Citrus Sinensis ID: 035927

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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---
Protein Sequence
MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHcccHHHHHHHHcccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccHHHHHHHHHcccccccEEHHHHHHHHHHccccccccccHHHHHHHHHHHcccccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccccEHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccHHHHHHHHcc
Coil and Loop (DISEMBL)
mknkdvisWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREAltlfpemqtsnirpdefTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLaisdpfptirpdevTYVGVLSActhngnetFVINSCNL
Flexible Loop (DISEMBL)
MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTlfpemqtsnirpdeFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSActhngnetfvinscnl
Low Complexity Region (SEG)
MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
Disordered region (IsUnstruct)
*****VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVIN****
Disordered Region (DISOPRED)
*KNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
Disordered Region (DISEMBL)
MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
Disordered Region (DISPRO)
***KDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCNL
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	153	2.2.26 [Sep-21-2011]
Q9LSB8	687	Putative pentatricopeptid	yes	no	0.928	0.206	0.449	2e-38
Q9SJZ3	681	Pentatricopeptide repeat-	no	no	0.928	0.208	0.342	1e-27
Q9C866	570	Pentatricopeptide repeat-	no	no	0.928	0.249	0.358	2e-27
Q1PEU4	555	Pentatricopeptide repeat-	no	no	0.928	0.255	0.347	1e-24
Q9SJG6	559	Pentatricopeptide repeat-	no	no	0.901	0.246	0.322	2e-24
Q9MA50	500	Pentatricopeptide repeat-	no	no	0.928	0.284	0.315	1e-23
Q38959	455	Pentatricopeptide repeat-	no	no	0.934	0.314	0.322	1e-23
Q9FFG8	657	Pentatricopeptide repeat-	no	no	0.928	0.216	0.315	2e-22
Q683I9	573	Pentatricopeptide repeat-	no	no	0.895	0.239	0.317	9e-22
Q9FJY7	620	Pentatricopeptide repeat-	no	no	0.901	0.222	0.306	3e-21

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

 Score =  157 bits (398), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 84/187 (44%), Positives = 107/187 (57%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK +DVISWT IV GY+ RG + +AR YF QMP RD + WT MIDGYLR   F E+L +F
Sbjct: 297 MKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRAGCFNESLEIF 356

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ++ + PDEFT+V +LTA                                  MY KC
Sbjct: 357 REMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVGNALIDMYFKC 416

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVL 135
           G  EKAQ+V   M ++DKFTWTAM+VGLA +                +I+PD++TY+GVL
Sbjct: 417 GCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQPDDITYLGVL 476

Query: 136 SACTHNG 142
           SAC H+G
Sbjct: 477 SACNHSG 483

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 =  121 bits (304), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 64/187 (34%), Positives = 97/187 (51%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           ++ + ++SWT ++SGY   G +D++R+ F  M E+D VLW AMI G ++  R ++AL LF
Sbjct: 318 LEKRTIVSWTTMISGYARCGLLDVSRKLFDDMEEKDVVLWNAMIGGSVQAKRGQDALALF 377

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQTSN +PDE T++  L+A                                  MY KC
Sbjct: 378 QEMQTSNTKPDEITMIHCLSACSQLGALDVGIWIHRYIEKYSLSLNVALGTSLVDMYAKC 437

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPT------------IRPDEVTYVGVL 135
           G++ +A  V   +  ++  T+TA+I GLA+     T            I PDE+T++G+L
Sbjct: 438 GNISEALSVFHGIQTRNSLTYTAIIGGLALHGDASTAISYFNEMIDAGIAPDEITFIGLL 497

Query: 136 SACTHNG 142
           SAC H G
Sbjct: 498 SACCHGG 504

Arabidopsis thaliana (taxid: 3702)

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

 Score =  121 bits (304), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 67/187 (35%), Positives = 97/187 (51%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M++K+V  WT +V GY++ G++D AR  F + P +D VLWTAM++GY++ NRF EAL LF
Sbjct: 208 MRDKNVKCWTSMVFGYVSTGRIDEARVLFERSPVKDVVLWTAMMNGYVQFNRFDEALELF 267

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
             MQT+ IRPD F +V +LT                                   MY KC
Sbjct: 268 RCMQTAGIRPDNFVLVSLLTGCAQTGALEQGKWIHGYINENRVTVDKVVGTALVDMYAKC 327

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVL 135
           G +E A  V  ++  +D  +WT++I GLA++                 +R D +T+V VL
Sbjct: 328 GCIETALEVFYEIKERDTASWTSLIYGLAMNGMSGRALDLYYEMENVGVRLDAITFVAVL 387

Query: 136 SACTHNG 142
           +AC H G
Sbjct: 388 TACNHGG 394

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (279), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 65/187 (34%), Positives = 96/187 (51%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M +K VI+WT ++ GY N   +D AR+ F  MPER+ V W  MI GY +  + +E + LF
Sbjct: 202 MTHKTVITWTTMIHGYCNIKDIDAARKLFDAMPERNLVSWNTMIGGYCQNKQPQEGIRLF 261

Query: 61  PEMQ-TSNIRPDEFTIVRILTAY---------------------------------MYCK 86
            EMQ T+++ PD+ TI+ +L A                                  MY K
Sbjct: 262 QEMQATTSLDPDDVTILSVLPAISDTGALSLGEWCHCFVQRKKLDKKVKVCTAILDMYSK 321

Query: 87  CGDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPFPTI----RPDEVTYVGVL 135
           CG++EKA+R+  +M  K   +W AMI G A++       D F T+    +PDE+T + V+
Sbjct: 322 CGEIEKAKRIFDEMPEKQVASWNAMIHGYALNGNARAALDLFVTMMIEEKPDEITMLAVI 381

Query: 136 SACTHNG 142
           +AC H G
Sbjct: 382 TACNHGG 388

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 =  111 bits (278), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 59/183 (32%), Positives = 91/183 (49%), Gaps = 45/183 (24%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQ 64
           DV++W  ++ G+   G +D A+  F +MP+R+ V W +MI G++R  RF++AL +F EMQ
Sbjct: 191 DVVAWNSMIMGFAKCGLIDQAQNLFDEMPQRNGVSWNSMISGFVRNGRFKDALDMFREMQ 250

Query: 65  TSNIRPDEFTIVRILTAY---------------------------------MYCKCGDVE 91
             +++PD FT+V +L A                                  MYCKCG +E
Sbjct: 251 EKDVKPDGFTMVSLLNACAYLGASEQGRWIHEYIVRNRFELNSIVVTALIDMYCKCGCIE 310

Query: 92  KAQRVLRKMLRKDKFTWTAMIVGLA-------ISDPFPT-----IRPDEVTYVGVLSACT 139
           +   V     +K    W +MI+GLA         D F       + PD V+++GVL+AC 
Sbjct: 311 EGLNVFECAPKKQLSCWNSMILGLANNGFEERAMDLFSELERSGLEPDSVSFIGVLTACA 370

Query: 140 HNG 142
           H+G
Sbjct: 371 HSG 373

Arabidopsis thaliana (taxid: 3702)

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

 Score =  108 bits (271), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 59/187 (31%), Positives = 91/187 (48%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M++K+ ++W  ++ GY+  GQVD A + F +MPERD + WTAMI+G+++     EAL  F
Sbjct: 135 MEDKNSVTWNTMIDGYMRSGQVDNAAKMFDKMPERDLISWTAMINGFVKKGYQEEALLWF 194

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ S ++PD   I+  L A                                  +YC+C
Sbjct: 195 REMQISGVKPDYVAIIAALNACTNLGALSFGLWVHRYVLSQDFKNNVRVSNSLIDLYCRC 254

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPF------------PTIRPDEVTYVGVL 135
           G VE A++V   M ++   +W ++IVG A +                  +PD VT+ G L
Sbjct: 255 GCVEFARQVFYNMEKRTVVSWNSVIVGFAANGNAHESLVYFRKMQEKGFKPDAVTFTGAL 314

Query: 136 SACTHNG 142
           +AC+H G
Sbjct: 315 TACSHVG 321

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 =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 61/189 (32%), Positives = 88/189 (46%), Gaps = 46/189 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M  + ++SWT ++ G ++  Q+D A   F QMP R+ V WTAMI  Y++  R  EA  LF
Sbjct: 180 MPGRSIVSWTTMLYGLVSNSQLDSAEIVFNQMPMRNVVSWTAMITAYVKNRRPDEAFQLF 239

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
             MQ  +++P+EFTIV +L A                                  MY KC
Sbjct: 240 RRMQVDDVKPNEFTIVNLLQASTQLGSLSMGRWVHDYAHKNGFVLDCFLGTALIDMYSKC 299

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISD-------------PFPTIRPDEVTYVGV 134
           G ++ A++V   M  K   TW +MI  L +                  ++ PD +T+VGV
Sbjct: 300 GSLQDARKVFDVMQGKSLATWNSMITSLGVHGCGEEALSLFEEMEEEASVEPDAITFVGV 359

Query: 135 LSACTHNGN 143
           LSAC + GN
Sbjct: 360 LSACANTGN 368

Arabidopsis thaliana (taxid: 3702)

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

 Score =  104 bits (260), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 60/190 (31%), Positives = 91/190 (47%), Gaps = 48/190 (25%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M  +DVISWT++++ Y   G ++ A + F  +P +D V WTAM+ G+ +  + +EAL  F
Sbjct: 210 MPERDVISWTELIAAYARVGNMECAAELFESLPTKDMVAWTAMVTGFAQNAKPQEALEYF 269

Query: 61  PEMQTSNIRPDEFTIVRILTAY-----------------------------------MYC 85
             M+ S IR DE T+   ++A                                    MY 
Sbjct: 270 DRMEKSGIRADEVTVAGYISACAQLGASKYADRAVQIAQKSGYSPSDHVVIGSALIDMYS 329

Query: 86  KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------------TIRPDEVTYV 132
           KCG+VE+A  V   M  K+ FT+++MI+GLA                    I+P+ VT+V
Sbjct: 330 KCGNVEEAVNVFMSMNNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFV 389

Query: 133 GVLSACTHNG 142
           G L AC+H+G
Sbjct: 390 GALMACSHSG 399

Arabidopsis thaliana (taxid: 3702)

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

 Score =  102 bits (254), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 62/195 (31%), Positives = 95/195 (48%), Gaps = 58/195 (29%)

Query: 3   NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPE 62
           +KD+ +W  +V+ Y   G +D AR+ F +MPER+ + W+ +I+GY+   +++EAL LF E
Sbjct: 125 SKDLPAWNSVVNAYAKAGLIDDARKLFDEMPERNVISWSCLINGYVMCGKYKEALDLFRE 184

Query: 63  MQTSN-----IRPDEFTIVRILTAY---------------------------------MY 84
           MQ        +RP+EFT+  +L+A                                  MY
Sbjct: 185 MQLPKPNEAFVRPNEFTMSTVLSACGRLGALEQGKWVHAYIDKYHVEIDIVLGTALIDMY 244

Query: 85  CKCGDVEKAQRVLRKM-LRKDKFTWTAMIVGLAI----------------SDPFPTIRPD 127
            KCG +E+A+RV   +  +KD   ++AMI  LA+                SD    I P+
Sbjct: 245 AKCGSLERAKRVFNALGSKKDVKAYSAMICCLAMYGLTDECFQLFSEMTTSD---NINPN 301

Query: 128 EVTYVGVLSACTHNG 142
            VT+VG+L AC H G
Sbjct: 302 SVTFVGILGACVHRG 316

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (249), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 89/183 (48%), Gaps = 45/183 (24%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQ 64
           D +SW  ++ GY+  G++DIA   F +M E++ + WT MI GY++ +  +EAL LF EMQ
Sbjct: 180 DDVSWNSVIKGYVKAGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQ 239

Query: 65  TSNIRPDEFTIVRILTAY---------------------------------MYCKCGDVE 91
            S++ PD  ++   L+A                                  MY KCG++E
Sbjct: 240 NSDVEPDNVSLANALSACAQLGALEQGKWIHSYLNKTRIRMDSVLGCVLIDMYAKCGEME 299

Query: 92  KAQRVLRKMLRKDKFTWTAMIVGL--------AISDPFPT----IRPDEVTYVGVLSACT 139
           +A  V + + +K    WTA+I G         AIS         I+P+ +T+  VL+AC+
Sbjct: 300 EALEVFKNIKKKSVQAWTALISGYAYHGHGREAISKFMEMQKMGIKPNVITFTAVLTACS 359

Query: 140 HNG 142
           + G
Sbjct: 360 YTG 362

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	153
356528966	712	PREDICTED: putative pentatricopeptide re	0.928	0.199	0.529	6e-47
255553251	512	pentatricopeptide repeat-containing prot	0.928	0.277	0.545	1e-46
449436619	723	PREDICTED: putative pentatricopeptide re	0.928	0.196	0.502	2e-45
449491161	744	PREDICTED: LOW QUALITY PROTEIN: putative	0.928	0.190	0.502	2e-45
357468161	874	Pentatricopeptide repeat-containing prot	0.928	0.162	0.497	2e-44
224134923	635	predicted protein [Populus trichocarpa]	0.908	0.218	0.505	2e-42
225442904	724	PREDICTED: putative pentatricopeptide re	0.928	0.196	0.497	3e-41
15233234	687	pentatricopeptide repeat-containing prot	0.928	0.206	0.449	1e-36
9294596	695	unnamed protein product [Arabidopsis tha	0.928	0.204	0.449	1e-36
413947530	649	hypothetical protein ZEAMMB73_142662 [Ze	0.928	0.218	0.427	7e-34

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

 Score =  191 bits (486), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 99/187 (52%), Positives = 119/187 (63%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MKN+DVISWT IV+G+ N GQ+D+AR+YF Q+PERDYV WTAMIDGYLR+NRF EAL LF
Sbjct: 269 MKNRDVISWTSIVTGFANIGQIDLARKYFDQIPERDYVSWTAMIDGYLRMNRFIEALALF 328

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ SN++PDEFT+V ILTA                                  MY KC
Sbjct: 329 REMQMSNVKPDEFTMVSILTACAHLGALELGEWVKTYIDKNSIKNDTFVGNALIDMYFKC 388

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPF------------PTIRPDEVTYVGVL 135
           G+V KA++V ++M  KDKFTWTAMIVGLAI+                +I PDE+TY+GVL
Sbjct: 389 GNVGKAKKVFKEMHHKDKFTWTAMIVGLAINGHGEEALAMFSNMIEASITPDEITYIGVL 448

Query: 136 SACTHNG 142
            ACTH G
Sbjct: 449 CACTHAG 455

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 =  190 bits (483), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 102/187 (54%), Positives = 120/187 (64%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK++DVISWT IV+G+ N GQ+DIAR+YF QMPERDYV WTAMIDGYL+VN F+EAL LF
Sbjct: 250 MKSRDVISWTAIVTGFANIGQLDIARKYFDQMPERDYVSWTAMIDGYLQVNCFKEALVLF 309

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQTSN++PDEFT+V ILTA                                  MY KC
Sbjct: 310 HEMQTSNVKPDEFTMVSILTACAQLGALELGEWVRTYIDKNKVKNDAYVGNALIDMYFKC 369

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPF-----PTIRPDEVTYVGVL 135
           G+VEKA+ +   M R DKFTWTAMIVGLAI+       D F      ++ PDE+TYVGVL
Sbjct: 370 GNVEKARSIFNSMPRPDKFTWTAMIVGLAINGYGEEALDMFVQMLKASVTPDEITYVGVL 429

Query: 136 SACTHNG 142
            ACTH G
Sbjct: 430 CACTHTG 436

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/187 (50%), Positives = 120/187 (64%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M N+D+ISWT IVSG+ N G++D+AR YF +MPE+DYV WTAMIDGY+R NRF+EAL LF
Sbjct: 280 MNNRDIISWTTIVSGFTNLGEIDVARNYFDKMPEKDYVSWTAMIDGYIRSNRFKEALELF 339

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
             MQ +N++PDEFT+V +LTA                                  MY KC
Sbjct: 340 RNMQATNVKPDEFTMVSVLTACAHLGALELGEWIRTYIDRNKIKNDLFVRNALIDMYFKC 399

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPF-----PTIRPDEVTYVGVL 135
           GDV+KA+ + R+M ++DKFTWTAMIVGLA++       D F      +I PDE+TY+GVL
Sbjct: 400 GDVDKAESIFREMSQRDKFTWTAMIVGLAVNGHGEKALDMFSNMLKASILPDEITYIGVL 459

Query: 136 SACTHNG 142
           SACTH G
Sbjct: 460 SACTHTG 466

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/187 (50%), Positives = 120/187 (64%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M N+D+ISWT IVSG+ N G++D+AR YF +MPE+DYV WTAMIDGY+R NRF+EAL LF
Sbjct: 301 MNNRDIISWTTIVSGFTNLGEIDVARNYFDKMPEKDYVSWTAMIDGYIRSNRFKEALELF 360

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
             MQ +N++PDEFT+V +LTA                                  MY KC
Sbjct: 361 RNMQATNVKPDEFTMVSVLTACAHLGALELGEWIRTYIDRNKIKNDLFVRNALIDMYFKC 420

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPF-----PTIRPDEVTYVGVL 135
           GDV+KA+ + R+M ++DKFTWTAMIVGLA++       D F      +I PDE+TY+GVL
Sbjct: 421 GDVDKAESIFREMSQRDKFTWTAMIVGLAVNGHGEKALDMFSNMLKASILPDEITYIGVL 480

Query: 136 SACTHNG 142
           SACTH G
Sbjct: 481 SACTHTG 487

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 =  183 bits (464), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/187 (49%), Positives = 118/187 (63%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK +DVISWT IV+G+ N  ++D+AR+YF QMPERDYV WTAMIDGYLR+NRF+E LTLF
Sbjct: 301 MKTRDVISWTSIVTGFANTCRIDLARKYFDQMPERDYVSWTAMIDGYLRMNRFKEVLTLF 360

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            +MQ SN++PDEFT+V ILTA                                  MY KC
Sbjct: 361 RDMQMSNVKPDEFTMVSILTACAHLGALELGEWAKTYIDKNKIKNDTFIGNALIDMYFKC 420

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPF------------PTIRPDEVTYVGVL 135
           G+VEKA+++  +M +KDKFTWTAMIVGLA +                ++ PDE+TY+GV+
Sbjct: 421 GNVEKAKKIFNEMQKKDKFTWTAMIVGLANNGHGEEALTMFSYMLEASVTPDEITYIGVM 480

Query: 136 SACTHNG 142
            ACTH G
Sbjct: 481 CACTHVG 487

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 93/184 (50%), Positives = 114/184 (61%), Gaps = 45/184 (24%)

Query: 4   KDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEM 63
           KDVISWT IV+G++N GQVD AR+YF +MPERD+V WTAMIDGYLR+N ++EAL LF EM
Sbjct: 195 KDVISWTAIVTGFVNTGQVDAARKYFHKMPERDHVSWTAMIDGYLRLNCYKEALMLFREM 254

Query: 64  QTSNIRPDEFTIVRILTAY---------------------------------MYCKCGDV 90
           QTS I+PDEFT+V +LTA                                  MY KCG+V
Sbjct: 255 QTSKIKPDEFTMVSVLTACAQLGALELGEWIRTYIDKNKVKNDTFVGNALIDMYFKCGNV 314

Query: 91  EKAQRVLRKMLRKDKFTWTAMIVGLAISDPF------------PTIRPDEVTYVGVLSAC 138
           E A  +   + ++DKFTWTAM+VGLAI+                ++ PDEVTYVGVLSAC
Sbjct: 315 EMALSIFNTLPQRDKFTWTAMVVGLAINGCGEEALNMFSQMLKASVTPDEVTYVGVLSAC 374

Query: 139 THNG 142
           TH G
Sbjct: 375 THTG 378

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 93/187 (49%), Positives = 115/187 (61%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK++DVISWT IV+G+ N GQV +AR YF +MPERD+V WTAMIDGYL+VNRF+E L+LF
Sbjct: 281 MKSRDVISWTAIVTGFTNLGQVGLARNYFDKMPERDFVSWTAMIDGYLQVNRFKEVLSLF 340

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ +NI+PDEFT+V ILTA                                  MY  C
Sbjct: 341 REMQAANIKPDEFTMVSILTACAHLGALELGEWIKAYIDKNEIKIDSFVGNALIDMYFNC 400

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPF-----PTIRPDEVTYVGVL 135
           G+VEKA R+   M  +DK +WTA+I GLAI+       D F      +I PDEVT +GVL
Sbjct: 401 GNVEKAIRIFNAMPHRDKISWTAVIFGLAINGYGEEALDMFSQMLKASITPDEVTCIGVL 460

Query: 136 SACTHNG 142
            ACTH+G
Sbjct: 461 CACTHSG 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/187 (44%), Positives = 107/187 (57%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK +DVISWT IV GY+ RG + +AR YF QMP RD + WT MIDGYLR   F E+L +F
Sbjct: 297 MKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRAGCFNESLEIF 356

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ++ + PDEFT+V +LTA                                  MY KC
Sbjct: 357 REMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVGNALIDMYFKC 416

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVL 135
           G  EKAQ+V   M ++DKFTWTAM+VGLA +                +I+PD++TY+GVL
Sbjct: 417 GCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQPDDITYLGVL 476

Query: 136 SACTHNG 142
           SAC H+G
Sbjct: 477 SACNHSG 483

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 84/187 (44%), Positives = 107/187 (57%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           MK +DVISWT IV GY+ RG + +AR YF QMP RD + WT MIDGYLR   F E+L +F
Sbjct: 297 MKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRAGCFNESLEIF 356

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ++ + PDEFT+V +LTA                                  MY KC
Sbjct: 357 REMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKTYIDKNKIKNDVVVGNALIDMYFKC 416

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVL 135
           G  EKAQ+V   M ++DKFTWTAM+VGLA +                +I+PD++TY+GVL
Sbjct: 417 GCSEKAQKVFHDMDQRDKFTWTAMVVGLANNGQGQEAIKVFFQMQDMSIQPDDITYLGVL 476

Query: 136 SACTHNG 142
           SAC H+G
Sbjct: 477 SACNHSG 483

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413947530|gb|AFW80179.1| hypothetical protein ZEAMMB73_142662 [Zea mays]

 Score =  148 bits (374), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 80/187 (42%), Positives = 107/187 (57%), Gaps = 45/187 (24%)

Query: 1   MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
           M+ + V+SWT ++SG    G+VD AR  F +MPERD V WTAMIDGY++  RFREAL +F
Sbjct: 206 MQVRSVVSWTSLLSGLTRLGRVDEARDLFGRMPERDTVSWTAMIDGYVQAARFREALEMF 265

Query: 61  PEMQTSNIRPDEFTIVRILTAY---------------------------------MYCKC 87
            EMQ SN+  DEFT+V ++TA                                  MY KC
Sbjct: 266 REMQCSNVSADEFTMVSVITACAQLGALEMGEWVRVYMSRQGIKMDAFVGNALIDMYSKC 325

Query: 88  GDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS-------DPFPTI-----RPDEVTYVGVL 135
           G +E+A  V + M  +DKFTWTA+I+GLA++       + F  +      PDEVT++GVL
Sbjct: 326 GSIERALDVFKDMHHRDKFTWTAIILGLAVNGYGEEAIEMFHRMIGVSETPDEVTFIGVL 385

Query: 136 SACTHNG 142
           +ACTH G
Sbjct: 386 TACTHAG 392

Source: Zea mays

Species: Zea mays

Genus: Zea

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	153
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.529	0.118	0.456	4.2e-26
TAIR|locus:2054966	555	AHG11 "ABA hypersensitive germ	0.529	0.145	0.439	2.9e-25
TAIR|locus:2093920	687	AT3G15930 "AT3G15930" [Arabido	0.764	0.170	0.462	2.2e-22
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.601	0.124	0.382	1.2e-20
TAIR|locus:2206164	570	AT1G31430 [Arabidopsis thalian	0.764	0.205	0.404	1.1e-18
TAIR|locus:505006163	761	AT1G32415 "AT1G32415" [Arabido	0.718	0.144	0.379	5.9e-16
TAIR|locus:2057986	625	AT2G36980 [Arabidopsis thalian	0.620	0.152	0.278	7.9e-08
TAIR|locus:2044797	627	AT2G35030 [Arabidopsis thalian	0.699	0.170	0.407	3.3e-16
TAIR|locus:2198678	500	PDE247 "pigment defective 247"	0.529	0.162	0.432	8.9e-16
TAIR|locus:2032955	790	AT1G25360 "AT1G25360" [Arabido	0.673	0.130	0.301	6.6e-08

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

 Score = 211 (79.3 bits), Expect = 4.2e-26, Sum P(2) = 4.2e-26
 Identities = 37/81 (45%), Positives = 57/81 (70%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             ++ + ++SWT ++SGY   G +D++R+ F  M E+D VLW AMI G ++  R ++AL LF
Sbjct:   318 LEKRTIVSWTTMISGYARCGLLDVSRKLFDDMEEKDVVLWNAMIGGSVQAKRGQDALALF 377

Query:    61 PEMQTSNIRPDEFTIVRILTA 81
              EMQTSN +PDE T++  L+A
Sbjct:   378 QEMQTSNTKPDEITMIHCLSA 398

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 181 (68.8 bits), Expect = 2.9e-25, Sum P(2) = 2.9e-25
 Identities = 36/82 (43%), Positives = 53/82 (64%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             M +K VI+WT ++ GY N   +D AR+ F  MPER+ V W  MI GY +  + +E + LF
Sbjct:   202 MTHKTVITWTTMIHGYCNIKDIDAARKLFDAMPERNLVSWNTMIGGYCQNKQPQEGIRLF 261

Query:    61 PEMQ-TSNIRPDEFTIVRILTA 81
              EMQ T+++ PD+ TI+ +L A
Sbjct:   262 QEMQATTSLDPDDVTILSVLPA 283

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 269 (99.8 bits), Expect = 2.2e-22, P = 2.2e-22
 Identities = 56/121 (46%), Positives = 79/121 (65%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             MK +DVISWT IV GY+ RG + +AR YF QMP RD + WT MIDGYLR   F E+L +F
Sbjct:   297 MKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRDRISWTIMIDGYLRAGCFNESLEIF 356

Query:    61 PEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDP 120
              EMQ++ + PDEFT+V +LTA  +   G +E  + + +  + K+K     ++VG A+ D 
Sbjct:   357 REMQSAGMIPDEFTMVSVLTACAHL--GSLEIGEWI-KTYIDKNKIK-NDVVVGNALIDM 412

Query:   121 F 121
             +
Sbjct:   413 Y 413

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 203 (76.5 bits), Expect = 1.2e-20, Sum P(2) = 1.2e-20
 Identities = 36/94 (38%), Positives = 63/94 (67%)

Query:     3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPE 62
             ++DV+S+T ++ GY +RG ++ A++ F ++P +D V W AMI GY     ++EAL LF +
Sbjct:   197 HRDVVSYTALIKGYASRGYIENAQKLFDEIPVKDVVSWNAMISGYAETGNYKEALELFKD 256

Query:    63 MQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRV 96
             M  +N+RPDE T+V +++A    + G +E  ++V
Sbjct:   257 MMKTNVRPDESTMVTVVSAC--AQSGSIELGRQV 288

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2206164 AT1G31430 [Arabidopsis thaliana (taxid:3702)]

 Score = 233 (87.1 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 49/121 (40%), Positives = 78/121 (64%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             M++K+V  WT +V GY++ G++D AR  F + P +D VLWTAM++GY++ NRF EAL LF
Sbjct:   208 MRDKNVKCWTSMVFGYVSTGRIDEARVLFERSPVKDVVLWTAMMNGYVQFNRFDEALELF 267

Query:    61 PEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDP 120
               MQT+ IRPD F +V +LT     + G +E+ + +    + +++ T    +VG A+ D 
Sbjct:   268 RCMQTAGIRPDNFVLVSLLTGC--AQTGALEQGKWI-HGYINENRVT-VDKVVGTALVDM 323

Query:   121 F 121
             +
Sbjct:   324 Y 324

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:505006163 AT1G32415 "AT1G32415" [Arabidopsis thaliana (taxid:3702)]

 Score = 210 (79.0 bits), Expect = 5.9e-16, P = 5.9e-16
 Identities = 44/116 (37%), Positives = 64/116 (55%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             M  ++V+SW  +V+G I  G ++ A+Q F  MP RD V W AMI GY+  +   EA  LF
Sbjct:   164 MPERNVVSWNTLVTGLIRNGDMEKAKQVFDAMPSRDVVSWNAMIKGYIENDGMEEAKLLF 223

Query:    61 PEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA 116
              +M   N+      +      Y YC+ GDV +A R+  +M  ++  +WTAMI G A
Sbjct:   224 GDMSEKNV------VTWTSMVYGYCRYGDVREAYRLFCEMPERNIVSWTAMISGFA 273

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2057986 AT2G36980 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 7.9e-08, P = 7.9e-08
 Identities = 27/97 (27%), Positives = 53/97 (54%)

Query:     6 VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQT 65
             ++  T  ++     G++  ARQ F  MPE D V W  M+  Y R+   +EA+ LF +++ 
Sbjct:     4 LVRLTSKIASLAKSGRIASARQVFDGMPELDTVAWNTMLTSYSRLGLHQEAIALFTQLRF 63

Query:    66 SNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR 102
             S+ +PD+++   IL+       G+V+  +++   ++R
Sbjct:    64 SDAKPDDYSFTAILSTC--ASLGNVKFGRKIQSLVIR 98

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2044797 AT2G35030 [Arabidopsis thaliana (taxid:3702)]

 Score = 211 (79.3 bits), Expect = 3.3e-16, P = 3.3e-16
 Identities = 46/113 (40%), Positives = 68/113 (60%)

Query:     4 KDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEM 63
             K+V++WT +VSGY+   Q+ IA   F +MPER+ V W  MIDGY +  R  +AL LF EM
Sbjct:   107 KNVVTWTAMVSGYLRSKQLSIAEMLFQEMPERNVVSWNTMIDGYAQSGRIDKALELFDEM 166

Query:    64 QTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA 116
                NI     ++V+ L      + G +++A  +  +M R+D  +WTAM+ GLA
Sbjct:   167 PERNIVSWN-SMVKALV-----QRGRIDEAMNLFERMPRRDVVSWTAMVDGLA 213

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2198678 PDE247 "pigment defective 247" [Arabidopsis thaliana (taxid:3702)]

 Score = 191 (72.3 bits), Expect = 8.9e-16, Sum P(2) = 8.9e-16
 Identities = 35/81 (43%), Positives = 53/81 (65%)

Query:     1 MKNKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLF 60
             M++K+ ++W  ++ GY+  GQVD A + F +MPERD + WTAMI+G+++     EAL  F
Sbjct:   135 MEDKNSVTWNTMIDGYMRSGQVDNAAKMFDKMPERDLISWTAMINGFVKKGYQEEALLWF 194

Query:    61 PEMQTSNIRPDEFTIVRILTA 81
              EMQ S ++PD   I+  L A
Sbjct:   195 REMQISGVKPDYVAIIAALNA 215

GO:0005739 "mitochondrion" evidence=ISM

GO:0009451 "RNA modification" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2032955 AT1G25360 "AT1G25360" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 32/106 (30%), Positives = 56/106 (52%)

Query:     4 KDVISWTDIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLRVNRFREALTLFPE 62
             KD  SWT +++GY+  G  D+  +    M +    V + AMI GY+    ++EAL +   
Sbjct:   217 KDERSWTTMMTGYVKNGYFDLGEELLEGMDDNMKLVAYNAMISGYVNRGFYQEALEMVRR 276

Query:    63 MQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTW 108
             M +S I  DEFT   ++ A      G ++  ++V   +LR++ F++
Sbjct:   277 MVSSGIELDEFTYPSVIRAC--ATAGLLQLGKQVHAYVLRREDFSF 320

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_scaffold_44000037 hypothetical protein (635 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	153
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-18
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-18
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-16
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	2e-16
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-13
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	5e-11
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	6e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-07
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-05
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-05
pfam01535	31	pfam01535, PPR, PPR repeat	4e-05
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	7e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.003

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

 Score = 80.7 bits (199), Expect = 2e-18
 Identities = 52/183 (28%), Positives = 80/183 (43%), Gaps = 46/183 (25%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFRE-ALTLFPEM 63
           DV     ++  Y++ G    A + F++M  +D V WTAMI GY + N   + AL  +  M
Sbjct: 322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEK-NGLPDKALETYALM 380

Query: 64  QTSNIRPDEFTIVRILTA------------------------Y---------MYCKCGDV 90
           +  N+ PDE TI  +L+A                        Y         MY KC  +
Sbjct: 381 EQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCI 440

Query: 91  EKAQRVLRKMLRKDKFTWTAMIVGLAISDP-----------FPTIRPDEVTYVGVLSACT 139
           +KA  V   +  KD  +WT++I GL +++              T++P+ VT +  LSAC 
Sbjct: 441 DKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACA 500

Query: 140 HNG 142
             G
Sbjct: 501 RIG 503

Length = 857

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

 Score = 80.3 bits (198), Expect = 3e-18
 Identities = 55/180 (30%), Positives = 81/180 (45%), Gaps = 45/180 (25%)

Query: 12  IVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD 71
           ++S ++  G++  A   F +MPERD   W  ++ GY +   F EAL L+  M  + +RPD
Sbjct: 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPD 186

Query: 72  EFT-----------------------IVR--------ILTAY--MYCKCGDVEKAQRVLR 98
            +T                       +VR        ++ A   MY KCGDV  A+ V  
Sbjct: 187 VYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFD 246

Query: 99  KMLRKDKFTWTAMIVG-------LAISDPFPTIR-----PDEVTYVGVLSACTHNGNETF 146
           +M R+D  +W AMI G       L   + F T+R     PD +T   V+SAC   G+E  
Sbjct: 247 RMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERL 306

Length = 857

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

 Score = 75.3 bits (185), Expect = 1e-16
 Identities = 50/173 (28%), Positives = 70/173 (40%), Gaps = 47/173 (27%)

Query: 12  IVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD 71
           +++ Y+  G V  AR  F +MP RD + W AMI GY       E L LF  M+  ++ PD
Sbjct: 228 LITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPD 287

Query: 72  EFTIVRILTA---------------------------------YMYCKCGDVEKAQRVLR 98
             TI  +++A                                  MY   G   +A++V  
Sbjct: 288 LMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFS 347

Query: 99  KMLRKDKFTWTAMIVGLAISDPFP-------------TIRPDEVTYVGVLSAC 138
           +M  KD  +WTAMI G    +  P              + PDE+T   VLSAC
Sbjct: 348 RMETKDAVSWTAMISGYE-KNGLPDKALETYALMEQDNVSPDEITIASVLSAC 399

Length = 857

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

 Score = 74.9 bits (184), Expect = 2e-16
 Identities = 47/171 (27%), Positives = 74/171 (43%), Gaps = 51/171 (29%)

Query: 20  GQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT---IV 76
           G ++ AR  F  MPE+  V W +M+ GY       EAL L+ EM+ S +  D+FT   ++
Sbjct: 273 GDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMI 332

Query: 77  RILTAY------------------------------MYCKCGDVEKAQRVLRKMLRKDKF 106
           RI +                                +Y K G +E A+ V  +M RK+  
Sbjct: 333 RIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLI 392

Query: 107 TWTAMIVGLA---------------ISDPFPTIRPDEVTYVGVLSACTHNG 142
           +W A+I G                 I++    + P+ VT++ VLSAC ++G
Sbjct: 393 SWNALIAGYGNHGRGTKAVEMFERMIAE---GVAPNHVTFLAVLSACRYSG 440

Length = 697

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

 Score = 64.5 bits (157), Expect = 8e-13
 Identities = 37/142 (26%), Positives = 56/142 (39%), Gaps = 33/142 (23%)

Query: 9   WTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEM--QTS 66
              ++  ++  G +  AR+ F +MPER+   W  +I G +    +REA  LF EM    S
Sbjct: 161 MNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGS 220

Query: 67  NIRPDEF-TIVRILTAY------------------------------MYCKCGDVEKAQR 95
           +  P  F  ++R                                   MY KCGD+E A+ 
Sbjct: 221 DAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARC 280

Query: 96  VLRKMLRKDKFTWTAMIVGLAI 117
           V   M  K    W +M+ G A+
Sbjct: 281 VFDGMPEKTTVAWNSMLAGYAL 302

Length = 697

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

 Score = 59.1 bits (143), Expect = 5e-11
 Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 2/107 (1%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQ 64
           D+++ T +V  Y   G+++ AR  F +MP ++ + W A+I GY    R  +A+ +F  M 
Sbjct: 359 DIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMI 418

Query: 65  TSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAM 111
              + P+  T + +L+A  Y   G  E+   + + M    +    AM
Sbjct: 419 AEGVAPNHVTFLAVLSACRY--SGLSEQGWEIFQSMSENHRIKPRAM 463

Length = 697

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

 Score = 56.0 bits (135), Expect = 6e-10
 Identities = 41/184 (22%), Positives = 72/184 (39%), Gaps = 51/184 (27%)

Query: 6   VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQT 65
           V+    ++  Y     +D A + F  +PE+D + WT++I G    NR  EAL  F +M  
Sbjct: 424 VVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL 483

Query: 66  SNIRPDEFTIVRILTAY---------------------------------MYCKCGDVEK 92
           + ++P+  T++  L+A                                  +Y +CG +  
Sbjct: 484 T-LKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNY 542

Query: 93  A--QRVLRKMLRKDKFTWTAMIVGLAISDPFPT------------IRPDEVTYVGVLSAC 138
           A  Q    +   KD  +W  ++ G                     + PDEVT++ +L AC
Sbjct: 543 AWNQFNSHE---KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCAC 599

Query: 139 THNG 142
           + +G
Sbjct: 600 SRSG 603

Length = 857

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

 Score = 45.5 bits (109), Expect = 1e-07
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT 74
          D V +  +IDGY +  +  EAL LF EM+   I+P+ +T
Sbjct: 2  DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYT 40

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

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

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 29/124 (23%), Positives = 56/124 (45%), Gaps = 16/124 (12%)

Query: 4   KDVISWTDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTL 59
           KDV+SW  +++GY+  G+  +A + F +M E     D V + +++    R     + L  
Sbjct: 552 KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEY 611

Query: 60  FPEMQTSNIRPDEFTIVRILTAY-----MYCKCGDVEKAQRVLRKM-LRKDKFTWTAMIV 113
           F  M+      ++++I   L  Y     +  + G + +A   + KM +  D   W A++ 
Sbjct: 612 FHSME------EKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLN 665

Query: 114 GLAI 117
              I
Sbjct: 666 ACRI 669

Length = 857

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

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 32  MPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVE 91
           +P   Y    A+++  + +   R    ++  +++S   PD++ + R+L   M+ KCG + 
Sbjct: 121 LPASTY---DALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLL--MHVKCGMLI 175

Query: 92  KAQRVLRKMLRKDKFTWTAMIVGL 115
            A+R+  +M  ++  +W  +I GL
Sbjct: 176 DARRLFDEMPERNLASWGTIIGGL 199

Length = 697

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

 Score = 42.9 bits (101), Expect = 2e-05
 Identities = 36/143 (25%), Positives = 64/143 (44%), Gaps = 25/143 (17%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLF 60
           D   +T ++S     G+VD   + F +M     E +   + A+IDG  R  +  +A   +
Sbjct: 471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAY 530

Query: 61  PEMQTSNIRPDEFTIVRILTAYMYC-KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISD 119
             M++ N++PD      +++A   C + G V++A  VL +M               A + 
Sbjct: 531 GIMRSKNVKPDRVVFNALISA---CGQSGAVDRAFDVLAEMK--------------AETH 573

Query: 120 PFPTIRPDEVTYVGVLSACTHNG 142
           P   I PD +T   ++ AC + G
Sbjct: 574 P---IDPDHITVGALMKACANAG 593

Length = 1060

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

 Score = 38.2 bits (90), Expect = 4e-05
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNI 68
          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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 37.8 bits (89), Expect = 7e-05
 Identities = 15/35 (42%), Positives = 19/35 (54%)

Query: 38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE 72
          V +  +IDG  +  R  EAL LF EM+   I PD 
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

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

 Score = 36.2 bits (85), Expect = 4e-04
 Identities = 13/48 (27%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 4  KDVISWTDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGY 47
           DV+++  ++ 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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 35.8 bits (84), Expect = 4e-04
 Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 4/37 (10%)

Query: 84  YCKCGDVEKAQRVLRKMLRK----DKFTWTAMIVGLA 116
           YCK G VE+A ++  +M ++    + +T++ +I GL 
Sbjct: 13  YCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 33.3 bits (77), Expect = 0.003
 Identities = 7/33 (21%), Positives = 15/33 (45%)

Query: 38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP 70
            + A++    +      AL +  EM+ S ++P
Sbjct: 2  ETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	153
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	99.97
PLN03077	857	Protein ECB2; Provisional	99.97
PLN03218	1060	maturation of RBCL 1; Provisional	99.96
PLN03077	857	Protein ECB2; Provisional	99.96
PLN03218	1060	maturation of RBCL 1; Provisional	99.96
PF13041	50	PPR_2: PPR repeat family	99.67
PF13041	50	PPR_2: PPR repeat family	99.56
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.21
PF12854	34	PPR_1: PPR repeat	99.18
PF12854	34	PPR_1: PPR repeat	99.18
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.14
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.11
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.11
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.97
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	98.96
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.92
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.82
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.68
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.65
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.62
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.5
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.48
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.45
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	98.36
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	98.35
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.33
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.31
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.3
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.3
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.28
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.27
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.27
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.21
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.19
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.13
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.1
PRK12370	553	invasion protein regulator; Provisional	98.1
PRK11189	296	lipoprotein NlpI; Provisional	98.08
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.06
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.04
KOG1126	638	consensus DNA-binding cell division cycle control	98.04
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.03
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.01
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.01
PRK15359	144	type III secretion system chaperone protein SscB;	97.93
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.9
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.89
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	97.89
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.87
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.87
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	97.87
PRK15359	144	type III secretion system chaperone protein SscB;	97.87
PRK11189	296	lipoprotein NlpI; Provisional	97.86
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.85
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.85
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.82
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	97.79
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.79
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.78
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.76
PRK12370	553	invasion protein regulator; Provisional	97.72
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.71
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.71
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	97.69
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	97.67
PRK14574	822	hmsH outer membrane protein; Provisional	97.65
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.63
PRK14574	822	hmsH outer membrane protein; Provisional	97.56
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.56
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.55
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	97.55
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	97.55
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	97.51
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.51
KOG2003	840	consensus TPR repeat-containing protein [General f	97.51
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.5
KOG1129	478	consensus TPR repeat-containing protein [General f	97.46
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.44
KOG1126	638	consensus DNA-binding cell division cycle control	97.42
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.39
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	97.35
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.32
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.29
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.28
KOG2003	840	consensus TPR repeat-containing protein [General f	97.27
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.26
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.26
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.23
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	97.23
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.21
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.2
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.16
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.16
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.14
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.13
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	97.13
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.13
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.13
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.12
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.07
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.06
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.03
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.01
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.99
KOG2076	895	consensus RNA polymerase III transcription factor	96.94
PF12688	120	TPR_5: Tetratrico peptide repeat	96.93
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.86
KOG3941	406	consensus Intermediate in Toll signal transduction	96.86
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.84
KOG1129	478	consensus TPR repeat-containing protein [General f	96.79
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	96.71
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.71
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.66
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	96.65
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.58
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	96.56
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	96.56
KOG0547	606	consensus Translocase of outer mitochondrial membr	96.53
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.52
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	96.52
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	96.48
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.44
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.37
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.34
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.34
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.3
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	96.3
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.28
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.24
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.23
PF13371	73	TPR_9: Tetratricopeptide repeat	96.19
KOG3785	557	consensus Uncharacterized conserved protein [Funct	96.17
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.16
KOG3616	1636	consensus Selective LIM binding factor [Transcript	96.08
PRK10803	263	tol-pal system protein YbgF; Provisional	95.97
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	95.94
PRK10803	263	tol-pal system protein YbgF; Provisional	95.86
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.86
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	95.85
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	95.83
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.79
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	95.77
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.72
PF13512	142	TPR_18: Tetratricopeptide repeat	95.66
COG4783	484	Putative Zn-dependent protease, contains TPR repea	95.66
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	95.56
PF13762	145	MNE1: Mitochondrial splicing apparatus component	95.54
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	95.5
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	95.49
PF13371	73	TPR_9: Tetratricopeptide repeat	95.46
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.42
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.39
KOG1128	777	consensus Uncharacterized conserved protein, conta	95.38
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	95.36
KOG1125	579	consensus TPR repeat-containing protein [General f	95.3
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	95.25
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	95.22
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	95.22
KOG1128	777	consensus Uncharacterized conserved protein, conta	95.21
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	95.06
KOG3941	406	consensus Intermediate in Toll signal transduction	94.99
PF12688	120	TPR_5: Tetratrico peptide repeat	94.97
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	94.91
COG4105	254	ComL DNA uptake lipoprotein [General function pred	94.91
PRK14720	906	transcript cleavage factor/unknown domain fusion p	94.85
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	94.81
KOG2047	835	consensus mRNA splicing factor [RNA processing and	94.69
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	94.51
KOG2376	652	consensus Signal recognition particle, subunit Srp	94.44
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.22
KOG2047	835	consensus mRNA splicing factor [RNA processing and	94.08
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	94.0
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	93.97
PRK14720	906	transcript cleavage factor/unknown domain fusion p	93.9
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.86
KOG2076	895	consensus RNA polymerase III transcription factor	93.77
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	93.62
KOG0547	606	consensus Translocase of outer mitochondrial membr	93.54
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	93.49
KOG3060	289	consensus Uncharacterized conserved protein [Funct	93.43
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	93.25
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.15
KOG0553	304	consensus TPR repeat-containing protein [General f	93.0
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	92.97
PLN02789	320	farnesyltranstransferase	92.95
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	92.87
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.72
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	92.71
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.65
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.35
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	92.35
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	92.04
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	92.03
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	91.98
KOG2796	366	consensus Uncharacterized conserved protein [Funct	91.88
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	91.86
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	91.68
PRK15331	165	chaperone protein SicA; Provisional	91.64
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	91.63
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	91.49
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	91.26
KOG0553	304	consensus TPR repeat-containing protein [General f	91.15
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	91.04
PF11848	48	DUF3368: Domain of unknown function (DUF3368); Int	91.0
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	90.98
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	90.46
PF13428	44	TPR_14: Tetratricopeptide repeat	90.38
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	90.36
COG3629	280	DnrI DNA-binding transcriptional activator of the	90.34
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	90.18
KOG0495	913	consensus HAT repeat protein [RNA processing and m	90.06
KOG4340	459	consensus Uncharacterized conserved protein [Funct	89.96
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	89.67
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	89.6
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	89.33
PRK10564	303	maltose regulon periplasmic protein; Provisional	88.99
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	88.95
PF13428	44	TPR_14: Tetratricopeptide repeat	88.91
KOG4570	418	consensus Uncharacterized conserved protein [Funct	88.74
KOG1125	579	consensus TPR repeat-containing protein [General f	88.72
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	88.64
KOG0495	913	consensus HAT repeat protein [RNA processing and m	87.85
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	87.7
PRK04841	903	transcriptional regulator MalT; Provisional	87.65
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	87.63
PRK15331	165	chaperone protein SicA; Provisional	87.18
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	87.02
KOG3060	289	consensus Uncharacterized conserved protein [Funct	86.9
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	86.83
smart00299	140	CLH Clathrin heavy chain repeat homology.	86.7
KOG2041	1189	consensus WD40 repeat protein [General function pr	86.65
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	86.39
COG4700	251	Uncharacterized protein conserved in bacteria cont	86.36
PLN02789	320	farnesyltranstransferase	86.26
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	86.22
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	86.17
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	85.82
COG3118	304	Thioredoxin domain-containing protein [Posttransla	85.03
KOG2376	652	consensus Signal recognition particle, subunit Srp	85.02
PF13431	34	TPR_17: Tetratricopeptide repeat	84.85
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	84.64
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	83.45
PF13934	226	ELYS: Nuclear pore complex assembly	83.4
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	83.28
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	83.26
COG4700	251	Uncharacterized protein conserved in bacteria cont	83.25
PF08311	126	Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro	83.21
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	82.72
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	82.61
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	82.52
COG4455	273	ImpE Protein of avirulence locus involved in tempe	82.46
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	82.37
KOG2610	491	consensus Uncharacterized conserved protein [Funct	82.15
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	81.74
PF03745	62	DUF309: Domain of unknown function (DUF309); Inter	80.97
COG3947	361	Response regulator containing CheY-like receiver a	80.92
PF13929	292	mRNA_stabil: mRNA stabilisation	80.62
COG4455	273	ImpE Protein of avirulence locus involved in tempe	80.52
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	80.26

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

Probab=100.00  E-value=2.2e-32  Score=219.94  Aligned_cols=150  Identities=31%  Similarity=0.521  Sum_probs=134.2

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      .||..+||+||++|++.|++++|.++|++|.++|..+||+||.+|++.|+.++|+++|++|++.|++||..||+++|.+|
T Consensus       256 ~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~  335 (697)
T PLN03081        256 VGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIF  335 (697)
T ss_pred             CccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            46777888888888888888888888888888888888888888888888888888888888888888888888888877


Q ss_pred             ---------------------------------HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC-------
Q 035927           83 ---------------------------------MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------  122 (153)
Q Consensus        83 ---------------------------------~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~-------  122 (153)
                                                       +|+++|++++|.++|++|.++|+.+||+||.+|++.|..+       
T Consensus       336 ~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~  415 (697)
T PLN03081        336 SRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFE  415 (697)
T ss_pred             HhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHH
Confidence                                             7899999999999999999999999999999999998877       


Q ss_pred             -----CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           |+.||..||++++.+|++.|..++|.++|+
T Consensus       416 ~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~  450 (697)
T PLN03081        416 RMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQ  450 (697)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHH
Confidence                 999999999999999999999999999885

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

Probab=99.97  E-value=7e-30  Score=205.49  Aligned_cols=150  Identities=27%  Similarity=0.439  Sum_probs=136.7

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      .||..+||.+++.|++.|++++|.++|++|.+||..+||++|.+|++.|++++|+++|++|++.|+.||..||+.++.+|
T Consensus       155 ~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~  234 (697)
T PLN03081        155 EPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRAS  234 (697)
T ss_pred             CcchHHHHHHHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999998888877777665555443


Q ss_pred             ---------------------------------HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC-------
Q 035927           83 ---------------------------------MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------  122 (153)
Q Consensus        83 ---------------------------------~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~-------  122 (153)
                                                       +|+++|++++|.++|+.|.++|+++||++|.+|++.|.++       
T Consensus       235 ~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~  314 (697)
T PLN03081        235 AGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYY  314 (697)
T ss_pred             hcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHH
Confidence                                             3799999999999999999999999999999999998887       


Q ss_pred             -----CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           |+.||..||++++.+|++.|.+++|.+++.
T Consensus       315 ~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~  349 (697)
T PLN03081        315 EMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHA  349 (697)
T ss_pred             HHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHH
Confidence                 889999999999999999999888888763

>PLN03077 Protein ECB2; Provisional

Probab=99.97  E-value=8.6e-30  Score=208.86  Aligned_cols=150  Identities=35%  Similarity=0.566  Sum_probs=130.5

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      +||..+||++|++|++.|++++|.++|++|++||..+||+||.+|++.|++++|+++|++|++.|++||..||+.+|.+|
T Consensus       219 ~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~  298 (857)
T PLN03077        219 ELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAC  298 (857)
T ss_pred             CcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHH
Confidence            47888888899999999999999999999998899999999999999999999999999998888888888888777776


Q ss_pred             ---------------------------------HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC-------
Q 035927           83 ---------------------------------MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------  122 (153)
Q Consensus        83 ---------------------------------~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~-------  122 (153)
                                                       +|+++|++++|.++|+.|.++|..+||++|.+|++.|.++       
T Consensus       299 ~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~  378 (857)
T PLN03077        299 ELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYA  378 (857)
T ss_pred             HhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHH
Confidence                                             5789999999999999999999999999999999998877       


Q ss_pred             -----CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           |+.||..||++++.+|++.|++++|.+++.
T Consensus       379 ~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~  413 (857)
T PLN03077        379 LMEQDNVSPDEITIASVLSACACLGDLDVGVKLHE  413 (857)
T ss_pred             HHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHH
Confidence                 788888888888888877777777777653

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.96  E-value=9e-29  Score=204.15  Aligned_cols=147  Identities=24%  Similarity=0.404  Sum_probs=88.8

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      +||..+||++|++|++.|++++|.++|++|.    .||..+|+.||.+|++.|++++|.++|++|++.|++||..||+.+
T Consensus       469 ~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsL  548 (1060)
T PLN03218        469 KADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNAL  548 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            3566666666666666666666666666665    356666666666666666666666666666666666666666666


Q ss_pred             HHHHHHhccCChHHHHHHHHhcc------cCChhhHHHHHHHHHhcCCCC------------CCCCCHhHHHHHHHHHhc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKML------RKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVLSACTH  140 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~------~~~~~~~~~li~~~~~~~~~~------------~~~p~~~t~~~ll~~~~~  140 (153)
                      |.+  |++.|++++|.++|+.|.      .||..+|+++|.+|++.|.++            ++.|+..+|+++|.+|++
T Consensus       549 I~a--~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k  626 (1060)
T PLN03218        549 ISA--CGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQ  626 (1060)
T ss_pred             HHH--HHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHh
Confidence            666  366666666666666663      245566666666666665544            455555555555555555


Q ss_pred             CCchhHhhhhc
Q 035927          141 NGNETFVINSC  151 (153)
Q Consensus       141 ~g~~~~a~~~~  151 (153)
                      .|++++|.++|
T Consensus       627 ~G~~deAl~lf  637 (1060)
T PLN03218        627 KGDWDFALSIY  637 (1060)
T ss_pred             cCCHHHHHHHH
Confidence            55555555554

>PLN03077 Protein ECB2; Provisional

Probab=99.96  E-value=7.1e-29  Score=203.46  Aligned_cols=149  Identities=34%  Similarity=0.569  Sum_probs=133.5

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      +||..+||+||++|++.|++++|.++|++|..||..+||+||.+|++.|++++|+++|++|++.|+.||..||+.+|.+|
T Consensus       320 ~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~  399 (857)
T PLN03077        320 AVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSAC  399 (857)
T ss_pred             ccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHH
Confidence            58899999999999999999999999999999999999999999999999999999999999999999988888888876


Q ss_pred             ---------------------------------HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC-------
Q 035927           83 ---------------------------------MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------  122 (153)
Q Consensus        83 ---------------------------------~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~-------  122 (153)
                                                       +|+++|++++|.++|++|.++|+.+||++|.+|++.+..+       
T Consensus       400 ~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~  479 (857)
T PLN03077        400 ACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFR  479 (857)
T ss_pred             hccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHH
Confidence                                             5899999999999999999999999999999999997765       


Q ss_pred             ----CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          123 ----TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       123 ----~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                          +++||..||+++|.+|++.|.++.+.+++
T Consensus       480 ~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~  512 (857)
T PLN03077        480 QMLLTLKPNSVTLIAALSACARIGALMCGKEIH  512 (857)
T ss_pred             HHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHH
Confidence                78899999988888877777777666654

>PLN03218 maturation of RBCL 1; Provisional

Probab=99.96  E-value=1.9e-28  Score=202.19  Aligned_cols=149  Identities=19%  Similarity=0.337  Sum_probs=81.3

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      +||..+|+++|++|++.|++++|.++|++|.+    |+..+||++|.+|++.|++++|+++|++|.+.|+.||..||+++
T Consensus       576 ~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsL  655 (1060)
T PLN03218        576 DPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSAL  655 (1060)
T ss_pred             CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            35555555555555555555555555555542    34455555555555555555555555555555555555555555


Q ss_pred             HHHH---------------------------------HHhccCChHHHHHHHHhcc----cCChhhHHHHHHHHHhcCCC
Q 035927           79 LTAY---------------------------------MYCKCGDVEKAQRVLRKML----RKDKFTWTAMIVGLAISDPF  121 (153)
Q Consensus        79 i~~~---------------------------------~~~~~g~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~~~  121 (153)
                      |.+|                                 +|++.|++++|.++|+.|.    .||..+||++|.+|++.|.+
T Consensus       656 I~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~  735 (1060)
T PLN03218        656 VDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQL  735 (1060)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCH
Confidence            5552                                 1355555555555555553    34555566666666555554


Q ss_pred             C------------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          122 P------------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       122 ~------------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +            |+.||..||+++|.+|++.|++++|.++|
T Consensus       736 eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~  777 (1060)
T PLN03218        736 PKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLL  777 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4            55566666666666666666666655554

>PF13041 PPR_2: PPR repeat family

Probab=99.67  E-value=2.5e-16  Score=85.70  Aligned_cols=50  Identities=38%  Similarity=0.776  Sum_probs=47.6

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927           35 RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      ||..+||++|++|++.|++++|+++|++|++.|++||..||+++|++|  +|
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~--~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGL--CK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH--cC
Confidence            789999999999999999999999999999999999999999999995  64

>PF13041 PPR_2: PPR repeat family

Probab=99.56  E-value=9.4e-15  Score=79.43  Aligned_cols=50  Identities=30%  Similarity=0.644  Sum_probs=46.7

Q ss_pred             CChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhc
Q 035927           70 PDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTH  140 (153)
Q Consensus        70 p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~  140 (153)
                      ||+.+||++|++  |++.|++++|.++|++|.+.                   |++||..||+++|++|++
T Consensus         1 P~~~~yn~li~~--~~~~~~~~~a~~l~~~M~~~-------------------g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISG--YCKAGKFEEALKLFKEMKKR-------------------GIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHH--HHHCcCHHHHHHHHHHHHHc-------------------CCCCCHHHHHHHHHHHcC
Confidence            899999999999  59999999999999999988                   788999999999999875

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.21  E-value=5.6e-10  Score=84.43  Aligned_cols=59  Identities=14%  Similarity=0.292  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      .+..+...|.+.|++++|..+|+++.+   .+..+++.++..+.+.|++++|.+.++.+.+.
T Consensus       109 ~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  170 (389)
T PRK11788        109 ALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKL  170 (389)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHh
Confidence            345555555555555555555555542   23445555555555555555555555555443

>PF12854 PPR_1: PPR repeat

Probab=99.18  E-value=5.1e-11  Score=59.22  Aligned_cols=34  Identities=29%  Similarity=0.581  Sum_probs=29.1

Q ss_pred             CCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           66 SNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        66 ~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      +|+.||..|||++|++  ||+.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~--~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDG--YCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHH--HHHCCCHHHHHHHHHhCc
Confidence            4788999999999998  599999999999998874

>PF12854 PPR_1: PPR repeat

Probab=99.18  E-value=4.5e-11  Score=59.41  Aligned_cols=31  Identities=32%  Similarity=0.688  Sum_probs=26.8

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP   33 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~   33 (153)
                      +||..|||+||++||+.|++++|.++|++|+
T Consensus         4 ~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    4 EPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            5888888888888888888888888888884

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.14  E-value=2.1e-09  Score=81.32  Aligned_cols=145  Identities=8%  Similarity=-0.012  Sum_probs=91.9

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCCC--C------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPER--D------YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~--~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      ++..+++.++..+.+.|++++|.+.++++.+.  +      ...|..+...+.+.|++++|...++++.+.. +.+...+
T Consensus       139 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~  217 (389)
T PRK11788        139 FAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRAS  217 (389)
T ss_pred             chHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHH
Confidence            44556777777777777777777777776431  1      1234556666667777777777777776543 1233344


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhccc--CC--hhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcC
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLR--KD--KFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHN  141 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~--~~--~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~  141 (153)
                      ..+...  |.+.|++++|.++|+++.+  |+  ...++.+..+|...|.++          ...|+...+..+...+.+.
T Consensus       218 ~~la~~--~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~  295 (389)
T PRK11788        218 ILLGDL--ALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQ  295 (389)
T ss_pred             HHHHHH--HHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHh
Confidence            444444  5777777777777777753  22  344666777777776666          4456666666777777777


Q ss_pred             CchhHhhhhc
Q 035927          142 GNETFVINSC  151 (153)
Q Consensus       142 g~~~~a~~~~  151 (153)
                      |+.++|.+++
T Consensus       296 g~~~~A~~~l  305 (389)
T PRK11788        296 EGPEAAQALL  305 (389)
T ss_pred             CCHHHHHHHH
Confidence            7777777665

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.11  E-value=1.3e-09  Score=82.01  Aligned_cols=143  Identities=17%  Similarity=0.253  Sum_probs=114.5

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      +.+..+|.++|.+.|+-...+.|.+++.+-..    -+..+||.+|.+-.-.    ...+++.+|.+...+||..|||++
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~----~~K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYS----VGKKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhh----ccHHHHHHHHHhhcCCchHhHHHH
Confidence            45667999999999999999999999998874    3778888888765433    237899999999999999999999


Q ss_pred             HHHHHHhccCChHHHHHH----HHhc----ccCChhhHHHHHHHHHhcCCCC--------------------CCCC-CHh
Q 035927           79 LTAYMYCKCGDVEKAQRV----LRKM----LRKDKFTWTAMIVGLAISDPFP--------------------TIRP-DEV  129 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~----~~~m----~~~~~~~~~~li~~~~~~~~~~--------------------~~~p-~~~  129 (153)
                      +.+  ..+-|+++.|.+.    +.+|    ++|...+|..+|..+++.++-+                    -+.| |..
T Consensus       280 L~c--~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~  357 (625)
T KOG4422|consen  280 LSC--AAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNK  357 (625)
T ss_pred             HHH--HHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhH
Confidence            998  5999988776555    4444    3578889999999999885553                    3334 346


Q ss_pred             HHHHHHHHHhcCCchhHhhhhc
Q 035927          130 TYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       130 t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .|.+.+..|.+..+.+.|.++-
T Consensus       358 FF~~AM~Ic~~l~d~~LA~~v~  379 (625)
T KOG4422|consen  358 FFQSAMSICSSLRDLELAYQVH  379 (625)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHH
Confidence            6888899999988888888764

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.11  E-value=1.4e-09  Score=81.84  Aligned_cols=113  Identities=14%  Similarity=0.227  Sum_probs=96.4

Q ss_pred             HHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhc----ccC
Q 035927           28 YFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKM----LRK  103 (153)
Q Consensus        28 l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m----~~~  103 (153)
                      ++-+....+..+|.+||.++|+-...+.|.+++++-.....+.+..+||.+|++..|.+      ..++..+|    ..|
T Consensus       198 L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~------~K~Lv~EMisqkm~P  271 (625)
T KOG4422|consen  198 LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSV------GKKLVAEMISQKMTP  271 (625)
T ss_pred             HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc------cHHHHHHHHHhhcCC
Confidence            44444445778999999999999999999999999999999999999999999852322      25666666    458


Q ss_pred             ChhhHHHHHHHHHhcCCCC----------------CCCCCHhHHHHHHHHHhcCCchhH
Q 035927          104 DKFTWTAMIVGLAISDPFP----------------TIRPDEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus       104 ~~~~~~~li~~~~~~~~~~----------------~~~p~~~t~~~ll~~~~~~g~~~~  146 (153)
                      |..|||+++.+.++.|.|+                |+.|...+|-.+|..+.+.++..+
T Consensus       272 nl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k  330 (625)
T KOG4422|consen  272 NLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK  330 (625)
T ss_pred             chHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh
Confidence            9999999999999999888                999999999999999999888754

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

Probab=98.97  E-value=4e-08  Score=80.45  Aligned_cols=112  Identities=13%  Similarity=0.191  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .+..+...+.+.|++++|..+++++..   .+...|..+...+.+.|++++|...++.+.+.+ +.+...+..+...  |
T Consensus       569 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~--~  645 (899)
T TIGR02917       569 PALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADA--Y  645 (899)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHH--H
Confidence            344444444444444444444444431   234445555555555555555555555554332 1223333333333  3


Q ss_pred             hccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           85 CKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      .+.|++++|.+.|+++.+.   +...|..+...+...|.++
T Consensus       646 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  686 (899)
T TIGR02917       646 AVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTE  686 (899)
T ss_pred             HHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHH
Confidence            5555555555555554321   3444444444444444443

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

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

Probab=98.96  E-value=3.2e-08  Score=81.06  Aligned_cols=94  Identities=11%  Similarity=0.201  Sum_probs=49.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...|..+...+.+.|++++|...|+++.+   .+...+..+...+.+.|++++|...++++.+.. +.+..++..+..
T Consensus       599 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  677 (899)
T TIGR02917       599 DSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQ  677 (899)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            3445566666666666666666666666532   244455555555555566666666665555432 123344444444


Q ss_pred             HHHHhccCChHHHHHHHHhc
Q 035927           81 AYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m  100 (153)
                      .  +.+.|++++|.++++.+
T Consensus       678 ~--~~~~~~~~~A~~~~~~~  695 (899)
T TIGR02917       678 L--LLAAKRTESAKKIAKSL  695 (899)
T ss_pred             H--HHHcCCHHHHHHHHHHH
Confidence            3  34444444444444444

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.92  E-value=2.5e-09  Score=52.99  Aligned_cols=35  Identities=43%  Similarity=0.703  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE   72 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   72 (153)
                      .+||++|++|++.|++++|.++|++|++.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999984

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.82  E-value=8.2e-09  Score=50.97  Aligned_cols=33  Identities=24%  Similarity=0.472  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP   70 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p   70 (153)
                      .+||.+|++|++.|+++.|+++|++|++.|++|
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            589999999999999999999999999999988

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.68  E-value=2.6e-06  Score=59.01  Aligned_cols=143  Identities=15%  Similarity=0.202  Sum_probs=93.2

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+..+...+.+.|++++|...+++..+  | +...+..+...+...|++++|.+.+++..+..- .+...+..+... 
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~-  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-NNGDVLNNYGTF-  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHHHHH-
Confidence            34567777778888888888888877642  2 456677777777778888888888877766531 233344444444 


Q ss_pred             HHhccCChHHHHHHHHhcccC-----ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhH
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK-----DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~  146 (153)
                       |...|++++|.+.+++..+.     ....+..+...+...|.++          ...|+ ...+..+...+...|+.++
T Consensus       109 -~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       109 -LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             -HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHH
Confidence             57778888888888777542     2344555555666666555          23333 4556667777777777777


Q ss_pred             hhhhc
Q 035927          147 VINSC  151 (153)
Q Consensus       147 a~~~~  151 (153)
                      |.+.+
T Consensus       188 A~~~~  192 (234)
T TIGR02521       188 ARAYL  192 (234)
T ss_pred             HHHHH
Confidence            77655

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

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.65  E-value=2.7e-06  Score=58.94  Aligned_cols=145  Identities=11%  Similarity=0.108  Sum_probs=112.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +...+..+...+...|++++|.+.+++..+   .+...+..+...+...|++++|...+++..+....| ....+..+..
T Consensus        64 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~  143 (234)
T TIGR02521        64 DYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGL  143 (234)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHH
Confidence            456788889999999999999999988763   356778888889999999999999999998754333 3334444444


Q ss_pred             HHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~  146 (153)
                      .  |.+.|++++|.+.+++..+.   +...+..+...+...+.++          ...| +...+..+...+...|+.++
T Consensus       144 ~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (234)
T TIGR02521       144 C--ALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAA  221 (234)
T ss_pred             H--HHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHH
Confidence            4  79999999999999998643   4667888888888887777          2233 55667778888889999999


Q ss_pred             hhhhc
Q 035927          147 VINSC  151 (153)
Q Consensus       147 a~~~~  151 (153)
                      |.++.
T Consensus       222 a~~~~  226 (234)
T TIGR02521       222 AQRYG  226 (234)
T ss_pred             HHHHH
Confidence            88763

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.

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

Probab=98.62  E-value=5e-08  Score=46.97  Aligned_cols=30  Identities=37%  Similarity=0.774  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      +||+||++|++.|++++|.++|++|++.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            677777777777777777777777777664

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.50  E-value=9.8e-06  Score=65.85  Aligned_cols=143  Identities=10%  Similarity=-0.029  Sum_probs=72.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+..+...+.+.|++++|...++++.  .| +...+..+ ..+.+.|++++|...++.+.+..-.++......+... 
T Consensus       144 ~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~-  221 (656)
T PRK15174        144 SQIFALHLRTLVLMDKELQAISLARTQAQEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDT-  221 (656)
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHH-
Confidence            4455566666666666666666665543  12 22222222 2345566666666666665544222223333333333 


Q ss_pred             HHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC--------------CCCCC-HhHHHHHHHHHhcCCch
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP--------------TIRPD-EVTYVGVLSACTHNGNE  144 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~--------------~~~p~-~~t~~~ll~~~~~~g~~  144 (153)
                       +.+.|+.++|+..+++..+.   +...+..+...+...|.++              ...|+ ...+..+...+.+.|+.
T Consensus       222 -l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~  300 (656)
T PRK15174        222 -LCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQN  300 (656)
T ss_pred             -HHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCH
Confidence             45666666666666665432   3445555555555555543              22343 34455555555566666


Q ss_pred             hHhhhhc
Q 035927          145 TFVINSC  151 (153)
Q Consensus       145 ~~a~~~~  151 (153)
                      ++|...+
T Consensus       301 ~eA~~~l  307 (656)
T PRK15174        301 EKAIPLL  307 (656)
T ss_pred             HHHHHHH
Confidence            6655544

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=98.48  E-value=1e-05  Score=65.25  Aligned_cols=144  Identities=12%  Similarity=-0.056  Sum_probs=115.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...|+.+...+...|++++|...|++..+  | +...|..+...+...|++++|...++...+.. +-+...+..+-.. 
T Consensus       331 a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~-  408 (615)
T TIGR00990       331 AIALNLRGTFKCLKGKHLEALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQL-  408 (615)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH-
Confidence            34577788888899999999999998863  4 46688888888999999999999999997753 2345566666555 


Q ss_pred             HHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~  148 (153)
                       |...|++++|+..|++..+  | +...|..+...+.+.|.++          ...|+ ...++.+...+...|++++|.
T Consensus       409 -~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~  487 (615)
T TIGR00990       409 -HFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAI  487 (615)
T ss_pred             -HHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHH
Confidence             6999999999999999865  3 5677778888888888777          44565 577888999999999999998


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      +.|+
T Consensus       488 ~~~~  491 (615)
T TIGR00990       488 EKFD  491 (615)
T ss_pred             HHHH
Confidence            8764

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

Probab=98.45  E-value=9.3e-07  Score=64.37  Aligned_cols=145  Identities=17%  Similarity=0.252  Sum_probs=90.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC-----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP-----ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVR   77 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~   77 (153)
                      ++...+...+..+.+.++++++.+++++..     .++...|..+...+.+.|+.++|+..+++..+.  .| |....+.
T Consensus       108 ~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~--~P~~~~~~~~  185 (280)
T PF13429_consen  108 GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRKALEL--DPDDPDARNA  185 (280)
T ss_dssp             ----------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHH---TT-HHHHHH
T ss_pred             cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHH
Confidence            556667888888899999999999888854     236778888888888999999999999988875  35 4666777


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGN  143 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~  143 (153)
                      ++..  +...|+.+++.++++...+   .|...|..+..++...|..+          ...| |......+..++.+.|+
T Consensus       186 l~~~--li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~  263 (280)
T PF13429_consen  186 LAWL--LIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDPLWLLAYADALEQAGR  263 (280)
T ss_dssp             HHHH--HCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT----
T ss_pred             HHHH--HHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccccccccccccccccccccccc
Confidence            7777  5888998887777777643   36677788888888887766          3345 67888889999999999


Q ss_pred             hhHhhhhcc
Q 035927          144 ETFVINSCN  152 (153)
Q Consensus       144 ~~~a~~~~~  152 (153)
                      .++|.++.+
T Consensus       264 ~~~A~~~~~  272 (280)
T PF13429_consen  264 KDEALRLRR  272 (280)
T ss_dssp             ---------
T ss_pred             ccccccccc
Confidence            999998764

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=98.36  E-value=2.1e-05  Score=63.96  Aligned_cols=136  Identities=15%  Similarity=0.056  Sum_probs=63.7

Q ss_pred             HHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHH----HHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927           13 VSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFRE----ALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~----a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      ...+.+.|++++|...+++..+  | +...+..+-..+.+.|++++    |+..+++..+.. +.+...+..+...  +.
T Consensus       219 ~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~--l~  295 (656)
T PRK15174        219 VDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADA--LI  295 (656)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHH--HH
Confidence            3344444444444444444431  1 33444444455555555443    455555444321 1123333333333  45


Q ss_pred             ccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCHhH-HHHHHHHHhcCCchhHhhhhc
Q 035927           86 KCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDEVT-YVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~~t-~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +.|++++|...+++..+  | +...+..+...+.+.|.++          ...|+... +..+..++...|+.++|.+.|
T Consensus       296 ~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l  375 (656)
T PRK15174        296 RTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVF  375 (656)
T ss_pred             HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHH
Confidence            55566666555555532  2 3344445555555555555          23454433 222344556666666666554

>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=98.35  E-value=2.2e-05  Score=63.30  Aligned_cols=145  Identities=7%  Similarity=-0.002  Sum_probs=87.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +..+|..+...+...|++++|...|++...  | +...+..+...+.+.|++++|+..+++..+.. +-+...++.+-..
T Consensus       398 ~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~  476 (615)
T TIGR00990       398 DPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKNF-PEAPDVYNYYGEL  476 (615)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            345566666677777777777777766642  2 45566666667777777777777777766531 2234455555444


Q ss_pred             HHHhccCChHHHHHHHHhcccC--C-hh-------hHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK--D-KF-------TWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTH  140 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~--~-~~-------~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~  140 (153)
                        |...|++++|++.|++..+-  + ..       .++.....+...+.++          .+.|+. ..+..+...+.+
T Consensus       477 --~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~  554 (615)
T TIGR00990       477 --LLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQ  554 (615)
T ss_pred             --HHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHH
Confidence              57778888888877776431  1 11       1111111222223333          344544 457788888888


Q ss_pred             CCchhHhhhhcc
Q 035927          141 NGNETFVINSCN  152 (153)
Q Consensus       141 ~g~~~~a~~~~~  152 (153)
                      .|++++|++.|+
T Consensus       555 ~g~~~eAi~~~e  566 (615)
T TIGR00990       555 QGDVDEALKLFE  566 (615)
T ss_pred             ccCHHHHHHHHH
Confidence            888888887764

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

Probab=98.33  E-value=5.7e-07  Score=65.49  Aligned_cols=144  Identities=16%  Similarity=0.151  Sum_probs=78.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~   82 (153)
                      ...+..++.. ...+++++|.+++.+.-  .++...+..++..+.+.++++++.++++...+.. .++|...|..+... 
T Consensus        78 ~~~~~~l~~l-~~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~-  155 (280)
T PF13429_consen   78 PQDYERLIQL-LQDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEI-  155 (280)
T ss_dssp             -----------------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHH-
T ss_pred             cccccccccc-cccccccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHH-
Confidence            3345566666 67888888888877663  2467778889999999999999999999987543 44566666666666 


Q ss_pred             HHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCchhHhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~~~a~  148 (153)
                       +.+.|+.++|++.+++..+  | |....+.++..+...|..+           ..+.|...+..+..++...|+.++|.
T Consensus       156 -~~~~G~~~~A~~~~~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al  234 (280)
T PF13429_consen  156 -YEQLGDPDKALRDYRKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEAL  234 (280)
T ss_dssp             -HHHCCHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHH
T ss_pred             -HHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccc
Confidence             6999999999999999864  5 5677777888877776555           23456677888999999999999999


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      ..|+
T Consensus       235 ~~~~  238 (280)
T PF13429_consen  235 EYLE  238 (280)
T ss_dssp             HHHH
T ss_pred             cccc
Confidence            8774

>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=98.31  E-value=2.4e-05  Score=59.70  Aligned_cols=121  Identities=18%  Similarity=0.125  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      .-.+|+..+...++++.|..+|+++.+.+......+.+.+...++-.+|..++.+..+.. +-|......-.+.  +.+.
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~f--Ll~k  247 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEF--LLSK  247 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHH--HHhc
Confidence            345677777888999999999999998777777788888888888889999998888542 2355555555554  5899


Q ss_pred             CChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCH-hHHHHHHHHHhcCCchhHhhhhcc
Q 035927           88 GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDE-VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        88 g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ++.+.|+++.++..+-                     .|+. .+|..|..+|.+.|+++.|+...|
T Consensus       248 ~~~~lAL~iAk~av~l---------------------sP~~f~~W~~La~~Yi~~~d~e~ALlaLN  292 (395)
T PF09295_consen  248 KKYELALEIAKKAVEL---------------------SPSEFETWYQLAECYIQLGDFENALLALN  292 (395)
T ss_pred             CCHHHHHHHHHHHHHh---------------------CchhHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence            9999999999999763                     3544 578888888888888888775543

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

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.30  E-value=2.1e-05  Score=66.34  Aligned_cols=97  Identities=16%  Similarity=0.022  Sum_probs=51.1

Q ss_pred             CChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC-----
Q 035927           51 NRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP-----  122 (153)
Q Consensus        51 ~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~-----  122 (153)
                      |++++|...+++..+.  .|+...+..+-..  +.+.|+.++|+..+++..+  | +...++.+...+...|.++     
T Consensus       590 Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~--l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~  665 (987)
T PRK09782        590 GQPELALNDLTRSLNI--APSANAYVARATI--YRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREM  665 (987)
T ss_pred             CCHHHHHHHHHHHHHh--CCCHHHHHHHHHH--HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            5555555555555433  2444444444443  4566666666666665543  2 3445555555555555554     


Q ss_pred             -----CCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927          123 -----TIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       123 -----~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                           ...|+ ...+..+-.++...|++++|...|
T Consensus       666 l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l  700 (987)
T PRK09782        666 LERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYA  700 (987)
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence                 33443 344566666666666666666544

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

Probab=98.30  E-value=7.2e-06  Score=62.94  Aligned_cols=112  Identities=15%  Similarity=0.175  Sum_probs=94.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC-C-----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE-R-----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~-~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      +......+++.+....+++++..++.+.+. |     -..|..++|+.|.+.|..++++.+++.=..-|+-||..|||.+
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~L  144 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLL  144 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHH
Confidence            344566778888888889999999999984 2     2346779999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc----CChhhHHHHHHHHHhc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR----KDKFTWTAMIVGLAIS  118 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~  118 (153)
                      |+.  +.+.|++..|.++...|..    .+..++...+.+|.+.
T Consensus       145 md~--fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  145 MDH--FLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHH--HhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            999  5999999999999998853    2667777777777766

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 [].

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.28  E-value=1.1e-06  Score=43.10  Aligned_cols=29  Identities=31%  Similarity=0.639  Sum_probs=27.0

Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      .+||++|.+  |++.|++++|.++|++|.+.
T Consensus         1 ~~~n~li~~--~~~~~~~~~a~~~~~~M~~~   29 (35)
T TIGR00756         1 VTYNTLIDG--LCKAGRVEEALELFKEMLER   29 (35)
T ss_pred             CcHHHHHHH--HHHCCCHHHHHHHHHHHHHc
Confidence            479999999  59999999999999999887

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.

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

Probab=98.27  E-value=8.1e-07  Score=42.58  Aligned_cols=29  Identities=34%  Similarity=0.696  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER   35 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~   35 (153)
                      .+||++|++|++.|++++|.++|++|.+.
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~   29 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRER   29 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHC
Confidence            48999999999999999999999999754

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

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

Probab=98.27  E-value=1.4e-05  Score=50.09  Aligned_cols=82  Identities=16%  Similarity=0.260  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCChhHHHHHHHHHHHhccC--------ChHHHHHHHHhcccCChhhHH
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPDEFTIVRILTAYMYCKCG--------DVEKAQRVLRKMLRKDKFTWT  109 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~~~g--------~~~~a~~~~~~m~~~~~~~~~  109 (153)
                      |-...|..+...+++.....+|+.+++.|+ .|++.+|+.++.+.  ++..        ++-..+.++..|...      
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si--~~R~lD~~~ie~kl~~LLtvYqDiL~~------   98 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSI--AKRELDSEDIENKLTNLLTVYQDILSN------   98 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHH--HHccccchhHHHHHHHHHHHHHHHHHh------
Confidence            345667777778999999999999999999 99999999999993  3322        233455666666655      


Q ss_pred             HHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcC
Q 035927          110 AMIVGLAISDPFPTIRPDEVTYVGVLSACTHN  141 (153)
Q Consensus       110 ~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~  141 (153)
                                   +++|+..||+.++.+..+.
T Consensus        99 -------------~lKP~~etYnivl~~Llkg  117 (120)
T PF08579_consen   99 -------------KLKPNDETYNIVLGSLLKG  117 (120)
T ss_pred             -------------ccCCcHHHHHHHHHHHHHh
Confidence                         6889999999998887653

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 [, , ].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.21  E-value=1.8e-06  Score=42.32  Aligned_cols=30  Identities=27%  Similarity=0.363  Sum_probs=27.6

Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.+|+++|.+|  ++.|+++.|.++|+.|.+.
T Consensus         1 v~ty~~ll~a~--~~~g~~~~a~~~~~~M~~~   30 (34)
T PF13812_consen    1 VHTYNALLRAC--AKAGDPDAALQLFDEMKEQ   30 (34)
T ss_pred             CcHHHHHHHHH--HHCCCHHHHHHHHHHHHHh
Confidence            36899999995  9999999999999999876

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.19  E-value=0.00013  Score=61.75  Aligned_cols=145  Identities=10%  Similarity=-0.018  Sum_probs=101.9

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH-H
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL-T   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li-~   80 (153)
                      |+......+...+.+.|++++|...|+++..  |+...+..+...+.+.|++++|...++..++.+  |+.......+ .
T Consensus       507 Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~  584 (987)
T PRK09782        507 PDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGDNALYWWLHA  584 (987)
T ss_pred             CchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CccHHHHHHHHH
Confidence            4433333334445678999999999987753  344556666777788899999999998888754  4332222222 2


Q ss_pred             HHHHhccCChHHHHHHHHhccc--CChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCchhHh
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--KDKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGNETFV  147 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~~~~a  147 (153)
                      .  ..+.|++++|...+++..+  |+...|..+...+.+.|..+          ...|+. ..++.+-.++...|+.++|
T Consensus       585 ~--l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeA  662 (987)
T PRK09782        585 Q--RYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQS  662 (987)
T ss_pred             H--HHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHH
Confidence            2  2456999999999998864  67778888888888888877          556764 5567777788899999999


Q ss_pred             hhhcc
Q 035927          148 INSCN  152 (153)
Q Consensus       148 ~~~~~  152 (153)
                      ++.|+
T Consensus       663 i~~l~  667 (987)
T PRK09782        663 REMLE  667 (987)
T ss_pred             HHHHH
Confidence            88764

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

Probab=98.13  E-value=2.3e-05  Score=64.04  Aligned_cols=76  Identities=21%  Similarity=0.364  Sum_probs=48.9

Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC----ChhhHHHHHHHHHhcCCCC---------CCCCCHhHHHHHH
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK----DKFTWTAMIVGLAISDPFP---------TIRPDEVTYVGVL  135 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~li~~~~~~~~~~---------~~~p~~~t~~~ll  135 (153)
                      .|+..+|.++++.  -...|+.+.|..+...|++.    +..-|..++.|--...-++         |+.|+..|+.-.+
T Consensus       201 ~~~s~~l~a~l~~--alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g~~~~q~~e~vlrgmqe~gv~p~seT~adyv  278 (1088)
T KOG4318|consen  201 APTSETLHAVLKR--ALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLGINAAQVFEFVLRGMQEKGVQPGSETQADYV  278 (1088)
T ss_pred             CCChHHHHHHHHH--HHhcCchhhHHHHHHHHHHcCCCcccccchhhhhcCccchHHHHHHHHHHHhcCCCCcchhHHHH
Confidence            4777777777777  37777788888887777664    3444555555511111111         7888888888877


Q ss_pred             HHHhcCCchhH
Q 035927          136 SACTHNGNETF  146 (153)
Q Consensus       136 ~~~~~~g~~~~  146 (153)
                      ..+..+|....
T Consensus       279 ip~l~N~~t~~  289 (1088)
T KOG4318|consen  279 IPQLSNGQTKY  289 (1088)
T ss_pred             Hhhhcchhhhh
Confidence            77777665443

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.10  E-value=0.0001  Score=56.57  Aligned_cols=139  Identities=14%  Similarity=0.232  Sum_probs=101.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .|..++....+..+.+...+++++++.   .+......+...+.+.|+.++|..++++..+.  .||....  ++.+  .
T Consensus       231 a~~~l~~~~~~~~~~~~l~~~w~~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~--~  304 (398)
T PRK10747        231 AWIGLMDQAMADQGSEGLKRWWKNQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIP--R  304 (398)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHhCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHh--h
Confidence            445555555566667778888888763   36777788888888888888888888887763  4444222  2222  3


Q ss_pred             hccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           85 CKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ...++.+++.+..+...+  | |.....++-..+.+.+.++          ...|+..++..+...+.+.|+.++|.++|
T Consensus       305 l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~  384 (398)
T PRK10747        305 LKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMR  384 (398)
T ss_pred             ccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            556888888888887754  2 5666777777777777777          67799999999999999999999999887


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      +
T Consensus       385 ~  385 (398)
T PRK10747        385 R  385 (398)
T ss_pred             H
Confidence            5

>PRK12370 invasion protein regulator; Provisional

Probab=98.10  E-value=0.00015  Score=57.90  Aligned_cols=135  Identities=10%  Similarity=-0.003  Sum_probs=86.5

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh-HHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF-TIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-t~~~li~   80 (153)
                      +...+..+-..+...|++++|...|++..  .| +...|..+-..+...|++++|...+++..+.+  |+.. .+..+..
T Consensus       337 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~--P~~~~~~~~~~~  414 (553)
T PRK12370        337 NPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKLD--PTRAAAGITKLW  414 (553)
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCChhhHHHHHH
Confidence            45567777777788888888888888865  34 45677777778888888888888888887653  3322 2223333


Q ss_pred             HHHHhccCChHHHHHHHHhccc---C-ChhhHHHHHHHHHhcCCCC----------CCCCCHhH-HHHHHHHHhcCCc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---K-DKFTWTAMIVGLAISDPFP----------TIRPDEVT-YVGVLSACTHNGN  143 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~-~~~~~~~li~~~~~~~~~~----------~~~p~~~t-~~~ll~~~~~~g~  143 (153)
                      .  +...|++++|++.+++..+   | +...+..+...+...|.++          ...|+..+ .+.+...|.+.|+
T Consensus       415 ~--~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  490 (553)
T PRK12370        415 I--TYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNSE  490 (553)
T ss_pred             H--HHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccHH
Confidence            3  3557888888888887743   3 3444555666666666655          23344333 4444455566663

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.08  E-value=0.00046  Score=50.85  Aligned_cols=143  Identities=15%  Similarity=0.037  Sum_probs=82.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...|+.+-..+.+.|++++|...|++..+  | +...|..+...+...|++++|.+.++...+.  .|+..........
T Consensus        97 ~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l  174 (296)
T PRK11189         97 MADAYNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYL  174 (296)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            445677777777777777777777776642  3 4556666666666777777777777776654  2432211111111


Q ss_pred             HHHhccCChHHHHHHHHhcccC-ChhhHHHHHHHHHhcCCCC----------C------CCCC-HhHHHHHHHHHhcCCc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK-DKFTWTAMIVGLAISDPFP----------T------IRPD-EVTYVGVLSACTHNGN  143 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~----------~------~~p~-~~t~~~ll~~~~~~g~  143 (153)
                        ....++.++|...|.+.... +...|..-+..+ ..+.+.          +      ..|+ ...|..+-..+.+.|+
T Consensus       175 --~~~~~~~~~A~~~l~~~~~~~~~~~~~~~~~~~-~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~  251 (296)
T PRK11189        175 --AESKLDPKQAKENLKQRYEKLDKEQWGWNIVEF-YLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGD  251 (296)
T ss_pred             --HHccCCHHHHHHHHHHHHhhCCccccHHHHHHH-HccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence              24556777777777554322 222332222111 122221          1      1122 3568888999999999


Q ss_pred             hhHhhhhcc
Q 035927          144 ETFVINSCN  152 (153)
Q Consensus       144 ~~~a~~~~~  152 (153)
                      .++|...|+
T Consensus       252 ~~~A~~~~~  260 (296)
T PRK11189        252 LDEAAALFK  260 (296)
T ss_pred             HHHHHHHHH
Confidence            999998875

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

Probab=98.06  E-value=6.1e-05  Score=52.58  Aligned_cols=104  Identities=13%  Similarity=0.163  Sum_probs=83.7

Q ss_pred             hHHHHHHHHhC--CCCCHHHHHHHHHHHHhc-----CChHHHHHHHHHHhhCCCCCChhHHHHHHHHH------------
Q 035927           22 VDIARQYFAQM--PERDYVLWTAMIDGYLRV-----NRFREALTLFPEMQTSNIRPDEFTIVRILTAY------------   82 (153)
Q Consensus        22 ~~~a~~l~~~m--~~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~------------   82 (153)
                      +......|++.  ..+|-.+|..+++.|.+.     |+.+-....+..|.+-|+.-|..+|+.||+.+            
T Consensus        30 l~~~~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ  109 (228)
T PF06239_consen   30 LAPHEELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQ  109 (228)
T ss_pred             ccchHHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHH
Confidence            33456677776  467999999999999864     78888888999999999999999999999985            


Q ss_pred             -HH-hccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCch
Q 035927           83 -MY-CKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNE  144 (153)
Q Consensus        83 -~~-~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~  144 (153)
                       ++ -...+-+-|++++++|...                   |+.||..|+..+++.+.+.+..
T Consensus       110 ~~F~hyp~Qq~c~i~lL~qME~~-------------------gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  110 AEFMHYPRQQECAIDLLEQMENN-------------------GVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             HHhccCcHHHHHHHHHHHHHHHc-------------------CCCCcHHHHHHHHHHhccccHH
Confidence             11 1122347789999999887                   8899999999999998876653

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

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

Probab=98.04  E-value=0.00019  Score=46.23  Aligned_cols=96  Identities=13%  Similarity=0.188  Sum_probs=76.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +......+...+.+.|++++|.+.|++...   .+...|..+-..+.+.|++++|...++...+.+ +.+..++..+-..
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~   94 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAEC   94 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHH
Confidence            445577788889999999999999988753   377888899999999999999999999887664 2334444444443


Q ss_pred             HHHhccCChHHHHHHHHhcccC
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                        |...|+.++|.+.|+...+.
T Consensus        95 --~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        95 --LLALGEPESALKALDLAIEI  114 (135)
T ss_pred             --HHHcCCHHHHHHHHHHHHHh
Confidence              79999999999999998763

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

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

Probab=98.04  E-value=2e-05  Score=62.33  Aligned_cols=140  Identities=14%  Similarity=0.159  Sum_probs=113.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC------------------------------------C-CHHHHHHHHHHHHhcC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE------------------------------------R-DYVLWTAMIDGYLRVN   51 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~------------------------------------~-~~~~~~~li~~~~~~~   51 (153)
                      ...+-.+|...+++++|.++|+..++                                    | .+.+|.++-..|.-.+
T Consensus       356 l~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~Li~~~~~sPesWca~GNcfSLQk  435 (638)
T KOG1126|consen  356 LSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQDLIDTDPNSPESWCALGNCFSLQK  435 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHHHHhhCCCCcHHHHHhcchhhhhh
Confidence            45677889999999999999998873                                    1 4568999999999999


Q ss_pred             ChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHH---HHHHHHhcCCCC-----
Q 035927           52 RFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTA---MIVGLAISDPFP-----  122 (153)
Q Consensus        52 ~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~---li~~~~~~~~~~-----  122 (153)
                      +.+.|+..|++..+.+  | .+.+|+.+=.-  +....++|+|.+-|+.....|+..||+   +-..|.+.+.++     
T Consensus       436 dh~~Aik~f~RAiQld--p~faYayTLlGhE--~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~  511 (638)
T KOG1126|consen  436 DHDTAIKCFKRAIQLD--PRFAYAYTLLGHE--SIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVYLKQEKLEFAEFH  511 (638)
T ss_pred             HHHHHHHHHHHhhccC--CccchhhhhcCCh--hhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhheeccchhhHHHHH
Confidence            9999999999887653  4 66777776666  688899999999999999888888887   455677777766     


Q ss_pred             -----CCCC-CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRP-DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           .+-| +.+....+...+-+.|+.|+|+++|+
T Consensus       512 fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~  547 (638)
T KOG1126|consen  512 FQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYE  547 (638)
T ss_pred             HHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHH
Confidence                 5556 45667778888899999999999886

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

Probab=98.03  E-value=0.00024  Score=46.76  Aligned_cols=122  Identities=9%  Similarity=0.073  Sum_probs=86.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC---CHH-HHH--HHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHH--HH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER---DYV-LWT--AMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIV--RI   78 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~-~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~--~l   78 (153)
                      ..|..++..+. .++...+...++.+...   +.. ...  .+-..+...|++++|...|+......-.|+.....  .+
T Consensus        13 ~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            45777777774 88889998888888743   211 222  23366667899999999999999876223222222  23


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ...  +...|++++|+..++....+.                     +....+...-..+.+.|+.++|...|+
T Consensus        92 A~~--~~~~~~~d~Al~~L~~~~~~~---------------------~~~~~~~~~Gdi~~~~g~~~~A~~~y~  142 (145)
T PF09976_consen   92 ARI--LLQQGQYDEALATLQQIPDEA---------------------FKALAAELLGDIYLAQGDYDEARAAYQ  142 (145)
T ss_pred             HHH--HHHcCCHHHHHHHHHhccCcc---------------------hHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            333  689999999999998865441                     344566677888999999999998875

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

Probab=98.01  E-value=6.7e-05  Score=47.08  Aligned_cols=75  Identities=11%  Similarity=0.316  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----CCHHHHHHHHHHHHhcC--------ChHHHHHHHHHHhhCCCCCChhH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVN--------RFREALTLFPEMQTSNIRPDEFT   74 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~~~~~~~~li~~~~~~~--------~~~~a~~~~~~m~~~~~~p~~~t   74 (153)
                      |-..-|..+...+++...-.+|+.+++     |+..+|+.++++.++..        ++.+.+.++++|...+++|+..|
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            345567777778999999999999874     68899999999999752        35688999999999999999999


Q ss_pred             HHHHHHHH
Q 035927           75 IVRILTAY   82 (153)
Q Consensus        75 ~~~li~~~   82 (153)
                      |+.+++..
T Consensus       107 Ynivl~~L  114 (120)
T PF08579_consen  107 YNIVLGSL  114 (120)
T ss_pred             HHHHHHHH
Confidence            99999983

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 [, , ].

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.01  E-value=0.00022  Score=58.33  Aligned_cols=124  Identities=12%  Similarity=0.117  Sum_probs=99.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .++..+-.|.....+.|+.++|..+++...+  | +......+...+.+.+++++|+...++..+.  .|+..+.-....
T Consensus        84 ~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a  161 (694)
T PRK15179         84 HTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEA  161 (694)
T ss_pred             ccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHH
Confidence            3466788888899999999999999999974  4 6678888899999999999999999999876  477777777777


Q ss_pred             HHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .+ +.+.|+.++|..+|++...++                     |+ ...+.+.-.++-..|+.++|...|
T Consensus       162 ~~-l~~~g~~~~A~~~y~~~~~~~---------------------p~~~~~~~~~a~~l~~~G~~~~A~~~~  211 (694)
T PRK15179        162 KS-WDEIGQSEQADACFERLSRQH---------------------PEFENGYVGWAQSLTRRGALWRARDVL  211 (694)
T ss_pred             HH-HHHhcchHHHHHHHHHHHhcC---------------------CCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            75 899999999999999998753                     33 456666666666677777666555

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.93  E-value=0.00065  Score=44.73  Aligned_cols=92  Identities=8%  Similarity=0.086  Sum_probs=75.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .+..+-..+.+.|++++|...|++...   .+...|..+-..+.+.|++++|...|+...+.+ +.+...+..+-.+  +
T Consensus        26 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~--l  102 (144)
T PRK15359         26 TVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVC--L  102 (144)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHH--H
Confidence            355567788999999999999998763   377889999999999999999999999999753 2355555555554  6


Q ss_pred             hccCChHHHHHHHHhccc
Q 035927           85 CKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~  102 (153)
                      .+.|+.++|...|+...+
T Consensus       103 ~~~g~~~eAi~~~~~Al~  120 (144)
T PRK15359        103 KMMGEPGLAREAFQTAIK  120 (144)
T ss_pred             HHcCCHHHHHHHHHHHHH
Confidence            999999999999999865

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.90  E-value=0.00037  Score=54.88  Aligned_cols=144  Identities=15%  Similarity=0.183  Sum_probs=104.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC----------CC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhC---CCCCC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE----------RD-YVLWTAMIDGYLRVNRFREALTLFPEMQTS---NIRPD   71 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~   71 (153)
                      ..+++.|-.+|.+.|++++|...+++..+          +. ..-++.+...+...+++++|..++....+-   -..++
T Consensus       283 a~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~  362 (508)
T KOG1840|consen  283 AATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGED  362 (508)
T ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhcccc
Confidence            34588888899999999887766665531          22 235777777788889999999998877432   12333


Q ss_pred             h----hHHHHHHHHHHHhccCChHHHHHHHHhcccC-----------ChhhHHHHHHHHHhcCCCC--------------
Q 035927           72 E----FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK-----------DKFTWTAMIVGLAISDPFP--------------  122 (153)
Q Consensus        72 ~----~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-----------~~~~~~~li~~~~~~~~~~--------------  122 (153)
                      .    .+++-+-..  |-+.|++++|.+++++.++.           .-...|.+...|.+.+..+              
T Consensus       363 ~~~~a~~~~nl~~l--~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~  440 (508)
T KOG1840|consen  363 NVNLAKIYANLAEL--YLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMK  440 (508)
T ss_pred             chHHHHHHHHHHHH--HHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHH
Confidence            2    455555555  79999999999999998542           2345677777887775555              


Q ss_pred             CCC---CCH-hHHHHHHHHHhcCCchhHhhhhc
Q 035927          123 TIR---PDE-VTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       123 ~~~---p~~-~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .+.   |+. .+|..|...|.+.|++|+|.++-
T Consensus       441 ~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~  473 (508)
T KOG1840|consen  441 LCGPDHPDVTYTYLNLAALYRAQGNYEAAEELE  473 (508)
T ss_pred             HhCCCCCchHHHHHHHHHHHHHcccHHHHHHHH
Confidence            233   443 67999999999999999998864

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.89  E-value=0.0008  Score=55.82  Aligned_cols=139  Identities=11%  Similarity=0.083  Sum_probs=83.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMY   84 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~   84 (153)
                      -...+......|+.++|+++|.+...   .+...+..+...+.+.|++++|..++++..+.  .|+ ......+...  +
T Consensus        18 ~~d~~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~--l   93 (765)
T PRK10049         18 IADWLQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSL--EPQNDDYQRGLILT--L   93 (765)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH--H
Confidence            34455566667777777777777653   24445667777777777777777777776654  232 2333333333  5


Q ss_pred             hccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCchhHhhhh
Q 035927           85 CKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      .+.|+.++|...+++..+  | +.. +..+...+...|..+          ...|+. ..+..+..++...|..++|++.
T Consensus        94 ~~~g~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~  172 (765)
T PRK10049         94 ADAGQYDEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGA  172 (765)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHH
Confidence            677777777777777643  2 344 666666666665555          445654 4455566666777777777765


Q ss_pred             cc
Q 035927          151 CN  152 (153)
Q Consensus       151 ~~  152 (153)
                      ++
T Consensus       173 l~  174 (765)
T PRK10049        173 ID  174 (765)
T ss_pred             HH
Confidence            43

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

Probab=97.89  E-value=2.7e-05  Score=63.73  Aligned_cols=86  Identities=21%  Similarity=0.337  Sum_probs=64.6

Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC----ChhhHHHHHHHHHhcCCCC-CCCCCHhHHH
Q 035927           58 TLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK----DKFTWTAMIVGLAISDPFP-TIRPDEVTYV  132 (153)
Q Consensus        58 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~li~~~~~~~~~~-~~~p~~~t~~  132 (153)
                      +++..++..|+.|+.+||..+|.-  ||..|+++.|- +|..|.-+    +...|+.++.+...+++.+ .-.|-..||.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiar--Yc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~aDtyt   87 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIAR--YCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLADTYT   87 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHH--HcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCchhHHH
Confidence            566777788888888888888887  68888888887 77777543    4556777777777777777 3457778888


Q ss_pred             HHHHHHhcCCchhH
Q 035927          133 GVLSACTHNGNETF  146 (153)
Q Consensus       133 ~ll~~~~~~g~~~~  146 (153)
                      .++.+|.+.|++.-
T Consensus        88 ~Ll~ayr~hGDli~  101 (1088)
T KOG4318|consen   88 NLLKAYRIHGDLIL  101 (1088)
T ss_pred             HHHHHHHhccchHH
Confidence            88888888887543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.87  E-value=0.00098  Score=57.69  Aligned_cols=138  Identities=11%  Similarity=0.082  Sum_probs=97.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCCh
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDV   90 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~   90 (153)
                      .+...+...|+.++|..+++.- ..+...+..+-..+.+.|++++|++.|+...+.. +.+......+...  |...|+.
T Consensus       578 ~~a~~l~~~G~~~eA~~~l~~~-p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~--~~~~g~~  653 (1157)
T PRK11447        578 ETANRLRDSGKEAEAEALLRQQ-PPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEV--DIAQGDL  653 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH--HHHCCCH
Confidence            3456677888888898888842 2355566777788888889999998888887653 2356667777776  6888899


Q ss_pred             HHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCC----C---CHhHHHHHHHHHhcCCchhHhhhh
Q 035927           91 EKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIR----P---DEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus        91 ~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~----p---~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      ++|++.++...+.   +...+..+..++...|.++          ...    |   +...+..+...+...|+.++|.+.
T Consensus       654 ~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~  733 (1157)
T PRK11447        654 AAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALET  733 (1157)
T ss_pred             HHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999888887653   4555566666666666655          221    2   223455566778899999999988


Q ss_pred             cc
Q 035927          151 CN  152 (153)
Q Consensus       151 ~~  152 (153)
                      |+
T Consensus       734 y~  735 (1157)
T PRK11447        734 YK  735 (1157)
T ss_pred             HH
Confidence            74

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.87  E-value=0.00093  Score=47.22  Aligned_cols=147  Identities=10%  Similarity=0.100  Sum_probs=100.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCCh-hHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPDE-FTI   75 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~-~t~   75 (153)
                      .....+-.+...+.+.|++++|...|++...  |+    ...+..+...+.+.|++++|...++++.+..- .|.. .++
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~  110 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAY  110 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHH
Confidence            3445677777888999999999999998763  32    24677788888999999999999999986531 1221 122


Q ss_pred             HHHHHHHHHhcc--------CChHHHHHHHHhccc--C-ChhhHH-----------------HHHHHHHhcCCCC-----
Q 035927           76 VRILTAYMYCKC--------GDVEKAQRVLRKMLR--K-DKFTWT-----------------AMIVGLAISDPFP-----  122 (153)
Q Consensus        76 ~~li~~~~~~~~--------g~~~~a~~~~~~m~~--~-~~~~~~-----------------~li~~~~~~~~~~-----  122 (153)
                      ..+-..  +.+.        |+.++|.+.|+.+.+  | +...+.                 .+...+.+.|.++     
T Consensus       111 ~~~g~~--~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~  188 (235)
T TIGR03302       111 YLRGLS--NYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINR  188 (235)
T ss_pred             HHHHHH--HHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHH
Confidence            222222  4443        788999999999864  3 222221                 2233444555555     


Q ss_pred             -----CCCC----CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRP----DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p----~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           ...|    ....+..+..++.+.|+.++|...++
T Consensus       189 ~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~  227 (235)
T TIGR03302       189 FETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAA  227 (235)
T ss_pred             HHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                 2223    34678899999999999999988763

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).

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=97.87  E-value=0.00057  Score=56.67  Aligned_cols=137  Identities=11%  Similarity=0.001  Sum_probs=70.1

Q ss_pred             HHHHHhcCChHHHHHHHHhCCCCC-------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-----------CCCCh--
Q 035927           13 VSGYINRGQVDIARQYFAQMPERD-------YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-----------IRPDE--   72 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~~-------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----------~~p~~--   72 (153)
                      ..++...|++++|...|+++.+.+       ......+..++.+.|++++|...++.+.+..           -.|+.  
T Consensus       279 a~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~  358 (765)
T PRK10049        279 ASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDW  358 (765)
T ss_pred             HHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchH
Confidence            445556666666666666553211       1234444445556666666666666665431           01221  


Q ss_pred             -hHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHH
Q 035927           73 -FTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSA  137 (153)
Q Consensus        73 -~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~  137 (153)
                       ..+......  +...|+.++|+++++++.+  | +...+..+...+...|..+          ...||. ..+......
T Consensus       359 ~~a~~~~a~~--l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~  436 (765)
T PRK10049        359 LQGQSLLSQV--AKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWT  436 (765)
T ss_pred             HHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHH
Confidence             112222222  4566666666666666543  2 4555555555555555554          444553 344444455


Q ss_pred             HhcCCchhHhhhhc
Q 035927          138 CTHNGNETFVINSC  151 (153)
Q Consensus       138 ~~~~g~~~~a~~~~  151 (153)
                      +.+.|++++|.+++
T Consensus       437 al~~~~~~~A~~~~  450 (765)
T PRK10049        437 ALDLQEWRQMDVLT  450 (765)
T ss_pred             HHHhCCHHHHHHHH
Confidence            56666666666554

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.87  E-value=0.00032  Score=46.25  Aligned_cols=103  Identities=9%  Similarity=-0.044  Sum_probs=74.4

Q ss_pred             HHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCCh
Q 035927           26 RQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDK  105 (153)
Q Consensus        26 ~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~  105 (153)
                      ..++++..+-+...+..+-..+.+.|++++|...|+...... +.+...+..+-..  +.+.|++++|...|++..+.+ 
T Consensus        13 ~~~~~~al~~~p~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~--~~~~g~~~~A~~~y~~Al~l~-   88 (144)
T PRK15359         13 EDILKQLLSVDPETVYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGT--WMMLKEYTTAINFYGHALMLD-   88 (144)
T ss_pred             HHHHHHHHHcCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHH--HHHHhhHHHHHHHHHHHHhcC-
Confidence            345555544455456667778889999999999999988654 2366666666666  699999999999999998753 


Q ss_pred             hhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          106 FTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       106 ~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                         +.+...+..+-.++...|+.++|.+.|
T Consensus        89 -------------------p~~~~a~~~lg~~l~~~g~~~eAi~~~  115 (144)
T PRK15359         89 -------------------ASHPEPVYQTGVCLKMMGEPGLAREAF  115 (144)
T ss_pred             -------------------CCCcHHHHHHHHHHHHcCCHHHHHHHH
Confidence                               124566666666777777777776655

>PRK11189 lipoprotein NlpI; Provisional

Probab=97.86  E-value=0.00075  Score=49.75  Aligned_cols=93  Identities=17%  Similarity=0.078  Sum_probs=75.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~   82 (153)
                      ..|..+-..+.+.|+.++|...|++..+  | +...|+.+-..+...|++++|.+.|+...+.  .|+ ..++..+-.. 
T Consensus        65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l--~P~~~~a~~~lg~~-  141 (296)
T PRK11189         65 QLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAYLNRGIA-  141 (296)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH-
Confidence            4577788889999999999999988863  3 6789999999999999999999999999875  354 3444444444 


Q ss_pred             HHhccCChHHHHHHHHhcccC
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~  103 (153)
                       +...|++++|.+.|+...+.
T Consensus       142 -l~~~g~~~eA~~~~~~al~~  161 (296)
T PRK11189        142 -LYYGGRYELAQDDLLAFYQD  161 (296)
T ss_pred             -HHHCCCHHHHHHHHHHHHHh
Confidence             68899999999999998653

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

Probab=97.85  E-value=0.00015  Score=53.31  Aligned_cols=114  Identities=18%  Similarity=0.247  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC--CHH---HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER--DYV---LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~--~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      .....+..+.+.+|++.|.+.++.|++.  |..   ...+++....-.+++.+|.-+|+++.+. ..++..+.|.+.-+ 
T Consensus       133 ~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~-  210 (290)
T PF04733_consen  133 LLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVC-  210 (290)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHH-
Confidence            3444556666666666666666666542  211   1222222222233566666666665433 44555666655555 


Q ss_pred             HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCch
Q 035927           83 MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNE  144 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~  144 (153)
                       ....|++++|++++.+..+.+                    +-|..|...++......|+.
T Consensus       211 -~l~~~~~~eAe~~L~~al~~~--------------------~~~~d~LaNliv~~~~~gk~  251 (290)
T PF04733_consen  211 -HLQLGHYEEAEELLEEALEKD--------------------PNDPDTLANLIVCSLHLGKP  251 (290)
T ss_dssp             -HHHCT-HHHHHHHHHHHCCC---------------------CCHHHHHHHHHHHHHHTT-T
T ss_pred             -HHHhCCHHHHHHHHHHHHHhc--------------------cCCHHHHHHHHHHHHHhCCC
Confidence             466666666666666655432                    12456766777777777776

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.

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

Probab=97.85  E-value=0.00029  Score=49.23  Aligned_cols=96  Identities=22%  Similarity=0.373  Sum_probs=73.5

Q ss_pred             CCchhHHHHHHHHHHhc-----CChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcC----------------ChHHHH
Q 035927            3 NKDVISWTDIVSGYINR-----GQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVN----------------RFREAL   57 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~-----g~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~----------------~~~~a~   57 (153)
                      ..|..+|..+++.|.+.     |.++=...-+..|.    +.|..+|+.||+.+-+..                +.+-|+
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i  123 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAI  123 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHH
Confidence            46788999999999876     55555555555555    469999999999988642                246899


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHhccCCh-HHHHHHHHhc
Q 035927           58 TLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDV-EKAQRVLRKM  100 (153)
Q Consensus        58 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~-~~a~~~~~~m  100 (153)
                      +++++|...|+.||..|+..+++.+  ++.+.+ .+.+++.-.|
T Consensus       124 ~lL~qME~~gV~Pd~Et~~~ll~iF--G~~s~p~~K~~rmmYWm  165 (228)
T PF06239_consen  124 DLLEQMENNGVMPDKETEQMLLNIF--GRKSHPMKKYRRMMYWM  165 (228)
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHh--ccccHHHHHHHHHHHHH
Confidence            9999999999999999999999994  776653 4444444444

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

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

Probab=97.82  E-value=0.00095  Score=49.15  Aligned_cols=114  Identities=13%  Similarity=0.131  Sum_probs=86.3

Q ss_pred             HHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC--Ch
Q 035927           13 VSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG--DV   90 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g--~~   90 (153)
                      ...+...|++++|++++++-  .+.......+..+.+.++++.|...++.|++.+   +..+...+..+......|  .+
T Consensus       109 A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~---eD~~l~qLa~awv~l~~g~e~~  183 (290)
T PF04733_consen  109 ATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQID---EDSILTQLAEAWVNLATGGEKY  183 (290)
T ss_dssp             HHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS---CCHHHHHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC---CcHHHHHHHHHHHHHHhCchhH
Confidence            34566789999999999876  566777888999999999999999999999763   335555555553122333  69


Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           91 EKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        91 ~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ++|..+|+++.++                    ..++..+.+.+..+....|++++|.+++
T Consensus       184 ~~A~y~f~El~~~--------------------~~~t~~~lng~A~~~l~~~~~~eAe~~L  224 (290)
T PF04733_consen  184 QDAFYIFEELSDK--------------------FGSTPKLLNGLAVCHLQLGHYEEAEELL  224 (290)
T ss_dssp             CHHHHHHHHHHCC--------------------S--SHHHHHHHHHHHHHCT-HHHHHHHH
T ss_pred             HHHHHHHHHHHhc--------------------cCCCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            9999999999774                    4577888888999999999999998764

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=97.79  E-value=0.0015  Score=56.62  Aligned_cols=69  Identities=16%  Similarity=0.073  Sum_probs=49.2

Q ss_pred             HhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhhh
Q 035927           84 YCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      |.+.|+.++|++.|++..+  | +...+..+...+...|.++          ...|+ ...+..+..++.+.|+.++|.+
T Consensus       613 ~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~  692 (1157)
T PRK11447        613 AQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQR  692 (1157)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHH
Confidence            5777888888888887754  3 5677777777777777766          34454 3456666777778888888887


Q ss_pred             hcc
Q 035927          150 SCN  152 (153)
Q Consensus       150 ~~~  152 (153)
                      +|+
T Consensus       693 ~~~  695 (1157)
T PRK11447        693 TFN  695 (1157)
T ss_pred             HHH
Confidence            764

>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=97.79  E-value=0.0012  Score=42.52  Aligned_cols=78  Identities=18%  Similarity=0.112  Sum_probs=62.5

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC-------------------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE-------------------RDYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      |..++.++|.++++.|+++....+.++.-.                   |+...-.+++.+|+..+++..|+.+++.+.+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            567889999999999999999988877642                   4677788888888888888888888888864


Q ss_pred             C-CCCCChhHHHHHHHHH
Q 035927           66 S-NIRPDEFTIVRILTAY   82 (153)
Q Consensus        66 ~-~~~p~~~t~~~li~~~   82 (153)
                      . +++.+..+|..|++=+
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HcCCCCCHHHHHHHHHHH
Confidence            4 7777788888888765

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

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

Probab=97.78  E-value=4.6e-05  Score=45.37  Aligned_cols=77  Identities=22%  Similarity=0.410  Sum_probs=57.1

Q ss_pred             cCChHHHHHHHHhCCC--C---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHH
Q 035927           19 RGQVDIARQYFAQMPE--R---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~--~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      .|+++.|+.+++++.+  |   +...+-.+...+.+.|++++|..+++. .  +..|+......++.-| +.+.|++++|
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~--~~~~~~~~~~~l~a~~-~~~l~~y~eA   77 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-L--KLDPSNPDIHYLLARC-LLKLGKYEEA   77 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-H--THHHCHHHHHHHHHHH-HHHTT-HHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-h--CCCCCCHHHHHHHHHH-HHHhCCHHHH
Confidence            5789999999999973  3   334455588999999999999999988 3  2334444555555555 8999999999


Q ss_pred             HHHHHh
Q 035927           94 QRVLRK   99 (153)
Q Consensus        94 ~~~~~~   99 (153)
                      ++++++
T Consensus        78 i~~l~~   83 (84)
T PF12895_consen   78 IKALEK   83 (84)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            999875

>TIGR00540 hemY_coli hemY protein

Probab=97.76  E-value=0.00061  Score=52.46  Aligned_cols=125  Identities=10%  Similarity=0.018  Sum_probs=72.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHH-HHHHHHH--HhcCChHHHHHHHHHHhhCCCCCChh--H-HH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLW-TAMIDGY--LRVNRFREALTLFPEMQTSNIRPDEF--T-IV   76 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~-~~li~~~--~~~~~~~~a~~~~~~m~~~~~~p~~~--t-~~   76 (153)
                      +...+-.+...+.+.|+.++|..++++..+  ||...- -.++..+  ...++.+.++..++...+.  .|+..  . ..
T Consensus       262 ~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~--~p~~~~~~ll~  339 (409)
T TIGR00540       262 NIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN--VDDKPKCCINR  339 (409)
T ss_pred             CHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh--CCCChhHHHHH
Confidence            455566666666666666666666666653  322210 0122222  2235556666666555443  23333  2 22


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ++-..  +.+.|++++|.+.|+....-                   ...|+...+..+...+.+.|+.++|.++++
T Consensus       340 sLg~l--~~~~~~~~~A~~~le~a~a~-------------------~~~p~~~~~~~La~ll~~~g~~~~A~~~~~  394 (409)
T TIGR00540       340 ALGQL--LMKHGEFIEAADAFKNVAAC-------------------KEQLDANDLAMAADAFDQAGDKAEAAAMRQ  394 (409)
T ss_pred             HHHHH--HHHcccHHHHHHHHHHhHHh-------------------hcCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            33333  46666666666666632211                   235888888899999999999999988874

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.

>PRK12370 invasion protein regulator; Provisional

Probab=97.72  E-value=0.0011  Score=52.97  Aligned_cols=113  Identities=10%  Similarity=0.020  Sum_probs=81.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--CC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...+..+-..+...|++++|...+++..+  |+ ...+..+...+...|++++|...+++..+.. .|+.......+..
T Consensus       371 ~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~  449 (553)
T PRK12370        371 SADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVM  449 (553)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHH
Confidence            455688888899999999999999999864  43 2333444555667899999999999987653 3555554455555


Q ss_pred             HHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcC
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISD  119 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~  119 (153)
                      + |...|+.++|.+.+.++...   +....+.+...|+..+
T Consensus       450 ~-l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  489 (553)
T PRK12370        450 F-LSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS  489 (553)
T ss_pred             H-HHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH
Confidence            4 78999999999999998643   3444555555555554

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

Probab=97.71  E-value=0.0011  Score=46.17  Aligned_cols=97  Identities=12%  Similarity=0.157  Sum_probs=74.2

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHH-HhcCC--hHHHHHHHHHHhhCCCCC-ChhHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGY-LRVNR--FREALTLFPEMQTSNIRP-DEFTI   75 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~-~~~~~--~~~a~~~~~~m~~~~~~p-~~~t~   75 (153)
                      +.|...|..+-..|...|++++|...|++..+  | +...+..+-..+ .+.|+  .++|..++++..+.+  | +...+
T Consensus        70 P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d--P~~~~al  147 (198)
T PRK10370         70 PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALD--ANEVTAL  147 (198)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC--CCChhHH
Confidence            45677789999999999999999999998863  3 777788777764 56666  589999999998764  4 33444


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ..+-..  +.+.|++++|...|+++.+.
T Consensus       148 ~~LA~~--~~~~g~~~~Ai~~~~~aL~l  173 (198)
T PRK10370        148 MLLASD--AFMQADYAQAIELWQKVLDL  173 (198)
T ss_pred             HHHHHH--HHHcCCHHHHHHHHHHHHhh
Confidence            444443  68999999999999998653

>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=97.71  E-value=0.00066  Score=39.48  Aligned_cols=92  Identities=20%  Similarity=0.292  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      ++..+...+.+.|++++|...+++..+  | +...+..+...+...+++++|.+.++...+..- .+..++..+...  +
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~--~   78 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLA--Y   78 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHH--H
Confidence            466778888999999999999998753  3 446788888888899999999999999877542 233456666665  6


Q ss_pred             hccCChHHHHHHHHhccc
Q 035927           85 CKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~  102 (153)
                      ...|+.+.|.+.+....+
T Consensus        79 ~~~~~~~~a~~~~~~~~~   96 (100)
T cd00189          79 YKLGKYEEALEAYEKALE   96 (100)
T ss_pred             HHHHhHHHHHHHHHHHHc
Confidence            899999999999988754

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=97.69  E-value=0.0041  Score=47.80  Aligned_cols=82  Identities=18%  Similarity=0.122  Sum_probs=44.8

Q ss_pred             HhcCChHHHHHHHHhCCC--CCHHHHH--HHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHhccCChH
Q 035927           17 INRGQVDIARQYFAQMPE--RDYVLWT--AMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMYCKCGDVE   91 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~--~~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~g~~~   91 (153)
                      .+.|+++.|.+.+.++.+  |+.....  .....+...|++++|...++...+..  |+ ......+...  |.+.|+|+
T Consensus       129 ~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~--P~~~~al~ll~~~--~~~~gdw~  204 (398)
T PRK10747        129 QQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA--PRHPEVLRLAEQA--YIRTGAWS  204 (398)
T ss_pred             HHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHH--HHHHHhHH
Confidence            566666666666666653  2322222  12345555666666666666665543  43 3333333333  56666666


Q ss_pred             HHHHHHHhccc
Q 035927           92 KAQRVLRKMLR  102 (153)
Q Consensus        92 ~a~~~~~~m~~  102 (153)
                      +|.+++..+.+
T Consensus       205 ~a~~~l~~l~k  215 (398)
T PRK10747        205 SLLDILPSMAK  215 (398)
T ss_pred             HHHHHHHHHHH
Confidence            66666666653

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

Probab=97.67  E-value=0.0022  Score=48.39  Aligned_cols=144  Identities=15%  Similarity=0.194  Sum_probs=92.0

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCC---------------------------------------------CH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPER---------------------------------------------DY   37 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~---------------------------------------------~~   37 (153)
                      +.++..-.....+|.+.|++.....+..+|.+.                                             ++
T Consensus       184 pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p  263 (400)
T COG3071         184 PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDP  263 (400)
T ss_pred             cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcCh
Confidence            345556777777888888888888888887641                                             23


Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHH
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVG  114 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~  114 (153)
                      ..-.+++.-+.+.|+.++|.++..+-.+++..|.   .-.++..   .+-++.+.-++..++-.+   .++-.+.++-.-
T Consensus       264 ~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L~~~~~~---l~~~d~~~l~k~~e~~l~~h~~~p~L~~tLG~L  337 (400)
T COG3071         264 ELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---LCRLIPR---LRPGDPEPLIKAAEKWLKQHPEDPLLLSTLGRL  337 (400)
T ss_pred             hHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---HHHHHhh---cCCCCchHHHHHHHHHHHhCCCChhHHHHHHHH
Confidence            3344445555555556666666665555554444   2222322   444444444444444322   145566667777


Q ss_pred             HHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          115 LAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       115 ~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      |.+.+.|.          ...|+..+|+.+-.++.+.|+.++|-++++
T Consensus       338 ~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~  385 (400)
T COG3071         338 ALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRR  385 (400)
T ss_pred             HHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHH
Confidence            77777776          677999999999999999999999988764

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.65  E-value=0.0013  Score=54.85  Aligned_cols=138  Identities=11%  Similarity=0.055  Sum_probs=80.9

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCCCCHHH-HHHH--HHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPERDYVL-WTAM--IDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~~~~~-~~~l--i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      .++..+...|+.++|...+++...|+... +..+  ...+...|++++|.++++++.+..- -+...+..++..  |.+.
T Consensus        73 dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~dP-~n~~~l~gLa~~--y~~~  149 (822)
T PRK14574         73 DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSSLKKDP-TNPDLISGMIMT--QADA  149 (822)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHHHHH--Hhhc
Confidence            66777777777777777777776553222 2222  3455566777777777777765531 123333344444  5777


Q ss_pred             CChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC------------CCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           88 GDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------------TIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        88 g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~------------~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ++.++|++.++++.+.+......+..++...+.-.            ...|+ ...+.-++.+..+.|....|.++.
T Consensus       150 ~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~  226 (822)
T PRK14574        150 GRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLA  226 (822)
T ss_pred             CCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            77777777777776543333233444555532111            44454 455566667777777777766653

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

Probab=97.63  E-value=0.00094  Score=42.97  Aligned_cols=93  Identities=14%  Similarity=0.099  Sum_probs=67.9

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +......+...+.+.|++++|...++.....+ +.+...+..+-..  |.+.|+++.|...++...+.+           
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~--~~~~~~~~~A~~~~~~~~~~~-----------   81 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAAC--CQMLKEYEEAIDAYALAAALD-----------   81 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhcC-----------
Confidence            45566777788889999999999999998754 2344555555554  789999999999999987642           


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                               +.+...+..+-..+...|+.++|.+.|
T Consensus        82 ---------p~~~~~~~~la~~~~~~g~~~~A~~~~  108 (135)
T TIGR02552        82 ---------PDDPRPYFHAAECLLALGEPESALKAL  108 (135)
T ss_pred             ---------CCChHHHHHHHHHHHHcCCHHHHHHHH
Confidence                     124555666666777777777776655

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

>PRK14574 hmsH outer membrane protein; Provisional

Probab=97.56  E-value=0.0093  Score=49.96  Aligned_cols=138  Identities=11%  Similarity=0.075  Sum_probs=92.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--CCH--HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--RDY--VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      |...| ...+.|+++.|...|.+..+  |+.  ..+ .++..+...|+.++|+..+++... .-.........+...  |
T Consensus        38 y~~ai-i~~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~-p~n~~~~~llalA~l--y  112 (822)
T PRK14574         38 YDSLI-IRARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQS-SMNISSRGLASAARA--Y  112 (822)
T ss_pred             HHHHH-HHHhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhcc-CCCCCHHHHHHHHHH--H
Confidence            43333 46789999999999999974  432  234 888888899999999999999982 111222333333334  6


Q ss_pred             hccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           85 CKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ...|++++|.++|+++.+.   +...+..++..+...+..+          ...|+...+..++..+...++..+|++.+
T Consensus       113 ~~~gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~  192 (822)
T PRK14574        113 RNEKRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQAS  192 (822)
T ss_pred             HHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHH
Confidence            8889999999999999653   4566666667677775555          55677666633333333344444466554

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

Probab=97.56  E-value=0.0025  Score=44.29  Aligned_cols=66  Identities=17%  Similarity=0.290  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC--hHHHHHHHHhcccC
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD--VEKAQRVLRKMLRK  103 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~--~~~a~~~~~~m~~~  103 (153)
                      |...|..+-..+...|++++|...++...+.. +-+...+..+-.+. |.+.|+  .++|.+++++..+.
T Consensus        72 ~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL-~~~~g~~~~~~A~~~l~~al~~  139 (198)
T PRK10370         72 NSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVL-YYQAGQHMTPQTREMIDKALAL  139 (198)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH-HHhcCCCCcHHHHHHHHHHHHh
Confidence            66778888888888888888888888877653 12455555555542 466676  48888888888654

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

Probab=97.55  E-value=0.00075  Score=49.43  Aligned_cols=121  Identities=12%  Similarity=0.166  Sum_probs=85.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHH-----HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPERDYVL-----WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~-----~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      .+|..+|...-+.+.++.|..+|.+..+.+..+     ..++|..+ ..++.+.|..+|+...+. +.-+...|...++.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~-~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            478999999999999999999999998643333     33333322 256777799999999865 56688888999987


Q ss_pred             HHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC---HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD---EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~---~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                        +.+.|+.+.|..+|++..+.                    +.++   ...|...++.=.+.|+++.+.++.
T Consensus        80 --l~~~~d~~~aR~lfer~i~~--------------------l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~  130 (280)
T PF05843_consen   80 --LIKLNDINNARALFERAISS--------------------LPKEKQSKKIWKKFIEFESKYGDLESVRKVE  130 (280)
T ss_dssp             --HHHTT-HHHHHHHHHHHCCT--------------------SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHH
T ss_pred             --HHHhCcHHHHHHHHHHHHHh--------------------cCchhHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence              69999999999999999874                    1122   235666666666667666665543

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.

>TIGR00540 hemY_coli hemY protein

Probab=97.55  E-value=0.0053  Score=47.29  Aligned_cols=141  Identities=12%  Similarity=0.126  Sum_probs=84.7

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhH-------HHHHHHH
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT-------IVRILTA   81 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t-------~~~li~~   81 (153)
                      ....+...|++++|...++++.+  | +......+...+.+.|++++|.+++..+.+.+..++...       +...+..
T Consensus       159 ~a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~  238 (409)
T TIGR00540       159 RTRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDE  238 (409)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            45666677888888888888763  3 666777888888888888888888888877764322211       1111100


Q ss_pred             ---------H-----------------------HHhccCChHHHHHHHHhccc--CChhh-HHHHHHHHHhc--CCCC--
Q 035927           82 ---------Y-----------------------MYCKCGDVEKAQRVLRKMLR--KDKFT-WTAMIVGLAIS--DPFP--  122 (153)
Q Consensus        82 ---------~-----------------------~~~~~g~~~~a~~~~~~m~~--~~~~~-~~~li~~~~~~--~~~~--  122 (153)
                               +                       .+.+.|+.++|.+++++..+  ||... ...++..+...  +..+  
T Consensus       239 ~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~  318 (409)
T TIGR00540       239 AMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKL  318 (409)
T ss_pred             HHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHH
Confidence                     0                       35667777777777777654  22211 00122222222  1111  


Q ss_pred             --------CCCCCHh---HHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 --------TIRPDEV---TYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 --------~~~p~~~---t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                              ...|+..   ...++-..|.+.|++++|.+.|+
T Consensus       319 ~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le  359 (409)
T TIGR00540       319 EKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFK  359 (409)
T ss_pred             HHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHH
Confidence                    3445544   45677888889999999988775

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=97.55  E-value=0.0019  Score=50.97  Aligned_cols=143  Identities=14%  Similarity=0.192  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC-------CHHHHHH----HHHHHHhcCChHHHHHHHHHHhh---CCCCCChh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER-------DYVLWTA----MIDGYLRVNRFREALTLFPEMQT---SNIRPDEF   73 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~-------~~~~~~~----li~~~~~~~~~~~a~~~~~~m~~---~~~~p~~~   73 (153)
                      ++..|...|...|+++.|..++.+-.+.       +.....+    +-..|...+++++|..+|+++..   ....++..
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~  280 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHP  280 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            4555999999999999999999877532       3333333    44466677999999999999964   22334333


Q ss_pred             H----HHHHHHHHHHhccCChHHHHHHHHhccc-------C---C-hhhHHHHHHHHHhcCCCC---------------C
Q 035927           74 T----IVRILTAYMYCKCGDVEKAQRVLRKMLR-------K---D-KFTWTAMIVGLAISDPFP---------------T  123 (153)
Q Consensus        74 t----~~~li~~~~~~~~g~~~~a~~~~~~m~~-------~---~-~~~~~~li~~~~~~~~~~---------------~  123 (153)
                      .    ++-|-..  |.+.|++++|...++...+       .   . ....+.+...++..+.++               -
T Consensus       281 ~va~~l~nLa~l--y~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  281 AVAATLNNLAVL--YYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             HHHHHHHHHHHH--HhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence            3    3333333  7999999998888777632       1   1 223555666666666666               1


Q ss_pred             CCCC----HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          124 IRPD----EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       124 ~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..++    ..+++.+-..|.+.|++++|.++|+
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k  391 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYK  391 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHH
Confidence            2232    3779999999999999999999875

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

Probab=97.51  E-value=0.00082  Score=51.82  Aligned_cols=142  Identities=15%  Similarity=0.075  Sum_probs=86.2

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .||..+-+.|+-.++-++|...|++-.+-   ....|+.|-.-|..-.+...|.+-++..++-+ +-|-..|=.+=++  
T Consensus       331 ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQa--  407 (559)
T KOG1155|consen  331 ETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQA--  407 (559)
T ss_pred             cceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHH--
Confidence            46666777777777777777777766532   34567777777777677777777776666543 3466666666666  


Q ss_pred             HhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCchhHhhh
Q 035927           84 YCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      |.-.+-..-|+-.|++..+  | |...|.+|-..|.+.+.++           .-..+...+..+-+.|-+.++.++|.+
T Consensus       408 Yeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~  487 (559)
T KOG1155|consen  408 YEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQ  487 (559)
T ss_pred             HHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHH
Confidence            4666666666666666532  2 5555555555555554444           011233556666666666666666655


Q ss_pred             hc
Q 035927          150 SC  151 (153)
Q Consensus       150 ~~  151 (153)
                      .|
T Consensus       488 ~y  489 (559)
T KOG1155|consen  488 YY  489 (559)
T ss_pred             HH
Confidence            54

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.51  E-value=0.0022  Score=39.98  Aligned_cols=95  Identities=16%  Similarity=0.207  Sum_probs=73.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCC-ChhHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRP-DEFTIVRI   78 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p-~~~t~~~l   78 (153)
                      .++-.+...+.+.|++++|...|.++.+  |+    ...+..+...+.+.|++++|.+.++...... -.| ....+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            4567778888999999999999999963  32    3467778899999999999999999998642 111 23344444


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccC
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ...  |.+.|+.++|.+.++.+.+.
T Consensus        83 ~~~--~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        83 GMS--LQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHH--HHHhCChHHHHHHHHHHHHH
Confidence            444  68999999999999998653

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.

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

Probab=97.51  E-value=0.0026  Score=49.26  Aligned_cols=131  Identities=15%  Similarity=0.202  Sum_probs=66.6

Q ss_pred             hcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHH
Q 035927           18 NRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      +.|++++|+++|-++..   .+......+.+-|-...+..+|.+++.+.  ..+.| |......+-..  |-+.|+-..|
T Consensus       536 ~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~--~slip~dp~ilskl~dl--ydqegdksqa  611 (840)
T KOG2003|consen  536 ALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQA--NSLIPNDPAILSKLADL--YDQEGDKSQA  611 (840)
T ss_pred             HhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHh--cccCCCCHHHHHHHHHH--hhcccchhhh
Confidence            44555566555555432   24444444444444445555555554332  22333 33334444443  5666666555


Q ss_pred             HHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHh-cCCchhHhhhhcc
Q 035927           94 QRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACT-HNGNETFVINSCN  152 (153)
Q Consensus        94 ~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~-~~g~~~~a~~~~~  152 (153)
                      .+.+-.--.  | |..+-..+..-|.....++          -+.|+.+-|..++..|. +.|++.+|+++|+
T Consensus       612 fq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk  684 (840)
T KOG2003|consen  612 FQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYK  684 (840)
T ss_pred             hhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHH
Confidence            554332211  1 3333333333333332222          34588888888887777 6788888887764

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

Probab=97.50  E-value=0.00099  Score=51.43  Aligned_cols=75  Identities=15%  Similarity=0.188  Sum_probs=67.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      |..++|..|.+.|..+.+++++..=..    ||..+||.||+.+.+.|++..|.++...|...+...+..|+...+.+|
T Consensus       105 t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~  183 (429)
T PF10037_consen  105 THHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSC  183 (429)
T ss_pred             cHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHH
Confidence            456999999999999999999977554    799999999999999999999999999998888778888888888887

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

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

Probab=97.46  E-value=0.0022  Score=47.76  Aligned_cols=116  Identities=13%  Similarity=0.048  Sum_probs=67.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      |-+.||--|-+.|.+..++..|+.++.+-..  | |+.--..+.+-+-.-++.++|.++++...+.. ..++.....+-.
T Consensus       254 ~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~  332 (478)
T KOG1129|consen  254 PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAV  332 (478)
T ss_pred             CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhHHHHHHHHHHHHhcC-Cccceeeeeeee
Confidence            5556666666777777777777776666542  2 33333334444444456666666666555432 223334444444


Q ss_pred             HHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      +  |.-.++++-|++.++++.+-   +...|+.+--+|...+.++
T Consensus       333 ~--yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  333 G--YFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQID  375 (478)
T ss_pred             c--cccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchh
Confidence            4  56677777777777777653   5666777666666665555

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

Probab=97.44  E-value=0.013  Score=41.95  Aligned_cols=116  Identities=19%  Similarity=0.223  Sum_probs=80.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .|....+.......+.|++..|...|++...   +|...|+.+--+|-+.|+.++|..-|.+..+-  .|+..+.-.=+.
T Consensus        98 ~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlg  175 (257)
T COG5010          98 KDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALEL--APNEPSIANNLG  175 (257)
T ss_pred             ccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHH
Confidence            3444556677888888999999888888864   37888888888888889998888888887764  332222222222


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  122 (153)
                      .. |.-.|+.+.|..++..-..   .|...-..+.......|+++
T Consensus       176 ms-~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~  219 (257)
T COG5010         176 MS-LLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFR  219 (257)
T ss_pred             HH-HHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChH
Confidence            21 5778888888888887642   25556666666666666665

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

Probab=97.42  E-value=0.0019  Score=51.49  Aligned_cols=144  Identities=15%  Similarity=0.146  Sum_probs=84.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC----------------------------------CCHHHHH---HHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE----------------------------------RDYVLWT---AMIDGY   47 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~----------------------------------~~~~~~~---~li~~~   47 (153)
                      .+.+|.++-+.|+-.++-+.|++.|++-.+                                  .|+.+||   .|--.|
T Consensus       420 sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~rhYnAwYGlG~vy  499 (638)
T KOG1126|consen  420 SPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPRHYNAWYGLGTVY  499 (638)
T ss_pred             CcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCchhhHHHHhhhhhe
Confidence            356777777777777777777777777653                                  2333333   344445


Q ss_pred             HhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC--
Q 035927           48 LRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP--  122 (153)
Q Consensus        48 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~--  122 (153)
                      .+.++++.|+-.|+..++  +.|.-...-.-++.. +-+.|+.++|++++++..-  | |+.+---.+..+...+..+  
T Consensus       500 ~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~-~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~ea  576 (638)
T KOG1126|consen  500 LKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRI-QHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEA  576 (638)
T ss_pred             eccchhhHHHHHHHhhhc--CCccchhHHhhhhHH-HHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHH
Confidence            566666666666665554  345444333334442 6777777777777777632  2 3222111222222222211  


Q ss_pred             --------CCCCCH-hHHHHHHHHHhcCCchhHhhhhc
Q 035927          123 --------TIRPDE-VTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       123 --------~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                              .+.|+. ..|..+.+.|-+.|+.+.|+.-|
T Consensus       577 l~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f  614 (638)
T KOG1126|consen  577 LQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHF  614 (638)
T ss_pred             HHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhh
Confidence                    666876 44778889999999999998755

>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=97.39  E-value=0.0022  Score=37.20  Aligned_cols=90  Identities=18%  Similarity=0.201  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhc
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAIS  118 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~  118 (153)
                      .+..+...+...|++++|...+++..+..- .+...+..+...  +...|++++|.+.|+...+..              
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~--~~~~~~~~~a~~~~~~~~~~~--------------   64 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDP-DNADAYYNLAAA--YYKLGKYEEALEDYEKALELD--------------   64 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCC-ccHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhCC--------------
Confidence            355677778889999999999999876531 233445445554  688999999999999986642              


Q ss_pred             CCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          119 DPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       119 ~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                            +.+...+..+...+...|+.++|.+.+
T Consensus        65 ------~~~~~~~~~~~~~~~~~~~~~~a~~~~   91 (100)
T cd00189          65 ------PDNAKAYYNLGLAYYKLGKYEEALEAY   91 (100)
T ss_pred             ------CcchhHHHHHHHHHHHHHhHHHHHHHH
Confidence                  123356777778888888888887765

>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=97.35  E-value=0.0037  Score=40.34  Aligned_cols=66  Identities=18%  Similarity=0.247  Sum_probs=56.6

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHH--h-------------hCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEM--Q-------------TSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m--~-------------~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      |..++..+|-++++.|+++...++++..  +             .....|+..+..+++.+  |+..|++..|.++.+.+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~s--f~~n~~i~~al~~vd~f   78 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHS--FGYNGDIFSALKLVDFF   78 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHH--HHhcccHHHHHHHHHHH
Confidence            4678899999999999999999988765  1             12356999999999999  69999999999999999


Q ss_pred             ccC
Q 035927          101 LRK  103 (153)
Q Consensus       101 ~~~  103 (153)
                      .+.
T Consensus        79 s~~   81 (126)
T PF12921_consen   79 SRK   81 (126)
T ss_pred             HHH
Confidence            765

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

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

Probab=97.32  E-value=0.0099  Score=42.08  Aligned_cols=141  Identities=13%  Similarity=0.172  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      +...|--.|.+.|+...|..-+++..+  | +..+|.++-..|-+.|+.+.|.+-|+...+.  .|+.....-=-+++ +
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG~F-L  113 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSL--APNNGDVLNNYGAF-L  113 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc--CCCccchhhhhhHH-H
Confidence            456677788899999999999988874  3 5668888888888999999999999888765  35444433344454 6


Q ss_pred             hccCChHHHHHHHHhccc-CC----hhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhh
Q 035927           85 CKCGDVEKAQRVLRKMLR-KD----KFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~-~~----~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~  148 (153)
                      |..|++++|...|+.... |+    ..+|..+--+..+.|.+.          ..-|+ ..+...+.......|+.-.|.
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar  193 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPAR  193 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHH
Confidence            889999999999988754 42    345555555555556655          23343 355666667777777777666


Q ss_pred             hhc
Q 035927          149 NSC  151 (153)
Q Consensus       149 ~~~  151 (153)
                      ..+
T Consensus       194 ~~~  196 (250)
T COG3063         194 LYL  196 (250)
T ss_pred             HHH
Confidence            554

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

Probab=97.29  E-value=0.0076  Score=45.02  Aligned_cols=87  Identities=17%  Similarity=0.222  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      +.+.-|.-+...|+...|.++-.+..-|+..-|-..+++++..+++++-..+-.   +   +-+.+.|..++.+|  .+.
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~---s---kKsPIGyepFv~~~--~~~  250 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAK---S---KKSPIGYEPFVEAC--LKY  250 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHh---C---CCCCCChHHHHHHH--HHC
Confidence            345567777888999999999999998999999999999999999987665432   2   22458899999997  788


Q ss_pred             CChHHHHHHHHhccc
Q 035927           88 GDVEKAQRVLRKMLR  102 (153)
Q Consensus        88 g~~~~a~~~~~~m~~  102 (153)
                      |..++|..++.++..
T Consensus       251 ~~~~eA~~yI~k~~~  265 (319)
T PF04840_consen  251 GNKKEASKYIPKIPD  265 (319)
T ss_pred             CCHHHHHHHHHhCCh
Confidence            889999988888443

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.28  E-value=0.016  Score=38.93  Aligned_cols=89  Identities=12%  Similarity=-0.013  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      ..|..+...+...|++++|...|++..  .+    ...+|..+-..+.+.|+.++|+..++...+.. +....++..+..
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~  114 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHH
Confidence            346677777778888888888888774  22    23467778788888888888888888877542 122333443333


Q ss_pred             HHHHh-------ccCChHHHHHHHH
Q 035927           81 AYMYC-------KCGDVEKAQRVLR   98 (153)
Q Consensus        81 ~~~~~-------~~g~~~~a~~~~~   98 (153)
                      .  |.       +.|+++.|+..++
T Consensus       115 i--~~~~~~~~~~~g~~~~A~~~~~  137 (168)
T CHL00033        115 I--CHYRGEQAIEQGDSEIAEAWFD  137 (168)
T ss_pred             H--HHHhhHHHHHcccHHHHHHHHH
Confidence            3  34       6777664444443

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

Probab=97.27  E-value=0.017  Score=45.04  Aligned_cols=135  Identities=15%  Similarity=0.079  Sum_probs=87.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .+.-.+.+.|--..+..+|++++-+..+   .|+...+-|-+.|-+.|+-.+|.+.+-+--+ =++.+..|..++-..  
T Consensus       559 evl~qianiye~led~aqaie~~~q~~slip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ay--  635 (840)
T KOG2003|consen  559 EVLVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAY--  635 (840)
T ss_pred             HHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHH--
Confidence            3444566666667777777777766653   2677777777777777777777665543221 134466666666554  


Q ss_pred             HhccCChHHHHHHHHhc--ccCChhhHHHHHHHHHhc-CCCC-----------CCCCCHhHHHHHHHHHhcCCch
Q 035927           84 YCKCGDVEKAQRVLRKM--LRKDKFTWTAMIVGLAIS-DPFP-----------TIRPDEVTYVGVLSACTHNGNE  144 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m--~~~~~~~~~~li~~~~~~-~~~~-----------~~~p~~~t~~~ll~~~~~~g~~  144 (153)
                      |....=+++++..|++.  .+|+..-|-.|+..|.++ |.++           .++-|.....-+++-|...|..
T Consensus       636 yidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl~  710 (840)
T KOG2003|consen  636 YIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGLK  710 (840)
T ss_pred             HHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccch
Confidence            57777777777777764  577777777777776665 4444           4445667777777777776654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.26  E-value=0.0062  Score=37.86  Aligned_cols=95  Identities=9%  Similarity=0.053  Sum_probs=63.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      .++-.+...+.+.|++++|.+.++.+.+..- .| .......+...  +.+.|+++.|.+.|+.+.+.+.          
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~A~~~~~~~~~~~p----------   70 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEA--YYAQGKYADAAKAFLAVVKKYP----------   70 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHH--HHhhccHHHHHHHHHHHHHHCC----------
Confidence            3556677788899999999999999986431 11 12233344444  7999999999999999875310          


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                             +-......+..+..++.+.|+.++|.+.+
T Consensus        71 -------~~~~~~~~~~~~~~~~~~~~~~~~A~~~~   99 (119)
T TIGR02795        71 -------KSPKAPDALLKLGMSLQELGDKEKAKATL   99 (119)
T ss_pred             -------CCCcccHHHHHHHHHHHHhCChHHHHHHH
Confidence                   01112344556666666777777776655

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.

>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=97.26  E-value=0.0028  Score=35.73  Aligned_cols=52  Identities=23%  Similarity=0.475  Sum_probs=36.1

Q ss_pred             HhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           48 LRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        48 ~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      .+.|++++|+.+|+...+..  | +....-.+..+  |.+.|++++|.++++.+...
T Consensus         2 l~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~--~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN--PDNPEARLLLAQC--YLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT--TTSHHHHHHHHHH--HHHTT-HHHHHHHHHCCHGG
T ss_pred             hhccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHH
Confidence            46788888888888887652  4 44444445554  68888888888888888654

...

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

Probab=97.23  E-value=0.0094  Score=47.99  Aligned_cols=141  Identities=15%  Similarity=0.159  Sum_probs=84.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~   82 (153)
                      ..||.|.+++-..|++.+|...+.+-..  | -..+.+.|-..+-..|.+++|..+|....+-  .|. ...++-+-.. 
T Consensus       321 ~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i-  397 (966)
T KOG4626|consen  321 DAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASI-  397 (966)
T ss_pred             HHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHH-
Confidence            3466666666666666666666665542  2 2344555556666666666666666655542  232 2334444443 


Q ss_pred             HHhccCChHHHHHHHHhccc--CC-hhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCchhHhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLR--KD-KFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~~~~a~  148 (153)
                       |-+.|++++|+.-+++..+  |+ .-.|+.+-..|-..|+.+          .+.|.- ..++.+-..|-..|++.+|+
T Consensus       398 -~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI  476 (966)
T KOG4626|consen  398 -YKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAI  476 (966)
T ss_pred             -HHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHH
Confidence             5677777777777776643  33 335555555555555555          455653 55777777778888888877


Q ss_pred             hhc
Q 035927          149 NSC  151 (153)
Q Consensus       149 ~~~  151 (153)
                      +-|
T Consensus       477 ~sY  479 (966)
T KOG4626|consen  477 QSY  479 (966)
T ss_pred             HHH
Confidence            765

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

Probab=97.23  E-value=0.009  Score=48.10  Aligned_cols=61  Identities=13%  Similarity=0.122  Sum_probs=51.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      ..+|+.+-+.+-..|++++|..+++.+.+  | ....|-.+-.++...|+.+.|.+.|.+.++-
T Consensus       116 ae~ysn~aN~~kerg~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~alql  179 (966)
T KOG4626|consen  116 AEAYSNLANILKERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEALQL  179 (966)
T ss_pred             HHHHHHHHHHHHHhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc
Confidence            35788899999999999999999999864  3 5678888999999999999888888777664

>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=97.21  E-value=0.002  Score=42.25  Aligned_cols=66  Identities=15%  Similarity=0.228  Sum_probs=33.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh-----CCCCCChhH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT-----SNIRPDEFT   74 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t   74 (153)
                      ...++..+...|++++|..+..+...  | +...|..+|.++.+.|+..+|...|+.+.+     -|+.|+..+
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            33444455556666666666666542  2 555666666666666666666666665532     356665544

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

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

Probab=97.20  E-value=0.041  Score=39.09  Aligned_cols=142  Identities=11%  Similarity=0.018  Sum_probs=105.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +..+|..+...|-+.|..+.|.+-|++-.+   .+....|.---.+|..|.+++|...|++......-| -..||.-+.-
T Consensus        68 ~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~  147 (250)
T COG3063          68 YYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGL  147 (250)
T ss_pred             cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHH
Confidence            345699999999999999999999998763   366777777778889999999999999998875433 3345554444


Q ss_pred             HHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~~~  146 (153)
                      +  ..+.|+.+.|...|++-.+.   ...+.-.+..-..+.+..-           +..++..+...-|+---..|+-+.
T Consensus       148 C--al~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~  225 (250)
T COG3063         148 C--ALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAA  225 (250)
T ss_pred             H--HhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHHHHHHHhcccccHHHHHHHHHHHHHhccHHH
Confidence            3  58999999999999998653   3444445555555554443           455888888888887777787766


Q ss_pred             hh
Q 035927          147 VI  148 (153)
Q Consensus       147 a~  148 (153)
                      +-
T Consensus       226 a~  227 (250)
T COG3063         226 AQ  227 (250)
T ss_pred             HH
Confidence            53

>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=97.16  E-value=0.0013  Score=37.10  Aligned_cols=61  Identities=18%  Similarity=0.296  Sum_probs=49.7

Q ss_pred             HhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927           17 INRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      .+.|++++|.++|++..  .| +...+-.+...+.+.|++++|..+++.....  .|+...|..++
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            46899999999999986  34 7788889999999999999999999999875  46656665554

...

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

Probab=97.16  E-value=0.012  Score=43.92  Aligned_cols=135  Identities=13%  Similarity=0.133  Sum_probs=82.1

Q ss_pred             HHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927           14 SGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      ..+...|++++|..++++..+  | +...+.. ...+..    .+....+...+..  ..+..|+......++..+ +..
T Consensus        51 ~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~-~~~  126 (355)
T cd05804          51 LSAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFG-LEE  126 (355)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHH-HHH
Confidence            345667888888888887652  3 3434442 222222    3444444444433  122234433333333332 688


Q ss_pred             cCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CC---CCCH--hHHHHHHHHHhcCCchhHhh
Q 035927           87 CGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TI---RPDE--VTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~---~p~~--~t~~~ll~~~~~~g~~~~a~  148 (153)
                      .|++++|.+.+++..+  | +...+..+...+...|.++          ..   .|+.  ..|..+...+...|+.++|.
T Consensus       127 ~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~  206 (355)
T cd05804         127 AGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAAL  206 (355)
T ss_pred             cCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHH
Confidence            8999999999888854  2 4666777777777777766          22   1333  34667888889999999998


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      ++|+
T Consensus       207 ~~~~  210 (355)
T cd05804         207 AIYD  210 (355)
T ss_pred             HHHH
Confidence            8774

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.

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

Probab=97.14  E-value=0.014  Score=45.38  Aligned_cols=125  Identities=18%  Similarity=0.139  Sum_probs=77.0

Q ss_pred             HhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHH
Q 035927           17 INRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      ...|++++|+..++.+.  .| |+.-+....+.+.+.++.++|.+.++.++..  .|+.........- +|.+.|++++|
T Consensus       317 ~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~-all~~g~~~ea  393 (484)
T COG4783         317 YLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQ-ALLKGGKPQEA  393 (484)
T ss_pred             HHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHH-HHHhcCChHHH
Confidence            34566777777777764  34 5556666667777788888888888887764  4654333333332 26788888888


Q ss_pred             HHHHHhcccC---ChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhh
Q 035927           94 QRVLRKMLRK---DKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus        94 ~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      +++++.....   |...|..+..+|...|...      .-....-.+++..|++++|+..
T Consensus       394 i~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~------~a~~A~AE~~~~~G~~~~A~~~  447 (484)
T COG4783         394 IRILNRYLFNDPEDPNGWDLLAQAYAELGNRA------EALLARAEGYALAGRLEQAIIF  447 (484)
T ss_pred             HHHHHHHhhcCCCCchHHHHHHHHHHHhCchH------HHHHHHHHHHHhCCCHHHHHHH
Confidence            8888777542   5666666666666665433      2223344555556666655543

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.13  E-value=0.026  Score=37.70  Aligned_cols=74  Identities=11%  Similarity=-0.016  Sum_probs=42.1

Q ss_pred             HHHHHhCC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           26 RQYFAQMP-ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        26 ~~l~~~m~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +..+..+. +.+....-.+-..+...|++++|..+|+....-  -|....|--=+.+| +-..|++++|+..|.....
T Consensus        23 l~~l~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~-~Q~~g~~~~AI~aY~~A~~   97 (157)
T PRK15363         23 LRMLLDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGEC-CQAQKHWGEAIYAYGRAAQ   97 (157)
T ss_pred             HHHHHCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHH-HHHHhhHHHHHHHHHHHHh
Confidence            33444444 344444445555555677777777777766553  24444444444444 5677777777777776643

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

Probab=97.13  E-value=0.012  Score=43.69  Aligned_cols=100  Identities=18%  Similarity=0.240  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-CCH------HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-RDY------VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      +--+|-+.|-+.|.+|.|+++-..+.. ||.      ..--.|-.-|-..|-++.|+++|..+.+.|. .-......++.
T Consensus        71 ~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~e-fa~~AlqqLl~  149 (389)
T COG2956          71 AHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEGE-FAEGALQQLLN  149 (389)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcchh-hhHHHHHHHHH
Confidence            345677788889999999999888764 432      2345566666778889999999988887653 34456677777


Q ss_pred             HHHHhccCChHHHHHHHHhcccCChhhHHH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRKDKFTWTA  110 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  110 (153)
                      .  |-+..+|++|+++-+++.+.+...|+.
T Consensus       150 I--YQ~treW~KAId~A~~L~k~~~q~~~~  177 (389)
T COG2956         150 I--YQATREWEKAIDVAERLVKLGGQTYRV  177 (389)
T ss_pred             H--HHHhhHHHHHHHHHHHHHHcCCccchh
Confidence            7  688889999988888776544333333

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

Probab=97.13  E-value=0.012  Score=44.53  Aligned_cols=87  Identities=15%  Similarity=0.125  Sum_probs=71.1

Q ss_pred             HHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC
Q 035927           13 VSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD   89 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~   89 (153)
                      ...+...|++++|+++|++..+  | +...|..+..++.+.|++++|+..+++.++.. +.+...|..+-.+  |.+.|+
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~--~~~lg~   85 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTA--CMKLEE   85 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHH--HHHhCC
Confidence            4567788999999999999873  3 67788889999999999999999999998753 2245555555555  699999


Q ss_pred             hHHHHHHHHhccc
Q 035927           90 VEKAQRVLRKMLR  102 (153)
Q Consensus        90 ~~~a~~~~~~m~~  102 (153)
                      +++|+..|++..+
T Consensus        86 ~~eA~~~~~~al~   98 (356)
T PLN03088         86 YQTAKAALEKGAS   98 (356)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999999865

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.13  E-value=0.032  Score=37.66  Aligned_cols=78  Identities=15%  Similarity=0.130  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILT   80 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~   80 (153)
                      .+..+...+.+.|++++|...|++..+  ++    ...+..+...+.+.|++++|...+++..+.  .|+ ...+..+..
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~  114 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHH
Confidence            466666777778888888888877652  22    356777777788888888888888887764  243 333333333


Q ss_pred             HHHHhccCC
Q 035927           81 AYMYCKCGD   89 (153)
Q Consensus        81 ~~~~~~~g~   89 (153)
                      .  |...|+
T Consensus       115 ~--~~~~g~  121 (172)
T PRK02603        115 I--YHKRGE  121 (172)
T ss_pred             H--HHHcCC
Confidence            2  566555

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

Probab=97.12  E-value=0.0026  Score=35.59  Aligned_cols=56  Identities=16%  Similarity=0.258  Sum_probs=34.9

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           44 IDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        44 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      -..+.+.|++++|...|++.++..  |+..-....+.-+ +.+.|++++|...|+...+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~-~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRI-LYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHH-HHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHH
Confidence            345566777777777777777654  5444444444443 6777777777777777643

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

Probab=97.07  E-value=0.032  Score=43.66  Aligned_cols=90  Identities=21%  Similarity=0.282  Sum_probs=73.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      |=..+..=-..|++..|.++|++-.  +|+...|.+.|+.=.+-..++.|..+++.++-..  |++.+|--..+-  =.+
T Consensus       144 WyKY~ymEE~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~H--P~v~~wikyarF--E~k  219 (677)
T KOG1915|consen  144 WYKYIYMEEMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVH--PKVSNWIKYARF--EEK  219 (677)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheec--ccHHHHHHHHHH--HHh
Confidence            3334444556788999999998875  6899999999999999999999999999998543  899888888876  378


Q ss_pred             cCChHHHHHHHHhccc
Q 035927           87 CGDVEKAQRVLRKMLR  102 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~  102 (153)
                      +|....+..+|....+
T Consensus       220 ~g~~~~aR~VyerAie  235 (677)
T KOG1915|consen  220 HGNVALARSVYERAIE  235 (677)
T ss_pred             cCcHHHHHHHHHHHHH
Confidence            9999999998887754

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

Probab=97.06  E-value=0.013  Score=42.46  Aligned_cols=50  Identities=20%  Similarity=0.363  Sum_probs=27.8

Q ss_pred             CChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           51 NRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        51 ~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.+.+|.-+|++|.++ ..|+..+.+...-++  ...|++++|+.+++....+
T Consensus       187 ek~qdAfyifeE~s~k-~~~T~~llnG~Av~~--l~~~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  187 EKIQDAFYIFEELSEK-TPPTPLLLNGQAVCH--LQLGRYEEAESLLEEALDK  236 (299)
T ss_pred             hhhhhHHHHHHHHhcc-cCCChHHHccHHHHH--HHhcCHHHHHHHHHHHHhc
Confidence            3455566666665442 345555555555553  5566666666666665543

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

Probab=97.03  E-value=0.0012  Score=39.22  Aligned_cols=79  Identities=15%  Similarity=0.239  Sum_probs=55.1

Q ss_pred             cCChHHHHHHHHHHhhCCC-CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-
Q 035927           50 VNRFREALTLFPEMQTSNI-RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-  127 (153)
Q Consensus        50 ~~~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-  127 (153)
                      .|+++.|+.+++++.+..- .|+...+-.+..+  |.+.|++++|..+++. .+.                     .|+ 
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~--~~~~~~y~~A~~~~~~-~~~---------------------~~~~   57 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQC--YFQQGKYEEAIELLQK-LKL---------------------DPSN   57 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHH--HHHTTHHHHHHHHHHC-HTH---------------------HHCH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHH--HHHCCCHHHHHHHHHH-hCC---------------------CCCC
Confidence            5789999999999987642 2233333334444  7999999999999999 332                     233 


Q ss_pred             HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          128 EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ......+..+|.+.|++++|+++|.
T Consensus        58 ~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen   58 PDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            3444455788889999999998874

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

Probab=97.01  E-value=0.0075  Score=39.58  Aligned_cols=84  Identities=17%  Similarity=0.285  Sum_probs=61.4

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC--CCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE--RDY----VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~--~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      +-..+...|++++|...|+....  ++.    ...-.|...+...|++++|+..++......+.|  . +..+.+-. |.
T Consensus        54 lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~~~~~~--~-~~~~~Gdi-~~  129 (145)
T PF09976_consen   54 LAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQIPDEAFKA--L-AAELLGDI-YL  129 (145)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccCcchHH--H-HHHHHHHH-HH
Confidence            44678889999999999999874  332    244456777788999999999997754433322  2 33344443 89


Q ss_pred             ccCChHHHHHHHHh
Q 035927           86 KCGDVEKAQRVLRK   99 (153)
Q Consensus        86 ~~g~~~~a~~~~~~   99 (153)
                      +.|+.++|...|+.
T Consensus       130 ~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  130 AQGDYDEARAAYQK  143 (145)
T ss_pred             HCCCHHHHHHHHHH
Confidence            99999999999975

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

Probab=96.99  E-value=0.019  Score=41.26  Aligned_cols=99  Identities=18%  Similarity=0.131  Sum_probs=82.6

Q ss_pred             CCCchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            2 KNKDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         2 ~~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      .+||-..||.+--+|-+.|++++|..-|.+..+   .+....|.|...+.-.|++++|..++......+-....+-=|..
T Consensus       130 ~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLA  209 (257)
T COG5010         130 APTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLA  209 (257)
T ss_pred             CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHH
Confidence            368999999999999999999999999988763   47788888888899999999999999999887765555555544


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccC
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +-   ....|++++|+++...-..+
T Consensus       210 l~---~~~~g~~~~A~~i~~~e~~~  231 (257)
T COG5010         210 LV---VGLQGDFREAEDIAVQELLS  231 (257)
T ss_pred             HH---HhhcCChHHHHhhccccccc
Confidence            44   48999999999998876655

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

Probab=96.94  E-value=0.027  Score=46.70  Aligned_cols=128  Identities=18%  Similarity=0.314  Sum_probs=95.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCCC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      +...|..+..++.+.|++++|+.+|..+...    +...|--+-+.|-..|..++|.+.++..+..  .||..--.+=+.
T Consensus       413 ~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~--~p~~~D~Ri~La  490 (895)
T KOG2076|consen  413 DVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLIL--APDNLDARITLA  490 (895)
T ss_pred             hHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCchhhhhhHH
Confidence            4566889999999999999999999999742    6778999999999999999999999999864  466555555555


Q ss_pred             HHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~  146 (153)
                      .. |-+.|+.++|.+++..|..||...           ..-++..|+...-......+.+.|+.|+
T Consensus       491 sl-~~~~g~~EkalEtL~~~~~~D~~~-----------~e~~a~~~e~ri~~~r~d~l~~~gk~E~  544 (895)
T KOG2076|consen  491 SL-YQQLGNHEKALETLEQIINPDGRN-----------AEACAWEPERRILAHRCDILFQVGKREE  544 (895)
T ss_pred             HH-HHhcCCHHHHHHHHhcccCCCccc-----------hhhccccHHHHHHHHHHHHHHHhhhHHH
Confidence            54 789999999999999997765220           0000334555554555555556665554

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.93  E-value=0.041  Score=35.15  Aligned_cols=103  Identities=17%  Similarity=0.119  Sum_probs=75.4

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCCC---C---HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC---hhHHHHHHHHH
Q 035927           12 IVSGYINRGQVDIARQYFAQMPER---D---YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD---EFTIVRILTAY   82 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~---~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~t~~~li~~~   82 (153)
                      +-.++-..|+.++|+.+|++-...   +   ...+-.+-+.+-..|++++|..++++....-  |+   ......+...+
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~   84 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALA   84 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHH
Confidence            345677789999999999987632   1   2356667777888899999999999987642  44   33344443332


Q ss_pred             HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHh
Q 035927           83 MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAI  117 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~  117 (153)
                       +...|+.++|...+-....++...|.--|..|+.
T Consensus        85 -L~~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   85 -LYNLGRPKEALEWLLEALAETLPRYRRAIRFYAD  118 (120)
T ss_pred             -HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             6889999999999988777766677777776654

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.86  E-value=0.057  Score=44.57  Aligned_cols=105  Identities=12%  Similarity=0.076  Sum_probs=84.8

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .....+...+.+.+++++|....++...  | +....+.+-..+.+.|+.++|..+|++....+ .-+..++..+-..  
T Consensus       121 ~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~--  197 (694)
T PRK15179        121 EAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQS--  197 (694)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHH--
Confidence            3477788899999999999999999974  4 66778888888899999999999999999832 2346777777777  


Q ss_pred             HhccCChHHHHHHHHhccc---CChhhHHHHHHH
Q 035927           84 YCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVG  114 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~  114 (153)
                      +-+.|+.++|...|++..+   ++...|+..+.-
T Consensus       198 l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~~~  231 (694)
T PRK15179        198 LTRRGALWRARDVLQAGLDAIGDGARKLTRRLVD  231 (694)
T ss_pred             HHHcCCHHHHHHHHHHHHHhhCcchHHHHHHHHH
Confidence            5899999999999999853   456666655443

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

Probab=96.86  E-value=0.019  Score=42.12  Aligned_cols=99  Identities=16%  Similarity=0.130  Sum_probs=77.4

Q ss_pred             HHHHHHHhCC--CCCHHHHHHHHHHHHhc-----CChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC-------
Q 035927           24 IARQYFAQMP--ERDYVLWTAMIDGYLRV-----NRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD-------   89 (153)
Q Consensus        24 ~a~~l~~~m~--~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~-------   89 (153)
                      .....|+...  ++|-.+|-.++..|...     ++++--...++.|.+-|+.-|..+|+.||+.+   -.|.       
T Consensus        52 ~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~Llnvf---PKgkfiP~nvf  128 (406)
T KOG3941|consen   52 HVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVF---PKGKFIPQNVF  128 (406)
T ss_pred             chhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhC---cccccccHHHH
Confidence            3455666666  56888999999888754     56787788889999999999999999999984   3333       


Q ss_pred             ----------hHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCch
Q 035927           90 ----------VEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNE  144 (153)
Q Consensus        90 ----------~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~  144 (153)
                                -+-+++++++|...                   |+.||..+-..+++++.+-|..
T Consensus       129 Q~~F~HYP~QQ~C~I~vLeqME~h-------------------GVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  129 QKVFLHYPQQQNCAIKVLEQMEWH-------------------GVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             HHHHhhCchhhhHHHHHHHHHHHc-------------------CCCCchHHHHHHHHHhcccccc
Confidence                      24466667777666                   8999999999999999887764

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

Probab=96.84  E-value=0.012  Score=42.63  Aligned_cols=126  Identities=15%  Similarity=0.176  Sum_probs=78.8

Q ss_pred             HHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH--HHhccCChH
Q 035927           14 SGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY--MYCKCGDVE   91 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~--~~~~~g~~~   91 (153)
                      ..|+..|++++|.+..+..  .+......=...+.+..+++-|.+.++.|++.   -+..|.+.|..+.  ...-.+...
T Consensus       116 ~i~~~~~~~deAl~~~~~~--~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i---ded~tLtQLA~awv~la~ggek~q  190 (299)
T KOG3081|consen  116 IIYMHDGDFDEALKALHLG--ENLEAAALNVQILLKMHRFDLAEKELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQ  190 (299)
T ss_pred             HHhhcCCChHHHHHHHhcc--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc---chHHHHHHHHHHHHHHhccchhhh
Confidence            4577889999999998884  33333333344456777888899999999874   4556777665552  012345688


Q ss_pred             HHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCch
Q 035927           92 KAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNE  144 (153)
Q Consensus        92 ~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~  144 (153)
                      +|.-+|++|.++   +..+-|-+..++...+.++           .-.-+..|...++-.-...|..
T Consensus       191 dAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~Nliv~a~~~Gkd  257 (299)
T KOG3081|consen  191 DAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLANLIVLALHLGKD  257 (299)
T ss_pred             hHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCC
Confidence            899999999774   4444455555555556666           2223445555555444445544

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

Probab=96.79  E-value=0.0082  Score=44.82  Aligned_cols=137  Identities=14%  Similarity=0.099  Sum_probs=96.2

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHH-HHHHHHHHhc
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIV-RILTAYMYCK   86 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~-~li~~~~~~~   86 (153)
                      +.+-+.|.+.|-+.+|...++.-.  .|-..||-.|-+.|.+..+++.|+.++.+-+++  .|-.+||- ...+.  +..
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi--~ea  302 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARI--HEA  302 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHH--HHH
Confidence            567788999999999999988765  457778999999999999999999999887764  45445554 44444  688


Q ss_pred             cCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC------------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           87 CGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~------------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .++.++|.++++...+-   +++.-.++..+|.-.+.-+            |+ -+...|+.+--+|...+.+|.++-.|
T Consensus       303 m~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~-~speLf~NigLCC~yaqQ~D~~L~sf  381 (478)
T KOG1129|consen  303 MEQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGA-QSPELFCNIGLCCLYAQQIDLVLPSF  381 (478)
T ss_pred             HHhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcC-CChHHHhhHHHHHHhhcchhhhHHHH
Confidence            99999999999998653   3443333333333332222            22 34566777777777777777665544

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

Probab=96.71  E-value=0.064  Score=45.71  Aligned_cols=136  Identities=13%  Similarity=0.184  Sum_probs=101.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      ...|+.+.++=.+.|.+.+|.+-|=+  ..|+..|-.+++...++|.+++-..++...++..-.|...+  .+|-+  |+
T Consensus      1104 p~vWsqlakAQL~~~~v~dAieSyik--adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~A--yA 1177 (1666)
T KOG0985|consen 1104 PAVWSQLAKAQLQGGLVKDAIESYIK--ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFA--YA 1177 (1666)
T ss_pred             hHHHHHHHHHHHhcCchHHHHHHHHh--cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHH--HH
Confidence            34699999999999999999988844  46888999999999999999999888876677666676654  56777  69


Q ss_pred             ccCChHHHHHHHHhcc-----------------------cCChhhHHHHHHHHHhcCCCCC------CCCCHhHHHHHHH
Q 035927           86 KCGDVEKAQRVLRKML-----------------------RKDKFTWTAMIVGLAISDPFPT------IRPDEVTYVGVLS  136 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~-----------------------~~~~~~~~~li~~~~~~~~~~~------~~p~~~t~~~ll~  136 (153)
                      +.+++.+.++.+..=.                       =.++.-|..+...++..|.++|      -.-+..||..+.-
T Consensus      1178 kt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAns~ktWK~Vcf 1257 (1666)
T KOG0985|consen 1178 KTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKANSTKTWKEVCF 1257 (1666)
T ss_pred             HhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHH
Confidence            9999888877643210                       0155667777777887777772      2234577888888


Q ss_pred             HHhcCCchhHh
Q 035927          137 ACTHNGNETFV  147 (153)
Q Consensus       137 ~~~~~g~~~~a  147 (153)
                      +|...+.+..|
T Consensus      1258 aCvd~~EFrlA 1268 (1666)
T KOG0985|consen 1258 ACVDKEEFRLA 1268 (1666)
T ss_pred             HHhchhhhhHH
Confidence            87776666554

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

Probab=96.71  E-value=0.0075  Score=33.68  Aligned_cols=55  Identities=18%  Similarity=0.240  Sum_probs=47.0

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      +...+.+.|++++|...|++..+  | +...+..+-..+.+.|++++|...|++.++.
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            45678899999999999999974  3 6778999999999999999999999999754

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

Probab=96.66  E-value=0.0089  Score=43.79  Aligned_cols=92  Identities=12%  Similarity=0.199  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      .+|..+|+..-+.+.++.|..+|.+.++.+ ...++....+.+.   |...++.+.|.++|+...+.             
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E---~~~~~d~~~A~~Ife~glk~-------------   65 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALME---YYCNKDPKRARKIFERGLKK-------------   65 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHH---HHTCS-HHHHHHHHHHHHHH-------------
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHH---HHhCCCHHHHHHHHHHHHHH-------------
Confidence            578999999999999999999999998654 3455555555554   35567788899999999764             


Q ss_pred             hcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                             ..-+...|...+.-+.+.|+.+.|..+|+
T Consensus        66 -------f~~~~~~~~~Y~~~l~~~~d~~~aR~lfe   94 (280)
T PF05843_consen   66 -------FPSDPDFWLEYLDFLIKLNDINNARALFE   94 (280)
T ss_dssp             -------HTT-HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             -------CCCCHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence                   23356667777788888888888887764

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.

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

Probab=96.65  E-value=0.047  Score=40.83  Aligned_cols=92  Identities=17%  Similarity=0.109  Sum_probs=70.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCChh--HHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPDEF--TIVRILTAY   82 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~--t~~~li~~~   82 (153)
                      ...+...+...|++++|...+++..+  | +...+..+-..+...|++++|...+++.....- .|+..  .|..+... 
T Consensus       117 ~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~-  195 (355)
T cd05804         117 LGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALF-  195 (355)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHH-
Confidence            34555678889999999999999863  3 566788888889999999999999998876432 23332  33345454 


Q ss_pred             HHhccCChHHHHHHHHhccc
Q 035927           83 MYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~  102 (153)
                       +...|+.++|.+++++...
T Consensus       196 -~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         196 -YLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             -HHHCCCHHHHHHHHHHHhc
Confidence             7999999999999999753

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.

>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=96.58  E-value=0.013  Score=33.06  Aligned_cols=62  Identities=24%  Similarity=0.337  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC-ChHHHHHHHHhcc
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG-DVEKAQRVLRKML  101 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g-~~~~a~~~~~~m~  101 (153)
                      ...|..+-..+.+.|++++|+..|++..+.+  |+....-..+..+ |.+.| ++++|++.|++..
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~~~~~~~~~g~~-~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--PNNAEAYYNLGLA-YMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--TTHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHH-HHHhCccHHHHHHHHHHHH
Confidence            4556666666666677777777776666542  4333333333332 56666 5667766666554

...

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=96.56  E-value=0.063  Score=35.91  Aligned_cols=89  Identities=13%  Similarity=0.191  Sum_probs=68.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      .+-..+...|++++|..+|+-...  | +..-|-.|--.+=..|++++|.+.|......+  ||...----...| |.+.
T Consensus        40 ~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~--~ddp~~~~~ag~c-~L~l  116 (157)
T PRK15363         40 RYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK--IDAPQAPWAAAEC-YLAC  116 (157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCchHHHHHHHH-HHHc
Confidence            344567789999999999998863  3 55666677766767899999999999998765  4433333344444 8999


Q ss_pred             CChHHHHHHHHhccc
Q 035927           88 GDVEKAQRVLRKMLR  102 (153)
Q Consensus        88 g~~~~a~~~~~~m~~  102 (153)
                      |+.+.|.+-|+..+.
T Consensus       117 G~~~~A~~aF~~Ai~  131 (157)
T PRK15363        117 DNVCYAIKALKAVVR  131 (157)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999999998764

>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=96.56  E-value=0.056  Score=41.61  Aligned_cols=92  Identities=16%  Similarity=0.101  Sum_probs=75.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTA   81 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~   81 (153)
                      ......+...+...++-.+|.+++++..+  | +....+.-.+.|.+.++.+.|+.+.+++.+.  .| +-.+|..|..+
T Consensus       200 pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~  277 (395)
T PF09295_consen  200 PEVAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAEC  277 (395)
T ss_pred             CcHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHH
Confidence            33555688888888899999999988864  2 6666777777888999999999999999875  46 45588888888


Q ss_pred             HHHhccCChHHHHHHHHhcc
Q 035927           82 YMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~  101 (153)
                        |.+.|+++.|+..+..++
T Consensus       278 --Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  278 --YIQLGDFENALLALNSCP  295 (395)
T ss_pred             --HHhcCCHHHHHHHHhcCc
Confidence              799999999999999985

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

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

Probab=96.53  E-value=0.04  Score=43.22  Aligned_cols=141  Identities=11%  Similarity=0.045  Sum_probs=93.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      +|----..+.-.+++++|..=|++-.+  | +...|-.+-.+.-+.+.+++++..|++.+++ ++-....|+-.-..  +
T Consensus       396 vYyHRgQm~flL~q~e~A~aDF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAei--L  472 (606)
T KOG0547|consen  396 VYYHRGQMRFLLQQYEEAIADFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEI--L  472 (606)
T ss_pred             hhHhHHHHHHHHHHHHHHHHHHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHH--H
Confidence            344444445555666777777766653  2 5667777777777888999999999888754 55567777777777  5


Q ss_pred             hccCChHHHHHHHHhccc--CC-------hh--hHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCC
Q 035927           85 CKCGDVEKAQRVLRKMLR--KD-------KF--TWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNG  142 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~--~~-------~~--~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g  142 (153)
                      ...++++.|.+.|+..++  |+       .-  .=-+++-.-.+ ++|.          .+-|-. ..|.+|-..-.+.|
T Consensus       473 tDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qwk-~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~  551 (606)
T KOG0547|consen  473 TDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQWK-EDINQAENLLRKAIELDPKCEQAYETLAQFELQRG  551 (606)
T ss_pred             hhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhchh-hhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHh
Confidence            889999999999988743  21       11  11111111111 2222          444543 55888888899999


Q ss_pred             chhHhhhhcc
Q 035927          143 NETFVINSCN  152 (153)
Q Consensus       143 ~~~~a~~~~~  152 (153)
                      ++++|+++|+
T Consensus       552 ~i~eAielFE  561 (606)
T KOG0547|consen  552 KIDEAIELFE  561 (606)
T ss_pred             hHHHHHHHHH
Confidence            9999999986

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

Probab=96.52  E-value=0.025  Score=42.89  Aligned_cols=74  Identities=12%  Similarity=0.069  Sum_probs=51.7

Q ss_pred             HHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCC
Q 035927           45 DGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDP  120 (153)
Q Consensus        45 ~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~  120 (153)
                      ..+...|++++|++.|++.++..  | +...|..+-.+  |.+.|++++|+..+++..+.   +...|..+..+|...|.
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~--P~~~~a~~~~a~~--~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD--PNNAELYADRAQA--NIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCC
Confidence            44557899999999999998753  4 44444444444  79999999999999999653   34445555555555554


Q ss_pred             CC
Q 035927          121 FP  122 (153)
Q Consensus       121 ~~  122 (153)
                      ++
T Consensus        86 ~~   87 (356)
T PLN03088         86 YQ   87 (356)
T ss_pred             HH
Confidence            44

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

Probab=96.52  E-value=0.036  Score=48.28  Aligned_cols=143  Identities=12%  Similarity=0.174  Sum_probs=75.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER--DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .+|.++++.-..-|.-+...++|++..+-  -...|-.|..-|.+.+..++|-++++.|.+. ++-....|...+..  +
T Consensus      1498 NiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~f--L 1574 (1710)
T KOG1070|consen 1498 NIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADF--L 1574 (1710)
T ss_pred             HHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHH--H
Confidence            35666666666666556666666666542  2345666666666666666666666666543 22344455555555  4


Q ss_pred             hccCChHHHHHHHHhcccC-------C-hhhHHHHHHHHHhcCC----CCCC---CC-CHhHHHHHHHHHhcCCchhHhh
Q 035927           85 CKCGDVEKAQRVLRKMLRK-------D-KFTWTAMIVGLAISDP----FPTI---RP-DEVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~-------~-~~~~~~li~~~~~~~~----~~~~---~p-~~~t~~~ll~~~~~~g~~~~a~  148 (153)
                      .+..+.+.|..++.+..+.       . +.-|..|.-.|+..+.    |+|.   -| -...|+..+..-.+.|+.+.+.
T Consensus      1575 l~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR 1654 (1710)
T KOG1070|consen 1575 LRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVR 1654 (1710)
T ss_pred             hcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHH
Confidence            6666666666665554321       1 1122223323332211    2211   12 2355777777777777776666


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      .+|+
T Consensus      1655 ~lfe 1658 (1710)
T KOG1070|consen 1655 DLFE 1658 (1710)
T ss_pred             HHHH
Confidence            6653

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

Probab=96.48  E-value=0.17  Score=40.43  Aligned_cols=127  Identities=15%  Similarity=0.230  Sum_probs=91.8

Q ss_pred             CCchhHH--HHHHHHHHhcCChHHHHHHHHhCCC--CC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHH
Q 035927            3 NKDVISW--TDIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         3 ~pd~~~~--~~li~~~~~~g~~~~a~~l~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      +|+...|  .-+-..|-..|++++|++..++--+  |+ +..|..-.+.+-+.|++++|.+.++..++... -|...=+-
T Consensus       189 ~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DRyiNsK  267 (517)
T PF12569_consen  189 PPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELDL-ADRYINSK  267 (517)
T ss_pred             CchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhHHHHHH
Confidence            3555445  4556778889999999999997753  43 55788888888889999999999999988753 46566666


Q ss_pred             HHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-----Hh-HH--HHHHHHHhcCCchhHhhh
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-----EV-TY--VGVLSACTHNGNETFVIN  149 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-----~~-t~--~~ll~~~~~~g~~~~a~~  149 (153)
                      ....  +.|+|++++|.+++...-+++.                   .|-     .. .|  .-.-.+|.+.|++..|++
T Consensus       268 ~aKy--~LRa~~~e~A~~~~~~Ftr~~~-------------------~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk  326 (517)
T PF12569_consen  268 CAKY--LLRAGRIEEAEKTASLFTREDV-------------------DPLSNLNDMQCMWFETECAEAYLRQGDYGLALK  326 (517)
T ss_pred             HHHH--HHHCCCHHHHHHHHHhhcCCCC-------------------CcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            6666  6999999999999999876641                   121     11 22  122366778888888776


Q ss_pred             hc
Q 035927          150 SC  151 (153)
Q Consensus       150 ~~  151 (153)
                      .|
T Consensus       327 ~~  328 (517)
T PF12569_consen  327 RF  328 (517)
T ss_pred             HH
Confidence            55

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 [], [].

>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=96.44  E-value=0.015  Score=32.73  Aligned_cols=61  Identities=18%  Similarity=0.382  Sum_probs=53.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcC-ChHHHHHHHHHHhh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVN-RFREALTLFPEMQT   65 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~   65 (153)
                      +..+|..+-..+.+.|++++|+..|.+..+  | +...|..+-.++.+.| ++++|+..++...+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            456789999999999999999999999863  3 6778999999999999 79999999988765

...

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

Probab=96.37  E-value=0.038  Score=41.31  Aligned_cols=84  Identities=17%  Similarity=0.256  Sum_probs=68.9

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      -||..-|-..+.++++.++|++-..+...  +..+..|-..+..|.+.|+..+|..++..          .++..-+.. 
T Consensus       205 v~dkrfw~lki~aLa~~~~w~eL~~fa~s--kKsPIGyepFv~~~~~~~~~~eA~~yI~k----------~~~~~rv~~-  271 (319)
T PF04840_consen  205 VPDKRFWWLKIKALAENKDWDELEKFAKS--KKSPIGYEPFVEACLKYGNKKEASKYIPK----------IPDEERVEM-  271 (319)
T ss_pred             CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--CCCCCChHHHHHHHHHCCCHHHHHHHHHh----------CChHHHHHH-
Confidence            48888999999999999999999988765  44668999999999999999999988876          223566676 


Q ss_pred             HHhccCChHHHHHHHHhc
Q 035927           83 MYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m  100 (153)
                       |.++|++.+|.+.-.+.
T Consensus       272 -y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  272 -YLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             -HHHCCCHHHHHHHHHHc
Confidence             68899998887774444

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

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.34  E-value=0.12  Score=34.67  Aligned_cols=65  Identities=18%  Similarity=0.146  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-C-hhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-D-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ...|..+...+...|++++|+..++......-.| + ..++..+-..  |.+.|+.++|++.+++..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~--~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLI--HTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHh
Confidence            4567788888888999999999999997653222 1 2345554444  79999999999999998653

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.34  E-value=0.061  Score=40.77  Aligned_cols=104  Identities=13%  Similarity=0.184  Sum_probs=59.1

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhc-------CChHHHHHHHHHHhhCCCCCChhHHHHHHHHH--
Q 035927           12 IVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRV-------NRFREALTLFPEMQTSNIRPDEFTIVRILTAY--   82 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~-------~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~--   82 (153)
                      |+-.|.+.+++++|..+..++...++.-|-.---.++..       .+++-|.+.|.-.-+++...|+..=..-+.+|  
T Consensus       291 L~iYyL~q~dVqeA~~L~Kdl~PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fF  370 (557)
T KOG3785|consen  291 LIIYYLNQNDVQEAISLCKDLDPTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFF  370 (557)
T ss_pred             heeeecccccHHHHHHHHhhcCCCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHH
Confidence            455678889999999999888654443332111111222       23566666665444444443333222222222  


Q ss_pred             -------------------------------HHhccCChHHHHHHHHhcccC---ChhhHHHHHHHH
Q 035927           83 -------------------------------MYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGL  115 (153)
Q Consensus        83 -------------------------------~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~  115 (153)
                                                     .++..|...+|+++|-.+..+   |-.+|..++..|
T Consensus       371 L~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArC  437 (557)
T KOG3785|consen  371 LSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARC  437 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHH
Confidence                                           456778888888888888665   556666555443

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.30  E-value=0.066  Score=39.73  Aligned_cols=141  Identities=18%  Similarity=0.209  Sum_probs=91.5

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCCCC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC-------------CCh
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR-------------PDE   72 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-------------p~~   72 (153)
                      +..-....+.|+.+.|.+-|..-.+-    ....||..+.-| +.++.+.|++...+.+++|++             ||+
T Consensus       148 in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDv  226 (459)
T KOG4340|consen  148 INLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDV  226 (459)
T ss_pred             ccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCch
Confidence            33334455677888887777766532    456777777655 667788888888888777653             333


Q ss_pred             hHH--------HHHHHHH-----HHhccCChHHHHHHHHhcccC-----ChhhHHHHHHHHHhcCCCC---------CCC
Q 035927           73 FTI--------VRILTAY-----MYCKCGDVEKAQRVLRKMLRK-----DKFTWTAMIVGLAISDPFP---------TIR  125 (153)
Q Consensus        73 ~t~--------~~li~~~-----~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~---------~~~  125 (153)
                      .+.        ..++.++     .+.+.|+.+.|.+.+..|+-+     |++|-+.+.-.=+..+.-+         ++.
T Consensus       227 rsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqFLL~~n  306 (459)
T KOG4340|consen  227 RSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQFLLQQN  306 (459)
T ss_pred             hcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcccCCccccHHHHHHHHhcC
Confidence            221        2233332     456888889999998888643     6666665544333332222         455


Q ss_pred             C-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          126 P-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       126 p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      | -..||..++--||++.-++.|-+++
T Consensus       307 PfP~ETFANlLllyCKNeyf~lAADvL  333 (459)
T KOG4340|consen  307 PFPPETFANLLLLYCKNEYFDLAADVL  333 (459)
T ss_pred             CCChHHHHHHHHHHhhhHHHhHHHHHH
Confidence            5 3589999999999999888876653

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

Probab=96.30  E-value=0.089  Score=44.88  Aligned_cols=131  Identities=12%  Similarity=0.167  Sum_probs=100.0

Q ss_pred             HHHHhcCChHHHHHHHHhCCC-------------------------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927           14 SGYINRGQVDIARQYFAQMPE-------------------------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~-------------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      ..+...+.+++|..+|++...                         .....|+.+..+-.+.|...+|.+-|-+      
T Consensus      1056 ~iai~~~LyEEAF~ifkkf~~n~~A~~VLie~i~~ldRA~efAe~~n~p~vWsqlakAQL~~~~v~dAieSyik------ 1129 (1666)
T KOG0985|consen 1056 EIAIENQLYEEAFAIFKKFDMNVSAIQVLIENIGSLDRAYEFAERCNEPAVWSQLAKAQLQGGLVKDAIESYIK------ 1129 (1666)
T ss_pred             HHHhhhhHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHHHHHhhCChHHHHHHHHHHHhcCchHHHHHHHHh------
Confidence            344555667777777776642                         1445788888888888888888776622      


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC--ChhhHHHHHHHHHhcCCCC-----CCCCCHhHHHHHHHHHhcC
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK--DKFTWTAMIVGLAISDPFP-----TIRPDEVTYVGVLSACTHN  141 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~li~~~~~~~~~~-----~~~p~~~t~~~ll~~~~~~  141 (153)
                      --|...|.-+|+.+  .+.|.|++..+.+...+++  ....-+.+|-+|++.+.+.     -..||..-...+-.-|...
T Consensus      1130 adDps~y~eVi~~a--~~~~~~edLv~yL~MaRkk~~E~~id~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~ 1207 (1666)
T KOG0985|consen 1130 ADDPSNYLEVIDVA--SRTGKYEDLVKYLLMARKKVREPYIDSELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEE 1207 (1666)
T ss_pred             cCCcHHHHHHHHHH--HhcCcHHHHHHHHHHHHHhhcCccchHHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhh
Confidence            24678899999996  9999999999988776553  4455678999999998777     3568888888899999999


Q ss_pred             CchhHhhhhcc
Q 035927          142 GNETFVINSCN  152 (153)
Q Consensus       142 g~~~~a~~~~~  152 (153)
                      |.++.|.-+|+
T Consensus      1208 ~~y~aAkl~y~ 1218 (1666)
T KOG0985|consen 1208 KMYEAAKLLYS 1218 (1666)
T ss_pred             hhhHHHHHHHH
Confidence            99998877664

>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=96.28  E-value=0.014  Score=33.80  Aligned_cols=26  Identities=19%  Similarity=0.420  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      +|+.+-..|...|++++|++.+++..
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al   32 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKAL   32 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444444455555555444443

...

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.24  E-value=0.036  Score=45.72  Aligned_cols=97  Identities=18%  Similarity=0.178  Sum_probs=61.4

Q ss_pred             HHHhcCChHHHHHHHHhCCCCCHHH--HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHH
Q 035927           15 GYINRGQVDIARQYFAQMPERDYVL--WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEK   92 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~~~~~--~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~   92 (153)
                      +-.+...+.+|+.+++.++..++.+  |..+.+-|+..|+++.|+.+|-+-         ..++-.|..  |.+.|+|..
T Consensus       741 aai~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~---------~~~~dai~m--y~k~~kw~d  809 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDM--YGKAGKWED  809 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHH--HhccccHHH
Confidence            4445567777888887777544332  666667777778888887777432         345556666  688888888


Q ss_pred             HHHHHHhcccC--ChhhHHHHHHHHHhcCCCC
Q 035927           93 AQRVLRKMLRK--DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        93 a~~~~~~m~~~--~~~~~~~li~~~~~~~~~~  122 (153)
                      |.++-.+...|  ....|-+-..-+-..|.|.
T Consensus       810 a~kla~e~~~~e~t~~~yiakaedldehgkf~  841 (1636)
T KOG3616|consen  810 AFKLAEECHGPEATISLYIAKAEDLDEHGKFA  841 (1636)
T ss_pred             HHHHHHHhcCchhHHHHHHHhHHhHHhhcchh
Confidence            88877777655  4445554444444444444

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

Probab=96.23  E-value=0.14  Score=40.23  Aligned_cols=131  Identities=14%  Similarity=0.226  Sum_probs=79.6

Q ss_pred             cCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHH
Q 035927           19 RGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQR   95 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~   95 (153)
                      .+++..|..+|++...   ++...|---+..=-++..+..|.+++++.+.---+.|..=|. .+..  =...|++.+|.+
T Consensus        86 q~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyK-Y~ym--EE~LgNi~gaRq  162 (677)
T KOG1915|consen   86 QKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYK-YIYM--EEMLGNIAGARQ  162 (677)
T ss_pred             HHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHH-HHHH--HHHhcccHHHHH
Confidence            3455667777776653   344555555555556666777777777666532222322222 2222  156677777777


Q ss_pred             HHHhcc--cCChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           96 VLRKML--RKDKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        96 ~~~~m~--~~~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +|++-.  +|+.-.|++.|.-=.+...++          -+.|+..+|--....=-+.|+...|..+|.
T Consensus       163 iferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~Vye  231 (677)
T KOG1915|consen  163 IFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYE  231 (677)
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            777654  467777777666555543333          466888888777777778888877777663

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.19  E-value=0.021  Score=32.52  Aligned_cols=55  Identities=22%  Similarity=0.280  Sum_probs=33.6

Q ss_pred             HHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           45 DGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        45 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..+.+.+++++|++.++.+...  .|+....-.....| |.+.|++++|.+.|+...+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~~~a~~-~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALEL--DPDDPELWLQRARC-LFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHh--CcccchhhHHHHHH-HHHhccHHHHHHHHHHHHH
Confidence            3456667777777777777665  24433333333333 6777777777777777654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.17  E-value=0.042  Score=41.63  Aligned_cols=59  Identities=17%  Similarity=0.219  Sum_probs=42.0

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           43 MIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        43 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +..+.+..|++.+|+++|-......+ -|..+|-+++.-| |.++++++.|++++-++..|
T Consensus       399 ~AQAk~atgny~eaEelf~~is~~~i-kn~~~Y~s~LArC-yi~nkkP~lAW~~~lk~~t~  457 (557)
T KOG3785|consen  399 LAQAKLATGNYVEAEELFIRISGPEI-KNKILYKSMLARC-YIRNKKPQLAWDMMLKTNTP  457 (557)
T ss_pred             HHHHHHHhcChHHHHHHHhhhcChhh-hhhHHHHHHHHHH-HHhcCCchHHHHHHHhcCCc
Confidence            34555666778888888866554444 3557777777776 88888888888888877665

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.16  E-value=0.2  Score=40.11  Aligned_cols=126  Identities=7%  Similarity=-0.014  Sum_probs=73.5

Q ss_pred             CCchhHHHHHHHHHHhcC-----ChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhc--------CChHHHHHHHHHHhhC
Q 035927            3 NKDVISWTDIVSGYINRG-----QVDIARQYFAQMPE--R-DYVLWTAMIDGYLRV--------NRFREALTLFPEMQTS   66 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g-----~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~--------~~~~~a~~~~~~m~~~   66 (153)
                      +.|...|...+.+.....     ..++|..+|++..+  | ....|..+..++...        +++..+.+........
T Consensus       334 ~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al  413 (517)
T PRK10153        334 PHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVAL  413 (517)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhc
Confidence            466778888888765533     26789999998874  4 344555544433322        1223344444433332


Q ss_pred             C-CCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchh
Q 035927           67 N-IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNET  145 (153)
Q Consensus        67 ~-~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~  145 (153)
                      . ...+...+.++--.  ....|++++|...+++..+-+                     |+...|..+-+.+...|+.+
T Consensus       414 ~~~~~~~~~~~ala~~--~~~~g~~~~A~~~l~rAl~L~---------------------ps~~a~~~lG~~~~~~G~~~  470 (517)
T PRK10153        414 PELNVLPRIYEILAVQ--ALVKGKTDEAYQAINKAIDLE---------------------MSWLNYVLLGKVYELKGDNR  470 (517)
T ss_pred             ccCcCChHHHHHHHHH--HHhcCCHHHHHHHHHHHHHcC---------------------CCHHHHHHHHHHHHHcCCHH
Confidence            1 33455666665433  356799999999999987642                     44445555555555555555


Q ss_pred             Hhhhhc
Q 035927          146 FVINSC  151 (153)
Q Consensus       146 ~a~~~~  151 (153)
                      +|.+.|
T Consensus       471 eA~~~~  476 (517)
T PRK10153        471 LAADAY  476 (517)
T ss_pred             HHHHHH
Confidence            555443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=96.08  E-value=0.077  Score=43.94  Aligned_cols=87  Identities=20%  Similarity=0.329  Sum_probs=64.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG   88 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g   88 (153)
                      |..+.+-|+..|+++.|.++|.+     ..-++..|..|.+.|++++|..+-.+.-  |-......|-+-..-  +-++|
T Consensus       768 y~~iadhyan~~dfe~ae~lf~e-----~~~~~dai~my~k~~kw~da~kla~e~~--~~e~t~~~yiakaed--ldehg  838 (1636)
T KOG3616|consen  768 YGEIADHYANKGDFEIAEELFTE-----ADLFKDAIDMYGKAGKWEDAFKLAEECH--GPEATISLYIAKAED--LDEHG  838 (1636)
T ss_pred             chHHHHHhccchhHHHHHHHHHh-----cchhHHHHHHHhccccHHHHHHHHHHhc--CchhHHHHHHHhHHh--HHhhc
Confidence            77788899999999999999954     4567888999999999999998876654  222233444444444  46788


Q ss_pred             ChHHHHHHHHhcccCC
Q 035927           89 DVEKAQRVLRKMLRKD  104 (153)
Q Consensus        89 ~~~~a~~~~~~m~~~~  104 (153)
                      ++.+|++++-.+..|+
T Consensus       839 kf~eaeqlyiti~~p~  854 (1636)
T KOG3616|consen  839 KFAEAEQLYITIGEPD  854 (1636)
T ss_pred             chhhhhheeEEccCch
Confidence            8888888877776664

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.97  E-value=0.14  Score=37.23  Aligned_cols=94  Identities=13%  Similarity=0.111  Sum_probs=69.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCC-ChhHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRP-DEFTIVRI   78 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p-~~~t~~~l   78 (153)
                      ..|...+..+.+.|++++|...|+.+.+  |+    ...+--+-..+...|++++|...|+.+.+.- -.| ....+-.+
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~kl  223 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHH
Confidence            4477877777888999999999999873  43    3567778888889999999999999998541 111 11222222


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ...  |.+.|+.++|.++|+.+.+
T Consensus       224 g~~--~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        224 GVI--MQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHH--HHHcCCHHHHHHHHHHHHH
Confidence            222  6789999999999999875

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=95.94  E-value=0.18  Score=34.00  Aligned_cols=82  Identities=15%  Similarity=0.145  Sum_probs=56.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-C-hhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-D-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTA  110 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~  110 (153)
                      ....|..+...+.+.|++++|...|++..+.+-.+ + ...+..+...  |.+.|++++|.+.+++..+.   +...+..
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~--~~~~g~~~~A~~~~~~al~~~p~~~~~~~~  111 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGII--YASNGEHDKALEYYHQALELNPKQPSALNN  111 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhCcccHHHHHH
Confidence            45578888888889999999999999998654322 2 2345444444  79999999999999998653   3334444


Q ss_pred             HHHHHHhcC
Q 035927          111 MIVGLAISD  119 (153)
Q Consensus       111 li~~~~~~~  119 (153)
                      +...+...+
T Consensus       112 lg~~~~~~g  120 (172)
T PRK02603        112 IAVIYHKRG  120 (172)
T ss_pred             HHHHHHHcC
Confidence            444444333

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=95.86  E-value=0.12  Score=37.61  Aligned_cols=94  Identities=12%  Similarity=0.055  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh----hHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE----FTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMI  112 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li  112 (153)
                      ...|...+..+.+.|++++|...|+.+.+.-  |+.    ..+-.+-..  |...|++++|...|+.+.+..+       
T Consensus       143 ~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y--P~s~~a~~A~y~LG~~--y~~~g~~~~A~~~f~~vv~~yP-------  211 (263)
T PRK10803        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKKY--PDSTYQPNANYWLGQL--NYNKGKKDDAAYYFASVVKNYP-------  211 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCcchHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHHCC-------
Confidence            3457777777677899999999999998652  332    234444444  7899999999999999975310       


Q ss_pred             HHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          113 VGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       113 ~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                +-......+..+...+...|+.++|.+.|
T Consensus       212 ----------~s~~~~dAl~klg~~~~~~g~~~~A~~~~  240 (263)
T PRK10803        212 ----------KSPKAADAMFKVGVIMQDKGDTAKAKAVY  240 (263)
T ss_pred             ----------CCcchhHHHHHHHHHHHHcCCHHHHHHHH
Confidence                      00112233444455555677777777665

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

Probab=95.86  E-value=0.079  Score=34.58  Aligned_cols=95  Identities=19%  Similarity=0.216  Sum_probs=65.9

Q ss_pred             chhHHHHHHH---HHHhcCChHHHHHHHHhCCC----C---------------------CHHHHHHHHHHHHhcCChHHH
Q 035927            5 DVISWTDIVS---GYINRGQVDIARQYFAQMPE----R---------------------DYVLWTAMIDGYLRVNRFREA   56 (153)
Q Consensus         5 d~~~~~~li~---~~~~~g~~~~a~~l~~~m~~----~---------------------~~~~~~~li~~~~~~~~~~~a   56 (153)
                      |...|-.++.   .....|+.+.+...+.+...    +                     =......++..+...|++++|
T Consensus         2 D~~~F~~~~~~a~~~~~~~~~~~~~~~~~~al~ly~G~~l~~~~~~~W~~~~r~~l~~~~~~~~~~l~~~~~~~~~~~~a   81 (146)
T PF03704_consen    2 DVDRFEALVREARAAARAGDPEEAIELLEEALALYRGDFLPDLDDEEWVEPERERLRELYLDALERLAEALLEAGDYEEA   81 (146)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCHHHH
Confidence            3444555533   23456777777776666542    1                     112455566666678999999


Q ss_pred             HHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           57 LTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        57 ~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..+.+.+.... +.|...|..+|.+  |.+.|+...|.++|+.+.+
T Consensus        82 ~~~~~~~l~~d-P~~E~~~~~lm~~--~~~~g~~~~A~~~Y~~~~~  124 (146)
T PF03704_consen   82 LRLLQRALALD-PYDEEAYRLLMRA--LAAQGRRAEALRVYERYRR  124 (146)
T ss_dssp             HHHHHHHHHHS-TT-HHHHHHHHHH--HHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CCCHHHHHHHHHH--HHHCcCHHHHHHHHHHHHH
Confidence            99999998764 4689999999999  6999999999999999954

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

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

Probab=95.85  E-value=0.31  Score=38.21  Aligned_cols=114  Identities=17%  Similarity=0.230  Sum_probs=91.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      ....|+.+-+-|....+...|.+-+++-.   ..|-..|-.|-.+|.--+...-|+-.|++...  ++| |...|.+|-+
T Consensus       363 ~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kPnDsRlw~aLG~  440 (559)
T KOG1155|consen  363 YLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKPNDSRLWVALGE  440 (559)
T ss_pred             hhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCCCchHHHHHHHH
Confidence            44569999999999999999999998876   34888999999999999999999999988876  466 5666666555


Q ss_pred             HHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.+++++|++-|+....-   +...+..+...|-+.++.+
T Consensus       441 C--Y~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~  483 (559)
T KOG1155|consen  441 C--YEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLN  483 (559)
T ss_pred             H--HHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHH
Confidence            4  89999999999999998542   3466777777776665554

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

Probab=95.83  E-value=0.15  Score=44.80  Aligned_cols=146  Identities=13%  Similarity=0.122  Sum_probs=109.8

Q ss_pred             CCchh-HHHHHHHHHHhcCChHHHHHHHHhCCCC--------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh
Q 035927            3 NKDVI-SWTDIVSGYINRGQVDIARQYFAQMPER--------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF   73 (153)
Q Consensus         3 ~pd~~-~~~~li~~~~~~g~~~~a~~l~~~m~~~--------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~   73 (153)
                      .|+.. .|-..|.-..+.+.++.|.+++++....        ....|.++++.-...|.-+....+|++..+-.  -.-.
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~ 1531 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYT 1531 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHH
Confidence            35544 4999999999999999999999998742        45689999988888898889999999998642  1234


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCCCCH---hHHHHHHHH
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIRPDE---VTYVGVLSA  137 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~p~~---~t~~~ll~~  137 (153)
                      .|..|.+.  |.+.++.++|.++++.|.++   ....|...+..+.+...-+          .+-|-.   ....-...-
T Consensus      1532 V~~~L~~i--y~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1532 VHLKLLGI--YEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHH--HHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHH
Confidence            56666666  79999999999999999765   6778999888888885533          444552   222333344


Q ss_pred             HhcCCchhHhhhhcc
Q 035927          138 CTHNGNETFVINSCN  152 (153)
Q Consensus       138 ~~~~g~~~~a~~~~~  152 (153)
                      -.+.|+.|++.-+|.
T Consensus      1610 EFk~GDaeRGRtlfE 1624 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFE 1624 (1710)
T ss_pred             HhhcCCchhhHHHHH
Confidence            457888888777663

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

Probab=95.79  E-value=0.031  Score=32.34  Aligned_cols=55  Identities=18%  Similarity=0.361  Sum_probs=39.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC---------C-CHHHHHHHHHHHHhcCChHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE---------R-DYVLWTAMIDGYLRVNRFREALTLFP   61 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---------~-~~~~~~~li~~~~~~~~~~~a~~~~~   61 (153)
                      .+|+.+-..|.+.|++++|+..|++..+         + ...+++.+-..+...|++++|++.++
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~   70 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQ   70 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            4589999999999999999998876641         1 24456666666666777777776664

...

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

Probab=95.77  E-value=0.63  Score=35.62  Aligned_cols=141  Identities=14%  Similarity=0.130  Sum_probs=107.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .|..-..+--+.|+.+.+-..+.+..++    +...+-+..+.....|++..|..-+++..+.+- -.........++  
T Consensus       120 ~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~p-r~~~vlrLa~r~--  196 (400)
T COG3071         120 AYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMTP-RHPEVLRLALRA--  196 (400)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhCc-CChHHHHHHHHH--
Confidence            3555556667788899999988888754    556677777888889999999999999988753 355677888888  


Q ss_pred             HhccCChHHHHHHHHhcccCC-----------hhhHHHHHHHHHhcCCCCC-----------CCCCHhHHHHHHHHHhcC
Q 035927           84 YCKCGDVEKAQRVLRKMLRKD-----------KFTWTAMIVGLAISDPFPT-----------IRPDEVTYVGVLSACTHN  141 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~~-----------~~~~~~li~~~~~~~~~~~-----------~~p~~~t~~~ll~~~~~~  141 (153)
                      |.+.|++.....+..++.+.+           ..+|+.++.=....+..+|           .+-+...-.+++.-+.++
T Consensus       197 y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l  276 (400)
T COG3071         197 YIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRL  276 (400)
T ss_pred             HHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHc
Confidence            799999999999999997652           2367777777666655552           334556667778888899


Q ss_pred             CchhHhhhhc
Q 035927          142 GNETFVINSC  151 (153)
Q Consensus       142 g~~~~a~~~~  151 (153)
                      |+.++|.++.
T Consensus       277 ~~~~~A~~~i  286 (400)
T COG3071         277 GDHDEAQEII  286 (400)
T ss_pred             CChHHHHHHH
Confidence            9999998764

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.72  E-value=0.38  Score=37.57  Aligned_cols=98  Identities=10%  Similarity=0.067  Sum_probs=70.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CCC-H---HHHHHHHHHHHhcCChHHHHHHHHHHhhCC-C-------C
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ERD-Y---VLWTAMIDGYLRVNRFREALTLFPEMQTSN-I-------R   69 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~-~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~-------~   69 (153)
                      .+...|+.+-.+|.+.|++++|+..|++-.  .|+ .   .+|..+-.+|.+.|+.++|++.+++..+.+ .       -
T Consensus        73 ~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALelsn~~f~~i~~D  152 (453)
T PLN03098         73 KTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRDYNLKFSTILND  152 (453)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcchhHHHHHhC
Confidence            456679999999999999999999999864  454 2   469999999999999999999999988751 1       1


Q ss_pred             CCh------hHHHHHHHHHHHhccCC-----hHHHHHHHHhcccC
Q 035927           70 PDE------FTIVRILTAYMYCKCGD-----VEKAQRVLRKMLRK  103 (153)
Q Consensus        70 p~~------~t~~~li~~~~~~~~g~-----~~~a~~~~~~m~~~  103 (153)
                      ||.      ..|..++..  +.+-|.     ...-.++..+...|
T Consensus       153 pdL~plR~~pef~eLlee--~rk~G~~~g~~~~~~~kL~~E~~aP  195 (453)
T PLN03098        153 PDLAPFRASPEFKELQEE--ARKGGEDIGSSFRRDLKLISEVQAP  195 (453)
T ss_pred             cchhhhcccHHHHHHHHH--HHHhCCccCCchhhHHHHHHHHhch
Confidence            221      256666665  355553     33345555555555

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.66  E-value=0.35  Score=31.85  Aligned_cols=67  Identities=10%  Similarity=0.209  Sum_probs=47.6

Q ss_pred             HHHHhcCChHHHHHHHHhCCCC------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCChhHHHHHHHH
Q 035927           14 SGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPDEFTIVRILTA   81 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~   81 (153)
                      ....+.|+++.|.+.|+.+..+      ....-=.|+.++.+.+++++|...++++++..- -|+ +-|...+.|
T Consensus        18 ~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~-vdYa~Y~~g   91 (142)
T PF13512_consen   18 QEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPN-VDYAYYMRG   91 (142)
T ss_pred             HHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCC-ccHHHHHHH
Confidence            3455678899999999888742      455666788888899999999999998877542 233 444444444

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

Probab=95.66  E-value=0.39  Score=37.65  Aligned_cols=93  Identities=11%  Similarity=0.025  Sum_probs=71.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--CC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--RD-YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      |+.-+....+.+.+.++.++|.+-++++..  |+ ...+-.+-.++.+.|++.+|..+++.-... .+-|...|.-|-++
T Consensus       339 N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqa  417 (484)
T COG4783         339 NPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQA  417 (484)
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHH
Confidence            344456667789999999999999999974  44 556677788899999999999999888755 35688999999999


Q ss_pred             HHHhccCChHHHHHHHHhc
Q 035927           82 YMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m  100 (153)
                      |  ...|+..++..-..+.
T Consensus       418 y--~~~g~~~~a~~A~AE~  434 (484)
T COG4783         418 Y--AELGNRAEALLARAEG  434 (484)
T ss_pred             H--HHhCchHHHHHHHHHH
Confidence            5  6666655555544443

>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=95.56  E-value=0.23  Score=39.65  Aligned_cols=97  Identities=18%  Similarity=0.162  Sum_probs=77.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhH----HHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT----IVRI   78 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t----~~~l   78 (153)
                      +..|..-...+-+.|++++|.+.++.-++   .|...=+-....+.++|++++|.+++..+-+.+..|-...    +.+.
T Consensus       228 ~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf  307 (517)
T PF12569_consen  228 VELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWF  307 (517)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHH
Confidence            56688888999999999999999998875   3778889999999999999999999999987765443222    2333


Q ss_pred             HHHH--HHhccCChHHHHHHHHhccc
Q 035927           79 LTAY--MYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        79 i~~~--~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +..|  .|.+.|++..|++-|..+.+
T Consensus       308 ~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  308 ETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            3332  57899999999998888754

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 [], [].

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=95.54  E-value=0.18  Score=33.26  Aligned_cols=82  Identities=11%  Similarity=0.066  Sum_probs=65.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC---------CCHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE---------RDYVLWTAMIDGYLRVNR-FREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~---------~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      .|.++.-....+++.....+++.+..         .+..+|++++.+.++... --.+..+|..|++.+.+++..-|..+
T Consensus        42 iN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~l  121 (145)
T PF13762_consen   42 INCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCL  121 (145)
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            68888888888888888888888852         267789999999987765 56778899999888899999999999


Q ss_pred             HHHHHHhccCChHHH
Q 035927           79 LTAYMYCKCGDVEKA   93 (153)
Q Consensus        79 i~~~~~~~~g~~~~a   93 (153)
                      |.+   +.+|...+.
T Consensus       122 i~~---~l~g~~~~~  133 (145)
T PF13762_consen  122 IKA---ALRGYFHDS  133 (145)
T ss_pred             HHH---HHcCCCCcc
Confidence            999   555554443

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

Probab=95.50  E-value=0.098  Score=41.63  Aligned_cols=122  Identities=20%  Similarity=0.239  Sum_probs=74.3

Q ss_pred             HHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CC---CC-ChhHHHHHHHHHHHhc
Q 035927           16 YINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS--NI---RP-DEFTIVRILTAYMYCK   86 (153)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~---~p-~~~t~~~li~~~~~~~   86 (153)
                      |.+.++++.|.++|.+-..  | |+...+-+--...+.+.+.+|...|+.-+..  .+   ++ -..+++-+-.+  |-+
T Consensus       390 y~~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~--~Rk  467 (611)
T KOG1173|consen  390 YMRTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHA--YRK  467 (611)
T ss_pred             HHHhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHH--HHH
Confidence            4556667777777766652  2 6666666666556667777777777766521  11   11 22334444444  577


Q ss_pred             cCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHh
Q 035927           87 CGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACT  139 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~  139 (153)
                      .+..++|+..+++...   .|..++.++.-.|...|.++          .++||-.+...+++.+.
T Consensus       468 l~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~ai  533 (611)
T KOG1173|consen  468 LNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAI  533 (611)
T ss_pred             HhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHH
Confidence            7777888777777642   36666666666666666666          56677666666665443

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

Probab=95.49  E-value=0.043  Score=46.08  Aligned_cols=100  Identities=13%  Similarity=0.131  Sum_probs=75.6

Q ss_pred             CChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHH
Q 035927           20 GQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRV   96 (153)
Q Consensus        20 g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~   96 (153)
                      +..++|.++|.+...   .|...=|.+-..++..|++.+|.++|.+.++... -+..+|--+-+.  |..+|++..|.++
T Consensus       626 k~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~--~~e~~qy~~AIqm  702 (1018)
T KOG2002|consen  626 KHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHC--YVEQGQYRLAIQM  702 (1018)
T ss_pred             HHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHH--HHHHHHHHHHHHH
Confidence            456789999987763   3778888898999999999999999999987754 222344445555  6999999999999


Q ss_pred             HHhcccC-----ChhhHHHHHHHHHhcCCCC
Q 035927           97 LRKMLRK-----DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        97 ~~~m~~~-----~~~~~~~li~~~~~~~~~~  122 (153)
                      |+...+.     +...-+.|..++.+.+.+.
T Consensus       703 Ye~~lkkf~~~~~~~vl~~Lara~y~~~~~~  733 (1018)
T KOG2002|consen  703 YENCLKKFYKKNRSEVLHYLARAWYEAGKLQ  733 (1018)
T ss_pred             HHHHHHHhcccCCHHHHHHHHHHHHHhhhHH
Confidence            9998543     5666666666666666555

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.46  E-value=0.061  Score=30.53  Aligned_cols=60  Identities=20%  Similarity=0.294  Sum_probs=49.9

Q ss_pred             HHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhH
Q 035927           13 VSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT   74 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   74 (153)
                      -..|.+.+++++|.++++++..  | +...|...-..+.+.|++++|...++...+.+  |+...
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~--p~~~~   64 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELS--PDDPD   64 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC--CCcHH
Confidence            3578899999999999999973  3 67778888889999999999999999998754  44433

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

Probab=95.42  E-value=0.19  Score=36.86  Aligned_cols=74  Identities=16%  Similarity=0.239  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh-----CCCCCChhHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT-----SNIRPDEFTIVRIL   79 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t~~~li   79 (153)
                      ++..++..+...|+++.+.+.++++-.  | +...|..+|.+|.+.|+...|+..|+.+.+     .|+.|...+.....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~  234 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYE  234 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHH
Confidence            456677777777777777777777753  2 667788888888888877777777777754     46777766666665


Q ss_pred             HH
Q 035927           80 TA   81 (153)
Q Consensus        80 ~~   81 (153)
                      ..
T Consensus       235 ~~  236 (280)
T COG3629         235 EI  236 (280)
T ss_pred             HH
Confidence            54

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

Probab=95.39  E-value=0.14  Score=42.79  Aligned_cols=120  Identities=13%  Similarity=0.218  Sum_probs=70.0

Q ss_pred             hcCChHHHHHHHHhCCCC-CHHHHHHHHHHHH--hcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHH
Q 035927           18 NRGQVDIARQYFAQMPER-DYVLWTAMIDGYL--RVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQ   94 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~-~~~~~~~li~~~~--~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~   94 (153)
                      ..+++.+|....+++.+. .-..|...++++.  +.|+.++|..+++....-+.. |..|...+-..  |-+.|+.++|.
T Consensus        21 d~~qfkkal~~~~kllkk~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~--y~d~~~~d~~~   97 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKHPNALYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNV--YRDLGKLDEAV   97 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHH--HHHHhhhhHHH
Confidence            345666666666666421 2233455555554  567777777777666544332 66666666555  67778888888


Q ss_pred             HHHHhcccC--ChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhc
Q 035927           95 RVLRKMLRK--DKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTH  140 (153)
Q Consensus        95 ~~~~~m~~~--~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~  140 (153)
                      .+|++..+.  +...-..+..+|++.+.+.           ..+-+...|+++++-..+
T Consensus        98 ~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk~~yyfWsV~Slilq  156 (932)
T KOG2053|consen   98 HLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFPKRAYYFWSVISLILQ  156 (932)
T ss_pred             HHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHH
Confidence            888777653  3333334444555554443           333345667777766654

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

Probab=95.38  E-value=0.13  Score=42.04  Aligned_cols=54  Identities=22%  Similarity=0.211  Sum_probs=23.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFPE   62 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~   62 (153)
                      |..+|..|+..|+-++|..+..+-.+  ||..-|..+.+......-+++|+++.+.
T Consensus       427 w~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~yEkawElsn~  482 (777)
T KOG1128|consen  427 WDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLYEKAWELSNY  482 (777)
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHHHHHHHHhhh
Confidence            33444444444444444444443332  3444444444444333334444444443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=95.36  E-value=0.68  Score=33.26  Aligned_cols=138  Identities=10%  Similarity=0.017  Sum_probs=79.4

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC--CCH-HH---HHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChhHHHHHHHHHHH
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE--RDY-VL---WTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEFTIVRILTAYMY   84 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~--~~~-~~---~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~~~~   84 (153)
                      ....+.+.|++++|.+.|+++..  |+. ..   .-.+..++.+.+++++|...++++.+.- -.|+. -+...+.+..+
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~-~~a~Y~~g~~~  116 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNI-DYVLYMRGLTN  116 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCch-HHHHHHHHHhh
Confidence            34455668999999999999974  322 22   2345567778999999999999998652 23332 33333333101


Q ss_pred             hccC---------------C---hHHHHHHHHhccc--CChh------hHH------------HHHHHHHhcCCCC----
Q 035927           85 CKCG---------------D---VEKAQRVLRKMLR--KDKF------TWT------------AMIVGLAISDPFP----  122 (153)
Q Consensus        85 ~~~g---------------~---~~~a~~~~~~m~~--~~~~------~~~------------~li~~~~~~~~~~----  122 (153)
                      ...+               +   ..+|.+.|+.+++  |+..      ..-            .+..-|.+.|.+.    
T Consensus       117 ~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~~A~~rl~~l~~~la~~e~~ia~~Y~~~~~y~AA~~  196 (243)
T PRK10866        117 MALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVN  196 (243)
T ss_pred             hhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchHHHHH
Confidence            1111               2   2345566666643  2111      000            1111133333332    


Q ss_pred             ----------CCCCCHhHHHHHHHHHhcCCchhHhhhh
Q 035927          123 ----------TIRPDEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       123 ----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                                +-+........+..+|.+.|..++|.+.
T Consensus       197 r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~  234 (243)
T PRK10866        197 RVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKV  234 (243)
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHH
Confidence                      4445567778889999999999988764

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

Probab=95.30  E-value=0.1  Score=41.54  Aligned_cols=92  Identities=20%  Similarity=0.221  Sum_probs=75.4

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC--hhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD--EFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~t~~~l   78 (153)
                      +|..+++.|-=.|--.|.+++|...|+...  +| |...||-|-..++...+.++|.+-|.+.++-  +|.  .+=||.-
T Consensus       428 ~DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlg  505 (579)
T KOG1125|consen  428 IDPDVQSGLGVLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLG  505 (579)
T ss_pred             CChhHHhhhHHHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhh
Confidence            667777777778888899999999999886  34 8899999999999999999999999999874  443  3456666


Q ss_pred             HHHHHHhccCChHHHHHHHHhc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      |.   +...|.+++|.+.|-..
T Consensus       506 IS---~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  506 IS---CMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             hh---hhhhhhHHHHHHHHHHH
Confidence            65   49999999998887665

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

Probab=95.25  E-value=0.69  Score=37.03  Aligned_cols=27  Identities=11%  Similarity=0.198  Sum_probs=20.2

Q ss_pred             CCCCH--hHHHHHHHHHhcCCchhHhhhh
Q 035927          124 IRPDE--VTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       124 ~~p~~--~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      +.||.  ..|..+|..=+..|++.-+.++
T Consensus       466 l~~~ks~~Iw~r~l~yES~vGdL~si~~l  494 (656)
T KOG1914|consen  466 LSADKSKEIWDRMLEYESNVGDLNSILKL  494 (656)
T ss_pred             CChhhhHHHHHHHHHHHHhcccHHHHHHH
Confidence            45554  7788888888888888777654

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

Probab=95.22  E-value=0.94  Score=34.08  Aligned_cols=52  Identities=15%  Similarity=0.284  Sum_probs=27.6

Q ss_pred             HHHhcCChHHHHHHHHhCCC-C--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927           15 GYINRGQVDIARQYFAQMPE-R--DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~-~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      -|-..|-+|.|+.+|..+.. +  -...-..|+.-|-+..++++|.+.-++..+.
T Consensus       116 Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~  170 (389)
T COG2956         116 DYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKL  170 (389)
T ss_pred             HHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHc
Confidence            34455666666666666654 2  2234444555555555555555555555443

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

Probab=95.22  E-value=0.55  Score=39.86  Aligned_cols=94  Identities=14%  Similarity=0.246  Sum_probs=65.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCCCC------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh--hHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPERD------YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE--FTI   75 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~   75 (153)
                      -|+...+.|-+.|.-.|+++.+..+.+.+-..+      ..+|-.+-++|...|++++|...|.+-.+.  .||.  ..+
T Consensus       268 ~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~  345 (1018)
T KOG2002|consen  268 ENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPL  345 (1018)
T ss_pred             CCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCccccc
Confidence            355567778888888888888888888876432      345777888888888888888888666543  3333  223


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      -.+-+.  |.+.|+++.+..-|+++.
T Consensus       346 ~GlgQm--~i~~~dle~s~~~fEkv~  369 (1018)
T KOG2002|consen  346 VGLGQM--YIKRGDLEESKFCFEKVL  369 (1018)
T ss_pred             cchhHH--HHHhchHHHHHHHHHHHH
Confidence            334444  677777777777777763

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

Probab=95.21  E-value=0.28  Score=40.31  Aligned_cols=134  Identities=14%  Similarity=0.124  Sum_probs=94.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG   88 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g   88 (153)
                      --.+...+.+.|-...|..+|++.     ..|...|..|+..|+-.+|..+..+-.++  +||...|..+-+.  .-...
T Consensus       401 q~~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGDv--~~d~s  471 (777)
T KOG1128|consen  401 QRLLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGDV--LHDPS  471 (777)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhhh--ccChH
Confidence            345667888899999999999876     56788888999999999999999888873  6888888888887  34444


Q ss_pred             ChHHHHHHHHhcccC-------------------------------ChhhHHHHHHHHHhcCCCC----------CCCCC
Q 035927           89 DVEKAQRVLRKMLRK-------------------------------DKFTWTAMIVGLAISDPFP----------TIRPD  127 (153)
Q Consensus        89 ~~~~a~~~~~~m~~~-------------------------------~~~~~~~li~~~~~~~~~~----------~~~p~  127 (153)
                      -+++|+++++....+                               -..+|-.+-.+..+.+.++          ...||
T Consensus       472 ~yEkawElsn~~sarA~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~aF~rcvtL~Pd  551 (777)
T KOG1128|consen  472 LYEKAWELSNYISARAQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVKAFHRCVTLEPD  551 (777)
T ss_pred             HHHHHHHHhhhhhHHHHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence            567777777665221                               1112222222222333333          56687


Q ss_pred             H-hHHHHHHHHHhcCCchhHhhhhc
Q 035927          128 E-VTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       128 ~-~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      . ..||.+-.+|.+.|...+|...+
T Consensus       552 ~~eaWnNls~ayi~~~~k~ra~~~l  576 (777)
T KOG1128|consen  552 NAEAWNNLSTAYIRLKKKKRAFRKL  576 (777)
T ss_pred             chhhhhhhhHHHHHHhhhHHHHHHH
Confidence            6 55999999999988888887654

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=95.06  E-value=0.35  Score=32.11  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=51.5

Q ss_pred             HHHHHHHHHH---hcCChHHHHHHHHHHhhC-CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCC-hhhHHHHHH
Q 035927           39 LWTAMIDGYL---RVNRFREALTLFPEMQTS-NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKD-KFTWTAMIV  113 (153)
Q Consensus        39 ~~~~li~~~~---~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~li~  113 (153)
                      .-+.||+...   ..++++++..+++.|+-. .-.|...+|...+.    .+.|+|++|.++|+.+.+.. ...|..-+-
T Consensus         9 iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~----i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~   84 (153)
T TIGR02561         9 LLGGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKELDMFDGWLL----IARGNYDEAARILRELLSSAGAPPYGKALL   84 (153)
T ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchhHHHHH----HHcCCHHHHHHHHHhhhccCCCchHHHHHH
Confidence            3344444443   368888999999888643 33466777777774    78999999999999997653 335555555


Q ss_pred             HHHhc
Q 035927          114 GLAIS  118 (153)
Q Consensus       114 ~~~~~  118 (153)
                      ++|-.
T Consensus        85 A~CL~   89 (153)
T TIGR02561        85 ALCLN   89 (153)
T ss_pred             HHHHH
Confidence            55544

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

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

Probab=94.99  E-value=0.24  Score=36.59  Aligned_cols=96  Identities=18%  Similarity=0.261  Sum_probs=69.5

Q ss_pred             CCchhHHHHHHHHHHhc-----CChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCC----------------hHHHH
Q 035927            3 NKDVISWTDIVSGYINR-----GQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNR----------------FREAL   57 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~-----g~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~----------------~~~a~   57 (153)
                      +.|...|-+.+..+...     +.++-.---+..|.    ++|..+|+.||+.+-+...                -+=+.
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            56777888888877665     33443333333443    5799999999999876532                24578


Q ss_pred             HHHHHHhhCCCCCChhHHHHHHHHHHHhccCCh-HHHHHHHHhc
Q 035927           58 TLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDV-EKAQRVLRKM  100 (153)
Q Consensus        58 ~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~-~~a~~~~~~m  100 (153)
                      +++++|...|+.||..+=..+|++  +++.+-. .+..++.-.|
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~--FGr~~~p~~K~~Rm~yWm  185 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNA--FGRWNFPTKKVKRMLYWM  185 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHH--hccccccHHHHHHHHHhh
Confidence            899999999999999999999999  4777653 4455555555

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=94.97  E-value=0.55  Score=29.99  Aligned_cols=56  Identities=14%  Similarity=0.234  Sum_probs=42.5

Q ss_pred             HHHHhcCChHHHHHHHHHHhhCCCCCChh--HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           45 DGYLRVNRFREALTLFPEMQTSNIRPDEF--TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        45 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .++-..|+.++|..+|++-...|...+..  .+-.+-..  |-..|++++|..++++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~last--lr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLAST--LRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence            44556799999999999999988755422  22233333  7899999999999999865

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

Probab=94.91  E-value=0.22  Score=42.41  Aligned_cols=114  Identities=15%  Similarity=0.154  Sum_probs=82.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .|+.|-..|+...+...|...|++--+   .+...+....+.|+...+++.|..+.-.--+ .-+--...+|++-.+-.|
T Consensus       494 af~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~q-ka~a~~~k~nW~~rG~yy  572 (1238)
T KOG1127|consen  494 AFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQ-KAPAFACKENWVQRGPYY  572 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhh-hchHHHHHhhhhhccccc
Confidence            577788888887788888888888764   3677889999999999999999998332221 122234445555454347


Q ss_pred             hccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           85 CKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      .+.++.+++..-|+.-...   |...|..+..+|.+.|...
T Consensus       573 Lea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~  613 (1238)
T KOG1127|consen  573 LEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYS  613 (1238)
T ss_pred             cCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCcee
Confidence            7888999998888887543   6667777777777777666

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=94.91  E-value=0.99  Score=32.65  Aligned_cols=74  Identities=14%  Similarity=0.226  Sum_probs=52.9

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCC------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCChhHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPDEFTIVRI   78 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~l   78 (153)
                      ...|+.-+.. .+.|++++|.+.|+.+.+.      ...+--.++.++-+.+++++|...++++.+. +-.|| .-|...
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-LQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPN-ADYAYY  112 (254)
T ss_pred             HHHHHHHHHH-HhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCC-hhHHHH
Confidence            3456665544 4689999999999999742      4556667777788899999999999999765 33444 345555


Q ss_pred             HHH
Q 035927           79 LTA   81 (153)
Q Consensus        79 i~~   81 (153)
                      |.+
T Consensus       113 lkg  115 (254)
T COG4105         113 LKG  115 (254)
T ss_pred             HHH
Confidence            555

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

Probab=94.85  E-value=0.32  Score=41.36  Aligned_cols=52  Identities=8%  Similarity=0.147  Sum_probs=24.1

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      +..+|-+.|+.++|..+|+++.+   .|..+-|-+-..++.. ++++|++++...+
T Consensus       122 LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV  176 (906)
T PRK14720        122 LAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAITYLKKAI  176 (906)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHHHHHHHHH
Confidence            33334444555555555555442   1444444444444444 5555555444443

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=94.81  E-value=0.67  Score=33.92  Aligned_cols=91  Identities=20%  Similarity=0.337  Sum_probs=52.8

Q ss_pred             HHHHHHHHhc-CChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-----CCChhH
Q 035927           10 TDIVSGYINR-GQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-----RPDEFT   74 (153)
Q Consensus        10 ~~li~~~~~~-g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-----~p~~~t   74 (153)
                      ..+-..|-+. |++++|.+.|++-..     .    -..++..+...+++.|++++|.++|++......     ++++..
T Consensus       118 ~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~  197 (282)
T PF14938_consen  118 KELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKE  197 (282)
T ss_dssp             HHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHH
Confidence            3344444444 555555555544431     1    123577778888888999999999998865432     222322


Q ss_pred             --HHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           75 --IVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        75 --~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                        +.++|  | +...|++-.|.+.|++..+.
T Consensus       198 ~~l~a~l--~-~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  198 YFLKAIL--C-HLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             HHHHHHH--H-HHHTT-HHHHHHHHHHHGTT
T ss_pred             HHHHHHH--H-HHHcCCHHHHHHHHHHHHhh
Confidence              22322  2 57788999999999987643

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

Probab=94.69  E-value=1.6  Score=35.80  Aligned_cols=108  Identities=7%  Similarity=0.096  Sum_probs=74.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC----------ChhhH
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK----------DKFTW  108 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~----------~~~~~  108 (153)
                      .|...+...-..+-++.+..++++.++    .+...-+-.|..  +++.+++++|-+.+..+...          +-..|
T Consensus       140 IW~lyl~Fv~~~~lPets~rvyrRYLk----~~P~~~eeyie~--L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw  213 (835)
T KOG2047|consen  140 IWDLYLKFVESHGLPETSIRVYRRYLK----VAPEAREEYIEY--LAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLW  213 (835)
T ss_pred             chHHHHHHHHhCCChHHHHHHHHHHHh----cCHHHHHHHHHH--HHhccchHHHHHHHHHhcCchhhhhhcccchhhHH
Confidence            355666666666667777777777764    233336666776  59999999999999888532          34456


Q ss_pred             HHHHHHHHhcCC----CC---------CCCCCH--hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          109 TAMIVGLAISDP----FP---------TIRPDE--VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       109 ~~li~~~~~~~~----~~---------~~~p~~--~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +-+-.-.++.-.    ++         +.-||.  ..|.+|.+.|.++|.+|+|..+|.
T Consensus       214 ~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvye  272 (835)
T KOG2047|consen  214 LELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYE  272 (835)
T ss_pred             HHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence            655555555511    11         344675  679999999999999999998874

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=94.51  E-value=0.53  Score=33.07  Aligned_cols=65  Identities=18%  Similarity=0.225  Sum_probs=50.6

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh----hHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           35 RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE----FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      .....+-.+...+.+.|++++|...+++..+..  |+.    ..+..+-..  |.+.|++++|...++++.+.
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~--~~~~~~~~~A~~~~~~~l~~   99 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYA--YYKSGDYAEAIAAADRFIRL   99 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHH--HHhcCCHHHHHHHHHHHHHH
Confidence            466778888888999999999999999997653  322    244444444  79999999999999999653

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).

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

Probab=94.44  E-value=1  Score=36.38  Aligned_cols=68  Identities=12%  Similarity=0.064  Sum_probs=40.4

Q ss_pred             HhccCChHHHHHHHHhcccCChhhHHHHH-----HHHHhc-C-CCC--CCCCCHhHHHHHHHH---HhcCCchhHhhhhc
Q 035927           84 YCKCGDVEKAQRVLRKMLRKDKFTWTAMI-----VGLAIS-D-PFP--TIRPDEVTYVGVLSA---CTHNGNETFVINSC  151 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~~~~~~~~li-----~~~~~~-~-~~~--~~~p~~~t~~~ll~~---~~~~g~~~~a~~~~  151 (153)
                      +.|.|++++|.++|..+.+.+...+-.-+     .+-... . ..+  ...| ..||..+.+.   +...|++.+|++++
T Consensus       120 lYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL  198 (652)
T KOG2376|consen  120 LYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVP-EDSYELLYNTACILIENGKYNQAIELL  198 (652)
T ss_pred             HHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHH
Confidence            47899999999999999766433333322     222222 1 122  2223 3356555543   34689999999875


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      .
T Consensus       199 ~  199 (652)
T KOG2376|consen  199 E  199 (652)
T ss_pred             H
Confidence            3

>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=94.22  E-value=1  Score=30.75  Aligned_cols=96  Identities=8%  Similarity=0.125  Sum_probs=68.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC---CChhHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR---PDEFTIVR   77 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~---p~~~t~~~   77 (153)
                      ..+..+.+.|++.|+.+.|.+.|.++...      ....+=.+|+...-.+++..+...+.+....-..   ++...--.
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            35778899999999999999999999854      2345677788888889999888888877654222   22222112


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +..+..+...+++.+|-+.|-....
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~~  141 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSLS  141 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccCc
Confidence            2222234678899999999888864

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.

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

Probab=94.08  E-value=1.3  Score=36.28  Aligned_cols=107  Identities=17%  Similarity=0.198  Sum_probs=71.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC----------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCCh--hHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE----------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPDE--FTI   75 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~--~t~   75 (153)
                      -+.-|..+++.+++++|.+.+.....          .+...|..+-+..+++.+.-..+++=..|+.. +.-+|.  ..|
T Consensus       172 ~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw  251 (835)
T KOG2047|consen  172 REEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLW  251 (835)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHH
Confidence            45667788888999998888888763          25667888888887775544444433233221 123554  457


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcccC--ChhhHHHHHHHHHh
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLRK--DKFTWTAMIVGLAI  117 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~li~~~~~  117 (153)
                      .+|.+.  |.+.|++++|..+|++-.+.  ++.-|..+..+|+.
T Consensus       252 ~SLAdY--YIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~  293 (835)
T KOG2047|consen  252 CSLADY--YIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQ  293 (835)
T ss_pred             HHHHHH--HHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHH
Confidence            778887  79999999999999987654  44445555554443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=94.00  E-value=1.4  Score=30.60  Aligned_cols=56  Identities=11%  Similarity=0.190  Sum_probs=41.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCC--C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      .....+.+.|++++|...|+++..  |    -....-.+..++.+.|++++|...++++.+.
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344566778999999999999973  2    2345556778888999999999999998764

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

Probab=93.97  E-value=2.2  Score=33.38  Aligned_cols=140  Identities=10%  Similarity=-0.044  Sum_probs=62.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHH---HHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAM---IDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~l---i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .....+-+.+...|+.++|...|++.+.-|..+..+|   --.+.+.|+.++...+...+.+..   +...=.+++.+|.
T Consensus       233 hLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~---~~ta~~wfV~~~~  309 (564)
T KOG1174|consen  233 HLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV---KYTASHWFVHAQL  309 (564)
T ss_pred             HHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh---hcchhhhhhhhhh
Confidence            3345555566666666666666666554333222211   111224445544444444443321   1111122222222


Q ss_pred             HhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHhhh
Q 035927           84 YCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      +....+++.|+.+-++.++.   +...|-.--+.+...+..+          ...| +...|.-++.+|...|...+|+-
T Consensus       310 l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~  389 (564)
T KOG1174|consen  310 LYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANA  389 (564)
T ss_pred             hhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHH
Confidence            23334444444444444322   2222222222222223332          3444 45778888888888888777654

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

Probab=93.90  E-value=0.91  Score=38.73  Aligned_cols=124  Identities=10%  Similarity=0.140  Sum_probs=75.4

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHH-HHHHHHHHHHhcCChHHHHHH------------------HH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYV-LWTAMIDGYLRVNRFREALTL------------------FP   61 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~-~~~~li~~~~~~~~~~~a~~~------------------~~   61 (153)
                      +.+...+-.|+..+-..+++++|.++.+.-..  |+.. .|-.+-..+.+.++..++..+                  ..
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv~~l~~~~~~~~~~~ve~~~~  107 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLLNLIDSFSQNLKWAIVEHICD  107 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhhhhhhhcccccchhHHHHHHH
Confidence            35566789999999999999999999886542  3322 222222244455555554444                  22


Q ss_pred             HHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcC
Q 035927           62 EMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHN  141 (153)
Q Consensus        62 ~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~  141 (153)
                      .|...+  -+...+-.+..+  |-+.|+.+++..+|+++.+-|.                    -|....|.+-..|+..
T Consensus       108 ~i~~~~--~~k~Al~~LA~~--Ydk~g~~~ka~~~yer~L~~D~--------------------~n~~aLNn~AY~~ae~  163 (906)
T PRK14720        108 KILLYG--ENKLALRTLAEA--YAKLNENKKLKGVWERLVKADR--------------------DNPEIVKKLATSYEEE  163 (906)
T ss_pred             HHHhhh--hhhHHHHHHHHH--HHHcCChHHHHHHHHHHHhcCc--------------------ccHHHHHHHHHHHHHh
Confidence            222111  011233334443  6888999999999999987531                    1455566666666666


Q ss_pred             CchhHhhhhc
Q 035927          142 GNETFVINSC  151 (153)
Q Consensus       142 g~~~~a~~~~  151 (153)
                       ++++|.+++
T Consensus       164 -dL~KA~~m~  172 (906)
T PRK14720        164 -DKEKAITYL  172 (906)
T ss_pred             -hHHHHHHHH
Confidence             777776654

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.86  E-value=0.14  Score=25.04  Aligned_cols=24  Identities=8%  Similarity=0.225  Sum_probs=13.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHH
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEM   63 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m   63 (153)
                      |+.|-..|.+.|++++|.+++++.
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            445555555556666666555553

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

Probab=93.77  E-value=2.6  Score=35.67  Aligned_cols=133  Identities=12%  Similarity=0.189  Sum_probs=84.6

Q ss_pred             HHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCCh
Q 035927           15 GYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDV   90 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~   90 (153)
                      ...-.|++++|.+++.+.-+   .+...|-.|-..|=+.|+.+++...+-  +.....| |..-|-.+-..  ..+.|.+
T Consensus       148 ~lfarg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~l--lAAHL~p~d~e~W~~ladl--s~~~~~i  223 (895)
T KOG2076|consen  148 NLFARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWL--LAAHLNPKDYELWKRLADL--SEQLGNI  223 (895)
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHH--HHHhcCCCChHHHHHHHHH--HHhcccH
Confidence            33444999999999988863   377889999999999999999887763  3333344 55666666665  5888889


Q ss_pred             HHHHHHHHhcccCChhhHHH---HHHHHHhcCCCC----------CCCC------CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           91 EKAQRVLRKMLRKDKFTWTA---MIVGLAISDPFP----------TIRP------DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        91 ~~a~~~~~~m~~~~~~~~~~---li~~~~~~~~~~----------~~~p------~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +.|.-.|.+.++.++.-|..   -+.-|-+.|...          ...|      ...+...+++.+-..+..+.|.+.+
T Consensus       224 ~qA~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~l  303 (895)
T KOG2076|consen  224 NQARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKAL  303 (895)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            99999999987653332222   222233332222          2223      2234445556666666667766654

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=93.62  E-value=2.8  Score=34.96  Aligned_cols=123  Identities=15%  Similarity=0.120  Sum_probs=84.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      ..|......+.+.+..++|...+.+..+-   -...|.-.-..+...|..++|.+.|.....-  -|+.+--..-+..+ 
T Consensus       651 ~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~l--dP~hv~s~~Ala~~-  727 (799)
T KOG4162|consen  651 KLWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALAL--DPDHVPSMTALAEL-  727 (799)
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhc--CCCCcHHHHHHHHH-
Confidence            34566677777888888888777777643   3344555545556678888888888777653  46555544445554 


Q ss_pred             HhccCChHHHHH--HHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           84 YCKCGDVEKAQR--VLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        84 ~~~~g~~~~a~~--~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.+.|+..-|.+  ++..+.+-|                    +-+..-|-.+-..+-+.|+.++|-++|.
T Consensus       728 lle~G~~~la~~~~~L~dalr~d--------------------p~n~eaW~~LG~v~k~~Gd~~~Aaecf~  778 (799)
T KOG4162|consen  728 LLELGSPRLAEKRSLLSDALRLD--------------------PLNHEAWYYLGEVFKKLGDSKQAAECFQ  778 (799)
T ss_pred             HHHhCCcchHHHHHHHHHHHhhC--------------------CCCHHHHHHHHHHHHHccchHHHHHHHH
Confidence            788888777777  888887644                    1256777777788888888888877763

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

Probab=93.54  E-value=0.91  Score=35.99  Aligned_cols=120  Identities=9%  Similarity=0.166  Sum_probs=65.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMY   84 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~   84 (153)
                      |--+-..|....+.++....|.+-..   .|..+|..=-....-.+++++|..=|++.++-  .| +...|-.+.-+  .
T Consensus       363 yI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L--~pe~~~~~iQl~~a--~  438 (606)
T KOG0547|consen  363 YIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAISL--DPENAYAYIQLCCA--L  438 (606)
T ss_pred             HHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhc--ChhhhHHHHHHHHH--H
Confidence            55556666666666666666666542   24444444444444455666666666665543  23 23333333322  4


Q ss_pred             hccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           85 CKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .|.++++++...|+..+++                    .+--+..|+..-..+...+++++|.+-|+
T Consensus       439 Yr~~k~~~~m~~Fee~kkk--------------------FP~~~Evy~~fAeiLtDqqqFd~A~k~YD  486 (606)
T KOG0547|consen  439 YRQHKIAESMKTFEEAKKK--------------------FPNCPEVYNLFAEILTDQQQFDKAVKQYD  486 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHh--------------------CCCCchHHHHHHHHHhhHHhHHHHHHHHH
Confidence            5667777777777777653                    11123445555566666666666655543

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

Probab=93.49  E-value=0.6  Score=37.39  Aligned_cols=76  Identities=14%  Similarity=0.207  Sum_probs=60.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      ...+++.|-++|-+.+++++|+..+++-.   ..+..+++++--.+...|+++.|.+.|.+-+.  ++||-.+...+++.
T Consensus       454 w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~  531 (611)
T KOG1173|consen  454 WEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKL  531 (611)
T ss_pred             hhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHH
Confidence            45568888888888999999998888765   34788888888888888999999888887664  57887777777776


Q ss_pred             H
Q 035927           82 Y   82 (153)
Q Consensus        82 ~   82 (153)
                      +
T Consensus       532 a  532 (611)
T KOG1173|consen  532 A  532 (611)
T ss_pred             H
Confidence            4

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.43  E-value=2.2  Score=31.06  Aligned_cols=129  Identities=10%  Similarity=0.071  Sum_probs=78.8

Q ss_pred             cCChHHHHHHHHhCCC--------CCH-HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC
Q 035927           19 RGQVDIARQYFAQMPE--------RDY-VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD   89 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~--------~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~   89 (153)
                      ..+.++..+++.++..        ++. ..|-.++-+....|+.+.|..-++++...=  |...=...+=... +...|+
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~-lEa~~~  101 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAML-LEATGN  101 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHH-HHHhhc
Confidence            3567777777777752        122 245556666667788888888888876542  4433333333332 566888


Q ss_pred             hHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCC-C----------CCCCCHhHHHHHHHHHhcCCchhHhhhh
Q 035927           90 VEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPF-P----------TIRPDEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus        90 ~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~-~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      +++|+++++.+.+.   |..++---+...-..|.= +          .+.-|...|.-+-.-|...|++++|.-+
T Consensus       102 ~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fC  176 (289)
T KOG3060|consen  102 YKEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFC  176 (289)
T ss_pred             hhhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHH
Confidence            88888888888653   444444333332222111 1          4556778888888888888888877543

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=93.25  E-value=1.2  Score=34.98  Aligned_cols=63  Identities=17%  Similarity=0.094  Sum_probs=51.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh----HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF----TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +...|+.+-.+|.+.|++++|+..|++.++.  .|+..    +|..+-.+  |.+.|+.++|++.+++..+
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAca--ya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACC--HAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence            5678999999999999999999999998775  46643    34444444  8999999999999998765

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.15  E-value=1.1  Score=35.54  Aligned_cols=85  Identities=14%  Similarity=0.121  Sum_probs=56.8

Q ss_pred             HHHhcCChHHHHHHHHhCCCC-------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927           15 GYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~-------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      .+...|++++|.+.|++....       ....+--+.-.+.-..++++|.+.|..+.+.+ +-+..+|.=+..+| |...
T Consensus       276 ~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c-~~~l  353 (468)
T PF10300_consen  276 LERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAAC-LLML  353 (468)
T ss_pred             HHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHH-HHhh
Confidence            344468888888888864421       23344444445556678888888888887654 23556666666666 7888


Q ss_pred             CCh-------HHHHHHHHhcc
Q 035927           88 GDV-------EKAQRVLRKML  101 (153)
Q Consensus        88 g~~-------~~a~~~~~~m~  101 (153)
                      |+.       ++|.++|.+++
T Consensus       354 ~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  354 GREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             ccchhhhhhHHHHHHHHHHHH
Confidence            887       78888888773

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.

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

Probab=93.00  E-value=0.25  Score=36.38  Aligned_cols=69  Identities=13%  Similarity=0.127  Sum_probs=51.6

Q ss_pred             HhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhhh
Q 035927           84 YCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      +.+.+++++|...|.+.++   .|.+-|..-..+|.+.|.++          .+-|. ..+|..|-.+|...|++++|.+
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~~  170 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAIE  170 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHHH
Confidence            3567788888888888754   36777888888888887777          33343 3668888888888998888887


Q ss_pred             hcc
Q 035927          150 SCN  152 (153)
Q Consensus       150 ~~~  152 (153)
                      -|+
T Consensus       171 ayk  173 (304)
T KOG0553|consen  171 AYK  173 (304)
T ss_pred             HHH
Confidence            764

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.97  E-value=1.4  Score=36.55  Aligned_cols=85  Identities=18%  Similarity=0.231  Sum_probs=60.0

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD   89 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~   89 (153)
                      +.-+.-+...|+-.+|.++-.+.+-||-..|---+.+++..+++++-+++-..++      +...|.-++.+|  .+.|+
T Consensus       688 ~dTv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c--~~~~n  759 (829)
T KOG2280|consen  688 HDTVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEAC--LKQGN  759 (829)
T ss_pred             HHHHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHH--Hhccc
Confidence            4445566667788888888888888888888888888888887776444433332      146677778886  78888


Q ss_pred             hHHHHHHHHhccc
Q 035927           90 VEKAQRVLRKMLR  102 (153)
Q Consensus        90 ~~~a~~~~~~m~~  102 (153)
                      .++|.+.+-++..
T Consensus       760 ~~EA~KYiprv~~  772 (829)
T KOG2280|consen  760 KDEAKKYIPRVGG  772 (829)
T ss_pred             HHHHhhhhhccCC
Confidence            8888887776644

>PLN02789 farnesyltranstransferase

Probab=92.95  E-value=3  Score=31.30  Aligned_cols=112  Identities=14%  Similarity=0.113  Sum_probs=71.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVN-RFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      ++..+-..+.+.++.++|..+.++..+.   +..+|+.--..+.+.| +++++++.++.+.+.+-+ +...|+---..  
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npk-nyqaW~~R~~~--  115 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPK-NYQIWHHRRWL--  115 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCc-chHHhHHHHHH--
Confidence            4455556677788899999999988743   4445555444555556 578999999988876532 22344433222  


Q ss_pred             HhccCC--hHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           84 YCKCGD--VEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        84 ~~~~g~--~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      +.+.|+  .+++...++++.+.   |..+|+...-.+...+.++
T Consensus       116 l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~  159 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWE  159 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHH
Confidence            244554  36677888777543   6667777666666665555

>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=92.87  E-value=2  Score=28.93  Aligned_cols=51  Identities=22%  Similarity=0.212  Sum_probs=34.0

Q ss_pred             hcCChHHHHHHHHHHhhC-CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           49 RVNRFREALTLFPEMQTS-NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        49 ~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.++.+++..+++.++-. .-.|...++...+    +.+.|+|.+|+.+|+.+.+.
T Consensus        22 ~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l----~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLRPEFPELDLFDGWL----HIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             ccCChHHHHHHHHHHHHhCCCchHHHHHHHHH----HHHhCCHHHHHHHHHHHhcc
Confidence            456777888888777643 2234555555555    36788888888888887653

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.72  E-value=0.38  Score=23.45  Aligned_cols=22  Identities=18%  Similarity=0.395  Sum_probs=10.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFA   30 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~   30 (153)
                      |+.|-..|.+.|++++|+++|+
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~   23 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYE   23 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHH
Confidence            3444444455555555544443

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=92.71  E-value=2.3  Score=31.11  Aligned_cols=62  Identities=10%  Similarity=0.223  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHhc-CChHHHHHHHHHHhhC----CCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           39 LWTAMIDGYLRV-NRFREALTLFPEMQTS----NIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        39 ~~~~li~~~~~~-~~~~~a~~~~~~m~~~----~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .+..+-..|-+. |++++|.+.|++..+.    |-+- -...+..+...  +.+.|++++|.++|+++..
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l--~~~l~~y~~A~~~~e~~~~  183 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADL--YARLGRYEEAIEIYEEVAK  183 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--HHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHH--HHHhCCHHHHHHHHHHHHH
Confidence            566667777777 8999999988887542    3111 12333444444  7999999999999999843

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.65  E-value=0.65  Score=34.84  Aligned_cols=93  Identities=17%  Similarity=0.236  Sum_probs=70.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-CCH-----HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-RDY-----VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-~~~-----~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+-..++..-....+++++...+=+++. |+.     .+-..+++.+.+. ++++++.++..-.+-|+-||..+++.+|+
T Consensus        65 ~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky-~pq~~i~~l~npIqYGiF~dqf~~c~l~D  143 (418)
T KOG4570|consen   65 LTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKY-DPQKAIYTLVNPIQYGIFPDQFTFCLLMD  143 (418)
T ss_pred             eehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHcc-ChHHHHHHHhCcchhccccchhhHHHHHH
Confidence            3445556666667889999999888874 321     2333445544443 57799999999999999999999999999


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .  +.+.++..+|..+...|..
T Consensus       144 ~--flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  144 S--FLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             H--HHhcccHHHHHHHHHHHHH
Confidence            9  5999999999999888754

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.35  E-value=2  Score=27.70  Aligned_cols=87  Identities=15%  Similarity=0.196  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ..-...++..+.+.+.++....+++.+...   +...+|.++..+++.+ ..+.++.+..      ..+......+++.|
T Consensus         7 ~~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c   79 (140)
T smart00299        7 PIDVSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLC   79 (140)
T ss_pred             cCCHHHHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHH
Confidence            334578899999899999999999988643   6778999999999875 3444455442      13344455567765


Q ss_pred             HHhccCChHHHHHHHHhcc
Q 035927           83 MYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~  101 (153)
                        .+.+.++++.-++.++.
T Consensus        80 --~~~~l~~~~~~l~~k~~   96 (140)
T smart00299       80 --EKAKLYEEAVELYKKDG   96 (140)
T ss_pred             --HHcCcHHHHHHHHHhhc
Confidence              55666666666666653

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=92.35  E-value=3.5  Score=30.49  Aligned_cols=97  Identities=13%  Similarity=0.165  Sum_probs=77.3

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcC---ChHHHHHHHHHHhhCCCCCChhHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVN---RFREALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      -|...|--|-.+|.+.|+++.|..-|++-.   .+|...+..+-..+....   .-.++.++|+++++.  .|+.++-..
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHHHHH
Confidence            467789999999999999999999998775   457777777777776543   457899999999875  366666666


Q ss_pred             HHHHHHHhccCChHHHHHHHHhcccC
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ++..- +...|++.+|...|+.|.+.
T Consensus       232 lLA~~-afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         232 LLAFA-AFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHH-HHHcccHHHHHHHHHHHHhc
Confidence            66553 79999999999999999764

>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=92.04  E-value=2.4  Score=28.55  Aligned_cols=75  Identities=17%  Similarity=0.263  Sum_probs=54.4

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCC--CC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927           11 DIVSGYINRGQVDIARQYFAQMP--ER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~--~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      .++..-.+.++.+++..+++-++  +|   ...++-.++.  ++.|++.+|+.+|++..+..  |.......|+..| +.
T Consensus        15 e~~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~--i~r~~w~dA~rlLr~l~~~~--~~~p~~kALlA~C-L~   89 (160)
T PF09613_consen   15 EVLSVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLH--IVRGDWDDALRLLRELEERA--PGFPYAKALLALC-LY   89 (160)
T ss_pred             HHHHHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHH--HHhCCHHHHHHHHHHHhccC--CCChHHHHHHHHH-HH
Confidence            34445566789999999999987  44   4455666655  78999999999999987653  5556666777776 55


Q ss_pred             ccCCh
Q 035927           86 KCGDV   90 (153)
Q Consensus        86 ~~g~~   90 (153)
                      ..|+.
T Consensus        90 ~~~D~   94 (160)
T PF09613_consen   90 ALGDP   94 (160)
T ss_pred             HcCCh
Confidence            55553

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=92.03  E-value=3.3  Score=33.31  Aligned_cols=63  Identities=13%  Similarity=0.014  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +...|.++--.....|++++|...+++..+.+  |+...|..+-..  +...|+.++|.+.+++...
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~--~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKV--YELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHh
Confidence            55677777666667899999999999998875  788888888887  6999999999999998754

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

Probab=91.98  E-value=5  Score=31.48  Aligned_cols=137  Identities=14%  Similarity=0.056  Sum_probs=82.4

Q ss_pred             HHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH-HHHHHHhccC
Q 035927           13 VSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI-LTAYMYCKCG   88 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l-i~~~~~~~~g   88 (153)
                      -.++.+.+++++|.--|+.-.  .| +..+|..|+..|...|++++|.-+-+.-.+. ++-+..+.+.+ -..| +-...
T Consensus       341 G~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~-~~dp~  418 (564)
T KOG1174|consen  341 GRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVL-FPDPR  418 (564)
T ss_pred             cHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceee-ccCch
Confidence            345667788888877776654  33 7778888888888888888776654443221 12344444433 1222 23333


Q ss_pred             ChHHHHHHHHhccc--CC-hhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           89 DVEKAQRVLRKMLR--KD-KFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        89 ~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      -=++|.+++++-.+  |+ +..-+.+..-+...|...          ..-||....+.+-..+.....+.+|++.|
T Consensus       419 ~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y  494 (564)
T KOG1174|consen  419 MREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYY  494 (564)
T ss_pred             hHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHH
Confidence            34566666666532  32 333444444444444444          34588888888888888888888887765

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.88  E-value=1.8  Score=31.85  Aligned_cols=91  Identities=9%  Similarity=0.149  Sum_probs=50.2

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCCC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH---HH
Q 035927           12 IVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY---MY   84 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~---~~   84 (153)
                      ++..+--.|.+.-....+++..+.    ++..-+.|.+.--+.|+.+.|...|++..+..-+.|..+++.++.--   .|
T Consensus       183 ~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~  262 (366)
T KOG2796|consen  183 MANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLH  262 (366)
T ss_pred             HHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhhe
Confidence            333344445555555555555432    44555555555556677777777777666555556666666655432   23


Q ss_pred             hccCChHHHHHHHHhccc
Q 035927           85 CKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~  102 (153)
                      .-..+...|...|++++.
T Consensus       263 lg~nn~a~a~r~~~~i~~  280 (366)
T KOG2796|consen  263 LGQNNFAEAHRFFTEILR  280 (366)
T ss_pred             ecccchHHHHHHHhhccc
Confidence            344455555555555543

>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=91.86  E-value=1.6  Score=28.62  Aligned_cols=81  Identities=17%  Similarity=0.243  Sum_probs=45.4

Q ss_pred             cCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHH
Q 035927           19 RGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLR   98 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~   98 (153)
                      +|++......+..+- .+.......++.+.+.|+-++-.+++.++.+ +-.++....-.+-.+  |.+.|+..++.++++
T Consensus        69 C~NlKrVi~C~~~~n-~~se~vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~A--y~klg~~r~~~ell~  144 (161)
T PF09205_consen   69 CGNLKRVIECYAKRN-KLSEYVDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANA--YKKLGNTREANELLK  144 (161)
T ss_dssp             -S-THHHHHHHHHTT----HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHH--HHHTT-HHHHHHHHH
T ss_pred             hcchHHHHHHHHHhc-chHHHHHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHH--HHHhcchhhHHHHHH
Confidence            456666666665552 2334456667777777777777777777654 335666666666666  577888777777777


Q ss_pred             hcccC
Q 035927           99 KMLRK  103 (153)
Q Consensus        99 ~m~~~  103 (153)
                      +.-++
T Consensus       145 ~ACek  149 (161)
T PF09205_consen  145 EACEK  149 (161)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            66443

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

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

Probab=91.68  E-value=1.6  Score=37.54  Aligned_cols=95  Identities=22%  Similarity=0.350  Sum_probs=54.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--------------------------------------C-CHHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--------------------------------------R-DYVLWTAMI   44 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--------------------------------------~-~~~~~~~li   44 (153)
                      .|...+..+.+.|++...++.|..+.-.-.+                                      | |...|..+.
T Consensus       524 tdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLG  603 (1238)
T KOG1127|consen  524 TDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLG  603 (1238)
T ss_pred             hhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHH
Confidence            3455567777788888888887777333322                                      1 455566666


Q ss_pred             HHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           45 DGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        45 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      .+|...|.+..|+.+|.+...  ++|+ .+|...-.+-+.+..|+..++...+..+.
T Consensus       604 eAY~~sGry~~AlKvF~kAs~--LrP~-s~y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  604 EAYPESGRYSHALKVFTKASL--LRPL-SKYGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             HHHHhcCceehHHHhhhhhHh--cCcH-hHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            666666666666666655543  2343 23333322223456666666666666553

>PRK15331 chaperone protein SicA; Provisional

Probab=91.64  E-value=2.5  Score=28.61  Aligned_cols=51  Identities=18%  Similarity=0.070  Sum_probs=25.5

Q ss_pred             HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhc
Q 035927           47 YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        47 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      +-..|++++|..+|..+..-+. -+.. |..=+.+| +-..+++++|...|...
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~-~n~~-Y~~GLaa~-~Q~~k~y~~Ai~~Y~~A   97 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDF-YNPD-YTMGLAAV-CQLKKQFQKACDLYAVA   97 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCc-CcHH-HHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence            3355666666666666554332 1222 33333333 45556666666665554

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

Probab=91.63  E-value=2.8  Score=33.19  Aligned_cols=90  Identities=16%  Similarity=0.229  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHH-HHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTI-VRILTA   81 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~-~~li~~   81 (153)
                      +|+..|++--+..-++.|..+|.+.++     +++..++++|..++ .|+...|..+|+-=...  -||...| +-.+.-
T Consensus       399 v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl~f  475 (660)
T COG5107         399 VFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYLLF  475 (660)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHHHH
Confidence            578888888888889999999988874     47788999998775 46677788888654432  2444443 444444


Q ss_pred             HHHhccCChHHHHHHHHhccc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~  102 (153)
                        +.+.++-+.|..+|+.-++
T Consensus       476 --Li~inde~naraLFetsv~  494 (660)
T COG5107         476 --LIRINDEENARALFETSVE  494 (660)
T ss_pred             --HHHhCcHHHHHHHHHHhHH
Confidence              6888999999999986543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.49  E-value=5.3  Score=33.39  Aligned_cols=70  Identities=17%  Similarity=0.259  Sum_probs=54.7

Q ss_pred             HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC------CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           83 MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+...|+-..|.++-.+.+=||-..|..-+.+++..+.|+      +-+-.+.-|.-.+.+|.+.|+.++|.+.+.
T Consensus       693 ~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskksPIGy~PFVe~c~~~~n~~EA~KYip  768 (829)
T KOG2280|consen  693 TLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKKSPIGYLPFVEACLKQGNKDEAKKYIP  768 (829)
T ss_pred             HHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccCCCCCchhHHHHHHhcccHHHHhhhhh
Confidence            4566777777777777777788889999999999998888      223336778888999999999999887653

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=91.26  E-value=0.76  Score=22.54  Aligned_cols=27  Identities=26%  Similarity=0.406  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      .+++.|-..|...|++++|+.++++..
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            456666666666666666666666654

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

Probab=91.15  E-value=4.8  Score=29.88  Aligned_cols=97  Identities=14%  Similarity=0.172  Sum_probs=67.0

Q ss_pred             HHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChH
Q 035927           15 GYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVE   91 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~   91 (153)
                      -+.+.+++++|+..|.+-.+   .|.+-|.-=-.+|++.|.++.|++=-+..++-+ .-...+|..|=.+  |...|+++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iD-p~yskay~RLG~A--~~~~gk~~  166 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSID-PHYSKAYGRLGLA--YLALGKYE  166 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcC-hHHHHHHHHHHHH--HHccCcHH
Confidence            34566788888888887753   377788888888889998888877665555422 1245566666666  68889999


Q ss_pred             HHHHHHHhccc--CChhhHHHHHHH
Q 035927           92 KAQRVLRKMLR--KDKFTWTAMIVG  114 (153)
Q Consensus        92 ~a~~~~~~m~~--~~~~~~~~li~~  114 (153)
                      +|++.|++..+  |+-.+|..=+..
T Consensus       167 ~A~~aykKaLeldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  167 EAIEAYKKALELDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHHhhhccCCCcHHHHHHHHH
Confidence            99999888854  544444443333

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=91.04  E-value=0.18  Score=32.78  Aligned_cols=120  Identities=17%  Similarity=0.270  Sum_probs=70.5

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      ..+++.+.+.+.++....+++.+.    ..+....+.++..|++.++.++.+.+++.       .+..-...+++.|  .
T Consensus        11 ~~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c--~   81 (143)
T PF00637_consen   11 SEVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLC--E   81 (143)
T ss_dssp             CCCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHH--H
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHH--H
Confidence            345677777788888777777776    23688899999999999887887777761       1113334555655  5


Q ss_pred             ccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC------CCCCCHhHHHHHHHHHhcCCc
Q 035927           86 KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP------TIRPDEVTYVGVLSACTHNGN  143 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~------~~~p~~~t~~~ll~~~~~~g~  143 (153)
                      +.|-++++.-++.++...+...     .-+...+.++      .-.++...|..+++.|...+.
T Consensus        82 ~~~l~~~a~~Ly~~~~~~~~al-----~i~~~~~~~~~a~e~~~~~~~~~l~~~l~~~~l~~~~  140 (143)
T PF00637_consen   82 KHGLYEEAVYLYSKLGNHDEAL-----EILHKLKDYEEAIEYAKKVDDPELWEQLLKYCLDSKP  140 (143)
T ss_dssp             TTTSHHHHHHHHHCCTTHTTCS-----STSSSTHCSCCCTTTGGGCSSSHHHHHHHHHHCTSTC
T ss_pred             hcchHHHHHHHHHHcccHHHHH-----HHHHHHccHHHHHHHHHhcCcHHHHHHHHHHHHhcCc
Confidence            6666666666666653321000     0000111111      223567778788777776654

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.

>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised

Probab=91.00  E-value=1.2  Score=23.47  Aligned_cols=35  Identities=23%  Similarity=0.192  Sum_probs=29.9

Q ss_pred             HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927           47 YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus        47 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      ..+.|-++++...+++|++.|+..+...++.+++-
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            34778888999999999999999999999888764

This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.

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

Probab=90.98  E-value=3.3  Score=35.14  Aligned_cols=106  Identities=15%  Similarity=0.268  Sum_probs=79.4

Q ss_pred             HHHHHHHHH--HhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            8 SWTDIVSGY--INRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         8 ~~~~li~~~--~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      .|..++.++  .|.|+.++|..+++....+   |..|...+-..|-..++.++|..+|++....  -|+......+..+ 
T Consensus        43 ~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFma-  119 (932)
T KOG2053|consen   43 LYAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMA-  119 (932)
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHH-
Confidence            466666665  5679999999999988743   8889999999999999999999999999875  4778888888887 


Q ss_pred             HHhccCChHH----HHHHHHhcccCChhhHHHHHHHHHhc
Q 035927           83 MYCKCGDVEK----AQRVLRKMLRKDKFTWTAMIVGLAIS  118 (153)
Q Consensus        83 ~~~~~g~~~~----a~~~~~~m~~~~~~~~~~li~~~~~~  118 (153)
                       |.|.+++.+    |.++++...++ ...|.+.++-+...
T Consensus       120 -yvR~~~yk~qQkaa~~LyK~~pk~-~yyfWsV~Slilqs  157 (932)
T KOG2053|consen  120 -YVREKSYKKQQKAALQLYKNFPKR-AYYFWSVISLILQS  157 (932)
T ss_pred             -HHHHHHHHHHHHHHHHHHHhCCcc-cchHHHHHHHHHHh
Confidence             688888765    55566654443 44444444444443

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=90.46  E-value=7.6  Score=30.82  Aligned_cols=89  Identities=13%  Similarity=0.190  Sum_probs=52.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCCCC----------CHHHHHHHHHHHHhc----CChHHHHHHHHHHhhCCCCCChhHH
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMPER----------DYVLWTAMIDGYLRV----NRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~~~----------~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      ..++...+=.|+-+.+++++.+-.+.          -...|+..+..++..    .+.+.|.++++.+++.  -|+...|
T Consensus       192 ~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lf  269 (468)
T PF10300_consen  192 LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALF  269 (468)
T ss_pred             HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHH
Confidence            34455555556666666666554321          223466666555543    3567777777777654  4665555


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      ...-.= .+...|++++|++.|+...
T Consensus       270 l~~~gR-~~~~~g~~~~Ai~~~~~a~  294 (468)
T PF10300_consen  270 LFFEGR-LERLKGNLEEAIESFERAI  294 (468)
T ss_pred             HHHHHH-HHHHhcCHHHHHHHHHHhc
Confidence            544444 3667777777777777654

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=90.38  E-value=0.76  Score=23.38  Aligned_cols=26  Identities=27%  Similarity=0.440  Sum_probs=12.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      |..+-..+.+.|++++|.+.+++.++
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            33444444444555555555554444

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=90.36  E-value=0.11  Score=33.70  Aligned_cols=94  Identities=14%  Similarity=0.132  Sum_probs=60.7

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCC
Q 035927           42 AMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPF  121 (153)
Q Consensus        42 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~  121 (153)
                      .+|..+.+.+.++....+++.....+-.-+....+.++..  |++.++.++..++++.-..   .-...++..|-+.+  
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~l--y~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~--   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLEL--YIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHG--   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHH--HHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTT--
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHH--HHhcCCchHHHHHcccccc---cCHHHHHHHHHhcc--
Confidence            3566777788889999999999977766677888888887  6999888888888773322   22222333333222  


Q ss_pred             CCCCCCHhHHHHHHHHHhcCCchhHhhhh
Q 035927          122 PTIRPDEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       122 ~~~~p~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                              .|...+-.|.+.|+.++|.++
T Consensus        85 --------l~~~a~~Ly~~~~~~~~al~i  105 (143)
T PF00637_consen   85 --------LYEEAVYLYSKLGNHDEALEI  105 (143)
T ss_dssp             --------SHHHHHHHHHCCTTHTTCSST
T ss_pred             --------hHHHHHHHHHHcccHHHHHHH
Confidence                    333445566677777776654

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.

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

Probab=90.34  E-value=1.7  Score=31.95  Aligned_cols=62  Identities=18%  Similarity=0.266  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .++..+++.+...|+.+.+...++++.... +-|...|..++.+  |.+.|+...|++.|+++.+
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~--y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEA--YLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHH--HHHcCCchHHHHHHHHHHH
Confidence            467778888888899999999999998764 4689999999999  6999999999999999954

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=90.18  E-value=2.7  Score=35.77  Aligned_cols=59  Identities=17%  Similarity=0.299  Sum_probs=41.5

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC-------------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE-------------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~-------------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      +..+|..+...|.+..+++-|.-.+.+|..             + +...=.+.  ..+..|.+++|+.+|++-++
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~e~eakvAv--LAieLgMlEeA~~lYr~ckR  828 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGEEDEAKVAV--LAIELGMLEEALILYRQCKR  828 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCcchhhHHHH--HHHHHhhHHHHHHHHHHHHH
Confidence            456899999999999999999999999974             1 11111222  22456778888887776654

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

Probab=90.06  E-value=10  Score=31.63  Aligned_cols=142  Identities=14%  Similarity=0.126  Sum_probs=72.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      ..+|-.-+..-+....++.|..+|.+-.  .++...|---+..---.++.++|+.++++.++.  -|+-+-+-.+++-. 
T Consensus       618 eeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~--fp~f~Kl~lmlGQi-  694 (913)
T KOG0495|consen  618 EEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALRLLEEALKS--FPDFHKLWLMLGQI-  694 (913)
T ss_pred             HHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh--CCchHHHHHHHhHH-
Confidence            3445555555566666666666666655  245445544444444455566666666555543  34433333333332 


Q ss_pred             HhccCChHHHHHHHHhccc--CC-hhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCchhHhhh
Q 035927           84 YCKCGDVEKAQRVLRKMLR--KD-KFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      +.+.++++.|.+.|..=.+  |+ ++.|-.+..-=-+.+.+-           .-+-|...|...|+.=.+.|+.+.|..
T Consensus       695 ~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~  774 (913)
T KOG0495|consen  695 EEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAEL  774 (913)
T ss_pred             HHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHH
Confidence            4556666666665555433  22 333332222111111111           222355678888888888888887765


Q ss_pred             h
Q 035927          150 S  150 (153)
Q Consensus       150 ~  150 (153)
                      +
T Consensus       775 l  775 (913)
T KOG0495|consen  775 L  775 (913)
T ss_pred             H
Confidence            4

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.96  E-value=6.6  Score=29.55  Aligned_cols=142  Identities=16%  Similarity=0.142  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      -+++.+..+.+..++++|++++..-.++   +....+.|-..|-...++..|-+-++++...  -|...-|...-.- .+
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQ-SL   88 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQ-SL   88 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHH-HH
Confidence            4778888889999999999998877643   6677888888888888999999999888653  4666666554333 25


Q ss_pred             hccCChHHHHHHHHhcccC-ChhhHHHHHHHHH--hcCCCCC------CCCCHhHHHHHH-HHH--hcCCchhHhhhhcc
Q 035927           85 CKCGDVEKAQRVLRKMLRK-DKFTWTAMIVGLA--ISDPFPT------IRPDEVTYVGVL-SAC--THNGNETFVINSCN  152 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~--~~~~~~~------~~p~~~t~~~ll-~~~--~~~g~~~~a~~~~~  152 (153)
                      .+.+.+.+|+++...|... +...-..-+.+-.  ..+++.|      -.|...+-..++ .+|  .+.|+.|.|.+-|+
T Consensus        89 Y~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFq  168 (459)
T KOG4340|consen   89 YKACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQ  168 (459)
T ss_pred             HHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHH
Confidence            7889999999999998763 3222222222211  2244442      234322222222 223  36777777776653

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=89.67  E-value=0.83  Score=22.40  Aligned_cols=27  Identities=11%  Similarity=0.300  Sum_probs=22.9

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQM   32 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m   32 (153)
                      ..+++.|-..|...|++++|..++++.
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~a   28 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEA   28 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHH
Confidence            357899999999999999999999765

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=89.60  E-value=3.6  Score=32.09  Aligned_cols=105  Identities=12%  Similarity=0.009  Sum_probs=69.1

Q ss_pred             HHhcCChHHHHHHHHhCCCC-CHHHHHHHHHHHHh--cCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH----------
Q 035927           16 YINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLR--VNRFREALTLFPEMQTSNIRPDEFTIVRILTAY----------   82 (153)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~~-~~~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~----------   82 (153)
                      +.-.|+.++|...-....+- ....+...+++.+-  .++.+.|...|++-++.+  ||...-.+.-..+          
T Consensus       179 l~~~~~~~~a~~ea~~ilkld~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ld--pdh~~sk~~~~~~k~le~~k~~g  256 (486)
T KOG0550|consen  179 LAFLGDYDEAQSEAIDILKLDATNAEALYVRGLCLYYNDNADKAINHFQQALRLD--PDHQKSKSASMMPKKLEVKKERG  256 (486)
T ss_pred             hhhcccchhHHHHHHHHHhcccchhHHHHhcccccccccchHHHHHHHhhhhccC--hhhhhHHhHhhhHHHHHHHHhhh
Confidence            33456667766666555543 44566777776664  578888888888887654  6666555554443          


Q ss_pred             -HHhccCChHHHHHHHHhcccC-------ChhhHHHHHHHHHhcCCCC
Q 035927           83 -MYCKCGDVEKAQRVLRKMLRK-------DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        83 -~~~~~g~~~~a~~~~~~m~~~-------~~~~~~~li~~~~~~~~~~  122 (153)
                       ...+.|...+|.+.+..-+..       +...|.....+..+.|...
T Consensus       257 N~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~  304 (486)
T KOG0550|consen  257 NDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLR  304 (486)
T ss_pred             hhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCch
Confidence             567999999999999998643       4445555555555555554

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=89.33  E-value=2.1  Score=26.63  Aligned_cols=47  Identities=21%  Similarity=0.207  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           55 EALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        55 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +...-++.+-...+.|+.....+.+++|  -|-+++..|.++|+.++.+
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAc--RRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRAC--RRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHH--HHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHH--HHhhhHHHHHHHHHHHHHH
Confidence            4445555666677889999999999998  8999999999999998653

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 ....

>PRK10564 maltose regulon periplasmic protein; Provisional

Probab=88.99  E-value=1.2  Score=32.94  Aligned_cols=45  Identities=13%  Similarity=0.161  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      +..=|+..|+..++.|++++|+.++++.++.|+.--..+|-.-++
T Consensus       256 Te~Yy~~aI~~AVk~gDi~KAL~LldEAe~LG~~~Ar~tFik~V~  300 (303)
T PRK10564        256 TESYFNQAIKQAVKKGDVDKALKLLDEAERLGSTSARSTFISSVK  300 (303)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCchHHHHHHHHhh
Confidence            445588999999999999999999999999998766666655443

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.95  E-value=6.8  Score=28.60  Aligned_cols=59  Identities=20%  Similarity=0.365  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCC----CCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSN----IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .|+.-++.+ +.|++.+|.+-|...++..    +.|+.  +=+|-..  +...|+.++|..+|..+.+
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA--~yWLGe~--~y~qg~y~~Aa~~f~~~~k  206 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNA--YYWLGES--LYAQGDYEDAAYIFARVVK  206 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchh--HHHHHHH--HHhcccchHHHHHHHHHHH
Confidence            366555544 5555666666666665541    22332  2234444  4666666666666666644

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=88.91  E-value=1.3  Score=22.49  Aligned_cols=26  Identities=31%  Similarity=0.565  Sum_probs=20.0

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ..+-..  |.+.|++++|+++|++..+.
T Consensus         5 ~~la~~--~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    5 LALARA--YRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHH--HHHcCCHHHHHHHHHHHHHH
Confidence            344455  68999999999999998753

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.74  E-value=0.82  Score=34.30  Aligned_cols=82  Identities=16%  Similarity=0.299  Sum_probs=47.9

Q ss_pred             CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc-C--------ChhhHHHHHHHHHhc-------CCCC-CCCCCHh
Q 035927           67 NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR-K--------DKFTWTAMIVGLAIS-------DPFP-TIRPDEV  129 (153)
Q Consensus        67 ~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~-~--------~~~~~~~li~~~~~~-------~~~~-~~~p~~~  129 (153)
                      |...++.+....+..  -....++++++..+-+++. +        +.++|--++.-|-..       ..++ |+.||..
T Consensus        59 g~~~s~~~Vd~~V~v--~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDV--ISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhc--cccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHccChHHHHHHHhCcchhccccchh
Confidence            334444555555544  1335555555555555532 1        233333333222221       2233 8999999


Q ss_pred             HHHHHHHHHhcCCchhHhhhh
Q 035927          130 TYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       130 t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      |++.+|..+.+.|+..+|.++
T Consensus       137 ~~c~l~D~flk~~n~~~aa~v  157 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASV  157 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHH
Confidence            999999999999999888765

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

Probab=88.72  E-value=1.8  Score=34.79  Aligned_cols=139  Identities=17%  Similarity=0.243  Sum_probs=85.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC----------CHHHHHHHHHHHHhcCChHHHHHHHHHHh-hCC--CCCC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER----------DYVLWTAMIDGYLRVNRFREALTLFPEMQ-TSN--IRPD   71 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~-~~~--~~p~   71 (153)
                      ...-+|.-.|.+.|.-.+|...++...  .|          +...=+.  +.+.....+.+...+|.++. ..+  +-||
T Consensus       354 eaLmaLAVSytNeg~q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~Dpd  431 (579)
T KOG1125|consen  354 EALMALAVSYTNEGLQNQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPD  431 (579)
T ss_pred             HHHHHHHHHHhhhhhHHHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChh
Confidence            334445555666666666666666552  11          0000000  23333344556666666664 445  3444


Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHH
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSA  137 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~  137 (153)
                      +.+.-.+|    |--.|+++.|.+-|+...+  | |...||-+-..++....-+          .+.|+- +....|--+
T Consensus       432 vQ~~LGVL----y~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS  507 (579)
T KOG1125|consen  432 VQSGLGVL----YNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGIS  507 (579)
T ss_pred             HHhhhHHH----HhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhh
Confidence            44443333    5778999999999999854  4 7888988887777775555          667874 445566777


Q ss_pred             HhcCCchhHhhhhc
Q 035927          138 CTHNGNETFVINSC  151 (153)
Q Consensus       138 ~~~~g~~~~a~~~~  151 (153)
                      |...|.+++|.+.|
T Consensus       508 ~mNlG~ykEA~~hl  521 (579)
T KOG1125|consen  508 CMNLGAYKEAVKHL  521 (579)
T ss_pred             hhhhhhHHHHHHHH
Confidence            88899998887654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=88.64  E-value=2.7  Score=25.90  Aligned_cols=57  Identities=19%  Similarity=0.208  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHH
Q 035927           55 EALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIV  113 (153)
Q Consensus        55 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~  113 (153)
                      ++..-++.+......|+.....+.+++|  -|-+++..|.++|+.++.+   +...|..++.
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAc--RRvND~alAVR~lE~vK~K~~~~~~~y~~~lq   84 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRAC--RRVNDFALAVRILEAIKDKCGAHKEIYPYILQ   84 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHH--HHhhhHHHHHHHHHHHHHHccCchhhHHHHHH
Confidence            4455555666677889999999999998  8999999999999988643   2334554443

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.

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

Probab=87.85  E-value=15  Score=30.72  Aligned_cols=140  Identities=16%  Similarity=0.145  Sum_probs=70.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh-hHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE-FTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~li~~~   82 (153)
                      .||+.--..|.+.+.++=|..+|....+   .+...|......=-..|..+.-..+|++.+..  .|-+ ..|--.... 
T Consensus       517 ~tw~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~--~pkae~lwlM~ake-  593 (913)
T KOG0495|consen  517 STWLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ--CPKAEILWLMYAKE-  593 (913)
T ss_pred             hHHhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCcchhHHHHHHHH-
Confidence            3466666666666777777777766653   24555555555444456666666666666544  2322 222222222 


Q ss_pred             HHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHHHHHhcCCchhHhhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                       +-..|+...|..++....+.   +...|-+-+.--.....++          +..|+...|.--++.---.|+.|+|.+
T Consensus       594 -~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~r  672 (913)
T KOG0495|consen  594 -KWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALR  672 (913)
T ss_pred             -HHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHH
Confidence             34556666666666655332   3333433333333332222          344555444444444444455555444


Q ss_pred             h
Q 035927          150 S  150 (153)
Q Consensus       150 ~  150 (153)
                      +
T Consensus       673 l  673 (913)
T KOG0495|consen  673 L  673 (913)
T ss_pred             H
Confidence            4

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

Probab=87.70  E-value=4.4  Score=32.12  Aligned_cols=76  Identities=16%  Similarity=0.276  Sum_probs=50.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .|...|-+||..+...|..++..+.+++|..|   =...|..-|++=....+++..+.+|.+-+....  +...|...+.
T Consensus        40 tnI~S~fqLiq~~~tq~s~~~~re~yeq~~~pfp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~l--~ldLW~lYl~  117 (660)
T COG5107          40 TNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKSL--NLDLWMLYLE  117 (660)
T ss_pred             hhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCCccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhhc--cHhHHHHHHH
Confidence            45556777777777777777777777777766   334566666666666677777777777765533  3555666655


Q ss_pred             H
Q 035927           81 A   81 (153)
Q Consensus        81 ~   81 (153)
                      .
T Consensus       118 Y  118 (660)
T COG5107         118 Y  118 (660)
T ss_pred             H
Confidence            3

>PRK04841 transcriptional regulator MalT; Provisional

Probab=87.65  E-value=8  Score=32.94  Aligned_cols=91  Identities=12%  Similarity=0.061  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC-------C--CHHHHHHHHHHHHhcCChHHHHHHHHHHhh----CCCC--C-Ch
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFPEMQT----SNIR--P-DE   72 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~--p-~~   72 (153)
                      .+.+-..+...|++++|...+++...       +  -..+...+-..+...|++++|...+++...    .+..  + ..
T Consensus       494 ~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~  573 (903)
T PRK04841        494 TSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHE  573 (903)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHH
Confidence            34455556677888887777766642       1  122344455556677888888877776643    2211  1 11


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      ..+..+-..  +...|++++|...+.+..
T Consensus       574 ~~~~~la~~--~~~~G~~~~A~~~~~~al  600 (903)
T PRK04841        574 FLLRIRAQL--LWEWARLDEAEQCARKGL  600 (903)
T ss_pred             HHHHHHHHH--HHHhcCHHHHHHHHHHhH
Confidence            222222222  455688888877777663

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.63  E-value=6.2  Score=28.83  Aligned_cols=92  Identities=12%  Similarity=0.219  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCC--hhHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPD--EFTIVRI   78 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~--~~t~~~l   78 (153)
                      .|+.-++.+ +.|++..|..-|....+  |    ....+-=|-..+...|++++|-.+|..+.+. +-.|-  ...|..-
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            588777655 56779999999988864  2    3445556889999999999999999999764 22221  2223222


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccC
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      . .  ..+.|+-++|..+|+++.+.
T Consensus       223 ~-~--~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 V-S--LGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             H-H--HHHhcCHHHHHHHHHHHHHH
Confidence            2 2  58999999999999999774

>PRK15331 chaperone protein SicA; Provisional

Probab=87.18  E-value=7.2  Score=26.40  Aligned_cols=86  Identities=13%  Similarity=0.078  Sum_probs=61.4

Q ss_pred             HHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCChhHHHHHHHHHHHhccCC
Q 035927           14 SGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPDEFTIVRILTAYMYCKCGD   89 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~t~~~li~~~~~~~~g~   89 (153)
                      ..+-..|++++|..+|.-+..  + |..-|-.|-..+-..+++++|.+.|...-..+. -|-. .|.  ..-| |...|+
T Consensus        45 y~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p-~f~--agqC-~l~l~~  120 (165)
T PRK15331         45 YEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRP-VFF--TGQC-QLLMRK  120 (165)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCc-cch--HHHH-HHHhCC
Confidence            345678999999999988763  3 555566666666667999999999988765432 1222 222  2334 789999


Q ss_pred             hHHHHHHHHhcccC
Q 035927           90 VEKAQRVLRKMLRK  103 (153)
Q Consensus        90 ~~~a~~~~~~m~~~  103 (153)
                      .+.|..-|....+.
T Consensus       121 ~~~A~~~f~~a~~~  134 (165)
T PRK15331        121 AAKARQCFELVNER  134 (165)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999988664

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=87.02  E-value=7  Score=26.06  Aligned_cols=71  Identities=11%  Similarity=0.076  Sum_probs=48.9

Q ss_pred             HHHHhcCChHHHHHHHHhCC--CC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC
Q 035927           14 SGYINRGQVDIARQYFAQMP--ER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG   88 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~--~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g   88 (153)
                      ..-...++++++..+++.|+  .|   ...+|-.++.  ++.|++++|+.+|++..+.+.  ...--..|+-.| +.-.|
T Consensus        18 ~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~--i~rg~w~eA~rvlr~l~~~~~--~~p~~kAL~A~C-L~al~   92 (153)
T TIGR02561        18 MYALRSADPYDAQAMLDALRVLRPNLKELDMFDGWLL--IARGNYDEAARILRELLSSAG--APPYGKALLALC-LNAKG   92 (153)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHhCCCccccchhHHHHH--HHcCCHHHHHHHHHhhhccCC--CchHHHHHHHHH-HHhcC
Confidence            33345789999999999887  44   4556776665  789999999999999987752  223344455444 44444


Q ss_pred             C
Q 035927           89 D   89 (153)
Q Consensus        89 ~   89 (153)
                      +
T Consensus        93 D   93 (153)
T TIGR02561        93 D   93 (153)
T ss_pred             C
Confidence            4

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.90  E-value=10  Score=27.78  Aligned_cols=111  Identities=14%  Similarity=0.223  Sum_probs=75.2

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHH-HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDG-YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~-~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      |-.++-+....|+.+.|...++++..  |+..=...|=.. +-..|++++|.++++..++.+ +.|.+++.-=+-.  .-
T Consensus        55 ~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAi--lk  131 (289)
T KOG3060|consen   55 YEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYKEAIEYYESLLEDD-PTDTVIRKRKLAI--LK  131 (289)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchhhHHHHHHHHhccC-cchhHHHHHHHHH--HH
Confidence            55666677777888888888888753  211111111111 124688999999999998876 5577777665555  35


Q ss_pred             ccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC
Q 035927           86 KCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  122 (153)
                      ..|+--+|++-+....+   .|...|.-+..-|...+.|+
T Consensus       132 a~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~  171 (289)
T KOG3060|consen  132 AQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFE  171 (289)
T ss_pred             HcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHH
Confidence            56766677776666654   38889999999888888887

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=86.83  E-value=5.6  Score=24.76  Aligned_cols=75  Identities=12%  Similarity=0.071  Sum_probs=43.0

Q ss_pred             hHHHHHHHHhCCC-CCHHHHHHHHH--HHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHH
Q 035927           22 VDIARQYFAQMPE-RDYVLWTAMID--GYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLR   98 (153)
Q Consensus        22 ~~~a~~l~~~m~~-~~~~~~~~li~--~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~   98 (153)
                      -++|.-+-+.+.. ++..-...||+  .+.+.|++++|+.+.+..    ..||...|-++..    .|.|..+++..-+.
T Consensus        21 HqEA~tIAdwL~~~~~~~E~v~lIRlsSLmNrG~Yq~Al~l~~~~----~~pdlepw~ALce----~rlGl~s~l~~rl~   92 (115)
T TIGR02508        21 HQEANTIADWLHLKGESEEAVQLIRLSSLMNRGDYQSALQLGNKL----CYPDLEPWLALCE----WRLGLGSALESRLN   92 (115)
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHHHHccchHHHHHHhcCCC----CCchHHHHHHHHH----HhhccHHHHHHHHH
Confidence            3455555554442 22233333433  344567777777766555    3677777777665    46777776666666


Q ss_pred             hcccCC
Q 035927           99 KMLRKD  104 (153)
Q Consensus        99 ~m~~~~  104 (153)
                      .|.+++
T Consensus        93 rla~sg   98 (115)
T TIGR02508        93 RLAASG   98 (115)
T ss_pred             HHHhCC
Confidence            665543

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.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=86.70  E-value=6.4  Score=25.27  Aligned_cols=81  Identities=10%  Similarity=0.140  Sum_probs=54.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +...-..++..+.+.+..+....+++.+...+ ..+....+.+|..  |++.. .++..+.++.  .++.......+.-|
T Consensus         6 ~~~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~l--y~~~~-~~~ll~~l~~--~~~~yd~~~~~~~c   79 (140)
T smart00299        6 DPIDVSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIEL--YAKYD-PQKEIERLDN--KSNHYDIEKVGKLC   79 (140)
T ss_pred             CcCCHHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHH--HHHHC-HHHHHHHHHh--ccccCCHHHHHHHH
Confidence            33445678888888899999999999998877 3677788899988  57664 4444455552  33344444466666


Q ss_pred             HhcCCCC
Q 035927          116 AISDPFP  122 (153)
Q Consensus       116 ~~~~~~~  122 (153)
                      -+.+.++
T Consensus        80 ~~~~l~~   86 (140)
T smart00299       80 EKAKLYE   86 (140)
T ss_pred             HHcCcHH
Confidence            5555554

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=86.65  E-value=4.4  Score=33.90  Aligned_cols=120  Identities=14%  Similarity=0.107  Sum_probs=53.5

Q ss_pred             CChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCChhHHHHHHHHHHHhccCChHHHHHHHH
Q 035927           20 GQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLR   98 (153)
Q Consensus        20 g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~   98 (153)
                      |++++|.+++-+|.++|..     |...-+.|++-.+.++++.=-.. .-..-...|+.+-..  ++...+|++|.+.+.
T Consensus       748 g~feeaek~yld~drrDLA-----ielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~--fa~~~~We~A~~yY~  820 (1189)
T KOG2041|consen  748 GEFEEAEKLYLDADRRDLA-----IELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGET--FAEMMEWEEAAKYYS  820 (1189)
T ss_pred             cchhHhhhhhhccchhhhh-----HHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence            4555556666555554432     33334444444444443211000 001112334444444  355555555555555


Q ss_pred             hcccCChhhHHHHHHHHHhcCCCC-------CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           99 KMLRKDKFTWTAMIVGLAISDPFP-------TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        99 ~m~~~~~~~~~~li~~~~~~~~~~-------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .....     ...+.++.+.++|+       .++-|+...-.+...+.+.|.-++|.+.|
T Consensus       821 ~~~~~-----e~~~ecly~le~f~~LE~la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~  875 (1189)
T KOG2041|consen  821 YCGDT-----ENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSVGMCDQAVEAY  875 (1189)
T ss_pred             hccch-----HhHHHHHHHHHhhhhHHHHHHhcCcccchHHHHHHHHHhhchHHHHHHHH
Confidence            44321     11333444444444       23334455555666666666666665543

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=86.39  E-value=13  Score=28.84  Aligned_cols=86  Identities=14%  Similarity=0.244  Sum_probs=63.4

Q ss_pred             HHHHhcCChHHHHHHHHhCCC------------------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHH
Q 035927           14 SGYINRGQVDIARQYFAQMPE------------------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      +.+.+.|++..|..-|++...                  .-..++..+.-.+.+.+++..|+..-+.-+..+ ++|+...
T Consensus       216 n~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KAL  294 (397)
T KOG0543|consen  216 NVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKAL  294 (397)
T ss_pred             hHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHH
Confidence            478899999999988887431                  134567778888889999999998888877654 2344433


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      =-==++  +...|+++.|+..|.++.+
T Consensus       295 yRrG~A--~l~~~e~~~A~~df~ka~k  319 (397)
T KOG0543|consen  295 YRRGQA--LLALGEYDLARDDFQKALK  319 (397)
T ss_pred             HHHHHH--HHhhccHHHHHHHHHHHHH
Confidence            333445  5888999999999999954

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=86.36  E-value=9.3  Score=26.81  Aligned_cols=95  Identities=13%  Similarity=0.186  Sum_probs=60.3

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC---CCCChhHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN---IRPDEFTIV   76 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~---~~p~~~t~~   76 (153)
                      |++..--.|-.+..+.|+..+|...|++-..    .|+...-.+-++....+++..|...+++.-+.+   -.||..  -
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~--L  164 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH--L  164 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch--H
Confidence            4444445566677777777777777776653    266666667777777777777777777765443   234322  2


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhccc
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .+-+.  |...|+..+|+.-|+...+
T Consensus       165 l~aR~--laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         165 LFART--LAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             HHHHH--HHhcCCchhHHHHHHHHHH
Confidence            33333  4667777777777777654

>PLN02789 farnesyltranstransferase

Probab=86.26  E-value=12  Score=28.11  Aligned_cols=108  Identities=9%  Similarity=0.104  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHhcC-ChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCC--hHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            8 SWTDIVSGYINRG-QVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNR--FREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         8 ~~~~li~~~~~~g-~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      .|+..-..+.+.| ++++++.+++++.+  | +..+|+----.+-+.|.  .++++++++.+.+.+- -+...|+---..
T Consensus        73 aW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~dp-kNy~AW~~R~w~  151 (320)
T PLN02789         73 VWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDA-KNYHAWSHRQWV  151 (320)
T ss_pred             HHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHhCc-ccHHHHHHHHHH
Confidence            4666666666667 57888888887753  2 55556644333444444  3667788877776542 355666666655


Q ss_pred             HHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAIS  118 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~  118 (153)
                        +.+.|+++++++.++++++.   |...|+.....+.+.
T Consensus       152 --l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~  189 (320)
T PLN02789        152 --LRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRS  189 (320)
T ss_pred             --HHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhc
Confidence              47778888888888888652   667777766665544

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=86.22  E-value=12  Score=30.16  Aligned_cols=114  Identities=14%  Similarity=0.222  Sum_probs=67.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHH-------HHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMID-------GYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~-------~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      ++..-.+|...|...++...-+.-.+.   ...-|+.+-.       ++.+.++++.|...|.+-+..-.+||..+=..-
T Consensus       260 ~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~  339 (539)
T KOG0548|consen  260 LNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKE  339 (539)
T ss_pred             HHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHH
Confidence            445555566666655555544442211   1122333333       333445667777777666554444443322221


Q ss_pred             HHHH-----------------------HHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           79 LTAY-----------------------MYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        79 i~~~-----------------------~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      ..--                       .+.+.|++..|.+-++++++.   |...|.....+|.+.+.+.
T Consensus       340 ~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~Da~lYsNRAac~~kL~~~~  409 (539)
T KOG0548|consen  340 AEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPEDARLYSNRAACYLKLGEYP  409 (539)
T ss_pred             HHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhhHH
Confidence            1111                       567999999999999998653   7888998888888887777

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

Probab=86.17  E-value=7.8  Score=31.89  Aligned_cols=95  Identities=18%  Similarity=0.263  Sum_probs=55.4

Q ss_pred             CCchhHHHH--HHHHHHhcCChHHHHHHHHhCCCCCHH---HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHH
Q 035927            3 NKDVISWTD--IVSGYINRGQVDIARQYFAQMPERDYV---LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         3 ~pd~~~~~~--li~~~~~~g~~~~a~~l~~~m~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      +|....|+.  +...+-+.|+++.|....+.--.-+++   -|-.--+-+...|++++|..++++.++.+. ||...=.-
T Consensus       366 ~PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~INsK  444 (700)
T KOG1156|consen  366 PPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAINSK  444 (700)
T ss_pred             CchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHHHH
Confidence            566655554  455666777788887777766542222   233334566667777777777777776542 44333324


Q ss_pred             HHHHHHHhccCChHHHHHHHHhc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      ..+.  ..+..+.++|.++....
T Consensus       445 cAKY--mLrAn~i~eA~~~~skF  465 (700)
T KOG1156|consen  445 CAKY--MLRANEIEEAEEVLSKF  465 (700)
T ss_pred             HHHH--HHHccccHHHHHHHHHh
Confidence            4444  35566666666665555

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

Probab=85.82  E-value=12  Score=30.31  Aligned_cols=64  Identities=14%  Similarity=0.195  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      -..+|...|+.--+...++.|..+|.+.++.+..+ .+...++++..   -..++..-|.++|+-=.+
T Consensus       365 ~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy---~cskD~~~AfrIFeLGLk  429 (656)
T KOG1914|consen  365 LTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEY---YCSKDKETAFRIFELGLK  429 (656)
T ss_pred             CceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHH---HhcCChhHHHHHHHHHHH
Confidence            34578888888888888888899998888888777 77777778774   567788888888876543

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=85.03  E-value=13  Score=27.71  Aligned_cols=53  Identities=21%  Similarity=0.267  Sum_probs=25.9

Q ss_pred             HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           47 YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        47 ~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ....|++.+|..+|+......-. +...--.+..+  |...|+.+.|..++..+..
T Consensus       144 ~~~~e~~~~a~~~~~~al~~~~~-~~~~~~~la~~--~l~~g~~e~A~~iL~~lP~  196 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQAAPE-NSEAKLLLAEC--LLAAGDVEAAQAILAALPL  196 (304)
T ss_pred             hhhccchhhHHHHHHHHHHhCcc-cchHHHHHHHH--HHHcCChHHHHHHHHhCcc
Confidence            34556666666666555443211 11222233333  4666666666666666643

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

Probab=85.02  E-value=20  Score=29.41  Aligned_cols=111  Identities=12%  Similarity=0.139  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHH--------hCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CCCCChhHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFA--------QMPE--RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS--NIRPDEFTI   75 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~--------~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~t~   75 (153)
                      +-=.++......|+++.|.+++.        .+.+  .-+.+...+...+.+.++-+.|-++++....+  .-.+.....
T Consensus       378 v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l  457 (652)
T KOG2376|consen  378 VLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIAL  457 (652)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHH
Confidence            34456677788899999999998        3331  24556677777778887777777777777543  112333333


Q ss_pred             HHHHHHH--HHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhc
Q 035927           76 VRILTAY--MYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAIS  118 (153)
Q Consensus        76 ~~li~~~--~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~  118 (153)
                      .+++.-.  .-.+.|..++|..+++++.+-   |+.+-..++.+|++-
T Consensus       458 ~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~  505 (652)
T KOG2376|consen  458 LSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL  505 (652)
T ss_pred             HhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc
Confidence            3333321  145779999999999999762   455555555555544

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=84.85  E-value=1.2  Score=21.37  Aligned_cols=23  Identities=13%  Similarity=0.193  Sum_probs=19.8

Q ss_pred             CHhHHHHHHHHHhcCCchhHhhh
Q 035927          127 DEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus       127 ~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      |...|+.+-..+...|+.++|++
T Consensus        12 n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen   12 NAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             CHHHHHHHHHHHHHCcCHHhhcC
Confidence            56789999999999999999874

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=84.64  E-value=16  Score=28.15  Aligned_cols=90  Identities=16%  Similarity=0.137  Sum_probs=63.3

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCCC-------CHHHHHHHHHHHHh---cCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLR---VNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~-------~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .++-+|-...+++...++.+.++..       +...=-...-++.+   .|+-++|++++.........++..||..+-+
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            4555688889999999999999854       11111122233335   7999999999999877777788889888877


Q ss_pred             HH--HHhc-----cCChHHHHHHHHhc
Q 035927           81 AY--MYCK-----CGDVEKAQRVLRKM  100 (153)
Q Consensus        81 ~~--~~~~-----~g~~~~a~~~~~~m  100 (153)
                      .+  .+..     ...+++|+..|.+-
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kg  252 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKG  252 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHH
Confidence            75  2222     23477788888776

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=83.45  E-value=14  Score=26.50  Aligned_cols=82  Identities=17%  Similarity=0.184  Sum_probs=52.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC----ChhhHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK----DKFTWTAM  111 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~l  111 (153)
                      +...+-.....+.+.|++++|...|+.+...--.+.......+.-+..|.+.++.++|...+++..+.    .-..|...
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y  110 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLY  110 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHH
Confidence            44433344455567899999999999998753222211111122222379999999999999999652    34456666


Q ss_pred             HHHHHh
Q 035927          112 IVGLAI  117 (153)
Q Consensus       112 i~~~~~  117 (153)
                      +.|.+.
T Consensus       111 ~~g~~~  116 (243)
T PRK10866        111 MRGLTN  116 (243)
T ss_pred             HHHHhh
Confidence            666653

>PF13934 ELYS: Nuclear pore complex assembly

Probab=83.40  E-value=14  Score=26.32  Aligned_cols=103  Identities=12%  Similarity=0.097  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHh--cCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            8 SWTDIVSGYIN--RGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         8 ~~~~li~~~~~--~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      .|...+.++--  .+++++|.+.+-+-.-+ ...-.-++..+...|+.+.|+.+++...-..-  +......++..   .
T Consensus        78 ~~~~~~~g~W~LD~~~~~~A~~~L~~ps~~-~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~--s~~~~~~~~~~---L  151 (226)
T PF13934_consen   78 KYIKFIQGFWLLDHGDFEEALELLSHPSLI-PWFPDKILQALLRRGDPKLALRYLRAVGPPLS--SPEALTLYFVA---L  151 (226)
T ss_pred             HHHHHHHHHHHhChHhHHHHHHHhCCCCCC-cccHHHHHHHHHHCCChhHHHHHHHhcCCCCC--CHHHHHHHHHH---H
Confidence            34555665554  35677777776433211 11122477777778888888887766542211  22222333333   5


Q ss_pred             ccCChHHHHHHHHhcccCC-hhhHHHHHHHHH
Q 035927           86 KCGDVEKAQRVLRKMLRKD-KFTWTAMIVGLA  116 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~~~-~~~~~~li~~~~  116 (153)
                      .++.+.+|...-+...++. ...+..++..+.
T Consensus       152 a~~~v~EAf~~~R~~~~~~~~~l~e~l~~~~~  183 (226)
T PF13934_consen  152 ANGLVTEAFSFQRSYPDELRRRLFEQLLEHCL  183 (226)
T ss_pred             HcCCHHHHHHHHHhCchhhhHHHHHHHHHHHH
Confidence            6788888888877776642 445555555555

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=83.28  E-value=2.9  Score=31.13  Aligned_cols=76  Identities=14%  Similarity=0.389  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHHHHhc--CChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc-------CChHHHHHHHHhcccC---
Q 035927           36 DYVLWTAMIDGYLRV--NRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC-------GDVEKAQRVLRKMLRK---  103 (153)
Q Consensus        36 ~~~~~~~li~~~~~~--~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~-------g~~~~a~~~~~~m~~~---  103 (153)
                      ...++.+++..-...  ..+++.+++++.|.+.|++-+..+|-+..-.   ...       .....|..+|+.|++.   
T Consensus        59 ~~~~la~~l~~~~~~p~~~~~~~~~~y~~L~~~gFk~~~y~~laA~~i---~~~~~~~~~~~~~~ra~~iy~~mKk~H~f  135 (297)
T PF13170_consen   59 HRFILAALLDISFEDPEEAFKEVLDIYEKLKEAGFKRSEYLYLAALII---LEEEEKEDYDEIIQRAKEIYKEMKKKHPF  135 (297)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhccCccChHHHHHHHH---HHhcccccHHHHHHHHHHHHHHHHHhCcc
Confidence            455666666543331  2357778899999999999888777664443   233       3467799999999763   


Q ss_pred             ----ChhhHHHHHHH
Q 035927          104 ----DKFTWTAMIVG  114 (153)
Q Consensus       104 ----~~~~~~~li~~  114 (153)
                          +-.++.+++..
T Consensus       136 LTs~~D~~~a~lLA~  150 (297)
T PF13170_consen  136 LTSPEDYPFAALLAM  150 (297)
T ss_pred             ccCccchhHHHHHhc
Confidence                44555555554

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=83.26  E-value=15  Score=26.51  Aligned_cols=144  Identities=15%  Similarity=0.053  Sum_probs=76.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCH-HHHHHHHHHHH--hcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPERDY-VLWTAMIDGYL--RVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~-~~~~~li~~~~--~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ..+||-+--.+...|+++.|.+.|+..-+-|+ .-|..+=++..  -.|+++-|.+=+...=+.+-+-.-.+....+.  
T Consensus        99 ~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~~YY~gR~~LAq~d~~~fYQ~D~~DPfR~LWLYl~--  176 (297)
T COG4785          99 PEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRYKLAQDDLLAFYQDDPNDPFRSLWLYLN--  176 (297)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhccceeeeecCchHhhHHHHHHHHhcCCCChHHHHHHHHH--
Confidence            34577777777777888888888877765322 23333333322  24666666655544433321111111111121  


Q ss_pred             HHhccCChHHHH-HHHHhcccCChhhHHHHHHHHHhcCCCC---------CCC-------CCHhHHHHHHHHHhcCCchh
Q 035927           83 MYCKCGDVEKAQ-RVLRKMLRKDKFTWTAMIVGLAISDPFP---------TIR-------PDEVTYVGVLSACTHNGNET  145 (153)
Q Consensus        83 ~~~~~g~~~~a~-~~~~~m~~~~~~~~~~li~~~~~~~~~~---------~~~-------p~~~t~~~ll~~~~~~g~~~  145 (153)
                        .+.-++.+|. ++.++..+.|..-|..-|-.|.--..-+         +-.       --..||..+-+-+...|+++
T Consensus       177 --E~k~dP~~A~tnL~qR~~~~d~e~WG~~iV~~yLgkiS~e~l~~~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~  254 (297)
T COG4785         177 --EQKLDPKQAKTNLKQRAEKSDKEQWGWNIVEFYLGKISEETLMERLKADATDNTSLAEHLTETYFYLGKYYLSLGDLD  254 (297)
T ss_pred             --HhhCCHHHHHHHHHHHHHhccHhhhhHHHHHHHHhhccHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHhccccHH
Confidence              2233444443 2333334445555655555543321111         111       12478889999999999999


Q ss_pred             HhhhhccC
Q 035927          146 FVINSCNL  153 (153)
Q Consensus       146 ~a~~~~~~  153 (153)
                      +|..+|+|
T Consensus       255 ~A~~LfKL  262 (297)
T COG4785         255 EATALFKL  262 (297)
T ss_pred             HHHHHHHH
Confidence            99988864

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=83.25  E-value=13  Score=26.05  Aligned_cols=66  Identities=12%  Similarity=0.198  Sum_probs=58.0

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           35 RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      |+...--.|-.++...|+..+|...|++-..--+--|....-.+-++  ....+++..|...++++-+
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~A--qfa~~~~A~a~~tLe~l~e  152 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQA--QFAIQEFAAAQQTLEDLME  152 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHH--HHhhccHHHHHHHHHHHhh
Confidence            56677778889999999999999999999877677899888899998  6899999999999999854

>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division

Probab=83.21  E-value=9.7  Score=24.41  Aligned_cols=43  Identities=14%  Similarity=0.176  Sum_probs=33.7

Q ss_pred             HHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHhccCChHHHHHHHHh
Q 035927           55 EALTLFPEMQTSNIRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRK   99 (153)
Q Consensus        55 ~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~   99 (153)
                      ++.++|..|.+.|+.-. +..|...-..  +.+.|++++|.++|..
T Consensus        81 ~~~~if~~l~~~~IG~~~A~fY~~wA~~--le~~~~~~~A~~I~~~  124 (126)
T PF08311_consen   81 DPREIFKFLYSKGIGTKLALFYEEWAEF--LEKRGNFKKADEIYQL  124 (126)
T ss_dssp             HHHHHHHHHHHHTTSTTBHHHHHHHHHH--HHHTT-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCccHHHHHHHHHHHHH--HHHcCCHHHHHHHHHh
Confidence            89999999999988554 4555555555  6999999999999874

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.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=82.72  E-value=3.5  Score=21.29  Aligned_cols=25  Identities=16%  Similarity=0.347  Sum_probs=16.4

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhCC
Q 035927           43 MIDGYLRVNRFREALTLFPEMQTSN   67 (153)
Q Consensus        43 li~~~~~~~~~~~a~~~~~~m~~~~   67 (153)
                      |-.+|...|+.+.|.+++++....|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            4556667777777777777766543

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.

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=82.61  E-value=3.2  Score=18.44  Aligned_cols=20  Identities=15%  Similarity=0.340  Sum_probs=10.5

Q ss_pred             HHHHHHHhcCChHHHHHHHH
Q 035927           11 DIVSGYINRGQVDIARQYFA   30 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~   30 (153)
                      .+-.++...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34445555555555555543

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

>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=82.52  E-value=1.8  Score=28.24  Aligned_cols=30  Identities=20%  Similarity=0.262  Sum_probs=25.6

Q ss_pred             cCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927           50 VNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus        50 ~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      .|.-.+|..+|..|++.|-+||  .|+.|+..
T Consensus       108 ygsk~DaY~VF~kML~~G~pPd--dW~~Ll~~  137 (140)
T PF11663_consen  108 YGSKTDAYAVFRKMLERGNPPD--DWDALLKE  137 (140)
T ss_pred             hccCCcHHHHHHHHHhCCCCCc--cHHHHHHH
Confidence            4666789999999999999997  58888876

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 [].

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=82.46  E-value=13  Score=26.67  Aligned_cols=74  Identities=20%  Similarity=0.224  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHH-HHHHHHHhccCChHHHHHHHHhccc------CChhhHHHHH
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVR-ILTAYMYCKCGDVEKAQRVLRKMLR------KDKFTWTAMI  112 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~-li~~~~~~~~g~~~~a~~~~~~m~~------~~~~~~~~li  112 (153)
                      .+.-++.+.+.+.+.+|+...++=++.  +|.-.+... +++.  ||-.|+|++|..-++-.-+      +....|..+|
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVka--kPtda~~RhflfqL--lcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~li   79 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKA--KPTDAGGRHFLFQL--LCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLI   79 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhc--CCccccchhHHHHH--HhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHH
Confidence            344566667777777777776665554  454333333 3443  6777777777665555421      2455676666


Q ss_pred             HHHHh
Q 035927          113 VGLAI  117 (153)
Q Consensus       113 ~~~~~  117 (153)
                      .+-..
T Consensus        80 r~ea~   84 (273)
T COG4455          80 RCEAA   84 (273)
T ss_pred             HHHHH
Confidence            65433

>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=82.37  E-value=23  Score=28.06  Aligned_cols=81  Identities=16%  Similarity=0.135  Sum_probs=46.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      ..-.+.++..+-+.|-.+.|+++-..     .   ..=.+...+.|+++.|.++.++.      .+...|..|-...  .
T Consensus       295 ~~~~~~i~~fL~~~G~~e~AL~~~~D-----~---~~rFeLAl~lg~L~~A~~~a~~~------~~~~~W~~Lg~~A--L  358 (443)
T PF04053_consen  295 KDQGQSIARFLEKKGYPELALQFVTD-----P---DHRFELALQLGNLDIALEIAKEL------DDPEKWKQLGDEA--L  358 (443)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHSS------H---HHHHHHHHHCT-HHHHHHHCCCC------STHHHHHHHHHHH--H
T ss_pred             hhHHHHHHHHHHHCCCHHHHHhhcCC-----h---HHHhHHHHhcCCHHHHHHHHHhc------CcHHHHHHHHHHH--H
Confidence            33478888888888888888877632     2   12233444566666665554322      2445666666653  6


Q ss_pred             ccCChHHHHHHHHhccc
Q 035927           86 KCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~  102 (153)
                      +.|+++-|++-|.+...
T Consensus       359 ~~g~~~lAe~c~~k~~d  375 (443)
T PF04053_consen  359 RQGNIELAEECYQKAKD  375 (443)
T ss_dssp             HTTBHHHHHHHHHHCT-
T ss_pred             HcCCHHHHHHHHHhhcC
Confidence            66666666666666543

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.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.15  E-value=21  Score=27.47  Aligned_cols=133  Identities=11%  Similarity=0.040  Sum_probs=86.3

Q ss_pred             cCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CC-CCChhHHHHHHHHHHHhccCChHHH
Q 035927           19 RGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NI-RPDEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~-~p~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      .|+..+|...|+++.+   .|...++-.=+++.-.|+.+.....+++.... +- .|...-.+.+..-+ +..+|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFg-L~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFG-LEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhh-HHHhccchhH
Confidence            4666667777777763   37778888888888899999888988888643 31 23334444444443 7899999999


Q ss_pred             HHHHHhcccCC---hhhHHHHHHHHHhcCCCC---------------CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           94 QRVLRKMLRKD---KFTWTAMIVGLAISDPFP---------------TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        94 ~~~~~~m~~~~---~~~~~~li~~~~~~~~~~---------------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ++.-++-.+-|   .=.-++....+-..+.+.               +-.--.+.|+...-.+...+.++.|.++|+
T Consensus       195 Ek~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD  271 (491)
T KOG2610|consen  195 EKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYD  271 (491)
T ss_pred             HHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHH
Confidence            99998887643   333334444444444433               111123445566666667789999998885

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

Probab=81.74  E-value=29  Score=28.82  Aligned_cols=45  Identities=11%  Similarity=0.199  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChhHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEFTIVRILTA   81 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~li~~   81 (153)
                      ...|-....+..-.|+...|..++++..+.. -.|+...+.-....
T Consensus       143 ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~  188 (700)
T KOG1156|consen  143 RASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELL  188 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHH
Confidence            3457777777777899999999999998664 46777777665544

>PF03745 DUF309: Domain of unknown function (DUF309); InterPro: IPR005500 This family consists of eubacterial and archaebacterial proteins of unknown function

Probab=80.97  E-value=7.5  Score=21.63  Aligned_cols=50  Identities=18%  Similarity=0.258  Sum_probs=30.4

Q ss_pred             HhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH---HHhccCChHHHHHHH
Q 035927           48 LRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY---MYCKCGDVEKAQRVL   97 (153)
Q Consensus        48 ~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~---~~~~~g~~~~a~~~~   97 (153)
                      .+.|++=+|.+++++.=...-.|....+..+|+.+   ...+.|+.+.|.+++
T Consensus        10 ~n~g~f~EaHEvlE~~W~~~~~~~~~~lqglIq~A~a~~h~~~gn~~gA~~l~   62 (62)
T PF03745_consen   10 FNAGDFFEAHEVLEELWKAAPGPERDFLQGLIQLAVALYHLRRGNPRGARRLL   62 (62)
T ss_dssp             HHTT-HHHHHHHHHHHCCCT-CCHHHHHHHHHHHHHHHHHHHCTSHHHHHHHH
T ss_pred             HcCCCHHHhHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHHHhCCHHHHHHhC
Confidence            35677777888887774322233566666666654   344777777777664

The proteins contain a motif HXXXEXX(W/Y) where X can be any amino acid. This motif is likely to be functionally important and may be involved in metal binding.; PDB: 2CXD_B 2CWY_A 2IJQ_B.

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=80.92  E-value=18  Score=27.14  Aligned_cols=50  Identities=10%  Similarity=0.088  Sum_probs=22.3

Q ss_pred             HHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHH
Q 035927           14 SGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEM   63 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m   63 (153)
                      ..|..+|.+.+|.++-++...-   +...|-.+|..++..|+--.|..-++.+
T Consensus       287 ~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyery  339 (361)
T COG3947         287 RAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERY  339 (361)
T ss_pred             HHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHH
Confidence            3444445555555544444321   3444444555555444444444433333

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=80.62  E-value=21  Score=26.54  Aligned_cols=101  Identities=12%  Similarity=0.110  Sum_probs=73.8

Q ss_pred             CChHHHHHHHHhCCC-----CCHHHHHHHHHHHHhc--CChHHHHHHHHHHhh-CCCCCChhHHHHHHHHHHHhccCChH
Q 035927           20 GQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRV--NRFREALTLFPEMQT-SNIRPDEFTIVRILTAYMYCKCGDVE   91 (153)
Q Consensus        20 g~~~~a~~l~~~m~~-----~~~~~~~~li~~~~~~--~~~~~a~~~~~~m~~-~~~~p~~~t~~~li~~~~~~~~g~~~   91 (153)
                      ..+.+|..+|+....     .|...-.-+++.....  ..+..-.++.+.+.+ .|-.++..+...+|..  +++.++|.
T Consensus       142 ~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~--L~~~~dW~  219 (292)
T PF13929_consen  142 KIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEI--LAESRDWN  219 (292)
T ss_pred             HHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHH--HHhcccHH
Confidence            346788888884432     3777788888888762  245555566666653 3556888899999999  69999999


Q ss_pred             HHHHHHHhcccC-----ChhhHHHHHHHHHhcCCCC
Q 035927           92 KAQRVLRKMLRK-----DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        92 ~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~  122 (153)
                      +-.++|+.....     |...|...|......|+-+
T Consensus       220 kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~  255 (292)
T PF13929_consen  220 KLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQE  255 (292)
T ss_pred             HHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHH
Confidence            999999998543     7777888777777775544

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=80.52  E-value=11  Score=27.11  Aligned_cols=74  Identities=9%  Similarity=-0.004  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CCCCChhHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS--NIRPDEFTIVRILTA   81 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~t~~~li~~   81 (153)
                      |.+..++.+.+.+++++++.....=.  +| |..+=..++..+|-.|++++|..-++-.-..  ...+-..+|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            45667788889999999888776543  34 6777788999999999999999888776443  466778888888886

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=80.26  E-value=4.6  Score=18.76  Aligned_cols=27  Identities=15%  Similarity=0.411  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      +|..+-..+...|++++|+..|++.++
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            344555555555555555555555543

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 ....

---

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	153
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-07
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	3e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 48.3 bits (113), Expect = 2e-07
 Identities = 14/108 (12%), Positives = 36/108 (33%), Gaps = 10/108 (9%)

Query: 5   DVISWTDIVSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLRVNRFREAL 57
                       +   Q+ +A         +          ++ A++ G+ R   F+E +
Sbjct: 126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELV 185

Query: 58  TLFPEMQTSNIRPDEFTIVRILTAYMYCKCG-DVEKAQRVLRKMLRKD 104
            +   ++ + + PD  +    L      +   D    +R L +M ++ 
Sbjct: 186 YVLFMVKDAGLTPDLLSYAAAL--QCMGRQDQDAGTIERCLEQMSQEG 231

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus} Length = 291

 Score = 41.3 bits (96), Expect = 3e-05
 Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 8/105 (7%)

Query: 16  YINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTI 75
           Y      D A +   Q    + +  T  I   L+++R   A     +MQ  +   D  T+
Sbjct: 111 YFYDQNPDAALRTLHQGDSLECMAMTVQI--LLKLDRLDLARKELKKMQ--DQDED-ATL 165

Query: 76  VRILTAYMYCKCGD--VEKAQRVLRKMLRKDKFTWTAMIVGLAIS 118
            ++ TA++    G   ++ A  + ++M  K   T   +  G A  
Sbjct: 166 TQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLL-NGQAAC 209

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	153
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.96
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.91
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.6
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.55
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.17
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.14
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.14
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.13
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.09
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.08
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.07
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.07
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.07
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.06
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.06
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.05
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.05
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.04
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.03
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.99
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	98.98
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	98.97
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	98.93
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	98.92
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.91
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.91
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	98.9
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.89
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	98.89
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	98.86
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.81
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.8
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.79
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	98.79
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	98.79
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.76
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.74
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.73
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.72
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.7
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	98.7
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.66
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.64
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.64
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	98.63
2gw1_A	514	Mitochondrial precursor proteins import receptor;	98.61
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.61
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.6
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.56
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.55
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	98.52
3u4t_A	272	TPR repeat-containing protein; structural genomics	98.51
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	98.51
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.5
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.48
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.48
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.48
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.46
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.45
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.41
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.4
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.39
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	98.38
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.36
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.35
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.34
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.31
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.29
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.29
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.29
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.27
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.27
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.27
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.26
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	98.26
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.24
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.23
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.22
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.22
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.21
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.19
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.19
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.18
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.17
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.15
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.14
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.14
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.13
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.13
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.12
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.1
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.08
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.08
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.07
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.05
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.04
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.03
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.02
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.01
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.01
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.99
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.97
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.96
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.95
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	97.94
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.94
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.94
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	97.92
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	97.92
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.92
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.91
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.91
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	97.91
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	97.91
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.9
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.9
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.89
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	97.89
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.86
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.84
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	97.84
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.84
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.84
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.82
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.82
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.82
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.82
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	97.81
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	97.81
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.81
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.81
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.8
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.78
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	97.78
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.77
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.76
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.76
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.73
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.71
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.68
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.64
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.64
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.63
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.63
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.62
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.6
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	97.59
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.58
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	97.54
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.54
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.54
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.53
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.52
4g1t_A	472	Interferon-induced protein with tetratricopeptide	97.48
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	97.46
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.43
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.41
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	97.36
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.35
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.34
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.33
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.31
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	97.3
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.3
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.26
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	97.25
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.24
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	97.21
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.19
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	97.19
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.19
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	97.17
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.13
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.02
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	96.98
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.96
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	96.9
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.89
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.86
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	96.86
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.75
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.75
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.75
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.74
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.73
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	96.71
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.66
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.59
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	96.46
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.45
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	96.41
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.36
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.05
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	95.95
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	95.75
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.73
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.69
1klx_A	138	Cysteine rich protein B; structural genomics, heli	95.16
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.05
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.02
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.62
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	94.4
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	94.31
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	94.28
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.16
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	94.05
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	94.01
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.73
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.71
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	93.57
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	92.97
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.75
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	92.36
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	92.03
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.02
1klx_A	138	Cysteine rich protein B; structural genomics, heli	91.75
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	91.63
1pc2_A	152	Mitochondria fission protein; unknown function; NM	90.96
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	90.87
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	90.16
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	89.45
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	89.37
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	88.04
1pc2_A	152	Mitochondria fission protein; unknown function; NM	87.34
2p58_C	116	Putative type III secretion protein YSCG; type III	87.3
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	87.15
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	87.02
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	86.88
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	85.97
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	85.9
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.31
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	85.25
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	84.89
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.54
2p58_C	116	Putative type III secretion protein YSCG; type III	84.09
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	83.96
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	83.38
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	83.29
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	81.5

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=7.4e-31  Score=203.16  Aligned_cols=145  Identities=12%  Similarity=0.153  Sum_probs=135.8

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCC---------hHHHHHHHHHHhhCCCCCCh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNR---------FREALTLFPEMQTSNIRPDE   72 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~---------~~~a~~~~~~m~~~~~~p~~   72 (153)
                      ...++.+|++|++.|++++|.++|++|.    +||..+||+||.+|++.+.         +++|.++|++|++.|+.||.
T Consensus        26 e~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~  105 (501)
T 4g26_A           26 EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE  105 (501)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCH
Confidence            3468899999999999999999999997    5899999999999997654         68999999999999999999


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcc----cCChhhHHHHHHHHHhcCCCC------------CCCCCHhHHHHHHH
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKML----RKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVGVLS  136 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~~~~------------~~~p~~~t~~~ll~  136 (153)
                      .||+++|.+  |++.|++++|.++|++|.    .||..+||++|.+|++.|.++            |+.||..||++||.
T Consensus       106 ~tyn~lI~~--~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~  183 (501)
T 4g26_A          106 ATFTNGARL--AVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLK  183 (501)
T ss_dssp             HHHHHHHHH--HHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHH--HHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            999999999  599999999999999996    469999999999999999888            99999999999999


Q ss_pred             HHhcCCchhHhhhhcc
Q 035927          137 ACTHNGNETFVINSCN  152 (153)
Q Consensus       137 ~~~~~g~~~~a~~~~~  152 (153)
                      +|++.|+.++|.++|+
T Consensus       184 ~~~~~g~~d~A~~ll~  199 (501)
T 4g26_A          184 VSMDTKNADKVYKTLQ  199 (501)
T ss_dssp             HHHHTTCHHHHHHHHH
T ss_pred             HHhhCCCHHHHHHHHH
Confidence            9999999999999874

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.96  E-value=2.4e-28  Score=189.09  Aligned_cols=139  Identities=13%  Similarity=0.068  Sum_probs=130.1

Q ss_pred             CCchhHHHHHHHHHHhcCC---------hHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC
Q 035927            3 NKDVISWTDIVSGYINRGQ---------VDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR   69 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~---------~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   69 (153)
                      +||..|||+||++|++.+.         +++|.++|++|.    .||..|||+||++|++.|++++|+++|++|++.|+.
T Consensus        58 ~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~  137 (501)
T 4g26_A           58 QLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQ  137 (501)
T ss_dssp             CCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCC
T ss_pred             CCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Confidence            5999999999999998765         688999999997    589999999999999999999999999999999999


Q ss_pred             CChhHHHHHHHHHHHhccCChHHHHHHHHhcc----cCChhhHHHHHHHHHhcCCCC------------CCCCCHhHHHH
Q 035927           70 PDEFTIVRILTAYMYCKCGDVEKAQRVLRKML----RKDKFTWTAMIVGLAISDPFP------------TIRPDEVTYVG  133 (153)
Q Consensus        70 p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~~li~~~~~~~~~~------------~~~p~~~t~~~  133 (153)
                      ||..|||++|.+  |++.|++++|.++|+.|.    .||..+|+++|.+|++.|.++            ++.|+..||+.
T Consensus       138 Pd~~tyn~lI~~--~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~  215 (501)
T 4g26_A          138 PRLRSYGPALFG--FCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDM  215 (501)
T ss_dssp             CCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHH
T ss_pred             CccceehHHHHH--HHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHH
Confidence            999999999999  599999999999999995    469999999999999999888            89999999999


Q ss_pred             HHHHHhcCCc
Q 035927          134 VLSACTHNGN  143 (153)
Q Consensus       134 ll~~~~~~g~  143 (153)
                      ++..++..+.
T Consensus       216 l~~~F~s~~a  225 (501)
T 4g26_A          216 IEEWFKSEVA  225 (501)
T ss_dssp             HHHHHHSHHH
T ss_pred             HHHHHhcCcc
Confidence            9999886543

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.91  E-value=6.6e-25  Score=178.05  Aligned_cols=110  Identities=12%  Similarity=0.173  Sum_probs=95.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC-------CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP-------ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      ..|||++|++||+.|++++|.++|++|.       .||..|||+||++||+.|++++|.++|++|.+.|++||++|||++
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            4589999999999999999999997764       589999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhccCCh-HHHHHHHHhcccC----ChhhHHHHHHHHHh
Q 035927           79 LTAYMYCKCGDV-EKAQRVLRKMLRK----DKFTWTAMIVGLAI  117 (153)
Q Consensus        79 i~~~~~~~~g~~-~~a~~~~~~m~~~----~~~~~~~li~~~~~  117 (153)
                      |++  +++.|+. ++|.++|++|.+.    |..+|++++.+..+
T Consensus       207 I~g--lcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR  248 (1134)
T 3spa_A          207 LQC--MGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR  248 (1134)
T ss_dssp             HHH--HHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHH
T ss_pred             HHH--HHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhH
Confidence            998  5999985 7899999999765    44444444333333

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.80  E-value=1.4e-19  Score=147.22  Aligned_cols=112  Identities=12%  Similarity=0.019  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhh---CCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcc----cCChhhHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQT---SNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKML----RKDKFTWT  109 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~----~~~~~~~~  109 (153)
                      +.|||+||++||+.|++++|.++|++|.+   .|+.||++|||+||++  ||+.|++++|.++|++|.    +||++|||
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~G--lck~G~~~eA~~Lf~eM~~~G~~PDvvTYn  204 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLG--WARQGAFKELVYVLFMVKDAGLTPDLLSYA  204 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHH--HHhCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence            46899999999999999999999998864   4899999999999999  699999999999999995    57999999


Q ss_pred             HHHHHHHhcCCC-C------------CCCCCHhHHHHHHHHHhcCCchhHhhhh
Q 035927          110 AMIVGLAISDPF-P------------TIRPDEVTYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       110 ~li~~~~~~~~~-~------------~~~p~~~t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      ++|.++|+.|.. +            |+.||..||++++.++-+.+-++.+.++
T Consensus       205 tLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv  258 (1134)
T 3spa_A          205 AALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKV  258 (1134)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGG
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHh
Confidence            999999999875 2            9999999999999999888877777665

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.60  E-value=2.1e-14  Score=111.63  Aligned_cols=146  Identities=12%  Similarity=0.153  Sum_probs=101.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+..+|+.+...|.+.|++++|.++|+++.   ..+..+|+.++..+.+.|++++|+++|+++.+.+ +.+..+++.+..
T Consensus       371 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  449 (597)
T 2xpi_A          371 EKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGM  449 (597)
T ss_dssp             TSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHH
Confidence            456667777777777777777777777764   2356677777777777777777777777776553 346677777777


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------------CCCCC--HhHHHHHHHHHh
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------------TIRPD--EVTYVGVLSACT  139 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------------~~~p~--~~t~~~ll~~~~  139 (153)
                      +  |.+.|++++|+++|+++.+   .+..+|+.++..|.+.|.++                +..|+  ..+|..+..+|.
T Consensus       450 ~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~  527 (597)
T 2xpi_A          450 Q--HMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYR  527 (597)
T ss_dssp             H--HHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHH
Confidence            6  4777777777777777643   35667777777777776665                23565  566777777777


Q ss_pred             cCCchhHhhhhcc
Q 035927          140 HNGNETFVINSCN  152 (153)
Q Consensus       140 ~~g~~~~a~~~~~  152 (153)
                      +.|++++|.+.|+
T Consensus       528 ~~g~~~~A~~~~~  540 (597)
T 2xpi_A          528 KLKMYDAAIDALN  540 (597)
T ss_dssp             HTTCHHHHHHHHH
T ss_pred             HhcCHHHHHHHHH
Confidence            7777777776653

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.55  E-value=2.5e-14  Score=111.15  Aligned_cols=116  Identities=9%  Similarity=0.053  Sum_probs=63.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      +|..+|+.++..|.+.|++++|.++|+++.+   .+..+|+.++..+.+.|++++|..+++++.+.. +.+..+++.+..
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  381 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGI  381 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHH
Confidence            6677777777777777777777777777741   244445555555555555555555555554321 234444444444


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|.++
T Consensus       382 ~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  424 (597)
T 2xpi_A          382 Y--YLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHD  424 (597)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             H--HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            4  3555555555555555432   13445555555555554444

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.17  E-value=5.4e-11  Score=90.34  Aligned_cols=131  Identities=11%  Similarity=0.126  Sum_probs=67.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      +.+.+.++.+|.+.|+++++.++++   +|+..+|+.+...|...|.+++|...|..+         ..|..+..+  +.
T Consensus        94 ~~i~~~Li~~Y~Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~--L~  159 (449)
T 1b89_A           94 SYVETELIFALAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLAST--LV  159 (449)
T ss_dssp             ---------------CHHHHTTTTT---CC----------------CTTTHHHHHHHT---------TCHHHHHHH--HH
T ss_pred             chhHHHHHHHHHHhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHH--HH
Confidence            3455556666666666666555553   255556666666666666666666666654         356666665  57


Q ss_pred             ccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC-------CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           86 KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP-------TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~-------~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.|++++|.+.+++.  .++.+|..++.+|+..|.|+       .+..++.-...++..|.+.|.+++|..+++
T Consensus       160 ~Lg~yq~AVea~~KA--~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~~ad~l~~lv~~Yek~G~~eEai~lLe  231 (449)
T 1b89_A          160 HLGEYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLE  231 (449)
T ss_dssp             TTTCHHHHHHHHHHH--TCHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHc--CCchhHHHHHHHHHHcCcHHHHHHHHHHHHhCHhhHHHHHHHHHHCCCHHHHHHHHH
Confidence            777777777777777  36788888888888887766       222333334467788888888888877653

>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=99.14  E-value=2.9e-09  Score=73.94  Aligned_cols=145  Identities=9%  Similarity=0.015  Sum_probs=91.0

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +...+..+...+.+.|++++|.+.+++..   ..+...|..+...+.+.|++++|...+++..+.+..| +...+..+..
T Consensus        70 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~  149 (252)
T 2ho1_A           70 SADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGL  149 (252)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHH
Confidence            44556666667777777777777776654   2255666777777777777777777777776633344 3334444444


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~  146 (153)
                      .  |.+.|++++|.+.|++..+  | +...|..+...+...|.++          ...| +...+..+...+...|+.++
T Consensus       150 ~--~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  227 (252)
T 2ho1_A          150 V--SLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDT  227 (252)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHH
Confidence            4  5677777777777777643  2 4666666666676666655          3333 34556666677777777777


Q ss_pred             hhhhc
Q 035927          147 VINSC  151 (153)
Q Consensus       147 a~~~~  151 (153)
                      |.+.+
T Consensus       228 A~~~~  232 (252)
T 2ho1_A          228 AASYG  232 (252)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

>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=99.14  E-value=1.1e-09  Score=82.23  Aligned_cols=94  Identities=16%  Similarity=0.192  Sum_probs=52.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...+..+...+.+.|++++|..+|+++.+   .+...|..+...+.+.|++++|...++++.+.+ +.+...+..+...
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  103 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHL  103 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHH
Confidence            344566666666666666666666665541   245556666666666666666666666665442 1234444444444


Q ss_pred             HHHhccCChHHHHHHHHhcc
Q 035927           82 YMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~  101 (153)
                        |.+.|++++|.+.|+++.
T Consensus       104 --~~~~g~~~~A~~~~~~~~  121 (450)
T 2y4t_A          104 --LLKQGKLDEAEDDFKKVL  121 (450)
T ss_dssp             --HHHTTCHHHHHHHHHHHH
T ss_pred             --HHHcCCHHHHHHHHHHHH
Confidence              455666666666665554

>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=99.13  E-value=1.7e-09  Score=79.89  Aligned_cols=141  Identities=10%  Similarity=0.040  Sum_probs=94.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      |..+...+.+.|++++|...|++..  .| +..++..+...+.+.|++++|...++++.+.+ +.+..++..+...  |.
T Consensus       206 ~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~--~~  282 (388)
T 1w3b_A          206 YINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANA--LK  282 (388)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH--HH
Confidence            3333344444444444444443332  12 45677777788888888888888888887653 1245566666666  58


Q ss_pred             ccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           86 KCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +.|++++|.+.|+++.+   .+..+|+.+...+...|.++          ...|+ ..++..+...+.+.|++++|.+.|
T Consensus       283 ~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  362 (388)
T 1w3b_A          283 EKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHY  362 (388)
T ss_dssp             HHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            88888888888888753   26777888888888777766          44454 567888888888888888888776


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      +
T Consensus       363 ~  363 (388)
T 1w3b_A          363 K  363 (388)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.09  E-value=3.3e-09  Score=78.41  Aligned_cols=143  Identities=11%  Similarity=0.110  Sum_probs=84.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-----------------
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSN-----------------   67 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----------------   67 (153)
                      .+..+...+.+.|++++|.+.|+++.  .| +..+|+.+...+.+.|++++|...|+++.+.+                 
T Consensus       137 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~  216 (388)
T 1w3b_A          137 VRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEA  216 (388)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHc
Confidence            34445555555555555555555553  12 34455555555555555555555555544321                 


Q ss_pred             ---------------CCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC------
Q 035927           68 ---------------IRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP------  122 (153)
Q Consensus        68 ---------------~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~------  122 (153)
                                     ..| +..++..+...  |.+.|++++|.+.|+++.+  | +..+|..+...+.+.|.++      
T Consensus       217 ~~~~~A~~~~~~al~~~p~~~~~~~~l~~~--~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  294 (388)
T 1w3b_A          217 RIFDRAVAAYLRALSLSPNHAVVHGNLACV--YYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCY  294 (388)
T ss_dssp             TCTTHHHHHHHHHHHHCTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhCcCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence                           123 34455555554  5777777777777777743  2 4667777777777777666      


Q ss_pred             -----CCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -----TIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -----~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                           ..+.+..++..+...+.+.|++++|.+.|+
T Consensus       295 ~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  329 (388)
T 1w3b_A          295 NTALRLCPTHADSLNNLANIKREQGNIEEAVRLYR  329 (388)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                 223456777777788888888888777653

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.08  E-value=6.9e-09  Score=71.38  Aligned_cols=146  Identities=11%  Similarity=0.106  Sum_probs=120.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...+++..   ..+...+..+...+.+.|++++|...+++..+.. +.+...+..+..
T Consensus        55 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~  133 (243)
T 2q7f_A           55 EDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGT  133 (243)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            456778889999999999999999999875   2377889999999999999999999999998754 235566666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~  146 (153)
                      .  |.+.|++++|.+.+++..+   .+...|..+...+...|.++          ...| +...+..+...+.+.|+.++
T Consensus       134 ~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  211 (243)
T 2q7f_A          134 V--LVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREK  211 (243)
T ss_dssp             H--HHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTH
T ss_pred             H--HHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHH
Confidence            6  6999999999999999854   36788888999999998887          2334 46788899999999999999


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |.+.|+
T Consensus       212 A~~~~~  217 (243)
T 2q7f_A          212 ALEMLD  217 (243)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988764

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.07  E-value=5.8e-09  Score=70.75  Aligned_cols=144  Identities=10%  Similarity=-0.002  Sum_probs=84.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...|..+...+.+.|++++|...|++..   ..+...|..+...+...|++++|...+++..+.. +.+..++..+...
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~   85 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            34456666666777777777777666654   2245566666666666666777766666665532 1234445545444


Q ss_pred             HHHhcc-CChHHHHHHHHhccc--C---ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCch
Q 035927           82 YMYCKC-GDVEKAQRVLRKMLR--K---DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNE  144 (153)
Q Consensus        82 ~~~~~~-g~~~~a~~~~~~m~~--~---~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~  144 (153)
                        |... |++++|.+.++++.+  .   +...|..+...+...|.++          ...|+ ...+..+...+.+.|+.
T Consensus        86 --~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           86 --LCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             --HHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCH
T ss_pred             --HHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCH
Confidence              4666 667776666666654  1   2455566666666665555          22232 45566666666666666


Q ss_pred             hHhhhhc
Q 035927          145 TFVINSC  151 (153)
Q Consensus       145 ~~a~~~~  151 (153)
                      ++|.+.+
T Consensus       164 ~~A~~~~  170 (225)
T 2vq2_A          164 GDADYYF  170 (225)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6666554

>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=99.07  E-value=6.8e-09  Score=68.18  Aligned_cols=144  Identities=12%  Similarity=0.070  Sum_probs=118.8

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...|..+...+.+.|++++|...+++..+   .+...+..+...+...|++++|...+++..+.. +.+...+..+... 
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~-   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLT-   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH-
Confidence            34578888899999999999999999874   367889999999999999999999999998753 2356666666666 


Q ss_pred             HHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a~  148 (153)
                       |.+.|++++|.+.+++..+   .+...+..+...+...|.++          ...| +...+..+...+...|+.++|.
T Consensus        86 -~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           86 -YVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             -HHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             -HHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHH
Confidence             6999999999999999854   36778888888898888877          2234 5678889999999999999999


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      +.++
T Consensus       165 ~~~~  168 (186)
T 3as5_A          165 PHFK  168 (186)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8764

>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=99.07  E-value=3.7e-09  Score=79.27  Aligned_cols=148  Identities=13%  Similarity=0.119  Sum_probs=122.7

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh----hHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE----FTI   75 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~t~   75 (153)
                      +.+...|..+...+.+.|++++|...|+++.+   .+...|..+...+.+.|++++|...|+++.+.+  |+.    ..+
T Consensus        57 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~  134 (450)
T 2y4t_A           57 PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN--PSENEEKEAQ  134 (450)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC--CCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCChhhHHHH
Confidence            35677899999999999999999999999863   367899999999999999999999999998753  443    455


Q ss_pred             HHHHHH----------HHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCC-CCHhHH
Q 035927           76 VRILTA----------YMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIR-PDEVTY  131 (153)
Q Consensus        76 ~~li~~----------~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~-p~~~t~  131 (153)
                      ..+...          ..|.+.|++++|.+.|+++.+   .+...+..+...|...|.++          ... .+..+|
T Consensus       135 ~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  214 (450)
T 2y4t_A          135 SQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLKNDNTEAF  214 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHH
Confidence            544332          126899999999999999864   37888999999999999988          223 457889


Q ss_pred             HHHHHHHhcCCchhHhhhhcc
Q 035927          132 VGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       132 ~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+...|.+.|+.++|.+.|+
T Consensus       215 ~~l~~~~~~~g~~~~A~~~~~  235 (450)
T 2y4t_A          215 YKISTLYYQLGDHELSLSEVR  235 (450)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHH
Confidence            999999999999999998874

>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=99.06  E-value=5.7e-09  Score=64.90  Aligned_cols=123  Identities=19%  Similarity=0.317  Sum_probs=101.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      ..|..+...+.+.|++++|..+++++.   ..+...|..+...+...|++++|...++++.+.+ +.+...+..+...  
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~--   78 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNA--   78 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHH--
Confidence            357888999999999999999999875   2467889999999999999999999999998754 3355667767666  


Q ss_pred             HhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           84 YCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.+.|++++|.+.++++.+.+                    +.+...+..+...+.+.|+.++|.+.|+
T Consensus        79 ~~~~~~~~~A~~~~~~~~~~~--------------------~~~~~~~~~la~~~~~~~~~~~A~~~~~  127 (136)
T 2fo7_A           79 YYKQGDYDEAIEYYQKALELD--------------------PRSAEAWYNLGNAYYKQGDYDEAIEYYQ  127 (136)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHC--------------------TTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHhC--------------------CCChHHHHHHHHHHHHHccHHHHHHHHH
Confidence            699999999999999987642                    1356778888899999999999988764

>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=99.06  E-value=4.9e-11  Score=90.55  Aligned_cols=134  Identities=9%  Similarity=0.150  Sum_probs=26.9

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      .+|..+..++.+.|++++|++.|.+  .+|..+|..+++.+.+.|++++|...++..++.  .+++.+.+.++.+  |.+
T Consensus        33 ~vWs~La~A~l~~g~~~eAIdsfik--a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~--Y~K  106 (449)
T 1b89_A           33 AVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFA--LAK  106 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHc--CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHH--HHH
Confidence            4778888888888888888888855  356667777777777777777777766555542  3445666666666  577


Q ss_pred             cCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC---------------------------------CCCCCHhHHHH
Q 035927           87 CGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP---------------------------------TIRPDEVTYVG  133 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~---------------------------------~~~p~~~t~~~  133 (153)
                      .|++++++++++.   |+..+|+.+...|...|.++                                 .. .+..+|..
T Consensus       107 lg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~n~~~LA~~L~~Lg~yq~AVea~~KA-~~~~~Wk~  182 (449)
T 1b89_A          107 TNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKA-NSTRTWKE  182 (449)
T ss_dssp             --CHHHHTTTTTC---C----------------CTTTHHHHHHHTTCHHHHHHHHHTTTCHHHHHHHHHHH-TCHHHHHH
T ss_pred             hCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHhhhHHHHHHHHHHhccHHHHHHHHHHc-CCchhHHH
Confidence            7777776666542   44445555555555555555                                 11 36677777


Q ss_pred             HHHHHhcCCchhHhhhh
Q 035927          134 VLSACTHNGNETFVINS  150 (153)
Q Consensus       134 ll~~~~~~g~~~~a~~~  150 (153)
                      ++.+|...|+++.|..+
T Consensus       183 v~~aCv~~~ef~lA~~~  199 (449)
T 1b89_A          183 VCFACVDGKEFRLAQMC  199 (449)
T ss_dssp             HHHHHHHTTCHHHHHHT
T ss_pred             HHHHHHHcCcHHHHHHH
Confidence            77777777777777543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.05  E-value=3.9e-09  Score=76.11  Aligned_cols=140  Identities=10%  Similarity=0.043  Sum_probs=78.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC----CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP----ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~----~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      |+..++..+...+.+.|+.++|.+.++++.    .| +...+..+-..+.+.|++++|+..+++      +.+...+..+
T Consensus        63 ~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l  136 (291)
T 3mkr_A           63 PELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMT  136 (291)
T ss_dssp             HHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHH
T ss_pred             hhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHH
Confidence            455556666666666666666666666642    13 444455555666666666666666655      3455555555


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc--CChhhHHHHHHHHH----hcCCCC-----------CCCCCHhHHHHHHHHHhcC
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR--KDKFTWTAMIVGLA----ISDPFP-----------TIRPDEVTYVGVLSACTHN  141 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~----~~~~~~-----------~~~p~~~t~~~ll~~~~~~  141 (153)
                      ...  |.+.|++++|.+.|+++.+  |+.. ...+..++.    ..|.++           ..+.+...++.+..++.+.
T Consensus       137 ~~~--~~~~g~~~~A~~~l~~~~~~~p~~~-~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~  213 (291)
T 3mkr_A          137 VQI--LLKLDRLDLARKELKKMQDQDEDAT-LTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQ  213 (291)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHHHCTTCH-HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHT
T ss_pred             HHH--HHHCCCHHHHHHHHHHHHhhCcCcH-HHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHc
Confidence            555  5677777777777777643  2211 111212211    112222           2234556677777777777


Q ss_pred             CchhHhhhhcc
Q 035927          142 GNETFVINSCN  152 (153)
Q Consensus       142 g~~~~a~~~~~  152 (153)
                      |++++|.+.|+
T Consensus       214 g~~~eA~~~l~  224 (291)
T 3mkr_A          214 GRWEAAEGVLQ  224 (291)
T ss_dssp             TCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            77777776653

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.05  E-value=2.6e-09  Score=73.55  Aligned_cols=143  Identities=13%  Similarity=0.006  Sum_probs=74.3

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li   79 (153)
                      ++...+..+-..+.+.|++++|...|++..+  | +...|..+-..+.+.|++++|...+++..+..  | +...+..+-
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVART--PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHH
Confidence            5555666666667777777777776666532  2 45566666666666666666666666665432  3 233333333


Q ss_pred             HHHHHhcc-----------CChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCHhHHHHHH
Q 035927           80 TAYMYCKC-----------GDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDEVTYVGVL  135 (153)
Q Consensus        80 ~~~~~~~~-----------g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~~t~~~ll  135 (153)
                      ..  |.+.           |++++|+..|++..+  | +...|..+-..+...|.++          .+..+...+..+-
T Consensus        81 ~~--~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la  158 (217)
T 2pl2_A           81 EA--YVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALA  158 (217)
T ss_dssp             HH--HHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_pred             HH--HHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHH
Confidence            33  3555           556666655555532  2 3444444444554444444          0003334444444


Q ss_pred             HHHhcCCchhHhhhh
Q 035927          136 SACTHNGNETFVINS  150 (153)
Q Consensus       136 ~~~~~~g~~~~a~~~  150 (153)
                      ..+...|+.++|.+.
T Consensus       159 ~~~~~~g~~~~A~~~  173 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQ  173 (217)
T ss_dssp             HHHHHHTCHHHHHHH
T ss_pred             HHHHHcCCHHHHHHH
Confidence            444444444444443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.04  E-value=7.6e-09  Score=68.79  Aligned_cols=145  Identities=10%  Similarity=0.072  Sum_probs=118.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +..+|..+-..+.+.|++++|...|++..  .| +...|..+...+.+.|++++|...+.......- -+...+..+-..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHHHH
Confidence            56689999999999999999999999976  33 788999999999999999999999999876532 233344444343


Q ss_pred             HHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHh
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFV  147 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a  147 (153)
                        +...++++.+.+.+.+..+   .+...+..+...+.+.|.++          .+.| +...|..+-..|.+.|+.++|
T Consensus        83 --~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           83 --NFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             --HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             --HHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHH
Confidence              6899999999999998854   36788888999999998888          4455 457799999999999999999


Q ss_pred             hhhcc
Q 035927          148 INSCN  152 (153)
Q Consensus       148 ~~~~~  152 (153)
                      .+.|+
T Consensus       161 ~~~~~  165 (184)
T 3vtx_A          161 VKYFK  165 (184)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98874

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.03  E-value=1.2e-08  Score=69.20  Aligned_cols=147  Identities=13%  Similarity=0.027  Sum_probs=119.9

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhc-CChHHHHHHHHHHhhCCCCCC-hhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRV-NRFREALTLFPEMQTSNIRPD-EFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p~-~~t~~~l   78 (153)
                      .+...+..+...+...|++++|...+++..   ..+...+..+...+... |++++|...+++..+.+..|+ ...+..+
T Consensus        40 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l  119 (225)
T 2vq2_A           40 KNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNK  119 (225)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHH
Confidence            456788999999999999999999999885   23778899999999999 999999999999988444444 4556666


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCC--CHhHHHHHHHHHhcCCc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRP--DEVTYVGVLSACTHNGN  143 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p--~~~t~~~ll~~~~~~g~  143 (153)
                      ...  |.+.|++++|.+.|+++.+  | +...+..+...+...|.++          ...|  +...+..+...+...|+
T Consensus       120 ~~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  197 (225)
T 2vq2_A          120 GIC--SAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGN  197 (225)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTC
T ss_pred             HHH--HHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCc
Confidence            665  6999999999999999854  3 5788899999999998887          3334  56677788888889999


Q ss_pred             hhHhhhhcc
Q 035927          144 ETFVINSCN  152 (153)
Q Consensus       144 ~~~a~~~~~  152 (153)
                      .+.|..+++
T Consensus       198 ~~~a~~~~~  206 (225)
T 2vq2_A          198 AQAAYEYEA  206 (225)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887653

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.99  E-value=9.5e-09  Score=75.23  Aligned_cols=61  Identities=11%  Similarity=0.087  Sum_probs=33.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      +...|..+...+.+.|++++|...|++..+   .+..+|..+...+.+.|++++|...++++.+
T Consensus        98 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  161 (365)
T 4eqf_A           98 DAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVSYTNTSHQQDACEALKNWIK  161 (365)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHccccHHHHHHHHHHHHH
Confidence            344455555555555555555555555431   2445555555555556666666666655543

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=98.98  E-value=1.3e-08  Score=70.68  Aligned_cols=144  Identities=8%  Similarity=-0.027  Sum_probs=120.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...|..+...+...|++++|...|++..   ..+...|..+...+.+.|++++|...+++..+.. +.+...+..+... 
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~-  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF-  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH-
Confidence            4668889999999999999999999886   2377889999999999999999999999998753 2356677777776 


Q ss_pred             HHhccCChHHHHHHHHhccc----C-ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhH
Q 035927           83 MYCKCGDVEKAQRVLRKMLR----K-DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~----~-~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~  146 (153)
                       |.+.|++++|.+.++++.+    + +...|..+...+...|.++          ...| +...+..+...+.+.|+.++
T Consensus       115 -~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 -LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             -HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHH
T ss_pred             -HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHH
Confidence             6999999999999999876    2 4667888888888888877          3334 46788899999999999999


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |.+.|+
T Consensus       194 A~~~~~  199 (252)
T 2ho1_A          194 ARQYYD  199 (252)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988764

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=98.97  E-value=3.8e-09  Score=77.34  Aligned_cols=92  Identities=8%  Similarity=0.043  Sum_probs=52.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+..+...+.+.|++++|..+|+++.+   .+...|..+...+.+.|++++|...|++..+.. +.+..++..+... 
T Consensus        65 ~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~-  142 (365)
T 4eqf_A           65 WPGAFEEGLKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVS-  142 (365)
T ss_dssp             CTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH-
Confidence            34456666666666666666666666542   255566666666666666666666666665432 1234445555544 


Q ss_pred             HHhccCChHHHHHHHHhc
Q 035927           83 MYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m  100 (153)
                       |.+.|++++|.+.|+++
T Consensus       143 -~~~~g~~~~A~~~~~~a  159 (365)
T 4eqf_A          143 -YTNTSHQQDACEALKNW  159 (365)
T ss_dssp             -HHHTTCHHHHHHHHHHH
T ss_pred             -HHccccHHHHHHHHHHH
Confidence             45555555555555554

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=98.93  E-value=3.3e-08  Score=71.19  Aligned_cols=141  Identities=11%  Similarity=0.063  Sum_probs=112.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHH---HHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIV---RILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~---~li~~   81 (153)
                      +...+..+-..+.+.|++++|.+.+++  ..+...+..+...+.+.|++++|...++.+.+..  |+....+   .++..
T Consensus       100 ~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~l~~a~~~l  175 (291)
T 3mkr_A          100 NTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQD--EDATLTQLATAWVSL  175 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHH
Confidence            344566777899999999999999999  5688899999999999999999999999998764  6643222   22333


Q ss_pred             HHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhH-
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETF-  146 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~-  146 (153)
                        +...|++++|..+|+++.+  | +...|+.+..++.+.|.++          ...| +..++..+...+...|+.++ 
T Consensus       176 --~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~ea  253 (291)
T 3mkr_A          176 --AAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEV  253 (291)
T ss_dssp             --HHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHH
T ss_pred             --HhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHH
Confidence              3556899999999999964  3 7889999999999999998          4456 56789999999999999865 


Q ss_pred             hhhhc
Q 035927          147 VINSC  151 (153)
Q Consensus       147 a~~~~  151 (153)
                      +.+++
T Consensus       254 a~~~~  258 (291)
T 3mkr_A          254 TNRYL  258 (291)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=98.92  E-value=2.6e-08  Score=68.56  Aligned_cols=146  Identities=14%  Similarity=0.096  Sum_probs=109.8

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhc-----------CChHHHHHHHHHHhhCCC
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRV-----------NRFREALTLFPEMQTSNI   68 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~-----------~~~~~a~~~~~~m~~~~~   68 (153)
                      +.+...+..+-..+.+.|++++|...|++..  .| +...|..+-..+.+.           |++++|...+++..+.  
T Consensus        36 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--  113 (217)
T 2pl2_A           36 PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--  113 (217)
T ss_dssp             SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--
Confidence            3456778899999999999999999999876  34 677899999999999           9999999999999875  


Q ss_pred             CCC-hhHHHHHHHHHHHhccCChHHHHHHHHhccc--CChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHH
Q 035927           69 RPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--KDKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGV  134 (153)
Q Consensus        69 ~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~l  134 (153)
                      .|+ ...+..+-..  |.+.|++++|++.|++..+  .+...+..+...+...|.++          ...|+ ...+..+
T Consensus       114 ~P~~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~l  191 (217)
T 2pl2_A          114 NPRYAPLHLQRGLV--YALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRY  191 (217)
T ss_dssp             CTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             CcccHHHHHHHHHH--HHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHH
Confidence            354 4445444444  7999999999999999754  56788899999999999888          44564 5778889


Q ss_pred             HHHHhcCCchhHhhhhcc
Q 035927          135 LSACTHNGNETFVINSCN  152 (153)
Q Consensus       135 l~~~~~~g~~~~a~~~~~  152 (153)
                      ...+.+.|+.++|.+.|+
T Consensus       192 a~~~~~~g~~~~A~~~~~  209 (217)
T 2pl2_A          192 ASALLLKGKAEEAARAAA  209 (217)
T ss_dssp             HHHHTC------------
T ss_pred             HHHHHHccCHHHHHHHHH
Confidence            999999999999998875

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=98.91  E-value=5.1e-08  Score=69.74  Aligned_cols=143  Identities=14%  Similarity=0.155  Sum_probs=72.1

Q ss_pred             hhHHHHHHHHHHhcC-ChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            6 VISWTDIVSGYINRG-QVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         6 ~~~~~~li~~~~~~g-~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      ...|..+...+...| ++++|...|++..+   .+...|..+...+...|++++|...+++..+..- .+...+..+...
T Consensus        90 ~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~  168 (330)
T 3hym_B           90 PVSWFAVGCYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLE  168 (330)
T ss_dssp             THHHHHHHHHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHH
Confidence            444555555555555 56666666555432   2344555555555555666666666555554321 122333333333


Q ss_pred             HHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------C----------CCCCHhHHHHHHHHH
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------T----------IRPDEVTYVGVLSAC  138 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~----------~~p~~~t~~~ll~~~  138 (153)
                        |.+.|++++|.+.+++..+.   +...|..+...+...|.++          .          .+.+...+..+...+
T Consensus       169 --~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~  246 (330)
T 3hym_B          169 --YGLTNNSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVC  246 (330)
T ss_dssp             --HHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHH
T ss_pred             --HHHHhhHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHH
Confidence              45555666666555555331   3445555555555554444          0          012234555555555


Q ss_pred             hcCCchhHhhhhc
Q 035927          139 THNGNETFVINSC  151 (153)
Q Consensus       139 ~~~g~~~~a~~~~  151 (153)
                      .+.|++++|.+.|
T Consensus       247 ~~~g~~~~A~~~~  259 (330)
T 3hym_B          247 RKLKKYAEALDYH  259 (330)
T ss_dssp             HHTTCHHHHHHHH
T ss_pred             HHhcCHHHHHHHH
Confidence            5556655555544

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=98.91  E-value=5.4e-08  Score=70.95  Aligned_cols=145  Identities=13%  Similarity=0.151  Sum_probs=79.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-------------
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-------------   68 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-------------   68 (153)
                      +...|..+...+.+.|++++|...|++..   ..+..++..+...+.+.|++++|...++++.+..-             
T Consensus        97 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  176 (368)
T 1fch_A           97 HMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGA  176 (368)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC------
T ss_pred             CHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHh
Confidence            44455666666666666666666666553   22555666666666666666666666665544321             


Q ss_pred             ----------------------------------CC---ChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhH
Q 035927           69 ----------------------------------RP---DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTW  108 (153)
Q Consensus        69 ----------------------------------~p---~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~  108 (153)
                                                        .|   +..++..+...  |.+.|++++|...|++..+  | +...|
T Consensus       177 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~  254 (368)
T 1fch_A          177 GGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL--FNLSGEYDKAVDCFTAALSVRPNDYLLW  254 (368)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             hhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhCcCCHHHH
Confidence                                              01   23344444444  4566666666666665532  2 34555


Q ss_pred             HHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          109 TAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       109 ~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ..+...+...|.++          ...| +...+..+...|.+.|++++|.+.|
T Consensus       255 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  308 (368)
T 1fch_A          255 NKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHF  308 (368)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            55666666555555          2223 3455566666666666666666554

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=98.90  E-value=3.9e-08  Score=70.39  Aligned_cols=146  Identities=12%  Similarity=0.068  Sum_probs=109.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...|..+...+.+.|++++|...|++..+  | +...+..+...+...|++++|...+++..+.. +.+...+..+..
T Consensus       123 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~  201 (330)
T 3hym_B          123 TYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGV  201 (330)
T ss_dssp             TCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            3456788888888888888888888888752  2 45667778888888888888888888887653 234566666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc-----------C-ChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR-----------K-DKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSA  137 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~-----------~-~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~  137 (153)
                      .  |.+.|++++|.+.+++..+           + +...|..+...+...|.++          ...| +...+..+...
T Consensus       202 ~--~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~  279 (330)
T 3hym_B          202 V--AFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYI  279 (330)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHH
T ss_pred             H--HHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHH
Confidence            5  6888888888888888743           2 3567888888888887777          3334 45677888888


Q ss_pred             HhcCCchhHhhhhcc
Q 035927          138 CTHNGNETFVINSCN  152 (153)
Q Consensus       138 ~~~~g~~~~a~~~~~  152 (153)
                      +.+.|+.++|.+.|+
T Consensus       280 ~~~~g~~~~A~~~~~  294 (330)
T 3hym_B          280 HSLMGNFENAVDYFH  294 (330)
T ss_dssp             HHHHTCHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHH
Confidence            888888888887764

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.89  E-value=2e-08  Score=69.47  Aligned_cols=147  Identities=14%  Similarity=0.220  Sum_probs=106.6

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-C-------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC------
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-D-------YVLWTAMIDGYLRVNRFREALTLFPEMQTSN------   67 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~-------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------   67 (153)
                      ++...|..+...+.+.|++++|...+++..+  | +       ...|..+...+.+.|++++|...+++..+..      
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  115 (258)
T 3uq3_A           36 KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTEHRTADIL  115 (258)
T ss_dssp             CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHH
T ss_pred             ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCchhHHH
Confidence            3456777788888888888888888887753  2 1       5778888888888888888888888887632      


Q ss_pred             ------------------CCCC-hhHHHHHHHHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC---
Q 035927           68 ------------------IRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP---  122 (153)
Q Consensus        68 ------------------~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~---  122 (153)
                                        ..|+ ...+..+...  |.+.|++++|.+.|++..+   .+...|..+...+...|.++   
T Consensus       116 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~  193 (258)
T 3uq3_A          116 TKLRNAEKELKKAEAEAYVNPEKAEEARLEGKE--YFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAI  193 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHH--HHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHH
Confidence                              2232 3334444444  6888888888888888753   25777888888888887777   


Q ss_pred             -------CCCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 -------TIRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 -------~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                             ...|+ ...|..+...+.+.|+.++|.+.|+
T Consensus       194 ~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  231 (258)
T 3uq3_A          194 ADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLD  231 (258)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence                   33344 6778888888888898888887764

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=98.89  E-value=5.5e-08  Score=70.86  Aligned_cols=94  Identities=11%  Similarity=0.082  Sum_probs=80.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...+..+...+.+.|++++|...|+++.+   .+...|..+...+.+.|++++|...+++..+.. +.+..++..+...
T Consensus        63 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~  141 (368)
T 1fch_A           63 DHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVS  141 (368)
T ss_dssp             TCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            456788999999999999999999999863   377889999999999999999999999998764 3466777777776


Q ss_pred             HHHhccCChHHHHHHHHhcc
Q 035927           82 YMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~  101 (153)
                        |.+.|++++|.+.++++.
T Consensus       142 --~~~~g~~~~A~~~~~~~~  159 (368)
T 1fch_A          142 --FTNESLQRQACEILRDWL  159 (368)
T ss_dssp             --HHHTTCHHHHHHHHHHHH
T ss_pred             --HHHcCCHHHHHHHHHHHH
Confidence              699999999999998764

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=98.86  E-value=6.8e-09  Score=71.42  Aligned_cols=147  Identities=12%  Similarity=0.078  Sum_probs=103.3

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      +.....|..+...+.+.|++++|..+|++..+   .+...+..+...+.+.|++++|...+++..+.. +.+...+..+.
T Consensus        20 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la   98 (243)
T 2q7f_A           20 HMASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAG   98 (243)
T ss_dssp             ----------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHH
Confidence            34556688888899999999999999998853   367889999999999999999999999998753 23566677777


Q ss_pred             HHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchh
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNET  145 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~  145 (153)
                      ..  |.+.|++++|.+.++++.+   .+...|..+...+...|.++          ...| +...+..+...+.+.|+++
T Consensus        99 ~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  176 (243)
T 2q7f_A           99 NV--YVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLD  176 (243)
T ss_dssp             HH--HHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCH
T ss_pred             HH--HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHH
Confidence            66  6999999999999999854   36788888999999988887          3334 5678888999999999999


Q ss_pred             Hhhhhcc
Q 035927          146 FVINSCN  152 (153)
Q Consensus       146 ~a~~~~~  152 (153)
                      +|.+.|+
T Consensus       177 ~A~~~~~  183 (243)
T 2q7f_A          177 EALSQFA  183 (243)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9988764

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=98.81  E-value=2.1e-07  Score=66.48  Aligned_cols=145  Identities=12%  Similarity=0.094  Sum_probs=85.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-------------
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-------------   68 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-------------   68 (153)
                      +...+..+...+.+.|++++|...+++..+   .+...+..+...+.+.|++++|...+++..+..-             
T Consensus        54 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  133 (327)
T 3cv0_A           54 REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQAD  133 (327)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTTTC--------
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHH
Confidence            445566666667777777777777766542   2556666666666667777777666666654310             


Q ss_pred             -----------------------------------CCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHH
Q 035927           69 -----------------------------------RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTA  110 (153)
Q Consensus        69 -----------------------------------~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~  110 (153)
                                                         +.+...+..+...  |.+.|++++|.+.+++..+  | +...|..
T Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  211 (327)
T 3cv0_A          134 VDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVL--YNLSNNYDSAAANLRRAVELRPDDAQLWNK  211 (327)
T ss_dssp             ------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHH--HHHhccHHHHHHHHHHHHHhCCCcHHHHHH
Confidence                                               1123333333333  4666667777666666643  2 4556666


Q ss_pred             HHHHHHhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          111 MIVGLAISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       111 li~~~~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +...+...|.++          ...| +...+..+...+.+.|++++|.+.|
T Consensus       212 l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  263 (327)
T 3cv0_A          212 LGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQL  263 (327)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHH
Confidence            666666666555          2223 3456666667777777777776655

>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=98.80  E-value=2e-07  Score=63.12  Aligned_cols=140  Identities=10%  Similarity=-0.020  Sum_probs=103.7

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      +...+..+...+.+.|++++|...|++...++...|..+...+.+.|++++|...+++..+.. +.+...+..+-..  |
T Consensus         5 ~~~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~--~   81 (213)
T 1hh8_A            5 EAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGML--Y   81 (213)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--H
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHH--H
Confidence            344566778889999999999999999988899999999999999999999999999998754 2355666666665  7


Q ss_pred             hccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCH-hHHHHHHHHHhcCCchhHhhhhcc
Q 035927           85 CKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDE-VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+.|++++|.+.|++..+.+...-.  + .+...+.  ...|+. ..+..+...+.+.|+.++|.+.|+
T Consensus        82 ~~~~~~~~A~~~~~~al~~~~~~~~--~-~~~~~~~--~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  145 (213)
T 1hh8_A           82 YQTEKYDLAIKDLKEALIQLRGNQL--I-DYKILGL--QFKLFACEVLYNIAFMYAKKEEWKKAEEQLA  145 (213)
T ss_dssp             HHTTCHHHHHHHHHHHHHTTTTCSE--E-ECGGGTB--CCEEEHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHcccHHHHHHHHHHHHHhCCCccH--H-HHHHhcc--ccCccchHHHHHHHHHHHHccCHHHHHHHHH
Confidence            9999999999999998653100000  0 0000000  123333 667888888999999999988764

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.79  E-value=4.6e-08  Score=78.85  Aligned_cols=144  Identities=12%  Similarity=0.063  Sum_probs=123.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +...|+.|-..+.+.|++++|+..|++..  .| +...|+.+-..+.+.|++++|+..|++..+.  .| +...|..+-.
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            45679999999999999999999999876  34 6889999999999999999999999999875  35 4566776666


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhH
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~  146 (153)
                      .  |.+.|++++|++.|++..+  | +...|+.+...+...|.++          .+.|+ ...+..+...+...|++++
T Consensus        86 ~--l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           86 T--LKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTT
T ss_pred             H--HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHH
Confidence            6  7999999999999999854  3 6889999999999999888          56676 4678899999999999999


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |.+.|+
T Consensus       164 A~~~~~  169 (723)
T 4gyw_A          164 YDERMK  169 (723)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887653

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=98.79  E-value=7.4e-08  Score=66.55  Aligned_cols=145  Identities=18%  Similarity=0.162  Sum_probs=117.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC--CCCC----hhHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN--IRPD----EFTIVR   77 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~   77 (153)
                      ...|..+...+.+.|++++|...|++..+  .+...|..+...+...|++++|...+++..+..  ..|+    ...+..
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45788899999999999999999988742  677889999999999999999999999997642  2233    466666


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc--------------------------C---ChhhHHHHHHHHHhcCCCC------
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR--------------------------K---DKFTWTAMIVGLAISDPFP------  122 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~--------------------------~---~~~~~~~li~~~~~~~~~~------  122 (153)
                      +...  |.+.|++++|.+.|++..+                          .   +...|..+...+...|.++      
T Consensus        85 l~~~--~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~  162 (258)
T 3uq3_A           85 IGNA--YHKLGDLKKTIEYYQKSLTEHRTADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWPNAVKAY  162 (258)
T ss_dssp             HHHH--HHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHH--HHHcccHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            6666  6999999999999998865                          2   3556777888888888777      


Q ss_pred             ----CCCC-CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 ----TIRP-DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 ----~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                          ...| +...|..+...+.+.|++++|.+.|+
T Consensus       163 ~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  197 (258)
T 3uq3_A          163 TEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCN  197 (258)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence                2334 56778899999999999999988764

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=98.79  E-value=1.5e-07  Score=67.19  Aligned_cols=134  Identities=10%  Similarity=0.002  Sum_probs=68.4

Q ss_pred             HHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHH
Q 035927           16 YINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEK   92 (153)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~   92 (153)
                      +...|++++|...+++..+   .+...+..+...+.+.|++++|...+++..+.. +.+...+..+...  |.+.|++++
T Consensus       148 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~--~~~~~~~~~  224 (327)
T 3cv0_A          148 FAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGAT--LANGNRPQE  224 (327)
T ss_dssp             TTSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHH
T ss_pred             HHHcccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHH--HHHcCCHHH
Confidence            3344444444444444431   134444444444444455555555544444321 1123333333333  344455555


Q ss_pred             HHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCC-------------CHhHHHHHHHHHhcCCchhH
Q 035927           93 AQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRP-------------DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        93 a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p-------------~~~t~~~ll~~~~~~g~~~~  146 (153)
                      |.+.|++..+  | +...|..+...+...|.++          ...|             +...|..+..++.+.|+.++
T Consensus       225 A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  304 (327)
T 3cv0_A          225 ALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDL  304 (327)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHH
Confidence            5554444422  1 3444444444444444443          1123             36788999999999999999


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |.++++
T Consensus       305 A~~~~~  310 (327)
T 3cv0_A          305 VELTYA  310 (327)
T ss_dssp             HHHHTT
T ss_pred             HHHHHH
Confidence            998875

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.76  E-value=7.6e-08  Score=72.97  Aligned_cols=64  Identities=8%  Similarity=0.155  Sum_probs=49.3

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSN   67 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   67 (153)
                      ||...|..+..++.+.|++++|...+++..  .| +...|..+...+.+.|++++|...|+.+.+.+
T Consensus        37 p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  103 (514)
T 2gw1_A           37 EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEGLGKFADAMFDLSVLSLNG  103 (514)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSS
T ss_pred             ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            677778888888888888888888888765  23 56678888888888888888888887776543

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.74  E-value=3.1e-07  Score=66.18  Aligned_cols=145  Identities=11%  Similarity=0.083  Sum_probs=98.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC----ChhHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP----DEFTIV   76 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p----~~~t~~   76 (153)
                      .+...+..+...+.+.|++++|...|++..+  | +...|..+...+.+.|++++|...+++..+.  .|    +...+.
T Consensus        35 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~  112 (359)
T 3ieg_A           35 DNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAES  112 (359)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCcccChHHHHH
Confidence            3455677777777777777777777777652  3 5667777777777778888888888777654  24    222232


Q ss_pred             HH------------HHHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCC-CHhH
Q 035927           77 RI------------LTAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRP-DEVT  130 (153)
Q Consensus        77 ~l------------i~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p-~~~t  130 (153)
                      .+            ...  +...|++++|.+.++++.+   .+...+..+...+...|.++          ...| +...
T Consensus       113 ~l~~~~~~~~~~~~a~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  190 (359)
T 3ieg_A          113 QLVKADEMQRLRSQALD--AFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEA  190 (359)
T ss_dssp             HHHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHH
T ss_pred             HHHHHHHHHHHHHHHHH--HHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHH
Confidence            22            123  5778888888888877743   25667777777777777766          3344 4567


Q ss_pred             HHHHHHHHhcCCchhHhhhhcc
Q 035927          131 YVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       131 ~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +..+...+...|++++|.+.|+
T Consensus       191 ~~~la~~~~~~~~~~~A~~~~~  212 (359)
T 3ieg_A          191 FYKISTLYYQLGDHELSLSEVR  212 (359)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHH
Confidence            7788888888888888877653

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.73  E-value=5e-08  Score=74.80  Aligned_cols=145  Identities=8%  Similarity=0.011  Sum_probs=118.1

Q ss_pred             CchhHHHHHHHHHHhcCCh-HHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQV-DIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~-~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      .+...+..+-..+...|++ ++|...|++..  .| +...|..+-..+.+.|++++|...|++..+..  |+...+..+-
T Consensus       100 ~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg  177 (474)
T 4abn_A          100 VEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLS  177 (474)
T ss_dssp             CCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHH
Confidence            3566788888899999999 99999998875  33 67889999999999999999999999998764  7766666666


Q ss_pred             HHHHHhcc---------CChHHHHHHHHhccc--C-ChhhHHHHHHHHHhc--------CCCC----------CCCC---
Q 035927           80 TAYMYCKC---------GDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAIS--------DPFP----------TIRP---  126 (153)
Q Consensus        80 ~~~~~~~~---------g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~--------~~~~----------~~~p---  126 (153)
                      ..  |.+.         |++++|++.|++..+  | +...|..+..+|...        +.++          .+.|   
T Consensus       178 ~~--~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~  255 (474)
T 4abn_A          178 MV--LRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKAS  255 (474)
T ss_dssp             HH--HTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             HH--HHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCcc
Confidence            66  6888         999999999999854  3 677888888888776        5555          4456   


Q ss_pred             -CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          127 -DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       127 -~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                       +...|..+-..|.+.|++++|.+.|+
T Consensus       256 ~~~~~~~~lg~~~~~~g~~~~A~~~~~  282 (474)
T 4abn_A          256 SNPDLHLNRATLHKYEESYGEALEGFS  282 (474)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence             66788899999999999999988764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.72  E-value=4e-07  Score=65.66  Aligned_cols=147  Identities=12%  Similarity=0.104  Sum_probs=115.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHH-HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYV-LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      -+...|..+...+.+.|++++|..+|++..+  | +.. .|..+...+.+.|++++|..+|++..+.+ +++...|....
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a  175 (308)
T 2ond_A           97 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAA  175 (308)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHH
Confidence            3455799999999999999999999999864  4 343 89999999999999999999999998764 23444454443


Q ss_pred             HHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------C---CCCC--HhHHHHHHHHHhcC
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------T---IRPD--EVTYVGVLSACTHN  141 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~---~~p~--~~t~~~ll~~~~~~  141 (153)
                      ... +...|+.++|.++|++..+  | +...|..++..+.+.|.++          .   +.|+  ...|..++....+.
T Consensus       176 ~~~-~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~  254 (308)
T 2ond_A          176 LME-YYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNI  254 (308)
T ss_dssp             HHH-HHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHH
T ss_pred             HHH-HHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHc
Confidence            331 2347999999999999864  3 6788999998888888777          2   3554  45788888888899


Q ss_pred             CchhHhhhhcc
Q 035927          142 GNETFVINSCN  152 (153)
Q Consensus       142 g~~~~a~~~~~  152 (153)
                      |+.+.|..+++
T Consensus       255 g~~~~a~~~~~  265 (308)
T 2ond_A          255 GDLASILKVEK  265 (308)
T ss_dssp             SCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            99999987753

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.70  E-value=3.7e-07  Score=63.77  Aligned_cols=142  Identities=8%  Similarity=-0.036  Sum_probs=85.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh--hHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE--FTIVRILTAY   82 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~--~t~~~li~~~   82 (153)
                      .+-.....+.+.|++++|...|++..  .| +...+..+...+.+.|++++|...+++..+.+-.|+.  ..|..+-.. 
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~-   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI-   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH-
Confidence            34455666777777777777777764  22 4456777777777777777777777777663322222  124444444 


Q ss_pred             HHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCchhHhh
Q 035927           83 MYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~~~~a~  148 (153)
                       |.+.|++++|++.|++..+  | +...|..+...+...|.++          ...|+. ..|..+...+...+++++|.
T Consensus        84 -~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~  162 (272)
T 3u4t_A           84 -LMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKAD  162 (272)
T ss_dssp             -HHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             -HHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence             5777777777777777643  2 4566666777776666665          334433 34444442444445677666


Q ss_pred             hhc
Q 035927          149 NSC  151 (153)
Q Consensus       149 ~~~  151 (153)
                      +.|
T Consensus       163 ~~~  165 (272)
T 3u4t_A          163 SSF  165 (272)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=98.70  E-value=3.1e-07  Score=66.18  Aligned_cols=145  Identities=13%  Similarity=0.131  Sum_probs=114.3

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      |...+..+...+.+.|++++|...|++..+   .+...|..+...+...|++++|...+++..+.. +-+...+..+...
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   80 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHH
Confidence            456788899999999999999999998862   367899999999999999999999999998753 2255666666666


Q ss_pred             HHHhccCChHHHHHHHHhcccC------ChhhHHHH------------HHHHHhcCCCC----------CCCC-CHhHHH
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK------DKFTWTAM------------IVGLAISDPFP----------TIRP-DEVTYV  132 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~------~~~~~~~l------------i~~~~~~~~~~----------~~~p-~~~t~~  132 (153)
                        |.+.|++++|.+.|++..+.      +...+..+            ...+...|.++          ...| +...+.
T Consensus        81 --~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  158 (359)
T 3ieg_A           81 --LLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRE  158 (359)
T ss_dssp             --HHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             --HHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHH
Confidence              79999999999999999653      23344433            45666666666          2334 567788


Q ss_pred             HHHHHHhcCCchhHhhhhcc
Q 035927          133 GVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       133 ~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+...+...|++++|.+.++
T Consensus       159 ~~~~~~~~~~~~~~A~~~~~  178 (359)
T 3ieg_A          159 LRAECFIKEGEPRKAISDLK  178 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHH
Confidence            89999999999999998764

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.66  E-value=1.4e-07  Score=65.95  Aligned_cols=143  Identities=11%  Similarity=-0.009  Sum_probs=103.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +..+|..+...+.+.|++++|...|++..   ..+...|..+...+.+.|++++|...+++..+.. +.+...+..+...
T Consensus        42 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~  120 (275)
T 1xnf_A           42 RAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIA  120 (275)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHH
Confidence            45678899999999999999999999876   2368899999999999999999999999998753 2345667766666


Q ss_pred             HHHhccCChHHHHHHHHhccc--CChhhHHHHHHHHHhcCCCC-----------CCCCCHhHHHHHHHHHhcCCchhHhh
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR--KDKFTWTAMIVGLAISDPFP-----------TIRPDEVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~-----------~~~p~~~t~~~ll~~~~~~g~~~~a~  148 (153)
                        |.+.|++++|.+.|+++.+  |+.......+..+...+.++           ..+++...+ .+...+...++.++|.
T Consensus       121 --~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~a~  197 (275)
T 1xnf_A          121 --LYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGW-NIVEFYLGNISEQTLM  197 (275)
T ss_dssp             --HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCSTHH-HHHHHHTTSSCHHHHH
T ss_pred             --HHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCcchHHH-HHHHHHHHhcCHHHHH
Confidence              6999999999999999864  43333333333333333333           222333333 4667777777777777


Q ss_pred             hhc
Q 035927          149 NSC  151 (153)
Q Consensus       149 ~~~  151 (153)
                      +.+
T Consensus       198 ~~~  200 (275)
T 1xnf_A          198 ERL  200 (275)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            655

>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=98.64  E-value=8.9e-07  Score=60.67  Aligned_cols=137  Identities=9%  Similarity=0.044  Sum_probs=103.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---C-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh-hHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---E-RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE-FTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~l   78 (153)
                      .|...+..+-..+.+.|++++|...|++..   . ++...+..+-..+.+.|++++|+..+++..+.  .|+. ..+..+
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l   82 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGK   82 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHH
Confidence            456788888899999999999999999875   2 56777777888888999999999999998865  3544 444444


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc--C-Ch-------hhHHHHHHHHHhcCCCC----------CCCCC---HhHHHHHH
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR--K-DK-------FTWTAMIVGLAISDPFP----------TIRPD---EVTYVGVL  135 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~--~-~~-------~~~~~li~~~~~~~~~~----------~~~p~---~~t~~~ll  135 (153)
                      -..  |.+.|++++|++.|++..+  | +.       ..|..+-..+...|.++          ...|+   ...|..+-
T Consensus        83 ~~~--~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~  160 (228)
T 4i17_A           83 SAA--YRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLG  160 (228)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             HHH--HHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence            444  7999999999999999864  3 34       34666666666667666          56676   35677777


Q ss_pred             HHHhcCCch
Q 035927          136 SACTHNGNE  144 (153)
Q Consensus       136 ~~~~~~g~~  144 (153)
                      ..|...|..
T Consensus       161 ~~~~~~~~~  169 (228)
T 4i17_A          161 VLFYNNGAD  169 (228)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777777776

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.64  E-value=1.2e-06  Score=53.57  Aligned_cols=94  Identities=20%  Similarity=0.395  Sum_probs=80.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...|..+...+.+.|++++|...|++..+   .+...+..+...+.+.|++++|...++++.+.. +.+..++..+... 
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~-   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA-   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH-
Confidence            56788999999999999999999998852   367889999999999999999999999998753 3456677777776 


Q ss_pred             HHhccCChHHHHHHHHhccc
Q 035927           83 MYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~  102 (153)
                       |.+.|++++|.+.|+++.+
T Consensus        87 -~~~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           87 -YYKQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             -HHHTTCHHHHHHHHHHHHH
T ss_pred             -HHHhcCHHHHHHHHHHHHH
Confidence             6999999999999999864

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=98.63  E-value=3.5e-07  Score=63.87  Aligned_cols=144  Identities=13%  Similarity=-0.024  Sum_probs=106.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...|..+...+.+.|++++|...|++..+  | +...|..+...+.+.|++++|...++++.+.  .|+.......+.
T Consensus        75 ~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~  152 (275)
T 1xnf_A           75 DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLY  152 (275)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHH
Confidence            4577899999999999999999999998863  3 6789999999999999999999999999874  355555555555


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCCC-----HhHHHHHHHHHhcCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRPD-----EVTYVGVLSACTHNG  142 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p~-----~~t~~~ll~~~~~~g  142 (153)
                      .  +.+.|++++|...+++..+   ++...|. +...+...+..+          ...|+     ...+..+...+.+.|
T Consensus       153 ~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g  229 (275)
T 1xnf_A          153 L--AEQKLDEKQAKEVLKQHFEKSDKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLG  229 (275)
T ss_dssp             H--HHHHHCHHHHHHHHHHHHHHSCCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             H--HHHhcCHHHHHHHHHHHHhcCCcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcC
Confidence            5  3677999999999977643   2333333 333333333222          22232     467888888888999


Q ss_pred             chhHhhhhcc
Q 035927          143 NETFVINSCN  152 (153)
Q Consensus       143 ~~~~a~~~~~  152 (153)
                      +.++|.+.|+
T Consensus       230 ~~~~A~~~~~  239 (275)
T 1xnf_A          230 DLDSATALFK  239 (275)
T ss_dssp             CHHHHHHHHH
T ss_pred             CHHHHHHHHH
Confidence            9999888764

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=98.61  E-value=3.9e-07  Score=69.07  Aligned_cols=81  Identities=9%  Similarity=-0.119  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHH
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVG  114 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~  114 (153)
                      ..|..+...+.+.|++++|...+++..+.+  |+...+..+...  |.+.|++++|.+.+++..+.   +...|..+...
T Consensus       238 ~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  313 (514)
T 2gw1_A          238 ISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALI--MADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQM  313 (514)
T ss_dssp             HHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHH--HHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHH--HHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHH
Confidence            344444444445555555555555544332  223333333333  34455555555554444321   33444444444


Q ss_pred             HHhcCCCC
Q 035927          115 LAISDPFP  122 (153)
Q Consensus       115 ~~~~~~~~  122 (153)
                      +...|.++
T Consensus       314 ~~~~~~~~  321 (514)
T 2gw1_A          314 NFILQNYD  321 (514)
T ss_dssp             HHHTTCTT
T ss_pred             HHHhCCHH
Confidence            44444444

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.61  E-value=2.3e-07  Score=65.78  Aligned_cols=146  Identities=15%  Similarity=0.183  Sum_probs=112.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--------C---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC------C
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--------R---DYVLWTAMIDGYLRVNRFREALTLFPEMQTS------N   67 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--------~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~   67 (153)
                      +..++..+...+...|++++|..+|++..+        .   ....+..+...+...|++++|...+++..+.      +
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            456688999999999999999999998864        1   4567888999999999999999999998754      2


Q ss_pred             CCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccC-----------ChhhHHHHHHHHHhcCCCC----------CC-
Q 035927           68 IRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK-----------DKFTWTAMIVGLAISDPFP----------TI-  124 (153)
Q Consensus        68 ~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-----------~~~~~~~li~~~~~~~~~~----------~~-  124 (153)
                      -.| ....+..+...  |...|++++|.+.|++..+.           ....+..+...+...|.++          .. 
T Consensus       106 ~~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~  183 (311)
T 3nf1_A          106 DHPAVAATLNNLAVL--YGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIY  183 (311)
T ss_dssp             TCHHHHHHHHHHHHH--HHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHH--HHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            233 34455555555  79999999999999988531           3556777888888887776          11 


Q ss_pred             -------CCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          125 -------RPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       125 -------~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                             .|+ ...+..+...+.+.|++++|.+.|+
T Consensus       184 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  219 (311)
T 3nf1_A          184 QTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYK  219 (311)
T ss_dssp             HHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                   333 3568888899999999999998764

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.60  E-value=4.5e-07  Score=69.25  Aligned_cols=142  Identities=11%  Similarity=-0.015  Sum_probs=116.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      .+..+...+...|++++|...|++..  .|+...|..+...+.+.|++++|...+++..+.. +.+..++..+...  |.
T Consensus       245 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~--~~  321 (537)
T 3fp2_A          245 ALCYTGIFHFLKNNLLDAQVLLQESINLHPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQM--YF  321 (537)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHH--HH
Confidence            46677788889999999999999986  4667888889999999999999999999998754 2356667777666  69


Q ss_pred             ccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           86 KCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +.|++++|.+.|++..+  | +...|..+...+...|.++          ...|+ ...+..+...+.+.|++++|.+.|
T Consensus       322 ~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  401 (537)
T 3fp2_A          322 ILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQY  401 (537)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHH
Confidence            99999999999999854  3 5778889999999998887          33454 567888999999999999999876


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      +
T Consensus       402 ~  402 (537)
T 3fp2_A          402 D  402 (537)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.56  E-value=1.6e-07  Score=65.48  Aligned_cols=25  Identities=8%  Similarity=-0.032  Sum_probs=21.1

Q ss_pred             HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          128 EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ...+..+...|.+.|++++|.++|+
T Consensus       252 ~~~~~~la~~~~~~g~~~~A~~~~~  276 (283)
T 3edt_B          252 NTTLRSLGALYRRQGKLEAAHTLED  276 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            3568888899999999999998774

>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=98.55  E-value=3.9e-06  Score=58.98  Aligned_cols=108  Identities=10%  Similarity=0.003  Sum_probs=63.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCCC-CHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      +...+..+-..+.+.|++++|...|++..++ +...+..+-..+.+    .+++++|...|++..+.+   +...+..+-
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg   81 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLG   81 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHH
Confidence            4445566666666666777766666665433 44556666666666    666666666666666554   444444444


Q ss_pred             HHHHHhc----cCChHHHHHHHHhcccC-ChhhHHHHHHHHHh
Q 035927           80 TAYMYCK----CGDVEKAQRVLRKMLRK-DKFTWTAMIVGLAI  117 (153)
Q Consensus        80 ~~~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~  117 (153)
                      ..  |.+    .+++++|++.|++..+. +...+..+-..|..
T Consensus        82 ~~--~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~  122 (273)
T 1ouv_A           82 NL--YYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHD  122 (273)
T ss_dssp             HH--HHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HH--HhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHc
Confidence            44  455    66666666666665443 44555555555555

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=98.52  E-value=2.4e-07  Score=65.64  Aligned_cols=145  Identities=13%  Similarity=0.118  Sum_probs=101.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC----------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC------CC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS------NI   68 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~   68 (153)
                      ...+..+...+...|++++|...+++..+          + ....+..+...+...|++++|...+++..+.      +.
T Consensus       111 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~  190 (311)
T 3nf1_A          111 AATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPD  190 (311)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTT
T ss_pred             HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            45688899999999999999999988752          2 4457888999999999999999999999764      22


Q ss_pred             CCC-hhHHHHHHHHHHHhccCChHHHHHHHHhcccC------------ChhhHHHH------HHHHHhcCCCC-------
Q 035927           69 RPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK------------DKFTWTAM------IVGLAISDPFP-------  122 (153)
Q Consensus        69 ~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~------------~~~~~~~l------i~~~~~~~~~~-------  122 (153)
                      .|+ ..++..+...  |.+.|++++|.+.+++..+.            ....|...      ...+...+.+.       
T Consensus       191 ~~~~~~~~~~la~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  268 (311)
T 3nf1_A          191 DPNVAKTKNNLASC--YLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYK  268 (311)
T ss_dssp             CHHHHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC----
T ss_pred             CHHHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHh
Confidence            343 3455555555  79999999999999998642            11112111      11122222222       


Q ss_pred             ---CCCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          123 ---TIRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       123 ---~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                         ...|+ ..++..+...|.+.|++++|.+.|+
T Consensus       269 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  302 (311)
T 3nf1_A          269 ACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEE  302 (311)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence               12343 4678899999999999999998874

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=98.51  E-value=3.6e-06  Score=58.71  Aligned_cols=24  Identities=8%  Similarity=-0.153  Sum_probs=18.4

Q ss_pred             hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          129 VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       129 ~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..|..+-..|.+.|+.++|.+.|+
T Consensus       222 ~~~~~l~~~~~~~~~~~~A~~~~~  245 (272)
T 3u4t_A          222 EANEYIAYYYTINRDKVKADAAWK  245 (272)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHH
Confidence            467777778888888888887764

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=98.51  E-value=1.2e-06  Score=66.78  Aligned_cols=145  Identities=12%  Similarity=0.053  Sum_probs=90.7

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +..+|..+...+.+.|++++|...|++..+   .+...|..+...+.+.|++++|...+++..+.. +.+...+..+...
T Consensus       309 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  387 (537)
T 3fp2_A          309 YPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEI  387 (537)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            455667777777777777777777776642   245667777777777777777777777776542 2234455555554


Q ss_pred             HHHhccCChHHHHHHHHhcccC---------ChhhHHHHHHHHHhc----------CCCC----------CCCC-CHhHH
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK---------DKFTWTAMIVGLAIS----------DPFP----------TIRP-DEVTY  131 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~----------~~~~----------~~~p-~~~t~  131 (153)
                        |.+.|++++|.+.|++..+.         ....+......+...          |.++          ...| +...+
T Consensus       388 --~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~  465 (537)
T 3fp2_A          388 --LTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAK  465 (537)
T ss_dssp             --HHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             --HHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHH
Confidence              57777777777777776431         111122223334333          3333          2234 45678


Q ss_pred             HHHHHHHhcCCchhHhhhhcc
Q 035927          132 VGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       132 ~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+...+.+.|+.++|.+.|+
T Consensus       466 ~~l~~~~~~~g~~~~A~~~~~  486 (537)
T 3fp2_A          466 IGLAQLKLQMEKIDEAIELFE  486 (537)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHH
Confidence            888888888888888887764

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=98.50  E-value=2.5e-06  Score=55.64  Aligned_cols=116  Identities=16%  Similarity=0.146  Sum_probs=96.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...+++..   ..+...+..+...+...|++++|.+.+++..+.. +.+...+..+..
T Consensus        40 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~  118 (186)
T 3as5_A           40 FDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGV  118 (186)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHH
Confidence            466778999999999999999999999875   2367889999999999999999999999998753 345666666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.|++++|.+.+++..+   .+...|..+...+...|.++
T Consensus       119 ~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~  161 (186)
T 3as5_A          119 A--LDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHE  161 (186)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             H--HHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHH
Confidence            6  6999999999999999854   26778888888888887655

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.48  E-value=4e-06  Score=51.50  Aligned_cols=114  Identities=8%  Similarity=0.028  Sum_probs=88.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+...|++++|...|++..   ..+...|..+...+...|++++|...++...+.. +.+...+..+..
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~   88 (131)
T 2vyi_A           10 AEAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHH
Confidence            345678888999999999999999999875   2377889999999999999999999999998753 234556666666


Q ss_pred             HHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDP  120 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~  120 (153)
                      .  |.+.|++++|.+.|++..+.   +...+..+...+...+.
T Consensus        89 ~--~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           89 A--LSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTT
T ss_pred             H--HHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhc
Confidence            5  69999999999999998652   44455555555544443

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.48  E-value=4.3e-06  Score=51.78  Aligned_cols=110  Identities=16%  Similarity=0.064  Sum_probs=86.1

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      +.+...|..+...+.+.|++++|...|++..+   .+...|..+...+...|++++|+..+++..+.. +.+...+..+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la   91 (133)
T 2lni_A           13 PDLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKA   91 (133)
T ss_dssp             SCHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHH
Confidence            45566789999999999999999999998753   377889999999999999999999999998753 23456666666


Q ss_pred             HHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHH
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGL  115 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~  115 (153)
                      ..  |.+.|++++|.+.|++..+.   +...+..+...+
T Consensus        92 ~~--~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~  128 (133)
T 2lni_A           92 AA--LEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCM  128 (133)
T ss_dssp             HH--HHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHH
T ss_pred             HH--HHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHH
Confidence            65  69999999999999998653   333444444443

>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=98.48  E-value=3.6e-06  Score=51.81  Aligned_cols=96  Identities=20%  Similarity=0.387  Sum_probs=81.0

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...++++.   ..+...+..+...+.+.|++++|...++++.+.. +.+...+..+..
T Consensus        33 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~  111 (136)
T 2fo7_A           33 RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGN  111 (136)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            456678889999999999999999999885   2367788999999999999999999999998753 235667777777


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .  |.+.|++++|.+.++.+.+
T Consensus       112 ~--~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A          112 A--YYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             H--HHTTTCHHHHHHHHHHHHH
T ss_pred             H--HHHHccHHHHHHHHHHHHc
Confidence            6  6999999999999998754

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.46  E-value=1.3e-06  Score=59.58  Aligned_cols=141  Identities=15%  Similarity=0.071  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHH----------------HHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTA----------------MIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~----------------li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      .+-.....+.+.|++++|...|++..+  | +...|..                +-..+.+.|++++|...+++..+.. 
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-   84 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA-   84 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-
Confidence            344455677889999999999999863  3 4455666                8888999999999999999998753 


Q ss_pred             CC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCC---------C-CCCCCH--hHHH
Q 035927           69 RP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPF---------P-TIRPDE--VTYV  132 (153)
Q Consensus        69 ~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~---------~-~~~p~~--~t~~  132 (153)
                       | +...+..+-..  |.+.|++++|+..|++..+  | +...|..+...|...+..         . -..|+.  ..+.
T Consensus        85 -p~~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  161 (208)
T 3urz_A           85 -PNNVDCLEACAEM--QVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSSPTKMQYARY  161 (208)
T ss_dssp             -TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHHH
T ss_pred             -CCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCchhHHHH
Confidence             5 45566666555  7999999999999999864  4 677788777776543211         1 123443  3344


Q ss_pred             HHHHHHhcCCchhHhhhhcc
Q 035927          133 GVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       133 ~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..-.++...|++++|.+.|+
T Consensus       162 ~~g~~~~~~~~~~~A~~~~~  181 (208)
T 3urz_A          162 RDGLSKLFTTRYEKARNSLQ  181 (208)
T ss_dssp             HHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHH
Confidence            44556667888999887764

>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=98.45  E-value=3.1e-06  Score=54.54  Aligned_cols=123  Identities=11%  Similarity=0.054  Sum_probs=92.8

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+..+...+.+.|++++|...|++..   ..+...|..+...+.+.|++++|...+++..+.. +.+...+..+... 
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~-   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS-   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHH-
Confidence            3457778888999999999999999875   3378889999999999999999999999998753 2345566666555 


Q ss_pred             HHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHH--HHHHHHHhcCCchhHhhhhc
Q 035927           83 MYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTY--VGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~--~~ll~~~~~~g~~~~a~~~~  151 (153)
                       |.+.|++++|.+.|++..+.+.                    -+...+  ......+.+.|++++|.+.+
T Consensus        91 -~~~~~~~~~A~~~~~~a~~~~p--------------------~~~~~~~~~~~~~~~~~~~~~~~A~~~~  140 (166)
T 1a17_A           91 -NMALGKFRAALRDYETVVKVKP--------------------HDKDAKMKYQECNKIVKQKAFERAIAGD  140 (166)
T ss_dssp             -HHHTTCHHHHHHHHHHHHHHST--------------------TCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHHhccHHHHHHHHHHHHHhCC--------------------CCHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence             7999999999999999876320                    123333  33344466778888887765

>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=98.41  E-value=2.2e-06  Score=56.66  Aligned_cols=142  Identities=11%  Similarity=0.027  Sum_probs=102.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMY   84 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~   84 (153)
                      .+......+.+.|++++|...|++..+  | +...+..+-..+.+.|++++|...++...+..  |+........... +
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~-~   84 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLE-L   84 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHH-H
Confidence            456677788899999999999999874  3 67788889999999999999999998876542  3433322221111 2


Q ss_pred             hccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC---HhHHHHHHHHHhcCCchhHhh
Q 035927           85 CKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD---EVTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~---~~t~~~ll~~~~~~g~~~~a~  148 (153)
                      .+.++..+|...+++..+  | +...+..+...+...|.++          ...|+   ...+..+...+...|+.++|.
T Consensus        85 ~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~  164 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIA  164 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHH
T ss_pred             HhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHH
Confidence            333333456777777643  3 5778888888888888777          45565   457888999999999999998


Q ss_pred             hhcc
Q 035927          149 NSCN  152 (153)
Q Consensus       149 ~~~~  152 (153)
                      ..|+
T Consensus       165 ~~y~  168 (176)
T 2r5s_A          165 SKYR  168 (176)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7764

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.40  E-value=1.6e-06  Score=66.41  Aligned_cols=146  Identities=10%  Similarity=0.038  Sum_probs=120.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhc---------CChHHHHHHHHHHhhCCCCCCh
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRV---------NRFREALTLFPEMQTSNIRPDE   72 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~---------~~~~~a~~~~~~m~~~~~~p~~   72 (153)
                      -+...|..+-..|.+.|++++|...|++..  .|+...+..+-..+.+.         |++++|...+++..+.. +-+.
T Consensus       135 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~  213 (474)
T 4abn_A          135 ELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDG  213 (474)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCH
Confidence            346789999999999999999999999886  46778899999999999         99999999999998753 2356


Q ss_pred             hHHHHHHHHHHHhcc--------CChHHHHHHHHhccc--C----ChhhHHHHHHHHHhcCCCC----------CCCCC-
Q 035927           73 FTIVRILTAYMYCKC--------GDVEKAQRVLRKMLR--K----DKFTWTAMIVGLAISDPFP----------TIRPD-  127 (153)
Q Consensus        73 ~t~~~li~~~~~~~~--------g~~~~a~~~~~~m~~--~----~~~~~~~li~~~~~~~~~~----------~~~p~-  127 (153)
                      ..+..+-..  |.+.        |++++|++.|++..+  |    +...|..+...|...|.++          ...|+ 
T Consensus       214 ~~~~~lg~~--~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~  291 (474)
T 4abn_A          214 RSWYILGNA--YLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAW  291 (474)
T ss_dssp             HHHHHHHHH--HHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHH--HHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence            666666666  5777        899999999999854  3    6788999999999998888          44565 


Q ss_pred             HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          128 EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ...+..+...+...|+.++|++.+.
T Consensus       292 ~~a~~~l~~~~~~lg~~~eAi~~~~  316 (474)
T 4abn_A          292 PEPQQREQQLLEFLSRLTSLLESKG  316 (474)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4568888899999999999987653

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.39  E-value=8.1e-06  Score=58.72  Aligned_cols=145  Identities=7%  Similarity=0.078  Sum_probs=106.6

Q ss_pred             CchhHHHHHHHHHH-------hcCCh-------HHHHHHHHhCCC---C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            4 KDVISWTDIVSGYI-------NRGQV-------DIARQYFAQMPE---R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         4 pd~~~~~~li~~~~-------~~g~~-------~~a~~l~~~m~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      -+...|..+...+.       +.|++       ++|..+|++..+   | +...|..+...+.+.|++++|..+|++..+
T Consensus        48 ~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  127 (308)
T 2ond_A           48 HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA  127 (308)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            34556777777765       45886       899999998753   3 567899999999999999999999999997


Q ss_pred             CCCCCChh--HHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHH-hcCCCC----------CCCC-CH
Q 035927           66 SNIRPDEF--TIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLA-ISDPFP----------TIRP-DE  128 (153)
Q Consensus        66 ~~~~p~~~--t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~-~~~~~~----------~~~p-~~  128 (153)
                      .  .|+..  .|..+...  +.+.|++++|.++|++..+.   +...|........ ..|..+          ...| +.
T Consensus       128 ~--~p~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~p~~~  203 (308)
T 2ond_A          128 I--EDIDPTLVYIQYMKF--ARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIP  203 (308)
T ss_dssp             S--SSSCTHHHHHHHHHH--HHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCH
T ss_pred             c--cccCccHHHHHHHHH--HHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcH
Confidence            4  45432  68888777  58999999999999998763   3333432222211 134443          2234 45


Q ss_pred             hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          129 VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       129 ~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..|..++..+.+.|+.++|..+|+
T Consensus       204 ~~~~~~~~~~~~~g~~~~A~~~~~  227 (308)
T 2ond_A          204 EYVLAYIDYLSHLNEDNNTRVLFE  227 (308)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHH
Confidence            778888999999999999998874

>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=98.38  E-value=1.4e-05  Score=56.16  Aligned_cols=106  Identities=12%  Similarity=0.022  Sum_probs=54.9

Q ss_pred             hHHHHHHHHHHh----cCChHHHHHHHHhCCC-CCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChhHHHH
Q 035927            7 ISWTDIVSGYIN----RGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         7 ~~~~~li~~~~~----~g~~~~a~~l~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      ..+..+-..+.+    .+++++|...|++..+ .+...+..+-..+.+    .+++++|...|++..+.+   +...+..
T Consensus        39 ~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~  115 (273)
T 1ouv_A           39 SGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCAS  115 (273)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHH
Confidence            345555555555    6666666666655432 245555555555555    556666666666555543   3344444


Q ss_pred             HHHHHHHhc----cCChHHHHHHHHhcccC-ChhhHHHHHHHHHh
Q 035927           78 ILTAYMYCK----CGDVEKAQRVLRKMLRK-DKFTWTAMIVGLAI  117 (153)
Q Consensus        78 li~~~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~  117 (153)
                      +-..  |.+    .+++++|++.|++..+. +...+..+...|..
T Consensus       116 lg~~--~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~  158 (273)
T 1ouv_A          116 LGGI--YHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDA  158 (273)
T ss_dssp             HHHH--HHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHH--HHcCCCcccCHHHHHHHHHHHHhcCcHHHHHHHHHHHHc
Confidence            4443  344    55555555555555433 33444444444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.36  E-value=3.4e-06  Score=55.04  Aligned_cols=94  Identities=11%  Similarity=0.128  Sum_probs=76.0

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~   80 (153)
                      +...+..+-..+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|...|++..+..  |+ ...+..+-.
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~--P~~~~~~~~lg~  112 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG--KNDYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--SSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC--CCCcHHHHHHHH
Confidence            45567788889999999999999999886  34 77889999999999999999999999998753  43 444444444


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +  |.+.|++++|.+.|++..+
T Consensus       113 ~--~~~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          113 C--QLRLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHH
Confidence            4  7999999999999999865

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.35  E-value=8.9e-06  Score=48.63  Aligned_cols=99  Identities=9%  Similarity=0.021  Sum_probs=81.7

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC-CChhHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR-PDEFTIVRI   78 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~~t~~~l   78 (153)
                      +.+...+..+...+.+.|++++|...|++..   ..+...|..+...+.+.|++++|...+++..+..-. .+...+..+
T Consensus         3 p~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l   82 (112)
T 2kck_A            3 DQNPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAK   82 (112)
T ss_dssp             CSSTTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHH
Confidence            3456778889999999999999999999875   346788999999999999999999999999876311 146666666


Q ss_pred             HHHHHHhcc-CChHHHHHHHHhcccC
Q 035927           79 LTAYMYCKC-GDVEKAQRVLRKMLRK  103 (153)
Q Consensus        79 i~~~~~~~~-g~~~~a~~~~~~m~~~  103 (153)
                      ...  |.+. |++++|.+.++...+.
T Consensus        83 ~~~--~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           83 ADA--LRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HHH--HTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHH--HHHHhCCHHHHHHHHHHHhhc
Confidence            666  6999 9999999999998764

>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=98.34  E-value=9.7e-06  Score=60.66  Aligned_cols=138  Identities=7%  Similarity=0.024  Sum_probs=112.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNR-FREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      ...|+.+-..+.+.|++++|+..+++..  .| +...|+.+-..+.+.|+ +++|+..+++..+..  | +...|..+-.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHHH
Confidence            4568888889999999999999999886  34 67889999999999996 999999999998753  4 4555665555


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhc-CCchh
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTH-NGNET  145 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~-~g~~~  145 (153)
                      .  |.+.|++++|+..|++..+  | +...|..+..++...|.++          .+.|+ ...|+.+-.++.+ .|..+
T Consensus       175 ~--~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          175 L--VEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             H--HHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             H--HHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcch
Confidence            5  6999999999999999864  3 7889999999999999998          44564 5778888888888 66656


Q ss_pred             Hh
Q 035927          146 FV  147 (153)
Q Consensus       146 ~a  147 (153)
                      +|
T Consensus       253 eA  254 (382)
T 2h6f_A          253 RA  254 (382)
T ss_dssp             HH
T ss_pred             HH
Confidence            66

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.31  E-value=1.5e-05  Score=61.48  Aligned_cols=146  Identities=13%  Similarity=0.115  Sum_probs=111.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CH-HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DY-VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      .+...|..+...+.+.|++++|..+|++..  .| +. ..|...+..+.+.|++++|..+|++..+.. +.+...|-...
T Consensus       319 ~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~-~~~~~~~~~~a  397 (530)
T 2ooe_A          319 KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAA  397 (530)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT-TCCTHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhcc-CCchHHHHHHH
Confidence            356779999999999999999999999886  34 33 589999999999999999999999998753 12333333333


Q ss_pred             HHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------C---CCCC--HhHHHHHHHHHhcC
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------T---IRPD--EVTYVGVLSACTHN  141 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~---~~p~--~~t~~~ll~~~~~~  141 (153)
                      ..+ +...|+.++|.++|+...+  | +...|..++..+.+.|..+          .   ..|+  ...|...+......
T Consensus       398 ~~~-~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~  476 (530)
T 2ooe_A          398 LME-YYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNI  476 (530)
T ss_dssp             HHH-HHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHS
T ss_pred             HHH-HHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHc
Confidence            332 4579999999999998854  3 6788888888888877766          1   2333  34677888888889


Q ss_pred             CchhHhhhhc
Q 035927          142 GNETFVINSC  151 (153)
Q Consensus       142 g~~~~a~~~~  151 (153)
                      |+.+.+.+++
T Consensus       477 G~~~~~~~~~  486 (530)
T 2ooe_A          477 GDLASILKVE  486 (530)
T ss_dssp             SCHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            9999888765

>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=98.29  E-value=8.1e-06  Score=65.27  Aligned_cols=133  Identities=10%  Similarity=0.007  Sum_probs=108.6

Q ss_pred             HhcCChHHHHHHHHhCC-----------CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927           17 INRGQVDIARQYFAQMP-----------ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~-----------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      ...|++++|.+.+++..           ..+...|..+...+.+.|++++|++.+++..+.+ +-+...+..+-..  |.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~--~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVA--EL  478 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHH--HH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHH--HH
Confidence            77899999999999875           2367789999999999999999999999998753 2244555555555  79


Q ss_pred             ccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCCC---------CCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           86 KCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFPT---------IRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~---------~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.|++++|++.|++..+  | +...|..+...+.+.|.++.         ..|+ ...|..+-.++.+.|+.++|.+.|+
T Consensus       479 ~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~  558 (681)
T 2pzi_A          479 LTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDEHKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLD  558 (681)
T ss_dssp             HHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCTTCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHHHHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            99999999999999864  3 67889999999999988874         3354 4678889999999999999998775

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.29  E-value=1.5e-05  Score=55.74  Aligned_cols=148  Identities=14%  Similarity=0.133  Sum_probs=105.0

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-C---HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCC-hhH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-D---YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPD-EFT   74 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~-~~t   74 (153)
                      +.+...+-.+...+.+.|++++|...|++..+  | +   ...+..+-..+.+.|++++|...|+...+.. -.|. ...
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            34556677778888999999999999999863  3 3   5678888889999999999999999998752 1222 223


Q ss_pred             HHHHHHHHHHhc--------cCChHHHHHHHHhccc--C-ChhhH-----------------HHHHHHHHhcCCCC----
Q 035927           75 IVRILTAYMYCK--------CGDVEKAQRVLRKMLR--K-DKFTW-----------------TAMIVGLAISDPFP----  122 (153)
Q Consensus        75 ~~~li~~~~~~~--------~g~~~~a~~~~~~m~~--~-~~~~~-----------------~~li~~~~~~~~~~----  122 (153)
                      +..+-.+  |.+        .|++++|++.|++..+  | +...+                 ..+...|...|.++    
T Consensus        92 ~~~lg~~--~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  169 (261)
T 3qky_A           92 EYERAMC--YYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAV  169 (261)
T ss_dssp             HHHHHHH--HHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHH--HHHhcccccccchhHHHHHHHHHHHHHHCcCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            3333333  577        9999999999999864  3 23333                 34456666777766    


Q ss_pred             ------CCCCC----HhHHHHHHHHHhcC----------CchhHhhhhcc
Q 035927          123 ------TIRPD----EVTYVGVLSACTHN----------GNETFVINSCN  152 (153)
Q Consensus       123 ------~~~p~----~~t~~~ll~~~~~~----------g~~~~a~~~~~  152 (153)
                            ...|+    ...+..+..+|...          |++++|.+.|+
T Consensus       170 ~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~  219 (261)
T 3qky_A          170 TYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYE  219 (261)
T ss_dssp             HHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHH
Confidence                  23354    34567777777765          78888887764

>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=98.29  E-value=1.4e-05  Score=62.26  Aligned_cols=124  Identities=10%  Similarity=0.026  Sum_probs=85.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...|..+...+.+.|++++|.+.|++..+   .+...|..+-..+.+.|++++|...+++..+.. +-+...+..+-..
T Consensus        22 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~  100 (568)
T 2vsy_A           22 DFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLLQQASDAA-PEHPGIALWLGHA  100 (568)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            455677777788888888888888877653   256677778888888888888888888877643 2244555555555


Q ss_pred             HHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcC---CchhHhhhhc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHN---GNETFVINSC  151 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~---g~~~~a~~~~  151 (153)
                        |.+.|++++|.+.|++..+.+                    +-+...+..+...+...   |+.++|.+.|
T Consensus       101 --~~~~g~~~~A~~~~~~al~~~--------------------p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~  151 (568)
T 2vsy_A          101 --LEDAGQAEAAAAAYTRAHQLL--------------------PEEPYITAQLLNWRRRLCDWRALDVLSAQV  151 (568)
T ss_dssp             --HHHTTCHHHHHHHHHHHHHHC--------------------TTCHHHHHHHHHHHHHTTCCTTHHHHHHHH
T ss_pred             --HHHcCCHHHHHHHHHHHHHhC--------------------CCCHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence              688888888888888875431                    11345566666666666   7777766654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.27  E-value=1.8e-05  Score=49.65  Aligned_cols=94  Identities=14%  Similarity=0.135  Sum_probs=79.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+...-..+.+.|++++|.+.|++..   ..+...|..+-..+.+.|++++|+..+++.++.+ +.+...|..+-.+ 
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~-   90 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAAC-   90 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHH-
Confidence            3457888899999999999999999875   3378899999999999999999999999998753 2345566666665 


Q ss_pred             HHhccCChHHHHHHHHhccc
Q 035927           83 MYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~  102 (153)
                       |.+.|++++|++.|++..+
T Consensus        91 -~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           91 -LVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             -HHHTTCHHHHHHHHHHHHH
T ss_pred             -HHHCCCHHHHHHHHHHHHH
Confidence             7999999999999999865

>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=98.27  E-value=1.1e-05  Score=60.37  Aligned_cols=145  Identities=8%  Similarity=0.093  Sum_probs=116.6

Q ss_pred             CchhHHHHHHHHHHhcCC-hHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQ-VDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~-~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      -+...|+.+-..+.+.|+ +++|+..|++..+  | +...|+.+-..+.+.|++++|+..|++.++.. +-+...|..+-
T Consensus       129 ~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg  207 (382)
T 2h6f_A          129 ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQ  207 (382)
T ss_dssp             TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHH
Confidence            345679999999999997 9999999999873  3 77899999999999999999999999998753 23566666666


Q ss_pred             HHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHh-cCCCC---------------CCCCC-HhHHHHHHHHHh
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAI-SDPFP---------------TIRPD-EVTYVGVLSACT  139 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~-~~~~~---------------~~~p~-~~t~~~ll~~~~  139 (153)
                      .+  +.+.|++++|++.|+++.+  | +...|+.+...+.. .+..+               .+.|+ ...|+.+...+.
T Consensus       208 ~~--~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~  285 (382)
T 2h6f_A          208 WV--IQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQ  285 (382)
T ss_dssp             HH--HHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHT
T ss_pred             HH--HHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            65  6999999999999999965  3 68899999999998 45533               34565 466888888888


Q ss_pred             cCC--chhHhhhhc
Q 035927          140 HNG--NETFVINSC  151 (153)
Q Consensus       140 ~~g--~~~~a~~~~  151 (153)
                      +.|  +.++|++.+
T Consensus       286 ~~g~~~~~~a~~~~  299 (382)
T 2h6f_A          286 DRGLSKYPNLLNQL  299 (382)
T ss_dssp             TTCGGGCHHHHHHH
T ss_pred             ccCccchHHHHHHH
Confidence            888  577777654

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.27  E-value=3.4e-06  Score=60.36  Aligned_cols=144  Identities=8%  Similarity=-0.046  Sum_probs=104.4

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ...+..+...+.+.|++++|...|++..  .| +...+..+...+.+.|++++|...+++....  .|+.......... 
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~-  193 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQI-  193 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHH-
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHH-
Confidence            3456667777888899999999998875  33 6778888888889999999999998887654  3554443333333 


Q ss_pred             HHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC---HhHHHHHHHHHhcCCchhH
Q 035927           83 MYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD---EVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~---~~t~~~ll~~~~~~g~~~~  146 (153)
                      .+.+.++.++|.+.+++..+  | +...+..+...+...|.++          ...|+   ...+..+...+...|+.++
T Consensus       194 ~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  273 (287)
T 3qou_A          194 ELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDA  273 (287)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCH
T ss_pred             HHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCc
Confidence            25677777777777777643  3 5677777777777777776          33454   4568888888888998888


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |...|+
T Consensus       274 a~~~~r  279 (287)
T 3qou_A          274 LASXYR  279 (287)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876653

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.26  E-value=1.4e-05  Score=58.12  Aligned_cols=121  Identities=14%  Similarity=0.089  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-----ChhHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-----DEFTIVR   77 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-----~~~t~~~   77 (153)
                      +...+..++...|++++|++++++...     .+...+..++..+.+.|+.+.|...++.|++.  .|     +..+...
T Consensus       102 ~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~--~~d~~~~~d~~l~~  179 (310)
T 3mv2_B          102 ELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTNA--IEDTVSGDNEMILN  179 (310)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CccccccchHHHHH
Confidence            334455555555555555555555421     13444555555555555555555555555443  23     2333333


Q ss_pred             HHHHHHHhccC--ChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           78 ILTAYMYCKCG--DVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        78 li~~~~~~~~g--~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +..+......|  +.++|..+|+++.+.                     .|+..+-..++.++.+.|++++|.+.+
T Consensus       180 Laea~v~l~~g~~~~q~A~~~f~El~~~---------------------~p~~~~~~lLln~~~~~g~~~eAe~~L  234 (310)
T 3mv2_B          180 LAESYIKFATNKETATSNFYYYEELSQT---------------------FPTWKTQLGLLNLHLQQRNIAEAQGIV  234 (310)
T ss_dssp             HHHHHHHHHHTCSTTTHHHHHHHHHHTT---------------------SCSHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHhCCccHHHHHHHHHHHHHh---------------------CCCcccHHHHHHHHHHcCCHHHHHHHH
Confidence            43331111122  555555555555442                     466444455555888999999998875

>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=98.26  E-value=2.9e-05  Score=66.33  Aligned_cols=58  Identities=10%  Similarity=0.249  Sum_probs=46.9

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      ..+|..+-.++.+.|++++|..-|.+-  .|...|..++..+.+.|++++|...+...++
T Consensus      1105 p~vWsqLAKAql~~G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk 1162 (1630)
T 1xi4_A         1105 PAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARK 1162 (1630)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            457888888888889999998888663  6777888888888888888888888865443

>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=98.24  E-value=6e-05  Score=45.23  Aligned_cols=96  Identities=16%  Similarity=0.120  Sum_probs=79.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--C-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--E-RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...+..+...+...|++++|...|++..  . .+...+..+...+.+.|++++|...+++..+.. +.+...+..+...
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~   81 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHH
Confidence            45678889999999999999999999875  2 377889999999999999999999999998753 2345566666666


Q ss_pred             HHHhccCChHHHHHHHHhcccC
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                        |.+.|++++|.+.+++..+.
T Consensus        82 --~~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           82 --LEFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             --HHHTTCHHHHHHHHHHHHTT
T ss_pred             --HHHHhhHHHHHHHHHHHHHc
Confidence              69999999999999998654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.23  E-value=1.5e-05  Score=48.46  Aligned_cols=92  Identities=17%  Similarity=0.255  Sum_probs=70.3

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      ...|..+...+.+.|++++|...++++.+.. +.+...+..+...  |.+.|++++|...|+++.+.+            
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~--~~~~~~~~~A~~~~~~~~~~~------------   73 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA--YYKQGDYDEAIEYYQKALELD------------   73 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH--HHHhCCHHHHHHHHHHHHHhC------------
Confidence            5678889999999999999999999998753 2356677777776  699999999999999986532            


Q ss_pred             hcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          117 ISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       117 ~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                              +.+...+..+...+.+.|++++|.+.|
T Consensus        74 --------~~~~~~~~~la~~~~~~~~~~~A~~~~  100 (125)
T 1na0_A           74 --------PNNAEAWYNLGNAYYKQGDYDEAIEYY  100 (125)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             --------CccHHHHHHHHHHHHHhcCHHHHHHHH
Confidence                    124455666666677777777776655

>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=98.22  E-value=7.6e-06  Score=52.91  Aligned_cols=102  Identities=11%  Similarity=-0.026  Sum_probs=58.9

Q ss_pred             HhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHH
Q 035927           17 INRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEK   92 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~   92 (153)
                      ...|++++|+..+.+....   +...+-.+-..|.+.|++++|...|++..+.  .| +...|..+-..  |.+.|++++
T Consensus         8 ~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~--~~~~~~~~~   83 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLL--YELEENTDK   83 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH--HHHTTCHHH
T ss_pred             HHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH--HHHcCchHH
Confidence            3445666666666665532   3334555666666777777777777766654  24 33334333333  567777777


Q ss_pred             HHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC
Q 035927           93 AQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        93 a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~  122 (153)
                      |+..|++..+  | +...|..+...+.+.+.++
T Consensus        84 A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~  116 (150)
T 4ga2_A           84 AVECYRRSVELNPTQKDLVLKIAELLCKNDVTD  116 (150)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSS
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChH
Confidence            7777776643  3 4555555555565555554

>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=98.22  E-value=3.6e-05  Score=48.06  Aligned_cols=97  Identities=9%  Similarity=-0.008  Sum_probs=81.1

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      +.+...|..+...+.+.|++++|...|.+..   ..+...|..+...+.+.|++++|...++...+.. +-+...+..+-
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   84 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   84 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHH
Confidence            4567789999999999999999999999875   2367889999999999999999999999998753 22455565555


Q ss_pred             HHHHHhccCChHHHHHHHHhccc
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..  |.+.|++++|.+.|++..+
T Consensus        85 ~~--~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           85 QC--QLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HH--HHHHhhHHHHHHHHHHHHH
Confidence            55  7999999999999999865

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.21  E-value=1.8e-05  Score=52.20  Aligned_cols=116  Identities=9%  Similarity=0.057  Sum_probs=92.9

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      -+...|..+...+.+.|++++|...+.+..   ..+...+..+...+...++++.|...+.+..+.. +-+...+..+-.
T Consensus        37 ~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~  115 (184)
T 3vtx_A           37 NNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGL  115 (184)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHH
Confidence            456678899999999999999999998875   2366778888888888999999999999887643 224445555555


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.|++++|++.|++..+  | +...|..+...+.+.|.++
T Consensus       116 ~--~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A          116 V--YDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             H--HHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHH
Confidence            4  7999999999999999854  3 6788999999999988876

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.19  E-value=6.8e-06  Score=53.59  Aligned_cols=115  Identities=8%  Similarity=-0.075  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMYC   85 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~   85 (153)
                      +...+.+.+...+.++++.++     .| +...+..+-..+.+.|++++|...|+...+.  .|+ ...|..+-.+  |.
T Consensus        11 ~~~~l~~~~~~~~~l~~al~l-----~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~--~~   81 (151)
T 3gyz_A           11 ISTAVIDAINSGATLKDINAI-----PDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY--DFYNVDYIMGLAAI--YQ   81 (151)
T ss_dssp             HHHHHHHHHHTSCCTGGGCCS-----CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHCCCCHHHHhCC-----CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH--HH
Confidence            445566666655555444332     23 5667888888999999999999999999875  354 4455555444  79


Q ss_pred             ccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           86 KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.|++++|+..|++..+-+                     | +...|..+-.+|.+.|++++|.+.|+
T Consensus        82 ~~g~~~~Ai~~~~~al~l~---------------------P~~~~~~~~lg~~~~~lg~~~eA~~~~~  128 (151)
T 3gyz_A           82 IKEQFQQAADLYAVAFALG---------------------KNDYTPVFHTGQCQLRLKAPLKAKECFE  128 (151)
T ss_dssp             HTTCHHHHHHHHHHHHHHS---------------------SSCCHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhC---------------------CCCcHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999999997632                     3 45667788888888888888887764

>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=98.19  E-value=1.5e-05  Score=51.40  Aligned_cols=94  Identities=9%  Similarity=0.048  Sum_probs=77.3

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +...+..+...+.+.|++++|...|++..   ..+...|..+-..+.+.|++++|...|++..+..  | +...+..+-.
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~lg~   97 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD--IXEPRFPFHAAE   97 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCchHHHHHHH
Confidence            45567788889999999999999999875   3378889999999999999999999999998753  4 3444544444


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +  |...|++++|.+.|++..+
T Consensus        98 ~--~~~~g~~~~A~~~~~~al~  117 (148)
T 2vgx_A           98 C--LLQXGELAEAESGLFLAQE  117 (148)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHH
Confidence            4  7999999999999999864

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.18  E-value=1.7e-05  Score=50.45  Aligned_cols=94  Identities=11%  Similarity=0.060  Sum_probs=76.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~   80 (153)
                      +...+..+...+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|...|+...+.+  |+ ...+..+-.
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~   94 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD--INEPRFPFHAAE   94 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCcHHHHHHHH
Confidence            44557777888999999999999999875  33 77889999999999999999999999998753  43 344444444


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +  |...|++++|.+.|++..+
T Consensus        95 ~--~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           95 C--HLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHH
Confidence            4  7999999999999999865

>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=98.17  E-value=7.6e-05  Score=53.15  Aligned_cols=142  Identities=9%  Similarity=0.040  Sum_probs=102.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC-----CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC-CCh----hH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR-PDE----FT   74 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p~~----~t   74 (153)
                      +...+..+.+.|++++|..++++...     ++    ...+..+...+...+++++|+..+++..+.... ++.    ..
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence            33447788999999999999998653     12    123445666666778999999999999874322 232    24


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHhccc------C----ChhhHHHHHHHHHhcCCCC----------------CCCCC-
Q 035927           75 IVRILTAYMYCKCGDVEKAQRVLRKMLR------K----DKFTWTAMIVGLAISDPFP----------------TIRPD-  127 (153)
Q Consensus        75 ~~~li~~~~~~~~g~~~~a~~~~~~m~~------~----~~~~~~~li~~~~~~~~~~----------------~~~p~-  127 (153)
                      ++.+-..  |.+.|++++|+..|++..+      .    ...+|..+...|.+.|.++                +..+. 
T Consensus       158 ~~~lg~~--y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~  235 (293)
T 3u3w_A          158 ENAIANI--YAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTH
T ss_pred             HHHHHHH--HHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHH
Confidence            6666555  7999999999999999862      1    2347788888888888877                22233 


Q ss_pred             HhHHHHHHHHHhcCCc-hhHhhhhcc
Q 035927          128 EVTYVGVLSACTHNGN-ETFVINSCN  152 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~-~~~a~~~~~  152 (153)
                      ...|..+-.++.+.|+ .++|.+.|+
T Consensus       236 ~~~~~~lg~~~~~~g~~~~~A~~~~~  261 (293)
T 3u3w_A          236 GQLYYQRGECLRKLEYEEAEIEDAYK  261 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcHHHHHHHHH
Confidence            5678888888999995 588887663

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.15  E-value=4.2e-05  Score=52.44  Aligned_cols=143  Identities=10%  Similarity=-0.010  Sum_probs=99.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh----HH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF----TI   75 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----t~   75 (153)
                      ...+-.+...+.+.|++++|...|+++.+  |+    ...+..+...+.+.|++++|...|++..+..  |+..    .+
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~a~   81 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDYVM   81 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHHHH
Confidence            34555667788999999999999999863  32    3567788889999999999999999998643  3322    22


Q ss_pred             HHHHHHHHHh------------------ccCChHHHHHHHHhcccC---ChhhHH-----------------HHHHHHHh
Q 035927           76 VRILTAYMYC------------------KCGDVEKAQRVLRKMLRK---DKFTWT-----------------AMIVGLAI  117 (153)
Q Consensus        76 ~~li~~~~~~------------------~~g~~~~a~~~~~~m~~~---~~~~~~-----------------~li~~~~~  117 (153)
                      -.+-.+  |.                  ..|+.++|...|+++.+.   +...+.                 .+...+.+
T Consensus        82 ~~~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~~~~~~~~~~~~~~a~~~~~  159 (225)
T 2yhc_A           82 YMRGLT--NMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTE  159 (225)
T ss_dssp             HHHHHH--HHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHH--HHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            222222  23                  367899999999999753   233332                 23334555


Q ss_pred             cCCCC----------CCCCCH----hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          118 SDPFP----------TIRPDE----VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       118 ~~~~~----------~~~p~~----~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .|.++          ..-|+.    ..+..+..++.+.|+.++|.+.++
T Consensus       160 ~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~  208 (225)
T 2yhc_A          160 RGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAK  208 (225)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence            56665          334543    568889999999999999998764

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.14  E-value=2.1e-05  Score=52.32  Aligned_cols=130  Identities=13%  Similarity=0.022  Sum_probs=70.9

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC------C---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CCCCC---
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE------R---DYVLWTAMIDGYLRVNRFREALTLFPEMQTS--NIRPD---   71 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~------~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~---   71 (153)
                      ...+..+-..+...|++++|...+++...      .   ...+++.+-..+...|++++|...+++..+.  ....+   
T Consensus        26 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  105 (203)
T 3gw4_A           26 SGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLA  105 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHH
Confidence            34566666666666776666666665532      1   3345666666666667777777776666432  11101   


Q ss_pred             -hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCC-CCHhHHHHHHHHHhcCCchhHhhh
Q 035927           72 -EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIR-PDEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        72 -~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~-p~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                       ...+..+-..  |...|++++|.+.+++..+.....               +-. .-...+..+-..+...|++++|.+
T Consensus       106 ~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~~~~~~---------------~~~~~~~~~~~~la~~~~~~g~~~~A~~  168 (203)
T 3gw4_A          106 ASANAYEVATV--ALHFGDLAGARQEYEKSLVYAQQA---------------DDQVAIACAFRGLGDLAQQEKNLLEAQQ  168 (203)
T ss_dssp             HHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHHHHT---------------TCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHH--HHHhCCHHHHHHHHHHHHHHHHhc---------------cchHHHHHHHHHHHHHHHHCcCHHHHHH
Confidence             1222333333  566677777766666653210000               000 112446677778888888888877


Q ss_pred             hcc
Q 035927          150 SCN  152 (153)
Q Consensus       150 ~~~  152 (153)
                      .++
T Consensus       169 ~~~  171 (203)
T 3gw4_A          169 HWL  171 (203)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.14  E-value=3.1e-05  Score=50.31  Aligned_cols=96  Identities=10%  Similarity=0.017  Sum_probs=80.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...|..+-..+.+.|++++|...|++..+  | +...|..+-..+.+.|++++|+..+++..+.. +-+...+..+-.
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~   87 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            3556788899999999999999999998862  3 78899999999999999999999999998764 224556666655


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .  |.+.|++++|.+.|++..+
T Consensus        88 ~--~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           88 A--RFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHHccCHHHHHHHHHHHHH
Confidence            5  7999999999999999864

>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=98.13  E-value=1.2e-05  Score=55.83  Aligned_cols=132  Identities=11%  Similarity=0.043  Sum_probs=86.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC----------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC------CC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS------NI   68 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~   68 (153)
                      ..++..+...+...|++++|...+++...          | ...+|..+...+...|++++|...+++..+.      .-
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  122 (283)
T 3edt_B           43 ATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKF  122 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCC
Confidence            44577777788888888888877776641          1 3456777777888888888888888877653      11


Q ss_pred             CC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhH
Q 035927           69 RP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        69 ~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~  146 (153)
                      .| ...++..+...  |...|++++|.+.+++..+.-..             ...+-.| ....+..+...+...|++++
T Consensus       123 ~~~~~~~~~~la~~--~~~~g~~~~A~~~~~~al~~~~~-------------~~~~~~~~~~~~~~~la~~~~~~g~~~~  187 (283)
T 3edt_B          123 HPDVAKQLNNLALL--CQNQGKAEEVEYYYRRALEIYAT-------------RLGPDDPNVAKTKNNLASCYLKQGKYQD  187 (283)
T ss_dssp             CHHHHHHHHHHHHH--HHTTTCHHHHHHHHHHHHHHHHH-------------HSCTTCHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             ChHHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHHHHH-------------hcCCCCHHHHHHHHHHHHHHHHcCCHHH
Confidence            12 23444444444  67888888888888777542000             0000123 34678888899999999999


Q ss_pred             hhhhcc
Q 035927          147 VINSCN  152 (153)
Q Consensus       147 a~~~~~  152 (153)
                      |.+.|+
T Consensus       188 A~~~~~  193 (283)
T 3edt_B          188 AETLYK  193 (283)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988764

>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=98.13  E-value=3.9e-05  Score=47.48  Aligned_cols=95  Identities=13%  Similarity=0.026  Sum_probs=78.7

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...|..+-..+.+.|++++|...|++..   ..+...|..+-..+.+.|++++|+..+++..+.. +-+...+..+-.+
T Consensus         3 ~a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   81 (126)
T 3upv_A            3 KAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            44568888899999999999999999875   2378899999999999999999999999998753 2245555555555


Q ss_pred             HHHhccCChHHHHHHHHhccc
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~  102 (153)
                        |.+.|++++|.+.|++..+
T Consensus        82 --~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           82 --QIAVKEYASALETLDAART  100 (126)
T ss_dssp             --HHHTTCHHHHHHHHHHHHH
T ss_pred             --HHHHhCHHHHHHHHHHHHH
Confidence              7999999999999999854

>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=98.12  E-value=3.5e-05  Score=47.21  Aligned_cols=95  Identities=15%  Similarity=0.157  Sum_probs=78.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC--CCCC----hhHHH
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN--IRPD----EFTIV   76 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~   76 (153)
                      ...|..+...+.+.|++++|...|++..   ..+...+..+...+...|++++|...++...+..  ..++    ...+.
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            4568888999999999999999999875   2377889999999999999999999999997653  1233    55666


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhccc
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .+...  |.+.|++++|.+.|+...+
T Consensus        84 ~la~~--~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           84 RIGNS--YFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHH--HHHhccHHHHHHHHHHHHH
Confidence            66666  6999999999999999865

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.10  E-value=0.0001  Score=46.25  Aligned_cols=96  Identities=17%  Similarity=0.094  Sum_probs=79.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      .+...+..+...+.+.|++++|...|++..+  |+    ...|..+...+.+.|++++|...++...+.. +.+...+..
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~  104 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALYR  104 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHHH
Confidence            4566788999999999999999999998763  44    6788889999999999999999999988653 224555555


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +-..  |.+.|++++|.+.|++..+
T Consensus       105 ~a~~--~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          105 RSQA--LEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHH--HHHHTCHHHHHHHHHHHHH
T ss_pred             HHHH--HHHcCCHHHHHHHHHHHHH
Confidence            5555  7999999999999999865

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=98.08  E-value=7.3e-05  Score=60.35  Aligned_cols=114  Identities=11%  Similarity=0.079  Sum_probs=98.3

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~   80 (153)
                      +...|+.+-.+|.+.|++++|...|++..  .| +...|+.+-..+.+.|++++|++.|++..+.  .| +...++.+-.
T Consensus        42 ~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~  119 (723)
T 4gyw_A           42 FAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLAS  119 (723)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            45679999999999999999999999875  34 6789999999999999999999999999875  35 4566777766


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.|++++|++.|++..+  | +...|..+...+...+.++
T Consensus       120 ~--~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A          120 I--HKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCT
T ss_pred             H--HHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHH
Confidence            6  7999999999999999854  4 6888999999999998887

>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=98.08  E-value=5.4e-05  Score=50.86  Aligned_cols=117  Identities=12%  Similarity=0.012  Sum_probs=87.7

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC------------
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN------------   67 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------------   67 (153)
                      +|+...|..+...+.+.|++++|...|++..   ..+...|..+-..+.+.|++++|...++...+..            
T Consensus        34 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  113 (213)
T 1hh8_A           34 DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILG  113 (213)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGT
T ss_pred             CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhc
Confidence            4677889999999999999999999999875   3477889999999999999999999999998743            


Q ss_pred             --CCCCh-hHHHHHHHHHHHhccCChHHHHHHHHhcccC----ChhhHHHHHHHHHhcCCC
Q 035927           68 --IRPDE-FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK----DKFTWTAMIVGLAISDPF  121 (153)
Q Consensus        68 --~~p~~-~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~----~~~~~~~li~~~~~~~~~  121 (153)
                        ..|+. ..+..+-..  |.+.|++++|.+.|++..+.    ........+..+.+...+
T Consensus       114 ~~~~~~~~~~~~~l~~~--~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~  172 (213)
T 1hh8_A          114 LQFKLFACEVLYNIAFM--YAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLY  172 (213)
T ss_dssp             BCCEEEHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHTTCCSGGGGHHHHHHHHHHTTCCC
T ss_pred             cccCccchHHHHHHHHH--HHHccCHHHHHHHHHHHHHcCcccccchHHHHHHHHHhcccc
Confidence              12222 444444444  79999999999999998653    223334444444444433

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.07  E-value=8.3e-05  Score=57.30  Aligned_cols=144  Identities=6%  Similarity=0.091  Sum_probs=107.2

Q ss_pred             chhHHHHHHHHHHh-------cCChH-------HHHHHHHhCCC---C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            5 DVISWTDIVSGYIN-------RGQVD-------IARQYFAQMPE---R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         5 d~~~~~~li~~~~~-------~g~~~-------~a~~l~~~m~~---~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      +...|......+.+       .|+++       +|..+|++..+   | +...|..+...+.+.|++++|..+|++..+.
T Consensus       271 ~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~  350 (530)
T 2ooe_A          271 HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI  350 (530)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc
Confidence            45567777777775       79987       89999998763   4 6788999999999999999999999999984


Q ss_pred             CCCCCh--hHHHHHHHHHHHhccCChHHHHHHHHhcccCC---hhhHHHHHHH-HHhcCCCC----------CCCC-CHh
Q 035927           67 NIRPDE--FTIVRILTAYMYCKCGDVEKAQRVLRKMLRKD---KFTWTAMIVG-LAISDPFP----------TIRP-DEV  129 (153)
Q Consensus        67 ~~~p~~--~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~li~~-~~~~~~~~----------~~~p-~~~  129 (153)
                        .|+.  ..|..+...  +.+.|++++|.++|++..+..   ...|-..... +...|..+          ...| +..
T Consensus       351 --~p~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~  426 (530)
T 2ooe_A          351 --EDIDPTLVYIQYMKF--ARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPE  426 (530)
T ss_dssp             --SSSCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHH
T ss_pred             --cccCchHHHHHHHHH--HHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHH
Confidence              4542  467777776  588999999999999986532   2222221111 22344444          2335 467


Q ss_pred             HHHHHHHHHhcCCchhHhhhhcc
Q 035927          130 TYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       130 t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .|..++..+.+.|+.++|..+|+
T Consensus       427 ~~~~~~~~~~~~g~~~~Ar~~~~  449 (530)
T 2ooe_A          427 YVLAYIDYLSHLNEDNNTRVLFE  449 (530)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHhhHHHHHH
Confidence            88999999999999999998874

>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=98.05  E-value=6.2e-05  Score=51.29  Aligned_cols=115  Identities=10%  Similarity=0.003  Sum_probs=92.3

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMI  112 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li  112 (153)
                      |...|...-..+.+.|++++|...|+...+..-.++...+..+-..  |.+.|++++|++.|++..+  | +...|..+.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~   83 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVC--ADNIKKYKEAADYFDIAIKKNYNLANAYIGKS   83 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHH--HHHhhcHHHHHHHHHHHHHhCcchHHHHHHHH
Confidence            5677888888899999999999999999876543666666664444  7999999999999999864  3 577888899


Q ss_pred             HHHHhcCCCC----------CCCCC-H-------hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          113 VGLAISDPFP----------TIRPD-E-------VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       113 ~~~~~~~~~~----------~~~p~-~-------~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+...|.++          ...|+ .       ..|..+-..+.+.|++++|.+.|+
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~  141 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYK  141 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHH
Confidence            9999998888          34454 3       457777788889999999998774

>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=98.04  E-value=4.8e-05  Score=55.65  Aligned_cols=120  Identities=12%  Similarity=0.058  Sum_probs=91.6

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-C---------------HHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-D---------------YVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      +...|..+-..+.+.|++++|...|++..  .| +               ...|..+-..+.+.|++++|+..+++.++.
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            34568888899999999999999999875  23 3               478999999999999999999999999875


Q ss_pred             CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhH
Q 035927           67 NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        67 ~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~  146 (153)
                      . +.+...+..+-.+  |.+.|++++|++.|++..+.+                    +-+...+..+...+.+.|+.++
T Consensus       226 ~-p~~~~a~~~lg~~--~~~~g~~~~A~~~~~~al~l~--------------------P~~~~a~~~l~~~~~~~~~~~~  282 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEA--HLAVNDFELARADFQKVLQLY--------------------PNNKAAKTQLAVCQQRIRRQLA  282 (336)
T ss_dssp             C-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC--------------------SSCHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHH--HHHCCCHHHHHHHHHHHHHHC--------------------CCCHHHHHHHHHHHHHHHHHHH
Confidence            3 2356666666666  799999999999999986532                    0134455555556666666655


Q ss_pred             h
Q 035927          147 V  147 (153)
Q Consensus       147 a  147 (153)
                      |
T Consensus       283 a  283 (336)
T 1p5q_A          283 R  283 (336)
T ss_dssp             H
T ss_pred             H
Confidence            5

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.03  E-value=5.7e-05  Score=44.98  Aligned_cols=96  Identities=9%  Similarity=-0.050  Sum_probs=74.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +...|..+...+.+.|++++|...+++..+.. +.+...+..+-..  |.+.|++++|.+.|++..+.+.          
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~--~~~~~~~~~A~~~~~~a~~~~~----------   71 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKA--LYNLERYEEAVDCYNYVINVIE----------   71 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHTSC----------
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHH--HHHccCHHHHHHHHHHHHHhCc----------
Confidence            45667778888899999999999999998753 2345566666665  6999999999999999876430          


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcC-CchhHhhhhcc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHN-GNETFVINSCN  152 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~-g~~~~a~~~~~  152 (153)
                              -..+...+..+...+.+. |+.++|.+.++
T Consensus        72 --------~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~  101 (112)
T 2kck_A           72 --------DEYNKDVWAAKADALRYIEGKEVEAEIAEA  101 (112)
T ss_dssp             --------CTTCHHHHHHHHHHHTTCSSCSHHHHHHHH
T ss_pred             --------ccchHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence                    011467788888999999 99999988764

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.02  E-value=7.6e-05  Score=46.76  Aligned_cols=93  Identities=9%  Similarity=0.017  Sum_probs=70.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      ...+...-..+.+.|++++|++.|++..+.. +.+...|..+-.+  |.+.|++++|++.|++..+-+            
T Consensus        13 a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~--~~~~~~~~~A~~~~~~al~~~------------   77 (126)
T 4gco_A           13 AQEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAAC--LTKLMEFQRALDDCDTCIRLD------------   77 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhH--HHhhccHHHHHHHHHHHHHhh------------
Confidence            4567778888999999999999999998753 2355556555555  799999999999999987642            


Q ss_pred             hcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                              +.+...|..+-.++...|++++|.+.|+
T Consensus        78 --------p~~~~a~~~lg~~~~~~~~~~~A~~~~~  105 (126)
T 4gco_A           78 --------SKFIKGYIRKAACLVAMREWSKAQRAYE  105 (126)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             --------hhhhHHHHHHHHHHHHCCCHHHHHHHHH
Confidence                    1245667777777788888888877663

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.01  E-value=2.6e-05  Score=57.47  Aligned_cols=144  Identities=13%  Similarity=0.024  Sum_probs=104.8

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-Ch
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-DE   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~   72 (153)
                      .+++.+-..|...|++++|...|++..+     +    ...++..+-..+...|++++|...+++..+.    +..| ..
T Consensus       185 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  264 (383)
T 3ulq_A          185 QCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLP  264 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHH
Confidence            4688888999999999999999987752     1    2347888999999999999999999998762    3323 34


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccC-----C---hhhHHHHHHHHHhcCC---CC---------CCCCC-HhHH
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK-----D---KFTWTAMIVGLAISDP---FP---------TIRPD-EVTY  131 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-----~---~~~~~~li~~~~~~~~---~~---------~~~p~-~~t~  131 (153)
                      .++..+-..  |.+.|++++|.+.+++..+-     +   ...+..+-..+...+.   ++         +..|+ ...+
T Consensus       265 ~~~~~l~~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~  342 (383)
T 3ulq_A          265 QAYFLITQI--HYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFA  342 (383)
T ss_dssp             HHHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHH--HHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            455555555  79999999999999987531     2   2224455555555554   22         33333 3567


Q ss_pred             HHHHHHHhcCCchhHhhhhcc
Q 035927          132 VGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       132 ~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+-..|.+.|+.++|.+.|+
T Consensus       343 ~~la~~y~~~g~~~~A~~~~~  363 (383)
T 3ulq_A          343 IDVAKYYHERKNFQKASAYFL  363 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHH
Confidence            788899999999999998764

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.01  E-value=4.7e-05  Score=54.36  Aligned_cols=144  Identities=6%  Similarity=-0.086  Sum_probs=73.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-------C--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-Ch
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-DE   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~   72 (153)
                      ..|......|...|++++|...|.+...       +  ...+|+.+-..|.+.|++++|+..+++..+.    |-.. -.
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            3455555566666666555555544421       1  2566666666666666666666655555432    1100 02


Q ss_pred             hHHHHHHHHHHHhcc-CChHHHHHHHHhcccC-----C----hhhHHHHHHHHHhcCCCC----------CCCCCH----
Q 035927           73 FTIVRILTAYMYCKC-GDVEKAQRVLRKMLRK-----D----KFTWTAMIVGLAISDPFP----------TIRPDE----  128 (153)
Q Consensus        73 ~t~~~li~~~~~~~~-g~~~~a~~~~~~m~~~-----~----~~~~~~li~~~~~~~~~~----------~~~p~~----  128 (153)
                      .+++.+-..  |.+. |++++|+..|++..+-     +    ..+|+.+...+...|.++          .+.|+.    
T Consensus       118 ~~~~~lg~~--~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  195 (292)
T 1qqe_A          118 NFKFELGEI--LENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQ  195 (292)
T ss_dssp             HHHHHHHHH--HHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTG
T ss_pred             HHHHHHHHH--HHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCccc
Confidence            234444443  4553 6666666666555321     1    234555555555555554          122221    


Q ss_pred             ----hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          129 ----VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       129 ----~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                          ..|..+..++...|+.++|.+.|+
T Consensus       196 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~  223 (292)
T 1qqe_A          196 WSLKDYFLKKGLCQLAATDAVAAARTLQ  223 (292)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                145566666777777777776653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.99  E-value=2.5e-05  Score=57.21  Aligned_cols=114  Identities=10%  Similarity=0.072  Sum_probs=63.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-C----HHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCCC-h
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--R-D----YVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRPD-E   72 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~   72 (153)
                      ....+...-..+.+.|++++|...|++..+  | +    ...|..+...+...|++++|...+++..+.    +-.|. .
T Consensus         8 ~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   87 (406)
T 3sf4_A            8 SCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   87 (406)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHH
Confidence            344455566667777777777777766542  2 2    245666666666777777777777665332    22222 2


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccC-----C----hhhHHHHHHHHHhcCC
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK-----D----KFTWTAMIVGLAISDP  120 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-----~----~~~~~~li~~~~~~~~  120 (153)
                      ..+..+-..  |...|++++|...+++..+-     +    ...+..+...+...|.
T Consensus        88 ~~~~~la~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~  142 (406)
T 3sf4_A           88 KASGNLGNT--LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGK  142 (406)
T ss_dssp             HHHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCC
Confidence            233333333  56677777777766665321     1    2345555555555554

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=97.97  E-value=0.00012  Score=47.11  Aligned_cols=103  Identities=12%  Similarity=0.117  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~   82 (153)
                      ..+-.+-..|.+.|++++|.+.|++..  .| +...|..+-..+.+.|++++|...|+...+.  .| +...+..+-.. 
T Consensus        32 ~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~-  108 (150)
T 4ga2_A           32 IKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEENTDKAVECYRRSVEL--NPTQKDLVLKIAEL-  108 (150)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCCCHHHHHHHHHH-
Confidence            345678889999999999999999886  34 7889999999999999999999999999875  35 45666666666 


Q ss_pred             HHhccCChHHHHHH-HHhccc--C-ChhhHHHHHH
Q 035927           83 MYCKCGDVEKAQRV-LRKMLR--K-DKFTWTAMIV  113 (153)
Q Consensus        83 ~~~~~g~~~~a~~~-~~~m~~--~-~~~~~~~li~  113 (153)
                       |.+.|+.++|.+. +++..+  | +...|.....
T Consensus       109 -~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~  142 (150)
T 4ga2_A          109 -LCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQ  142 (150)
T ss_dssp             -HHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             -HHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHH
Confidence             6999999876665 466643  3 4444444433

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.96  E-value=0.00011  Score=45.22  Aligned_cols=93  Identities=11%  Similarity=0.042  Sum_probs=69.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +...|..+...+.+.|++++|...+++..+.. +.+...+..+...  |.+.|++++|++.+++..+.+           
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~--~~~~~~~~~A~~~~~~a~~~~-----------   80 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAAC--YTKLLEFQLALKDCEECIQLE-----------   80 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHH--HTTTTCHHHHHHHHHHHHHHC-----------
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHH--HHHhccHHHHHHHHHHHHHhC-----------
Confidence            56788999999999999999999999998753 2355666666665  699999999999999986532           


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                               +.+...+..+...+.+.|++++|.+.|
T Consensus        81 ---------~~~~~~~~~la~~~~~~~~~~~A~~~~  107 (133)
T 2lni_A           81 ---------PTFIKGYTRKAAALEAMKDYTKAMDVY  107 (133)
T ss_dssp             ---------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ---------CCchHHHHHHHHHHHHHhhHHHHHHHH
Confidence                     123455556666666666666666554

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=97.95  E-value=5.2e-05  Score=60.64  Aligned_cols=135  Identities=10%  Similarity=0.021  Sum_probs=106.3

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li   79 (153)
                      .+...+..+...+.+.|++++|...|++..+   .+...|..+-..+.+.|++++|...|++..+..  | +...+..+-
T Consensus       431 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~lg  508 (681)
T 2pzi_A          431 ESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLTGDYDSATKHFTEVLDTF--PGELAPKLALA  508 (681)
T ss_dssp             TCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCSHHHHHHH
T ss_pred             cchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHH
Confidence            4556788889999999999999999998873   377889999999999999999999999998753  5 344555555


Q ss_pred             HHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCc
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGN  143 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~  143 (153)
                      ..  |.+.|++++ ++.|++..+  | +...|..+..++.+.|.++          ...|+. ..+..+..++...|.
T Consensus       509 ~~--~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          509 AT--AELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HH--HHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HH--HHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            54  799999999 999999854  3 6788999999999998887          566764 567777777766554

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=97.94  E-value=0.00034  Score=49.83  Aligned_cols=95  Identities=12%  Similarity=-0.006  Sum_probs=70.6

Q ss_pred             hHHHHHHHHHHhc-CChHHHHHHHHhCCC--C---C----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh---
Q 035927            7 ISWTDIVSGYINR-GQVDIARQYFAQMPE--R---D----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF---   73 (153)
Q Consensus         7 ~~~~~li~~~~~~-g~~~~a~~l~~~m~~--~---~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~---   73 (153)
                      .+++.+-..|.+. |++++|...|++..+  |   +    ..+|+.+...+.+.|++++|...|++..+........   
T Consensus       118 ~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  197 (292)
T 1qqe_A          118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWS  197 (292)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGG
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHH
Confidence            4677888888886 999999988887653  1   1    3568888889999999999999999988754322221   


Q ss_pred             ---HHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           74 ---TIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        74 ---t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                         .+..+...  |.+.|++++|...|++..+-
T Consensus       198 ~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~l  228 (292)
T 1qqe_A          198 LKDYFLKKGLC--QLAATDAVAAARTLQEGQSE  228 (292)
T ss_dssp             HHHHHHHHHHH--HHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHH--HHHcCCHHHHHHHHHHHHhh
Confidence               34444444  68899999999999998653

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.94  E-value=7.7e-05  Score=47.37  Aligned_cols=93  Identities=10%  Similarity=-0.046  Sum_probs=67.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVG  114 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~  114 (153)
                      +...+..+-..+.+.|++++|...|+...+.  .| +...|..+-..  |.+.|++++|...|++..+.+          
T Consensus        17 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~~~----------   82 (142)
T 2xcb_A           17 TLEQLYALGFNQYQAGKWDDAQKIFQALCML--DHYDARYFLGLGAC--RQSLGLYEQALQSYSYGALMD----------   82 (142)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             HHHHHHHHHHHHHHHccHHHHHHHHHHHHHh--CCccHHHHHHHHHH--HHHHhhHHHHHHHHHHHHhcC----------
Confidence            4456677778888999999999999999875  35 44445444444  799999999999999987632          


Q ss_pred             HHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          115 LAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       115 ~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                                +-+...+..+-.++...|++++|.+.|+
T Consensus        83 ----------p~~~~~~~~lg~~~~~~g~~~~A~~~~~  110 (142)
T 2xcb_A           83 ----------INEPRFPFHAAECHLQLGDLDGAESGFY  110 (142)
T ss_dssp             ----------TTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ----------CCCcHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                      1134556666777777777777776653

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=97.94  E-value=7.6e-05  Score=48.06  Aligned_cols=93  Identities=8%  Similarity=-0.038  Sum_probs=67.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +...+..+-..+.+.|++++|...|+...+.. +.+...+..+-.+  |.+.|++++|++.|++..+-+           
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~l~-----------   85 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGAC--RQAMGQYDLAIHSYSYGAVMD-----------   85 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHS-----------
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHH--HHHHhhHHHHHHHHHHHHhcC-----------
Confidence            55677888888999999999999999998653 2355555555444  799999999999999987532           


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                               +-+...+..+-.++...|+.++|.+.|
T Consensus        86 ---------p~~~~~~~~lg~~~~~~g~~~~A~~~~  112 (148)
T 2vgx_A           86 ---------IXEPRFPFHAAECLLQXGELAEAESGL  112 (148)
T ss_dssp             ---------TTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ---------CCCchHHHHHHHHHHHcCCHHHHHHHH
Confidence                     013455666666666777777766655

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=97.92  E-value=6.8e-05  Score=53.39  Aligned_cols=142  Identities=9%  Similarity=0.021  Sum_probs=98.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CC------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC---CCC--hh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RD------YVLWTAMIDGYLRVNRFREALTLFPEMQTSNI---RPD--EF   73 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~---~p~--~~   73 (153)
                      .+...+..+...|++++|.+.+.+..+   .+      ...+..+...+...|++++|+..+++..+...   .+.  ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            455667788899999999998875431   11      12344455666778899999999998875321   121  33


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhccc-----CC-----hhhHHHHHHHHHhcCCCC----------CCCCC------
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLR-----KD-----KFTWTAMIVGLAISDPFP----------TIRPD------  127 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~-----~~-----~~~~~~li~~~~~~~~~~----------~~~p~------  127 (153)
                      +++.+-..  |...|++++|+..|++..+     ++     ..+|+.+...|...|.++          .+.++      
T Consensus       157 ~~~~lg~~--y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~  234 (293)
T 2qfc_A          157 IENAIANI--YAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSS
T ss_pred             HHHHHHHH--HHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHH
Confidence            55555555  7999999999999988751     22     257888888888888877          11121      


Q ss_pred             -HhHHHHHHHHHhcCCchhHh-hhhc
Q 035927          128 -EVTYVGVLSACTHNGNETFV-INSC  151 (153)
Q Consensus       128 -~~t~~~ll~~~~~~g~~~~a-~~~~  151 (153)
                       ...|..+-..|.+.|+.++| .+.|
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~  260 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAY  260 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence             56788888899999999998 5544

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=97.92  E-value=7.5e-05  Score=58.07  Aligned_cols=111  Identities=9%  Similarity=0.005  Sum_probs=75.7

Q ss_pred             cCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHH
Q 035927           19 RGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQR   95 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~   95 (153)
                      .|++++|...|++..+  | +...|..+-..+.+.|++++|.+.+++..+.. +-+...+..+-..  |.+.|++++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~--~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRV--RWTQQRHAEAAV   78 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHH--HHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH--HHHCCCHHHHHH
Confidence            4788999999998863  3 67889999999999999999999999998753 2345566666665  799999999999


Q ss_pred             HHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           96 VLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        96 ~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+++..+.+                    +-+...+..+...+.+.|+.++|.+.|+
T Consensus        79 ~~~~al~~~--------------------p~~~~~~~~la~~~~~~g~~~~A~~~~~  115 (568)
T 2vsy_A           79 LLQQASDAA--------------------PEHPGIALWLGHALEDAGQAEAAAAAYT  115 (568)
T ss_dssp             HHHHHHHHC--------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHhcC--------------------CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999987642                    1245678888888889999999887764

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.92  E-value=6.1e-05  Score=46.82  Aligned_cols=93  Identities=12%  Similarity=0.020  Sum_probs=75.9

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~   82 (153)
                      ..+-.+...+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|+..+++..+..  | +...+..+-.. 
T Consensus        18 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~--P~~~~~~~~la~~-   94 (121)
T 1hxi_A           18 ENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVS-   94 (121)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH-
T ss_pred             hhHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHH-
Confidence            346667788999999999999999986  34 78889999999999999999999999998753  5 44455555555 


Q ss_pred             HHhccCChHHHHHHHHhcccC
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~  103 (153)
                       |.+.|++++|+..|++..+.
T Consensus        95 -~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           95 -HTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             -HHHHHHHHHHHHHHHHHHC-
T ss_pred             -HHHcCCHHHHHHHHHHHHHh
Confidence             79999999999999998764

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.91  E-value=0.00046  Score=45.05  Aligned_cols=96  Identities=8%  Similarity=0.163  Sum_probs=75.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHH-HHhcCCh--HHHHHHHHHHhhCCCCCChhHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDG-YLRVNRF--REALTLFPEMQTSNIRPDEFTIVR   77 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~-~~~~~~~--~~a~~~~~~m~~~~~~p~~~t~~~   77 (153)
                      .+...|..+...+...|++++|...|++..+   .+...+..+... +.+.|++  ++|...++...+.. +-+...+..
T Consensus        42 ~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~  120 (177)
T 2e2e_A           42 QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQTRAMIDKALALD-SNEITALML  120 (177)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhC-CCcHHHHHH
Confidence            4567788899999999999999999998763   367778888887 7788988  99999999988753 123455555


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +...  |.+.|++++|...|++..+
T Consensus       121 la~~--~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          121 LASD--AFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHH--HHHcccHHHHHHHHHHHHh
Confidence            5555  6899999999999999865

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=97.91  E-value=2.9e-05  Score=50.91  Aligned_cols=113  Identities=12%  Similarity=0.150  Sum_probs=74.8

Q ss_pred             HhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCCh--H
Q 035927           17 INRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDV--E   91 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~--~   91 (153)
                      ...|++++|...+++..   ..+...|..+...+...|++++|...+++..+.. +.+...+..+...+ |.+.|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l-~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVL-YYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHH-HHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHH-HHhcCCcchH
Confidence            35677788888777654   3477889999999999999999999999998653 22455555555552 4688998  9


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           92 KAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        92 ~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      +|...|++..+.+                    +-+...+..+...+...|++++|.+.|
T Consensus        99 ~A~~~~~~al~~~--------------------p~~~~~~~~la~~~~~~g~~~~A~~~~  138 (177)
T 2e2e_A           99 QTRAMIDKALALD--------------------SNEITALMLLASDAFMQANYAQAIELW  138 (177)
T ss_dssp             HHHHHHHHHHHHC--------------------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhC--------------------CCcHHHHHHHHHHHHHcccHHHHHHHH
Confidence            9999999986532                    012344445555555555555555544

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=97.91  E-value=0.00011  Score=53.53  Aligned_cols=94  Identities=13%  Similarity=0.173  Sum_probs=71.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-----CHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--R-----DYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEF   73 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-----~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~   73 (153)
                      +...+-.++..+.+.|+++.|.+.+++|.+  |     +-.+...|..+.+.    .++..+|..+|+++.+.  .|+..
T Consensus       135 ~lea~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~  212 (310)
T 3mv2_B          135 TTELLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWK  212 (310)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcc
Confidence            456678899999999999999999999974  4     24566666666332    34899999999998764  35544


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +-..++.+  +.+.|++++|++.++.+.+
T Consensus       213 ~~~lLln~--~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          213 TQLGLLNL--HLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HHHHHHHH--HHHHTCHHHHHHHHHHHHS
T ss_pred             cHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence            44555554  7999999999999987654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=97.91  E-value=0.00014  Score=53.59  Aligned_cols=139  Identities=9%  Similarity=0.012  Sum_probs=102.5

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CC---CCC-hhHHH
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS--NI---RPD-EFTIV   76 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~---~p~-~~t~~   76 (153)
                      .-..+...|++++|...|++..+     +    ...+|..+-..+...|++++|...+++..+.  ..   .|. ..+++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            44567788999999999988753     2    3467888889999999999999999888643  11   122 23444


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhcccC-----C----hhhHHHHHHHHHhcCCCC----------------CCCCC-HhH
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLRK-----D----KFTWTAMIVGLAISDPFP----------------TIRPD-EVT  130 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~~-----~----~~~~~~li~~~~~~~~~~----------------~~~p~-~~t  130 (153)
                      .+-..  |...|++++|++.|++..+-     +    ..++..+...|...|.++                +..|+ ..+
T Consensus       189 ~lg~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  266 (383)
T 3ulq_A          189 LFATN--FLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQA  266 (383)
T ss_dssp             HHHHH--HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHH
T ss_pred             HHHHH--HHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHH
Confidence            44444  79999999999999887531     1    347888888888888877                22143 466


Q ss_pred             HHHHHHHHhcCCchhHhhhhcc
Q 035927          131 YVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       131 ~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +..+...+.+.|+.++|.+.|+
T Consensus       267 ~~~l~~~~~~~g~~~~A~~~~~  288 (383)
T 3ulq_A          267 YFLITQIHYKLGKIDKAHEYHS  288 (383)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHH
Confidence            8888899999999999988764

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.90  E-value=0.00017  Score=44.81  Aligned_cols=95  Identities=13%  Similarity=-0.031  Sum_probs=70.6

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHH
Q 035927           34 ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIV  113 (153)
Q Consensus        34 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~  113 (153)
                      ..+...|..+-..+.+.|++++|...|+...+.. +.+...+..+-..  |.+.|++++|...+++..+.+         
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~--~~~~~~~~~A~~~~~~al~~~---------   73 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALC--YLKMQQPEQALADCRRALELD---------   73 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC---------
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHH--HHHhcCHHHHHHHHHHHHHhC---------
Confidence            3467889999999999999999999999988753 2244555555555  799999999999999987632         


Q ss_pred             HHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          114 GLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       114 ~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                 +-+...+..+...+...|++++|.+.|
T Consensus        74 -----------p~~~~~~~~l~~~~~~~~~~~~A~~~~  100 (137)
T 3q49_B           74 -----------GQSVKAHFFLGQCQLEMESYDEAIANL  100 (137)
T ss_dssp             -----------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             -----------chhHHHHHHHHHHHHHHhhHHHHHHHH
Confidence                       113455666666777777777776655

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=97.90  E-value=0.00015  Score=44.78  Aligned_cols=93  Identities=14%  Similarity=0.038  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      ...|..+-..+.+.|++++|...|++..+.. +.+...+..+-.+  |.+.|++++|+..|++..+.+            
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~--~~~~~~~~~A~~~~~~al~~~------------   68 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAA--LAKLMSFPEAIADCNKAIEKD------------   68 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHH--HHHhcCHHHHHHHHHHHHHhC------------
Confidence            4567778888899999999999999998753 2345566666555  799999999999999987642            


Q ss_pred             hcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                              +-+...|..+-.++...|++++|.+.|+
T Consensus        69 --------p~~~~~~~~lg~~~~~~~~~~~A~~~~~   96 (126)
T 3upv_A           69 --------PNFVRAYIRKATAQIAVKEYASALETLD   96 (126)
T ss_dssp             --------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             --------CCcHHHHHHHHHHHHHHhCHHHHHHHHH
Confidence                    1145567777777777888877776653

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.89  E-value=2.6e-05  Score=57.55  Aligned_cols=110  Identities=11%  Similarity=0.089  Sum_probs=67.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--C-CH----HHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-ChhHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--R-DY----VLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-DEFTIV   76 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~t~~   76 (153)
                      +..+-..+.+.|++++|...|++..+  | +.    ..|..+...+...|++++|...+++..+.    +-.| ....+.
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  130 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSG  130 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHH
Confidence            44555667777888888888777652  2 22    46777777777778888888877776542    2122 223333


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhcccC---------ChhhHHHHHHHHHhcCC
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLRK---------DKFTWTAMIVGLAISDP  120 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~~~  120 (153)
                      .+-..  |...|++++|.+.+++..+.         ....+..+...+...|.
T Consensus       131 ~l~~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (411)
T 4a1s_A          131 NLGNT--LKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGK  181 (411)
T ss_dssp             HHHHH--HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH--HHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCc
Confidence            33333  67777877777777776321         23355556666665555

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=97.89  E-value=0.00023  Score=61.07  Aligned_cols=133  Identities=17%  Similarity=0.221  Sum_probs=94.8

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC-------------------------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE-------------------------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~-------------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      +-..+...|++++|..+|++...                         .+..+|..+-.++.+.|++++|.+-|.+-   
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~~~~~A~~VLie~i~nldrAiE~Aervn~p~vWsqLAKAql~~G~~kEAIdsYiKA--- 1131 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFDVNTSAVQVLIEHIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKA--- 1131 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHHHHhhHHHHHHHHHhcCCHHHHHHHHHHHHhCCCHHHHHHHHHhc---
Confidence            44455555666666666655542                         25667889999999999999999998553   


Q ss_pred             CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC--ChhhHHHHHHHHHhcCCCC-----CCCCCHhHHHHHHHHHh
Q 035927           67 NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK--DKFTWTAMIVGLAISDPFP-----TIRPDEVTYVGVLSACT  139 (153)
Q Consensus        67 ~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~li~~~~~~~~~~-----~~~p~~~t~~~ll~~~~  139 (153)
                         -|...|.-++..  +.+.|++++|.+.+...++.  +....+.++.+|++.+.++     --.|+...|..+-..|.
T Consensus      1132 ---dD~say~eVa~~--~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI~~~n~ad~~~iGd~le 1206 (1630)
T 1xi4_A         1132 ---DDPSSYMEVVQA--ANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAHIQQVGDRCY 1206 (1630)
T ss_pred             ---CChHHHHHHHHH--HHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHHhCCCHHHHHHHHHHHH
Confidence               466778888888  59999999999999876543  3334556888888886666     12355566667777777


Q ss_pred             cCCchhHhhhhcc
Q 035927          140 HNGNETFVINSCN  152 (153)
Q Consensus       140 ~~g~~~~a~~~~~  152 (153)
                      ..|++++|..+|.
T Consensus      1207 ~eg~YeeA~~~Y~ 1219 (1630)
T 1xi4_A         1207 DEKMYDAAKLLYN 1219 (1630)
T ss_pred             hcCCHHHHHHHHH
Confidence            7777777777664

>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=97.86  E-value=6.3e-05  Score=57.73  Aligned_cols=120  Identities=13%  Similarity=0.100  Sum_probs=86.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      +..+-..+.+.|++++|.+.|++..   ..+...|..+-..+.+.|++++|+..+++..+.. +-+...+..+-.+  |.
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~--~~   85 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS--NM   85 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH--HH
Confidence            3344455678899999999999875   2368899999999999999999999999998763 2345566666555  79


Q ss_pred             ccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHH--HhcCCchhHhhhhcc
Q 035927           86 KCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSA--CTHNGNETFVINSCN  152 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~--~~~~g~~~~a~~~~~  152 (153)
                      +.|++++|++.|++..+.+                     | +...+..+-.+  +.+.|++++|.+.++
T Consensus        86 ~~g~~~eA~~~~~~al~~~---------------------p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           86 ALGKFRAALRDYETVVKVK---------------------PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHTCHHHHHHHHHHHHHHS---------------------TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HcCCHHHHHHHHHHHHHhC---------------------CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999986532                     2 22233333333  667788888777654

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=97.84  E-value=0.0002  Score=42.86  Aligned_cols=93  Identities=16%  Similarity=0.031  Sum_probs=67.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      +...+..+...+...|++++|...++...+.. +.+...+..+...  |.+.|++++|...+++..+.+           
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~--~~~~~~~~~A~~~~~~~~~~~-----------   68 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAA--YAKKGDYQKAYEDGCKTVDLK-----------   68 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHC-----------
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHH--HHhhccHHHHHHHHHHHHHhC-----------
Confidence            34567888888999999999999999998753 2355566666665  699999999999999986532           


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                               +.+...+..+...+...|+.++|.+.|
T Consensus        69 ---------~~~~~~~~~~a~~~~~~~~~~~A~~~~   95 (118)
T 1elw_A           69 ---------PDWGKGYSRKAAALEFLNRFEEAKRTY   95 (118)
T ss_dssp             ---------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ---------cccHHHHHHHHHHHHHHhhHHHHHHHH
Confidence                     113455666666666667766666654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=97.84  E-value=3.1e-05  Score=57.18  Aligned_cols=24  Identities=13%  Similarity=0.004  Sum_probs=11.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQM   32 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m   32 (153)
                      +..+...+...|++++|...+++.
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~a  152 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERH  152 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHH
Confidence            444444555555555555554443

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.84  E-value=9.6e-05  Score=45.16  Aligned_cols=96  Identities=15%  Similarity=0.154  Sum_probs=72.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      ...|..+...+...|++++|...++...+.. +.+...+..+...  |.+.|++++|...+++..+.+..          
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~--~~~~~~~~~A~~~~~~~~~~~~~----------   70 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAV--YFEKGDYNKCRELCEKAIEVGRE----------   70 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHHHH----------
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHH--HHHhccHHHHHHHHHHHHhhccc----------
Confidence            4567888888999999999999999998754 2355566666665  69999999999999998653210          


Q ss_pred             hcCCCCCCCCC----HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPD----EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                             ..++    ...+..+...+.+.|++++|.+.|+
T Consensus        71 -------~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  103 (131)
T 1elr_A           71 -------NREDYRQIAKAYARIGNSYFKEEKYKDAIHFYN  103 (131)
T ss_dssp             -------STTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             -------cchhHHHHHHHHHHHHHHHHHhccHHHHHHHHH
Confidence                   1122    5667788888888899988887764

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.84  E-value=0.00015  Score=46.94  Aligned_cols=92  Identities=12%  Similarity=0.073  Sum_probs=68.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVG  114 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~  114 (153)
                      +...|..+-..+.+.|++++|+..|++..+..  | +...+..+-..  |.+.|++++|+..|++..+.+          
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~--~~~~g~~~~A~~~~~~al~~~----------   75 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIA--PANPIYLSNRAAA--YSASGQHEKAAEDAELATVVD----------   75 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC----------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHH--HHHccCHHHHHHHHHHHHHhC----------
Confidence            55678888899999999999999999998753  4 45555555555  799999999999999997642          


Q ss_pred             HHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          115 LAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       115 ~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                +-+...|..+-..+.+.|++++|.+.|
T Consensus        76 ----------p~~~~~~~~lg~~~~~~g~~~~A~~~~  102 (164)
T 3sz7_A           76 ----------PKYSKAWSRLGLARFDMADYKGAKEAY  102 (164)
T ss_dssp             ----------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ----------CCCHHHHHHHHHHHHHccCHHHHHHHH
Confidence                      013455666666666667766666655

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.82  E-value=0.00016  Score=53.27  Aligned_cols=137  Identities=9%  Similarity=0.020  Sum_probs=98.5

Q ss_pred             HHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----C-CCCC-hhHHHHH
Q 035927           14 SGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----N-IRPD-EFTIVRI   78 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~-~~p~-~~t~~~l   78 (153)
                      ..+...|++++|...|++..+     +    ...++..+-..+...|++++|...+++..+.    + ..+. ..+++.+
T Consensus       109 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  188 (378)
T 3q15_A          109 MYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVI  188 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHH
Confidence            345678999999999987653     2    3457888888888999999999999887642    1 1222 2333444


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc-----C----ChhhHHHHHHHHHhcCCCC----------C-----CCCC-HhHHHH
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR-----K----DKFTWTAMIVGLAISDPFP----------T-----IRPD-EVTYVG  133 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~-----~----~~~~~~~li~~~~~~~~~~----------~-----~~p~-~~t~~~  133 (153)
                      -..  |.+.|++++|.+.|++..+     .    ...+++.+...|...|.++          .     ..|+ ..++..
T Consensus       189 g~~--y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  266 (378)
T 3q15_A          189 AGN--YDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFG  266 (378)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             HHH--HHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHH
Confidence            443  7999999999999888743     1    2346777778888887777          1     2343 466888


Q ss_pred             HHHHHhcCCchhHhhhhcc
Q 035927          134 VLSACTHNGNETFVINSCN  152 (153)
Q Consensus       134 ll~~~~~~g~~~~a~~~~~  152 (153)
                      +...+.+.|+.++|.+.++
T Consensus       267 la~~~~~~g~~~~A~~~~~  285 (378)
T 3q15_A          267 LSWTLCKAGQTQKAFQFIE  285 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHH
Confidence            8889999999999988764

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.82  E-value=9.9e-05  Score=46.63  Aligned_cols=129  Identities=16%  Similarity=0.065  Sum_probs=92.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC-----C----HHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCCC-h
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER-----D----YVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRPD-E   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~-----~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~   72 (153)
                      .++..+-..+...|++++|...+++....     +    ..++..+-..+...|++++|...+++..+.    +-.+. .
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   89 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA   89 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            46788888999999999999999887531     1    247888888999999999999999998643    11111 2


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ..+..+-..  |...|++++|.+.+++..+.....               +-.+ ....+..+...+...|+.++|.+.+
T Consensus        90 ~~~~~l~~~--~~~~~~~~~A~~~~~~a~~~~~~~---------------~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  152 (164)
T 3ro3_A           90 QSCYSLGNT--YTLLQDYEKAIDYHLKHLAIAQEL---------------KDRIGEGRACWSLGNAYTALGNHDQAMHFA  152 (164)
T ss_dssp             HHHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHT---------------TCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHH--HHHHhhHHHHHHHHHHHHHHHHHc---------------cchHhHHHHHHHHHHHHHHccCHHHHHHHH
Confidence            344444444  789999999999999875420000               0111 2356777888888999999998776


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      +
T Consensus       153 ~  153 (164)
T 3ro3_A          153 E  153 (164)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.82  E-value=5.2e-05  Score=53.67  Aligned_cols=53  Identities=11%  Similarity=0.226  Sum_probs=26.3

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCCC--C-C----HHHHHHHHHHHHhcCChHHHHHHHHHH
Q 035927           11 DIVSGYINRGQVDIARQYFAQMPE--R-D----YVLWTAMIDGYLRVNRFREALTLFPEM   63 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~--~-~----~~~~~~li~~~~~~~~~~~a~~~~~~m   63 (153)
                      ..-..+.+.|++++|..+|++..+  | +    ...+..+...+...|++++|...+++.
T Consensus        10 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a   69 (338)
T 3ro2_A           10 LEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHD   69 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334445555555555555555431  1 1    234455555555555555555555544

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.82  E-value=0.00073  Score=45.89  Aligned_cols=143  Identities=11%  Similarity=0.042  Sum_probs=105.4

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCCC-CHHHHHHHHHHHHhcC----ChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPER-DYVLWTAMIDGYLRVN----RFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-~~~~~~~li~~~~~~~----~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      -|...+..+-..|.+.+++++|.+.|++..+. +...+..|-..|.. +    ++++|...|+...+.|   +...+..+
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~~L   91 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEIVL   91 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHHHH
Confidence            35667888888899999999999999987643 67778888887777 6    8999999999998765   34455555


Q ss_pred             HHHHHHhc----cCChHHHHHHHHhcccCC-----hhhHHHHHHHHHhc----CCCC----------CCCCCHhHHHHHH
Q 035927           79 LTAYMYCK----CGDVEKAQRVLRKMLRKD-----KFTWTAMIVGLAIS----DPFP----------TIRPDEVTYVGVL  135 (153)
Q Consensus        79 i~~~~~~~----~g~~~~a~~~~~~m~~~~-----~~~~~~li~~~~~~----~~~~----------~~~p~~~t~~~ll  135 (153)
                      -..  |..    .++.++|.+.|++..+.+     ...+..+-..|...    ++++          ...++...+..+-
T Consensus        92 g~~--y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~a~~~Lg  169 (212)
T 3rjv_A           92 ARV--LVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLSRTGYAEYWAG  169 (212)
T ss_dssp             HHH--HTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTSCTTHHHHHHH
T ss_pred             HHH--HHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            554  566    789999999999997753     57788887777773    2222          2234555666666


Q ss_pred             HHHhcC-C-----chhHhhhhcc
Q 035927          136 SACTHN-G-----NETFVINSCN  152 (153)
Q Consensus       136 ~~~~~~-g-----~~~~a~~~~~  152 (153)
                      ..|... |     +.++|.+.|+
T Consensus       170 ~~y~~g~gg~~~~d~~~A~~~~~  192 (212)
T 3rjv_A          170 MMFQQGEKGFIEPNKQKALHWLN  192 (212)
T ss_dssp             HHHHHCBTTTBCCCHHHHHHHHH
T ss_pred             HHHHcCCCCCCCCCHHHHHHHHH
Confidence            666643 3     7888888764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=97.81  E-value=0.00012  Score=53.82  Aligned_cols=145  Identities=12%  Similarity=0.024  Sum_probs=101.9

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCCCh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRPDE   72 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~~   72 (153)
                      ..+++.+-..|...|++++|.+.|++..+     +    ...+++.+-..+...|++++|...+++..+.    +.+...
T Consensus       182 ~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~  261 (378)
T 3q15_A          182 IQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLP  261 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHH
Confidence            34678889999999999999998887652     1    2457888888999999999999999998761    222235


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccC-----C---hhhHHHHHHHHHhcCC---CC---------CCCCCH-hHH
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRK-----D---KFTWTAMIVGLAISDP---FP---------TIRPDE-VTY  131 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-----~---~~~~~~li~~~~~~~~---~~---------~~~p~~-~t~  131 (153)
                      .++..+-..  |.+.|++++|...+++..+-     +   ...++.+-..+...+.   +.         +..|+. ..+
T Consensus       262 ~~~~~la~~--~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~  339 (378)
T 3q15_A          262 KVLFGLSWT--LCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACA  339 (378)
T ss_dssp             HHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHH--HHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHH
Confidence            556666665  79999999999999987431     1   2233333333333333   11         222333 456


Q ss_pred             HHHHHHHhcCCchhHhhhhcc
Q 035927          132 VGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       132 ~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+...|...|+.++|.+.|+
T Consensus       340 ~~la~~y~~~g~~~~A~~~~~  360 (378)
T 3q15_A          340 RSAAAVFESSCHFEQAAAFYR  360 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHH
Confidence            778888999999999998774

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=97.81  E-value=2.4e-05  Score=55.47  Aligned_cols=68  Identities=12%  Similarity=0.046  Sum_probs=35.2

Q ss_pred             HhccCChHHHHHHHHhcccC-----C----hhhHHHHHHHHHhcCCCC----------CCC---CC----HhHHHHHHHH
Q 035927           84 YCKCGDVEKAQRVLRKMLRK-----D----KFTWTAMIVGLAISDPFP----------TIR---PD----EVTYVGVLSA  137 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~-----~----~~~~~~li~~~~~~~~~~----------~~~---p~----~~t~~~ll~~  137 (153)
                      |...|++++|.+.+++..+.     +    ...+..+...+...|.++          .+.   ++    ..++..+...
T Consensus       193 ~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  272 (338)
T 3ro2_A          193 HYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNT  272 (338)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHH
Confidence            45666666666666655321     1    224555555555555554          000   11    3445555666


Q ss_pred             HhcCCchhHhhhhc
Q 035927          138 CTHNGNETFVINSC  151 (153)
Q Consensus       138 ~~~~g~~~~a~~~~  151 (153)
                      +...|++++|.+.+
T Consensus       273 ~~~~g~~~~A~~~~  286 (338)
T 3ro2_A          273 YTLLQDYEKAIDYH  286 (338)
T ss_dssp             HHHTTCHHHHHHHH
T ss_pred             HHHhcCHHHHHHHH
Confidence            66666666666554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.81  E-value=0.00021  Score=44.70  Aligned_cols=94  Identities=15%  Similarity=0.203  Sum_probs=74.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC--CCCCh----hHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN--IRPDE----FTIVR   77 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~~----~t~~~   77 (153)
                      ..+..+-..+.+.|++++|++.|++..   ..+...|+.+-..+.+.|++++|+..+++.++.+  ..++.    .+|..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            357788899999999999999999875   3378889999999999999999999999987532  22222    23444


Q ss_pred             HHHHHHHhccCChHHHHHHHHhccc
Q 035927           78 ILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        78 li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +-..  |...|++++|++.|++..+
T Consensus        89 lg~~--~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           89 AGNA--FQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHH--HHHcCCHHHHHHHHHHHHh
Confidence            4444  6899999999999998754

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.81  E-value=0.00026  Score=43.07  Aligned_cols=84  Identities=13%  Similarity=0.130  Sum_probs=61.9

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMI  112 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li  112 (153)
                      +...+..+...+...|++++|...+++..+.. +.+...+..+...  |...|++++|.+.+++..+.   +...|..+.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~   87 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAA--YSKLGNYAGAVQDCERAICIDPAYSKAYGRMG   87 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHH--HHHhhchHHHHHHHHHHHhcCccCHHHHHHHH
Confidence            45678888889999999999999999998653 2355666666665  69999999999999998652   344555555


Q ss_pred             HHHHhcCCCC
Q 035927          113 VGLAISDPFP  122 (153)
Q Consensus       113 ~~~~~~~~~~  122 (153)
                      ..+...+.++
T Consensus        88 ~~~~~~~~~~   97 (131)
T 2vyi_A           88 LALSSLNKHV   97 (131)
T ss_dssp             HHHHHTTCHH
T ss_pred             HHHHHhCCHH
Confidence            5555555444

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.80  E-value=8.9e-05  Score=53.29  Aligned_cols=142  Identities=11%  Similarity=0.057  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-------C--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-Chh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-------R--DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-DEF   73 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-------~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~~   73 (153)
                      .|+.....|...|++++|...|.+...       +  -..+|+.+...|.+.|++++|...+++..+.    |-.. -..
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  117 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAM  117 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            577777778888888888877776542       1  1347788888888888888888888876532    2111 123


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhcccC---------ChhhHHHHHHHHHhcCCCC----------CC------CCC-
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLRK---------DKFTWTAMIVGLAISDPFP----------TI------RPD-  127 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~~~~~----------~~------~p~-  127 (153)
                      +++.+-..  |.+ |++++|+..|++..+-         -..+++.+...+...|.++          .+      .+. 
T Consensus       118 ~~~~lg~~--~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  194 (307)
T 2ifu_A          118 ALDRAGKL--MEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTC  194 (307)
T ss_dssp             HHHHHHHH--HTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHH--HHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHH
Confidence            45555554  566 8888888888877431         1456777777777777766          11      111 


Q ss_pred             HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          128 EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ...+..+...+...|+.++|.+.|+
T Consensus       195 ~~~~~~~g~~~~~~g~~~~A~~~~~  219 (307)
T 2ifu_A          195 YKKCIAQVLVQLHRADYVAAQKCVR  219 (307)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            1256666667777788888887664

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.78  E-value=0.00033  Score=50.28  Aligned_cols=121  Identities=12%  Similarity=0.019  Sum_probs=85.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh---hHHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE---FTIVRILTAYM   83 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~---~t~~~li~~~~   83 (153)
                      +-.....+...|++++|.++|+.+.  .|+....-.+-..+.+.+++++|+..|+...+.   |+.   .-....+.. .
T Consensus       105 ~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~---~d~~~~~~a~~~LG~-a  180 (282)
T 4f3v_A          105 TMGFAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW---PDKFLAGAAGVAHGV-A  180 (282)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC---SCHHHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc---CCcccHHHHHHHHHH-H
Confidence            4556778889999999999999997  343335555555777899999999999855443   222   112233333 2


Q ss_pred             HhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC--HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           84 YCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD--EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~--~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.+.|++++|+..|++...-                   ...|.  .......-.++.+.|+.++|..+|+
T Consensus       181 l~~LG~~~eAl~~l~~a~~g-------------------~~~P~~~~da~~~~glaL~~lGr~deA~~~l~  232 (282)
T 4f3v_A          181 AANLALFTEAERRLTEANDS-------------------PAGEACARAIAWYLAMARRSQGNESAAVALLE  232 (282)
T ss_dssp             HHHTTCHHHHHHHHHHHHTS-------------------TTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHhcC-------------------CCCccccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            79999999999999998643                   12243  3355667777788999999988774

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=97.78  E-value=4.6e-05  Score=55.77  Aligned_cols=21  Identities=10%  Similarity=-0.064  Sum_probs=9.9

Q ss_pred             HHHHHHHHHhcCCchhHhhhh
Q 035927          130 TYVGVLSACTHNGNETFVINS  150 (153)
Q Consensus       130 t~~~ll~~~~~~g~~~~a~~~  150 (153)
                      ++..+...+...|++++|.+.
T Consensus       269 ~~~~la~~~~~~g~~~~A~~~  289 (406)
T 3sf4_A          269 SCYSLGNTYTLLQDYEKAIDY  289 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCcHHHHHHH
Confidence            344444444455555554443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.77  E-value=0.0003  Score=43.19  Aligned_cols=90  Identities=17%  Similarity=0.198  Sum_probs=71.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC--C-CH---HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC----hhHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE--R-DY---VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD----EFTIVRI   78 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~l   78 (153)
                      +-.+...+.+.|++++|...|++..+  | +.   ..+..+-..+.+.|++++|...++...+..  |+    ...+..+
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~l   82 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHH
Confidence            34566778899999999999998763  4 33   477888888999999999999999998753  43    3444444


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      -..  |.+.|++++|.+.|+.+.+
T Consensus        83 a~~--~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           83 GLS--QYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHH--HHHcCCHHHHHHHHHHHHH
Confidence            444  7999999999999999965

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.76  E-value=0.00056  Score=48.59  Aligned_cols=96  Identities=9%  Similarity=-0.002  Sum_probs=79.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|...+++..+.. +-+...+..+-.
T Consensus         2 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (281)
T 2c2l_A            2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   80 (281)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            456678889999999999999999999875  34 78889999999999999999999999988753 234556666655


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +  |.+.|++++|++.|++..+
T Consensus        81 ~--~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           81 C--QLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHHcCCHHHHHHHHHHHHH
Confidence            5  7999999999999998753

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.76  E-value=0.00049  Score=43.02  Aligned_cols=92  Identities=13%  Similarity=0.040  Sum_probs=67.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC----hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD----EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAM  111 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~l  111 (153)
                      +...+..+...+.+.|++++|...|++..+.  .|+    ...+..+...  |.+.|++++|++.+++..+.+       
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~--~~~~~~~~~A~~~~~~~~~~~-------   95 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAAC--HLKLEDYDKAETEASKAIEKD-------   95 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHT-------
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHH--HHHHccHHHHHHHHHHHHhhC-------
Confidence            6778899999999999999999999999875  465    4555555555  799999999999999986532       


Q ss_pred             HHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          112 IVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       112 i~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                   +.+...+..+...+...|+.++|.+.|
T Consensus        96 -------------~~~~~~~~~~a~~~~~~~~~~~A~~~~  122 (148)
T 2dba_A           96 -------------GGDVKALYRRSQALEKLGRLDQAVLDL  122 (148)
T ss_dssp             -------------SCCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             -------------ccCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence                         113444555555666666666665554

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=97.73  E-value=0.00015  Score=45.36  Aligned_cols=95  Identities=8%  Similarity=0.059  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGL  115 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~  115 (153)
                      ...+..+-..+.+.|++++|+..|++.++.  .|+ ...|..+-.+  |.+.|++++|++.|++..+-+..         
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~--~~~~~~~~~A~~~~~~al~~~~~---------   74 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAV--YFEEKKFAECVQFCEKAVEVGRE---------   74 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHH---------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHH--HHHhhhHHHHHHHHHHHHHhCcc---------
Confidence            356778888999999999999999999875  354 4455554444  79999999999999998653210         


Q ss_pred             HhcCCCCCCCCC----HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          116 AISDPFPTIRPD----EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       116 ~~~~~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                              ..++    ...|..+-.++...|++++|++.|+
T Consensus        75 --------~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~  107 (127)
T 4gcn_A           75 --------TRADYKLIAKAMSRAGNAFQKQNDLSLAVQWFH  107 (127)
T ss_dssp             --------TTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             --------cchhhHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                    1111    2356677778888899999888764

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.71  E-value=0.00041  Score=46.32  Aligned_cols=93  Identities=10%  Similarity=0.115  Sum_probs=72.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC---CCH----------------HHHHHHHHHHHhcCChHHHHHHHHHHhhCC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE---RDY----------------VLWTAMIDGYLRVNRFREALTLFPEMQTSN   67 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~----------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   67 (153)
                      ..+..+-..+.+.|++++|...|++..+   .+.                ..|..+-..+.+.|++++|+..++...+..
T Consensus        39 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~  118 (198)
T 2fbn_A           39 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID  118 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            3567777888899999999999987652   122                678888888889999999999999988753


Q ss_pred             CCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           68 IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        68 ~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                       +.+...+..+-.+  |.+.|++++|.+.|++..+
T Consensus       119 -p~~~~~~~~lg~~--~~~~~~~~~A~~~~~~al~  150 (198)
T 2fbn_A          119 -KNNVKALYKLGVA--NMYFGFLEEAKENLYKAAS  150 (198)
T ss_dssp             -TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHH
T ss_pred             -cccHHHHHHHHHH--HHHcccHHHHHHHHHHHHH
Confidence             2345555555555  6999999999999998854

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.68  E-value=0.00031  Score=41.90  Aligned_cols=62  Identities=16%  Similarity=0.196  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..|..+-..+.+.|++++|...+++..+.. +.+...+..+-.+  |.+.|++++|++.+++..+
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~--~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMA--LIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH--HHHhcCHHHHHHHHHHHHH
Confidence            445555556666666666666666665432 1133333333333  5666666666666666644

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.64  E-value=0.00048  Score=42.28  Aligned_cols=87  Identities=13%  Similarity=0.173  Sum_probs=61.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh----HHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           41 TAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF----TIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        41 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      ..+...+.+.|++++|...|+...+..  |+..    .+..+-..  |.+.|++++|...|++..+.+            
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~--~~~~~~~~~A~~~~~~~~~~~------------   69 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGES--YYATRNFQLAEAQFRDLVSRY------------   69 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC------------
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHH--HHHhccHHHHHHHHHHHHHHC------------
Confidence            345566778999999999999998753  3322    44444444  799999999999999987532            


Q ss_pred             hcCCCCCCCCC----HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPD----EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~----~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                               |+    ...+..+..++.+.|+.++|.+.|+
T Consensus        70 ---------p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  100 (129)
T 2xev_A           70 ---------PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQ  100 (129)
T ss_dssp             ---------TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ---------CCCcccHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                     22    3456666677777788777776653

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.64  E-value=0.00029  Score=43.66  Aligned_cols=89  Identities=16%  Similarity=0.041  Sum_probs=69.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHh
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAI  117 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~  117 (153)
                      .+..+-..+.+.|++++|...++...+.  .| +...+..+-..  +.+.|++++|+..|++..+.+             
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~--~~~~g~~~~A~~~~~~al~l~-------------   81 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLT--QAENEKDGLAIIALNHARMLD-------------   81 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC-------------
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhC-------------
Confidence            4556667788999999999999999875  35 44445444444  799999999999999987643             


Q ss_pred             cCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          118 SDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       118 ~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                              | +...+..+..++.+.|+.++|.+.|+
T Consensus        82 --------P~~~~~~~~la~~~~~~g~~~~A~~~~~  109 (121)
T 1hxi_A           82 --------PKDIAVHAALAVSHTNEHNANAALASLR  109 (121)
T ss_dssp             --------TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --------CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence                    3 45677888888889999999887764

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.63  E-value=0.002  Score=48.32  Aligned_cols=109  Identities=14%  Similarity=0.126  Sum_probs=72.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC-----------C-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-----C-
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP-----------E-RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS-----N-   67 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~-----------~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~-   67 (153)
                      ...||.|-..+...|+.++|++.|++-.           . ....+|+.+-..|...|++++|...+++..+.     + 
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~  130 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSP  130 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccc
Confidence            4568999999999999999999887642           1 24578999999999999999999988877542     1 


Q ss_pred             CCCC-hhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHH
Q 035927           68 IRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVG  114 (153)
Q Consensus        68 ~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~  114 (153)
                      ..++ ..++...-.++.....++.++|++.|++..+  | +...+..+...
T Consensus       131 ~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~  181 (472)
T 4g1t_A          131 YRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIA  181 (472)
T ss_dssp             SCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            1222 2334333223112334568888888888743  3 34444444433

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=97.63  E-value=0.00077  Score=42.97  Aligned_cols=97  Identities=11%  Similarity=0.043  Sum_probs=74.6

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...+++..   ..+...|..+...+.+.|++++|...+++..+..- .+...+..+-.
T Consensus        45 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~  123 (166)
T 1a17_A           45 SNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAALRDYETVVKVKP-HDKDAKMKYQE  123 (166)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            456778899999999999999999998875   23678899999999999999999999999986531 23333322222


Q ss_pred             HHHHhccCChHHHHHHHHhcc
Q 035927           81 AYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      +..+.+.|++++|++.+....
T Consensus       124 ~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A          124 CNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcccchH
Confidence            212477899999999988763

>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=97.62  E-value=0.0009  Score=50.96  Aligned_cols=94  Identities=14%  Similarity=0.154  Sum_probs=78.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--C-C---------------HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--R-D---------------YVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~---------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      ..|..+-..+.+.|++++|...|++..+  | +               ...|..+-.++.+.|++++|+..+++.++.. 
T Consensus       269 ~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  347 (457)
T 1kt0_A          269 AIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-  347 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-
Confidence            4577888899999999999999998752  2 3               5789999999999999999999999998753 


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +-+...+..+-.+  |.+.|++++|+..|++..+-
T Consensus       348 p~~~~a~~~~g~a--~~~~g~~~~A~~~~~~al~l  380 (457)
T 1kt0_A          348 SANEKGLYRRGEA--QLLMNEFESAKGDFEKVLEV  380 (457)
T ss_dssp             TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHTT
T ss_pred             CccHHHHHHHHHH--HHHccCHHHHHHHHHHHHHh
Confidence            2356666666666  69999999999999999764

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.60  E-value=0.0001  Score=44.07  Aligned_cols=93  Identities=10%  Similarity=0.104  Sum_probs=69.4

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh-------h
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE-------F   73 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-------~   73 (153)
                      ++...|..+-..+.+.|++++|...|++..   ..+...|..+-..+.+.|++++|+..+++..+.  .|+.       .
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~   79 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRY--TSTAEHVAIRSK   79 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS--CSSTTSHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCccHHHHHHH
Confidence            456778899999999999999999999875   237788999999999999999999999999875  3442       2


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhc
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      .+..+-.+  +...|+.+.|.+.++++
T Consensus        80 ~~~~~~~~--~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           80 LQYRLELA--QGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             HHHHHHHH--HHHHHCCCCCSSSSSSC
T ss_pred             HHHHHHHH--HHHHHhHhhhHhHHHHh
Confidence            33333333  45556666555555444

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=97.59  E-value=0.0022  Score=41.96  Aligned_cols=114  Identities=15%  Similarity=0.133  Sum_probs=81.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHHH--HhcCChHHHHHHHHHHhhCCCCCC-hhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGY--LRVNRFREALTLFPEMQTSNIRPD-EFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~~--~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~l   78 (153)
                      .+...+..+...+.+.|++++|...+++...  |+.. +..+...+  .+.+...+|...+++..+.  .|+ ...+..+
T Consensus        38 ~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~-~~~~~~~~~~~~~~~~~~a~~~~~~al~~--~P~~~~~~~~l  114 (176)
T 2r5s_A           38 SRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNS-YKSLIAKLELHQQAAESPELKRLEQELAA--NPDNFELACEL  114 (176)
T ss_dssp             TSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHH-HHHHHHHHHHHHHHTSCHHHHHHHHHHHH--STTCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChH-HHHHHHHHHHHhhcccchHHHHHHHHHHh--CCCCHHHHHHH
Confidence            3456788899999999999999999999974  3333 32222211  2223344578888888764  354 5556656


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccC-----ChhhHHHHHHHHHhcCCCC
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRK-----DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~  122 (153)
                      -..  |.+.|++++|+..|+++.+.     +...+..+...+...|..+
T Consensus       115 a~~--~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  161 (176)
T 2r5s_A          115 AVQ--YNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGN  161 (176)
T ss_dssp             HHH--HHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSC
T ss_pred             HHH--HHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCC
Confidence            555  79999999999999998653     2457888888888888765

>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=97.58  E-value=0.00077  Score=50.01  Aligned_cols=117  Identities=10%  Similarity=0.083  Sum_probs=88.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-------------------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-------------------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      .+..+-..+.+.|++++|...|++..+                   .+...|..+-..+.+.|++++|+..+++.++.. 
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  303 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  303 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-
Confidence            477888899999999999999988754                   145688899999999999999999999998753 


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHh
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETFV  147 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a  147 (153)
                      +-+...+..+-.+  |.+.|++++|++.|++..+.+                     | +...+..+-..+...|+.+++
T Consensus       304 p~~~~a~~~lg~~--~~~~g~~~eA~~~l~~Al~l~---------------------P~~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          304 PSNTKALYRRAQG--WQGLKEYDQALADLKKAQEIA---------------------PEDKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC---------------------TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHH--HHHccCHHHHHHHHHHHHHhC---------------------CCCHHHHHHHHHHHHHHHHHHHH
Confidence            2245566655555  799999999999999986532                     2 344455555555556665554


Q ss_pred             h
Q 035927          148 I  148 (153)
Q Consensus       148 ~  148 (153)
                      .
T Consensus       361 ~  361 (370)
T 1ihg_A          361 E  361 (370)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=97.54  E-value=0.0021  Score=45.73  Aligned_cols=116  Identities=15%  Similarity=0.005  Sum_probs=87.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHH-HHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTA-MIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~-li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      -+...+..+...+.+.|++++|...+++...  |+...... ....+.+.++.++|...+++..+.. +.+...+..+-.
T Consensus       149 ~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~  227 (287)
T 3qou_A          149 QNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLAL  227 (287)
T ss_dssp             SCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHH
Confidence            3556788899999999999999999999974  44332222 2223556778888999998887653 234555666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C---ChhhHHHHHHHHHhcCCCC
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~---~~~~~~~li~~~~~~~~~~  122 (153)
                      .  |.+.|++++|.+.|.++.+  |   +...+..+...+...|..+
T Consensus       228 ~--l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          228 Q--LHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             H--HHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence            5  7999999999999999965  3   2667899999988887765

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.54  E-value=0.00014  Score=48.69  Aligned_cols=137  Identities=15%  Similarity=0.034  Sum_probs=81.3

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-CCC--------------
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-RPD--------------   71 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~--------------   71 (153)
                      +.........|+++++.+.|+.-...   ....+..+-..+.+.|++++|...|++..+..- .|+              
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~   87 (198)
T 2fbn_A            8 HHHSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIE   87 (198)
T ss_dssp             --------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHH
T ss_pred             cchhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHH
Confidence            33444555567777777777544321   455688888888999999999999999986421 121              


Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHH
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSA  137 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~  137 (153)
                      ...+..+-.+  |.+.|++++|+..+++..+  | +...|..+..++...+.++          .+.|+ ...+..+...
T Consensus        88 ~~~~~~la~~--~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~  165 (198)
T 2fbn_A           88 ISCNLNLATC--YNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELC  165 (198)
T ss_dssp             HHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHH--HHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHH
Confidence            1455555554  6999999999999999865  2 5666666777777766666          33443 3445555555


Q ss_pred             HhcCCchhHhh
Q 035927          138 CTHNGNETFVI  148 (153)
Q Consensus       138 ~~~~g~~~~a~  148 (153)
                      +...|+.+++.
T Consensus       166 ~~~~~~~~~~~  176 (198)
T 2fbn_A          166 VNKLKEARKKD  176 (198)
T ss_dssp             HHHHHHHHC--
T ss_pred             HHHHHHHHHHH
Confidence            55555555444

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=97.54  E-value=0.0013  Score=46.67  Aligned_cols=92  Identities=13%  Similarity=-0.003  Sum_probs=70.4

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVG  114 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~  114 (153)
                      +...+..+-..+.+.|++++|...|++..+.  .| +...+..+-..  |.+.|++++|++.+++..+.+          
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~--~~~~~~~~~A~~~~~~al~~~----------   68 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALC--YLKMQQPEQALADCRRALELD----------   68 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHTTSC----------
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHHHH--HHHhcCHHHHHHHHHHHHHhC----------
Confidence            4566778888899999999999999999875  35 45555555554  799999999999999998743          


Q ss_pred             HHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          115 LAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       115 ~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                +-+...+..+-.++.+.|++++|.+.|
T Consensus        69 ----------p~~~~~~~~lg~~~~~~g~~~~A~~~~   95 (281)
T 2c2l_A           69 ----------GQSVKAHFFLGQCQLEMESYDEAIANL   95 (281)
T ss_dssp             ----------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ----------CCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence                      124556777777777888888877765

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.53  E-value=0.0014  Score=42.23  Aligned_cols=95  Identities=18%  Similarity=0.206  Sum_probs=76.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCCC---------------------CHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPER---------------------DYVLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~~---------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      ...+...-..+.+.|++++|...|.+...-                     +...|..+-.++.+.|++++|+..++..+
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            345778888999999999999999876431                     23678888999999999999999999998


Q ss_pred             hCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           65 TSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        65 ~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.. +.+...|..+-.+  |...|++++|...|++..+-
T Consensus        91 ~~~-p~~~~a~~~~g~~--~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           91 KRE-ETNEKALFRRAKA--RIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHS-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHH
T ss_pred             hcC-CcchHHHHHHHHH--HHHHhcHHHHHHHHHHHHhc
Confidence            753 2355666666665  79999999999999998653

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.52  E-value=0.0012  Score=48.14  Aligned_cols=143  Identities=10%  Similarity=0.020  Sum_probs=98.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--C------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh-hHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--R------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE-FTIVR   77 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~t~~~   77 (153)
                      ..+..+-..+...|++++|...+++...  +      ...+|..+...+...|++++|...+++..+..-.++. ..+..
T Consensus       136 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~  215 (373)
T 1hz4_A          136 FLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWIS  215 (373)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHH
Confidence            3466778889999999999999987531  1      2356778888888999999999999998653211111 12222


Q ss_pred             -----HHHHHHHhccCChHHHHHHHHhcccCC-------hhhHHHHHHHHHhcCCCC----------------CCCCCH-
Q 035927           78 -----ILTAYMYCKCGDVEKAQRVLRKMLRKD-------KFTWTAMIVGLAISDPFP----------------TIRPDE-  128 (153)
Q Consensus        78 -----li~~~~~~~~g~~~~a~~~~~~m~~~~-------~~~~~~li~~~~~~~~~~----------------~~~p~~-  128 (153)
                           ....  +...|+.++|...++...+++       ...+..+...+...|.++                +..++. 
T Consensus       216 ~~~~~~~~~--~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~  293 (373)
T 1hz4_A          216 NANKVRVIY--WQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLN  293 (373)
T ss_dssp             HHHHHHHHH--HHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHH--HHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHH
Confidence                 2222  578999999999999987642       224556666677766665                222233 


Q ss_pred             hHHHHHHHHHhcCCchhHhhhhc
Q 035927          129 VTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       129 ~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ..+..+-.++...|+.++|.+.+
T Consensus       294 ~~~~~la~~~~~~g~~~~A~~~l  316 (373)
T 1hz4_A          294 RNLLLLNQLYWQAGRKSDAQRVL  316 (373)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHH
Confidence            35666677778889998888765

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=97.48  E-value=0.00045  Score=51.85  Aligned_cols=27  Identities=7%  Similarity=-0.136  Sum_probs=16.9

Q ss_pred             CCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          126 PDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       126 p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+..+|..+-..|...|+.++|++.|+
T Consensus       428 ~~~~~~~~LG~~~~~~g~~~~A~~~y~  454 (472)
T 4g1t_A          428 ADSEALHVLAFLQELNEKMQQADEDSE  454 (472)
T ss_dssp             -CTTHHHHHHHHHHHHHHCC-------
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            356789999999999999999999875

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=97.46  E-value=0.0025  Score=45.17  Aligned_cols=112  Identities=14%  Similarity=0.036  Sum_probs=80.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChh---HHHHHHHHHHHhccCChHHHHHHHHhccc-----CC----hh
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEF---TIVRILTAYMYCKCGDVEKAQRVLRKMLR-----KD----KF  106 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~---t~~~li~~~~~~~~g~~~~a~~~~~~m~~-----~~----~~  106 (153)
                      +...+..+.+.|++++|..++++..+.. ..|+..   .|...+..+ |...|++++|+..|++..+     .+    ..
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~  156 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAY-VLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHH-HTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHH-HHcccCHHHHHHHHHHHHHHhcccccHHHHHH
Confidence            4445778889999999999999998743 233322   122223443 6788899999999999853     13    33


Q ss_pred             hHHHHHHHHHhcCCCC--------------C---CCCCH-hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          107 TWTAMIVGLAISDPFP--------------T---IRPDE-VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       107 ~~~~li~~~~~~~~~~--------------~---~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .|+.+...|...|.++              .   ..|.. .++..+...|.+.|++++|.+.++
T Consensus       157 ~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~  220 (293)
T 3u3w_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVN  220 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            6888888898888777              1   12222 468888899999999999998764

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.43  E-value=0.00029  Score=43.04  Aligned_cols=81  Identities=14%  Similarity=0.162  Sum_probs=60.3

Q ss_pred             hcCChHHHHHHHHhCCC-----C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHhccCCh
Q 035927           18 NRGQVDIARQYFAQMPE-----R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMYCKCGDV   90 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~~-----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~g~~   90 (153)
                      ..|++++|...|++..+     | +...|..+-..+.+.|++++|...+++..+..  |+ ...+..+-.+  |.+.|++
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~--~~~~g~~   77 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF--PNHQALRVFYAMV--LYNLGRY   77 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH--HHHHTCH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHHH--HHHcCCH
Confidence            46788888888888753     2 45678889999999999999999999998753  43 4445444444  7999999


Q ss_pred             HHHHHHHHhccc
Q 035927           91 EKAQRVLRKMLR  102 (153)
Q Consensus        91 ~~a~~~~~~m~~  102 (153)
                      ++|+..|++..+
T Consensus        78 ~~A~~~~~~al~   89 (117)
T 3k9i_A           78 EQGVELLLKIIA   89 (117)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999864

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.41  E-value=0.0006  Score=52.68  Aligned_cols=122  Identities=10%  Similarity=-0.053  Sum_probs=82.4

Q ss_pred             HHHhcCChHHHHHHHHhCCC-------C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC---CCCCC----hhHHH
Q 035927           15 GYINRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS---NIRPD----EFTIV   76 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~----~~t~~   76 (153)
                      .+-..|++++|..++++...       +    ...+++.|...|...|++++|+.++++.++-   -+.|+    ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            35578999999988877641       2    4578999999999999999999999987542   12333    34556


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCCH-hHHHHHHHHHhcCCchhHhhhhc
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPDE-VTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .+-..  |...|++++|+.++++..+.-..+             +..-.|+. .+.+.+-.++...|.+++|..+|
T Consensus       398 nLa~~--~~~~G~~~eA~~~~~~Al~i~~~~-------------lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~  458 (490)
T 3n71_A          398 RAGLT--NWHAGHIEVGHGMICKAYAILLVT-------------HGPSHPITKDLEAMRMQTEMELRMFRQNEFMY  458 (490)
T ss_dssp             HHHHH--HHHTTCHHHHHHHHHHHHHHHHHH-------------TCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH--HHHCCCHHHHHHHHHHHHHHHHHH-------------hCCCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66665  799999999999999875320000             00012333 34555556666777777776655

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=97.36  E-value=0.00042  Score=48.22  Aligned_cols=110  Identities=10%  Similarity=0.024  Sum_probs=81.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCCC--C----CHHHHHHHHHHHHh--------cCChHHHHHHHHHHhhCCCCCC
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMPE--R----DYVLWTAMIDGYLR--------VNRFREALTLFPEMQTSNIRPD   71 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~----~~~~~~~li~~~~~--------~~~~~~a~~~~~~m~~~~~~p~   71 (153)
                      ...+..+..++.+.|++++|...|++..+  |    ....+..+-..+.+        .|++++|...|++..+..  |+
T Consensus        52 ~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~  129 (261)
T 3qky_A           52 ADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PN  129 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TT
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cC
Confidence            45678888999999999999999999863  3    24567777778888        899999999999998653  43


Q ss_pred             h-hHHH----------------HHHHHHHHhccCChHHHHHHHHhccc--CC----hhhHHHHHHHHHhc
Q 035927           72 E-FTIV----------------RILTAYMYCKCGDVEKAQRVLRKMLR--KD----KFTWTAMIVGLAIS  118 (153)
Q Consensus        72 ~-~t~~----------------~li~~~~~~~~g~~~~a~~~~~~m~~--~~----~~~~~~li~~~~~~  118 (153)
                      . ....                ..+..+ |.+.|++++|+..|+++.+  |+    ...+..+..+|...
T Consensus       130 ~~~~~~a~~~~~~~~~~~~~~~~~la~~-~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~  198 (261)
T 3qky_A          130 HELVDDATQKIRELRAKLARKQYEAARL-YERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAY  198 (261)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHH-HHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHh
Confidence            2 2221                222332 7999999999999999864  32    34666777777655

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.35  E-value=0.0078  Score=45.78  Aligned_cols=14  Identities=14%  Similarity=-0.009  Sum_probs=6.2

Q ss_pred             cCChHHHHHHHHhc
Q 035927           87 CGDVEKAQRVLRKM  100 (153)
Q Consensus        87 ~g~~~~a~~~~~~m  100 (153)
                      .++.++|.+.|++.
T Consensus       200 ~~~~~~A~~~~~~a  213 (490)
T 2xm6_A          200 ERNDAISAQWYRKS  213 (490)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH
Confidence            34444444444443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.34  E-value=0.00074  Score=43.53  Aligned_cols=84  Identities=10%  Similarity=0.111  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhC-------CC---------CCCh-hHHHHHHHHHHHhccCChHHHHHHHHh
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTS-------NI---------RPDE-FTIVRILTAYMYCKCGDVEKAQRVLRK   99 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-------~~---------~p~~-~t~~~li~~~~~~~~g~~~~a~~~~~~   99 (153)
                      ...+...-..+.+.|++++|...|....+.       .-         .|.. ..|..+-.+  |.+.|++++|+..+++
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~--~~~~~~~~~A~~~~~~   88 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQC--YLNIGDLHEAEETSSE   88 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHH--HHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHH--HHhcCcHHHHHHHHHH
Confidence            456777888889999999999999998764       00         2222 344444444  7999999999999999


Q ss_pred             cccC---ChhhHHHHHHHHHhcCCCC
Q 035927          100 MLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus       100 m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      ..+-   +...|..+..++...|.++
T Consensus        89 al~~~p~~~~a~~~~g~~~~~~g~~~  114 (162)
T 3rkv_A           89 VLKREETNEKALFRRAKARIAAWKLD  114 (162)
T ss_dssp             HHHHSTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHhcCCcchHHHHHHHHHHHHHhcHH
Confidence            8653   3333444444444444333

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.33  E-value=0.0081  Score=43.07  Aligned_cols=99  Identities=12%  Similarity=-0.085  Sum_probs=71.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCCC-C----HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPER-D----YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~~-~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      |+....-.+-..+.+.+++++|+..|+...+. +    ...+.-+-.++.+.|++++|+..|++.......|....=..+
T Consensus       133 p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~  212 (282)
T 4f3v_A          133 SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAW  212 (282)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHH
T ss_pred             CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHH
Confidence            43335455566899999999999999876543 2    336777788889999999999999998855443542221111


Q ss_pred             HHHHHHhccCChHHHHHHHHhccc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      -.+..+.+.|+.++|..+|+++.+
T Consensus       213 ~~glaL~~lGr~deA~~~l~~a~a  236 (282)
T 4f3v_A          213 YLAMARRSQGNESAAVALLEWLQT  236 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            111127999999999999999964

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=97.31  E-value=0.0017  Score=47.38  Aligned_cols=95  Identities=11%  Similarity=0.021  Sum_probs=75.2

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC--------------hhHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD--------------EFTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~--------------~~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      +...|..+-..+.+.|++++|...|++..+..-...              ...+..+-.+  |.+.|++++|++.+++..
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~--~~~~g~~~~A~~~~~~al  223 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMC--HLKLQAFSAAIESCNKAL  223 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHH--HHHcCCHHHHHHHHHHHH
Confidence            456788899999999999999999999987532111              3566666665  799999999999999997


Q ss_pred             cCChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          102 RKDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       102 ~~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      +.+                    +-+...|..+-.+|...|++++|.+.|+
T Consensus       224 ~~~--------------------p~~~~a~~~lg~~~~~~g~~~~A~~~~~  254 (336)
T 1p5q_A          224 ELD--------------------SNNEKGLSRRGEAHLAVNDFELARADFQ  254 (336)
T ss_dssp             HHC--------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HhC--------------------CCcHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            642                    1256778888889999999999988764

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=97.30  E-value=0.011  Score=44.93  Aligned_cols=108  Identities=9%  Similarity=0.031  Sum_probs=57.4

Q ss_pred             chhHHHHHHHHHHh----cCChHHHHHHHHhCCC-CCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChhHH
Q 035927            5 DVISWTDIVSGYIN----RGQVDIARQYFAQMPE-RDYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus         5 d~~~~~~li~~~~~----~g~~~~a~~l~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      |...+..+-..|..    .+++++|...|++..+ .+...+..|-..|..    .+++++|...|++..+.|   +...+
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~  114 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQ  114 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            34444555555555    5666666666665542 355555556666665    566666666666665544   23333


Q ss_pred             HHHHHHHHHhc----cCChHHHHHHHHhcccC-ChhhHHHHHHHHHh
Q 035927           76 VRILTAYMYCK----CGDVEKAQRVLRKMLRK-DKFTWTAMIVGLAI  117 (153)
Q Consensus        76 ~~li~~~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~  117 (153)
                      ..+-..  |..    .+++++|.+.|++..+. +...+..+...|..
T Consensus       115 ~~Lg~~--y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~  159 (490)
T 2xm6_A          115 QNLGVM--YHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFE  159 (490)
T ss_dssp             HHHHHH--HHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHH--HHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            333333  344    55666666666665443 34444444444443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.30  E-value=0.00013  Score=44.65  Aligned_cols=80  Identities=14%  Similarity=0.107  Sum_probs=49.9

Q ss_pred             hcCChHHHHHHHHHHhhCCC-CCC-hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC
Q 035927           49 RVNRFREALTLFPEMQTSNI-RPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP  126 (153)
Q Consensus        49 ~~~~~~~a~~~~~~m~~~~~-~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p  126 (153)
                      ..|++++|+..|++..+.+. .|+ ...+..+-..  |.+.|++++|++.|++..+.+                     |
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~--~~~~~~~~~A~~~~~~al~~~---------------------p   58 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGST--FRTLGEYRKAEAVLANGVKQF---------------------P   58 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC---------------------T
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHhC---------------------C
Confidence            35789999999999988642 143 3444444444  799999999999999997532                     2


Q ss_pred             -CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          127 -DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       127 -~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                       +...+..+..++.+.|++++|.+.|
T Consensus        59 ~~~~~~~~l~~~~~~~g~~~~A~~~~   84 (117)
T 3k9i_A           59 NHQALRVFYAMVLYNLGRYEQGVELL   84 (117)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHcCCHHHHHHHH
Confidence             2344555555555555555555544

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.26  E-value=0.0018  Score=47.29  Aligned_cols=94  Identities=14%  Similarity=0.105  Sum_probs=75.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CCCH------------------HHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ERDY------------------VLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~------------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      ..+..+-..+.+.|++++|...|++..  .|+.                  ..|..+-..+.+.|++++|+..++..++.
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  259 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLTE  259 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            446777788889999999999999865  2332                  27888888999999999999999999875


Q ss_pred             CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           67 NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        67 ~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      . +-+...+..+-.+  |...|++++|++.|++..+.
T Consensus       260 ~-p~~~~a~~~lg~a--~~~~g~~~~A~~~l~~al~l  293 (338)
T 2if4_A          260 E-EKNPKALFRRGKA--KAELGQMDSARDDFRKAQKY  293 (338)
T ss_dssp             C-TTCHHHHHHHHHH--HHTTTCHHHHHHHHHHTTC-
T ss_pred             C-CCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHH
Confidence            3 2356667766666  69999999999999999764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=97.25  E-value=0.0028  Score=46.14  Aligned_cols=125  Identities=6%  Similarity=-0.024  Sum_probs=71.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----CC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCC--CCh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----RD----YVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIR--PDE   72 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~--p~~   72 (153)
                      .++.+-..+...|++++|...+++...     .+    ..+++.+-..+...|++++|...+++..+.    +..  |..
T Consensus        55 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~  134 (373)
T 1hz4_A           55 ATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMH  134 (373)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHH
Confidence            355556667777888877777776542     11    123555666667778888888777776542    221  222


Q ss_pred             h-HHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC--CHhHHHHHHHHHhcCCchhHhhh
Q 035927           73 F-TIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP--DEVTYVGVLSACTHNGNETFVIN  149 (153)
Q Consensus        73 ~-t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p--~~~t~~~ll~~~~~~g~~~~a~~  149 (153)
                      . .+..+-..  |...|++++|...+++..+...                 ...|  ....+..+...+...|++++|.+
T Consensus       135 ~~~~~~la~~--~~~~g~~~~A~~~~~~al~~~~-----------------~~~~~~~~~~~~~la~~~~~~g~~~~A~~  195 (373)
T 1hz4_A          135 EFLVRIRAQL--LWAWARLDEAEASARSGIEVLS-----------------SYQPQQQLQCLAMLIQCSLARGDLDNARS  195 (373)
T ss_dssp             HHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHTT-----------------TSCGGGGHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHH--HHHhcCHHHHHHHHHHHHHHhh-----------------ccCcHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            2 22323333  5777888888888777643100                 0111  12445566666667777777766


Q ss_pred             hc
Q 035927          150 SC  151 (153)
Q Consensus       150 ~~  151 (153)
                      .+
T Consensus       196 ~l  197 (373)
T 1hz4_A          196 QL  197 (373)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.24  E-value=0.0035  Score=35.66  Aligned_cols=57  Identities=18%  Similarity=0.488  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      .+..+-..+.+.|++++|...|++..   ..+...+..+-..+.+.|++++|...+++..
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~   70 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKAL   70 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            34444444444444444444444432   1133344444444444444444444444443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=97.21  E-value=0.0013  Score=43.39  Aligned_cols=105  Identities=13%  Similarity=0.059  Sum_probs=73.1

Q ss_pred             HHhcCChHHHHH---HHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhh----CCCCCC-hhHHHHHHHHHHHhcc
Q 035927           16 YINRGQVDIARQ---YFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQT----SNIRPD-EFTIVRILTAYMYCKC   87 (153)
Q Consensus        16 ~~~~g~~~~a~~---l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~p~-~~t~~~li~~~~~~~~   87 (153)
                      ....|++++|.+   ++..-+......+..+-..+...|++++|...+++..+    .+..|. ...+..+-..  |...
T Consensus         2 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~--~~~~   79 (203)
T 3gw4_A            2 AFEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMV--ERMA   79 (203)
T ss_dssp             -----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--HHHT
T ss_pred             ccccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH--HHHc
Confidence            346799999999   76664445678899999999999999999999998865    233332 3344444444  7999


Q ss_pred             CChHHHHHHHHhccc-----C-C----hhhHHHHHHHHHhcCCCC
Q 035927           88 GDVEKAQRVLRKMLR-----K-D----KFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        88 g~~~~a~~~~~~m~~-----~-~----~~~~~~li~~~~~~~~~~  122 (153)
                      |++++|.+.+++..+     + +    ...+..+...+...|.++
T Consensus        80 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~  124 (203)
T 3gw4_A           80 GNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLA  124 (203)
T ss_dssp             TCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             CCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHH
Confidence            999999999988743     1 2    345677777777777766

>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=97.19  E-value=0.0037  Score=50.21  Aligned_cols=145  Identities=11%  Similarity=0.076  Sum_probs=98.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC-------------CC------------HHHHHHHHHHHHhcCChHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE-------------RD------------YVLWTAMIDGYLRVNRFREALT   58 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~-------------~~------------~~~~~~li~~~~~~~~~~~a~~   58 (153)
                      .+...|-..+...-+.|++++|..+|++...             |+            ...|...++..-+.|+++.|..
T Consensus       376 ~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~  455 (679)
T 4e6h_A          376 NSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRK  455 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHH
Confidence            4555677888888889999999999998763             21            2358888888778899999999


Q ss_pred             HHHHHhhC-C-CCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC----------C
Q 035927           59 LFPEMQTS-N-IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP----------T  123 (153)
Q Consensus        59 ~~~~m~~~-~-~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~----------~  123 (153)
                      +|...++. + ..+......+.+.   +...++.+.|.++|+...+.   +...|...+.-....+..+          .
T Consensus       456 vf~~A~~~~~~~~~~lyi~~A~lE---~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~  532 (679)
T 4e6h_A          456 IFGKCRRLKKLVTPDIYLENAYIE---YHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSID  532 (679)
T ss_dssp             HHHHHHHTGGGSCTHHHHHHHHHH---HTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHhcCCCChHHHHHHHHHH---HHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            99999876 3 2233332223332   22335589999999988652   5556666666555555444          2


Q ss_pred             CCC----CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          124 IRP----DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       124 ~~p----~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ..|    ....|...+..-.+.|+.+.+.++.
T Consensus       533 ~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~  564 (679)
T 4e6h_A          533 KISDSHLLKMIFQKVIFFESKVGSLNSVRTLE  564 (679)
T ss_dssp             TSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            234    2356777777777889888887764

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=97.19  E-value=0.0042  Score=44.44  Aligned_cols=94  Identities=10%  Similarity=-0.006  Sum_probs=57.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHhCC-------CC--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-C
Q 035927            6 VISWTDIVSGYINRGQVDIARQYFAQMP-------ER--DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-D   71 (153)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~a~~l~~~m~-------~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~   71 (153)
                      ..+|+.+...|.+.|++++|...|++..       .+  -..+++.+-..|.+ |++++|+..+++..+.    |-.+ .
T Consensus        76 a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~  154 (307)
T 2ifu_A           76 AKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQA  154 (307)
T ss_dssp             HHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHH
Confidence            4567777777777777766666555432       12  35667777777766 7777777777766532    1111 1


Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..++..+-..  |.+.|++++|+..|++..+
T Consensus       155 ~~~~~~lg~~--~~~~g~~~~A~~~~~~al~  183 (307)
T 2ifu_A          155 AELIGKASRL--LVRQQKFDEAAASLQKEKS  183 (307)
T ss_dssp             HHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence            2344455554  5777777777777777643

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.19  E-value=0.0031  Score=41.38  Aligned_cols=94  Identities=15%  Similarity=0.064  Sum_probs=73.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC--CC-------------HHHHHHHHHHHHhcCChHHHHHHHHHHhhC-----
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE--RD-------------YVLWTAMIDGYLRVNRFREALTLFPEMQTS-----   66 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~-------------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-----   66 (153)
                      ..+...-..+.+.|++++|...|++..+  |+             ...|+.+-.++.+.|++++|+..++..++.     
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            3466677788999999999999998763  32             238999999999999999999999998874     


Q ss_pred             CCCCCh-hHH----HHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           67 NIRPDE-FTI----VRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        67 ~~~p~~-~t~----~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .+.||. ..|    .-.-.+  +...|++++|+..|++..+
T Consensus        92 e~~pd~~~A~~~~~~~rG~a--L~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALA--LDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHhHHHH--HHHCCCHHHHHHHHHHHHh
Confidence            225643 344    344444  6999999999999999854

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=97.17  E-value=0.0072  Score=40.66  Aligned_cols=93  Identities=11%  Similarity=0.158  Sum_probs=69.3

Q ss_pred             HHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhcc
Q 035927           12 IVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKC   87 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~   87 (153)
                      +-..+.+.|++++|...|++..  .| +...|..+-..+...|++++|...|++..+..  | +...+..+-..  |...
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~--~~~~  135 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE--ADNLAANIFLGNY--YYLT  135 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH--HHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHH--HHHH
Confidence            8889999999999999999886  34 78899999999999999999999999998753  5 45555555554  3444


Q ss_pred             C--ChHHHHHHHHhcccCChhhH
Q 035927           88 G--DVEKAQRVLRKMLRKDKFTW  108 (153)
Q Consensus        88 g--~~~~a~~~~~~m~~~~~~~~  108 (153)
                      |  +.+.+...++....++...|
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~  158 (208)
T 3urz_A          136 AEQEKKKLETDYKKLSSPTKMQY  158 (208)
T ss_dssp             HHHHHHHHHHHHC---CCCHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCchhH
Confidence            3  45567777777777665443

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=97.13  E-value=0.0034  Score=42.52  Aligned_cols=122  Identities=8%  Similarity=0.001  Sum_probs=88.7

Q ss_pred             HHHHHHhCC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC----ChHHHHHHHHh
Q 035927           25 ARQYFAQMP-ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG----DVEKAQRVLRK   99 (153)
Q Consensus        25 a~~l~~~m~-~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g----~~~~a~~~~~~   99 (153)
                      |.+.|.+.. ..+...+..|-..+...+++++|...|++..+.|   +...+..+-..  |.. +    +.++|.+.|++
T Consensus         5 A~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~--y~~-~g~~~~~~~A~~~~~~   78 (212)
T 3rjv_A            5 PGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQL--KIR-NPQQADYPQARQLAEK   78 (212)
T ss_dssp             TTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHH--TTS-STTSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHH--HHc-CCCCCCHHHHHHHHHH
Confidence            444444443 3477888888889999999999999999998876   44555555554  566 6    89999999999


Q ss_pred             cccC-ChhhHHHHHHHHHh----cCCCC----------CCCCC---HhHHHHHHHHHhc----CCchhHhhhhcc
Q 035927          100 MLRK-DKFTWTAMIVGLAI----SDPFP----------TIRPD---EVTYVGVLSACTH----NGNETFVINSCN  152 (153)
Q Consensus       100 m~~~-~~~~~~~li~~~~~----~~~~~----------~~~p~---~~t~~~ll~~~~~----~g~~~~a~~~~~  152 (153)
                      ..++ +...+..+-..|..    .++++          ...|.   ...+..|-..|..    .++.++|++.|+
T Consensus        79 A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~  153 (212)
T 3rjv_A           79 AVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFK  153 (212)
T ss_dssp             HHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            8766 67777777777765    33333          44453   6777788888877    778999988764

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.02  E-value=0.0038  Score=36.95  Aligned_cols=62  Identities=19%  Similarity=0.195  Sum_probs=30.9

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      +...|..+-..+.+.|++++|...|++..+..  | +...|..+-.+  |.+.|++++|.+.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~--~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKL--YERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHH--HHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHH--HHHcCCHHHHHHHHHHHH
Confidence            34445555555555555555555555555432  2 22233333333  455555555555555553

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.98  E-value=0.012  Score=43.47  Aligned_cols=127  Identities=11%  Similarity=0.071  Sum_probs=84.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----CC---HHHHHHHHHHHH-hcCChHHHHHHHHHHhh----CCCCCC-hh
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----RD---YVLWTAMIDGYL-RVNRFREALTLFPEMQT----SNIRPD-EF   73 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~~---~~~~~~li~~~~-~~~~~~~a~~~~~~m~~----~~~~p~-~~   73 (153)
                      .+..+...|.+.|++++|.+.+.+..+     ++   .......+..+. ..|+.++|..++.....    .+..+. ..
T Consensus        57 al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  136 (434)
T 4b4t_Q           57 SILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHS  136 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHH
Confidence            477889999999999999999998863     11   122333333333 45889999999988753    333343 34


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ++..+...  |...|++++|..+++.......              .. .-+| ....+..+...|...|++++|..++
T Consensus       137 ~~~~la~~--~~~~g~~~~A~~~l~~~~~~~~--------------~~-~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~  198 (434)
T 4b4t_Q          137 LSIKLATL--HYQKKQYKDSLALINDLLREFK--------------KL-DDKPSLVDVHLLESKVYHKLRNLAKSKASL  198 (434)
T ss_dssp             HHHHHHHH--HHHHTCHHHHHHHHHHHHHHHT--------------TS-SCSTHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHH--HHHccChHHHHHHHHHHHHHHH--------------hc-ccchhHHHHHHHHHHHHHHhCcHHHHHHHH
Confidence            45555555  7999999999999998743100              00 0112 2356777778888888888887765

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.96  E-value=0.011  Score=33.49  Aligned_cols=77  Identities=16%  Similarity=0.216  Sum_probs=56.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMI  112 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li  112 (153)
                      +...|..+-..+.+.|++++|...+++..+.. +.+...+..+-..  |.+.|++++|.+.|++..+  | +...+..+.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~--~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~   84 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA--YYKQGDYDEAIEYYQKALELDPNNAEAKQNLG   84 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH--HHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence            45678888888999999999999999998753 2245555555555  7999999999999999864  3 344444444


Q ss_pred             HHH
Q 035927          113 VGL  115 (153)
Q Consensus       113 ~~~  115 (153)
                      ..+
T Consensus        85 ~~~   87 (91)
T 1na3_A           85 NAK   87 (91)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=96.90  E-value=0.0061  Score=38.02  Aligned_cols=93  Identities=16%  Similarity=0.253  Sum_probs=70.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCCC-h
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRPD-E   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p~-~   72 (153)
                      .++..+...+...|++++|...+++..+     +    ....+..+-..+...|++++|...+++..+.    +..+. .
T Consensus        50 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  129 (164)
T 3ro3_A           50 IAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEG  129 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHH
Confidence            3688888999999999999999988652     1    2457888888888999999999999988643    22222 2


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      ..+..+-..  |...|++++|.+.+++..
T Consensus       130 ~~~~~la~~--~~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A          130 RACWSLGNA--YTALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHHHHHHH--HHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--HHHccCHHHHHHHHHHHH
Confidence            344444444  789999999999998764

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.89  E-value=0.008  Score=35.51  Aligned_cols=78  Identities=12%  Similarity=0.126  Sum_probs=60.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPDEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~t~~~li   79 (153)
                      -+...+..+-..+.+.|++++|...|++..+  | +...|..+-..+.+.|++++|...+++..+.. -.++......+-
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~l~   84 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLSELQ   84 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHHHHH
Confidence            3566789999999999999999999999863  3 67789999999999999999999999887532 224444444444


Q ss_pred             HH
Q 035927           80 TA   81 (153)
Q Consensus        80 ~~   81 (153)
                      ..
T Consensus        85 ~~   86 (100)
T 3ma5_A           85 DA   86 (100)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.86  E-value=0.0023  Score=49.45  Aligned_cols=95  Identities=6%  Similarity=-0.123  Sum_probs=74.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC----------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh---CCCCC--
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT---SNIRP--   70 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p--   70 (153)
                      .+++.|..+|...|++++|..++++...          | ...+++.|-..|...|++++|+.++++..+   .-+.|  
T Consensus       352 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~H  431 (490)
T 3n71_A          352 RLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSH  431 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTS
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            4599999999999999999998888652          2 567899999999999999999999998853   11234  


Q ss_pred             -ChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           71 -DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        71 -~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                       ++.....++.-+ +...+..++|+.++.++.+
T Consensus       432 p~~~~~~~~l~~~-~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          432 PITKDLEAMRMQT-EMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH
Confidence             344444455554 7788899999999999864

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=96.86  E-value=0.0043  Score=43.92  Aligned_cols=114  Identities=8%  Similarity=-0.044  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhC--------CCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCC-----
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQM--------PER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPD-----   71 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m--------~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~-----   71 (153)
                      ..+..+...+...|++++|...+.+.        ... ...+|+.+-..|...|++++|+..+++..+. ...|+     
T Consensus       116 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~  195 (293)
T 2qfc_A          116 QWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFD  195 (293)
T ss_dssp             HHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccch
Confidence            44455666777777777777766542        233 3447777777777777777777777776521 01111     


Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhcccC---------ChhhHHHHHHHHHhcCCCC
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---------DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---------~~~~~~~li~~~~~~~~~~  122 (153)
                      ..++..+-..  |.+.|++++|++.+++..+-         -..+|..+...|.+.|.++
T Consensus       196 ~~~~~nlg~~--y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~  253 (293)
T 2qfc_A          196 VKVRYNHAKA--LYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEE  253 (293)
T ss_dssp             HHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCH
T ss_pred             HHHHHhHHHH--HHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcH
Confidence            1344444444  57777777777777765321         1445666666666666554

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=96.75  E-value=0.0082  Score=45.63  Aligned_cols=109  Identities=9%  Similarity=0.064  Sum_probs=81.8

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC----------------hhHHHHHHHHHHHhccCChHHHHHHHHh
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD----------------EFTIVRILTAYMYCKCGDVEKAQRVLRK   99 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~----------------~~t~~~li~~~~~~~~g~~~~a~~~~~~   99 (153)
                      ....|..+-..+.+.|++++|...|++..+..  |+                ...|..+-.+  |.+.|++++|+..+++
T Consensus       267 ~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~--~~~~g~~~~A~~~~~~  342 (457)
T 1kt0_A          267 QAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMC--YLKLREYTKAVECCDK  342 (457)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHH--HHHhcCHHHHHHHHHH
Confidence            45578888899999999999999999998642  32                3555555555  7999999999999999


Q ss_pred             ccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCCH-hHHHHHHHHHhcCCchhHhh
Q 035927          100 MLR--K-DKFTWTAMIVGLAISDPFP----------TIRPDE-VTYVGVLSACTHNGNETFVI  148 (153)
Q Consensus       100 m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~~-~t~~~ll~~~~~~g~~~~a~  148 (153)
                      ..+  | +...|..+..+|...+.++          .+.|+. ..+..+-..+.+.|+.+++.
T Consensus       343 al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          343 ALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             HHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            864  3 6777888888888887777          556644 55777777777777777664

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.75  E-value=0.0097  Score=35.74  Aligned_cols=75  Identities=13%  Similarity=0.093  Sum_probs=53.6

Q ss_pred             HHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcc
Q 035927           25 ARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        25 a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      |...|++..   ..+...|..+-..+.+.|++++|...+++..+.. +.+...+..+-..  |.+.|++++|...|++..
T Consensus         4 a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~--~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            4 ITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKT--LQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHH--HHHcCCHHHHHHHHHHHH
Confidence            444444442   2367788888888888999999999998887653 2234555555555  688999999999998875


Q ss_pred             c
Q 035927          102 R  102 (153)
Q Consensus       102 ~  102 (153)
                      +
T Consensus        81 ~   81 (115)
T 2kat_A           81 A   81 (115)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.75  E-value=0.0068  Score=36.46  Aligned_cols=63  Identities=11%  Similarity=0.045  Sum_probs=54.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTS   66 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~   66 (153)
                      .+...+..+...+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|...|+...+.
T Consensus        17 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   82 (115)
T 2kat_A           17 DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAA   82 (115)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            456778899999999999999999999875  23 6778999999999999999999999988753

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.74  E-value=0.0073  Score=45.79  Aligned_cols=89  Identities=9%  Similarity=0.053  Sum_probs=67.8

Q ss_pred             HHHHHHhcCChHHHHHHHHhCCC-------C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC---CCCC----Chh
Q 035927           12 IVSGYINRGQVDIARQYFAQMPE-------R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS---NIRP----DEF   73 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p----~~~   73 (153)
                      .+..+.+.|++++|..++++...       +    ...+++.|...|...|++++|+.++++.+.-   -+.|    -..
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            35567788999999999986642       2    4568999999999999999999999988642   1223    234


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +++.+-..  |...|++++|+.++++..+
T Consensus       373 ~l~nLa~~--~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKL--QLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--HHhcCCHHHHHHHHHHHHH
Confidence            45555555  7999999999999998753

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=96.73  E-value=0.0097  Score=44.07  Aligned_cols=93  Identities=9%  Similarity=0.061  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhC--------------CCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTS--------------NIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..|..+-..+.+.|++++|+..|++.++.              ...| +...|..+-.+  |.+.|++++|++.+++..+
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~--~~~~g~~~~A~~~~~~al~  301 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGAC--KLKMSDWQGAVDSCLEALE  301 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHH--HHhccCHHHHHHHHHHHHH
Confidence            45788888899999999999999988761              1223 33455555554  7999999999999999987


Q ss_pred             CChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          103 KDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       103 ~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+                    +-+...|..+-.+|.+.|++++|.+.|+
T Consensus       302 ~~--------------------p~~~~a~~~lg~~~~~~g~~~eA~~~l~  331 (370)
T 1ihg_A          302 ID--------------------PSNTKALYRRAQGWQGLKEYDQALADLK  331 (370)
T ss_dssp             TC--------------------TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hC--------------------chhHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            53                    1246678888888899999999887764

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=96.71  E-value=0.085  Score=38.14  Aligned_cols=145  Identities=6%  Similarity=-0.017  Sum_probs=107.0

Q ss_pred             chhHHHHHHHHH----Hhc---CChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChH--HHHHHHHHHhhCCCCCCh
Q 035927            5 DVISWTDIVSGY----INR---GQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFR--EALTLFPEMQTSNIRPDE   72 (153)
Q Consensus         5 d~~~~~~li~~~----~~~---g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~--~a~~~~~~m~~~~~~p~~   72 (153)
                      +..+|+---..+    .+.   +++++++.+++++.+   .|..+|+----.+.+.|.++  ++++.++.+.+.+. -|-
T Consensus       102 ~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~  180 (306)
T 3dra_A          102 NYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNN  180 (306)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCH
T ss_pred             cHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCH
Confidence            334455555555    555   789999999999973   37777777777777778887  99999999998653 456


Q ss_pred             hHHHHHHHHHHHhccCC------hHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC-----------CC----CCCH
Q 035927           73 FTIVRILTAYMYCKCGD------VEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP-----------TI----RPDE  128 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~------~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~-----------~~----~p~~  128 (153)
                      ..|+---..  +.+.|+      ++++++.+++..+  | |...|+.+-..+.+.|...           ..    ..+.
T Consensus       181 sAW~~R~~l--l~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~  258 (306)
T 3dra_A          181 SAWSHRFFL--LFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSS  258 (306)
T ss_dssp             HHHHHHHHH--HHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCH
T ss_pred             HHHHHHHHH--HHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCH
Confidence            666655444  355565      8889999888754  3 8899999888887776543           11    2355


Q ss_pred             hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          129 VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       129 ~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+..+...+.+.|+.++|.++|+
T Consensus       259 ~al~~la~~~~~~~~~~~A~~~~~  282 (306)
T 3dra_A          259 FALETLAKIYTQQKKYNESRTVYD  282 (306)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCHHHHHHHHH
Confidence            778888899999999999999875

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=96.66  E-value=0.017  Score=37.79  Aligned_cols=99  Identities=14%  Similarity=0.077  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC-C-----Chh-----HHHHHHHHHHHhccCChHHHHHHHHhcccCChh
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSNIR-P-----DEF-----TIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKF  106 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~-p-----~~~-----t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~  106 (153)
                      ..+...-..+.+.|++++|...|+...+-.-. |     +..     .|.-.-.+  +.+.|++++|+..+++..+-   
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~a--l~~Lgr~~eAl~~~~kAL~l---   86 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEA--LAGLRSFDEALHSADKALHY---   86 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHH---
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHH--HHHCCCHHHHHHHHHHHHHh---
Confidence            34556666777899999999999999764211 1     222     55555554  79999999999999988653   


Q ss_pred             hHHHHHHHHHhcCCCCCCCCCH-hHH----HHHHHHHhcCCchhHhhhhcc
Q 035927          107 TWTAMIVGLAISDPFPTIRPDE-VTY----VGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       107 ~~~~li~~~~~~~~~~~~~p~~-~t~----~~ll~~~~~~g~~~~a~~~~~  152 (153)
                       ||       +.+   .+.|+. ..|    ...-.++...|++++|++.|+
T Consensus        87 -~n-------~~~---e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~  126 (159)
T 2hr2_A           87 -FN-------RRG---ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFK  126 (159)
T ss_dssp             -HH-------HHC---CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             -hh-------ccc---cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHH
Confidence             00       000   234654 567    888899999999999998875

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=96.59  E-value=0.0049  Score=47.22  Aligned_cols=93  Identities=14%  Similarity=0.105  Sum_probs=68.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li   79 (153)
                      .+...|..+..++.+.|++++|.+.+++..+   .+...|..+-..+.+.|++++|+..+++..+..  | +...+..+-
T Consensus        38 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~--p~~~~~~~~l~  115 (477)
T 1wao_1           38 SNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAALRDYETVVKVK--PHDKDAKMKYQ  115 (477)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTCTTHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHH
Confidence            3467799999999999999999999998752   367889999999999999999999999998653  3 222333332


Q ss_pred             HHHHHhccCChHHHHHHHH
Q 035927           80 TAYMYCKCGDVEKAQRVLR   98 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~   98 (153)
                      .+..+.+.|++++|++.++
T Consensus       116 ~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1          116 ECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHHHHhcccc
Confidence            2211478899999999998

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=96.46  E-value=0.016  Score=39.26  Aligned_cols=64  Identities=20%  Similarity=0.273  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCC-hhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ...+-.+...+.+.|++++|...|+++.+.. -.|. ...+..+..+  |.+.|++++|+..|+++.+
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~--~~~~~~~~~A~~~~~~~l~   69 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYA--YYKNADLPLAQAAIDRFIR   69 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHH--HHhcCCHHHHHHHHHHHHH
Confidence            3455566677889999999999999998642 1222 2345555555  7999999999999999965

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.45  E-value=0.0061  Score=46.34  Aligned_cols=82  Identities=9%  Similarity=0.023  Sum_probs=62.6

Q ss_pred             cCChHHHHHHHHhCC-------CC----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC---CCCC----ChhHHHHHHH
Q 035927           19 RGQVDIARQYFAQMP-------ER----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS---NIRP----DEFTIVRILT   80 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~-------~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p----~~~t~~~li~   80 (153)
                      .|++++|..++++..       .+    ...+++.|...|...|++++|+.++++.++-   -+.|    -..+++-+-.
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            467888888887653       22    4578999999999999999999999998642   1223    3345666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .  |...|++++|+.++++..+
T Consensus       391 ~--~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          391 L--YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             H--HHHTTCHHHHHHHHHHHHH
T ss_pred             H--HHhccCHHHHHHHHHHHHH
Confidence            5  7999999999999998754

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=96.41  E-value=0.068  Score=40.42  Aligned_cols=105  Identities=11%  Similarity=0.021  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHhcC---ChHHHHHHHHhCCC---CCHHHHHHHHHHHHhc----CChHHHHHHHHHHhhCCCCCChhHHH
Q 035927            7 ISWTDIVSGYINRG---QVDIARQYFAQMPE---RDYVLWTAMIDGYLRV----NRFREALTLFPEMQTSNIRPDEFTIV   76 (153)
Q Consensus         7 ~~~~~li~~~~~~g---~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~----~~~~~a~~~~~~m~~~~~~p~~~t~~   76 (153)
                      ..+..|-..|.+.|   +.++|.+.|++..+   ++...+..|-..|.+.    +++++|...|+... .|.   ...+.
T Consensus       177 ~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g~---~~a~~  252 (452)
T 3e4b_A          177 ICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PGY---PASWV  252 (452)
T ss_dssp             THHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GGS---THHHH
T ss_pred             HHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CCC---HHHHH
Confidence            35556666666666   66666666665532   2334334555555443    56677777776665 322   22222


Q ss_pred             HHHHHHHH--hccCChHHHHHHHHhcccC-ChhhHHHHHHHHH
Q 035927           77 RILTAYMY--CKCGDVEKAQRVLRKMLRK-DKFTWTAMIVGLA  116 (153)
Q Consensus        77 ~li~~~~~--~~~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~  116 (153)
                      .+-..+ |  ...++.++|.+.|++..+. +...+..+-..|.
T Consensus       253 ~Lg~~~-~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~  294 (452)
T 3e4b_A          253 SLAQLL-YDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY  294 (452)
T ss_dssp             HHHHHH-HHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHH-HhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            222221 2  4566777777777776554 4555555555554

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.36  E-value=0.013  Score=42.65  Aligned_cols=82  Identities=11%  Similarity=0.010  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChh------------------HHHHHHHHHHHhccCChHHHHHHHH
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEF------------------TIVRILTAYMYCKCGDVEKAQRVLR   98 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~------------------t~~~li~~~~~~~~g~~~~a~~~~~   98 (153)
                      ...+..+-..+.+.|++++|...|++..+.  .|+..                  .|..+-.+  |.+.|++++|+..++
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~--~~~~g~~~~A~~~~~  254 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAAC--LIKLKRYDEAIGHCN  254 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHH--HHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHH--HHHcCCHHHHHHHHH
Confidence            445777778888899999999999998764  34433                  44444444  799999999999999


Q ss_pred             hccc--C-ChhhHHHHHHHHHhcCCCC
Q 035927           99 KMLR--K-DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        99 ~m~~--~-~~~~~~~li~~~~~~~~~~  122 (153)
                      +..+  | +...|..+..+|...+.++
T Consensus       255 ~al~~~p~~~~a~~~lg~a~~~~g~~~  281 (338)
T 2if4_A          255 IVLTEEEKNPKALFRRGKAKAELGQMD  281 (338)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            9864  3 5666666666776666665

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.05  E-value=0.029  Score=42.49  Aligned_cols=94  Identities=15%  Similarity=0.122  Sum_probs=66.9

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhC--C-CCCC----hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHH
Q 035927           44 IDGYLRVNRFREALTLFPEMQTS--N-IRPD----EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLA  116 (153)
Q Consensus        44 i~~~~~~~~~~~a~~~~~~m~~~--~-~~p~----~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  116 (153)
                      +..+.+.|++++|+.++++.++.  . +.|+    ..+++.+...  |...|++++|+.++++..+.-..          
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~--y~~~g~~~eA~~~~~~~L~i~~~----------  361 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDA--CINLGLLEEALFYGTRTMEPYRI----------  361 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHHHH----------
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHH--HHhhccHHHHHHHHHHHHHhHHH----------
Confidence            45566789999999999999753  2 3343    3567777777  68999999999999988542000          


Q ss_pred             hcCCCCCCCCCH-hHHHHHHHHHhcCCchhHhhhhcc
Q 035927          117 ISDPFPTIRPDE-VTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       117 ~~~~~~~~~p~~-~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                         .+..-.|+. .+++.|-..|...|++++|..+|+
T Consensus       362 ---~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~  395 (429)
T 3qwp_A          362 ---FFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLR  395 (429)
T ss_dssp             ---HSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ---HcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence               000123554 668889999999999999988764

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=95.95  E-value=0.21  Score=37.72  Aligned_cols=141  Identities=11%  Similarity=0.043  Sum_probs=93.5

Q ss_pred             hHHHHHHHHHHhcC----ChHHHHHHHHhCCCCCHHHHHHHHHHHHhcC---ChHHHHHHHHHHhhCCCCCChhHHHHHH
Q 035927            7 ISWTDIVSGYINRG----QVDIARQYFAQMPERDYVLWTAMIDGYLRVN---RFREALTLFPEMQTSNIRPDEFTIVRIL   79 (153)
Q Consensus         7 ~~~~~li~~~~~~g----~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~t~~~li   79 (153)
                      ..+..+-..|...+    ..+.+..++......+...+..|-..|.+.|   +.++|+..|+...+.|. ++...+..+-
T Consensus       142 ~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg  220 (452)
T 3e4b_A          142 EAGLAQVLLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVA  220 (452)
T ss_dssp             THHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHH
Confidence            34455555666666    3455666666666666668889999999999   89999999999988874 4444333344


Q ss_pred             HHHHHhcc----CChHHHHHHHHhcccC-ChhhHHHHHHHHH---hcCCCC--------CCC-CCHhHHHHHHHHHhcCC
Q 035927           80 TAYMYCKC----GDVEKAQRVLRKMLRK-DKFTWTAMIVGLA---ISDPFP--------TIR-PDEVTYVGVLSACTHNG  142 (153)
Q Consensus        80 ~~~~~~~~----g~~~~a~~~~~~m~~~-~~~~~~~li~~~~---~~~~~~--------~~~-p~~~t~~~ll~~~~~~g  142 (153)
                      ..  |...    ++.++|.+.|++.. + +...+..+-..|.   ..++++        ... -+...+..+-..|. .|
T Consensus       221 ~~--y~~g~~~~~d~~~A~~~~~~aa-~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G  296 (452)
T 3e4b_A          221 RV--LGDATLGTPDEKTAQALLEKIA-PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EG  296 (452)
T ss_dssp             HH--HTCGGGSSCCHHHHHHHHHHHG-GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HC
T ss_pred             HH--HhCCCCCCCCHHHHHHHHHHHc-CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cC
Confidence            43  4444    68999999999998 6 6677777766633   223332        011 14555656666665 45


Q ss_pred             -----chhHhhhhcc
Q 035927          143 -----NETFVINSCN  152 (153)
Q Consensus       143 -----~~~~a~~~~~  152 (153)
                           +.++|.+.|+
T Consensus       297 ~g~~~d~~~A~~~~~  311 (452)
T 3e4b_A          297 KWVPADAKAAEAHFE  311 (452)
T ss_dssp             SSSCCCHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHH
Confidence                 8888888775

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.75  E-value=0.015  Score=42.96  Aligned_cols=123  Identities=7%  Similarity=-0.029  Sum_probs=83.4

Q ss_pred             HHHHHhcCChHHHHHHHHhCCC--C------------------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC-CCCCC
Q 035927           13 VSGYINRGQVDIARQYFAQMPE--R------------------DYVLWTAMIDGYLRVNRFREALTLFPEMQTS-NIRPD   71 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~--~------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~~~p~   71 (153)
                      ...+.+.|++++|.+.|.+..+  +                  ...++..+...|.+.|++++|.+.+...... +-.++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            3567789999999999988742  1                  1134788999999999999999999988642 11122


Q ss_pred             ---hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-HhHHHHHHHHHhcCCchhHh
Q 035927           72 ---EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-EVTYVGVLSACTHNGNETFV  147 (153)
Q Consensus        72 ---~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~a  147 (153)
                         .......++.+ +...|+.+.|.++++...+....           .    +..+. ..++..+...+...|++++|
T Consensus        91 ~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~-----------~----~~~~~~~~~~~~la~~~~~~g~~~~A  154 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKF-EQVPDSLDDQIFVCEKSIEFAKR-----------E----KRVFLKHSLSIKLATLHYQKKQYKDS  154 (434)
T ss_dssp             HHHHHHHHHHHHHH-CSCCSCHHHHHHHHHHHHHHHHH-----------S----SCCSSHHHHHHHHHHHHHHHTCHHHH
T ss_pred             hHHHHHHHHHHHHH-HhCCCCHHHHHHHHHHHHHHHHH-----------h----CccHHHHHHHHHHHHHHHHccChHHH
Confidence               22344455553 66788999999998887432000           0    11222 35567777788888888888


Q ss_pred             hhhc
Q 035927          148 INSC  151 (153)
Q Consensus       148 ~~~~  151 (153)
                      .+++
T Consensus       155 ~~~l  158 (434)
T 4b4t_Q          155 LALI  158 (434)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7664

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.73  E-value=0.039  Score=31.86  Aligned_cols=51  Identities=20%  Similarity=0.300  Sum_probs=22.4

Q ss_pred             HHHhcCChHHHHHHHHhCC--CC-CHH-HHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927           15 GYINRGQVDIARQYFAQMP--ER-DYV-LWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~--~~-~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      .+.+.|++++|...|++..  .| +.. .|..+-..+.+.|++++|...|++..+
T Consensus         9 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            9 ELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3344444444444444433  11 233 444444444444444444444444443

>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=95.69  E-value=0.019  Score=43.64  Aligned_cols=71  Identities=8%  Similarity=-0.007  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC----------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh---CCCCCCh
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE----------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT---SNIRPDE   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~---~~~~p~~   72 (153)
                      .+++.|..+|...|++++|..++++...          | ...+++.|-..|...|++++|+.++++..+   .-+.||.
T Consensus       341 ~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~H  420 (433)
T 3qww_A          341 HMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIAIMEVAHGKDH  420 (433)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTC
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHcCCCC
Confidence            5699999999999999999999988752          2 557899999999999999999999998854   2234555


Q ss_pred             hHHHH
Q 035927           73 FTIVR   77 (153)
Q Consensus        73 ~t~~~   77 (153)
                      .....
T Consensus       421 p~~~~  425 (433)
T 3qww_A          421 PYISE  425 (433)
T ss_dssp             HHHHH
T ss_pred             hHHHH
Confidence            44443

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=95.16  E-value=0.16  Score=31.82  Aligned_cols=89  Identities=12%  Similarity=-0.041  Sum_probs=53.2

Q ss_pred             CChHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc----cCChHHHH
Q 035927           20 GQVDIARQYFAQMPER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK----CGDVEKAQ   94 (153)
Q Consensus        20 g~~~~a~~l~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~----~g~~~~a~   94 (153)
                      +++++|.+.|++..+. +....  |-..|...+..++|...|++..+.|   +...+..+-..  |.+    .++.++|.
T Consensus         9 ~d~~~A~~~~~~aa~~g~~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~--y~~G~g~~~d~~~A~   81 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNEMFGC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDF--YENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTCTTHH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHH--HHHCSSSCCCHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCHhhh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHH--HHcCCCCCccHHHHH
Confidence            4567777777766422 33333  5555555567777888888887764   34444444444  455    67888888


Q ss_pred             HHHHhcccC-ChhhHHHHHHHH
Q 035927           95 RVLRKMLRK-DKFTWTAMIVGL  115 (153)
Q Consensus        95 ~~~~~m~~~-~~~~~~~li~~~  115 (153)
                      +.|++..+. +...+..+-..|
T Consensus        82 ~~~~~Aa~~g~~~a~~~Lg~~y  103 (138)
T 1klx_A           82 QYYSKACGLNDQDGCLILGYKQ  103 (138)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHH
Confidence            888887654 344444443333

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.05  E-value=0.27  Score=39.32  Aligned_cols=78  Identities=13%  Similarity=0.011  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCG   88 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g   88 (153)
                      ...++..+.+.|..++|.++.+.   + .    .-.....+.|++++|+++.+.+      .+...|..+-..+  .+.|
T Consensus       632 ~~~~~~~l~~~~~~~~a~~~~~~---~-~----~~f~~~l~~~~~~~A~~~~~~~------~~~~~W~~la~~a--l~~~  695 (814)
T 3mkq_A          632 LTKIARFLEGQEYYEEALNISPD---Q-D----QKFELALKVGQLTLARDLLTDE------SAEMKWRALGDAS--LQRF  695 (814)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHCCC---H-H----HHHHHHHHHTCHHHHHHHHTTC------CCHHHHHHHHHHH--HHTT
T ss_pred             HHHHHHHHHhCCChHHheecCCC---c-c----hheehhhhcCCHHHHHHHHHhh------CcHhHHHHHHHHH--HHcC
Confidence            36667777777777777766531   1 1    1123345667777777775433      3456777777774  7777


Q ss_pred             ChHHHHHHHHhccc
Q 035927           89 DVEKAQRVLRKMLR  102 (153)
Q Consensus        89 ~~~~a~~~~~~m~~  102 (153)
                      +++.|++.|.++..
T Consensus       696 ~~~~A~~~y~~~~d  709 (814)
T 3mkq_A          696 NFKLAIEAFTNAHD  709 (814)
T ss_dssp             CHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHccC
Confidence            77777777777644

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.02  E-value=0.088  Score=30.26  Aligned_cols=57  Identities=21%  Similarity=0.227  Sum_probs=43.9

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhCCCCCCh-h-HHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           43 MIDGYLRVNRFREALTLFPEMQTSNIRPDE-F-TIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        43 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~-t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ....+.+.|++++|...++...+..  |+. . .+..+-..  |.+.|++++|.+.|++..+.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~lg~~--~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE--PVGKDEAYYLMGNA--YRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--SSTHHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHH--HHHcCCHHHHHHHHHHHHhc
Confidence            3456678899999999999998753  543 4 45554444  79999999999999998653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.62  E-value=0.3  Score=28.53  Aligned_cols=44  Identities=14%  Similarity=0.146  Sum_probs=19.8

Q ss_pred             hHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927           22 VDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus        22 ~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      .++|..++++..+  | +......+-..+.+.|++++|...|+.+.+
T Consensus        25 ~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A           25 TDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444444444431  1 333444444444444555555555555443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=94.40  E-value=0.68  Score=35.54  Aligned_cols=107  Identities=14%  Similarity=0.269  Sum_probs=70.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC--CHHHHH--HHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER--DYVLWT--AMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTA   81 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~--~~~~~~--~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~   81 (153)
                      .+|...+...-+.+.++.|..+|++...|  +...|.  +.+.... .++.+.|..+|+...+.-  |+ ...+...++.
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~~~~yid~  363 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHHHHHHHHH
Confidence            45777777777788899999999988433  223333  2333222 236999999999987642  33 3445566665


Q ss_pred             HHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcC
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISD  119 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~  119 (153)
                        ..+.|+.+.|..+|+...+ ....|...+.-=...|
T Consensus       364 --e~~~~~~~~aR~l~er~~k-~~~lw~~~~~fE~~~G  398 (493)
T 2uy1_A          364 --LLRIGDEENARALFKRLEK-TSRMWDSMIEYEFMVG  398 (493)
T ss_dssp             --HHHHTCHHHHHHHHHHSCC-BHHHHHHHHHHHHHHS
T ss_pred             --HHHcCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHCC
Confidence              5788999999999999854 3445555544333333

>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=94.31  E-value=0.52  Score=37.88  Aligned_cols=113  Identities=8%  Similarity=0.022  Sum_probs=79.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCCC----CHHHHHHHHHHHHhc-CChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPER----DYVLWTAMIDGYLRV-NRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~~----~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      .+|...+....+.|.++.|..+|.+..+.    ....|-.....-.+. ++.+.|..+|+...+. ++-+...+...++.
T Consensus       435 ~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~f  513 (679)
T 4e6h_A          435 YVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDF  513 (679)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHH
Confidence            36888888888899999999999988532    222332222222233 4589999999999876 43455666677775


Q ss_pred             HHHhccCChHHHHHHHHhcccCC------hhhHHHHHHHHHhcCCCC
Q 035927           82 YMYCKCGDVEKAQRVLRKMLRKD------KFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~~~------~~~~~~li~~~~~~~~~~  122 (153)
                        ....|+.+.|..+|+...+..      ...|...+.-=.+.|..+
T Consensus       514 --e~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~  558 (679)
T 4e6h_A          514 --LIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLN  558 (679)
T ss_dssp             --HHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSH
T ss_pred             --HHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHH
Confidence              578899999999999986542      356777766666667665

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=94.28  E-value=0.068  Score=34.92  Aligned_cols=82  Identities=20%  Similarity=0.138  Sum_probs=61.1

Q ss_pred             HhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCCh----------HHHHHHHHHHhhCCCCC-ChhHHHHHHHHH
Q 035927           17 INRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRF----------REALTLFPEMQTSNIRP-DEFTIVRILTAY   82 (153)
Q Consensus        17 ~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~----------~~a~~~~~~m~~~~~~p-~~~t~~~li~~~   82 (153)
                      .+.+++++|...+++..  .| +...|+.+-..+.+.+++          ++|+..|++.++.  .| +...|..+-.+ 
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~a-   89 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNA-   89 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHH-
T ss_pred             HHHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHH-
Confidence            45667888888888775  34 777888888888777654          5999999988875  34 45566666666 


Q ss_pred             HHhcc-----------CChHHHHHHHHhccc
Q 035927           83 MYCKC-----------GDVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~-----------g~~~~a~~~~~~m~~  102 (153)
                       |...           |++++|++.|++..+
T Consensus        90 -y~~lg~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           90 -YTSFAFLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             -HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHHhcccCcchhhhhccHHHHHHHHHHHHH
Confidence             4554           589999999999865

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.16  E-value=0.38  Score=28.06  Aligned_cols=65  Identities=9%  Similarity=0.007  Sum_probs=49.6

Q ss_pred             CHHHHHHHHHHHHhcCC---hHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           36 DYVLWTAMIDGYLRVNR---FREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~---~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      |...+..+-.++...++   .++|..++++.++.  .|+...-..++.-. +.+.|++++|...|+++.+.
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~-~~~~g~y~~Ai~~w~~~l~~   72 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIAND-HFISFRFQEAIDTWVLLLDS   72 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHH-HHHTTCHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHhh
Confidence            56667777777765544   79999999999875  46655555555553 79999999999999999764

>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=94.05  E-value=1.3  Score=32.65  Aligned_cols=145  Identities=8%  Similarity=-0.032  Sum_probs=90.2

Q ss_pred             chhHHHHHHHHHHhc-C-ChHHHHHHHHhCCCC---CHHHHHHHHHHHHhcCChH--------HHHHHHHHHhhCCCCCC
Q 035927            5 DVISWTDIVSGYINR-G-QVDIARQYFAQMPER---DYVLWTAMIDGYLRVNRFR--------EALTLFPEMQTSNIRPD   71 (153)
Q Consensus         5 d~~~~~~li~~~~~~-g-~~~~a~~l~~~m~~~---~~~~~~~li~~~~~~~~~~--------~a~~~~~~m~~~~~~p~   71 (153)
                      +..+|+-.--.+.+. + ++++++++++++.+.   |..+|+----.+.+.|.++        ++++.++++.+... -|
T Consensus       122 ny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N  200 (349)
T 3q7a_A          122 SYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RN  200 (349)
T ss_dssp             CHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TC
T ss_pred             cHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CC
Confidence            334455555555555 5 677777777777643   4455554333333334444        77777777776542 35


Q ss_pred             hhHHHHHHHHHHHhccCC-------hHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCC--------------------
Q 035927           72 EFTIVRILTAYMYCKCGD-------VEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPF--------------------  121 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~-------~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~--------------------  121 (153)
                      ...|+---..  +.+.++       ++++++.+++..+  | |...|+.+-..+.+.+.-                    
T Consensus       201 ~SAW~~R~~l--L~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (349)
T 3q7a_A          201 NSAWGWRWYL--RVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDI  278 (349)
T ss_dssp             HHHHHHHHHH--HTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC-------
T ss_pred             HHHHHHHHHH--HHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccc
Confidence            5666655554  466665       5778888777653  3 788888766666554432                    


Q ss_pred             C----------CC-------CCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          122 P----------TI-------RPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       122 ~----------~~-------~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .          +.       .+...-+..+...|...|+.++|.++|+
T Consensus       279 ~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~  326 (349)
T 3q7a_A          279 ETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFE  326 (349)
T ss_dssp             -------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            1          11       2456677888888999999999988774

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=94.01  E-value=0.76  Score=36.69  Aligned_cols=50  Identities=22%  Similarity=0.355  Sum_probs=38.3

Q ss_pred             HHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927           13 VSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      .....+.|+++.|.++...+  .+...|..+-..+.+.++++.|...|..+.
T Consensus       659 f~~~l~~~~~~~A~~~~~~~--~~~~~W~~la~~al~~~~~~~A~~~y~~~~  708 (814)
T 3mkq_A          659 FELALKVGQLTLARDLLTDE--SAEMKWRALGDASLQRFNFKLAIEAFTNAH  708 (814)
T ss_dssp             HHHHHHHTCHHHHHHHHTTC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             eehhhhcCCHHHHHHHHHhh--CcHhHHHHHHHHHHHcCCHHHHHHHHHHcc
Confidence            34456778888888888766  456788888888888888888888887764

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.73  E-value=0.58  Score=27.58  Aligned_cols=61  Identities=7%  Similarity=-0.006  Sum_probs=40.1

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC----------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE----------RDYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      +..-|-.|-..+.+.|+++.|...|+...+          +....+..+..++.+.|++++|+..+++..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            344566777777777777777777766431          1345566666777777777777777777664

>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=0.3  Score=36.35  Aligned_cols=71  Identities=20%  Similarity=0.240  Sum_probs=51.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh-----CCCCCChhHHHHHHH
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQT-----SNIRPDEFTIVRILT   80 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t~~~li~   80 (153)
                      ..++.++...|+.+++......+.  .| +...|..+|.++.+.|+..+|+..|+...+     -|+.|+..+-...-.
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~~~  253 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNER  253 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            345666777888888887777665  23 677888888888888888888888888744     388887665444433

>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=93.57  E-value=0.57  Score=34.85  Aligned_cols=63  Identities=10%  Similarity=-0.025  Sum_probs=47.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +..+|..+.-.+...|++++|...+++....+  |+...|..+-..  +.-.|++++|.+.|++...
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~--~~~~G~~~eA~e~~~~Alr  338 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKV--YEMKGMNREAADAYLTAFN  338 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHH--HHHCCCHHHHHHHHHHHHh
Confidence            55667777666667799999999999998875  776666333333  7889999999999988754

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=92.97  E-value=0.0015  Score=50.59  Aligned_cols=109  Identities=16%  Similarity=0.201  Sum_probs=51.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMPE--RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      |...|..+|.+..+.|.+++-...+...++  ++...=+.|+-+|++.+++.+-++++       -.|++.-...+-+=|
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~IDteLi~ayAk~~rL~elEefl-------~~~N~A~iq~VGDrc  154 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI-------NGPNNAHIQQVGDRC  154 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTTTHHHHHHHHTSCSSSTTTSTT-------SCCSSSCTHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccHHHHHHHHHhhCcHHHHHHHH-------cCCCcccHHHHHHHH
Confidence            344455555555555555555555544442  24444445555555555544322211       124444444444443


Q ss_pred             HHhccCChHHHHHHHHhcc------------------------cCChhhHHHHHHHHHhcCCCC
Q 035927           83 MYCKCGDVEKAQRVLRKML------------------------RKDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~------------------------~~~~~~~~~li~~~~~~~~~~  122 (153)
                        ...|..+.|.-+|..+.                        ..++.||.-.-.+|...+.|.
T Consensus       155 --f~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~Efr  216 (624)
T 3lvg_A          155 --YDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFR  216 (624)
T ss_dssp             --HHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTT
T ss_pred             --HHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHH
Confidence              44444444444444441                        125566666666666665554

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=92.75  E-value=0.69  Score=34.40  Aligned_cols=75  Identities=17%  Similarity=0.100  Sum_probs=58.7

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+..+|..+...+...|++++|...+++..  .|+...|..+-..+.-.|++++|.+.+++....  .|...||...=+
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~~~~~  351 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLYWIEN  351 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHHHHhC
Confidence            456667777777777899999999999987  567777767777777899999999999988765  477777665443

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=92.36  E-value=0.28  Score=31.97  Aligned_cols=76  Identities=16%  Similarity=0.128  Sum_probs=60.7

Q ss_pred             CchhHHHHHHHHHHhcCCh----------HHHHHHHHhCC--CC-CHHHHHHHHHHHHhcC-----------ChHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQV----------DIARQYFAQMP--ER-DYVLWTAMIDGYLRVN-----------RFREALTL   59 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~----------~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~-----------~~~~a~~~   59 (153)
                      .+...|+.+-.++.+.+++          ++|+..|++..  .| +...|..+-.+|.+.|           ++++|.+.
T Consensus        34 ~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~  113 (158)
T 1zu2_A           34 LDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQF  113 (158)
T ss_dssp             TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHH
Confidence            4667788888888887765          59999998886  34 6778999999998764           89999999


Q ss_pred             HHHHhhCCCCCChhHHHHHHHH
Q 035927           60 FPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus        60 ~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      |++.++.  .|+...|...+..
T Consensus       114 ~~kAl~l--~P~~~~y~~al~~  133 (158)
T 1zu2_A          114 FQQAVDE--QPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHh--CCCCHHHHHHHHH
Confidence            9999874  6888888777775

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=92.03  E-value=2.5  Score=30.40  Aligned_cols=136  Identities=10%  Similarity=0.034  Sum_probs=83.0

Q ss_pred             HHHHHHHHHHhcC--ChHHHHHHHHhCCC--C-CHHHHHHHHHHH----Hhc---CChHHHHHHHHHHhhCCCCCChhHH
Q 035927            8 SWTDIVSGYINRG--QVDIARQYFAQMPE--R-DYVLWTAMIDGY----LRV---NRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus         8 ~~~~li~~~~~~g--~~~~a~~l~~~m~~--~-~~~~~~~li~~~----~~~---~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      .|+.--..+...|  ++++++.+++.+..  | +..+|+.--..+    .+.   +++++++.+++.+.+.. +-+-..|
T Consensus        69 aWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~~~EL~~~~~~l~~~-pkny~aW  147 (306)
T 3dra_A           69 IWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDPYREFDILEAMLSSD-PKNHHVW  147 (306)
T ss_dssp             HHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCTHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence            3777777777777  78888888877752  3 445555443333    333   67788888888887643 2355555


Q ss_pred             HHHHHHHHHhccCChH--HHHHHHHhcccC---ChhhHHHHHHHHHhcCC------CC----------CCCC-CHhHHHH
Q 035927           76 VRILTAYMYCKCGDVE--KAQRVLRKMLRK---DKFTWTAMIVGLAISDP------FP----------TIRP-DEVTYVG  133 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~--~a~~~~~~m~~~---~~~~~~~li~~~~~~~~------~~----------~~~p-~~~t~~~  133 (153)
                      +---..  +.+.|+++  ++++.++++.+.   |-..|+..-..+...+.      ++          ...| |...|+.
T Consensus       148 ~~R~~v--l~~l~~~~~~~EL~~~~~~i~~d~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y  225 (306)
T 3dra_A          148 SYRKWL--VDTFDLHNDAKELSFVDKVIDTDLKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNY  225 (306)
T ss_dssp             HHHHHH--HHHTTCTTCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             HHHHHH--HHHhcccChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHH
Confidence            554444  36667777  888888888643   66677766555555443      22          2334 3455666


Q ss_pred             HHHHHhcCCchhH
Q 035927          134 VLSACTHNGNETF  146 (153)
Q Consensus       134 ll~~~~~~g~~~~  146 (153)
                      .-..+.+.|+...
T Consensus       226 ~~~ll~~~~~~~~  238 (306)
T 3dra_A          226 LLGIHERFDRSIT  238 (306)
T ss_dssp             HHHHHHHTTCCGG
T ss_pred             HHHHHHhcCCChH
Confidence            6666666666333

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.02  E-value=1.6  Score=28.09  Aligned_cols=82  Identities=13%  Similarity=0.017  Sum_probs=59.4

Q ss_pred             hcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHH
Q 035927           18 NRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVL   97 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~   97 (153)
                      .+|++....+.+..+. .+...+...++.+...|.-++-.+++.++.. +.+|+....-.+-.+  |.+.|+..++.+++
T Consensus        73 ~C~NlKrVi~C~~~~n-~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~A--y~Klg~~r~a~eLl  148 (172)
T 1wy6_A           73 KCQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANA--LRRVGDERDATTLL  148 (172)
T ss_dssp             GCSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHH--HHHTTCHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHH--HHHhcchhhHHHHH
Confidence            4577778888887774 3445567778888888888888888887644 446777777777777  68888888888888


Q ss_pred             HhcccC
Q 035927           98 RKMLRK  103 (153)
Q Consensus        98 ~~m~~~  103 (153)
                      .+.-++
T Consensus       149 ~~AC~k  154 (172)
T 1wy6_A          149 IEACKK  154 (172)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            877544

>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=91.75  E-value=1.5  Score=27.17  Aligned_cols=87  Identities=11%  Similarity=-0.040  Sum_probs=67.6

Q ss_pred             HHHHHHhcCChHHHHHHHHhCC-CCCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927           12 IVSGYINRGQVDIARQYFAQMP-ERDYVLWTAMIDGYLR----VNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~-~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      |-..|.+.+.+++|.+.|++-. ..+...+..|-..|.+    .+++++|...|+...+.|.   ...+..+-..  |..
T Consensus        31 lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~a~~~Lg~~--y~~  105 (138)
T 1klx_A           31 LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLND---QDGCLILGYK--QYA  105 (138)
T ss_dssp             HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHH--HHH
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHcCCC---HHHHHHHHHH--HHC
Confidence            5555666677888999998875 3477888888888887    7899999999999988764   4455555554  566


Q ss_pred             ----cCChHHHHHHHHhcccC
Q 035927           87 ----CGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        87 ----~g~~~~a~~~~~~m~~~  103 (153)
                          .++.++|.+.|++..+.
T Consensus       106 G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A          106 GKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             TSSSCCCHHHHHHHHHHHHHT
T ss_pred             CCCCCcCHHHHHHHHHHHHHC
Confidence                78999999999988654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=91.63  E-value=1.3  Score=34.04  Aligned_cols=60  Identities=12%  Similarity=0.094  Sum_probs=31.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      |...+....+.++++.|..+|+.. +.. +++...|-..... .+...++.+.|.++|+...+
T Consensus       289 w~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A~l-E~~~~~d~~~ar~ife~al~  348 (493)
T 2uy1_A          289 RINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCAFI-EYYATGSRATPYNIFSSGLL  348 (493)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHHHH-HHHHHCCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHHHH-HHHHCCChHHHHHHHHHHHH
Confidence            444444444556677777887777 221 1233333322222 12333467778888777654

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=90.96  E-value=0.9  Score=29.34  Aligned_cols=77  Identities=13%  Similarity=0.137  Sum_probs=50.6

Q ss_pred             HHHHHHHHhCC---CCCHHHHHHHHHHHHhcC---ChHHHHHHHHHHhhCCCCC---ChhHHHHHHHHHHHhccCChHHH
Q 035927           23 DIARQYFAQMP---ERDYVLWTAMIDGYLRVN---RFREALTLFPEMQTSNIRP---DEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        23 ~~a~~l~~~m~---~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p---~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      ..+.+-|.+-.   .++..+--.+--++++++   +++++..++++..+.+ .|   ....|+.-+.   |.+.|+.++|
T Consensus        15 ~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~---~~kl~~Y~~A   90 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVG---NYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHH---HHHTSCHHHH
T ss_pred             HHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHH---HHHccCHHHH
Confidence            34444444431   246666666666777877   6678888998887764 24   2334444443   5899999999


Q ss_pred             HHHHHhcccC
Q 035927           94 QRVLRKMLRK  103 (153)
Q Consensus        94 ~~~~~~m~~~  103 (153)
                      .+.++.+.+.
T Consensus        91 ~~y~~~lL~i  100 (152)
T 1pc2_A           91 LKYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhc
Confidence            9999988764

>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=90.87  E-value=1.2  Score=26.88  Aligned_cols=50  Identities=20%  Similarity=0.155  Sum_probs=40.5

Q ss_pred             ChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           52 RFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        52 ~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.=+...-++.+-...+.|+.....+.+++|  -|-+++..|.++|+.++.+
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAc--RRvND~alAVR~lE~iK~K   74 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRAC--RRLNDFASAVRILEVVKDK   74 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHH--HHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHH--HHhhhHHHHHHHHHHHHHH
Confidence            3345566666667778899999999999998  8999999999999998653

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=90.16  E-value=1.8  Score=25.36  Aligned_cols=64  Identities=11%  Similarity=-0.016  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhCC------CCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           37 YVLWTAMIDGYLRVNRFREALTLFPEMQTSN------IRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        37 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~------~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..-+..|-..+.+.+++..|..-++...+..      -.+....+..+..+  |.+.|+++.|...+++..+
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~--~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYA--VYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHH--HHHccCHHHHHHHHHHHHh
Confidence            3445677888889999999999998876531      12445566666666  7999999999999999854

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=89.45  E-value=3.2  Score=27.23  Aligned_cols=96  Identities=16%  Similarity=0.210  Sum_probs=67.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC-----CCC-------HHHHHHHHHHHHhcCChHHHHHHHHHHhhC--CC----
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP-----ERD-------YVLWTAMIDGYLRVNRFREALTLFPEMQTS--NI----   68 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~-----~~~-------~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~----   68 (153)
                      -++-.=+..+...|.++.|+-+.+.+.     .++       ..+..-+-+++...+++..|...|++.++.  .+    
T Consensus        21 ~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~  100 (167)
T 3ffl_A           21 MNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTS  100 (167)
T ss_dssp             CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC----
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            344555677888899999888877754     122       236677788888999999999999985321  00    


Q ss_pred             -----------------CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           69 -----------------RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        69 -----------------~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                                       .++..-..=-|.-| |.+.+++++|+.+++.++.+
T Consensus       101 s~~~~~~~~ss~p~s~~~~~e~Elkykia~C-~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A          101 KVRPSTGNSASTPQSQCLPSEIEVKYKLAEC-YTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             ----------------CCCCHHHHHHHHHHH-HHHTTCHHHHHHHHHTSCGG
T ss_pred             CccccccccCCCcccccccchHHHHHHHHHH-HHHHCCHHHHHHHHhcCCch
Confidence                             01112333446777 99999999999999999654

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=89.37  E-value=3.3  Score=27.39  Aligned_cols=50  Identities=16%  Similarity=0.242  Sum_probs=36.3

Q ss_pred             HHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 035927           13 VSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQ   64 (153)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~   64 (153)
                      .....+.|+++.|.++.+.+  .+...|..|-+...+.|+++-|..-|....
T Consensus        12 F~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~   61 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQH   61 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             HHHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhC
Confidence            44556778888888887766  466778888888888888777777776654

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=88.04  E-value=3.8  Score=26.36  Aligned_cols=65  Identities=17%  Similarity=0.106  Sum_probs=53.8

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhC-C--CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQM-P--ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR   69 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m-~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   69 (153)
                      +....+.-++.+...|+-++-.++...+ .  ++++...-.+-.+|-+.|+..+|.+++.+..+.|++
T Consensus        90 ~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           90 LNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            4455677788889999999999999884 3  457888888899999999999999999999888874

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=87.34  E-value=1.7  Score=28.01  Aligned_cols=75  Identities=7%  Similarity=0.075  Sum_probs=54.1

Q ss_pred             CCchhHHHHHHHHHHhcC---ChHHHHHHHHhCCC---C--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhH
Q 035927            3 NKDVISWTDIVSGYINRG---QVDIARQYFAQMPE---R--DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFT   74 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g---~~~~a~~l~~~m~~---~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t   74 (153)
                      +++..+.-.+--++++.+   ++++++.+++...+   |  +...+-.|--++.+.|++++|+..++..++.  .|+-.-
T Consensus        29 ~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i--eP~n~Q  106 (152)
T 1pc2_A           29 SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT--EPQNNQ  106 (152)
T ss_dssp             CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTTCHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCCHH
Confidence            367777777788889988   66799999988763   3  2344555566668999999999999999874  565444


Q ss_pred             HHHHH
Q 035927           75 IVRIL   79 (153)
Q Consensus        75 ~~~li   79 (153)
                      -..+.
T Consensus       107 A~~Lk  111 (152)
T 1pc2_A          107 AKELE  111 (152)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            33333

>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=87.30  E-value=3.3  Score=24.92  Aligned_cols=77  Identities=12%  Similarity=0.050  Sum_probs=47.3

Q ss_pred             ChHHHHHHHHhCC-CCCHHHHHHHHHH--HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHH
Q 035927           21 QVDIARQYFAQMP-ERDYVLWTAMIDG--YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVL   97 (153)
Q Consensus        21 ~~~~a~~l~~~m~-~~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~   97 (153)
                      .-++|.-+-+.+. +++ .-...||+.  +.+.|++++|+.+.+...    .||...|-++..    .|.|-.+++..-+
T Consensus        22 ~HqEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce----~rlGl~s~le~rL   92 (116)
T 2p58_C           22 YHEEANCIAEWLHLKGE-EEAVQLIRLSSLMNRGDYASALQQGNKLA----YPDLEPWLALCE----YRLGLGSALESRL   92 (116)
T ss_dssp             CHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHHHHTTSC----CGGGHHHHHHHH----HHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHH----HhcccHHHHHHHH
Confidence            3455555555554 223 444445443  446788888877765554    688887777765    5777777777777


Q ss_pred             HhcccCChh
Q 035927           98 RKMLRKDKF  106 (153)
Q Consensus        98 ~~m~~~~~~  106 (153)
                      ..+..++.+
T Consensus        93 ~~la~sg~p  101 (116)
T 2p58_C           93 NRLARSQDP  101 (116)
T ss_dssp             HHHTTCCCH
T ss_pred             HHHHhCCCH
Confidence            677655433

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=87.15  E-value=3.1  Score=25.02  Aligned_cols=76  Identities=13%  Similarity=-0.027  Sum_probs=45.4

Q ss_pred             ChHHHHHHHHhCC-CCCHHHHHHHHHH--HHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHH
Q 035927           21 QVDIARQYFAQMP-ERDYVLWTAMIDG--YLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVL   97 (153)
Q Consensus        21 ~~~~a~~l~~~m~-~~~~~~~~~li~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~   97 (153)
                      .-++|.-+-+.+. +++ .-...||+.  +.+.|++++|+.+.+...    .||...|-.+..    .|.|-.+++..-+
T Consensus        21 ~HqEA~tIAdwL~~~~~-~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c----~pdlepw~ALce----~rlGl~s~le~rL   91 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ-DEAARLIRISSLANQGRYQEALAFAHGNP----WPALEPWFALCE----WHLGLGAALDRRL   91 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHTTCHHHHHGGGTTCC----CGGGHHHHHHHH----HHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHcchhHHHHHHhcCCCC----CchHHHHHHHHH----HhcccHHHHHHHH
Confidence            3455555555544 223 444444443  446677887776655444    677777777765    5777777777777


Q ss_pred             HhcccCCh
Q 035927           98 RKMLRKDK  105 (153)
Q Consensus        98 ~~m~~~~~  105 (153)
                      ..+.+++.
T Consensus        92 ~~la~sg~   99 (115)
T 2uwj_G           92 AGLGGSSD   99 (115)
T ss_dssp             HHHHTCSS
T ss_pred             HHHHhCCC
Confidence            66655543

>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=87.02  E-value=1.9  Score=31.03  Aligned_cols=30  Identities=17%  Similarity=0.367  Sum_probs=14.5

Q ss_pred             CHHHHHHHHHHHHhc-----CChHHHHHHHHHHhh
Q 035927           36 DYVLWTAMIDGYLRV-----NRFREALTLFPEMQT   65 (153)
Q Consensus        36 ~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~   65 (153)
                      +...|..+...|.+.     |+.++|...|++.++
T Consensus       198 ~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~  232 (301)
T 3u64_A          198 EGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTR  232 (301)
T ss_dssp             HHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHH
Confidence            444444444444442     455555555555544

>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=86.88  E-value=4.2  Score=29.31  Aligned_cols=74  Identities=14%  Similarity=0.109  Sum_probs=60.1

Q ss_pred             hHHHHHHHHHHhc-----CChHHHHHHHHhCC--CC--CHHHHHHHHHHHHhc-CChHHHHHHHHHHhhCCCC--CChhH
Q 035927            7 ISWTDIVSGYINR-----GQVDIARQYFAQMP--ER--DYVLWTAMIDGYLRV-NRFREALTLFPEMQTSNIR--PDEFT   74 (153)
Q Consensus         7 ~~~~~li~~~~~~-----g~~~~a~~l~~~m~--~~--~~~~~~~li~~~~~~-~~~~~a~~~~~~m~~~~~~--p~~~t   74 (153)
                      ..|..+...|.+.     |+.++|.+.|++-.  .|  +..++...-+.+++. |+.+++...+++.++....  |+...
T Consensus       200 sA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~l  279 (301)
T 3u64_A          200 AVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKL  279 (301)
T ss_dssp             HHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHH
T ss_pred             HHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhH
Confidence            4688888889984     99999999999886  45  478888888988885 8999999999999988766  77665


Q ss_pred             HHHHHH
Q 035927           75 IVRILT   80 (153)
Q Consensus        75 ~~~li~   80 (153)
                      .|.+-+
T Consensus       280 an~~~q  285 (301)
T 3u64_A          280 LVILSQ  285 (301)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555544

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=85.97  E-value=6.2  Score=26.70  Aligned_cols=82  Identities=15%  Similarity=0.009  Sum_probs=54.2

Q ss_pred             HHHHHHHHhCC--CCCHHHHHHHHHHHHh--cCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHH
Q 035927           23 DIARQYFAQMP--ERDYVLWTAMIDGYLR--VNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVL   97 (153)
Q Consensus        23 ~~a~~l~~~m~--~~~~~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~   97 (153)
                      +++.+.|....  +.|..-....|...-.  .++..++.++|..|.+.|+.- -+..|...-..  +...|++++|.++|
T Consensus        61 Erc~~~F~~~~rYkND~RYLklWl~Ya~~~~~~~~~~p~~if~~L~~~~IG~~~AlfYe~wA~~--lE~~g~~~~A~~Vy  138 (202)
T 3esl_A           61 ERCLIYIQDMETYRNDPRFLKIWIWYINLFLSNNFHESENTFKYMFNKGIGTKLSLFYEEFSKL--LENAQFFLEAKVLL  138 (202)
T ss_dssp             HHHHHHHTTCGGGTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTSSTTBHHHHHHHHHH--HHHTTCHHHHHHHH
T ss_pred             HHHHHHhcccccccCCHHHHHHHHHHHHhhcccccCCHHHHHHHHHHCCCcHHHHHHHHHHHHH--HHHcCCHHHHHHHH
Confidence            44444454443  2355443333332222  555789999999999998865 44556666665  69999999999999


Q ss_pred             HhcccCChh
Q 035927           98 RKMLRKDKF  106 (153)
Q Consensus        98 ~~m~~~~~~  106 (153)
                      +.-++....
T Consensus       139 ~~GI~~~A~  147 (202)
T 3esl_A          139 ELGAENNCR  147 (202)
T ss_dssp             HHHHHTTCB
T ss_pred             HHHHHcCCc
Confidence            998765433

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=85.90  E-value=4.3  Score=30.09  Aligned_cols=60  Identities=15%  Similarity=0.150  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ...++..+...|+.++|...+....... +.+...+..+|.+  |.+.|+..+|++.|+.+.+
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~a--l~~~Gr~~~Al~~y~~~r~  233 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITA--YYLSDRQSDALGAYRRVKT  233 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHH--HHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHH
Confidence            3445666677899999999998887542 5688899999999  6999999999999999843

>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=85.31  E-value=5.4  Score=25.40  Aligned_cols=47  Identities=21%  Similarity=0.195  Sum_probs=39.6

Q ss_pred             HHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           55 EALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        55 ~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +...-++.+....+.|+.....+.+++|  -|-+++..|.++|+.++.+
T Consensus        71 ElrrglN~l~~~DlVPeP~Ii~AALrAc--RRvNDfalAVR~lE~vK~K  117 (152)
T 2y69_E           71 ELRKGMNTLVGYDLVPEPKIIDAALRAC--RRLNDFASAVRILEVVKDK  117 (152)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHH--HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHH--HHhhhHHHHHHHHHHHHHh
Confidence            4445555566778999999999999998  9999999999999999753

>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=85.25  E-value=12  Score=29.26  Aligned_cols=109  Identities=8%  Similarity=0.039  Sum_probs=84.4

Q ss_pred             hHHHHHHHHHHhcCC----------hHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcC--ChHHHHHHHHHHhhCCCCCC
Q 035927            7 ISWTDIVSGYINRGQ----------VDIARQYFAQMPE--R-DYVLWTAMIDGYLRVN--RFREALTLFPEMQTSNIRPD   71 (153)
Q Consensus         7 ~~~~~li~~~~~~g~----------~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~   71 (153)
                      ..|+---.++.+.|+          ++++.++++++.+  | +..+|+.---.+.+.+  +++++++.++.+.+... -+
T Consensus        64 taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d~-~N  142 (567)
T 1dce_A           64 TLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RN  142 (567)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TC
T ss_pred             HHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhcc-cc
Confidence            447766666666676          8999999999873  3 6777877777777778  67999999999998653 36


Q ss_pred             hhHHHHHHHHHHHhccC-ChHHHHHHHHhcccC---ChhhHHHHHHHHHhc
Q 035927           72 EFTIVRILTAYMYCKCG-DVEKAQRVLRKMLRK---DKFTWTAMIVGLAIS  118 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g-~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~  118 (153)
                      ...|+---..  +.+.| ..+++.+.++++.+.   |...|+.....+.+.
T Consensus       143 ~~aW~~R~~~--l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l  191 (567)
T 1dce_A          143 FHCWDYRRFV--AAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQL  191 (567)
T ss_dssp             HHHHHHHHHH--HHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHH--HHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhh
Confidence            6777665555  47778 899999999999764   788899888887774

>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=84.89  E-value=12  Score=29.16  Aligned_cols=118  Identities=8%  Similarity=-0.011  Sum_probs=81.4

Q ss_pred             CChHHHHHHHHhCCC--C-CHHHHHHHHHHHHhcCC----------hHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927           20 GQVDIARQYFAQMPE--R-DYVLWTAMIDGYLRVNR----------FREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus        20 g~~~~a~~l~~~m~~--~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      ..-++|.+.++++..  | +...|+.--..+.+.|+          ++++++.++.+.+..- =+...|..--..  +.+
T Consensus        43 ~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~p-K~y~aW~hR~w~--l~~  119 (567)
T 1dce_A           43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP-KSYGTWHHRCWL--LSR  119 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHH--HHT
T ss_pred             CCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHH--HHH
Confidence            345678999988863  4 56677765555555555          8999999999987542 255666655555  577


Q ss_pred             cC--ChHHHHHHHHhccc---CChhhHHHHHHHHHhcC-CCC----------CCCC-CHhHHHHHHHHHhc
Q 035927           87 CG--DVEKAQRVLRKMLR---KDKFTWTAMIVGLAISD-PFP----------TIRP-DEVTYVGVLSACTH  140 (153)
Q Consensus        87 ~g--~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~-~~~----------~~~p-~~~t~~~ll~~~~~  140 (153)
                      .|  +++++++.++++.+   .|...|+..--.+.+.+ ..+          ...| |...|+..-..+.+
T Consensus       120 l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~  190 (567)
T 1dce_A          120 LPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  190 (567)
T ss_dssp             CSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHh
Confidence            88  77999999999965   37888888777777766 322          3445 44556666655554

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.54  E-value=4.8  Score=24.20  Aligned_cols=60  Identities=15%  Similarity=0.128  Sum_probs=34.1

Q ss_pred             HHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHH
Q 035927           14 SGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIV   76 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~   76 (153)
                      ..+.+.|++++|..+.+.+.-||...|-+|-.  .+.|-.+++..-+.++..+| .|....|.
T Consensus        47 sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg-~p~~q~Fa  106 (115)
T 2uwj_G           47 SSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGGSS-DPALADFA  106 (115)
T ss_dssp             HHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHTCS-SHHHHHHH
T ss_pred             HHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC-CHHHHHHH
Confidence            45556666666666666666666666666655  35555555555554555554 24434443

>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=84.09  E-value=5.1  Score=24.13  Aligned_cols=52  Identities=21%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             HHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC
Q 035927           14 SGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN   67 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~   67 (153)
                      ..+.+.|++++|..+.+.+.-||...|-+|-.  .+.|-.+++..-+.++..+|
T Consensus        48 sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~sg   99 (116)
T 2p58_C           48 SSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLARSQ   99 (116)
T ss_dssp             HHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTTCC
T ss_pred             HHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHhCC
Confidence            34555566666666666666666666655544  34454444444444554444

>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=83.96  E-value=4.2  Score=26.39  Aligned_cols=97  Identities=16%  Similarity=0.222  Sum_probs=54.2

Q ss_pred             CCchhHHHHHHHHHHhcCCh------HHHHHHHHhCC---CCC-HHHHHHHHHHHHh------cCChHHHHHHHHHHhhC
Q 035927            3 NKDVISWTDIVSGYINRGQV------DIARQYFAQMP---ERD-YVLWTAMIDGYLR------VNRFREALTLFPEMQTS   66 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~------~~a~~l~~~m~---~~~-~~~~~~li~~~~~------~~~~~~a~~~~~~m~~~   66 (153)
                      +-|..+|=..+...-+.|++      ++..++|++.-   .|+ -..|..-|...++      .+++++|.++|+.+++.
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            45666777777777777777      66667666543   121 1222222222221      35777788888877764


Q ss_pred             CCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           67 NIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        67 ~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                       .  .....-.++.+=.=.+.|++..|.+++.+-..
T Consensus        90 -h--KkFAKiwi~~AqFEiRqgnl~kARkILg~AiG  122 (161)
T 4h7y_A           90 -C--KKFAFVHISFAQFELSQGNVKKSKQLLQKAVE  122 (161)
T ss_dssp             -C--TTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -h--HHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc
Confidence             2  22222222222123477788888888777655

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.38  E-value=5  Score=30.16  Aligned_cols=93  Identities=9%  Similarity=0.026  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC---CCCCChhHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS---NIRPDEFTIVRI   78 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---~~~p~~~t~~~l   78 (153)
                      +...+.+.|.+.|+++.|.+.+.++..      .....+-.+|+.+...+++..+...+.+....   +-.|+...--..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            456788899999999999999999973      24557888889999999999999999988543   222322211111


Q ss_pred             HHHHHHhccCChHHHHHHHHhc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKM  100 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m  100 (153)
                      -.+..+...+++..|-..|-..
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~  234 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDS  234 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHH
Confidence            1111245788899988888776

>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=83.29  E-value=11  Score=27.40  Aligned_cols=60  Identities=13%  Similarity=0.050  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHHhcCC--hHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhC
Q 035927            7 ISWTDIVSGYINRGQ--VDIARQYFAQMPE---RDYVLWTAMIDGYLRVNR-FREALTLFPEMQTS   66 (153)
Q Consensus         7 ~~~~~li~~~~~~g~--~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~   66 (153)
                      .+|+----.+.+.|+  ++++..+++++.+   .|..+|+----.+.+.|. ++++++.++.+.+.
T Consensus       109 ~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~  174 (331)
T 3dss_A          109 GTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITR  174 (331)
T ss_dssp             HHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence            334444444444442  4555555555542   244444444444444444 35555555555544

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=81.50  E-value=11  Score=30.87  Aligned_cols=120  Identities=15%  Similarity=0.128  Sum_probs=60.6

Q ss_pred             HHHHHHHHHhcCC-hHHHHHHHHhCCC--CCHH-HHH-HHHHHHHhcC-ChHHHHHHHHHHhhC------CCCC-ChhHH
Q 035927            9 WTDIVSGYINRGQ-VDIARQYFAQMPE--RDYV-LWT-AMIDGYLRVN-RFREALTLFPEMQTS------NIRP-DEFTI   75 (153)
Q Consensus         9 ~~~li~~~~~~g~-~~~a~~l~~~m~~--~~~~-~~~-~li~~~~~~~-~~~~a~~~~~~m~~~------~~~p-~~~t~   75 (153)
                      -..|+..+...|+ .+.|..+|+++..  |... .+. ++|..+.+.+ +--+|.+++.+..+.      ...+ +....
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~  330 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSA  330 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccccc
Confidence            3556666666666 5778888888864  3222 222 2333332322 122344444333211      1111 11111


Q ss_pred             ---H---HHHH--HHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-HhHHHHHHHHHhcCCchhH
Q 035927           76 ---V---RILT--AYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-EVTYVGVLSACTHNGNETF  146 (153)
Q Consensus        76 ---~---~li~--~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~  146 (153)
                         +   .|+.  +=.+...|+++-|+++-++...                     +.|+ -.||..|..+|.+.|++|.
T Consensus       331 ~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~---------------------~aPseF~tW~~La~vYi~l~d~e~  389 (754)
T 4gns_B          331 RLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE---------------------LALDSFESWYNLARCHIKKEEYEK  389 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---------------------HCSSCHHHHHHHHHHHHHTTCHHH
T ss_pred             cccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh---------------------cCchhhHHHHHHHHHHHHhccHHH
Confidence               0   1111  1023568899999998888754                     2233 3566666666666666666


Q ss_pred             hhh
Q 035927          147 VIN  149 (153)
Q Consensus       147 a~~  149 (153)
                      |+-
T Consensus       390 ALL  392 (754)
T 4gns_B          390 ALF  392 (754)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

---

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	153
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.81
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	98.68
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.53
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.31
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.29
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.27
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.21
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.13
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.12
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.11
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.01
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.92
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.87
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.86
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	97.83
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	97.79
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.79
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.78
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.63
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.59
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.57
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.53
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.35
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.34
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.32
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.27
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.24
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.23
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.12
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.12
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.05
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.03
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.88
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	96.88
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	96.74
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.68
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.68
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	96.64
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.54
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.06
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.7
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.47
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	95.34
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.25
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.08
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	94.66
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.85
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	93.52
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.0
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	90.27
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	88.18
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	86.35
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	85.01
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	83.71

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=6.9e-08  Score=68.31  Aligned_cols=145  Identities=10%  Similarity=0.028  Sum_probs=97.5

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTA   81 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~   81 (153)
                      +...|..+...+...|++++|...+.+..   ..+...+..+...+.+.|++++|...+++..+.. +-+..++..+...
T Consensus       202 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  280 (388)
T d1w3ba_         202 FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANA  280 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHH
T ss_pred             cHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34456677777777777777777777654   2355667777777777777777877777776542 1234455555555


Q ss_pred             HHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHh
Q 035927           82 YMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFV  147 (153)
Q Consensus        82 ~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a  147 (153)
                        |.+.|++++|++.++...+   .+...+..+...+...|.++          .+.|+ ...+..+...+.+.|++++|
T Consensus       281 --~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A  358 (388)
T d1w3ba_         281 --LKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEA  358 (388)
T ss_dssp             --HHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHH
T ss_pred             --HHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence              5777777777777776643   25566667777777766666          45565 45577777888888888888


Q ss_pred             hhhcc
Q 035927          148 INSCN  152 (153)
Q Consensus       148 ~~~~~  152 (153)
                      .+.|+
T Consensus       359 ~~~~~  363 (388)
T d1w3ba_         359 LMHYK  363 (388)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77663

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.68  E-value=9.4e-07  Score=62.28  Aligned_cols=137  Identities=12%  Similarity=0.144  Sum_probs=112.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC---CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP---ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      .+...+..+...+.+.|++++|...|++..   ..+..+|..+...+.+.|++++|.+.++...... +.+...+..+..
T Consensus       235 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  313 (388)
T d1w3ba_         235 NHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLAN  313 (388)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHH
Confidence            455678888899999999999999998864   3367889999999999999999999999887643 345566666666


Q ss_pred             HHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGN  143 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~  143 (153)
                      .  |.+.|++++|++.|++..+  | +...|..+...+...|.++          .+.|+ ...|..+...+.+.|+
T Consensus       314 ~--~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         314 I--KREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             H--HHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             H--HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            6  7999999999999999865  3 5778899999999999998          67786 5678888888877664

>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=98.53  E-value=1.1e-06  Score=61.49  Aligned_cols=146  Identities=12%  Similarity=0.129  Sum_probs=100.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC-------------
Q 035927            5 DVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI-------------   68 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~-------------   68 (153)
                      +...|..+...+...|++++|...|.+..  .| +...|..+...+...|++++|.+.++......-             
T Consensus        52 ~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  131 (323)
T d1fcha_          52 HMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGA  131 (323)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC------
T ss_pred             CHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccccccchhhHHHhccchHHHHHhhhhhh
Confidence            45567777788888888888888887764  23 566777777777788888877777776543210             


Q ss_pred             -------------------------------------CCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhH
Q 035927           69 -------------------------------------RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTW  108 (153)
Q Consensus        69 -------------------------------------~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~  108 (153)
                                                           .++...+..+-..  +.+.|++++|+..|++..+  | +...|
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~--~~~~~~~~~A~~~~~~al~~~p~~~~~~  209 (323)
T d1fcha_         132 GGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL--FNLSGEYDKAVDCFTAALSVRPNDYLLW  209 (323)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             hhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHH--HHHHHHHhhhhcccccccccccccccch
Confidence                                                 1122223333333  5778888888888888743  3 57778


Q ss_pred             HHHHHHHHhcCCCC----------CCCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          109 TAMIVGLAISDPFP----------TIRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       109 ~~li~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..+...+...|.++          .+.|+ ...|..+..+|.+.|++++|++.|+
T Consensus       210 ~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~  264 (323)
T d1fcha_         210 NKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFL  264 (323)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            88888888887777          44564 4567788888888888888887764

>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=98.31  E-value=1.3e-05  Score=56.14  Aligned_cols=147  Identities=12%  Similarity=0.102  Sum_probs=109.2

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHHhCCC--C-C-HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHH
Q 035927            3 NKDVISWTDIVSGYINRGQVDIARQYFAQMPE--R-D-YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRI   78 (153)
Q Consensus         3 ~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~--~-~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~l   78 (153)
                      +.+...|...+....+.|+++.|..+|+++.+  | + ...|...+....+.|++++|.++|+..++.+- .+...|...
T Consensus        96 p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~-~~~~~~~~~  174 (308)
T d2onda1          96 KKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTA  174 (308)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT-CCTHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CcHHHHHHH
Confidence            34556788888999999999999999998753  3 3 45789999999999999999999999987643 233333333


Q ss_pred             HHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCC-------------CCCCC--HhHHHHHHHHHhc
Q 035927           79 LTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFP-------------TIRPD--EVTYVGVLSACTH  140 (153)
Q Consensus        79 i~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~-------------~~~p~--~~t~~~ll~~~~~  140 (153)
                      ...- +...|+.+.|.++|+...+.   +...|...+.-+.+.|.++             +..|+  ...|...+..-..
T Consensus       175 a~~e-~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~  253 (308)
T d2onda1         175 ALME-YYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESN  253 (308)
T ss_dssp             HHHH-HHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHH
T ss_pred             HHHH-HHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHH
Confidence            3221 35578999999999999753   6778888888888887776             23443  2467777777778


Q ss_pred             CCchhHhhhhc
Q 035927          141 NGNETFVINSC  151 (153)
Q Consensus       141 ~g~~~~a~~~~  151 (153)
                      .|+.+.+.+++
T Consensus       254 ~G~~~~~~~~~  264 (308)
T d2onda1         254 IGDLASILKVE  264 (308)
T ss_dssp             HSCHHHHHHHH
T ss_pred             cCCHHHHHHHH
Confidence            88888877665

>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=98.29  E-value=2.9e-05  Score=50.80  Aligned_cols=133  Identities=9%  Similarity=0.027  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhcc
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKC   87 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~   87 (153)
                      .|+. -..+...|+++.|++.|+++..++...|..+-..+.+.|++++|++.|++.++.+ +-+...|..+-.+  |.+.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~--~~~~   83 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGML--YYQT   83 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHT
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHH--HHhh
Confidence            4554 5567889999999999999998999999999999999999999999999998754 2244455554444  7999


Q ss_pred             CChHHHHHHHHhcccC---ChhhHHHHHHHHHhcCCCCCCCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           88 GDVEKAQRVLRKMLRK---DKFTWTAMIVGLAISDPFPTIRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        88 g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      |+.++|.+.|++..+-   +...      .+...+.  ..+++ ..++..+-.++.+.|++++|.+.|+
T Consensus        84 g~~~~A~~~~~kAl~~~~~n~~~------~~~~~~~--~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~  144 (192)
T d1hh8a_          84 EKYDLAIKDLKEALIQLRGNQLI------DYKILGL--QFKLFACEVLYNIAFMYAKKEEWKKAEEQLA  144 (192)
T ss_dssp             TCHHHHHHHHHHHHHTTTTCSEE------ECGGGTB--CCEEEHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCccCchH------HHHHhhh--hcccchHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            9999999999886431   1000      0000000  11122 2456677778888999999887653

>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=98.27  E-value=4.1e-06  Score=56.56  Aligned_cols=92  Identities=16%  Similarity=0.078  Sum_probs=75.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--C-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--E-RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~   82 (153)
                      .+|..+-..|.+.|++++|...|++..  . .+..+|+.+-..+.+.|++++|+..|++..+..  |+ ..++..+-.. 
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~-  114 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PTYNYAHLNRGIA-  114 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH--hhhhhhHHHHHHH-
Confidence            356777889999999999999999886  3 378899999999999999999999999998753  43 4455555555 


Q ss_pred             HHhccCChHHHHHHHHhccc
Q 035927           83 MYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~  102 (153)
                       |.+.|++++|++.|+...+
T Consensus       115 -~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_         115 -LYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             -HHHTTCHHHHHHHHHHHHH
T ss_pred             -HHHHhhHHHHHHHHHHHHh
Confidence             6899999999999998854

>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=98.21  E-value=1.4e-05  Score=51.89  Aligned_cols=95  Identities=9%  Similarity=-0.012  Sum_probs=81.1

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRIL   79 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li   79 (153)
                      |+.......-+.+.+.|++++|+..|.+..  .| +...|+.+-.+|.+.|++++|+..|+..++.  .| +..+|..+-
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHHH
Confidence            777788888999999999999999998875  34 7889999999999999999999999999864  45 455666666


Q ss_pred             HHHHHhccCChHHHHHHHHhccc
Q 035927           80 TAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      .+  |.+.|++++|...|++..+
T Consensus        80 ~~--~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QC--QLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HH--HHHTTCHHHHHHHHHHHHH
T ss_pred             HH--HHHCCCHHHHHHHHHHHHH
Confidence            65  7999999999999998743

>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=98.13  E-value=4.2e-05  Score=53.06  Aligned_cols=86  Identities=10%  Similarity=0.126  Sum_probs=70.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhc
Q 035927           11 DIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCK   86 (153)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~   86 (153)
                      ..-..+.+.|++++|...|++..  .| +..+|..+...+...|++++|...+++..+..  | +...+..+...  |.+
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~--~~~   99 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVS--FTN   99 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH--HHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc--ccccccccccccc--ccc
Confidence            45567889999999999999985  34 67889999999999999999999999988653  4 44555555555  799


Q ss_pred             cCChHHHHHHHHhc
Q 035927           87 CGDVEKAQRVLRKM  100 (153)
Q Consensus        87 ~g~~~~a~~~~~~m  100 (153)
                      .|++++|.+.++..
T Consensus       100 ~~~~~~A~~~~~~~  113 (323)
T d1fcha_         100 ESLQRQACEILRDW  113 (323)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             cccccccccchhhH
Confidence            99999999998876

>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=98.12  E-value=2.1e-05  Score=50.97  Aligned_cols=93  Identities=14%  Similarity=-0.019  Sum_probs=70.5

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHH
Q 035927           35 RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVG  114 (153)
Q Consensus        35 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~  114 (153)
                      |+...+...-..+.+.|++++|+..|.+.++..  |+.......+..| |.+.|++++|+..|++..+-+          
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~--p~~~~~~~~lg~~-y~~~~~~~~Ai~~~~~al~l~----------   68 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALC-YLKMQQPEQALADCRRALELD----------   68 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHH-HHHTTCHHHHHHHHHHHTTSC----------
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHhHHHH-HhhhhhhhhhhHHHHHHHHhC----------
Confidence            556666777788999999999999999988753  5444444445554 899999999999999998742          


Q ss_pred             HHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          115 LAISDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       115 ~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                 | +...|..+-.+|.+.|++++|...|
T Consensus        69 -----------p~~~~a~~~lg~~~~~l~~~~~A~~~~   95 (201)
T d2c2la1          69 -----------GQSVKAHFFLGQCQLEMESYDEAIANL   95 (201)
T ss_dssp             -----------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             -----------CCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence                       3 3456777777777777777777655

>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=98.11  E-value=4.4e-05  Score=45.83  Aligned_cols=91  Identities=15%  Similarity=0.117  Sum_probs=77.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhc
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCK   86 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~   86 (153)
                      ..--+.+.+.|++++|+.+|++..  .| +...|..+-.++.+.|++++|+..+....+.+ +.+...|..+-.+  |.+
T Consensus         7 ~~~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~--~~~   83 (117)
T d1elwa_           7 KEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAA--LEF   83 (117)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHH--HHH
Confidence            445677899999999999999975  34 78889999999999999999999999998764 3466677666666  799


Q ss_pred             cCChHHHHHHHHhcccC
Q 035927           87 CGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~~  103 (153)
                      .|++++|+..|++..+.
T Consensus        84 ~~~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          84 LNRFEEAKRTYEEGLKH  100 (117)
T ss_dssp             TTCHHHHHHHHHHHHTT
T ss_pred             ccCHHHHHHHHHHHHHh
Confidence            99999999999999764

>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=98.01  E-value=5.5e-05  Score=47.70  Aligned_cols=91  Identities=14%  Similarity=0.147  Sum_probs=76.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHh
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYC   85 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~   85 (153)
                      +...-+.|.+.|++++|...|.+..+   .+...|..+-..+.+.|++++|+..|+..++.+ +-+...|..+..+  |.
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~--~~   89 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAAS--NM   89 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHH--HH
Confidence            44556688999999999999998862   378899999999999999999999999998764 2355677777777  69


Q ss_pred             ccCChHHHHHHHHhccc
Q 035927           86 KCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        86 ~~g~~~~a~~~~~~m~~  102 (153)
                      ..|++++|.+.+++..+
T Consensus        90 ~~g~~~eA~~~~~~a~~  106 (159)
T d1a17a_          90 ALGKFRAALRDYETVVK  106 (159)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            99999999999999965

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.92  E-value=1.2e-05  Score=49.04  Aligned_cols=92  Identities=12%  Similarity=0.138  Sum_probs=71.4

Q ss_pred             HHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcC---ChHHHHHHHHHHhhCCCCCChh-HHHHHHHHH
Q 035927           10 TDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVN---RFREALTLFPEMQTSNIRPDEF-TIVRILTAY   82 (153)
Q Consensus        10 ~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~~~~p~~~-t~~~li~~~   82 (153)
                      ..+++.+...+++++|.+.|++...   .+..++..+-.++.+.+   ++++|..++++..+.+-.|+.. .+.- +..+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~-Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFY-LAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHH-HHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHH-HHHH
Confidence            4678889999999999999999863   37788888888888765   4567999999998765444432 3333 3443


Q ss_pred             HHhccCChHHHHHHHHhcccC
Q 035927           83 MYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        83 ~~~~~g~~~~a~~~~~~m~~~  103 (153)
                       |.+.|++++|++.|++..+-
T Consensus        82 -y~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          82 -NYRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             -HHHTTCHHHHHHHHHHHHHH
T ss_pred             -HHHHhhhHHHHHHHHHHHHh
Confidence             79999999999999999753

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.87  E-value=9.5e-05  Score=51.91  Aligned_cols=112  Identities=7%  Similarity=0.033  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhCCCCCChhHHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVN-RFREALTLFPEMQTSNIRPDEFTIVRILTAYM   83 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~   83 (153)
                      .|+-+-..+.+.++.++|+.++++..  .| +...|+..-..+...| ++++|+..++...+.. +-+..+|...-..  
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~--  121 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL--  121 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHH--
Confidence            34444455555556666666666554  22 4445555555544443 3555665555554432 1123333333333  


Q ss_pred             HhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCCC
Q 035927           84 YCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  122 (153)
                      +.+.|++++|++.++++.+   .+...|..+...+...+.++
T Consensus       122 ~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~  163 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWD  163 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCT
T ss_pred             HHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhH
Confidence            4555555555555555543   14555555555555555555

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.86  E-value=5.6e-05  Score=45.02  Aligned_cols=88  Identities=10%  Similarity=0.005  Sum_probs=71.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMY   84 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~   84 (153)
                      +-.+-..+.+.|++++|...|++..  .| +...|..+-..+.+.|++++|+..++...+..  |+ ...+..+-..  |
T Consensus        19 ~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~la~~--y   94 (112)
T d1hxia_          19 PMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVS--H   94 (112)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHH--H
T ss_pred             HHHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccc--cccccchHHHHHH--H
Confidence            3345677889999999999999986  34 78899999999999999999999999988753  54 5555554444  7


Q ss_pred             hccCChHHHHHHHHhc
Q 035927           85 CKCGDVEKAQRVLRKM  100 (153)
Q Consensus        85 ~~~g~~~~a~~~~~~m  100 (153)
                      ...|++++|++.+++.
T Consensus        95 ~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          95 TNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHH
Confidence            9999999999999874

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=7.9e-05  Score=52.33  Aligned_cols=123  Identities=6%  Similarity=0.042  Sum_probs=88.8

Q ss_pred             chhHHHHHHHHHHhcCC-hHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHH
Q 035927            5 DVISWTDIVSGYINRGQ-VDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILT   80 (153)
Q Consensus         5 d~~~~~~li~~~~~~g~-~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~   80 (153)
                      +...|+..-.++.+.|+ +++|+..+++..  .| +..+|+.+-..+.+.|++++|++.++.+.+.. +-+...|..+..
T Consensus        76 ~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~  154 (315)
T d2h6fa1          76 NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQW  154 (315)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHH
Confidence            33457877778887764 889988888875  23 67788888888888899999999999888643 235677777776


Q ss_pred             HHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCc------hhHhhhhc
Q 035927           81 AYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGN------ETFVINSC  151 (153)
Q Consensus        81 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~------~~~a~~~~  151 (153)
                      .  +.+.|++++|++.+++..+.|                     | +...|+..-..+.+.|.      .++|++.+
T Consensus       155 ~--~~~~~~~~~Al~~~~~al~~~---------------------p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~  209 (315)
T d2h6fa1         155 V--IQEFKLWDNELQYVDQLLKED---------------------VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYT  209 (315)
T ss_dssp             H--HHHHTCCTTHHHHHHHHHHHC---------------------TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHH
T ss_pred             H--HHHHHhhHHHHHHHHHHHHHC---------------------CccHHHHHHHHHHHHHccccchhhhhHHhHHHH
Confidence            6  588899999999999887754                     3 45567666555544444      45666554

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.79  E-value=0.00022  Score=49.55  Aligned_cols=130  Identities=6%  Similarity=0.045  Sum_probs=93.3

Q ss_pred             ChHHHHHHHHhCC----CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHH
Q 035927           21 QVDIARQYFAQMP----ERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRV   96 (153)
Q Consensus        21 ~~~~a~~l~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~   96 (153)
                      ..++|..+|++..    ..+...|...+...-+.|+++.|..+|+.+.+..-......|...+..  ..+.|+.+.|.++
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~--~~~~~~~~~ar~i  156 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKF--ARRAEGIKSGRMI  156 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHH--HHHHHCHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHH--HHHcCChHHHHHH
Confidence            3577888888753    236667888888888999999999999999876433345578888887  4899999999999


Q ss_pred             HHhcccC---ChhhHHHHHHHH-HhcCCCC----------CCCC-CHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927           97 LRKMLRK---DKFTWTAMIVGL-AISDPFP----------TIRP-DEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus        97 ~~~m~~~---~~~~~~~li~~~-~~~~~~~----------~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      |++..+.   +...|-....-. ...+..+          ...| +...|...++...+.|+.++|..+|+
T Consensus       157 ~~~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe  227 (308)
T d2onda1         157 FKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFE  227 (308)
T ss_dssp             HHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            9998653   333333222211 1123222          2224 46779999999999999999999885

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.79  E-value=0.00011  Score=46.21  Aligned_cols=78  Identities=10%  Similarity=0.106  Sum_probs=60.4

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHHHHHHHhc
Q 035927           42 AMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAMIVGLAIS  118 (153)
Q Consensus        42 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~  118 (153)
                      ..-..+.+.|++++|...|++..+.+  |+...+-..+..| |.+.|++++|+..|++..+  | +...|..+..++...
T Consensus        15 ~~gn~~~~~~~y~~A~~~~~~al~~~--p~~~~~~~~lg~~-~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~   91 (159)
T d1a17a_          15 TQANDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLA-YLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMAL   91 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHH-HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHhhhccccc--hhhhhhhhhhHHH-HHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHc
Confidence            34556779999999999999998764  6555554555554 8999999999999999865  3 566777777777777


Q ss_pred             CCCC
Q 035927          119 DPFP  122 (153)
Q Consensus       119 ~~~~  122 (153)
                      |.++
T Consensus        92 g~~~   95 (159)
T d1a17a_          92 GKFR   95 (159)
T ss_dssp             TCHH
T ss_pred             CCHH
Confidence            7776

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=7.8e-05  Score=44.68  Aligned_cols=86  Identities=17%  Similarity=0.055  Sum_probs=61.8

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCC
Q 035927           43 MIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        43 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~  122 (153)
                      --..+.+.|++++|...|++..+.. +-+...|..+-.+  |.+.|++++|++.++...+-+                  
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~--~~~~~~~~~A~~~~~~al~~~------------------   67 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAA--YAKKGDYQKAYEDGCKTVDLK------------------   67 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHC------------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC-Ccchhhhhccccc--ccccccccccchhhhhHHHhc------------------
Confidence            3456778999999999999998753 2355556665555  799999999999999997532                  


Q ss_pred             CCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          123 TIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       123 ~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                        +.+...|..+..++...|++++|+..|
T Consensus        68 --p~~~~~~~~~g~~~~~~~~~~~A~~~~   94 (117)
T d1elwa_          68 --PDWGKGYSRKAAALEFLNRFEEAKRTY   94 (117)
T ss_dssp             --TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             --cchhhHHHHHHHHHHHccCHHHHHHHH
Confidence              124455666666666666666666554

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=0.00019  Score=43.48  Aligned_cols=90  Identities=9%  Similarity=0.051  Sum_probs=66.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCC---hHHHHHHHHhcccCChhhHHHHHHHHHh
Q 035927           41 TAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGD---VEKAQRVLRKMLRKDKFTWTAMIVGLAI  117 (153)
Q Consensus        41 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~---~~~a~~~~~~m~~~~~~~~~~li~~~~~  117 (153)
                      ..+++.+...+++++|.+.|+.....+ +.+..+..-+-.+  +.+.++   .++|+.+++++.+.+.            
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~--L~~s~~~~d~~~Ai~~l~~~l~~~~------------   67 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWC--LVRTRYNDDIRKGIVLLEELLPKGS------------   67 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHH--HTTSSSHHHHHHHHHHHHHHTTTSC------------
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHH--HHHhcchHHHHHHHHHHHHHHhccC------------
Confidence            567888999999999999999998754 2455666666665  576554   4569999999987531            


Q ss_pred             cCCCCCCCCC-HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          118 SDPFPTIRPD-EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       118 ~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                             .|+ ...|..+-.+|.+.|++++|.+.|+
T Consensus        68 -------~~~~~~~~~~Lg~~y~~~g~~~~A~~~~~   96 (122)
T d1nzna_          68 -------KEEQRDYVFYLAVGNYRLKEYEKALKYVR   96 (122)
T ss_dssp             -------HHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             -------CchHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence                   123 2367777888888888888887764

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.59  E-value=0.00014  Score=43.22  Aligned_cols=86  Identities=15%  Similarity=0.052  Sum_probs=68.4

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhCCCCCC-hhHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCC
Q 035927           43 MIDGYLRVNRFREALTLFPEMQTSNIRPD-EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPF  121 (153)
Q Consensus        43 li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~  121 (153)
                      +-..+.+.|++++|...|++.++.  .|+ ...|..+-..  |.+.|++++|+..|++..+-+                 
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~--~~~~~~~~~A~~~~~~al~~~-----------------   80 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLT--QAENEKDGLAIIALNHARMLD-----------------   80 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHC-----------------
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhh--hhhhhhHHHhhcccccccccc-----------------
Confidence            455667899999999999999875  354 5555555554  799999999999999987643                 


Q ss_pred             CCCCCCHhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          122 PTIRPDEVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       122 ~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                         +-+...|..+...|...|+.++|.+.++
T Consensus        81 ---p~~~~a~~~la~~y~~~g~~~~A~~~l~  108 (112)
T d1hxia_          81 ---PKDIAVHAALAVSHTNEHNANAALASLR  108 (112)
T ss_dssp             ---TTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ---cccccchHHHHHHHHHCCCHHHHHHHHH
Confidence               1256778889999999999999998764

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.57  E-value=0.0025  Score=41.13  Aligned_cols=99  Identities=14%  Similarity=0.050  Sum_probs=77.4

Q ss_pred             CCCchhHHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC-----------
Q 035927            2 KNKDVISWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN-----------   67 (153)
Q Consensus         2 ~~pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-----------   67 (153)
                      .+|+..+|..+-..+.+.|++++|.+.|++-.+   .+...|..+-..+.+.|++++|+..|+......           
T Consensus        32 ~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~  111 (192)
T d1hh8a_          32 QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKIL  111 (192)
T ss_dssp             SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGG
T ss_pred             CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHHHHHHhCccCchHHHHHh
Confidence            467888899999999999999999999999863   377899999999999999999999999876431           


Q ss_pred             -CCCCh---hHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           68 -IRPDE---FTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        68 -~~p~~---~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                       .....   .++..+-.+  |.+.|++++|.+.+....+
T Consensus       112 ~~~~~~~~~e~~~n~a~~--~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_         112 GLQFKLFACEVLYNIAFM--YAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             TBCCEEEHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHT
T ss_pred             hhhcccchHHHHHHHHHH--HHHCCCHHHHHHHHHHHHh
Confidence             11111   222222233  6899999999999998754

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.53  E-value=0.00016  Score=49.87  Aligned_cols=130  Identities=8%  Similarity=-0.062  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CC-CCCh
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NI-RPDE   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~-~p~~   72 (153)
                      ..|....+.|-..|++++|.+.|.+...     .    -..+|+.+-..|.+.|++++|...++...+.    |- ....
T Consensus        38 ~~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~  117 (290)
T d1qqea_          38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (290)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHH
Confidence            3588888899999999999999887752     1    2457899999999999999999999877542    21 1224


Q ss_pred             hHHHHHHHHHHHhccCChHHHHHHHHhcccCChhhHHHHHHHHHhcCCCCCCCCC-HhHHHHHHHHHhcCCchhHhhhhc
Q 035927           73 FTIVRILTAYMYCKCGDVEKAQRVLRKMLRKDKFTWTAMIVGLAISDPFPTIRPD-EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus        73 ~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~~~p~-~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ..+..+...+ +...|++++|++.+.+..+-....               +..+. ..++..+...+...|++++|.+.|
T Consensus       118 ~~~~~l~~~~-~~~~~~~~~A~~~~~~A~~l~~~~---------------~~~~~~~~~~~~la~~~~~~g~y~~A~~~~  181 (290)
T d1qqea_         118 NFKFELGEIL-ENDLHDYAKAIDCYELAGEWYAQD---------------QSVALSNKCFIKCADLKALDGQYIEASDIY  181 (290)
T ss_dssp             HHHHHHHHHH-HHTTCCHHHHHHHHHHHHHHHHHT---------------TCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhH-hhHHHHHHHHHHHHHHHHHHHHhc---------------CchhhhhhHHHHHHHHHHHcChHHHHHHHH
Confidence            4455555553 345799999999998874310000               11121 345777778888888888888776


Q ss_pred             c
Q 035927          152 N  152 (153)
Q Consensus       152 ~  152 (153)
                      +
T Consensus       182 ~  182 (290)
T d1qqea_         182 S  182 (290)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=97.35  E-value=0.00049  Score=44.40  Aligned_cols=68  Identities=21%  Similarity=0.316  Sum_probs=51.9

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh-----CCCCCChhH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQT-----SNIRPDEFT   74 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~t   74 (153)
                      ..+..+...+.+.|++++|...+++..  .| +...|..++.++.+.|+..+|+..|+++.+     .|+.|+..+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            346677778888888888888888875  23 777888888888888888888888888743     477787654

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=97.34  E-value=0.0009  Score=44.51  Aligned_cols=83  Identities=12%  Similarity=-0.013  Sum_probs=61.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhccc--C-ChhhHHHH
Q 035927           36 DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR--K-DKFTWTAM  111 (153)
Q Consensus        36 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~l  111 (153)
                      ....|..+-..|.+.|++++|.+.|++.++.  .| +..+|..+-.+  |.+.|++++|++.|++..+  | +...|..+
T Consensus        36 ~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~--~~~~g~~~~A~~~~~~al~~~p~~~~a~~~l  111 (259)
T d1xnfa_          36 RAQLLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIY--LTQAGNFDAAYEAFDSVLELDPTYNYAHLNR  111 (259)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHHCTTCTHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchH--HHHHHHHHHhhhhhhHHHHHHhhhhhhHHHH
Confidence            3457777888889999999999999999874  34 55566655555  7999999999999999965  3 34455555


Q ss_pred             HHHHHhcCCCC
Q 035927          112 IVGLAISDPFP  122 (153)
Q Consensus       112 i~~~~~~~~~~  122 (153)
                      ...+...|.++
T Consensus       112 g~~~~~~g~~~  122 (259)
T d1xnfa_         112 GIALYYGGRDK  122 (259)
T ss_dssp             HHHHHHTTCHH
T ss_pred             HHHHHHHhhHH
Confidence            55555555554

>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=97.32  E-value=0.00088  Score=40.47  Aligned_cols=91  Identities=15%  Similarity=0.167  Sum_probs=71.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--C-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCC--CCCC----hhHHHHHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--E-RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSN--IRPD----EFTIVRIL   79 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~~p~----~~t~~~li   79 (153)
                      +-.+-+.+.+.|++++|++.|.+..  . .+...|..+-..|.+.|++++|+..++..++..  ....    ..+|..+-
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            5566778999999999999998886  2 378899999999999999999999999987532  1111    12444444


Q ss_pred             HHHHHhccCChHHHHHHHHhcc
Q 035927           80 TAYMYCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        80 ~~~~~~~~g~~~~a~~~~~~m~  101 (153)
                      ..  +...+++++|.+.|.+..
T Consensus        87 ~~--~~~~~~~~~A~~~~~kal  106 (128)
T d1elra_          87 NS--YFKEEKYKDAIHFYNKSL  106 (128)
T ss_dssp             HH--HHHTTCHHHHHHHHHHHH
T ss_pred             HH--HHHhCCHHHHHHHHHHHH
Confidence            55  688899999999998865

>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=97.27  E-value=0.0018  Score=41.60  Aligned_cols=86  Identities=13%  Similarity=0.120  Sum_probs=71.7

Q ss_pred             HHHHhcCChHHHHHHHHhCCC----C---------------------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927           14 SGYINRGQVDIARQYFAQMPE----R---------------------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~----~---------------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      ......|++++|.+.|.+-..    +                     -...+..+...+.+.|++++|+..++...+.. 
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-   97 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREWRGPVLDDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIAELEALTFEH-   97 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-
Confidence            577888999999998887542    0                     12457888899999999999999999998753 


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +-+...|..++.+  |.+.|+.++|++.|+++.+
T Consensus        98 P~~e~~~~~l~~a--l~~~Gr~~eAl~~y~~~~~  129 (179)
T d2ff4a2          98 PYREPLWTQLITA--YYLSDRQSDALGAYRRVKT  129 (179)
T ss_dssp             TTCHHHHHHHHHH--HHTTTCHHHHHHHHHHHHH
T ss_pred             CccHHHHHHHHHH--HHHhcCHHHHHHHHHHHHH
Confidence            3588999999999  6999999999999999843

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.24  E-value=0.002  Score=40.78  Aligned_cols=92  Identities=15%  Similarity=0.129  Sum_probs=71.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC-----C-------------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE-----R-------------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR   69 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~-----~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   69 (153)
                      .+...-+.+.+.|++++|+..|.+...     +             -..+|+.+...|.+.|++++|+..++..++.+ +
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p   93 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-S   93 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-c
Confidence            345556689999999999999976531     0             13467778888899999999999999998763 2


Q ss_pred             CChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           70 PDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        70 p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      -++..+..+-.+  |...|++++|...|++..+
T Consensus        94 ~~~~a~~~~g~~--~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          94 NNEKGLSRRGEA--HLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             TCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             cchhhhHHHHHH--HHHhhhHHHHHHHHHHHHH
Confidence            256666665555  7999999999999999965

>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=97.23  E-value=0.0018  Score=40.24  Aligned_cols=92  Identities=10%  Similarity=0.126  Sum_probs=74.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--------C-----------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--------R-----------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--------~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      .+..--+.+.+.|++++|...|.+...        +           ...+|+.+...|.+.|++++|+..++..++.+ 
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-   97 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-   97 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc-
Confidence            345566788999999999999987431        1           23467778888899999999999999998764 


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      +.+..+|-.+..+  |.+.|++++|...|++..+
T Consensus        98 p~~~ka~~~~g~~--~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          98 KNNVKALYKLGVA--NMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHH
T ss_pred             chhhhhhHHhHHH--HHHcCCHHHHHHHHHHHHH
Confidence            3477888888777  7999999999999999865

>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=97.12  E-value=0.005  Score=38.61  Aligned_cols=92  Identities=10%  Similarity=0.097  Sum_probs=72.2

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCC------------------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCC
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPE------------------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIR   69 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~------------------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~   69 (153)
                      +......+.+.|++++|+..|.+..+                  | +...|..+-..+.+.|++++|+..++..++.. +
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p  108 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-P  108 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-T
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-h
Confidence            45556778899999999999877632                  1 44567778888889999999999999998754 3


Q ss_pred             CChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           70 PDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        70 p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      -+...|..+-.+  |.+.|++++|++.|++..+-
T Consensus       109 ~~~~a~~~~g~~--~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1         109 SNTKALYRRAQG--WQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             TCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhhHHHhHHHH--HHHccCHHHHHHHHHHHHHh
Confidence            356666666666  79999999999999999753

>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=97.12  E-value=0.002  Score=38.83  Aligned_cols=94  Identities=12%  Similarity=0.153  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHHHHH
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMIVGL  115 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~  115 (153)
                      .+-.+-..+.+.|++++|+..|.+.++.+ +.+...+..+-.+  |.+.|++++|+..++..++-   +...|..+    
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~--~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~----   78 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAV--YFEKGDYNKCRELCEKAIEVGRENREDYRQI----   78 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH--HHHHTCHHHHHHHHHHHHHHHHHSTTCHHHH----
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHH--HHHcCchHHHHHHHHHHHHhCcccHHHHHHH----
Confidence            34456677889999999999999998763 2345555555444  79999999999999998653   21111111    


Q ss_pred             HhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          116 AISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       116 ~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                  ..+|..+-..+...|++++|.+.|
T Consensus        79 ------------a~~~~~lg~~~~~~~~~~~A~~~~  102 (128)
T d1elra_          79 ------------AKAYARIGNSYFKEEKYKDAIHFY  102 (128)
T ss_dssp             ------------HHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ------------HHHHHHHHHHHHHhCCHHHHHHHH
Confidence                        134555566666667777776665

>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=97.05  E-value=0.0094  Score=41.16  Aligned_cols=102  Identities=10%  Similarity=0.062  Sum_probs=74.3

Q ss_pred             cCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcC--ChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHH
Q 035927           19 RGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVN--RFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKA   93 (153)
Q Consensus        19 ~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a   93 (153)
                      .|++++|..++++..  .| +...|..+...+...+  ++++|...+....+.. +++...+......+ +...+..++|
T Consensus        86 ~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~-~~~~~~~~~A  163 (334)
T d1dcea1          86 AALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVA-AQAAVAPAEE  163 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH-HHTCCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHH-HHhccccHHH
Confidence            345788888888875  23 6777777777777655  5889999999998753 24556665555543 6788999999


Q ss_pred             HHHHHhcccC---ChhhHHHHHHHHHhcCCCC
Q 035927           94 QRVLRKMLRK---DKFTWTAMIVGLAISDPFP  122 (153)
Q Consensus        94 ~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  122 (153)
                      +..++...+.   +...|+.+...+...|.++
T Consensus       164 l~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~  195 (334)
T d1dcea1         164 LAFTDSLITRNFSNYSSWHYRSCLLPQLHPQP  195 (334)
T ss_dssp             HHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHH
Confidence            9999998764   6777888777777765544

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.03  E-value=0.003  Score=39.94  Aligned_cols=90  Identities=11%  Similarity=0.050  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhCC-CCCC-------------hhHHHHHHHHHHHhccCChHHHHHHHHhcccCC
Q 035927           39 LWTAMIDGYLRVNRFREALTLFPEMQTSN-IRPD-------------EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKD  104 (153)
Q Consensus        39 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~-------------~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~  104 (153)
                      .+...-..+.+.|++++|...|.+.++.- ..+.             ..+|+-+ ..| |.+.|++++|+..++...+.+
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nl-a~~-y~k~~~~~~A~~~~~~al~~~   92 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNL-AMC-HLKLQAFSAAIESCNKALELD   92 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHH-HHH-HHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHH-HHH-HHhhhhcccccchhhhhhhcc
Confidence            34455567888999999999999886531 1111             1223333 333 799999999999999997532


Q ss_pred             hhhHHHHHHHHHhcCCCCCCCC-CHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          105 KFTWTAMIVGLAISDPFPTIRP-DEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       105 ~~~~~~li~~~~~~~~~~~~~p-~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                           | +...|..+..+|...|++++|.+.|
T Consensus        93 ---------------------p~~~~a~~~~g~~~~~~g~~~~A~~~~  119 (170)
T d1p5qa1          93 ---------------------SNNEKGLSRRGEAHLAVNDFELARADF  119 (170)
T ss_dssp             ---------------------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ---------------------ccchhhhHHHHHHHHHhhhHHHHHHHH
Confidence                                 2 3444555555555555555555544

>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=96.88  E-value=0.0079  Score=37.17  Aligned_cols=92  Identities=16%  Similarity=0.084  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhCC----CCCChh-----------HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           38 VLWTAMIDGYLRVNRFREALTLFPEMQTSN----IRPDEF-----------TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        38 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~----~~p~~~-----------t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..+..--..+.+.|++.+|+..|.+..+.-    ..++..           +|.-+ ..| |.+.|++++|++.++...+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nl-a~~-~~~l~~~~~Al~~~~~al~   95 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNL-ATC-YNKNKDYPKAIDHASKVLK   95 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHH-HHH-HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhH-HHH-HHHhcccchhhhhhhcccc
Confidence            345556677889999999999999887531    112221           23333 333 7999999999999999865


Q ss_pred             CChhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          103 KDKFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       103 ~~~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      .+                    +-+...|..+..++...|++++|+..|
T Consensus        96 ~~--------------------p~~~ka~~~~g~~~~~lg~~~~A~~~~  124 (153)
T d2fbna1          96 ID--------------------KNNVKALYKLGVANMYFGFLEEAKENL  124 (153)
T ss_dssp             HS--------------------TTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             cc--------------------chhhhhhHHhHHHHHHcCCHHHHHHHH
Confidence            32                    113455555555555555555555544

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.88  E-value=0.006  Score=41.61  Aligned_cols=94  Identities=6%  Similarity=0.044  Sum_probs=69.3

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-----C----CHHHHHHHHHHHHh-cCChHHHHHHHHHHhh----CCCCCC-
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-----R----DYVLWTAMIDGYLR-VNRFREALTLFPEMQT----SNIRPD-   71 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-----~----~~~~~~~li~~~~~-~~~~~~a~~~~~~m~~----~~~~p~-   71 (153)
                      .+|+.+...|.+.|++++|.+.+++...     .    -..++..+...+-. .|++++|...+.+..+    .+-.+. 
T Consensus        78 ~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~  157 (290)
T d1qqea_          78 NTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALS  157 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhh
Confidence            5688899999999999999998887542     1    24556777776644 6999999999988753    222222 


Q ss_pred             hhHHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           72 EFTIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        72 ~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..++..+...  |.+.|++++|...|++...
T Consensus       158 ~~~~~~la~~--~~~~g~y~~A~~~~~~~~~  186 (290)
T d1qqea_         158 NKCFIKCADL--KALDGQYIEASDIYSKLIK  186 (290)
T ss_dssp             HHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHH--HHHcChHHHHHHHHHHHHH
Confidence            2344555555  7999999999999999754

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=96.74  E-value=0.014  Score=36.50  Aligned_cols=94  Identities=14%  Similarity=0.122  Sum_probs=73.2

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC-------C-----------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCC
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE-------R-----------DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNI   68 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~-------~-----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~   68 (153)
                      ..+...-+.+.+.|++++|...|.+...       .           ....|+.+-.++.+.|++++|+..++..++.. 
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-   94 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-   94 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-
Confidence            3456677789999999999999876531       0           22346667777888999999999999998753 


Q ss_pred             CCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           69 RPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        69 ~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      +.+...|-..-.+  |...|++++|++.|.+..+-
T Consensus        95 p~~~~a~~~~~~~--~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          95 SANEKGLYRRGEA--QLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             TTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHS
T ss_pred             cchHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHh
Confidence            3466777777776  79999999999999999753

>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=96.68  E-value=0.015  Score=39.24  Aligned_cols=143  Identities=10%  Similarity=-0.009  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC--------CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhC----CCCC-Ch-h
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE--------RDYVLWTAMIDGYLRVNRFREALTLFPEMQTS----NIRP-DE-F   73 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~--------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~-~   73 (153)
                      .+..+-..+...|+++.+...+.....        .....+..+...+...++..++...+.+....    +..+ .. .
T Consensus       135 ~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~  214 (366)
T d1hz4a_         135 LVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISN  214 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHH
T ss_pred             HHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHH
Confidence            455566778888999999888877642        13445666666677778888888877766432    1111 11 1


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHhcccC-------ChhhHHHHHHHHHhcCCCC----------------CCCCCH-h
Q 035927           74 TIVRILTAYMYCKCGDVEKAQRVLRKMLRK-------DKFTWTAMIVGLAISDPFP----------------TIRPDE-V  129 (153)
Q Consensus        74 t~~~li~~~~~~~~g~~~~a~~~~~~m~~~-------~~~~~~~li~~~~~~~~~~----------------~~~p~~-~  129 (153)
                      .+......  +...|+++.|...+....+.       ....+..+...+...|.++                +..|+. .
T Consensus       215 ~~~~~~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  292 (366)
T d1hz4a_         215 ANKVRVIY--WQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNR  292 (366)
T ss_dssp             HHHHHHHH--HHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHH--HHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHH
Confidence            22333333  67888999999988887542       2334555666777776666                344543 5


Q ss_pred             HHHHHHHHHhcCCchhHhhhhcc
Q 035927          130 TYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       130 t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      .+..+-..|.+.|+.++|.+.++
T Consensus       293 ~~~~la~~~~~~g~~~~A~~~l~  315 (366)
T d1hz4a_         293 NLLLLNQLYWQAGRKSDAQRVLL  315 (366)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHH
Confidence            67778888999999999988763

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.68  E-value=0.0064  Score=38.10  Aligned_cols=90  Identities=10%  Similarity=0.097  Sum_probs=55.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhC--------------CCCC-ChhHHHHHHHHHHHhccCChHHHHHHHHhcccCC
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTS--------------NIRP-DEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRKD  104 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~--------------~~~p-~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~~  104 (153)
                      +......+.+.|++++|++.|.+..+.              .+.| ....+..+ ..| |.+.|++++|+..+++..+-+
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nl-a~~-~~~~~~~~~Ai~~~~~al~~~  107 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNI-GAC-KLKMSDWQGAVDSCLEALEID  107 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHH-HHH-HHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHH-HHH-HHhhcccchhhhhhhhhhhhh
Confidence            445566677889999998888776431              1122 22223333 333 799999999999999997642


Q ss_pred             hhhHHHHHHHHHhcCCCCCCCCCHhHHHHHHHHHhcCCchhHhhhhc
Q 035927          105 KFTWTAMIVGLAISDPFPTIRPDEVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       105 ~~~~~~li~~~~~~~~~~~~~p~~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                                          +-+...|..+-.++.+.|++++|++.|
T Consensus       108 --------------------p~~~~a~~~~g~~~~~l~~~~~A~~~~  134 (169)
T d1ihga1         108 --------------------PSNTKALYRRAQGWQGLKEYDQALADL  134 (169)
T ss_dssp             --------------------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             --------------------hhhhhHHHhHHHHHHHccCHHHHHHHH
Confidence                                113344555555555555555555544

>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=96.64  E-value=0.015  Score=39.28  Aligned_cols=94  Identities=18%  Similarity=0.229  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCCC-------CHHHHHHHHHHHHhcCChHHHHHHHHHHhh----CCCCCChhHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPER-------DYVLWTAMIDGYLRVNRFREALTLFPEMQT----SNIRPDEFTIV   76 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~~-------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~----~~~~p~~~t~~   76 (153)
                      .+..+...+...|+++.|...+.+....       ....+..+...+...|++++|...++....    .+..|+.....
T Consensus       215 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  294 (366)
T d1hz4a_         215 ANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNL  294 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHH
Confidence            4666777888999999999999987632       345567788889999999999999998753    35555544444


Q ss_pred             HHHHHHHHhccCChHHHHHHHHhccc
Q 035927           77 RILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        77 ~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                      ..+..+ |.+.|++++|.+.+++..+
T Consensus       295 ~~la~~-~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         295 LLLNQL-YWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHH-HHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHH-HHHCCCHHHHHHHHHHHHH
Confidence            444443 7999999999999988643

>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=96.54  E-value=0.0031  Score=43.03  Aligned_cols=24  Identities=4%  Similarity=-0.140  Sum_probs=17.4

Q ss_pred             HhHHHHHHHHHhcCCchhHhhhhc
Q 035927          128 EVTYVGVLSACTHNGNETFVINSC  151 (153)
Q Consensus       128 ~~t~~~ll~~~~~~g~~~~a~~~~  151 (153)
                      ...+......+.+.|+.++|.+++
T Consensus        99 ~~~~l~~a~~~~~~gd~~~A~~~~  122 (264)
T d1zbpa1          99 LTKSLVSFNLSMVSQDYEQVSELA  122 (264)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHH
Confidence            344555566777899999998765

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.06  E-value=0.066  Score=32.71  Aligned_cols=94  Identities=16%  Similarity=0.138  Sum_probs=68.4

Q ss_pred             hHHHHH--HHHHHhcCChHHHHHHHHhCCC-----C----------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhC---
Q 035927            7 ISWTDI--VSGYINRGQVDIARQYFAQMPE-----R----------DYVLWTAMIDGYLRVNRFREALTLFPEMQTS---   66 (153)
Q Consensus         7 ~~~~~l--i~~~~~~g~~~~a~~l~~~m~~-----~----------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---   66 (153)
                      ..|..+  ...+.+.|++++|+..|++-.+     |          ...+|+.+-.+|.+.|++++|..-+++.++.   
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~   87 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNR   87 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccc
Confidence            356665  5567788999999998888752     1          2467999999999999999999999888642   


Q ss_pred             --CCCCChh-----HHHHHHHHHHHhccCChHHHHHHHHhccc
Q 035927           67 --NIRPDEF-----TIVRILTAYMYCKCGDVEKAQRVLRKMLR  102 (153)
Q Consensus        67 --~~~p~~~-----t~~~li~~~~~~~~g~~~~a~~~~~~m~~  102 (153)
                        ...++..     .+..+-.+  |.+.|++++|+..|++..+
T Consensus        88 ~~~~~~~~~~~~~~a~~~~g~~--~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          88 RGELNQDEGKLWISAVYSRALA--LDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HCCTTSTHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHH
T ss_pred             cccccccccchhHHHHhhhHHH--HHHHHHHHHHHHHHHHHHH
Confidence              1222211     23333444  7999999999999999743

>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=95.70  E-value=0.068  Score=33.14  Aligned_cols=73  Identities=11%  Similarity=0.054  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHhCCC---CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            8 SWTDIVSGYINRGQVDIARQYFAQMPE---RDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         8 ~~~~li~~~~~~g~~~~a~~l~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      +|+.+-.+|.+.|++++|+..+++..+   .+..+|..+..++...|++++|...|...++.  -|+.......+..+
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~~~  141 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIFMC  141 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            466677788999999999999998863   37788999999999999999999999999875  46555555555553

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=95.47  E-value=0.039  Score=37.30  Aligned_cols=48  Identities=17%  Similarity=0.131  Sum_probs=26.4

Q ss_pred             hcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 035927           18 NRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQT   65 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~   65 (153)
                      +.|++++|+..+++-.  .| |...+..+...++..|++++|...++...+
T Consensus         8 ~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4455555555555543  22 555555555556666666555555555543

>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=95.34  E-value=0.2  Score=34.99  Aligned_cols=108  Identities=13%  Similarity=0.135  Sum_probs=58.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHHhCCC------------------------CCHHHHHHHHHHHHhcCChHHHHHH
Q 035927            4 KDVISWTDIVSGYINRGQVDIARQYFAQMPE------------------------RDYVLWTAMIDGYLRVNRFREALTL   59 (153)
Q Consensus         4 pd~~~~~~li~~~~~~g~~~~a~~l~~~m~~------------------------~~~~~~~~li~~~~~~~~~~~a~~~   59 (153)
                      ||..--..+.+.|.+.|.++.|..+|..+..                        .+..+|..+...+.+.....-|   
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d~~rl~~~~v~l~~~~~avd~~~k~~~~~~~k~~~~~l~~~~e~~la---   88 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLA---   88 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTCHHHHHHHHHTTTCHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHH---
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCCHHHHHHHHHhhccHHHHHHHHHHcCCHHHHHHHHHHHHhCcHHHHH---
Confidence            3433344455555566666666666655543                        1334555555555544433321   


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhccc---CChhhHHHHHHHHHhc
Q 035927           60 FPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAIS  118 (153)
Q Consensus        60 ~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~  118 (153)
                        .+...+...+......++..  |...|.+++...+++....   .+...++-++..|++.
T Consensus        89 --~i~~~~~~~~~d~l~~~v~~--ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~  146 (336)
T d1b89a_          89 --QMCGLHIVVHADELEELINY--YQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKF  146 (336)
T ss_dssp             --HHTTTTTTTCHHHHHHHHHH--HHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTT
T ss_pred             --HHHHHHhhcCHHHHHHHHHH--HHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHh
Confidence              22233344566667788887  6999999999999997643   3677788899988887

>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=95.25  E-value=0.15  Score=31.03  Aligned_cols=100  Identities=13%  Similarity=0.054  Sum_probs=65.3

Q ss_pred             HHHHHHH--HHHHHhcCChHHHHHHHHHHhhCC-CCCC----------hhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           37 YVLWTAM--IDGYLRVNRFREALTLFPEMQTSN-IRPD----------EFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        37 ~~~~~~l--i~~~~~~~~~~~a~~~~~~m~~~~-~~p~----------~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      ..+|..+  ...+.+.|++++|+..|++.++.. -.|+          ...|+.+-.+  |.+.|++++|.+-++...+-
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~--~~~lg~~~~A~~~~~~al~~   84 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEA--LAGLRSFDEALHSADKALHY   84 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHH--HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHH--HHHcCccchhhHhhhhhhhc
Confidence            3466666  445557799999999999997531 1122          2445555554  79999999999988887531


Q ss_pred             ChhhHHHHHHHHHhcCCCCCCCCC-----HhHHHHHHHHHhcCCchhHhhhhcc
Q 035927          104 DKFTWTAMIVGLAISDPFPTIRPD-----EVTYVGVLSACTHNGNETFVINSCN  152 (153)
Q Consensus       104 ~~~~~~~li~~~~~~~~~~~~~p~-----~~t~~~ll~~~~~~g~~~~a~~~~~  152 (153)
                      ..           +..   ...|+     ...++.+-.+|...|++++|++.|+
T Consensus        85 ~~-----------~~~---~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~  124 (156)
T d2hr2a1          85 FN-----------RRG---ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFK  124 (156)
T ss_dssp             HH-----------HHC---CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cc-----------ccc---cccccccchhHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence            00           000   01111     2346777888999999999988764

>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=95.08  E-value=0.042  Score=30.82  Aligned_cols=18  Identities=33%  Similarity=0.525  Sum_probs=9.8

Q ss_pred             HhccCChHHHHHHHHhcc
Q 035927           84 YCKCGDVEKAQRVLRKML  101 (153)
Q Consensus        84 ~~~~g~~~~a~~~~~~m~  101 (153)
                      |.+.|++++|++.+++..
T Consensus        56 ~~~~g~~~~A~~~y~~aL   73 (95)
T d1tjca_          56 VYQQGDLDKALLLTKKLL   73 (95)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHhcCChHHHHHHHHHHH
Confidence            455555555555555553

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=94.66  E-value=0.33  Score=32.90  Aligned_cols=143  Identities=7%  Similarity=-0.095  Sum_probs=87.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHH---HHh-------cCChHHHHHHHHHHhhCCCCCChhHH
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDG---YLR-------VNRFREALTLFPEMQTSNIRPDEFTI   75 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~---~~~-------~~~~~~a~~~~~~m~~~~~~p~~~t~   75 (153)
                      +..++....+....++|.+++++..  .| +...|+..-..   +..       .|.+++|+.+++...+.+ +-+...|
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~  110 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTW  110 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHH
Confidence            4444444444455689999999886  45 44455443322   222       344788999999987653 2244455


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHhcccC---ChhhHHHHH-HHHHhcCCCC----------CCCCC-HhHHHHHHHHHhc
Q 035927           76 VRILTAYMYCKCGDVEKAQRVLRKMLRK---DKFTWTAMI-VGLAISDPFP----------TIRPD-EVTYVGVLSACTH  140 (153)
Q Consensus        76 ~~li~~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li-~~~~~~~~~~----------~~~p~-~~t~~~ll~~~~~  140 (153)
                      .....+..+...+++++|...+....+.   +...|...+ ..+...+..+          ...|+ ...|+.+-..+.+
T Consensus       111 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~  190 (334)
T d1dcea1         111 HHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  190 (334)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            5444442123345689999999998543   455554443 3444444444          45564 5668888888899


Q ss_pred             CCchhHhhhhcc
Q 035927          141 NGNETFVINSCN  152 (153)
Q Consensus       141 ~g~~~~a~~~~~  152 (153)
                      .|+.++|...+.
T Consensus       191 ~~~~~~A~~~~~  202 (334)
T d1dcea1         191 LHPQPDSGPQGR  202 (334)
T ss_dssp             HSCCCCSSSCCS
T ss_pred             hcCHHHHHHHHH
Confidence            999988876654

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.85  E-value=0.24  Score=27.41  Aligned_cols=64  Identities=8%  Similarity=0.014  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCCC---------C-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCCh
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMPE---------R-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDE   72 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~~---------~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~   72 (153)
                      ..|-.+-..+.+.|++++|...|++-.+         + ...+++.+-.++.+.|++++|.+.+++.++.  .|+.
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l--~P~~   79 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh--CcCC
Confidence            4456778899999999999998877642         1 2567899999999999999999999999875  4653

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.52  E-value=0.15  Score=37.30  Aligned_cols=109  Identities=7%  Similarity=-0.140  Sum_probs=64.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHhCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCC-ChhHHHHHHHHHHHhc
Q 035927            9 WTDIVSGYINRGQVDIARQYFAQMPERD-YVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRP-DEFTIVRILTAYMYCK   86 (153)
Q Consensus         9 ~~~li~~~~~~g~~~~a~~l~~~m~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~t~~~li~~~~~~~   86 (153)
                      +..+-..+.+.|+.+.|..-+.+-.+++ ..++..+-..+...|++++|...|++..+.  .| +...|+.+-..  |..
T Consensus       123 ~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~--~~~  198 (497)
T d1ya0a1         123 SSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAIL--ASS  198 (497)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHH--HHH
T ss_pred             HHHhHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHH--HHH
Confidence            3444444444555555544443322221 245666777777889999999999998765  45 45677777776  689


Q ss_pred             cCChHHHHHHHHhccc---CChhhHHHHHHHHHhcCCC
Q 035927           87 CGDVEKAQRVLRKMLR---KDKFTWTAMIVGLAISDPF  121 (153)
Q Consensus        87 ~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~  121 (153)
                      .|+..+|...|.+-..   |-..++..+...+-+....
T Consensus       199 ~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~~~  236 (497)
T d1ya0a1         199 KGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALES  236 (497)
T ss_dssp             TTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhhhh
Confidence            9999999999998753   4577888888888776443

>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=93.00  E-value=0.13  Score=31.03  Aligned_cols=84  Identities=17%  Similarity=0.099  Sum_probs=56.4

Q ss_pred             HHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhc----------CChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927           16 YINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRV----------NRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~----------~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      |-+.+.+++|...|++..  .| +...+..+-..+...          +.+++|...|+..++.+ +-+..+|..+-.+ 
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~-   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNA-   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHH-
T ss_pred             HHHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHH-
Confidence            456677899999999885  34 667777777776643          44678888888887643 2355566665554 


Q ss_pred             HHhccC-----------ChHHHHHHHHhccc
Q 035927           83 MYCKCG-----------DVEKAQRVLRKMLR  102 (153)
Q Consensus        83 ~~~~~g-----------~~~~a~~~~~~m~~  102 (153)
                       |...|           .+++|.+.|++..+
T Consensus        85 -y~~~g~~~~~~~~~~~~~~~A~~~~~kal~  114 (145)
T d1zu2a1          85 -YTSFAFLTPDETEAKHNFDLATQFFQQAVD  114 (145)
T ss_dssp             -HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHHcccchhhHHHHHHhHHHhhhhhhcccc
Confidence             45443           35777777777754

>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=90.27  E-value=0.69  Score=26.26  Aligned_cols=49  Identities=20%  Similarity=0.161  Sum_probs=39.4

Q ss_pred             hHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHHHhcccC
Q 035927           53 FREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVLRKMLRK  103 (153)
Q Consensus        53 ~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~~~m~~~  103 (153)
                      .=+...-++.+-.....|+.....+.+++|  -|-+++..|.++|+.++.+
T Consensus        22 ~we~rrgmN~l~~~DlVPeP~Ii~aALrAc--RRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVPEPKIIDAALRAC--RRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHH--HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHH--HHhhhHHHHHHHHHHHHHH
Confidence            334555566666778899999999999998  9999999999999998653

>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=88.18  E-value=1.6  Score=26.10  Aligned_cols=82  Identities=13%  Similarity=0.017  Sum_probs=57.5

Q ss_pred             hcCChHHHHHHHHhCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChHHHHHHH
Q 035927           18 NRGQVDIARQYFAQMPERDYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVEKAQRVL   97 (153)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~~a~~~~   97 (153)
                      +++++......+-.+- .+...++-.++.+.+.|+-++-.++++++.+ +-+|+....-.+-.+  |.+-|...++.+++
T Consensus        68 ~C~Nlk~vv~C~~~~n-~~se~vdlALd~lv~~~kkd~Ld~i~~~l~k-n~~i~~~~llkia~A--~kkig~~re~nell  143 (161)
T d1wy6a1          68 KCQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANA--LRRVGDERDATTLL  143 (161)
T ss_dssp             GCSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHH--HHHTTCHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHHHHHHHHHHHHh-cCCCCHHHHHHHHHH--HHHhcchhhHHHHH
Confidence            3566777777776663 3444566777888888888888888888666 445666666667777  68888888888888


Q ss_pred             HhcccC
Q 035927           98 RKMLRK  103 (153)
Q Consensus        98 ~~m~~~  103 (153)
                      .+.-++
T Consensus       144 ~~ACe~  149 (161)
T d1wy6a1         144 IEACKK  149 (161)
T ss_dssp             HHHHHT
T ss_pred             HHHHHH
Confidence            776444

>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=86.35  E-value=2.4  Score=30.55  Aligned_cols=75  Identities=8%  Similarity=-0.035  Sum_probs=60.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHH
Q 035927            7 ISWTDIVSGYINRGQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus         7 ~~~~~li~~~~~~g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      ..+..+-+.+...|++++|...|.+..  .| +...|+.|-..+...|+..+|...|.+-.... .|-..++..|...+
T Consensus       153 ~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         153 HCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKAL  230 (497)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH
Confidence            356677888999999999999999876  34 77899999999999999999999888887654 35556666666653

>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=85.01  E-value=0.96  Score=26.92  Aligned_cols=77  Identities=14%  Similarity=0.109  Sum_probs=53.8

Q ss_pred             CchhHHHHHHHHHHhc----------CChHHHHHHHHhCC--CC-CHHHHHHHHHHHHhcC-----------ChHHHHHH
Q 035927            4 KDVISWTDIVSGYINR----------GQVDIARQYFAQMP--ER-DYVLWTAMIDGYLRVN-----------RFREALTL   59 (153)
Q Consensus         4 pd~~~~~~li~~~~~~----------g~~~~a~~l~~~m~--~~-~~~~~~~li~~~~~~~-----------~~~~a~~~   59 (153)
                      .|...+..+-.++...          +.+++|...|++..  .| +..+|..+-..|...|           .+++|.+.
T Consensus        29 ~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~  108 (145)
T d1zu2a1          29 LDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQF  108 (145)
T ss_dssp             TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhh
Confidence            4555677777676643          44578888888876  34 6778888888877644           35778888


Q ss_pred             HHHHhhCCCCCChhHHHHHHHHH
Q 035927           60 FPEMQTSNIRPDEFTIVRILTAY   82 (153)
Q Consensus        60 ~~~m~~~~~~p~~~t~~~li~~~   82 (153)
                      |+...+.  .|+...+..-+..+
T Consensus       109 ~~kal~l--~P~~~~~~~~L~~~  129 (145)
T d1zu2a1         109 FQQAVDE--QPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHHHHH--CTTCHHHHHHHHHH
T ss_pred             hhccccc--CCCHHHHHHHHHHH
Confidence            8877753  68878777777663

>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=83.71  E-value=5  Score=27.54  Aligned_cols=44  Identities=7%  Similarity=0.075  Sum_probs=21.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhCCCCCChhHHHHHHHHHHHhccCChH
Q 035927           40 WTAMIDGYLRVNRFREALTLFPEMQTSNIRPDEFTIVRILTAYMYCKCGDVE   91 (153)
Q Consensus        40 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~t~~~li~~~~~~~~g~~~   91 (153)
                      |.-++..+.+.++++.|.+.+...      -+..+|..+...|  .+..+..
T Consensus        43 ~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~~~l--~~~~e~~   86 (336)
T d1b89a_          43 FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFAC--VDGKEFR   86 (336)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHH--HHTTCHH
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHHHHH--HhCcHHH
Confidence            444555555555555555544322      1334555555554  4444433