 ...+..|...|. .|     ++++|.+.|+.....+...+..+...|..    ..+
T Consensus       276 ~Aa~~g~-----------------~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa~g~~~A~~~Lg~~y~~G~g~~~d  337 (452)
T 3e4b_A          276 NGRAADQ-----------------PRAELLLGKLYY-EGKWVPADAKAAEAHFEKAVGREVAADYYLGQIYRRGYLGKVY  337 (452)
T ss_dssp             HHHHTTC-----------------HHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTTTTCHHHHHHHHHHHHTTTTSSCC
T ss_pred             HHHHCCC-----------------HHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHCCCCCCcC
Confidence            9887761                 222234555555 44     77888888877772245555556555554    237


Q ss_pred             hhHHHHHHHHHHHCCC
Q 045555          143 GDTALDMFSQMLRASI  158 (175)
Q Consensus       143 ~~~a~~~~~~m~~~g~  158 (175)
                      +++|.+.|++..+.|.
T Consensus       338 ~~~A~~~~~~Aa~~g~  353 (452)
T 3e4b_A          338 PQKALDHLLTAARNGQ  353 (452)
T ss_dssp             HHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHhhCh
Confidence            7777777777766554

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.96  E-value=0.0002  Score=52.86  Aligned_cols=109  Identities=9%  Similarity=-0.027  Sum_probs=81.3

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ..+..+...+.+.|++++|+..|++.++.-.. |...........-+.+..+|..+..+|.+.|++++|.+.++...+  
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  303 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID  303 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC
Confidence            34778888999999999999999999872100 000000000000122356778899999999999999999999865  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      | +...|..+..+|...|++++|.+.|++..+.
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3 5678889999999999999999999999874

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.95  E-value=1.1e-05  Score=48.15  Aligned_cols=90  Identities=11%  Similarity=0.062  Sum_probs=57.2

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      ...+..+...+.+.|++++|+..|++..+..  |             .+...+..+..+|.+.|++++|.+.|+...+  
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p-------------~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   68 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQ--P-------------QNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT   68 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--C-------------CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            3456667777777888888888888777643  2             2334456677778888888888888887744  


Q ss_pred             CC-------hhhHHHHHHHHHhcCChhHHHHHHH
Q 045555          125 KD-------KFTWTAMIVGLAISGHGDTALDMFS  151 (175)
Q Consensus       125 ~~-------~~~~~~li~~~~~~g~~~~a~~~~~  151 (175)
                      |+       ...+..+..++...|+.+.|.+.++
T Consensus        69 p~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  102 (111)
T 2l6j_A           69 STAEHVAIRSKLQYRLELAQGAVGSVQIPVVEVD  102 (111)
T ss_dssp             SSTTSHHHHHHHHHHHHHHHHHHHCCCCCSSSSS
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHhHhhhHhHHH
Confidence            32       3344455555555555555544443

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=97.93  E-value=0.00072  Score=51.09  Aligned_cols=128  Identities=11%  Similarity=0.060  Sum_probs=76.3

Q ss_pred             cHHHHHHHHHHHHhcCC----hhHHHHHhhcCCCCChhHHHHHHHHHhccC---ChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           15 DVISWTTIVSGYINRGQ----VDIARQYFAQMPERDYVLWTAMIDGYLRVN---RFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~----~~~a~~~~~~m~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ++.....+...|...+.    .+.+..+++.....+...+..|...|.+.|   +.++|+..|++..+.|.....     
T Consensus       140 ~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~-----  214 (452)
T 3e4b_A          140 YPEAGLAQVLLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQ-----  214 (452)
T ss_dssp             CTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHH-----
T ss_pred             CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHH-----
Confidence            34455566666666553    344555565555556668888888888888   899999999999887732221     


Q ss_pred             hhhccCcchhHHHHHHHHHHhc----CCHHHHHHHHHhhcCCChhhHHHHHHH-H--HhcCChhHHHHHHHHHHHCC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKC----GDVEKAQRVFWKMLRKDKFTWTAMIVG-L--AISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~li~~-~--~~~g~~~~a~~~~~~m~~~g  157 (175)
                                .+..+...|...    +++++|.+.|+.....+...+..+... +  ...|++++|.+.|++..+.|
T Consensus       215 ----------~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g  281 (452)
T 3e4b_A          215 ----------RVDSVARVLGDATLGTPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD  281 (452)
T ss_dssp             ----------HHHHHHHHHTCGGGSSCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT
T ss_pred             ----------HHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC
Confidence                      112344444333    566666666666551144444444444 2  34556666666666655554

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.92  E-value=7.6e-06  Score=48.94  Aligned_cols=99  Identities=8%  Similarity=0.026  Sum_probs=72.5

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCC-ChHHHHHhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRR-DEFTTVRIL   89 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~l~   89 (175)
                      ++...+..+...+.+.|++++|...|++..+   .+...|..+..++.+.|++++|+..+++..+..... +...+    
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~----   77 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIR----   77 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHH----
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHH----
Confidence            3567788899999999999999999998763   477789999999999999999999999999854221 11111    


Q ss_pred             hccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           90 TTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                            ...+..+..++...|+.+.|.+.++++
T Consensus        78 ------~~~~~~~~~~~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           78 ------SKLQYRLELAQGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             ------HHHHHHHHHHHHHHHCCCCCSSSSSSC
T ss_pred             ------HHHHHHHHHHHHHHHhHhhhHhHHHHh
Confidence                  223345666666666666665555443

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.87  E-value=6.3e-05  Score=54.91  Aligned_cols=130  Identities=8%  Similarity=-0.033  Sum_probs=97.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-----CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-----RDY----VLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVR   87 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~   87 (175)
                      +++.+...+...|++++|...+++..+     ++.    .++..+...+...|++++|...+++..+.... .+.     
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~-----  129 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLE-----  129 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCT-----
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc-----
Confidence            567777888999999999999998653     222    33667788899999999999999998764210 000     


Q ss_pred             hhhccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           88 ILTTFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K------DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        88 l~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                          ..| ....+..+...+...|++++|...+++...  +      ...+|..+...+...|++++|...+++....
T Consensus       130 ----~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~  203 (373)
T 1hz4_A          130 ----QLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENL  203 (373)
T ss_dssp             ----TSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             ----cCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence                001 123456788899999999999999998732  1      1346778888899999999999999998753

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.87  E-value=0.00086  Score=48.20  Aligned_cols=140  Identities=6%  Similarity=0.053  Sum_probs=106.4

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChh--HHHHHhhcCCC---CChhHHHHHHHHHhccCC------hHHHH
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVD--IARQYFAQMPE---RDYVLWTAMIDGYLRVNR------FREAL   67 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~---~~~~~~~~li~~~~~~~~------~~~a~   67 (175)
                      ++++++++.+.+   .|..+|+--.-.+.+.|.++  ++++.++.+.+   .|...|+.....+.+.+.      +++++
T Consensus       127 ~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl  206 (306)
T 3dra_A          127 YREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKKHLATDNTIDEEL  206 (306)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSGGGCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccchhhhHHHHH
Confidence            356666666654   57788888888888888888  88888888875   477778877777777666      88888


Q ss_pred             HHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCH-HHHHHHHHhhcC------CChhhHHHHHHHHHhc
Q 045555           68 TLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDV-EKAQRVFWKMLR------KDKFTWTAMIVGLAIS  140 (175)
Q Consensus        68 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~~~------~~~~~~~~li~~~~~~  140 (175)
                      +.++++....               +-|...|+.+-..+.+.|+. +.+..+..+..+      ++...+..+...|.+.
T Consensus       207 ~~~~~aI~~~---------------p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~  271 (306)
T 3dra_A          207 NYVKDKIVKC---------------PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQ  271 (306)
T ss_dssp             HHHHHHHHHC---------------SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhC---------------CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHcc
Confidence            8888888754               33556677788888888884 445566666533      3677889999999999


Q ss_pred             CChhHHHHHHHHHHHC
Q 045555          141 GHGDTALDMFSQMLRA  156 (175)
Q Consensus       141 g~~~~a~~~~~~m~~~  156 (175)
                      |+.++|.++++.+.++
T Consensus       272 ~~~~~A~~~~~~l~~~  287 (306)
T 3dra_A          272 KKYNESRTVYDLLKSK  287 (306)
T ss_dssp             TCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHhc
Confidence            9999999999999863

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.86  E-value=0.00016  Score=53.69  Aligned_cols=125  Identities=10%  Similarity=-0.029  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC-----CCh----hHHHHHHHHHhccCChHHHHHHHHHhHhC----CCCCChHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE-----RDY----VLWTAMIDGYLRVNRFREALTLFREMQTS----NIRRDEFT   84 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~   84 (175)
                      ++..+...|.+.|++++|.+.+....+     ++.    .+.+.+-..+...|+++.+..++.+....    +..+.   
T Consensus        57 al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---  133 (434)
T 4b4t_Q           57 SILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFL---  133 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSS---
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHH---
Confidence            466777888888888888888877653     111    22333334444557788888877776542    11111   


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                                -..++..+...|...|++++|..+++....        + ...+|..++..|...|++++|...+++...
T Consensus       134 ----------~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  203 (434)
T 4b4t_Q          134 ----------KHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAART  203 (434)
T ss_dssp             ----------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ----------HHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHH
Confidence                      234567899999999999999999998732        1 345788899999999999999999988764

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.83  E-value=0.00015  Score=54.75  Aligned_cols=99  Identities=10%  Similarity=-0.006  Sum_probs=74.9

Q ss_pred             ccCChHHHHHHHHHhHhC---CCCCChHHHHHhhhccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------C--
Q 045555           59 RVNRFREALTLFREMQTS---NIRRDEFTTVRILTTFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR-------K--  125 (175)
Q Consensus        59 ~~~~~~~a~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~--  125 (175)
                      ..|++++|..++++.+..   -+.|+           .|+ ..+++.|..+|...|++++|+.++++..+       +  
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~-----------Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~H  378 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDS-----------NVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYS  378 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTT-----------SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSC
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChh-----------chHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence            457899999999988763   23343           222 45678999999999999999999999832       2  


Q ss_pred             --ChhhHHHHHHHHHhcCChhHHHHHHHHHHH---CCCCCcHHHHHHH
Q 045555          126 --DKFTWTAMIVGLAISGHGDTALDMFSQMLR---ASIRLDEVTYVGV  168 (175)
Q Consensus       126 --~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~l  168 (175)
                        ...+|+.+...|...|++++|..++++..+   .-+.||......+
T Consensus       379 p~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~l  426 (433)
T 3qww_A          379 LNVASMWLKLGRLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYISEI  426 (433)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHcCCCChHHHHH
Confidence              345799999999999999999999998764   2345555444443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.82  E-value=6.6e-05  Score=45.37  Aligned_cols=76  Identities=14%  Similarity=0.069  Sum_probs=65.4

Q ss_pred             CchHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            1 MGFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         1 ~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      +++|++.|+...+   .+...+..+...|.+.|++++|...|++..+   .+...|..+..++.+.|++++|...|++..
T Consensus         1 ~~~a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            1 MQAITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CCCHHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4678888887765   3678899999999999999999999998763   366789999999999999999999999987


Q ss_pred             hC
Q 045555           75 TS   76 (175)
Q Consensus        75 ~~   76 (175)
                      +.
T Consensus        81 ~~   82 (115)
T 2kat_A           81 AA   82 (115)
T ss_dssp             HH
T ss_pred             Hh
Confidence            74

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.81  E-value=0.0002  Score=53.91  Aligned_cols=107  Identities=10%  Similarity=0.003  Sum_probs=80.1

Q ss_pred             HHHHHHhccCChHHHHHHHHHhHhCC---CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----
Q 045555           52 AMIDGYLRVNRFREALTLFREMQTSN---IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----  124 (175)
Q Consensus        52 ~li~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----  124 (175)
                      ..+..+.+.|++++|..++++.+...   +.|+...          -..+++.|...|...|++++|+.++++..+    
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~----------~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~  361 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIY----------QLKVLDCAMDACINLGLLEEALFYGTRTMEPYRI  361 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHH----------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchH----------HHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHH
Confidence            33556778899999999999998642   2333222          245678999999999999999999998732    


Q ss_pred             ---C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH---CCCCCcHHHHHHH
Q 045555          125 ---K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR---ASIRLDEVTYVGV  168 (175)
Q Consensus       125 ---~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~l  168 (175)
                         +    ...+++.+...|...|++++|..++++..+   .-+.||......+
T Consensus       362 ~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~  415 (429)
T 3qwp_A          362 FFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDL  415 (429)
T ss_dssp             HSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHH
T ss_pred             HcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChHHHHH
Confidence               2    345799999999999999999999988764   3345555444444

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.80  E-value=0.00029  Score=42.42  Aligned_cols=77  Identities=14%  Similarity=0.171  Sum_probs=62.5

Q ss_pred             HHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcC
Q 045555           65 EALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISG  141 (175)
Q Consensus        65 ~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g  141 (175)
                      +|+..|++..+..               +.+...+..+...|.+.|++++|...|+...+  | +...|..+...|...|
T Consensus         3 ~a~~~~~~al~~~---------------p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g   67 (115)
T 2kat_A            3 AITERLEAMLAQG---------------TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQG   67 (115)
T ss_dssp             CHHHHHHHHHTTT---------------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC---------------CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcC
Confidence            4666777776643               22455667899999999999999999999843  3 5778999999999999


Q ss_pred             ChhHHHHHHHHHHHC
Q 045555          142 HGDTALDMFSQMLRA  156 (175)
Q Consensus       142 ~~~~a~~~~~~m~~~  156 (175)
                      ++++|.+.|++..+.
T Consensus        68 ~~~~A~~~~~~al~~   82 (115)
T 2kat_A           68 DRAGARQAWESGLAA   82 (115)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999998764

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.79  E-value=0.00015  Score=55.52  Aligned_cols=102  Identities=12%  Similarity=0.014  Sum_probs=76.9

Q ss_pred             HHHhccCChHHHHHHHHHhHhCC---CCCChHHHHHhhhccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhhcC------
Q 045555           55 DGYLRVNRFREALTLFREMQTSN---IRRDEFTTVRILTTFNND-IFVGIALIDMYCKCGDVEKAQRVFWKMLR------  124 (175)
Q Consensus        55 ~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~~~~~l~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~------  124 (175)
                      ..+...|++++|..++++.+...   +.|+           .|+ ..+++.|...|...|++++|+.++++..+      
T Consensus       317 ~~~~~qg~~~eA~~l~~~aL~~~~~~lg~~-----------Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~l  385 (490)
T 3n71_A          317 DKARSEGLYHEVVKLCRECLEKQEPVFADT-----------NLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLY  385 (490)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHTTTBCTT-----------SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHhcCCC-----------CHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHc
Confidence            34667899999999999887642   2233           222 45678999999999999999999998732      


Q ss_pred             -C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH---CCCCCcHHHHHH
Q 045555          125 -K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR---ASIRLDEVTYVG  167 (175)
Q Consensus       125 -~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~g~~p~~~t~~~  167 (175)
                       +    ...+++.|...|...|++++|..++++.++   .-+.||......
T Consensus       386 G~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~  436 (490)
T 3n71_A          386 HHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKD  436 (490)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHH
Confidence             2    345799999999999999999999998764   334555444333

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.77  E-value=0.00062  Score=51.59  Aligned_cols=123  Identities=11%  Similarity=0.012  Sum_probs=88.0

Q ss_pred             hhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh--HHHHHhhhccCcchhHHHHHHHHH
Q 045555           32 VDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE--FTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        32 ~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      +++|...|+...+   .....|..+...+.+.|++++|+..|++.++.......  .....-+  -......|..+..+|
T Consensus       250 ~~~A~~~~~~~~~~~~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~--~~~~~~~~~nla~~~  327 (457)
T 1kt0_A          250 FEKAKESWEMDTKEKLEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKAS--ESFLLAAFLNLAMCY  327 (457)
T ss_dssp             EECCCCGGGSCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHH--HHHHHHHHHHHHHHH
T ss_pred             cccCcchhhcCHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHH--HHHHHHHHHHHHHHH
Confidence            3344444443332   13456888899999999999999999999884311100  0000000  000135677899999


Q ss_pred             HhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          107 CKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+.|++++|...|+...+  | +...|..+..+|...|++++|...|++.++.
T Consensus       328 ~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l  380 (457)
T 1kt0_A          328 LKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  380 (457)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999854  3 6788999999999999999999999999864

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.76  E-value=0.00016  Score=45.62  Aligned_cols=112  Identities=14%  Similarity=0.016  Sum_probs=87.2

Q ss_pred             cCChhHHHHHhhcCCCC-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHH
Q 045555           29 RGQVDIARQYFAQMPER-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYC  107 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~  107 (175)
                      .+++++|...|++..+. +....  |-..|...+..++|++.|++..+.|                 +...+..|-..|.
T Consensus         8 ~~d~~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g-----------------~~~a~~~Lg~~y~   68 (138)
T 1klx_A            8 KKDLKKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACELN-----------------SGNGCRFLGDFYE   68 (138)
T ss_dssp             HHHHHHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHHTT-----------------CHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHcCC-----------------CHHHHHHHHHHHH
Confidence            45678888888876543 33333  6667777778888999999998875                 2334456777887


Q ss_pred             h----cCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHCCCC
Q 045555          108 K----CGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus       108 ~----~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~  159 (175)
                      .    .+++++|.+.|+...+. +...+..+-..|..    .+++++|.+.|++..+.|..
T Consensus        69 ~G~g~~~d~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~  129 (138)
T 1klx_A           69 NGKYVKKDLRKAAQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGSE  129 (138)
T ss_dssp             HCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             cCCCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCCH
Confidence            7    89999999999998654 77788888888888    89999999999999988743

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.70  E-value=0.00028  Score=44.41  Aligned_cols=98  Identities=16%  Similarity=0.136  Sum_probs=76.3

Q ss_pred             hHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           48 VLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        48 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      .++..+...+...|++++|+..+++..+.... ++...          -..++..+...|...|++++|.+.++...+  
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~----------~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~   79 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAA----------ERIAYSNLGNAYIFLGEFETASEYYKKTLLLA   79 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchH----------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            45788888899999999999999998774211 11110          123567899999999999999999999743  


Q ss_pred             ---CC----hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 ---KD----KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 ---~~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                         ++    ...+..+...+...|++++|.+.+++..+
T Consensus        80 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  117 (164)
T 3ro3_A           80 RQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  117 (164)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence               12    45678888899999999999999998775

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.69  E-value=0.00053  Score=40.42  Aligned_cols=62  Identities=18%  Similarity=0.173  Sum_probs=38.5

Q ss_pred             ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           46 DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        46 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      +...+..+...+.+.|++++|+..|++..+...               .+...|..+..+|.+.|++++|.+.|++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p---------------~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDP---------------DYVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST---------------TCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC---------------CcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            445566666667777777777777777666431               12334456666777777777776666654

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.69  E-value=0.00042  Score=50.37  Aligned_cols=105  Identities=12%  Similarity=0.016  Sum_probs=80.6

Q ss_pred             hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH------hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHH
Q 045555           47 YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR------ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFW  120 (175)
Q Consensus        47 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~------l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~  120 (175)
                      ...+..+...+.+.|++++|+..|++..+..  |+...+..      ....  .....|..+..+|.+.|++++|...++
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~--l~~~~~~nla~~~~~~g~~~~A~~~~~  254 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDFMFQLYGKYQDMALA--VKNPCHLNIAACLIKLKRYDEAIGHCN  254 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHHHHTCCHHHHHHHHH--HHTHHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccchhhhhcccHHHHHHH--HHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            3457788888999999999999999988742  33221100      0000  001267789999999999999999999


Q ss_pred             hhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          121 KMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       121 ~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ...+  | +...|..+..+|...|++++|.+.|++.++
T Consensus       255 ~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          255 IVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            9843  3 678899999999999999999999999875

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.67  E-value=0.00044  Score=40.76  Aligned_cols=76  Identities=16%  Similarity=0.098  Sum_probs=60.3

Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCCcHHHHHHHHh
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA-SIRLDEVTYVGVLS  170 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p~~~t~~~ll~  170 (175)
                      +...+..+...|.+.|++++|.+.|+...+  | +...|..+..+|...|++++|.+.|++..+. .-.++......+..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~~   85 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQD   85 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHHH
Confidence            456677899999999999999999999844  4 5778999999999999999999999998764 22345554444433

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.66  E-value=0.0011  Score=37.69  Aligned_cols=56  Identities=23%  Similarity=0.355  Sum_probs=26.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ..+...+.+.|++++|...|+...+  | +...|..+...+.+.|++++|.+.|++..+
T Consensus        13 ~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~   71 (91)
T 1na3_A           13 YNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE   71 (91)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            3444444445555555555544421  1 334444444555555555555555555444

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.63  E-value=0.00046  Score=39.30  Aligned_cols=63  Identities=17%  Similarity=0.452  Sum_probs=55.1

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +...+..+...+.+.|++++|...|++..+   .+...+..+...+.+.|++++|...+++..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~   73 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD   73 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            456788899999999999999999998653   467788999999999999999999999998853

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.58  E-value=0.00014  Score=46.97  Aligned_cols=100  Identities=15%  Similarity=0.030  Sum_probs=76.7

Q ss_pred             hccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCC----------HHHHHHHHHhhcC--C
Q 045555           58 LRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGD----------VEKAQRVFWKMLR--K  125 (175)
Q Consensus        58 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~----------~~~a~~~~~~~~~--~  125 (175)
                      .+.+.+++|+..+++..+..               +.+...|+.+..++.+.++          +++|...|++..+  |
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~---------------P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP   77 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSN---------------PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDP   77 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHhHHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCc
Confidence            45567899999999998854               2345556667777777765          4699999999843  4


Q ss_pred             -ChhhHHHHHHHHHhcC-----------ChhHHHHHHHHHHHCCCCCcHHHHHHHHhhhcC
Q 045555          126 -DKFTWTAMIVGLAISG-----------HGDTALDMFSQMLRASIRLDEVTYVGVLSACTH  174 (175)
Q Consensus       126 -~~~~~~~li~~~~~~g-----------~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~~  174 (175)
                       +...|..+..+|...|           ++++|.+.|++.++  +.|+...|..-+..+.+
T Consensus        78 ~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~~~k  136 (158)
T 1zu2_A           78 KKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMTAK  136 (158)
T ss_dssp             TCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHh
Confidence             6778999999998764           89999999999987  47888888777665543

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.48  E-value=0.0021  Score=50.10  Aligned_cols=149  Identities=9%  Similarity=0.051  Sum_probs=112.5

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCC----------hhHHHHHhhcCCC---CChhHHHHHHHHHhccC--Ch
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQ----------VDIARQYFAQMPE---RDYVLWTAMIDGYLRVN--RF   63 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~--~~   63 (175)
                      ++|++.++.+.+  | +..+|+.--..+.+.|+          ++++...++.+.+   .+..+|+.--..+.+.+  ++
T Consensus        46 eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~~  125 (567)
T 1dce_A           46 ESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNW  125 (567)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCH
T ss_pred             HHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccccH
Confidence            467777777765  4 56678877777777776          8999999998874   46778888888888999  77


Q ss_pred             HHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcC-CHHHHHHHHHhhcCC---ChhhHHHHHHHHHh
Q 045555           64 REALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCG-DVEKAQRVFWKMLRK---DKFTWTAMIVGLAI  139 (175)
Q Consensus        64 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~---~~~~~~~li~~~~~  139 (175)
                      +++++.++++.+..               +-+-..|+.-...+.+.| .++++.+.++++.+.   +...|+.....+.+
T Consensus       126 ~~el~~~~k~l~~d---------------~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~  190 (567)
T 1dce_A          126 ARELELCARFLEAD---------------ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  190 (567)
T ss_dssp             HHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhc---------------cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHh
Confidence            99999999999965               234556677777778888 899999999999764   66778877777665


Q ss_pred             c--------------CChhHHHHHHHHHHHCCCCC-cHHHHHH
Q 045555          140 S--------------GHGDTALDMFSQMLRASIRL-DEVTYVG  167 (175)
Q Consensus       140 ~--------------g~~~~a~~~~~~m~~~g~~p-~~~t~~~  167 (175)
                      .              +.++++.+.+++....  .| |...|..
T Consensus       191 l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~--~P~~~saW~y  231 (567)
T 1dce_A          191 LHPQPDSGPQGRLPENVLLKELELVQNAFFT--DPNDQSAWFY  231 (567)
T ss_dssp             HSCCCCSSSCCSSCHHHHHHHHHHHHHHHHH--CSSCSHHHHH
T ss_pred             hcccccccccccccHHHHHHHHHHHHHHHhh--CCCCccHHHH
Confidence            3              5578899999888764  34 3444443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.44  E-value=0.00045  Score=51.24  Aligned_cols=129  Identities=12%  Similarity=-0.036  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--------C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--------R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRI   88 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l   88 (175)
                      +.+.+-..+...|+.+.|..++.....        + -..++..|...+...|++++|..++.+....-...+..     
T Consensus        97 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~-----  171 (434)
T 4b4t_Q           97 LKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDK-----  171 (434)
T ss_dssp             HHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCS-----
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccc-----
Confidence            344455556677899999999887542        1 23467889999999999999999999987642221110     


Q ss_pred             hhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-----CC-----hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           89 LTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-----KD-----KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        89 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                          .....++..++..|...|++++|...++....     ++     ...+..+...+...|++++|.+.|.+..+
T Consensus       172 ----~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          172 ----PSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             ----THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             ----hhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence                11245678899999999999999999988732     11     34667777788889999999988877754

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.41  E-value=0.001  Score=50.13  Aligned_cols=94  Identities=6%  Similarity=-0.039  Sum_probs=70.8

Q ss_pred             HHHHHHHhcCChhHHHHHhhcCCC-------C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           21 TIVSGYINRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        21 ~li~~~~~~~~~~~a~~~~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      ..+.-+.+.|++++|..++++..+       +    ...+++.|...|...|++++|..++++.+..-        ...+
T Consensus       292 ~~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~--------~~~l  363 (429)
T 3qwp_A          292 KKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPY--------RIFF  363 (429)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH--------HHHS
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhH--------HHHc
Confidence            335556688999999999986542       2    24579999999999999999999999987531        1111


Q ss_pred             hccCcc-hhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           90 TTFNND-IFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        90 ~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      ....|+ ..+++.|...|...|++++|+.++++.
T Consensus       364 g~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~A  397 (429)
T 3qwp_A          364 PGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLA  397 (429)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            111333 346789999999999999999999987

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.33  E-value=0.00068  Score=51.13  Aligned_cols=87  Identities=8%  Similarity=0.032  Sum_probs=66.0

Q ss_pred             hcCChhHHHHHhhcCCC-------C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcc-
Q 045555           28 NRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNND-   95 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-   95 (175)
                      +.|++++|..++++..+       +    ...+++.|...|...|++++|..++++.+..        +...+..-.|+ 
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i--------~~~~lG~~Hp~~  381 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKP--------YSKHYPVYSLNV  381 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------HHHHSCSSCHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH--------HHHHcCCCChHH
Confidence            35788999998886542       2    2357999999999999999999999998763        11111112333 


Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      ..+++.|...|...|++++|+.++++.
T Consensus       382 a~~l~nLa~~~~~qg~~~eA~~~~~~A  408 (433)
T 3qww_A          382 ASMWLKLGRLYMGLENKAAGEKALKKA  408 (433)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCHHHHHHHHHHH
Confidence            346789999999999999999999986

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.29  E-value=0.0062  Score=43.73  Aligned_cols=140  Identities=14%  Similarity=0.044  Sum_probs=90.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcC--ChhHHHHHhhcCCC--C-ChhHHHHHHHHH----hcc---CChHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRG--QVDIARQYFAQMPE--R-DYVLWTAMIDGY----LRV---NRFREA   66 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~--~-~~~~~~~li~~~----~~~---~~~~~a   66 (175)
                      ++|+++++.+.+  | +..+|+.--..+...|  ++++++..++.+..  | +..+|+.--..+    ...   ++++++
T Consensus        50 ~~aL~~t~~~L~~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~~E  129 (306)
T 3dra_A           50 ERALHITELGINELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPYRE  129 (306)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTHHH
T ss_pred             HHHHHHHHHHHHHCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHHHH
Confidence            356666666654  4 4566777777777777  88888888887663  3 445566554444    444   678888


Q ss_pred             HHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHH--HHHHHHHhhcC---CChhhHHHHHHHHHhcC
Q 045555           67 LTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVE--KAQRVFWKMLR---KDKFTWTAMIVGLAISG  141 (175)
Q Consensus        67 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~--~a~~~~~~~~~---~~~~~~~~li~~~~~~g  141 (175)
                      +++++++.+..               +-+-..|+.-.-.+.+.|+++  ++.+.++.+.+   .|...|+...-.+.+.|
T Consensus       130 L~~~~~~l~~~---------------pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~  194 (306)
T 3dra_A          130 FDILEAMLSSD---------------PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKK  194 (306)
T ss_dssp             HHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSG
T ss_pred             HHHHHHHHHhC---------------CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcc
Confidence            88888887753               223444555555666666666  77777777744   25556665555555555


Q ss_pred             C------hhHHHHHHHHHHHC
Q 045555          142 H------GDTALDMFSQMLRA  156 (175)
Q Consensus       142 ~------~~~a~~~~~~m~~~  156 (175)
                      +      ++++++.+++++..
T Consensus       195 ~~~~~~~~~eEl~~~~~aI~~  215 (306)
T 3dra_A          195 HLATDNTIDEELNYVKDKIVK  215 (306)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHHHHHHh
Confidence            5      66777777766654

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.24  E-value=0.0025  Score=39.95  Aligned_cols=105  Identities=13%  Similarity=-0.005  Sum_probs=83.1

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhc----cCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~   75 (175)
                      ++|+++|+...+ .++...  +-..|..-+.+++|.+.|++..+ .+...+..|-..|..    .+++++|+..|++..+
T Consensus        12 ~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~   89 (138)
T 1klx_A           12 KKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACG   89 (138)
T ss_dssp             HHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHc
Confidence            467888887665 344444  77888888889999999998765 577788888888888    7899999999999998


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcCC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~  125 (175)
                      .|.                 ...+..|-..|..    .+++++|.+.|+...+.
T Consensus        90 ~g~-----------------~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           90 LND-----------------QDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             TTC-----------------HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             CCC-----------------HHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            762                 3344568888888    89999999999987544

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.13  E-value=0.00096  Score=38.79  Aligned_cols=57  Identities=18%  Similarity=0.173  Sum_probs=41.6

Q ss_pred             HHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh-HHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           53 MIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF-VGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        53 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      ....+.+.|++++|+..|++..+..  |+             +.. .+..+..+|.+.|++++|.+.|+...+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~--p~-------------~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE--PV-------------GKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--SS-------------THHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC--CC-------------cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3456777888888888888887753  22             233 456778888888888888888888744

>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=97.11  E-value=0.016  Score=46.27  Aligned_cols=71  Identities=10%  Similarity=0.040  Sum_probs=55.6

Q ss_pred             HHhhccCC---CcHHHHHHHHHHHHhcCChhHHH-HHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            6 EIFGNMKN---KDVISWTTIVSGYINRGQVDIAR-QYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         6 ~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~-~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      .+|++...   .+...|-..+..+.+.|+.++|. ++|+....  | +...|-..+...-+.|+++.|.++|++++..
T Consensus       330 ~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~  407 (679)
T 4e6h_A          330 YVYMQAAQHVCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDR  407 (679)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            44555443   36677888888888899999996 99988653  3 5566777888888999999999999999874

>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=97.03  E-value=0.016  Score=42.44  Aligned_cols=32  Identities=9%  Similarity=0.092  Sum_probs=27.3

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 ~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ++...+.-+.+.|...|+.++|.++++.+.++
T Consensus       300 ~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          300 PVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            35667788999999999999999999998754

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=96.99  E-value=0.00098  Score=43.07  Aligned_cols=110  Identities=15%  Similarity=0.081  Sum_probs=76.8

Q ss_pred             HhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCCh----------HHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           27 INRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRF----------REALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        27 ~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~----------~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      .+.+.+++|...++...+   .+...|..+-.++.+.+++          ++|+..|++.++..  |+            
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ld--P~------------   78 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID--PK------------   78 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC--TT------------
T ss_pred             HHHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhC--cC------------
Confidence            355667788888887653   4677788788888877764          59999999998854  22            


Q ss_pred             cchhHHHHHHHHHHhc-----------CCHHHHHHHHHhhc--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           94 NDIFVGIALIDMYCKC-----------GDVEKAQRVFWKML--RKDKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~-----------~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                       ....|..+..+|...           |++++|.+.|++..  +|+...|..-+..      .++|.++.-++...+
T Consensus        79 -~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~al~~------~~ka~el~~~~~~~~  148 (158)
T 1zu2_A           79 -KDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEM------TAKAPQLHAEAYKQG  148 (158)
T ss_dssp             -CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH------HHTHHHHHHHHHHSS
T ss_pred             -cHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHHHHH------HHhCHhccCcccccc
Confidence             345567788888876           48999999999984  5766655444443      345666666655544

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.95  E-value=0.026  Score=43.23  Aligned_cols=123  Identities=13%  Similarity=0.189  Sum_probs=90.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCCCC--hhHHHHHHHH-HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPERD--YVLWTAMIDG-YLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      ..|...+....+.++.+.|+.+|+....|.  ...|...... +...++.+.|..+|+...+..  |+            
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~--~~------------  352 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKH--PD------------  352 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHC--TT------------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC--CC------------
Confidence            467777777778889999999999884343  2333321111 112346999999999998853  22            


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                       +...+...++...+.|+.+.|..+|+... .....|...+..-...|+.+.+.+++++..+
T Consensus       353 -~~~~~~~yid~e~~~~~~~~aR~l~er~~-k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          353 -STLLKEEFFLFLLRIGDEENARALFKRLE-KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHSC-CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             -CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             12234456777788999999999999984 4678899999988889999999999988874

>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=96.86  E-value=0.016  Score=42.05  Aligned_cols=143  Identities=11%  Similarity=0.021  Sum_probs=101.3

Q ss_pred             hHHHHhhccCC---CcHHHHHHHHHHHHhcC--ChhHHHHHhhcCCC---CChhHHHHHHHHHhccCC-hHHHHHHHHHh
Q 045555            3 FALEIFGNMKN---KDVISWTTIVSGYINRG--QVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNR-FREALTLFREM   73 (175)
Q Consensus         3 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~-~~~a~~~~~~m   73 (175)
                      +++.+++.+..   .+..+|+.-.-.+.+.|  .+++++.+++.+.+   .|...|+.-.-.+.+.|. ++++++.++++
T Consensus        92 ~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~  171 (331)
T 3dss_A           92 AELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSL  171 (331)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHH
Confidence            45666666654   47788887777777777  48899999998875   577888888888888888 69999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhc--------------CCHHHHHHHHHhhc--CC-ChhhHHHHHHH
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKC--------------GDVEKAQRVFWKML--RK-DKFTWTAMIVG  136 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~--------------~~~~~a~~~~~~~~--~~-~~~~~~~li~~  136 (175)
                      .+..+               .+...|+.....+.+.              +.++++.+.++...  .| |...|+-+-..
T Consensus       172 I~~~p---------------~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~l  236 (331)
T 3dss_A          172 ITRNF---------------SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWL  236 (331)
T ss_dssp             HHHCS---------------CCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHCC---------------CCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            98652               2233334444444333              45888999888884  34 66777755555


Q ss_pred             HHhc-----------CChhHHHHHHHHHHHCCCCCcH
Q 045555          137 LAIS-----------GHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       137 ~~~~-----------g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      +.+.           +.++++.+.++++.+.  .||.
T Consensus       237 l~~~~~~~~~~~~~~~~l~~el~~~~elle~--~pd~  271 (331)
T 3dss_A          237 LGAGSGRCELSVEKSTVLQSELESCKELQEL--EPEN  271 (331)
T ss_dssp             HHSSSCGGGCCHHHHHHHHHHHHHHHHHHHH--CTTC
T ss_pred             HHhccCccccchHHHHHHHHHHHHHHHHHhh--Cccc
Confidence            5444           4578899999999874  4553

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.79  E-value=0.016  Score=46.54  Aligned_cols=46  Identities=24%  Similarity=0.408  Sum_probs=26.8

Q ss_pred             hcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           28 NRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      +.|++++|.++.+.+  .+...|..|...+.+.|+++.|.+.|.++..
T Consensus       664 ~~~~~~~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~d  709 (814)
T 3mkq_A          664 KVGQLTLARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAHD  709 (814)
T ss_dssp             HHTCHHHHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC
T ss_pred             hcCCHHHHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC
Confidence            344444444444433  2345667777777777777777777776644

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=96.77  E-value=0.027  Score=41.16  Aligned_cols=140  Identities=11%  Similarity=0.068  Sum_probs=99.8

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcC-ChhHHHHHhhcCCC---CChhHHHHHHHHHhcc-C-ChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRG-QVDIARQYFAQMPE---RDYVLWTAMIDGYLRV-N-RFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~-~-~~~~a~~~~~~   72 (175)
                      ++|+++++.+..  | +..+|+.--..+...| .+++++.+++.+..   .+..+|+.--..+.+. + +++++++++++
T Consensus        71 e~AL~lt~~~L~~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~EL~~~~k  150 (349)
T 3q7a_A           71 ERALELTEIIVRMNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVSEIEYIHG  150 (349)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence            357777777665  3 5667887777777778 58999999988764   3666788777777666 6 78899999999


Q ss_pred             hHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHH--------HHHHHHHhhcC---CChhhHHHHHHHHHhcC
Q 045555           73 MQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVE--------KAQRVFWKMLR---KDKFTWTAMIVGLAISG  141 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~--------~a~~~~~~~~~---~~~~~~~~li~~~~~~g  141 (175)
                      +.+...               .+-..|+.-.-.+.+.|+++        ++.+.++++.+   .|...|+.....+.+.+
T Consensus       151 ~L~~dp---------------kNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~N~SAW~~R~~lL~~l~  215 (349)
T 3q7a_A          151 SLLPDP---------------KNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGRNNSAWGWRWYLRVSRP  215 (349)
T ss_dssp             HTSSCT---------------TCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHTTST
T ss_pred             HHHhCC---------------CCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcc
Confidence            987542               23344454444444444454        88888888854   37778888888887777


Q ss_pred             C-------hhHHHHHHHHHHHC
Q 045555          142 H-------GDTALDMFSQMLRA  156 (175)
Q Consensus       142 ~-------~~~a~~~~~~m~~~  156 (175)
                      +       ++++++.+++.+..
T Consensus       216 ~~~~~~~~~~eELe~~~~aI~~  237 (349)
T 3q7a_A          216 GAETSSRSLQDELIYILKSIHL  237 (349)
T ss_dssp             TCCCCHHHHHHHHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHHHHHHh
Confidence            6       68888888888764

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.70  E-value=0.069  Score=42.80  Aligned_cols=93  Identities=15%  Similarity=0.228  Sum_probs=60.3

Q ss_pred             hHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCCh
Q 045555            3 FALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDE   82 (175)
Q Consensus         3 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   82 (175)
                      +|.++.+.+  .+...|..+...+.+.|+++.|.+.|..+..     |..+...+...|+.+....+-+.....|.    
T Consensus       670 ~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~d-----~~~l~~l~~~~~~~~~~~~~~~~a~~~~~----  738 (814)
T 3mkq_A          670 LARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAHD-----LESLFLLHSSFNNKEGLVTLAKDAETTGK----  738 (814)
T ss_dssp             HHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC-----HHHHHHHHHHTTCHHHHHHHHHHHHHTTC----
T ss_pred             HHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC-----hhhhHHHHHHcCCHHHHHHHHHHHHHcCc----
Confidence            445554444  4567899999999999999999999998876     33344444446666655555555555442    


Q ss_pred             HHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           83 FTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        83 ~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                                      ++....+|.+.|++++|.+++.++
T Consensus       739 ----------------~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          739 ----------------FNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             ----------------HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             ----------------hHHHHHHHHHcCCHHHHHHHHHHc
Confidence                            133444555566666666666654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.53  E-value=0.043  Score=31.44  Aligned_cols=55  Identities=20%  Similarity=0.220  Sum_probs=48.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHhhcC--C-Chh-hHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          102 LIDMYCKCGDVEKAQRVFWKMLR--K-DKF-TWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~~--~-~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ....+.+.|++++|.+.|+...+  | +.. .|..+..+|...|++++|.+.|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            56678899999999999999843  4 566 8888999999999999999999999875

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.48  E-value=0.065  Score=35.15  Aligned_cols=49  Identities=16%  Similarity=0.265  Sum_probs=30.7

Q ss_pred             HHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555           25 GYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus        25 ~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      .-.+.|+++.|.++-+.+  .+...|..|.....+.|+++-|.+.|.+...
T Consensus        14 LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D   62 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS   62 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC
T ss_pred             HHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC
Confidence            344666666666665544  3455666666666666776666666666644

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.32  E-value=0.2  Score=36.89  Aligned_cols=139  Identities=9%  Similarity=-0.045  Sum_probs=86.6

Q ss_pred             CcHHHHHHHHHHHH--hc---CChhHHHHHhhcCCC--CC-hhHHHHHHHHHhc----cCCh-HHHH---HHHHHhHhCC
Q 045555           14 KDVISWTTIVSGYI--NR---GQVDIARQYFAQMPE--RD-YVLWTAMIDGYLR----VNRF-REAL---TLFREMQTSN   77 (175)
Q Consensus        14 ~~~~~~~~li~~~~--~~---~~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~----~~~~-~~a~---~~~~~m~~~~   77 (175)
                      .|..+|...+.+..  ..   ....+|..+|++..+  |+ ...|..+.-++..    .+.. ....   ..++......
T Consensus       192 ~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~~  271 (372)
T 3ly7_A          192 HRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLP  271 (372)
T ss_dssp             SSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTCG
T ss_pred             CCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhcc
Confidence            36677777776644  33   335789999998874  53 3344443333321    1111 1111   1111111111


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .             -+.+...+..+.-.+...|++++|.+.+++..  .|+...|..+-..+.-.|++++|.+.|.+...
T Consensus       272 ~-------------~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~Alr  338 (372)
T 3ly7_A          272 E-------------LNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFN  338 (372)
T ss_dssp             G-------------GTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             c-------------CCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            1             13344555666666777899999999999984  46766777777888899999999999999886


Q ss_pred             CCCCCcHHHHHH
Q 045555          156 ASIRLDEVTYVG  167 (175)
Q Consensus       156 ~g~~p~~~t~~~  167 (175)
                      .  .|...||..
T Consensus       339 L--~P~~~t~~~  348 (372)
T 3ly7_A          339 L--RPGANTLYW  348 (372)
T ss_dssp             H--SCSHHHHHH
T ss_pred             c--CCCcChHHH
Confidence            4  677777654

>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=96.20  E-value=0.22  Score=36.15  Aligned_cols=148  Identities=9%  Similarity=0.049  Sum_probs=102.0

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCC----------hhHHHHHhhcCCC---CChhHHHHHHHHHhccC--Ch
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQ----------VDIARQYFAQMPE---RDYVLWTAMIDGYLRVN--RF   63 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~--~~   63 (175)
                      ++|+.+++.+..  | +..+|+.--..+...+.          +++++.+++.+..   .+..+|+.-...+.+.+  .+
T Consensus        47 ~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~  126 (331)
T 3dss_A           47 ESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNW  126 (331)
T ss_dssp             HHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCH
T ss_pred             HHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccH
Confidence            467788887765  4 44566654444433333          5678888887663   47778888877777777  48


Q ss_pred             HHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCC-HHHHHHHHHhhcC---CChhhHHHHHHHHHh
Q 045555           64 REALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGD-VEKAQRVFWKMLR---KDKFTWTAMIVGLAI  139 (175)
Q Consensus        64 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~---~~~~~~~~li~~~~~  139 (175)
                      +++++.++++....               +-+-..|+.-.-...+.|+ ++++.+.++.+.+   .|...|+.....+.+
T Consensus       127 ~~EL~~~~k~l~~d---------------prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~R~~ll~~  191 (331)
T 3dss_A          127 ARELELCARFLEAD---------------ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  191 (331)
T ss_dssp             HHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC---------------CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence            99999999999864               2344556666666777788 6899999999854   367778776666655


Q ss_pred             c--------------CChhHHHHHHHHHHHCCCCC-cHHHHH
Q 045555          140 S--------------GHGDTALDMFSQMLRASIRL-DEVTYV  166 (175)
Q Consensus       140 ~--------------g~~~~a~~~~~~m~~~g~~p-~~~t~~  166 (175)
                      .              +.++++++.+.+....  .| |...++
T Consensus       192 l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~--~P~d~SaW~  231 (331)
T 3dss_A          192 LHPQPDSGPQGRLPENVLLKELELVQNAFFT--DPNDQSAWF  231 (331)
T ss_dssp             HSCCC------CCCHHHHHHHHHHHHHHHHH--STTCHHHHH
T ss_pred             hhhccccccccccchHHHHHHHHHHHHHHHh--CCCCHHHHH
Confidence            4              4578888888888764  34 444443

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=96.19  E-value=0.095  Score=37.30  Aligned_cols=126  Identities=13%  Similarity=0.100  Sum_probs=86.6

Q ss_pred             CChhHHHHHhhcCCCCCh--hHHHHHHHH-Hhcc--CC------hHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhH
Q 045555           30 GQVDIARQYFAQMPERDY--VLWTAMIDG-YLRV--NR------FREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFV   98 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~~~~--~~~~~li~~-~~~~--~~------~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~   98 (175)
                      ++.....+.+....+.++  ..|..++.+ +...  |.      ...|...+++.++..  |+           ..+...
T Consensus       135 ~~~~~~~~~l~~~~~~dve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAleLD--P~-----------~~~GsA  201 (301)
T 3u64_A          135 GDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLW--PS-----------YQEGAV  201 (301)
T ss_dssp             SCHHHHHHHHTTCCGGGHHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHHHC--TT-----------HHHHHH
T ss_pred             cchhhHHHHHHHcCccccHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHHhC--CC-----------cccCHH
Confidence            333444555555554333  346655543 3332  32      567777777777743  33           112445


Q ss_pred             HHHHHHHHHh-----cCCHHHHHHHHHhhc--CC--ChhhHHHHHHHHHhc-CChhHHHHHHHHHHHCCCC--CcHHHHH
Q 045555           99 GIALIDMYCK-----CGDVEKAQRVFWKML--RK--DKFTWTAMIVGLAIS-GHGDTALDMFSQMLRASIR--LDEVTYV  166 (175)
Q Consensus        99 ~~~li~~~~~-----~~~~~~a~~~~~~~~--~~--~~~~~~~li~~~~~~-g~~~~a~~~~~~m~~~g~~--p~~~t~~  166 (175)
                      |..+...|.+     .|+.++|++.|++..  .|  +..++....+.+++. |+.++|.+.+++.+.....  |+....+
T Consensus       202 ~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          202 WNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             HHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHH
T ss_pred             HHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHH
Confidence            6788889998     599999999999984  46  488888999999985 9999999999999998766  7766555


Q ss_pred             HH
Q 045555          167 GV  168 (175)
Q Consensus       167 ~l  168 (175)
                      .+
T Consensus       282 ~~  283 (301)
T 3u64_A          282 IL  283 (301)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=96.07  E-value=0.17  Score=39.54  Aligned_cols=113  Identities=8%  Similarity=0.053  Sum_probs=88.5

Q ss_pred             CChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCC----------hHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch
Q 045555           30 GQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNR----------FREALTLFREMQTSNIRRDEFTTVRILTTFNNDI   96 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~   96 (175)
                      ...++|.+.++.+.+  | +..+|+.--..+...|+          ++++++.++++.+..               +-+.
T Consensus        43 ~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~---------------pK~y  107 (567)
T 1dce_A           43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN---------------PKSY  107 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC---------------TTCH
T ss_pred             CCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC---------------CCCH
Confidence            345678999998774  4 55668877666766666          899999999998854               2345


Q ss_pred             hHHHHHHHHHHhcC--CHHHHHHHHHhhcC---CChhhHHHHHHHHHhcC-ChhHHHHHHHHHHHCC
Q 045555           97 FVGIALIDMYCKCG--DVEKAQRVFWKMLR---KDKFTWTAMIVGLAISG-HGDTALDMFSQMLRAS  157 (175)
Q Consensus        97 ~~~~~li~~~~~~~--~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g-~~~~a~~~~~~m~~~g  157 (175)
                      .+|+.-.-.+.+.+  +++++.+.++++.+   .+...|+.-.-.+.+.| .++++.+.+.++++..
T Consensus       108 ~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~  174 (567)
T 1dce_A          108 GTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN  174 (567)
T ss_dssp             HHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT
T ss_pred             HHHHHHHHHHHHcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC
Confidence            56677777788888  77999999999954   47788888888888888 8999999999998753

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.03  E-value=0.031  Score=32.46  Aligned_cols=65  Identities=12%  Similarity=0.073  Sum_probs=53.1

Q ss_pred             CcHHHHHHHHHHHHhcCC---hhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555           14 KDVISWTTIVSGYINRGQ---VDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      +|+..+..+..++...++   .++|..++++..+  | +......+...+.+.|++++|+..|+++++...
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p   74 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSND   74 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            466777777777765544   7999999998774  4 677888888999999999999999999998754

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.00  E-value=0.12  Score=38.01  Aligned_cols=114  Identities=11%  Similarity=0.077  Sum_probs=75.6

Q ss_pred             chHHHHhhccCC--Cc-HHHHHHHHHHHHh---cC-C-------hhHHHHHhhcCC--CCChhHHHHHHHHHhccCChHH
Q 045555            2 GFALEIFGNMKN--KD-VISWTTIVSGYIN---RG-Q-------VDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFRE   65 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~-~~~~~~li~~~~~---~~-~-------~~~a~~~~~~m~--~~~~~~~~~li~~~~~~~~~~~   65 (175)
                      .+|+.+|++..+  |+ ...|..+..+|..   .+ .       ...+..-...+.  ..+..+|..+...+...|++++
T Consensus       216 ~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~~~~~~~a~~~~alal~~l~~gd~d~  295 (372)
T 3ly7_A          216 NRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELNNLSIIYQIKAVSALVKGKTDE  295 (372)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTCGGGTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHhCCCHHH
Confidence            468888888876  53 3445544444321   11 1       111222111221  3477788888777888899999


Q ss_pred             HHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc--CCChhhHH
Q 045555           66 ALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML--RKDKFTWT  131 (175)
Q Consensus        66 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~--~~~~~~~~  131 (175)
                      |...+++....+  |+...|              ..+...+.-.|++++|.+.|++..  .|...+|.
T Consensus       296 A~~~l~rAl~Ln--~s~~a~--------------~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~t~~  347 (372)
T 3ly7_A          296 SYQAINTGIDLE--MSWLNY--------------VLLGKVYEMKGMNREAADAYLTAFNLRPGANTLY  347 (372)
T ss_dssp             HHHHHHHHHHHC--CCHHHH--------------HHHHHHHHHTTCHHHHHHHHHHHHHHSCSHHHHH
T ss_pred             HHHHHHHHHhcC--CCHHHH--------------HHHHHHHHHCCCHHHHHHHHHHHHhcCCCcChHH
Confidence            999999999975  554443              578888999999999999999884  46666654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.93  E-value=0.085  Score=30.56  Aligned_cols=63  Identities=11%  Similarity=0.008  Sum_probs=49.9

Q ss_pred             cchhHHHHHHHHHHhcCC---HHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           94 NDIFVGIALIDMYCKCGD---VEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      .+...+..+..++...++   .++|..++++...  | ++.....+...+.+.|++++|.+.++++++.
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            445566667777754444   7999999999854  4 5677777888999999999999999999975

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=95.75  E-value=0.078  Score=39.29  Aligned_cols=122  Identities=14%  Similarity=0.129  Sum_probs=81.1

Q ss_pred             ChhHHHHHHHHHh---ccCChHHHHHHHHHhHhC--CC-CCChH--HHHHhhh-c-cCcchhHHHHHHHHHHhcCCHHHH
Q 045555           46 DYVLWTAMIDGYL---RVNRFREALTLFREMQTS--NI-RRDEF--TTVRILT-T-FNNDIFVGIALIDMYCKCGDVEKA  115 (175)
Q Consensus        46 ~~~~~~~li~~~~---~~~~~~~a~~~~~~m~~~--~~-~p~~~--~~~~l~~-~-~~~~~~~~~~li~~~~~~~~~~~a  115 (175)
                      |...|..++..-.   ..|+.+.|.+.+++....  |. -++..  .|..-.. . -.--......+++.+...|++++|
T Consensus       111 D~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~~~~w~~~~r~~l~~~~~~a~~~~~~~~l~~g~~~~a  190 (388)
T 2ff4_A          111 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAV  190 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            4555666665433   357888888888888764  31 12211  0100000 0 000112344677888899999999


Q ss_pred             HHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH-----CCCCCcHHHHHH
Q 045555          116 QRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR-----ASIRLDEVTYVG  167 (175)
Q Consensus       116 ~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~-----~g~~p~~~t~~~  167 (175)
                      .........  | +...|..+|.++.+.|+..+|.+.|++..+     -|+.|...+-..
T Consensus       191 ~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l  250 (388)
T 2ff4_A          191 IAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRAL  250 (388)
T ss_dssp             HHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            988888743  4 777999999999999999999999988643     499998876443

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.69  E-value=0.082  Score=31.10  Aligned_cols=65  Identities=14%  Similarity=0.044  Sum_probs=53.0

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhhcC----------CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555           96 IFVGIALIDMYCKCGDVEKAQRVFWKMLR----------KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus        96 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      ..-+-.|...+.+.|+++.|...|+...+          +...++..+..++.+.|++++|...+++..+  +.|+.
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~--l~P~~   79 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE--LDPEH   79 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTC
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh--cCCCC
Confidence            33445789999999999999999998732          1356789999999999999999999999986  35654

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.40  E-value=0.27  Score=31.38  Aligned_cols=89  Identities=11%  Similarity=0.031  Sum_probs=61.6

Q ss_pred             hHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcC---CHHHHHHHHHhhcCCC-----hhhHHHHH
Q 045555           63 FREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCG---DVEKAQRVFWKMLRKD-----KFTWTAMI  134 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~~~~~~-----~~~~~~li  134 (175)
                      ...+.+-|.+....|.               ++..+.-.+.-++++.+   +++++..++++..+.+     ...+-.+-
T Consensus        14 l~~~~~~y~~e~~~~~---------------~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LA   78 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS---------------VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLA   78 (152)
T ss_dssp             HHHHHHHHHHHHHTTC---------------CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCC---------------CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHH
Confidence            4555666666666554               22333335777888888   6779999999885543     34566677


Q ss_pred             HHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHH
Q 045555          135 VGLAISGHGDTALDMFSQMLRASIRLDEVTYVGV  168 (175)
Q Consensus       135 ~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~l  168 (175)
                      -+|.+.|++++|.+.++.+++.  .|+..--..|
T Consensus        79 v~~~kl~~Y~~A~~y~~~lL~i--eP~n~QA~~L  110 (152)
T 1pc2_A           79 VGNYRLKEYEKALKYVRGLLQT--EPQNNQAKEL  110 (152)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHhc--CCCCHHHHHH
Confidence            7889999999999999999974  6754443333

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.36  E-value=0.13  Score=30.28  Aligned_cols=62  Identities=6%  Similarity=-0.015  Sum_probs=52.7

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC----------CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE----------RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ++..+..|...+.+.|++..|..-|+...+          +....+..|..++.+.|+++.|+..+++..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            456677899999999999999999987542          23457899999999999999999999999884

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=94.98  E-value=0.08  Score=37.70  Aligned_cols=80  Identities=11%  Similarity=0.086  Sum_probs=63.7

Q ss_pred             HHHHhhccCC--Cc---HHHHHHHHHHHHhc-----CChhHHHHHhhcCCC--C--ChhHHHHHHHHHhcc-CChHHHHH
Q 045555            4 ALEIFGNMKN--KD---VISWTTIVSGYINR-----GQVDIARQYFAQMPE--R--DYVLWTAMIDGYLRV-NRFREALT   68 (175)
Q Consensus         4 A~~~~~~m~~--~~---~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~--~--~~~~~~~li~~~~~~-~~~~~a~~   68 (175)
                      |...+++..+  |+   ...|..+...|.+.     |+.++|.+.|++..+  |  +..++......+++. |+.+++.+
T Consensus       182 A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~  261 (301)
T 3u64_A          182 AVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDE  261 (301)
T ss_dssp             HHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHH
Confidence            4444444443  44   66899999999995     999999999999763  5  478888889999885 99999999


Q ss_pred             HHHHhHhCCCC--CChH
Q 045555           69 LFREMQTSNIR--RDEF   83 (175)
Q Consensus        69 ~~~~m~~~~~~--p~~~   83 (175)
                      .+++.++....  |+..
T Consensus       262 ~L~kAL~a~p~~~P~~~  278 (301)
T 3u64_A          262 ALDRALAIDPESVPHNK  278 (301)
T ss_dssp             HHHHHHHCCGGGCSSCH
T ss_pred             HHHHHHcCCCCCCCChh
Confidence            99999998765  5543

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.97  E-value=0.44  Score=31.23  Aligned_cols=120  Identities=13%  Similarity=0.118  Sum_probs=78.2

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRD   81 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~   81 (175)
                      +.|.++.+.+  .+...|..|.....+.|+++.|.+.|.....     +..+.--|.-.|+.++-..+-+.....|-   
T Consensus        22 ~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D-----~~~L~~Ly~~tg~~e~L~kla~iA~~~g~---   91 (177)
T 3mkq_B           22 DAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS-----FDKLSFLYLVTGDVNKLSKMQNIAQTRED---   91 (177)
T ss_dssp             HHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC-----HHHHHHHHHHHTCHHHHHHHHHHHHHTTC---
T ss_pred             HHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC-----HHHHHHHHHHhCCHHHHHHHHHHHHHCcc---
Confidence            3455555544  4677899999999999999999999999876     44444455556777666655555444442   


Q ss_pred             hHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           82 EFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        82 ~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                                       ++.....+...|+++++.+++.+..+..     --.-.-...|.-+.|.++..++
T Consensus        92 -----------------~n~af~~~l~lGdv~~~i~lL~~~~r~~-----eA~~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           92 -----------------FGSMLLNTFYNNSTKERSSIFAEGGSLP-----LAYAVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             -----------------HHHHHHHHHHHTCHHHHHHHHHHTTCHH-----HHHHHHHHTTCHHHHHHHHHHT
T ss_pred             -----------------HHHHHHHHHHcCCHHHHHHHHHHCCChH-----HHHHHHHHcCcHHHHHHHHHHh
Confidence                             2456667777888888888887653311     1111111255667777776665

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.05  E-value=0.65  Score=29.29  Aligned_cols=134  Identities=11%  Similarity=0.086  Sum_probs=86.6

Q ss_pred             HHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhccCChHHHHHHHHHhHhCC-CCC--ChHHHHHhhhccCcchhHHHH
Q 045555           26 YINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLRVNRFREALTLFREMQTSN-IRR--DEFTTVRILTTFNNDIFVGIA  101 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p--~~~~~~~l~~~~~~~~~~~~~  101 (175)
                      +.-.|..++..++..+..+ .+..-||-+|--....-+=+-..++++.+=+.- +.+  +.-+-..-......+....+.
T Consensus        17 ~ildG~v~qGveii~k~~~ssni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~~~n~~se~vd~   96 (172)
T 1wy6_A           17 FLLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLNEHVNK   96 (172)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCCHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHcCCCCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHHHhcchHHHHHH
Confidence            4456777888888777664 344445555544444444444444444442210 000  100000000012345566788


Q ss_pred             HHHHHHhcCCHHHHHHHHHhhc---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 045555          102 LIDMYCKCGDVEKAQRVFWKML---RKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus       102 li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  159 (175)
                      .++.....|+-|.-.++..++.   .+++...-.+..+|.+-|+..+|.+++++.-++|++
T Consensus        97 ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           97 ALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            8999999999999999999952   346788888999999999999999999999999975

>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=93.71  E-value=0.29  Score=36.20  Aligned_cols=68  Identities=21%  Similarity=0.270  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh-----CCCCCChHHH
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT-----SNIRRDEFTT   85 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~   85 (175)
                      +...++..+...|++++|......+..  | +...|..+|.++.+.|+..+|++.|+++.+     .|+.|++.+-
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            344566777889999999988887663  4 777899999999999999999999999866     3888887665

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=93.15  E-value=0.26  Score=31.49  Aligned_cols=79  Identities=14%  Similarity=0.056  Sum_probs=53.7

Q ss_pred             hHHHHHhhcC---CCCChhHHHHHHHHHhccC---ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHH
Q 045555           33 DIARQYFAQM---PERDYVLWTAMIDGYLRVN---RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        33 ~~a~~~~~~m---~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      ..+++-|...   ..++..+.-.+..++++.+   +.++++.++++..+.+ .|+.            ....+=.+.-+|
T Consensus        15 ~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~------------~rd~lY~LAv~~   81 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEE------------QRDYVFYLAVGN   81 (152)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHH------------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-Cccc------------hHHHHHHHHHHH
Confidence            3444444432   1356677777778888888   6779999999999865 1210            011112477778


Q ss_pred             HhcCCHHHHHHHHHhhcC
Q 045555          107 CKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~~  124 (175)
                      .+.|++++|.+.++...+
T Consensus        82 ~kl~~Y~~A~~y~~~lL~   99 (152)
T 1pc2_A           82 YRLKEYEKALKYVRGLLQ   99 (152)
T ss_dssp             HHTSCHHHHHHHHHHHHH
T ss_pred             HHccCHHHHHHHHHHHHh
Confidence            999999999999999843

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=93.08  E-value=3.7  Score=34.91  Aligned_cols=131  Identities=13%  Similarity=0.141  Sum_probs=82.5

Q ss_pred             HHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCC--------------------------ChhHHHHHHHHHh
Q 045555            5 LEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPER--------------------------DYVLWTAMIDGYL   58 (175)
Q Consensus         5 ~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--------------------------~~~~~~~li~~~~   58 (175)
                      .++....+ .|+..--.+..+|...|++++|.+.|++....                          -..-|..++..+-
T Consensus       832 ~~l~~~~~-~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~YY~hv~~LFe  910 (1139)
T 4fhn_B          832 MQLIGWLN-SDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKYHHQNLLSCYYLHLSKKLF  910 (1139)
T ss_dssp             HHHHHHSC-CCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTTTSCCSSHHHHHHHHHHHH
T ss_pred             HHHhhhcc-CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccccccccccccHHHHHHHHHHHHH
Confidence            33333333 34444455667788889999999998876421                          0112566777777


Q ss_pred             ccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--ChhhHHHHHHH
Q 045555           59 RVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--DKFTWTAMIVG  136 (175)
Q Consensus        59 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~li~~  136 (175)
                      +.+.++.++++-....+... ++....         ....|..+.+++...|++++|...+-.+..+  -..+...+|..
T Consensus       911 ~~~~~~~vi~fa~lAi~~~~-~~~~~~---------~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r~~cLr~LV~~  980 (1139)
T 4fhn_B          911 EESAYIDALEFSLLADASKE-TDDEDL---------SIAITHETLKTACAAGKFDAAHVALMVLSTTPLKKSCLLDFVNQ  980 (1139)
T ss_dssp             HTSCCHHHHHHHHHHHHHCC-SCCHHH---------HHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhcc-CCChhh---------HHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            77777777776666555321 111110         1235788899999999999998888777443  34566777777


Q ss_pred             HHhcCChhHH
Q 045555          137 LAISGHGDTA  146 (175)
Q Consensus       137 ~~~~g~~~~a  146 (175)
                      +|..|+.+.-
T Consensus       981 lce~~~~~~L  990 (1139)
T 4fhn_B          981 LTKQGKINQL  990 (1139)
T ss_dssp             HHHHCCHHHH
T ss_pred             HHhCCChhhh
Confidence            7776665443

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=92.93  E-value=1.1  Score=28.59  Aligned_cols=110  Identities=9%  Similarity=0.089  Sum_probs=73.6

Q ss_pred             CCChhHHHHHHHHHhccCCh------HHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhH--HHHHHHHHHhcCCHHHH
Q 045555           44 ERDYVLWTAMIDGYLRVNRF------REALTLFREMQTSNIRRDEFTTVRILTTFNNDIFV--GIALIDMYCKCGDVEKA  115 (175)
Q Consensus        44 ~~~~~~~~~li~~~~~~~~~------~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~--~~~li~~~~~~~~~~~a  115 (175)
                      ..|..+|-..+.-.-+.|++      +...++|++.... ++|+..        ...-...  |-.-. .+...+++++|
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~--------~~wrrYI~LWIrYA-~~~ei~D~d~a   79 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKY--------GQNESFARIQVRFA-ELKAIQEPDDA   79 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGG--------TTCHHHHHHHHHHH-HHHHHHCGGGC
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCcccc--------ccHHHHHHHHHHHH-HHHHhcCHHHH
Confidence            34667777777777777887      7777888877664 555421        1111111  11111 12344899999


Q ss_pred             HHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHH
Q 045555          116 QRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEV  163 (175)
Q Consensus       116 ~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~  163 (175)
                      .++|+.+..   .=...|-....--.+.|++.+|.+++...+..+-+|...
T Consensus        80 R~vy~~a~~~hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~~  130 (161)
T 4h7y_A           80 RDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEM  130 (161)
T ss_dssp             HHHHHHHHHHCTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHHH
Confidence            999999842   124567777777789999999999999999887777653

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.37  E-value=2.4  Score=34.41  Aligned_cols=133  Identities=16%  Similarity=0.069  Sum_probs=81.0

Q ss_pred             HHHHHHHHHHhcCC-hhHHHHHhhcCCC--CChhH--HHHHHHHHhccCC-hHHHHHHHHHhHhC------CCCCChHHH
Q 045555           18 SWTTIVSGYINRGQ-VDIARQYFAQMPE--RDYVL--WTAMIDGYLRVNR-FREALTLFREMQTS------NIRRDEFTT   85 (175)
Q Consensus        18 ~~~~li~~~~~~~~-~~~a~~~~~~m~~--~~~~~--~~~li~~~~~~~~-~~~a~~~~~~m~~~------~~~p~~~~~   85 (175)
                      ....++..+.-.|+ .+.|.++|+.+.+  |...+  ...++..+.+.++ --+|+.+..+..+.      ...+.....
T Consensus       250 L~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~  329 (754)
T 4gns_B          250 LMYSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADS  329 (754)
T ss_dssp             HHHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHH
T ss_pred             HHHHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccc
Confidence            34566666666766 5778888888764  32222  2233433333332 33455555555431      122211111


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQM  153 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m  153 (175)
                      ..+.   +.+..+...-.+-+...|+++.|.++-+..+.  | +..+|..|..+|...|+++.|+=.++-+
T Consensus       330 ~~~~---~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          330 ARLM---NCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHH---HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             cccc---CcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            0000   11112233345556678999999999999854  5 7889999999999999999999988887

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=91.34  E-value=1.4  Score=26.09  Aligned_cols=60  Identities=12%  Similarity=0.020  Sum_probs=41.9

Q ss_pred             ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHH
Q 045555           62 RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIV  135 (175)
Q Consensus        62 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~  135 (175)
                      +.-+..+-++.+....+.|++...              .+.+.+|.|.+++..|.++|+.++.   ....+|..++.
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii--------------~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKII--------------DAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHH--------------HHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHH--------------HHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHH
Confidence            455666666777766665555444              7888899999999999999988843   23445666654

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.75  E-value=2.1  Score=32.33  Aligned_cols=96  Identities=13%  Similarity=0.121  Sum_probs=72.1

Q ss_pred             HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------
Q 045555           51 TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------  124 (175)
Q Consensus        51 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------  124 (175)
                      ..|...+-..|++.+|.+++.++...-...+....         -...+...+..|...+++..|..+..+...      
T Consensus       141 ~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~---------kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~  211 (445)
T 4b4t_P          141 KDLVEIKKEEGKIDEAADILCELQVETYGSMEMSE---------KIQFILEQMELSILKGDYSQATVLSRKILKKTFKNP  211 (445)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHH---------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHH---------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccC
Confidence            46677788899999999999999764222221111         134567889999999999999999988721      


Q ss_pred             C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 K----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 ~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +    -...|...+..+...+++.+|.+.|.+..+
T Consensus       212 ~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          212 KYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            1    234677788888899999999999888865

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.43  E-value=1.4  Score=32.98  Aligned_cols=96  Identities=10%  Similarity=0.015  Sum_probs=68.0

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----
Q 045555           49 LWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----  124 (175)
Q Consensus        49 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----  124 (175)
                      +...+...|.+.|++++|.+.|.+++.....+.            --..++-.++..+...+++..+.....+...    
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~------------~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~  200 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTG------------AKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEK  200 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCC------------SHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChH------------HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhc
Confidence            466788889999999999999999987543322            1234556789999999999999999888722    


Q ss_pred             -CChhhHH----HHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          125 -KDKFTWT----AMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       125 -~~~~~~~----~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                       ++...-+    .-...+...+++.+|.+.|.+....
T Consensus       201 ~~d~~~~~~lk~~~gl~~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          201 GGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             CCCTHHHHHHHHHHHHGGGGTSCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHhcc
Confidence             2222211    1122234578999999999887653

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=89.38  E-value=0.0051  Score=47.05  Aligned_cols=117  Identities=9%  Similarity=0.095  Sum_probs=83.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .+..|+.+..+..+.+++.+|.+.|-+..  |...|..+|....+.|.+++-+..+.-.++..-.|..            
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIkA~--Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~I------------  118 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIKAD--DPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYV------------  118 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCCCS--CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTT------------
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHhCC--ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccccc------------
Confidence            55678999999999999999988775544  5555788999999999999998887766655333322            


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQ  152 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  152 (175)
                          =+.|+-+|++.+++.+-+++...   |+..-...+.+-|...|.++.|.-+|..
T Consensus       119 ----DteLi~ayAk~~rL~elEefl~~---~N~A~iq~VGDrcf~e~lYeAAKilys~  169 (624)
T 3lvg_A          119 ----ETELIFALAKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNN  169 (624)
T ss_dssp             ----THHHHHHHHTSCSSSTTTSTTSC---CSSSCTHHHHHHHHHSCCSTTSSTTGGG
T ss_pred             ----HHHHHHHHHhhCcHHHHHHHHcC---CCcccHHHHHHHHHHccCHHHHHHHHHh
Confidence                25699999999998876655443   5555555666666666666666555443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=89.05  E-value=1.7  Score=26.71  Aligned_cols=81  Identities=11%  Similarity=0.010  Sum_probs=53.2

Q ss_pred             CChhHHHHHhhcCC---CCChhHHHHHHHHHhccCChHH---HHHHHHHhHhCCCCC-ChHHHHHhhhccCcchhHHHHH
Q 045555           30 GQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFRE---ALTLFREMQTSNIRR-DEFTTVRILTTFNNDIFVGIAL  102 (175)
Q Consensus        30 ~~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~---a~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~~l  102 (175)
                      .....+.+-|....   .++..+--.+..++++..+...   ++.+++++.+.+- | ...             ...=.|
T Consensus        15 ~~l~~~~~~y~~e~~~~~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~-p~~~R-------------d~lY~L   80 (126)
T 1nzn_A           15 EDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGS-KEEQR-------------DYVFYL   80 (126)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSC-HHHHH-------------HHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCC-cchHH-------------HHHHHH
Confidence            33344444454332   2566666667778888887655   9999999988641 2 111             111257


Q ss_pred             HHHHHhcCCHHHHHHHHHhhcC
Q 045555          103 IDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .-++.+.|++++|.+.++.+.+
T Consensus        81 Avg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           81 AVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHH
Confidence            7788999999999999999843

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=88.35  E-value=0.034  Score=42.64  Aligned_cols=115  Identities=14%  Similarity=0.111  Sum_probs=87.2

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      .|+..|..+|....+.|.+++-...+...++  ++..+=+.|+-+|++.++..+-.+++    .   .|+....      
T Consensus        81 ~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~IDteLi~ayAk~~rL~elEefl----~---~~N~A~i------  147 (624)
T 3lvg_A           81 DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI----N---GPNNAHI------  147 (624)
T ss_dssp             SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTTTHHHHHHHHTSCSSSTTTSTT----S---CCSSSCT------
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccHHHHHHHHHhhCcHHHHHHHH----c---CCCcccH------
Confidence            5788899999999999999999999988875  46677789999999999975533322    1   2332222      


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc------------------------CCChhhHHHHHHHHHhcCChhHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKML------------------------RKDKFTWTAMIVGLAISGHGDTAL  147 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~------------------------~~~~~~~~~li~~~~~~g~~~~a~  147 (175)
                              ..+.+-|...|.++.|.-+|..+.                        ..++.||-.+-.+|...+++.-|-
T Consensus       148 --------q~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAq  219 (624)
T 3lvg_A          148 --------QQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQ  219 (624)
T ss_dssp             --------HHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTT
T ss_pred             --------HHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHH
Confidence                    467888888888888888887761                        137789999999999888887664


Q ss_pred             HH
Q 045555          148 DM  149 (175)
Q Consensus       148 ~~  149 (175)
                      -.
T Consensus       220 ic  221 (624)
T 3lvg_A          220 MC  221 (624)
T ss_dssp             HH
T ss_pred             Hh
Confidence            33

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=88.35  E-value=1.7  Score=33.13  Aligned_cols=72  Identities=14%  Similarity=0.075  Sum_probs=37.8

Q ss_pred             chHHHHhhccCCC--cHHHHHHHHHHHHhc-CChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKNK--DVISWTTIVSGYINR-GQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~~--~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      +.|+++|+....|  +...|......-.+. ++.+.|+.+|+...+  | +...|...+.-..+.|+.+.|..+|+..
T Consensus       303 ~~AR~i~~~A~~~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          303 ELFRKLFIELGNEGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             HHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             HHHHHHHHHhhCCCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            4566666666322  333343222222222 257777777775542  2 2233444555556667777777777776

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=87.65  E-value=3.6  Score=25.73  Aligned_cols=59  Identities=12%  Similarity=0.009  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHH
Q 045555           63 FREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIV  135 (175)
Q Consensus        63 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~  135 (175)
                      .-+..+-++++....+.|              ++.+..+.+.+|.|.+++..|.++|+..+.   +...+|..++.
T Consensus        69 ~wElrrglN~l~~~DlVP--------------eP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~lq  130 (152)
T 2y69_E           69 AWELRKGMNTLVGYDLVP--------------EPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHHHHHHHHTTSSBCC--------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCC--------------CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHHH
Confidence            344445555555555444              444447888899999999999999988743   34445666654

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=87.60  E-value=12  Score=31.80  Aligned_cols=148  Identities=11%  Similarity=-0.027  Sum_probs=98.2

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCC------hHHHHHhhh--
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRD------EFTTVRILT--   90 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~------~~~~~~l~~--   90 (175)
                      ...++..+.+.+..+.+.++.....+.. ..-..+..++...|++++|.+.|.+.-. |+..+      ......+..  
T Consensus       815 ~~~l~~~l~~~~~~~~~~~l~~~~~~~~-~~~yl~g~~~L~~ge~~~A~~~F~kaa~-~~~~~~~l~~~~~~~~~~~~~~  892 (1139)
T 4fhn_B          815 VTELVEKLFLFKQYNACMQLIGWLNSDP-IAVYLKALIYLKSKEAVKAVRCFKTTSL-VLYSHTSQFAVLREFQEIAEKY  892 (1139)
T ss_dssp             HHHHHHHHHHHSCTTHHHHHHHHSCCCH-HHHHHHHHHHHHTTCHHHHHHHHHTCCC-SCTTCCCSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhccCCc-HHHHHHHHHHHhcCCHHHHHHHHHHHhh-hhcccchhhhhhcccccccccc
Confidence            3456667778888888888776665543 3345677789999999999999987632 22111      112222221  


Q ss_pred             -ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---C-C----hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555           91 -TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---K-D----KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus        91 -~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~-~----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                       ....-..-|..++..+.+.+.++.+.++-+...+   + +    ...|..+++++...|++++|...+-.+.+...+  
T Consensus       893 ~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r--  970 (1139)
T 4fhn_B          893 HHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLK--  970 (1139)
T ss_dssp             TSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSC--
T ss_pred             cccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHH--
Confidence             1122234678899999999999988877665521   2 2    226889999999999999999999887765443  


Q ss_pred             HHHHHHHHh
Q 045555          162 EVTYVGVLS  170 (175)
Q Consensus       162 ~~t~~~ll~  170 (175)
                      ......|+.
T Consensus       971 ~~cLr~LV~  979 (1139)
T 4fhn_B          971 KSCLLDFVN  979 (1139)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            233444444

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=87.51  E-value=3.8  Score=25.87  Aligned_cols=82  Identities=11%  Similarity=0.051  Sum_probs=59.4

Q ss_pred             hcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHH
Q 045555           28 NRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYC  107 (175)
Q Consensus        28 ~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~  107 (175)
                      ..|+.....+.|-.+...+.+ ...-++.+...|.-+.-.+++.++.... +              |++...-.+..+|.
T Consensus        73 ~C~NlKrVi~C~~~~n~~se~-vd~ALd~lv~~~KkDqLdki~~~~l~n~-~--------------~~~~~l~kia~Ay~  136 (172)
T 1wy6_A           73 KCQNLKSVVECGVINNTLNEH-VNKALDILVIQGKRDKLEEIGREILKNN-E--------------VSASILVAIANALR  136 (172)
T ss_dssp             GCSCTHHHHHHHHHTTCCCHH-HHHHHHHHHHTTCHHHHHHHHHHHC--C-C--------------SCHHHHHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHhcchHHH-HHHHHHHHHHhccHhHHHHHHHHHhccC-C--------------CChHHHHHHHHHHH
Confidence            356666666666666555554 5777888899999999999999965532 2              33334457999999


Q ss_pred             hcCCHHHHHHHHHhhcCC
Q 045555          108 KCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus       108 ~~~~~~~a~~~~~~~~~~  125 (175)
                      +.|+..+|.+++.+.-+.
T Consensus       137 Klg~~r~a~eLl~~AC~k  154 (172)
T 1wy6_A          137 RVGDERDATTLLIEACKK  154 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHT
T ss_pred             HhcchhhHHHHHHHHHHh
Confidence            999999999999887554

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=87.28  E-value=7.4  Score=28.91  Aligned_cols=141  Identities=11%  Similarity=-0.004  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--------CChhHHHHHHHHHhccC-ChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--------RDYVLWTAMIDGYLRVN-RFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--------~~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      .+...|...|.+.|+.++..+++...++        .....-..|+..+.... ..+.-+++..+..+.... +..+|  
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~-~~r~f--   96 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQ-EKRTF--   96 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHH-TTCHH--
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHH-HHHHH--
Confidence            4567889999999999999999998875        13445677888887753 455556666665542110 00111  


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC----CC-----hhhHHHHHHHHHhcCChhHHHHHHHHHHHC--
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR----KD-----KFTWTAMIVGLAISGHGDTALDMFSQMLRA--  156 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--  156 (175)
                            ....+-.-++..|...|++.+|.+++..+.+    .|     ..+|-.-+..|...+++.++...+......  
T Consensus        97 ------lr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~  170 (394)
T 3txn_A           97 ------LRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTAN  170 (394)
T ss_dssp             ------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhc
Confidence                  0011123689999999999999999988843    12     345667778899999999999999887642  


Q ss_pred             CCCCcHHHHH
Q 045555          157 SIRLDEVTYV  166 (175)
Q Consensus       157 g~~p~~~t~~  166 (175)
                      .+.|++.+..
T Consensus       171 ai~~~p~i~a  180 (394)
T 3txn_A          171 AIYCPPKVQG  180 (394)
T ss_dssp             HSCCCHHHHH
T ss_pred             cCCCCHHHHH
Confidence            3435554443

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=86.82  E-value=3.3  Score=24.41  Aligned_cols=73  Identities=14%  Similarity=0.073  Sum_probs=54.3

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHH--HHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVS--GYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~--~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +||..+=+++.. ++ .-.-.||+  .+.+.|++.+|..+.+.+.-||...|-.|..  -+.|..+++..-+.++..+|
T Consensus        23 qEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg   98 (115)
T 2uwj_G           23 EEALCIAEWLERLGQ-DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGGSS   98 (115)
T ss_dssp             HHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTCS
T ss_pred             HHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC
Confidence            345555554443 44 44444554  4778999999999999999999999988765  47788888888888888776

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=86.53  E-value=3.5  Score=24.36  Aligned_cols=73  Identities=16%  Similarity=0.120  Sum_probs=53.8

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHH--HHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVS--GYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~--~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +||..+=+++.. ++ .-.-.||+  .+.+.|++.+|..+.+.+.-||...|-.|..  -+.|..+++..-+.++..+|
T Consensus        24 qEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg   99 (116)
T 2p58_C           24 EEANCIAEWLHLKGE-EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLARSQ   99 (116)
T ss_dssp             HHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC
Confidence            345555554443 44 44444554  4778999999999999999999999988865  47788888888888887776

>3ltj_A Alpharep-4; protein engineering, heat-like repeat, protein binding; 1.80A {Synthetic}

Probab=85.77  E-value=5.4  Score=25.85  Aligned_cols=143  Identities=13%  Similarity=0.126  Sum_probs=67.6

Q ss_pred             hhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555            8 FGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus         8 ~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ++.+..+|...-..-+..+.+.+..+....+.+.+..++..+-...+.++.+.|..+ +...+.++...   ++...-..
T Consensus        20 i~~L~~~~~~vr~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~~L~~~~~~~-~~~~L~~~l~d---~~~~vr~~   95 (201)
T 3ltj_A           20 IKNLQDDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDER-AVEPLIKALKD---EDGWVRQS   95 (201)
T ss_dssp             HHHTTCSCHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGG-GHHHHHHHTTC---SSHHHHHH
T ss_pred             HHHhcCCCHHHHHHHHHHHHhcCChhHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHH-HHHHHHHHHcC---CCHHHHHH
Confidence            333444566666666666666666555555555555555554444445555544432 22222222221   12111111


Q ss_pred             hhh-----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHH
Q 045555           88 ILT-----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMF  150 (175)
Q Consensus        88 l~~-----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  150 (175)
                      .+.                 --.++..+-...+.++++.++.+....+...+..++..+-...+.++.+.|. +++...+
T Consensus        96 a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~A~~aL~~~~~-~~~~~~L  174 (201)
T 3ltj_A           96 AAVALGQIGDERAVEPLIKALKDEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGEIGG-ERVRAAM  174 (201)
T ss_dssp             HHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHTCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCS-HHHHHHH
T ss_pred             HHHHHHHhCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCc-hhHHHHH
Confidence            110                 0123334444556666666654444344444444555555666666666654 4455555


Q ss_pred             HHHHH
Q 045555          151 SQMLR  155 (175)
Q Consensus       151 ~~m~~  155 (175)
                      .++.+
T Consensus       175 ~~~l~  179 (201)
T 3ltj_A          175 EKLAE  179 (201)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            55554

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=85.55  E-value=5.7  Score=25.96  Aligned_cols=144  Identities=12%  Similarity=0.114  Sum_probs=73.3

Q ss_pred             HhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHH
Q 045555            7 IFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTV   86 (175)
Q Consensus         7 ~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~   86 (175)
                      +.+.+..+|...-...+..+++.|..+....+.+.+..++..+-...+.++.+.++. ++...+.++.+.   ++...-.
T Consensus        24 L~~~L~~~~~~vR~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~aL~~~~~~-~~~~~L~~~l~~---~~~~vr~   99 (211)
T 3ltm_A           24 YIKNLQDDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDE-RAVEPLIKALKD---EDGWVRQ   99 (211)
T ss_dssp             HHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSCHHHHHHHHHHHHHHCCG-GGHHHHHHHTTC---SSHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHhCCccHHHHHHHHHcCCCHHHHHHHHHHHHhhCCH-HHHHHHHHHHcC---CCHHHHH
Confidence            344444566666666666666666655555555656656555544555555555543 222223333221   1211111


Q ss_pred             Hhhh-----------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHH
Q 045555           87 RILT-----------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus        87 ~l~~-----------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                      ..+.                 --.++..+-...+.++++.+..+....+..-+..++..+-...+.++.+.+. +++...
T Consensus       100 ~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~-~~~~~~  178 (211)
T 3ltm_A          100 SAAVALGQIGDERAVEPLIKALKDEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGEIGG-ERVRAA  178 (211)
T ss_dssp             HHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCS-HHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCc-hhHHHH
Confidence            1110                 0123444555666666666665444444444445566666666777776665 455566


Q ss_pred             HHHHHH
Q 045555          150 FSQMLR  155 (175)
Q Consensus       150 ~~~m~~  155 (175)
                      +.++.+
T Consensus       179 L~~~l~  184 (211)
T 3ltm_A          179 MEKLAE  184 (211)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            666554

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=85.43  E-value=4  Score=24.07  Aligned_cols=63  Identities=13%  Similarity=0.021  Sum_probs=48.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      .-+..+...|++++|..+.+...-||...|-++-.  .+.|.-+++..-+.++..+| .|....|.
T Consensus        44 IR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg-~p~~q~Fa  106 (115)
T 2uwj_G           44 IRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGGSS-DPALADFA  106 (115)
T ss_dssp             HHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTCS-SHHHHHHH
T ss_pred             HHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC-CHHHHHHH
Confidence            34556778999999999999999999999887754  47888889998888888776 34443443

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=85.42  E-value=5.8  Score=25.92  Aligned_cols=60  Identities=18%  Similarity=0.185  Sum_probs=37.5

Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      ++..+-...+.++++.++.+....+...+..++..+-...+.++.+.|+. ++...+.++.
T Consensus        93 ~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~~-~~~~~L~~~l  152 (211)
T 3ltm_A           93 EDGWVRQSAAVALGQIGDERAVEPLIKALKDEDWFVRIAAAFALGEIGDE-RAVEPLIKAL  152 (211)
T ss_dssp             SSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCG-GGHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhCcHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCH-HHHHHHHHHH
Confidence            45556667777777777765555555555566776766777777776654 3444454444

>2ion_A PDCD4, programmed cell death 4, PDCD4; alpha-helical, antitumor protein; 1.57A {Mus musculus} SCOP: a.118.1.14 PDB: 2ios_A 2iol_A

Probab=85.04  E-value=5.5  Score=25.27  Aligned_cols=62  Identities=18%  Similarity=0.294  Sum_probs=45.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhcCCC---hhhHHHHHHHHHhcCC--hhHHHHHHHHHHHCCCCC
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKMLRKD---KFTWTAMIVGLAISGH--GDTALDMFSQMLRASIRL  160 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p  160 (175)
                      .+.+++=|...|+.++|.+.++++..|.   ..+...+..++-+.++  .+.+.+++..+...|+-+
T Consensus        12 i~~lL~EY~~~~D~~EA~~cl~EL~~p~f~~e~V~~~i~~alE~~~~~~re~~~~LL~~L~~~~~is   78 (152)
T 2ion_A           12 IDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTIT   78 (152)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcC
Confidence            3578999999999999999999997773   3355556666665432  456788888888776444

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=84.96  E-value=4.3  Score=23.98  Aligned_cols=62  Identities=18%  Similarity=0.144  Sum_probs=48.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHH
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY  165 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  165 (175)
                      .-+..+...|++++|..+.+...-||...|-++-.+  +.|.-+++..-+.++..+| .|....|
T Consensus        45 IR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce~--rlGl~s~le~rL~~la~sg-~p~~q~F  106 (116)
T 2p58_C           45 IRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCEY--RLGLGSALESRLNRLARSQ-DPRIQTF  106 (116)
T ss_dssp             HHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHHH--HHTCHHHHHHHHHHHTTCC-CHHHHHH
T ss_pred             HHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHHH--hcccHHHHHHHHHHHHhCC-CHHHHHH
Confidence            345567789999999999999999999998877554  6788888888888887766 3443344

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=84.41  E-value=3.3  Score=29.07  Aligned_cols=68  Identities=15%  Similarity=0.148  Sum_probs=48.9

Q ss_pred             HHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC--CCCCcHHHHHHHHhh
Q 045555          104 DMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA--SIRLDEVTYVGVLSA  171 (175)
Q Consensus       104 ~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~--g~~p~~~t~~~ll~~  171 (175)
                      ....+.|+++++.+....-++  | |...-..++..+|-.|++++|.+-++-..+.  ...|-..+|..+|.+
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~a   77 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKA   77 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHH
Confidence            345678888888888877754  3 6777778899999999999998888877653  344445556655543

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=83.71  E-value=6.1  Score=27.74  Aligned_cols=54  Identities=22%  Similarity=0.364  Sum_probs=43.8

Q ss_pred             HHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           54 IDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        54 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      +....+.|+++++++-..+-++..               +.|...-..+++.+|-.|+|+.|.+=++..
T Consensus         4 ~~~ll~~g~L~~al~~~~~~VR~~---------------P~da~~R~~LfqLLcv~G~w~RA~~QL~~~   57 (273)
T 1zbp_A            4 WKNALSEGQLQQALELLIEAIKAS---------------PKDASLRSSFIELLCIDGDFERADEQLMQS   57 (273)
T ss_dssp             HHHHTTTTCHHHHHHHHHHHHHTC---------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC---------------CcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            346778999999999988888865               345666678999999999999998766665

>2nsz_A Programmed cell death protein 4; PDCD4, tumor suppressor, translation, antitumor protein; 1.15A {Mus musculus} SCOP: a.118.1.14 PDB: 2kzt_B 2hm8_A 2ggf_A

Probab=82.64  E-value=6.3  Score=24.14  Aligned_cols=61  Identities=18%  Similarity=0.323  Sum_probs=45.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcCCC---hhhHHHHHHHHHhcCC--hhHHHHHHHHHHHCCCCC
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLRKD---KFTWTAMIVGLAISGH--GDTALDMFSQMLRASIRL  160 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~--~~~a~~~~~~m~~~g~~p  160 (175)
                      +.+++=|...|+.++|.+.++++..|.   ..+...+..++-+.++  .+.+.+++..+...|+-+
T Consensus        11 ~~ll~EY~~~~D~~Ea~~cl~eL~~p~f~~e~V~~~i~~alE~~~~~~~e~~~~LL~~L~~~~~is   76 (129)
T 2nsz_A           11 DMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTIT   76 (129)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHCCCcC
Confidence            578999999999999999999998773   2345556666666542  456788888888777444

>3ygs_P Procaspase 9; apoptosis, caspase activation, caspase recruitment, recognition complex; 2.50A {Homo sapiens} SCOP: a.77.1.3

Probab=82.54  E-value=1.7  Score=25.30  Aligned_cols=39  Identities=18%  Similarity=0.055  Sum_probs=31.4

Q ss_pred             CChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHH
Q 045555           30 GQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALT   68 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~   68 (175)
                      ...+.|..++..+..+....|..++.++...|+..-|..
T Consensus        51 t~~~~ar~Lld~L~~rG~~Af~~F~~aL~et~~~~La~l   89 (97)
T 3ygs_P           51 SRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASF   89 (97)
T ss_dssp             CHHHHHHHHHHHHTTSCTTHHHHHHHHHHTTTCHHHHHH
T ss_pred             ChHHHHHHHHHHHHHcChHHHHHHHHHHHHcCcHHHHHH
Confidence            467889999999988888889999999987777665543

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=81.99  E-value=3.5  Score=27.59  Aligned_cols=78  Identities=15%  Similarity=0.133  Sum_probs=53.4

Q ss_pred             hHHHHhhccCC--CcHH---HHHHHHHHHHhcCChhHHHHHhhcCCCC-----ChhHHHHHHHHHhccCChHHHHHHHHH
Q 045555            3 FALEIFGNMKN--KDVI---SWTTIVSGYINRGQVDIARQYFAQMPER-----DYVLWTAMIDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         3 ~A~~~~~~m~~--~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~~a~~~~~~   72 (175)
                      ++.+.|...++  .|+.   .|-..+..+ ..+....+.++|..|...     -..-|......+-..|++.+|.++|+.
T Consensus        62 rc~~~F~~~~rYkND~RYLklWl~Ya~~~-~~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~  140 (202)
T 3esl_A           62 RCLIYIQDMETYRNDPRFLKIWIWYINLF-LSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLEL  140 (202)
T ss_dssp             HHHHHHTTCGGGTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHhcccccccCCHHHHHHHHHHHHhh-cccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            44455555443  3433   344444443 244466889999988753     344588888888899999999999999


Q ss_pred             hHhCCCCCC
Q 045555           73 MQTSNIRRD   81 (175)
Q Consensus        73 m~~~~~~p~   81 (175)
                      -.+.+-.|-
T Consensus       141 GI~~~A~P~  149 (202)
T 3esl_A          141 GAENNCRPY  149 (202)
T ss_dssp             HHHTTCBSH
T ss_pred             HHHcCCccH
Confidence            999887764

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=81.60  E-value=14  Score=27.44  Aligned_cols=131  Identities=15%  Similarity=0.073  Sum_probs=81.6

Q ss_pred             cHHHHHHHHHHHHhcCC-hhHHHHHhhcCCC---CChhHH------HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHH
Q 045555           15 DVISWTTIVSGYINRGQ-VDIARQYFAQMPE---RDYVLW------TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFT   84 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~---~~~~~~------~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~   84 (175)
                      .......++..+....+ .+.-.++.....+   .+-.+|      ..|...|...|++.+|..++.++.+.=-..|..+
T Consensus        57 ~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~r~flr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~  136 (394)
T 3txn_A           57 AAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKN  136 (394)
T ss_dssp             HHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTH
T ss_pred             HHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccch
Confidence            45566777777776433 3333333333321   111223      2678889999999999999999988532223222


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC------CChhh----HHHHHHHHH-hcCChhHHHHHHHHH
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR------KDKFT----WTAMIVGLA-ISGHGDTALDMFSQM  153 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~------~~~~~----~~~li~~~~-~~g~~~~a~~~~~~m  153 (175)
                      +         -..++-.-+..|...+++.++...+.....      +++..    ...-...+. ..+++.+|...|-+.
T Consensus       137 ~---------llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~ea  207 (394)
T 3txn_A          137 L---------LVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYFYEA  207 (394)
T ss_dssp             H---------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             h---------HHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHhhHHHHHhccCHHHHHHHHHHH
Confidence            2         245567788889999999999988877621      22221    122223344 678999998888775


Q ss_pred             H
Q 045555          154 L  154 (175)
Q Consensus       154 ~  154 (175)
                      .
T Consensus       208 f  208 (394)
T 3txn_A          208 F  208 (394)
T ss_dssp             H
T ss_pred             H
Confidence            4

---

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	175
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.22
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.11
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	99.07
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.04
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.84
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.78
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.7
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.7
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.7
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.67
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.59
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.58
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.57
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.57
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.56
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.56
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.47
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.46
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.39
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.39
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.33
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.32
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.3
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.27
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.26
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.24
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.23
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.12
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.09
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.06
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.97
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.96
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.92
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.91
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.89
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.68
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.65
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.64
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	97.63
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.62
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.53
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.42
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.33
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.3
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.25
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.13
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.92
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.84
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	96.71
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.68
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.44
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.33
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.73
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	94.19
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.64
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	91.98
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	89.87
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.41
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	84.8
d2nsza1	129	Programmed cell death 4, PDCD4 {Mouse (Mus musculu	82.9
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	82.44

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=4.8e-10  Score=79.90  Aligned_cols=166  Identities=13%  Similarity=0.079  Sum_probs=111.6

Q ss_pred             hHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555            3 FALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus         3 ~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      +|...++...+  | +..++..+...+...|++++|...|+....   .+...+..+...+.+.|++++|+..|++..+.
T Consensus       187 ~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  266 (388)
T d1w3ba_         187 LAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL  266 (388)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            45555554432  2 455666677777777777777777765442   34455666666677777777777777776663


Q ss_pred             CCCCCh-HHHHHhhh--------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHH
Q 045555           77 NIRRDE-FTTVRILT--------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTA  132 (175)
Q Consensus        77 ~~~p~~-~~~~~l~~--------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~  132 (175)
                      .  |+. ..+..+-.                    ..+.+...+..+...+.+.|++++|.+.|++..+  | +..+|..
T Consensus       267 ~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~  344 (388)
T d1w3ba_         267 Q--PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSN  344 (388)
T ss_dssp             C--SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHH
T ss_pred             C--CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            2  321 12211111                    3345567778899999999999999999999854  4 5678888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHCCCCCc-HHHHHHHHhhh
Q 045555          133 MIVGLAISGHGDTALDMFSQMLRASIRLD-EVTYVGVLSAC  172 (175)
Q Consensus       133 li~~~~~~g~~~~a~~~~~~m~~~g~~p~-~~t~~~ll~~~  172 (175)
                      +...|.+.|++++|.+.|++.++.  .|+ ...+..+-..+
T Consensus       345 la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~~~  383 (388)
T d1w3ba_         345 LASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGNTL  383 (388)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHH
Confidence            999999999999999999998863  564 55566554443

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=2.4e-09  Score=75.32  Aligned_cols=155  Identities=15%  Similarity=0.174  Sum_probs=118.7

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+  | +..+|..+..+|.+.|++++|...|.+..+   .+...|..+...|...|++++|.+.+++...
T Consensus        36 ~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  115 (323)
T d1fcha_          36 PNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLR  115 (323)
T ss_dssp             HHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccccccchhhHHH
Confidence            578888888765  5 577899999999999999999999998653   3677889999999999999999999999877


Q ss_pred             CCCCCChH---------------------------HHHHhhh------cc---CcchhHHHHHHHHHHhcCCHHHHHHHH
Q 045555           76 SNIRRDEF---------------------------TTVRILT------TF---NNDIFVGIALIDMYCKCGDVEKAQRVF  119 (175)
Q Consensus        76 ~~~~p~~~---------------------------~~~~l~~------~~---~~~~~~~~~li~~~~~~~~~~~a~~~~  119 (175)
                      ........                           .+.....      ..   .++..++..+...+...|++++|...|
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~  195 (323)
T d1fcha_         116 YTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCF  195 (323)
T ss_dssp             TSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhccc
Confidence            43211000                           0000000      11   234567778888899999999999999


Q ss_pred             HhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          120 WKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       120 ~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      +....  | +...|..+...|...|++++|.+.|++.++.
T Consensus       196 ~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  235 (323)
T d1fcha_         196 TAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALEL  235 (323)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccccccccccccchhhhhhcccccccchhHHHHHHHHHHH
Confidence            98733  3 5778888888999999999999999988764

>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=99.07  E-value=2.2e-08  Score=65.77  Aligned_cols=136  Identities=9%  Similarity=-0.031  Sum_probs=109.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchh
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIF   97 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~   97 (175)
                      .|+- ...+...|+++.|++.|.++.+++..+|..+..++...|++++|++.|++.++..               +.+..
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld---------------p~~~~   71 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD---------------KHLAV   71 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh---------------hhhhh
Confidence            3443 5667889999999999999999999999999999999999999999999999854               23455


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhhcC---C----------------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCC
Q 045555           98 VGIALIDMYCKCGDVEKAQRVFWKMLR---K----------------DKFTWTAMIVGLAISGHGDTALDMFSQMLRASI  158 (175)
Q Consensus        98 ~~~~li~~~~~~~~~~~a~~~~~~~~~---~----------------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  158 (175)
                      .|..+..+|.+.|++++|...|++...   +                ...++..+..++.+.|++++|.+.+.+..+...
T Consensus        72 a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~  151 (192)
T d1hh8a_          72 AYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKS  151 (192)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             hHHHHHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            677899999999999999999998632   1                124566778889999999999999999887655


Q ss_pred             CCcHHHHHHHH
Q 045555          159 RLDEVTYVGVL  169 (175)
Q Consensus       159 ~p~~~t~~~ll  169 (175)
                      .|+......-+
T Consensus       152 ~~~~~~~~~Al  162 (192)
T d1hh8a_         152 EPRHSKIDKAM  162 (192)
T ss_dssp             SGGGGHHHHHH
T ss_pred             CcchHHHHHHH
Confidence            55444444333

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=1.1e-08  Score=72.68  Aligned_cols=151  Identities=10%  Similarity=0.101  Sum_probs=110.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh-
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT-   90 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~-   90 (175)
                      +...+..+...+...|++++|...++...+   .+...|..+...+...|++++|+..+++....+.... ..+..+-. 
T Consensus       168 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~l~~~  246 (388)
T d1w3ba_         168 FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHA-VVHGNLACV  246 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCH-HHHHHHHHH
T ss_pred             hhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHH-HHHHHHHHH
Confidence            567888899999999999999999997653   3667889999999999999999999999988653322 22211111 


Q ss_pred             ------------------ccC-cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHH
Q 045555           91 ------------------TFN-NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALD  148 (175)
Q Consensus        91 ------------------~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~  148 (175)
                                        ... .+...+..+...+.+.|++++|.+.++....   .+...+..+...+...|++++|.+
T Consensus       247 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  326 (388)
T d1w3ba_         247 YYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVR  326 (388)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHH
Confidence                              222 3456777788888888888888888877633   356677778888888888888888


Q ss_pred             HHHHHHHCCCCCc-HHHHHHH
Q 045555          149 MFSQMLRASIRLD-EVTYVGV  168 (175)
Q Consensus       149 ~~~~m~~~g~~p~-~~t~~~l  168 (175)
                      .|++.++.  .|+ ..++..+
T Consensus       327 ~~~~al~~--~p~~~~~~~~l  345 (388)
T d1w3ba_         327 LYRKALEV--FPEFAAAHSNL  345 (388)
T ss_dssp             HHHHHTTS--CTTCHHHHHHH
T ss_pred             HHHHHHHh--CCCCHHHHHHH
Confidence            88887753  444 3334433

>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=98.84  E-value=7.7e-08  Score=67.34  Aligned_cols=139  Identities=12%  Similarity=0.074  Sum_probs=105.4

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-------------------------------
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-------------------------------   45 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-------------------------------   45 (175)
                      ++|...|....+  | +...+..+...|...|++++|.+.++....  |                               
T Consensus        70 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (323)
T d1fcha_          70 LLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSD  149 (323)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHH
T ss_pred             HHHHHHHHhhhccccccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHh
Confidence            466777766554  3 677888899999999999999988876421  0                               


Q ss_pred             ---------------------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHH
Q 045555           46 ---------------------DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALID  104 (175)
Q Consensus        46 ---------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~  104 (175)
                                           +..++..+...+...|++++|+..|++.....               +.+...|..+..
T Consensus       150 ~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~---------------p~~~~~~~~lg~  214 (323)
T d1fcha_         150 SLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR---------------PNDYLLWNKLGA  214 (323)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc---------------cccccchhhhhh
Confidence                                 12234455556666677777777777666532               223556778999


Q ss_pred             HHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          105 MYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       105 ~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      .|.+.|++++|.+.|+...+  | +...|..+..+|.+.|++++|.+.|++.++
T Consensus       215 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         215 TLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999999999999853  4 677899999999999999999999999876

>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=98.78  E-value=3.7e-07  Score=63.84  Aligned_cols=154  Identities=11%  Similarity=0.180  Sum_probs=106.2

Q ss_pred             chHHHHhhccCC----CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-C-hhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555            2 GFALEIFGNMKN----KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-D-YVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus         2 ~~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~-~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ++|..+|+...+    .+...|...+..+-+.|+++.|..+|+.+.+  | + ..+|...+..+.+.|+.+.|.++|.+.
T Consensus        81 ~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~a  160 (308)
T d2onda1          81 DEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKA  160 (308)
T ss_dssp             HHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            456777776543    3566788888999999999999999998654  3 3 346899999999999999999999999


Q ss_pred             HhCCCCCC-hHHHHHhhh-------------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-------C
Q 045555           74 QTSNIRRD-EFTTVRILT-------------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-------D  126 (175)
Q Consensus        74 ~~~~~~p~-~~~~~~l~~-------------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~  126 (175)
                      .+.+.... .......+.                   .++.+...|...++.+.+.|+++.|..+|+.....       .
T Consensus       161 l~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~  240 (308)
T d2onda1         161 REDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKS  240 (308)
T ss_dssp             HTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGC
T ss_pred             HHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHH
Confidence            88754322 221111111                   22334566677777777777777777777775321       2


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      ...|...+..-...|+.+.+.++++++.+
T Consensus       241 ~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         241 GEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33577777766677777777777776654

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=1.4e-07  Score=61.81  Aligned_cols=123  Identities=15%  Similarity=0.034  Sum_probs=95.2

Q ss_pred             chHHHHhhccCCCcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCC
Q 045555            2 GFALEIFGNMKNKDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNI   78 (175)
Q Consensus         2 ~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   78 (175)
                      ++|++.|+.+..|+..+|..+..+|.+.|++++|.+.|++..+   .+...|..+..++.+.|++++|+..|++......
T Consensus        22 ~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~  101 (192)
T d1hh8a_          22 KGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLR  101 (192)
T ss_dssp             HHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCc
Confidence            5789999998889999999999999999999999999998764   4677899999999999999999999999876421


Q ss_pred             CCChHHHHHhhhccCc-chhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           79 RRDEFTTVRILTTFNN-DIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        79 ~p~~~~~~~l~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .-....|..+-....+ ...++..+..+|.+.|++++|.+.+.....
T Consensus       102 ~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_         102 GNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             TCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            1111111110001111 134556788899999999999999998854

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=2.4e-07  Score=65.27  Aligned_cols=139  Identities=7%  Similarity=0.080  Sum_probs=80.9

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcC-ChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRG-QVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQ   74 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   74 (175)
                      ++|+++++...+  | +..+|+....++...| ++++|...++...+   .+..+|+.+...+.+.|++++|+..++++.
T Consensus        60 ~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal  139 (315)
T d2h6fa1          60 ERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADIL  139 (315)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHHHHHHHHhhhh
Confidence            456666666654  3 4556666666666654 36677776666542   355566666666667777777777777776


Q ss_pred             hCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCC------hhH
Q 045555           75 TSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGH------GDT  145 (175)
Q Consensus        75 ~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~------~~~  145 (175)
                      +..               +.+...|..+...+.+.|++++|...|+...+  | +...|+.+...+.+.+.      +++
T Consensus       140 ~~d---------------p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~~~~~~~  204 (315)
T d2h6fa1         140 NQD---------------AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLER  204 (315)
T ss_dssp             HHC---------------TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHH
T ss_pred             hhh---------------hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccchhhhhHH
Confidence            642               22344555666666666666666666666633  2 44455555444444443      345


Q ss_pred             HHHHHHHHHH
Q 045555          146 ALDMFSQMLR  155 (175)
Q Consensus       146 a~~~~~~m~~  155 (175)
                      |.+.+.+.++
T Consensus       205 ai~~~~~al~  214 (315)
T d2h6fa1         205 EVQYTLEMIK  214 (315)
T ss_dssp             HHHHHHHHHH
T ss_pred             hHHHHHHHHH
Confidence            5555555544

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.70  E-value=3.6e-07  Score=59.54  Aligned_cols=95  Identities=11%  Similarity=0.010  Sum_probs=75.0

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~   90 (175)
                      |+..........|.+.|++++|...|++..+   .+...|+.+..+|.+.|++++|+..|++.++..  |+         
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~--p~---------   70 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD--GQ---------   70 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC--TT---------
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC--CC---------
Confidence            5666677778888888999999988887652   467778888888888899999998888887642  22         


Q ss_pred             ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           91 TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        91 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                          +...|..+..+|.+.|++++|...|+...
T Consensus        71 ----~~~a~~~lg~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          71 ----SVKAHFFLGQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             ----CHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ----cHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                45567788888888889988888888764

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=5.8e-07  Score=53.92  Aligned_cols=99  Identities=15%  Similarity=0.095  Sum_probs=82.8

Q ss_pred             HHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChh
Q 045555           52 AMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKF  128 (175)
Q Consensus        52 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~  128 (175)
                      .-.+.+.+.|++++|+..|++.++..               +.+...|..+..+|.+.|++++|...+....+   .+..
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~~~---------------p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~   72 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIKLD---------------PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGK   72 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcC---------------CcchhhhhcccccccccccccccchhhhhHHHhccchhh
Confidence            34567889999999999999998854               33566778999999999999999999999843   3788


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHH
Q 045555          129 TWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVG  167 (175)
Q Consensus       129 ~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  167 (175)
                      .|..+..++...|++++|...|++..+.  .|+...+..
T Consensus        73 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~--~p~~~~~~~  109 (117)
T d1elwa_          73 GYSRKAAALEFLNRFEEAKRTYEEGLKH--EANNPQLKE  109 (117)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTT--CTTCHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHH
Confidence            9999999999999999999999999864  565544443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=1.6e-06  Score=54.68  Aligned_cols=96  Identities=9%  Similarity=0.074  Sum_probs=80.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-C
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-D  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~  126 (175)
                      +....+.|.+.|++++|+..|.+..+..  |             .+...|..+..+|...|++++|.+.|+...+  | +
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~--p-------------~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~   77 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELN--P-------------SNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKY   77 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccc--h-------------hhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccc
Confidence            3445677889999999999999999854  2             3456678899999999999999999999844  4 6


Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcH
Q 045555          127 KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDE  162 (175)
Q Consensus       127 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~  162 (175)
                      ...|..+..++...|++++|.+.+++....  .|+.
T Consensus        78 ~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~--~p~~  111 (159)
T d1a17a_          78 IKGYYRRAASNMALGKFRAALRDYETVVKV--KPHD  111 (159)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTC
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCC
Confidence            689999999999999999999999999875  4543

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=1e-06  Score=55.62  Aligned_cols=117  Identities=15%  Similarity=0.065  Sum_probs=89.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCc
Q 045555           18 SWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNN   94 (175)
Q Consensus        18 ~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~   94 (175)
                      .+....+.|.+.|++++|...|++..+   .+...|..+..+|.+.|++++|+..|++.++..  |             .
T Consensus        12 ~l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~--p-------------~   76 (159)
T d1a17a_          12 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--K-------------K   76 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc--c-------------c
Confidence            345567788999999999999998764   477889999999999999999999999999854  2             2


Q ss_pred             chhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHH--HhcCChhHHHHH
Q 045555           95 DIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGL--AISGHGDTALDM  149 (175)
Q Consensus        95 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~--~~~g~~~~a~~~  149 (175)
                      +...|..+..+|...|++++|...+++...  | +...+..+..+.  ...+.+++|...
T Consensus        77 ~~~a~~~~g~~~~~~g~~~eA~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          77 YIKGYYRRAASNMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            455678899999999999999999999853  4 444444444332  233445555443

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.57  E-value=2e-06  Score=57.99  Aligned_cols=157  Identities=10%  Similarity=-0.048  Sum_probs=91.1

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+   .++.+|+.+..+|.+.|++++|...|++..+  | +..++..+...+...|++++|...|++..+
T Consensus        54 ~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_          54 ALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            456666666554   3667788888888888888888888887663  3 455677777788888888888888888877


Q ss_pred             CCCCCChHH-HHHhhh-----------------ccCcchhHHHHHHHHHHhcCC----HHHHHHHHHhhcC--C-ChhhH
Q 045555           76 SNIRRDEFT-TVRILT-----------------TFNNDIFVGIALIDMYCKCGD----VEKAQRVFWKMLR--K-DKFTW  130 (175)
Q Consensus        76 ~~~~p~~~~-~~~l~~-----------------~~~~~~~~~~~li~~~~~~~~----~~~a~~~~~~~~~--~-~~~~~  130 (175)
                      ......... +..+..                 ...+....+ .++..+.....    .+.+...+.....  | ...+|
T Consensus       134 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (259)
T d1xnfa_         134 DDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETN  212 (259)
T ss_dssp             HCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHH
T ss_pred             hccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHH
Confidence            542111111 111110                 111111111 12222221111    1111111111110  1 23467


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          131 TAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       131 ~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      ..+...|...|++++|.+.|++.+..  .|+
T Consensus       213 ~~lg~~~~~~g~~~~A~~~~~~al~~--~p~  241 (259)
T d1xnfa_         213 FYLGKYYLSLGDLDSATALFKLAVAN--NVH  241 (259)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTT--CCT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHc--CCC
Confidence            77889999999999999999998864  454

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.57  E-value=4.5e-06  Score=56.21  Aligned_cols=126  Identities=11%  Similarity=-0.015  Sum_probs=96.3

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ...+|..+...|.+.|++++|.+.|++..+   .+..+|+.+..++.+.|++++|+..|++..+..  |+          
T Consensus        36 ~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~----------  103 (259)
T d1xnfa_          36 RAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PT----------  103 (259)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TT----------
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH--hh----------
Confidence            445788889999999999999999998763   477889999999999999999999999999854  22          


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                         +...+..+..+|...|++++|...|+...+  | +......+..++.+.+..+.+..+......
T Consensus       104 ---~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  167 (259)
T d1xnfa_         104 ---YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  167 (259)
T ss_dssp             ---CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             ---hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc
Confidence               234556788999999999999999998854  3 344444444555566655555555555544

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.56  E-value=6.3e-07  Score=63.03  Aligned_cols=127  Identities=10%  Similarity=0.051  Sum_probs=109.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccC-ChHHHHHHHHHhHhCCCCCChHHHHHhhhc
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVN-RFREALTLFREMQTSNIRRDEFTTVRILTT   91 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~   91 (175)
                      ..+++.+-..+.+.+.+++|+++++++.+  | +...|+....++...| ++++|+..+++..+..              
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~--------------  108 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--------------  108 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--------------
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH--------------
Confidence            45788888889999999999999999874  4 6667898888888876 5999999999998854              


Q ss_pred             cCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCC
Q 045555           92 FNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRAS  157 (175)
Q Consensus        92 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g  157 (175)
                       +-+..+|..+...+.+.|++++|...++++.+  | +...|..+...+.+.|++++|.+.++++++..
T Consensus       109 -p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~  176 (315)
T d2h6fa1         109 -PKNYQVWHHRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED  176 (315)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC
T ss_pred             -HhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC
Confidence             23466778899999999999999999999954  3 68899999999999999999999999999853

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.56  E-value=5.9e-07  Score=58.45  Aligned_cols=74  Identities=14%  Similarity=0.075  Sum_probs=41.7

Q ss_pred             chHHHHhhccCC---CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN---KDVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|++.|+...+   .++..|+.+..+|.+.|++++|...|+...+  | +..+|..+..+|.+.|++++|+..|++..+
T Consensus        21 ~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          21 PEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345555554432   2455566666666666666666666665543  2 344555666666666666666666665544

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=2.7e-06  Score=50.86  Aligned_cols=91  Identities=13%  Similarity=0.053  Sum_probs=77.9

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDI   96 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~   96 (175)
                      ..-.+.+.+.|++++|...|++..+   .+...|..+..++.+.|++++|+..+.+..+.+               +.+.
T Consensus         7 ~~~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~---------------p~~~   71 (117)
T d1elwa_           7 KEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK---------------PDWG   71 (117)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC---------------TTCH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhc---------------cchh
Confidence            3456778899999999999999763   477789999999999999999999999999865               2345


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcCC
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLRK  125 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~  125 (175)
                      ..|..+..++...|++++|...|+...+.
T Consensus        72 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          72 KGYSRKAAALEFLNRFEEAKRTYEEGLKH  100 (117)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            56678999999999999999999999653

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.46  E-value=1.6e-06  Score=51.48  Aligned_cols=89  Identities=13%  Similarity=-0.025  Sum_probs=75.9

Q ss_pred             HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-Ch
Q 045555           51 TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DK  127 (175)
Q Consensus        51 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~  127 (175)
                      ..+...+.+.|++++|+..|++..+..  |             -+...|..+..++.+.|++++|...|+...+  | +.
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~--p-------------~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~   84 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKE--P-------------EREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDI   84 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS--T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccc--c-------------ccchhhhhhhhhhhhhhhHHHhhcccccccccccccc
Confidence            345667889999999999999999854  2             2455668899999999999999999999843  4 67


Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555          128 FTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus       128 ~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                      ..|..+...|...|++++|.+.+++.+
T Consensus        85 ~a~~~la~~y~~~g~~~~A~~~l~~~l  111 (112)
T d1hxia_          85 AVHAALAVSHTNEHNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            899999999999999999999998864

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.39  E-value=6.5e-06  Score=53.03  Aligned_cols=69  Identities=14%  Similarity=0.180  Sum_probs=60.4

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHH-----HCCCCCcHHHH
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQML-----RASIRLDEVTY  165 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~-----~~g~~p~~~t~  165 (175)
                      ..+..+..++.+.|++++|...++....  | +...|..++.+|.+.|+..+|.+.|+++.     +-|+.|...|-
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            4567899999999999999999999944  4 78899999999999999999999999974     35999998763

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=5.3e-06  Score=50.01  Aligned_cols=103  Identities=11%  Similarity=0.024  Sum_probs=79.7

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCH---HHHHHHHHhhcCCC
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDV---EKAQRVFWKMLRKD  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~---~~a~~~~~~~~~~~  126 (175)
                      ...+++.+...+++++|.+.|++.+..+               +.+..++..+..++.+.++.   ++|.+++++....+
T Consensus         2 ~~~l~n~~~~~~~l~~Ae~~Y~~aL~~~---------------p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~   66 (122)
T d1nzna_           2 MEAVLNELVSVEDLLKFEKKFQSEKAAG---------------SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG   66 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHS---------------CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhC---------------CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcc
Confidence            3568889999999999999999999965               23445556788888775554   56999999986532


Q ss_pred             -----hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHH
Q 045555          127 -----KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVL  169 (175)
Q Consensus       127 -----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll  169 (175)
                           ..+|..+..+|.+.|++++|.+.|++.++.  .|+..-...+.
T Consensus        67 ~~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~~--~P~~~~A~~l~  112 (122)
T d1nzna_          67 SKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQNNQAKELE  112 (122)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--CcCCHHHHHHH
Confidence                 236778899999999999999999999984  67655444443

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.33  E-value=3.8e-06  Score=58.09  Aligned_cols=131  Identities=7%  Similarity=-0.031  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----C----ChhHHHHHHHHHh-ccCChHHHHHHHHHhHhCCC-CCChHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYL-RVNRFREALTLFREMQTSNI-RRDEFT   84 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~----~~~~~~~li~~~~-~~~~~~~a~~~~~~m~~~~~-~p~~~~   84 (175)
                      ..+|..+..+|.+.|++++|.+.|+...+     .    ...++..+...|. ..|++++|+..+.+..+... ..+...
T Consensus        77 a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~  156 (290)
T d1qqea_          77 GNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVAL  156 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhh
Confidence            45788999999999999999999987553     1    2345666666664 46999999999998865210 011111


Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC--Ch--------hhHHHHHHHHHhcCChhHHHHHHHHHH
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK--DK--------FTWTAMIVGLAISGHGDTALDMFSQML  154 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--~~--------~~~~~li~~~~~~g~~~~a~~~~~~m~  154 (175)
                                -..++..+...|.+.|++++|...|+.....  +.        ..|...+..+...|+++.|.+.+.+..
T Consensus       157 ----------~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~  226 (290)
T d1qqea_         157 ----------SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQ  226 (290)
T ss_dssp             ----------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGG
T ss_pred             ----------hhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence                      1335678999999999999999999997432  11        123455566778899999999999987


Q ss_pred             HC
Q 045555          155 RA  156 (175)
Q Consensus       155 ~~  156 (175)
                      +.
T Consensus       227 ~~  228 (290)
T d1qqea_         227 SE  228 (290)
T ss_dssp             CC
T ss_pred             Hh
Confidence            64

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.32  E-value=8.1e-06  Score=52.00  Aligned_cols=109  Identities=11%  Similarity=0.026  Sum_probs=76.0

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCC-----CChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIR-----RDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-----p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      +....+.+.+.|++++|+..|.+.++....     ........     ..-..+|+.+..+|.+.|++++|...++....
T Consensus        16 l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~-----~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~   90 (170)
T d1p5qa1          16 VKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQ-----ALRLASHLNLAMCHLKLQAFSAAIESCNKALE   90 (170)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHH-----HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhc-----hhHHHHHHHHHHHHHhhhhcccccchhhhhhh
Confidence            444555677777777777777776653211     00000000     01123567788999999999999999999843


Q ss_pred             --C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHH
Q 045555          125 --K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY  165 (175)
Q Consensus       125 --~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  165 (175)
                        | ++..|..+..+|...|++++|...|++.++.  .|+....
T Consensus        91 ~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l--~P~n~~~  132 (170)
T d1p5qa1          91 LDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAA  132 (170)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHH
T ss_pred             ccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh--CCCCHHH
Confidence              4 7888999999999999999999999999874  4543333

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=0.00012  Score=50.58  Aligned_cols=132  Identities=14%  Similarity=0.108  Sum_probs=95.0

Q ss_pred             CChhHHHHHhhcCCC----CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---------------
Q 045555           30 GQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---------------   90 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---------------   90 (175)
                      +..++|..+|+...+    .+...|...+....+.|+++.|..+|+++++.........|...+.               
T Consensus        78 ~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~  157 (308)
T d2onda1          78 LFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIF  157 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHH
Confidence            345788888887542    3566788888889999999999999999988654333334444443               


Q ss_pred             -----ccCcchhHHHHHHHH-HHhcCCHHHHHHHHHhhcC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHC-CCCC
Q 045555           91 -----TFNNDIFVGIALIDM-YCKCGDVEKAQRVFWKMLR---KDKFTWTAMIVGLAISGHGDTALDMFSQMLRA-SIRL  160 (175)
Q Consensus        91 -----~~~~~~~~~~~li~~-~~~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-g~~p  160 (175)
                           ..+.+...|...... +...|+.+.|..+|+....   .+...|...+..+...|+++.|..+|++.... +..|
T Consensus       158 ~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         158 KKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence                 223334444443333 3446888999999998854   36778999999999999999999999998875 4565


Q ss_pred             c
Q 045555          161 D  161 (175)
Q Consensus       161 ~  161 (175)
                      +
T Consensus       238 ~  238 (308)
T d2onda1         238 E  238 (308)
T ss_dssp             G
T ss_pred             H
Confidence            4

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.27  E-value=3.8e-06  Score=49.77  Aligned_cols=88  Identities=11%  Similarity=0.001  Sum_probs=75.3

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcch
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDI   96 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~   96 (175)
                      -.+...+.+.|++++|...|++..+  | +...|..+..++.+.|++++|+..|++..+..  |             .+.
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p-------------~~~   84 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--P-------------KDI   84 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------TCH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccc--c-------------ccc
Confidence            3456778899999999999999774  4 67889999999999999999999999998854  2             245


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           97 FVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        97 ~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      ..+..+...|...|++++|.+.+++.
T Consensus        85 ~a~~~la~~y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          85 AVHAALAVSHTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            56678999999999999999999864

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.26  E-value=3.9e-06  Score=58.03  Aligned_cols=131  Identities=12%  Similarity=0.087  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC-----C----ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~   87 (175)
                      ..|......|-..|++++|.+.|.+..+     .    -..+|..+..+|.+.|++++|+..+++........+.     
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~-----  112 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQ-----  112 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-----
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhccc-----
Confidence            4588888999999999999999998653     1    2357899999999999999999999987663211110     


Q ss_pred             hhhccCcchhHHHHHHHHHHh-cCCHHHHHHHHHhhcC-----C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           88 ILTTFNNDIFVGIALIDMYCK-CGDVEKAQRVFWKMLR-----K----DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~-~~~~~~a~~~~~~~~~-----~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                          ......++..+...|.. .|++++|.+.++...+     .    -..+|..+...+...|++++|.+.|++....
T Consensus       113 ----~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~  187 (290)
T d1qqea_         113 ----FRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKS  187 (290)
T ss_dssp             ----HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             ----chhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHh
Confidence                01123445667777754 6999999999998732     1    2346888999999999999999999998764

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=1.1e-05  Score=48.88  Aligned_cols=99  Identities=10%  Similarity=0.132  Sum_probs=78.5

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-C
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-D  126 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~  126 (175)
                      +-.+.+.+.+.|++++|+..|++.++.+               +.+...+..+..+|.+.|++++|.+.++..++  | +
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~---------------p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~   71 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD---------------PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGREN   71 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC---------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC---------------cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCccc
Confidence            4567788999999999999999999864               23455668899999999999999999999854  2 2


Q ss_pred             -------hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHH
Q 045555          127 -------KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY  165 (175)
Q Consensus       127 -------~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  165 (175)
                             ..+|..+...+...+++++|.+.|++....  .|+....
T Consensus        72 ~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~  115 (128)
T d1elra_          72 REDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAE--HRTPDVL  115 (128)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCHHHH
Confidence                   236777778888999999999999887764  3444333

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.23  E-value=2.4e-05  Score=48.87  Aligned_cols=115  Identities=17%  Similarity=0.128  Sum_probs=79.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhCCC----CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTSNI----RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~----~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +..-.+.+.+.|++.+|+..|.+.++.-.    .++......   .......+++.+..+|.+.|++++|.+.++...+ 
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~---~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~   96 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDK---KKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI   96 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHH---HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHh---hhhHHHHHHhhHHHHHHHhcccchhhhhhhccccc
Confidence            44455667777788888877777765311    111111100   0111234667899999999999999999999843 


Q ss_pred             -C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHH
Q 045555          125 -K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVL  169 (175)
Q Consensus       125 -~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll  169 (175)
                       | ++..|..+..++...|++++|...|++.++.  .|+.......+
T Consensus        97 ~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~~~~~l  141 (153)
T d2fbna1          97 DKNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSY  141 (153)
T ss_dssp             STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHH
T ss_pred             cchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence             4 7789999999999999999999999999874  46544443333

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.12  E-value=3.4e-05  Score=48.99  Aligned_cols=111  Identities=14%  Similarity=0.044  Sum_probs=83.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-----C-------------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-----R-------------DYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ...+......+.+.|++++|...|.+...     +             -..+|+.+..+|.+.|++++|+..+++.++..
T Consensus        13 a~~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~   92 (170)
T d1p5qa1          13 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD   92 (170)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc
Confidence            34556677789999999999999986542     0             12467788889999999999999999999864


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcC
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISG  141 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g  141 (175)
                        |             .+...+..+..+|...|++++|...|+...+  | +......+-...-+.+
T Consensus        93 --p-------------~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~  144 (170)
T d1p5qa1          93 --S-------------NNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIR  144 (170)
T ss_dssp             --T-------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHH
T ss_pred             --c-------------cchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence              2             2455567899999999999999999999844  4 4444444444443333

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=1.3e-05  Score=48.28  Aligned_cols=92  Identities=11%  Similarity=0.067  Sum_probs=72.9

Q ss_pred             HHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCC---hHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           20 TTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNR---FREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        20 ~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      ..+++.+...+++++|.+.|+....   .+..++..+..++.+.++   +++|+.++++....+..|+.           
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~-----------   71 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQ-----------   71 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHH-----------
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchH-----------
Confidence            4678889999999999999998764   477788889989987654   56799999999876532221           


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                        ...+..+..+|.+.|++++|.+.|+...+
T Consensus        72 --~~~~~~Lg~~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          72 --RDYVFYLAVGNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             --HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence              12345789999999999999999999954

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.06  E-value=8.6e-05  Score=46.89  Aligned_cols=113  Identities=12%  Similarity=-0.010  Sum_probs=75.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHhHhC---CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--
Q 045555           50 WTAMIDGYLRVNRFREALTLFREMQTS---NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        50 ~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--  124 (175)
                      +.-..+.+.+.|++++|+..|.+....   ...++.......   -.-...+|+.+..+|.+.|++++|...++....  
T Consensus        18 ~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~---~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          18 VKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKAS---ESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHH---HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhc---chhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            445556666777777777777665542   111111100000   001134566788899999999999999999844  


Q ss_pred             C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHH
Q 045555          125 K-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVG  167 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~  167 (175)
                      | +...|..+..++...|++++|.+.|.+.++.  .|+......
T Consensus        95 p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~  136 (168)
T d1kt1a1          95 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARL  136 (168)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHH
Confidence            3 7788999999999999999999999999864  565444333

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.97  E-value=0.0001  Score=46.52  Aligned_cols=124  Identities=10%  Similarity=0.065  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-------C-----------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-------R-----------DYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      ...+.-....+.+.|++.+|...|.....       .           ....|+.+..+|.+.|++++|+..+++.++..
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            44566778889999999999999986441       0           22357778888999999999999999998854


Q ss_pred             CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCCh-hHHHHHHHHH
Q 045555           78 IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHG-DTALDMFSQM  153 (175)
Q Consensus        78 ~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~-~~a~~~~~~m  153 (175)
                                     +.+...+..+..+|...|++++|...|.....  | +......+-....+.++. +...++|..|
T Consensus        95 ---------------p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~e~~kk~~~~~  159 (168)
T d1kt1a1          95 ---------------SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKAKEHNERDRRTYANM  159 (168)
T ss_dssp             ---------------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence                           23455567899999999999999999999954  4 444444444444444433 2344555555


Q ss_pred             H
Q 045555          154 L  154 (175)
Q Consensus       154 ~  154 (175)
                      .
T Consensus       160 f  160 (168)
T d1kt1a1         160 F  160 (168)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.96  E-value=9e-05  Score=46.78  Aligned_cols=57  Identities=14%  Similarity=-0.016  Sum_probs=33.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           99 GIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        99 ~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                      +..+..+|.+.|++++|...++...+  | +...|..+..+|.+.|++++|.+.|++.++
T Consensus        80 ~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          80 VLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            34455556666666666666666533  2 444555566666666666666666666555

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.92  E-value=3.5e-05  Score=46.52  Aligned_cols=99  Identities=11%  Similarity=0.074  Sum_probs=77.2

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      ..+..+...|.+.|++++|...|.+..+   .+...+..+..+|.+.|++++|+..+++.++.... +...+       .
T Consensus         5 ~~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~-~~~~~-------~   76 (128)
T d1elra_           5 LKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRE-NREDY-------R   76 (128)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH-STTCH-------H
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcc-cHHHH-------H
Confidence            3566778889999999999999998763   47888999999999999999999999998874211 00001       0


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                      .-..+|..+...+...+++++|.+.|....
T Consensus        77 ~~a~~~~~lg~~~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          77 QIAKAYARIGNSYFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            012466788899999999999999998763

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.91  E-value=0.00014  Score=45.18  Aligned_cols=94  Identities=10%  Similarity=0.103  Sum_probs=76.4

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC--------C-----------ChhHHHHHHHHHhccCChHHHHHHHHHhHhC
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE--------R-----------DYVLWTAMIDGYLRVNRFREALTLFREMQTS   76 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~--------~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   76 (175)
                      ...+..-...+.+.|++.+|...|.+..+        +           ...+|+.+..+|.+.|++++|+..+++.+..
T Consensus        17 a~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~   96 (153)
T d2fbna1          17 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI   96 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccc
Confidence            34566677888899999999999986431        1           2346788999999999999999999999885


Q ss_pred             CCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC
Q 045555           77 NIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR  124 (175)
Q Consensus        77 ~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  124 (175)
                      .               +.+...|-.+..+|...|++++|...|+...+
T Consensus        97 ~---------------p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          97 D---------------KNNVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             S---------------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             c---------------chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            4               23456677899999999999999999999843

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.89  E-value=8e-05  Score=47.02  Aligned_cols=52  Identities=10%  Similarity=-0.058  Sum_probs=35.3

Q ss_pred             HHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--C-ChhhHHHHHHH
Q 045555           85 TVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--K-DKFTWTAMIVG  136 (175)
Q Consensus        85 ~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~  136 (175)
                      +..++.--+.+...|..+..+|.+.|++++|.+.|+...+  | +...+..+...
T Consensus       100 ~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~  154 (169)
T d1ihga1         100 CLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKV  154 (169)
T ss_dssp             HHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3334434445577888899999999999999999998844  4 34444444333

>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=97.68  E-value=0.00037  Score=47.90  Aligned_cols=129  Identities=11%  Similarity=0.024  Sum_probs=87.5

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC-------C---ChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHH
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE-------R---DYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTT   85 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~-------~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~   85 (175)
                      ..++......+...++...+...+.....       .   ....+..+...+...|++++|...+.+........+    
T Consensus       172 ~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~----  247 (366)
T d1hz4a_         172 LQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANN----  247 (366)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTC----
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccc----
Confidence            34455555666666777666666554321       1   223455566667777888888888777665432222    


Q ss_pred             HHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC--------C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555           86 VRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR--------K-DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus        86 ~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~--------~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                             ......+..+...+...|++++|.+.++....        | ....+..+...|.+.|++++|.+.+++.++
T Consensus       248 -------~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         248 -------HFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             -------GGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             -------hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                   11233456788899999999999999998742        1 345677888999999999999999988754

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.65  E-value=0.00014  Score=50.73  Aligned_cols=161  Identities=11%  Similarity=0.030  Sum_probs=94.7

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcC--ChhHHHHHhhcCCC---CChhHHHHH-HHHHhccCChHHHHHHHHH
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRG--QVDIARQYFAQMPE---RDYVLWTAM-IDGYLRVNRFREALTLFRE   72 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~---~~~~~~~~l-i~~~~~~~~~~~a~~~~~~   72 (175)
                      ++|+.+++...+  | +...|..+..++...+  ++++|...++...+   ++...+... ...+...+.+++|+..+++
T Consensus        90 ~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~  169 (334)
T d1dcea1          90 KAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDS  169 (334)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHH
Confidence            355666665543  2 4555555555555444  35666666666542   234444332 3445555666666666666


Q ss_pred             hHhCCCCCChHHHHHh--------------------------------------------------hhccCcchhHHHHH
Q 045555           73 MQTSNIRRDEFTTVRI--------------------------------------------------LTTFNNDIFVGIAL  102 (175)
Q Consensus        73 m~~~~~~p~~~~~~~l--------------------------------------------------~~~~~~~~~~~~~l  102 (175)
                      ..+.... +...|..+                                                  +...+++...+..+
T Consensus       170 ~i~~~p~-~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l  248 (334)
T d1dcea1         170 LITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELS  248 (334)
T ss_dssp             TTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCC
T ss_pred             HHHcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHH
Confidence            6554321 12222111                                                  11112222333345


Q ss_pred             HHHHHhcCCHHHHHHHHHhhcCCC---hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHH
Q 045555          103 IDMYCKCGDVEKAQRVFWKMLRKD---KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTY  165 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~  165 (175)
                      ...+...++.++|...+.+..+.+   ...|..+...+...|++++|.+.|++..+.  .|+..-|
T Consensus       249 ~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y  312 (334)
T d1dcea1         249 VEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAY  312 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHH
Confidence            666777788889999888887654   456777888899999999999999999874  6754333

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.64  E-value=0.00035  Score=44.63  Aligned_cols=89  Identities=12%  Similarity=0.088  Sum_probs=72.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHhhcCCC--C-----------------------ChhHHHHHHHHHhccCChHHHHHHHHHh
Q 045555           19 WTTIVSGYINRGQVDIARQYFAQMPE--R-----------------------DYVLWTAMIDGYLRVNRFREALTLFREM   73 (175)
Q Consensus        19 ~~~li~~~~~~~~~~~a~~~~~~m~~--~-----------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m   73 (175)
                      ...........|++++|.+.|.+...  +                       ....+..+...+.+.|++++|+..+++.
T Consensus        14 ~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~a   93 (179)
T d2ff4a2          14 EKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEAL   93 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHH
Confidence            33444567889999999999987543  1                       1235788899999999999999999999


Q ss_pred             HhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           74 QTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        74 ~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      .+..               +.+...|..++.+|.+.|+.++|.+.|+..
T Consensus        94 l~~~---------------P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~  127 (179)
T d2ff4a2          94 TFEH---------------PYREPLWTQLITAYYLSDRQSDALGAYRRV  127 (179)
T ss_dssp             HHHS---------------TTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHhC---------------CccHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9854               335667789999999999999999999986

>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=97.63  E-value=0.00053  Score=47.07  Aligned_cols=130  Identities=13%  Similarity=-0.019  Sum_probs=92.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHhhcCCC--CC------hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCC-CChHHHHH
Q 045555           17 ISWTTIVSGYINRGQVDIARQYFAQMPE--RD------YVLWTAMIDGYLRVNRFREALTLFREMQTSNIR-RDEFTTVR   87 (175)
Q Consensus        17 ~~~~~li~~~~~~~~~~~a~~~~~~m~~--~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~~~~~   87 (175)
                      .........+...|++++|..++++..+  |+      ...++.+...+...|++++|+..|++..+.... ++...   
T Consensus        13 e~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~---   89 (366)
T d1hz4a_          13 EFNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHY---   89 (366)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHH---
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHH---
Confidence            3444556667899999999999987542  22      346777888999999999999999998764211 11111   


Q ss_pred             hhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-------C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555           88 ILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-------K----DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus        88 l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                             ....+..+...+...|++..+...+.....       +    ....+..+...+...|+++.+...+......
T Consensus        90 -------~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~  162 (366)
T d1hz4a_          90 -------ALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEV  162 (366)
T ss_dssp             -------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHH
Confidence                   123445677888899999999888887622       1    1234556667788899999999998887753

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.62  E-value=0.00033  Score=43.50  Aligned_cols=103  Identities=17%  Similarity=0.099  Sum_probs=72.8

Q ss_pred             HHHHH--HHHHhccCChHHHHHHHHHhHhCCC-CCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC-
Q 045555           49 LWTAM--IDGYLRVNRFREALTLFREMQTSNI-RRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR-  124 (175)
Q Consensus        49 ~~~~l--i~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-  124 (175)
                      +|..+  ...+.+.|++++|+..|++.++... .|+.....    ........|+.+..+|.+.|++++|...+++... 
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~----~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~   84 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFD----HAGFDAFCHAGLAEALAGLRSFDEALHSADKALHY   84 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCC----HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcc----cchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhc
Confidence            45555  4456677999999999999987321 12210000    0001235678899999999999999999988732 


Q ss_pred             --------C-----ChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 045555          125 --------K-----DKFTWTAMIVGLAISGHGDTALDMFSQMLR  155 (175)
Q Consensus       125 --------~-----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~  155 (175)
                              +     ....|+.+..+|...|++++|.+.|++..+
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                    1     123577788999999999999999998764

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.53  E-value=0.00088  Score=41.43  Aligned_cols=99  Identities=17%  Similarity=0.082  Sum_probs=73.6

Q ss_pred             HHHHHHH--HHHHHhcCChhHHHHHhhcCCC-----C----------ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC-
Q 045555           16 VISWTTI--VSGYINRGQVDIARQYFAQMPE-----R----------DYVLWTAMIDGYLRVNRFREALTLFREMQTSN-   77 (175)
Q Consensus        16 ~~~~~~l--i~~~~~~~~~~~a~~~~~~m~~-----~----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-   77 (175)
                      ..+|..+  ...+.+.|++++|++.|++..+     |          ....|+.+..+|.+.|++++|+.-+++.++.. 
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~   86 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFN   86 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccc
Confidence            3466666  5556688999999999998653     2          13578899999999999999999999987631 


Q ss_pred             ----CCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc
Q 045555           78 ----IRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML  123 (175)
Q Consensus        78 ----~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  123 (175)
                          ..++....         ....++.+..+|...|++++|.+.|++..
T Consensus        87 ~~~~~~~~~~~~---------~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          87 RRGELNQDEGKL---------WISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             HHCCTTSTHHHH---------HHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccccch---------hHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence                11221111         12346778999999999999999999863

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.42  E-value=0.00032  Score=43.13  Aligned_cols=112  Identities=13%  Similarity=0.071  Sum_probs=74.9

Q ss_pred             HHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhcc----------CChHHHHHHHHHhHhCCCCCChHHHHHhhhcc
Q 045555           26 YINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRV----------NRFREALTLFREMQTSNIRRDEFTTVRILTTF   92 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~----------~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~   92 (175)
                      |-+.+.+++|+..|+...+  | +..++..+-.+|...          +.+++|+..|++.++..  |+           
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~--P~-----------   73 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID--PK-----------   73 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC--TT-----------
T ss_pred             HHHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc--ch-----------
Confidence            3456678888888888753  4 566677777776644          44578899998888743  32           


Q ss_pred             CcchhHHHHHHHHHHhcC-----------CHHHHHHHHHhh--cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCC
Q 045555           93 NNDIFVGIALIDMYCKCG-----------DVEKAQRVFWKM--LRKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASI  158 (175)
Q Consensus        93 ~~~~~~~~~li~~~~~~~-----------~~~~a~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~  158 (175)
                        +...|..+..+|...|           .+++|.+.|+..  ..|+...|..-+..+      .+|.+++.+..++|+
T Consensus        74 --~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          74 --KDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             --CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             --hhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence              3445566777776554           367788888887  456666555444433      467788888777764

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.33  E-value=0.00025  Score=48.23  Aligned_cols=116  Identities=9%  Similarity=-0.019  Sum_probs=78.3

Q ss_pred             HHhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHH
Q 045555           26 YINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIAL  102 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~l  102 (175)
                      ..+.|++++|...+++..+   .|...+..+...++..|++++|...++...+..  |+             +...+..+
T Consensus         6 aL~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~--P~-------------~~~~~~~l   70 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLF--PE-------------YLPGASQL   70 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--GG-------------GHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CC-------------cHHHHHHH
Confidence            4578999999999998653   477889999999999999999999999998853  32             22233344


Q ss_pred             HHHHHhcCCHHHHHHHHHhh-c--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHC
Q 045555          103 IDMYCKCGDVEKAQRVFWKM-L--RK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRA  156 (175)
Q Consensus       103 i~~~~~~~~~~~a~~~~~~~-~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  156 (175)
                      ...+...+..+++..-...- .  .| +...+......+.+.|+.++|.+.++++.+.
T Consensus        71 ~~ll~a~~~~~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          71 RHLVKAAQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHHHHHHHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhccccHHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            44444333333332222111 1  12 2233344456677899999999999998764

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.30  E-value=0.00039  Score=42.73  Aligned_cols=100  Identities=15%  Similarity=0.015  Sum_probs=71.3

Q ss_pred             HhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----------cCCHHHHHHHHHhhcC--
Q 045555           57 YLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----------CGDVEKAQRVFWKMLR--  124 (175)
Q Consensus        57 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----------~~~~~~a~~~~~~~~~--  124 (175)
                      |-+.+.+++|+..|+...+..  |+             +...+..+..+|..          .+++++|...|+...+  
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~--P~-------------~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~   71 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN--PL-------------DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID   71 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC--TT-------------CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHccHHHHHHHHHHHHhhC--Cc-------------chHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc
Confidence            445677999999999998854  33             34444556666653          4556889999988843  


Q ss_pred             C-ChhhHHHHHHHHHhcCC-----------hhHHHHHHHHHHHCCCCCcHHHHHHHHhhhc
Q 045555          125 K-DKFTWTAMIVGLAISGH-----------GDTALDMFSQMLRASIRLDEVTYVGVLSACT  173 (175)
Q Consensus       125 ~-~~~~~~~li~~~~~~g~-----------~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~~  173 (175)
                      | +...|..+..+|...|+           +++|.+.|++..+  +.|+..++..-+.-+.
T Consensus        72 P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~~  130 (145)
T d1zu2a1          72 PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMTA  130 (145)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHH
T ss_pred             chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHHH
Confidence            4 67788888888876553           5788888888876  4788777777665543

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.25  E-value=0.0014  Score=45.44  Aligned_cols=132  Identities=9%  Similarity=0.041  Sum_probs=90.9

Q ss_pred             chHHHHhhccCC--Cc-HHHHHHHHHHH----------HhcCChhHHHHHhhcCCC---CChhHHHHHHHHHhccC--Ch
Q 045555            2 GFALEIFGNMKN--KD-VISWTTIVSGY----------INRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVN--RF   63 (175)
Q Consensus         2 ~~A~~~~~~m~~--~~-~~~~~~li~~~----------~~~~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~--~~   63 (175)
                      ++|+++++...+  |+ ...|+..-..+          ...|.+++|+.+++...+   .+...|..+..++...+  ++
T Consensus        46 ~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~  125 (334)
T d1dcea1          46 ESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNW  125 (334)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCH
T ss_pred             HHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccH
Confidence            477888887764  54 34554433332          234457888888888653   36667777777766665  58


Q ss_pred             HHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHH-HHHHHHHHhcCCHHHHHHHHHhhcCC---ChhhHHHHHHHHHh
Q 045555           64 REALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVG-IALIDMYCKCGDVEKAQRVFWKMLRK---DKFTWTAMIVGLAI  139 (175)
Q Consensus        64 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~-~~li~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~  139 (175)
                      ++|+..+.+......               ++...+ ..+...+...+.+++|...++.....   +...|+.+...+.+
T Consensus       126 ~~a~~~~~~al~~~~---------------~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~  190 (334)
T d1dcea1         126 ARELELCARFLEADE---------------RNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  190 (334)
T ss_dssp             HHHHHHHHHHHHHCT---------------TCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCc---------------hhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            999999999988532               222222 24557778899999999999998653   66778888888888


Q ss_pred             cCChhHHHH
Q 045555          140 SGHGDTALD  148 (175)
Q Consensus       140 ~g~~~~a~~  148 (175)
                      .|++++|..
T Consensus       191 ~~~~~~A~~  199 (334)
T d1dcea1         191 LHPQPDSGP  199 (334)
T ss_dssp             HSCCCCSSS
T ss_pred             hcCHHHHHH
Confidence            888776533

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.13  E-value=0.0022  Score=47.33  Aligned_cols=125  Identities=7%  Similarity=-0.091  Sum_probs=68.5

Q ss_pred             CChhHHHHHhhcCCC---CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHH
Q 045555           30 GQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMY  106 (175)
Q Consensus        30 ~~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~  106 (175)
                      +.++.|...+...-+   ++...+..+...+.+.|+.++|...+.+..+..                 ....+..+.+.+
T Consensus       100 ~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-----------------~~~~~~~LG~l~  162 (497)
T d1ya0a1         100 GFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI-----------------CQHCLVHLGDIA  162 (497)
T ss_dssp             HHHHHHHHHHTC-------------------------------CCHHHHHH-----------------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC-----------------HHHHHHHHHHHH
Confidence            334444444443322   233445555555556666666655554443311                 123456789999


Q ss_pred             HhcCCHHHHHHHHHhhc--CC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHHHHHhhh
Q 045555          107 CKCGDVEKAQRVFWKML--RK-DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYVGVLSAC  172 (175)
Q Consensus       107 ~~~~~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~~ll~~~  172 (175)
                      ...|++++|...|++..  .| +...|+.+...+...|+..+|...|.+.+... .|...++..|...+
T Consensus       163 ~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         163 RYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKAL  230 (497)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH
Confidence            99999999999999984  35 66799999999999999999999999887643 45666666665544

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.92  E-value=0.0011  Score=37.52  Aligned_cols=62  Identities=6%  Similarity=-0.026  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHhhcCCC---------C-ChhHHHHHHHHHhccCChHHHHHHHHHhHhCC
Q 045555           16 VISWTTIVSGYINRGQVDIARQYFAQMPE---------R-DYVLWTAMIDGYLRVNRFREALTLFREMQTSN   77 (175)
Q Consensus        16 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   77 (175)
                      +..+-.+...+.+.|++++|...|++..+         + ...+++.|..++.+.|++++|+..+++.++..
T Consensus         5 addc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~   76 (95)
T d1tjca_           5 AEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC
Confidence            44566788889999999999999987642         1 24578999999999999999999999999853

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.84  E-value=0.002  Score=47.48  Aligned_cols=93  Identities=8%  Similarity=-0.156  Sum_probs=51.4

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCCCC-hhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccC
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPERD-YVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFN   93 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~   93 (175)
                      +...+..+...+.+.|+.+.|...+.....++ ...+..+...+...|++++|...|.+..+..  |             
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~--P-------------  183 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLV--P-------------  183 (497)
T ss_dssp             ------------------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--T-------------
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC--C-------------
Confidence            45566667777777777777777666554433 2356777888888899999999999888753  2             


Q ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           94 NDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        94 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      .+...|+.|...|...|+..+|...|.+.
T Consensus       184 ~~~~~~~~Lg~~~~~~~~~~~A~~~y~ra  212 (497)
T d1ya0a1         184 SNGQPYNQLAILASSKGDHLTTIFYYCRS  212 (497)
T ss_dssp             TBSHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            24556788888888899999888888776

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=96.71  E-value=0.028  Score=37.15  Aligned_cols=77  Identities=12%  Similarity=0.062  Sum_probs=43.0

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHh----cCChhHHHHHhhcCCCC-ChhHHHHHHHHHhc----cCChHHHHHHHH
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYIN----RGQVDIARQYFAQMPER-DYVLWTAMIDGYLR----VNRFREALTLFR   71 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~   71 (175)
                      ++|+++|+...+ -|..++-.|-..|..    ..+...|...+.....+ +......|...+..    ..+.+.|...++
T Consensus        19 ~~A~~~~~kAa~~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~   98 (265)
T d1ouva_          19 TQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYS   98 (265)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccchhhccccccccccccchhhHHHHHHHh
Confidence            356666665543 355555556666654    55666676666665443 33333444333332    355677777777


Q ss_pred             HhHhCCC
Q 045555           72 EMQTSNI   78 (175)
Q Consensus        72 ~m~~~~~   78 (175)
                      +....|.
T Consensus        99 ~a~~~g~  105 (265)
T d1ouva_          99 KACDLKY  105 (265)
T ss_dssp             HHHHTTC
T ss_pred             hhhhhhh
Confidence            7766553

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.0081  Score=33.62  Aligned_cols=59  Identities=15%  Similarity=0.077  Sum_probs=50.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhhcCC----------ChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCc
Q 045555          101 ALIDMYCKCGDVEKAQRVFWKMLRK----------DKFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLD  161 (175)
Q Consensus       101 ~li~~~~~~~~~~~a~~~~~~~~~~----------~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~  161 (175)
                      .+...+.+.|++++|...|++..+.          ...+++.+..++.+.|++++|.+.+++.++.  .|+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~   78 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPE   78 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcC
Confidence            5888899999999999999987321          2457899999999999999999999999874  465

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.44  E-value=0.074  Score=36.98  Aligned_cols=117  Identities=11%  Similarity=0.078  Sum_probs=62.9

Q ss_pred             CcHHHHHHHHHHHHhcCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhh---
Q 045555           14 KDVISWTTIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILT---   90 (175)
Q Consensus        14 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---   90 (175)
                      ||..--..+..-|.+.|.++.|..+|..+..     |..++..+.+.++++.|.+.+.+.-.      ..+|..+..   
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d-----~~rl~~~~v~l~~~~~avd~~~k~~~------~~~~k~~~~~l~   80 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN-----FGRLASTLVHLGEYQAAVDGARKANS------TRTWKEVCFACV   80 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC-----HHHHHHHHHTTTCHHHHHHHHHHHTC------HHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC-----HHHHHHHHHhhccHHHHHHHHHHcCC------HHHHHHHHHHHH
Confidence            5655556677777788888888888876654     44555555666666666555443310      111111111   


Q ss_pred             -------------ccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhc---CCChhhHHHHHHHHHhcC
Q 045555           91 -------------TFNNDIFVGIALIDMYCKCGDVEKAQRVFWKML---RKDKFTWTAMIVGLAISG  141 (175)
Q Consensus        91 -------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g  141 (175)
                                   ....+......++..|...|.+++...++....   ..+...++-++..|++.+
T Consensus        81 ~~~e~~la~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          81 DGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC
T ss_pred             hCcHHHHHHHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhC
Confidence                         122334444678999999999999999999763   346667888999888864

>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=96.33  E-value=0.00048  Score=46.77  Aligned_cols=107  Identities=10%  Similarity=0.046  Sum_probs=69.4

Q ss_pred             chHHHHhhccCC--C-cHHHHHHHHHHHHhcCChhHHHHHhhcCCC--C-ChhHHHHHHHHHhccCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN--K-DVISWTTIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   75 (175)
                      ++|+..+++..+  | |...+..+...|+..|++++|...|+...+  | +...+..+...+...+..+++..-.   ..
T Consensus        13 ~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a~~~~---~~   89 (264)
T d1zbpa1          13 QQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDFAQGA---AT   89 (264)
T ss_dssp             HHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHTTSC---CC
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHHHHHh---hh
Confidence            577888887764  4 788999999999999999999999999874  4 3444444444443333333322211   11


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhh
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKM  122 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  122 (175)
                      .....+           +++..........+.+.|+.++|.+.+...
T Consensus        90 ~~~~~~-----------p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a  125 (264)
T d1zbpa1          90 AKVLGE-----------NEELTKSLVSFNLSMVSQDYEQVSELALQI  125 (264)
T ss_dssp             EECCCS-----------CHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hhcccC-----------chHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            111111           112223345667788999999999999887

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=95.73  E-value=0.18  Score=34.98  Aligned_cols=83  Identities=14%  Similarity=0.156  Sum_probs=40.8

Q ss_pred             HHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcCC-----
Q 045555           51 TAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLRK-----  125 (175)
Q Consensus        51 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----  125 (175)
                      ..++..|-..|.+++.+.+++.....               -.++...++-++..|++.+. ++..+.++.....     
T Consensus       103 ~~~v~~ye~~~~~e~Li~~Le~~~~~---------------~~~~~~~~~~L~~lyak~~~-~kl~e~l~~~s~~y~~~k  166 (336)
T d1b89a_         103 EELINYYQDRGYFEELITMLEAALGL---------------ERAHMGMFTELAILYSKFKP-QKMREHLELFWSRVNIPK  166 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHTTS---------------TTCCHHHHHHHHHHHHTTCH-HHHHHHHHHHSTTSCHHH
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHcC---------------CccchHHHHHHHHHHHHhCh-HHHHHHHHhccccCCHHH
Confidence            34455555555555555555554322               12334455666777776543 3333333332111     


Q ss_pred             ------ChhhHHHHHHHHHhcCChhHHHHH
Q 045555          126 ------DKFTWTAMIVGLAISGHGDTALDM  149 (175)
Q Consensus       126 ------~~~~~~~li~~~~~~g~~~~a~~~  149 (175)
                            ....|.-++-.|.+.|++++|..+
T Consensus       167 ~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~  196 (336)
T d1b89a_         167 VLRAAEQAHLWAELVFLYDKYEEYDNAIIT  196 (336)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHcCChHHHHHHHHhcCCHHHHHHH
Confidence                  223455566666666666655433

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=94.19  E-value=0.25  Score=28.84  Aligned_cols=110  Identities=15%  Similarity=0.049  Sum_probs=69.9

Q ss_pred             ChhHHHHHhhcCCC-CChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh-
Q 045555           31 QVDIARQYFAQMPE-RDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK-  108 (175)
Q Consensus        31 ~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~-  108 (175)
                      ++++|...|++..+ .+......|.  .....+.++|+..+++..+.|.                 ...+..|-..|.. 
T Consensus         8 d~~~A~~~~~kaa~~g~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~-----------------~~a~~~Lg~~y~~g   68 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEMFGCLSLV--SNSQINKQKLFQYLSKACELNS-----------------GNGCRFLGDFYENG   68 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCTTHHHHHH--TCTTSCHHHHHHHHHHHHHTTC-----------------HHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHCCChhhhhhhc--cccccCHHHHHHHHhhhhcccc-----------------hhhhhhHHHhhhhc
Confidence            55666666666443 2333333332  2334578888888888877762                 1122234444443 


Q ss_pred             ---cCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHCCCC
Q 045555          109 ---CGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus       109 ---~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~g~~  159 (175)
                         ..+.++|.+.|+...+. +......|-..|..    ..+.++|.++|++..+.|..
T Consensus        69 ~~~~~d~~~A~~~~~~aa~~g~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~~  127 (133)
T d1klxa_          69 KYVKKDLRKAAQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGSE  127 (133)
T ss_dssp             SSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             cccchhhHHHHHHHhhhhccCcchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCCH
Confidence               56788999999988654 56666666666654    45889999999998887743

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.64  E-value=0.35  Score=28.56  Aligned_cols=132  Identities=11%  Similarity=0.122  Sum_probs=87.9

Q ss_pred             HHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhccCChHHHHHHHHHhHhC-CCCC--C--hHHHHHhhhccCcchhHH
Q 045555           26 YINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLRVNRFREALTLFREMQTS-NIRR--D--EFTTVRILTTFNNDIFVG   99 (175)
Q Consensus        26 ~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p--~--~~~~~~l~~~~~~~~~~~   99 (175)
                      +.-.|..++..++..+... .+..-||-.|--....-+-+-.+.+++.+=+. .+.|  +  .+.+.-+  ....+....
T Consensus        12 ~ildG~ve~Gveii~k~~~ss~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~--~~n~~se~v   89 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGV--INNTLNEHV   89 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHH--HTTCCCHHH
T ss_pred             HHHhhhHHhHHHHHHHHcccCCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHH--HhcchHHHH
Confidence            4456777888887777654 34445555555555555545555555544322 0111  1  1111111  123445666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhc---CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCC
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKML---RKDKFTWTAMIVGLAISGHGDTALDMFSQMLRASIR  159 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~  159 (175)
                      +..++.....|+-+.-.++++++.   ++++...-.+..+|.+-|...++-+++++.-++|++
T Consensus        90 dlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          90 NKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            788999999999999999988864   357778888899999999999999999999999875

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=91.98  E-value=0.61  Score=27.06  Aligned_cols=104  Identities=14%  Similarity=0.033  Sum_probs=67.7

Q ss_pred             chHHHHhhccCC-CcHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhc----cCChHHHHHHHHHhHh
Q 045555            2 GFALEIFGNMKN-KDVISWTTIVSGYINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFREMQT   75 (175)
Q Consensus         2 ~~A~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~   75 (175)
                      ++|+++|++..+ -+......|.  .....+.++|...|++..+ .+......|-..|..    ..+.++|++.|++..+
T Consensus        10 ~~A~~~~~kaa~~g~~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~   87 (133)
T d1klxa_          10 KKAIQYYVKACELNEMFGCLSLV--SNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACG   87 (133)
T ss_dssp             HHHHHHHHHHHHTTCTTHHHHHH--TCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCChhhhhhhc--cccccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHHHhhhhc
Confidence            467888887654 3444444443  3445678899999887664 355555556555544    4568999999999988


Q ss_pred             CCCCCChHHHHHhhhccCcchhHHHHHHHHHHh----cCCHHHHHHHHHhhcC
Q 045555           76 SNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK----CGDVEKAQRVFWKMLR  124 (175)
Q Consensus        76 ~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~  124 (175)
                      .|.                 +..+..|-..|..    ..+.++|.+.|+...+
T Consensus        88 ~g~-----------------~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~  123 (133)
T d1klxa_          88 LND-----------------QDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  123 (133)
T ss_dssp             TTC-----------------HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             cCc-----------------chHHHHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence            773                 1222345555554    5678888888887643

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=89.87  E-value=1.6  Score=28.11  Aligned_cols=125  Identities=11%  Similarity=0.042  Sum_probs=81.5

Q ss_pred             cHHHHHHHHHHHHhcCChhHHHHHhhcCCC-CChhHHHHHHHHHhc----cCChHHHHHHHHHhHhCCCCCChHHHHHhh
Q 045555           15 DVISWTTIVSGYINRGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFREMQTSNIRRDEFTTVRIL   89 (175)
Q Consensus        15 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~   89 (175)
                      |+..+..|...+.+.+++++|.+.|++..+ .+...+..|-..|..    ..+...|...+....+.+            
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~------------   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN------------   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT------------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc------------
Confidence            567778888888889999999999998765 477777777766665    557888888888877655            


Q ss_pred             hccCcchhHHHHHHHHHH----hcCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHh----cCChhHHHHHHHHHHHC
Q 045555           90 TTFNNDIFVGIALIDMYC----KCGDVEKAQRVFWKMLRK-DKFTWTAMIVGLAI----SGHGDTALDMFSQMLRA  156 (175)
Q Consensus        90 ~~~~~~~~~~~~li~~~~----~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~~~a~~~~~~m~~~  156 (175)
                           +......+...+.    ..++.+.|...++...+. .......+...+..    ......+...+......
T Consensus        69 -----~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~  139 (265)
T d1ouva_          69 -----YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL  139 (265)
T ss_dssp             -----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT
T ss_pred             -----ccchhhccccccccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCCCcccchhHHHHHHhhhhhcc
Confidence                 2222333434443    356788888888877554 33333333333332    34556667777666654

>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=87.41  E-value=1.4  Score=24.47  Aligned_cols=59  Identities=12%  Similarity=0.029  Sum_probs=38.8

Q ss_pred             ChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHhcCCHHHHHHHHHhhcC---CChhhHHHHH
Q 045555           62 RFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCKCGDVEKAQRVFWKMLR---KDKFTWTAMI  134 (175)
Q Consensus        62 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~li  134 (175)
                      +.-++.+-++.+....+.|++...              .+.+.+|.|.+++..|.++|+..+.   .+-..|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii--------------~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKII--------------DAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHH--------------HHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHH--------------HHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            445566666666666665554444              6888888888888888888887743   2334555444

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=84.80  E-value=2.5  Score=24.86  Aligned_cols=81  Identities=11%  Similarity=0.050  Sum_probs=55.2

Q ss_pred             cCChhHHHHHhhcCCCCChhHHHHHHHHHhccCChHHHHHHHHHhHhCCCCCChHHHHHhhhccCcchhHHHHHHHHHHh
Q 045555           29 RGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFREMQTSNIRRDEFTTVRILTTFNNDIFVGIALIDMYCK  108 (175)
Q Consensus        29 ~~~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~~li~~~~~  108 (175)
                      .++.......|-.+...+.+ .+.-++.+.+.|.-+.-.++++++.+.+               ++++...-.+..+|.+
T Consensus        69 C~Nlk~vv~C~~~~n~~se~-vdlALd~lv~~~kkd~Ld~i~~~l~kn~---------------~i~~~~llkia~A~kk  132 (161)
T d1wy6a1          69 CQNLKSVVECGVINNTLNEH-VNKALDILVIQGKRDKLEEIGREILKNN---------------EVSASILVAIANALRR  132 (161)
T ss_dssp             CSCTHHHHHHHHHTTCCCHH-HHHHHHHHHHTTCHHHHHHHHHHHC--C---------------CSCHHHHHHHHHHHHH
T ss_pred             hhcHHHHHHHHHHhcchHHH-HHHHHHHHHHhccHHHHHHHHHHHHhcC---------------CCCHHHHHHHHHHHHH
Confidence            34444444444444443443 5677888889999999999999977755               2333344579999999


Q ss_pred             cCCHHHHHHHHHhhcCC
Q 045555          109 CGDVEKAQRVFWKMLRK  125 (175)
Q Consensus       109 ~~~~~~a~~~~~~~~~~  125 (175)
                      -|...++-+++.+.-+.
T Consensus       133 ig~~re~nell~~ACe~  149 (161)
T d1wy6a1         133 VGDERDATTLLIEACKK  149 (161)
T ss_dssp             TTCHHHHHHHHHHHHHT
T ss_pred             hcchhhHHHHHHHHHHH
Confidence            99999999988876544

>d2nsza1 a.118.1.14 (A:322-450) Programmed cell death 4, PDCD4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: MIF4G domain-like
domain: Programmed cell death 4, PDCD4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.90  E-value=2.9  Score=24.22  Aligned_cols=61  Identities=18%  Similarity=0.353  Sum_probs=46.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhhcCCC---hhhHHHHHHHHHhcCChh-H-HHHHHHHHHHCCCCC
Q 045555          100 IALIDMYCKCGDVEKAQRVFWKMLRKD---KFTWTAMIVGLAISGHGD-T-ALDMFSQMLRASIRL  160 (175)
Q Consensus       100 ~~li~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g~~~-~-a~~~~~~m~~~g~~p  160 (175)
                      ..+++=|...|+.++|.+.++++..|.   ..++..+..++-+.++-. + +.+++..+..+|+-+
T Consensus        11 ~~ll~EY~~~~D~~Ea~~~l~eL~~p~~~~e~V~~~i~~ale~~~~~r~~~~~~Ll~~L~~~~~is   76 (129)
T d2nsza1          11 DMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTIT   76 (129)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHHTCGGGHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCCchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHCCCCC
Confidence            579999999999999999999997663   345556666666665543 3 577999999887544

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.44  E-value=1.9  Score=24.93  Aligned_cols=55  Identities=7%  Similarity=0.074  Sum_probs=40.9

Q ss_pred             CCHHHHHHHHHhhcC--C-C-hhhHHHHHHHHHhcCChhHHHHHHHHHHHCCCCCcHHHHH
Q 045555          110 GDVEKAQRVFWKMLR--K-D-KFTWTAMIVGLAISGHGDTALDMFSQMLRASIRLDEVTYV  166 (175)
Q Consensus       110 ~~~~~a~~~~~~~~~--~-~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~g~~p~~~t~~  166 (175)
                      .+++++..++++..+  | + ...+-.+.-+|.+.|++++|.+.++.+++.  .|+..-..
T Consensus        52 ~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~i--eP~n~qA~  110 (124)
T d2pqrb1          52 NDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEH--ERNNKQVG  110 (124)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHcc--CCCcHHHH
Confidence            456778888888854  2 2 246667788899999999999999999874  56544333