Query 007621
Match_columns 595
No_of_seqs 346 out of 1223
Neff 7.4
Searched_HMMs 46136
Date Thu Mar 28 13:06:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 1.1E-60 2.5E-65 521.6 29.7 371 150-582 69-447 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 9.7E-50 2.1E-54 422.2 11.3 338 183-572 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 2E-44 4.3E-49 393.9 24.9 364 85-542 59-440 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.1E-39 1.1E-43 340.3 5.3 308 119-517 1-325 (345)
5 KOG1267 Mitochondrial transcri 100.0 6E-29 1.3E-33 269.2 16.2 331 90-550 59-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 1.2E-19 2.7E-24 196.6 13.6 241 280-542 90-334 (413)
7 smart00733 Mterf Mitochondrial 97.0 0.00061 1.3E-08 44.9 2.8 30 489-519 2-31 (31)
8 smart00733 Mterf Mitochondrial 96.6 0.0014 3.1E-08 43.1 2.0 28 337-365 3-30 (31)
9 PF11955 PORR: Plant organelle 94.6 0.35 7.5E-06 51.1 11.7 236 290-542 46-324 (335)
10 cd04790 HTH_Cfa-like_unk Helix 83.4 5.8 0.00012 37.9 8.3 23 179-201 48-70 (172)
11 cd04790 HTH_Cfa-like_unk Helix 75.5 18 0.00039 34.5 9.0 113 283-406 49-167 (172)
12 PF04695 Pex14_N: Peroxisomal 69.6 4.5 9.7E-05 37.1 3.1 39 339-381 13-51 (136)
13 PRK00117 recX recombination re 64.7 1.1E+02 0.0025 28.2 11.7 73 283-376 80-152 (157)
14 PF04695 Pex14_N: Peroxisomal 63.2 12 0.00027 34.2 4.7 31 468-498 21-51 (136)
15 PRK14135 recX recombination re 58.9 76 0.0016 32.2 10.2 23 355-377 237-259 (263)
16 TIGR01616 nitro_assoc nitrogen 58.4 20 0.00043 32.4 5.1 104 248-379 13-118 (126)
17 KOG2561 Adaptor protein NUB1, 53.6 51 0.0011 36.0 7.8 44 438-486 430-473 (568)
18 PF11212 DUF2999: Protein of u 53.5 45 0.00097 26.9 5.6 57 354-415 2-61 (82)
19 cd08306 Death_FADD Fas-associa 51.2 56 0.0012 27.3 6.4 38 287-328 19-57 (86)
20 PF10975 DUF2802: Protein of u 49.4 9.5 0.00021 30.8 1.3 34 78-111 32-65 (70)
21 TIGR00601 rad23 UV excision re 48.8 1E+02 0.0022 33.4 9.4 127 313-494 152-361 (378)
22 PF02787 CPSase_L_D3: Carbamoy 46.3 26 0.00056 31.6 3.8 72 211-304 11-84 (123)
23 PF00627 UBA: UBA/TS-N domain; 45.9 49 0.0011 22.7 4.4 23 283-305 4-26 (37)
24 PF14490 HHH_4: Helix-hairpin- 44.0 50 0.0011 28.0 5.0 66 177-266 7-73 (94)
25 PF00627 UBA: UBA/TS-N domain; 42.5 41 0.00088 23.2 3.5 21 473-493 5-25 (37)
26 COG1125 OpuBA ABC-type proline 42.0 46 0.00099 34.1 5.1 64 469-532 72-138 (309)
27 PRK09875 putative hydrolase; P 41.9 1.7E+02 0.0036 30.5 9.5 27 317-343 262-288 (292)
28 COG2137 OraA Uncharacterized p 41.3 2.1E+02 0.0046 27.4 9.3 23 282-304 88-110 (174)
29 smart00165 UBA Ubiquitin assoc 40.2 44 0.00096 22.7 3.5 19 474-492 5-23 (37)
30 PF14490 HHH_4: Helix-hairpin- 39.8 77 0.0017 26.8 5.6 22 283-304 10-31 (94)
31 PF07499 RuvA_C: RuvA, C-termi 39.3 44 0.00095 24.5 3.5 24 282-305 4-27 (47)
32 cd00194 UBA Ubiquitin Associat 38.4 48 0.001 22.7 3.4 20 473-492 4-23 (38)
33 PF08004 DUF1699: Protein of u 37.8 71 0.0015 28.8 5.0 80 292-376 27-116 (131)
34 PRK09875 putative hydrolase; P 37.2 4.2E+02 0.0091 27.5 11.6 29 386-414 262-290 (292)
35 PF11955 PORR: Plant organelle 36.8 60 0.0013 34.5 5.4 113 297-415 22-149 (335)
36 smart00165 UBA Ubiquitin assoc 36.5 53 0.0012 22.3 3.4 23 283-305 3-25 (37)
37 PF03960 ArsC: ArsC family; I 34.4 42 0.00091 29.2 3.2 79 249-349 9-91 (110)
38 KOG0011 Nucleotide excision re 34.3 1.1E+02 0.0023 32.3 6.4 116 283-416 137-266 (340)
39 cd08316 Death_FAS_TNFRSF6 Deat 33.4 3.1E+02 0.0068 23.5 8.8 41 286-330 25-66 (97)
40 PF02631 RecX: RecX family; I 31.4 44 0.00095 29.6 2.9 20 284-303 48-67 (121)
41 PF00356 LacI: Bacterial regul 30.8 62 0.0013 23.8 3.0 39 221-263 7-45 (46)
42 KOG0871 Class 2 transcription 30.6 81 0.0018 29.2 4.3 48 441-488 73-120 (156)
43 PF02631 RecX: RecX family; I 30.0 3.2E+02 0.0069 24.0 8.2 56 177-235 10-67 (121)
44 cd08315 Death_TRAILR_DR4_DR5 D 28.3 1.9E+02 0.0041 24.7 6.1 39 287-330 25-64 (96)
45 PF02022 Integrase_Zn: Integra 28.2 1.1E+02 0.0023 21.9 3.8 30 469-498 7-37 (40)
46 cd08319 Death_RAIDD Death doma 27.8 1.9E+02 0.0041 24.1 5.8 42 277-328 15-57 (83)
47 PRK14136 recX recombination re 27.3 6.4E+02 0.014 26.5 10.7 74 284-380 231-305 (309)
48 cd03035 ArsC_Yffb Arsenate Red 26.9 1.7E+02 0.0036 25.4 5.7 75 249-349 12-92 (105)
49 COG3620 Predicted transcriptio 25.0 2.5E+02 0.0054 26.7 6.5 82 221-330 15-97 (187)
50 PRK14134 recX recombination re 24.6 7.9E+02 0.017 25.3 14.9 22 388-409 257-278 (283)
51 cd01392 HTH_LacI Helix-turn-he 23.8 1.1E+02 0.0024 22.2 3.4 42 221-266 5-46 (52)
52 cd08779 Death_PIDD Death Domai 23.7 3E+02 0.0065 22.9 6.4 37 287-327 19-55 (86)
53 PRK00117 recX recombination re 23.6 5.8E+02 0.013 23.4 10.8 25 316-340 128-152 (157)
54 PRK10026 arsenate reductase; P 23.5 2.3E+02 0.005 26.1 6.2 77 249-349 15-96 (141)
55 PF14698 ASL_C2: Argininosucci 23.3 74 0.0016 25.5 2.5 23 90-113 5-27 (70)
56 TIGR01448 recD_rel helicase, p 23.0 2.6E+02 0.0056 33.0 8.0 74 182-265 81-159 (720)
57 cd08805 Death_ank1 Death domai 22.6 3.1E+02 0.0067 22.9 6.2 42 277-328 17-59 (84)
58 cd08804 Death_ank2 Death domai 22.1 3.2E+02 0.0069 22.7 6.2 38 287-328 21-59 (84)
59 cd03034 ArsC_ArsC Arsenate Red 21.6 2.7E+02 0.0059 24.2 6.1 77 249-349 12-93 (112)
60 PRK14135 recX recombination re 21.5 4.6E+02 0.01 26.4 8.6 23 388-410 237-259 (263)
61 TIGR01448 recD_rel helicase, p 21.5 1.6E+02 0.0035 34.7 5.9 82 214-304 78-166 (720)
62 smart00354 HTH_LACI helix_turn 21.2 1.3E+02 0.0028 23.8 3.6 40 221-264 8-47 (70)
63 cd03033 ArsC_15kD Arsenate Red 20.5 4.4E+02 0.0095 23.1 7.1 94 249-373 13-111 (113)
64 PF07499 RuvA_C: RuvA, C-termi 20.5 1.8E+02 0.0039 21.2 3.9 26 471-496 4-29 (47)
65 PF09098 Dehyd-heme_bind: Quin 20.4 44 0.00095 31.5 0.7 25 85-109 52-76 (167)
66 PF02742 Fe_dep_repr_C: Iron d 20.1 1.7E+02 0.0037 23.3 4.0 42 85-126 11-57 (71)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.1e-60 Score=521.56 Aligned_cols=371 Identities=20% Similarity=0.327 Sum_probs=335.0
Q ss_pred HHHHCCCCcCCCccccCccccccCCcchhhhHHHHHhhcCCCcchHHHHHHhcccccccC-chhhHHHHHHHHHCCCChH
Q 007621 150 FFESLGLSQSELSPLLPRHLMFLSDDEVLLDNFHVLCDYGIPRSKMGKMYVEATEIFRHD-RGVLASKLWAYENLGLSKN 228 (595)
Q Consensus 150 fl~slGls~~~l~~ll~~~~l~~s~d~~l~p~~~~L~~~g~s~~~i~~~~k~~p~ll~~~-~~~l~~~l~~L~~lGls~~ 228 (595)
||+++|++++++..+..| +.-..+.+.++||+++|++.+++. ++|++|+++ .+++.|+++||+++|++..
T Consensus 69 ~L~~lgi~~~~l~~~~~p-----~~~~~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~ 139 (487)
T PLN03196 69 FLRGIGIDPDELDGLELP-----STVDVMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRS 139 (487)
T ss_pred HHHHcCCCchhhhccCCC-----ccHHHHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHH
Confidence 999999999999876443 222478999999999999999997 689999999 7899999999999999999
Q ss_pred HHHHHHHhCCcceecCccchHHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCc
Q 007621 229 TVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPAL 308 (595)
Q Consensus 229 ~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~i 308 (595)
+|++++.++|.+|.++++.++.|++++|++ +|+++++|.+++.++|++
T Consensus 140 ~i~~lI~~~P~lL~~sve~~L~P~v~fL~~--------------------------------lGvs~~~i~~~l~r~P~L 187 (487)
T PLN03196 140 SLPELLRRYPQVLHASVVVDLAPVVKYLQG--------------------------------LDVKRQDIPRVLERYPEL 187 (487)
T ss_pred HHHHHHHhCCceecccHHHHHHHHHHHHHH--------------------------------cCCCHHHHHHHHHhCchh
Confidence 999999999999999999889998776655 899999999999999999
Q ss_pred cccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHHHHHhCCChhhHHHHHHhcCcccccc---c
Q 007621 309 VFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIEIGMGMKDISNMVLMHAELMGSC---S 385 (595)
Q Consensus 309 L~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s---~ 385 (595)
|+++.++++.++++||.++|++.++++++|.++|++|+++++++++|+++||+++|++.++|++++.++|++|+++ +
T Consensus 188 L~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~ 267 (487)
T PLN03196 188 LGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEET 267 (487)
T ss_pred hcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999996 6
Q ss_pred ccchHHHHHhcCCChhHHHHHHHhCCcccccccccchhhcccccccCCCCchHHHHHHH-HHcCCCCChh-HHHH-HHHH
Q 007621 386 LKGPKTVCSKLKVGRESLCQIIKDDPLKLFHLASKTEVKIDEQVDCQNPSKDVEKTEFL-LRLGYVENSE-EVTK-ALKQ 462 (595)
Q Consensus 386 lk~~i~~L~~lGv~~~~l~~lI~~~P~~L~~~~~~~~~~~~l~~s~~~~~~~~~k~~fl-~~lGf~~~~~-~~~~-al~~ 462 (595)
+++++++|+++|++++.++.+|..+|.++.. ...+++..+++|+ .++|++++.- .++. .+..
T Consensus 268 lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~---------------s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~i 332 (487)
T PLN03196 268 VKPNVECLLEFGVRKEALPSVIAQYPDILGL---------------DLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQI 332 (487)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCceeEe---------------cHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchh
Confidence 8999999999999999999999999999851 1123567788888 5799987653 2333 3333
Q ss_pred hhcChhHHHHHHHHHHHhCCCHHHHHHHHHhCCcccccChHHHHHHHHHHHHHhCCChHHHhhcCcccccccc-cccchH
Q 007621 463 FRGRGDQLQERFDCLVQAGLDSNVVRNIVKRAPMVLNQSKDVLEKKIDYLKNYLCYPLESVVAFPAYLCYDMG-RINHRC 541 (595)
Q Consensus 463 ~~~~~~~l~~r~~~L~~~G~s~~ev~~mi~~~P~iL~~s~e~L~~k~~fL~~~mg~~~~~l~~~P~~L~~sle-ri~pR~ 541 (595)
+..+.++|++|++||+++||+.+||..||+++|++|++|+++|++|++||+++||++.++|++||+||+||+| ||+|||
T Consensus 333 l~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~ 412 (487)
T PLN03196 333 VSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRY 412 (487)
T ss_pred hcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHH
Confidence 3445569999999999999999999999999999999999999999999999999999999999999999999 999999
Q ss_pred HHHHHHHHcCCCCCCCCcccccccChHHHHHHHhhhCCChH
Q 007621 542 KMYVWLRERGVAKPTLSLSTILACSDAKFEKYFVDVHPEGP 582 (595)
Q Consensus 542 ~~~~~L~~kgl~~~~~~l~~il~~sek~F~~~~v~~~~~~~ 582 (595)
++ |+++|+ +++++++++|||++|+++|+..|.|+.
T Consensus 413 ~~---L~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e~~ 447 (487)
T PLN03196 413 ER---VAKKGI---KCSLAWFLNCSDDKFEQRMSGDFIEGE 447 (487)
T ss_pred HH---HHHcCC---CCCHHHHhccCHHHHHHHHhhhccccc
Confidence 75 889998 689999999999999999999997653
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=9.7e-50 Score=422.20 Aligned_cols=338 Identities=26% Similarity=0.426 Sum_probs=223.8
Q ss_pred HHHhhcCCCcchHHHHHHhcccccccC-chhhHHHHHHHHHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCC
Q 007621 183 HVLCDYGIPRSKMGKMYVEATEIFRHD-RGVLASKLWAYENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGF 261 (595)
Q Consensus 183 ~~L~~~g~s~~~i~~~~k~~p~ll~~~-~~~l~~~l~~L~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv 261 (595)
++++++|+++.+|.++++++|.++.++ ++++.|+++||++.|++..+|++++..+|.+|..+.++++.|.++++++
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~--- 78 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKS--- 78 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTT---
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHH---
Confidence 467777777777777777777777777 6777788888877888877888888888888777766667666655544
Q ss_pred CCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHcCCChhHHHHHHhhC
Q 007621 262 KNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQN 341 (595)
Q Consensus 262 ~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~ 341 (595)
+|.+++|+.+++.++|++|..+.++++.+.++||.++|++.+.+.+++..+
T Consensus 79 -----------------------------~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~ 129 (345)
T PF02536_consen 79 -----------------------------IGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISR 129 (345)
T ss_dssp -----------------------------TSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-
T ss_pred -----------------------------HcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhc
Confidence 677777777777777777766666677777777777777776666777766
Q ss_pred CceeeccccccHHHHHHHHHHhCCChhhHHHHHHhcCcccccc---cccchHHHHHhcCCChhHHHHHHHhCCccccccc
Q 007621 342 PQILSSKFVKNLLQAVGFLIEIGMGMKDISNMVLMHAELMGSC---SLKGPKTVCSKLKVGRESLCQIIKDDPLKLFHLA 418 (595)
Q Consensus 342 P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s---~lk~~i~~L~~lGv~~~~l~~lI~~~P~~L~~~~ 418 (595)
|.++... .++.+.+++|.++|++.+++.+++.++|+++... .+++++++|+++|++.+++.+++.++|.++.
T Consensus 130 ~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~--- 204 (345)
T PF02536_consen 130 PPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLS--- 204 (345)
T ss_dssp CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGG---
T ss_pred Cccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceec---
Confidence 6655544 5677777777777777777777777777555442 4677777777777777777777777777774
Q ss_pred ccchhhcccccccCCCCchHHHHHHHHHcCCCCChhHHHHHHHHh-hcChhHHHHHHHHHHHhCCCHHHHHHHHHhCCcc
Q 007621 419 SKTEVKIDEQVDCQNPSKDVEKTEFLLRLGYVENSEEVTKALKQF-RGRGDQLQERFDCLVQAGLDSNVVRNIVKRAPMV 497 (595)
Q Consensus 419 ~~~~~~~~l~~s~~~~~~~~~k~~fl~~lGf~~~~~~~~~al~~~-~~~~~~l~~r~~~L~~~G~s~~ev~~mi~~~P~i 497 (595)
.+.++..+....+.+.|..++. ++......+ ....++++++++||.++||+.+||+.|++++|+|
T Consensus 205 -------------~s~~~~l~~~~~l~~~~~~~~~-~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~i 270 (345)
T PF02536_consen 205 -------------LSVEKILEPVLYLLSSGGVEEE-RVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQI 270 (345)
T ss_dssp -------------CGCHC----------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGG
T ss_pred -------------cccccccccccccccccccccc-ccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcch
Confidence 1223333344444444444333 333333222 3334589999999999999999999999999999
Q ss_pred cccChHHHHHHHHHHHHHhCCChHHHhhcCcccccccc-cccchHHHHHHHHHcCCCCCCCCcccccccChHHHHH
Q 007621 498 LNQSKDVLEKKIDYLKNYLCYPLESVVAFPAYLCYDMG-RINHRCKMYVWLRERGVAKPTLSLSTILACSDAKFEK 572 (595)
Q Consensus 498 L~~s~e~L~~k~~fL~~~mg~~~~~l~~~P~~L~~sle-ri~pR~~~~~~L~~kgl~~~~~~l~~il~~sek~F~~ 572 (595)
|++|.++|++|++||+++||++.++|+++|+||+||+| ||+|||+++++|+++|+ +..+++.+++.+||++|++
T Consensus 271 L~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 271 LSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp GGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred hhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcC-CCCCCHHHHhhccHHHhcC
Confidence 99999999999999999999999999999999999999 99999999999999997 6789999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2e-44 Score=393.90 Aligned_cols=364 Identities=13% Similarity=0.212 Sum_probs=315.2
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHhccCchHH------HHHHhcCC-CchhHHhhhccccccCccccchh---HHHHC
Q 007621 85 RTEAQEVLFDYLHSTRSLGYMDAEHISKNSPDFV------LNLLSKID-SGKDVTRSLMRFLRYNPINEFEP---FFESL 154 (595)
Q Consensus 85 ~~~a~~~~~~YL~~tcgLs~~~A~~~Sk~sP~~v------~~lL~~~~-s~~~v~~~~p~~L~~~p~~~l~p---fl~sl 154 (595)
..+....+.+||. +-|+....+++.- -|..| .+||+++| +.+|+. +.|.+|.++|++++.| ||+++
T Consensus 59 ~~~~~~~~~~~L~-~lgi~~~~l~~~~--~p~~~~~~~~~l~~L~s~G~~~~~i~-~~P~iL~~~v~~~l~Pvl~fL~~l 134 (487)
T PLN03196 59 KLVNREKVLDFLR-GIGIDPDELDGLE--LPSTVDVMRERVEFLHKLGLTIEDIN-EYPLVLGCSVKKNMIPVLDYLEKL 134 (487)
T ss_pred hhhhHHHHHHHHH-HcCCCchhhhccC--CCccHHHHHHHHHHHHHcCCChHHhc-cCcHHhhcCHhhhhHHHHHHHHHc
Confidence 5566778899995 5999998886643 34444 48999999 888887 6899999999999998 99999
Q ss_pred CCCcCCCccccC--ccccccCCcchhhhHHHHHhhcCCCcchHHHHHHhcccccccC-chhhHHHHHHHHHCCCChHHHH
Q 007621 155 GLSQSELSPLLP--RHLMFLSDDEVLLDNFHVLCDYGIPRSKMGKMYVEATEIFRHD-RGVLASKLWAYENLGLSKNTVI 231 (595)
Q Consensus 155 Gls~~~l~~ll~--~~~l~~s~d~~l~p~~~~L~~~g~s~~~i~~~~k~~p~ll~~~-~~~l~~~l~~L~~lGls~~~I~ 231 (595)
|++.+++++++. |.+|..+.++++.|+++||+++|++++++++++.++|++|+++ ++.+.|+++||+++|++..+|+
T Consensus 135 G~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~ 214 (487)
T PLN03196 135 GVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIG 214 (487)
T ss_pred CCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHH
Confidence 999999998877 8888888889999999999999999999999999999999999 7889999999999999999999
Q ss_pred HHHHhCCcceecCccchHHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCcccc
Q 007621 232 KLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFE 311 (595)
Q Consensus 232 klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~ 311 (595)
+++.++|++|+.++++++.|.+++|++ +|++.++|++++.++|++|++
T Consensus 215 ~il~~~P~iL~~sve~~i~P~v~fL~~--------------------------------lGv~~~~I~~il~~~P~iL~~ 262 (487)
T PLN03196 215 PMLTRFPEILGMRVGNNIKPKVDYLES--------------------------------LGLPRLAVARILEKRPYILGF 262 (487)
T ss_pred HHHHhCcHHhhcChhhhHHHHHHHHHH--------------------------------cCCCHHHHHHHHHhCCceeEc
Confidence 999999999999999888887776654 889999999999999999998
Q ss_pred CchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHHH-HHhCCChhhHHHHHHhcCcccccc--cccc
Q 007621 312 GSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFL-IEIGMGMKDISNMVLMHAELMGSC--SLKG 388 (595)
Q Consensus 312 ~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL-~~~Gl~~~~I~~il~~~P~lL~~s--~lk~ 388 (595)
+.+++++|+++||.++|++.++++.+|.++|.++++++++++.|++.|| +++|++.+++.+++.++|++++.+ .+++
T Consensus 263 sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~ 342 (487)
T PLN03196 263 DLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALK 342 (487)
T ss_pred CHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHH
Confidence 8888999999999999999999999999999999999999999999998 689999999999999999999886 5788
Q ss_pred hHHHHHhcCCChhHHHHHHHhCCcccccccccchhhcccccccCCCCchHHHHHHHHHcCCCCChhHHHHHHHHhhcChh
Q 007621 389 PKTVCSKLKVGRESLCQIIKDDPLKLFHLASKTEVKIDEQVDCQNPSKDVEKTEFLLRLGYVENSEEVTKALKQFRGRGD 468 (595)
Q Consensus 389 ~i~~L~~lGv~~~~l~~lI~~~P~~L~~~~~~~~~~~~l~~s~~~~~~~~~k~~fl~~lGf~~~~~~~~~al~~~~~~~~ 468 (595)
+++||+++|++.++++.++.++|++|. . +.+
T Consensus 343 kvefL~~~Gls~edI~~mv~k~P~lL~-------------~------------------------------------S~~ 373 (487)
T PLN03196 343 HVEFLRGRGFSAQDVAKMVVRCPQILA-------------L------------------------------------NLE 373 (487)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCCceee-------------c------------------------------------cHH
Confidence 999999999999999999999999985 1 125
Q ss_pred HHHHHHHHHH-HhCCCHHHHHHHHHhCCcccccChH-HHHHHHHHHHHHhCCChHHHhhcCcccccccccccchHH
Q 007621 469 QLQERFDCLV-QAGLDSNVVRNIVKRAPMVLNQSKD-VLEKKIDYLKNYLCYPLESVVAFPAYLCYDMGRINHRCK 542 (595)
Q Consensus 469 ~l~~r~~~L~-~~G~s~~ev~~mi~~~P~iL~~s~e-~L~~k~~fL~~~mg~~~~~l~~~P~~L~~sleri~pR~~ 542 (595)
+++++++||+ ++|++.++| .++|.+|+||.| +|+|++++|.+ -|+.. .-..+|.+|-++..-|+.
T Consensus 374 ~l~~k~dFlvneMg~~~~~I----v~fP~~LsySLEkRI~PR~~~L~~-kGl~~----sL~~~L~~sd~~F~~r~v 440 (487)
T PLN03196 374 IMKPSLEFFKKEMKRPLKEL----VEFPAYFTYGLESRIKPRYERVAK-KGIKC----SLAWFLNCSDDKFEQRMS 440 (487)
T ss_pred HHHHHHHHHHHHhCCCHHHH----HhChHHhccChhhhhHHHHHHHHH-cCCCC----CHHHHhccCHHHHHHHHh
Confidence 7899999999 899998875 699999999975 99999999987 48732 223567777667777764
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=5.1e-39 Score=340.30 Aligned_cols=308 Identities=20% Similarity=0.335 Sum_probs=227.6
Q ss_pred HHHHhcCC-Cchh---HHhhhccccccCccccchh---HHHHCCCCcCCCccccC--ccccccCCcchhhhHHHHHhhcC
Q 007621 119 LNLLSKID-SGKD---VTRSLMRFLRYNPINEFEP---FFESLGLSQSELSPLLP--RHLMFLSDDEVLLDNFHVLCDYG 189 (595)
Q Consensus 119 ~~lL~~~~-s~~~---v~~~~p~~L~~~p~~~l~p---fl~slGls~~~l~~ll~--~~~l~~s~d~~l~p~~~~L~~~g 189 (595)
++++++|| ++++ ++++.|++|.++|++++.| ||.|+|++.+++++++. |.++.++.++++.|+++||+++|
T Consensus 1 ~~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~ 80 (345)
T PF02536_consen 1 EDLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIG 80 (345)
T ss_dssp -HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTS
T ss_pred ChHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHc
Confidence 36889999 6665 6778899999999999999 99999999999999988 99999999999999999999999
Q ss_pred CCcchHHHHHHhcccccccC-chhhHHHHHHHHHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCCCCccccc
Q 007621 190 IPRSKMGKMYVEATEIFRHD-RGVLASKLWAYENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWIGR 268 (595)
Q Consensus 190 ~s~~~i~~~~k~~p~ll~~~-~~~l~~~l~~L~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~~~ 268 (595)
++++++++++.++|++|..+ .+++.+|+++|+++|++.+.+.+++...|..+... .++.+.++++
T Consensus 81 ~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l------------ 146 (345)
T PF02536_consen 81 LSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFL------------ 146 (345)
T ss_dssp S-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHH------------
T ss_pred CCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHH------------
Confidence 99999999999999999987 56999999999999999998999999999877666 3466655544
Q ss_pred ccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeecc
Q 007621 269 YLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSK 348 (595)
Q Consensus 269 ~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~s 348 (595)
.++|++++++.+++.++|.++...++++++++++||.+.|++.+++.+++.++|.++..+
T Consensus 147 --------------------~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s 206 (345)
T PF02536_consen 147 --------------------KELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLS 206 (345)
T ss_dssp --------------------CCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCG
T ss_pred --------------------HHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccc
Confidence 458999999999999999888878899999999999999999999999999999999999
Q ss_pred ccccHHHHHHHHHHhCCChhhHHHHHHhcCcccccc--cccchHHHHHhcCCChhHHHHHHHhCCcccccccccchhhcc
Q 007621 349 FVKNLLQAVGFLIEIGMGMKDISNMVLMHAELMGSC--SLKGPKTVCSKLKVGRESLCQIIKDDPLKLFHLASKTEVKID 426 (595)
Q Consensus 349 le~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s--~lk~~i~~L~~lGv~~~~l~~lI~~~P~~L~~~~~~~~~~~~ 426 (595)
.++.+.+...++...|...+ .++.++|.+++++ .+++++++|+++|++.+++++|+.++|++|.
T Consensus 207 ~~~~l~~~~~l~~~~~~~~~---~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~----------- 272 (345)
T PF02536_consen 207 VEKILEPVLYLLSSGGVEEE---RVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILS----------- 272 (345)
T ss_dssp CHC------------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGG-----------
T ss_pred cccccccccccccccccccc---ccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhh-----------
Confidence 99888777666666555544 8889999999886 5889999999999999999999999999995
Q ss_pred cccccCCCCchHHHHHHHHHcCCCCChhHHHHHHHHhhcChhHHHHHHHHHH-HhCCCHHHHHHHHHhCCcccccChH-H
Q 007621 427 EQVDCQNPSKDVEKTEFLLRLGYVENSEEVTKALKQFRGRGDQLQERFDCLV-QAGLDSNVVRNIVKRAPMVLNQSKD-V 504 (595)
Q Consensus 427 l~~s~~~~~~~~~k~~fl~~lGf~~~~~~~~~al~~~~~~~~~l~~r~~~L~-~~G~s~~ev~~mi~~~P~iL~~s~e-~ 504 (595)
. ..++++++++||. ++|++.++| .++|.+|+||.| +
T Consensus 273 --~------------------------------------s~e~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~r 310 (345)
T PF02536_consen 273 --Y------------------------------------SIEKLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKR 310 (345)
T ss_dssp --S-------------------------------------HHHHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHH
T ss_pred --c------------------------------------chhhhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhh
Confidence 1 1246899999999 899999886 489999999985 7
Q ss_pred HHHH---HHHHHHHhC
Q 007621 505 LEKK---IDYLKNYLC 517 (595)
Q Consensus 505 L~~k---~~fL~~~mg 517 (595)
|+|+ +++|.+ .|
T Consensus 311 i~PR~~~~~~l~~-~g 325 (345)
T PF02536_consen 311 IKPRYEVLKVLKS-KG 325 (345)
T ss_dssp HHHHHHHHHTT---TT
T ss_pred hhhHHHHHHHHHH-Cc
Confidence 9999 666655 46
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.96 E-value=6e-29 Score=269.18 Aligned_cols=331 Identities=25% Similarity=0.373 Sum_probs=262.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHhcc-------CchHHHHHHhcCC-Cchh---HHhhhccccccCccccchh---HHHHCC
Q 007621 90 EVLFDYLHSTRSLGYMDAEHISKN-------SPDFVLNLLSKID-SGKD---VTRSLMRFLRYNPINEFEP---FFESLG 155 (595)
Q Consensus 90 ~~~~~YL~~tcgLs~~~A~~~Sk~-------sP~~v~~lL~~~~-s~~~---v~~~~p~~L~~~p~~~l~p---fl~slG 155 (595)
.+...|++.++|++...|..+++. .|+++.++|.++| ++++ ++...|++|.+++++.+.| ++.+.|
T Consensus 59 ~f~~s~~~~s~~~~~~~~~~~~~~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g 138 (413)
T KOG1267|consen 59 NFESSYLVDSLGLSIKLARKLSREVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLG 138 (413)
T ss_pred CcceeeeccccccchhhHHHHHHHHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccC
Confidence 778899999999999999999864 6999999999999 6555 5555589999999999998 778899
Q ss_pred CCcCCCccccC--ccccccCCcchhhhHHHHHhhcC--CCcchHHHHHHhcccccccC-c-hhhHHHHHHHHHCCCChHH
Q 007621 156 LSQSELSPLLP--RHLMFLSDDEVLLDNFHVLCDYG--IPRSKMGKMYVEATEIFRHD-R-GVLASKLWAYENLGLSKNT 229 (595)
Q Consensus 156 ls~~~l~~ll~--~~~l~~s~d~~l~p~~~~L~~~g--~s~~~i~~~~k~~p~ll~~~-~-~~l~~~l~~L~~lGls~~~ 229 (595)
++.+++.+++. |.++..+.+.++.+.++|+.+++ .....+.+.. +.+.... . ..+. ++++++++|.++.+
T Consensus 139 ~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~---~~~~~~~~~~~~v~-~~~~~~~lg~~~~~ 214 (413)
T KOG1267|consen 139 LPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLL---TPVPSFLLNENSVE-RLDIRRELGVKPRL 214 (413)
T ss_pred ccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhc---cccccccccccccc-cchhhHHhCCCHHH
Confidence 99999998877 46677777788899999999985 4444444444 3344222 2 3344 88999999999999
Q ss_pred HHHHHHhCCcceecCccchHHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCcc
Q 007621 230 VIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALV 309 (595)
Q Consensus 230 I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL 309 (595)
+..++..+|.+..... .+...+.++.++|++|. . +++.+.|.++
T Consensus 215 L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~--------------------------------~--~~~v~~~~~~ 258 (413)
T KOG1267|consen 215 LKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPK--------------------------------T--REFVKAPILL 258 (413)
T ss_pred HHHHHhcCccceeeeh--hhhhhhhhHHHhccCCc--------------------------------h--hHHHhhhhhh
Confidence 9999998888887653 25555555555544443 3 6777888888
Q ss_pred ccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHHHHHhCCChhhHHHHHHhcCcccccccccch
Q 007621 310 FEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIEIGMGMKDISNMVLMHAELMGSCSLKGP 389 (595)
Q Consensus 310 ~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s~lk~~ 389 (595)
.+.++++|++++++|...|++.+|++.++.++|.+|+++.++ +..++.|+... .++ +.++|+++.+
T Consensus 259 ~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~-~~~~~~~~~~~---~~~----~~k~p~~l~~------ 324 (413)
T KOG1267|consen 259 SYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKK-NLKTTEYLLKN---PKH----ILKFPQLLRS------ 324 (413)
T ss_pred cccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhh-hhHHHHHHHhc---chh----hhhhhhhhhc------
Confidence 888888888888888888888888888888888888888764 45566665444 222 4455554422
Q ss_pred HHHHHhcCCChhHHHHHHHhCCcccccccccchhhcccccccCCCCchHHHHHHHHHcCCCCChhHHHHHHHHhhcChhH
Q 007621 390 KTVCSKLKVGRESLCQIIKDDPLKLFHLASKTEVKIDEQVDCQNPSKDVEKTEFLLRLGYVENSEEVTKALKQFRGRGDQ 469 (595)
Q Consensus 390 i~~L~~lGv~~~~l~~lI~~~P~~L~~~~~~~~~~~~l~~s~~~~~~~~~k~~fl~~lGf~~~~~~~~~al~~~~~~~~~ 469 (595)
.+..
T Consensus 325 ----------------------------------------------------------------------------s~~~ 328 (413)
T KOG1267|consen 325 ----------------------------------------------------------------------------SEDK 328 (413)
T ss_pred ----------------------------------------------------------------------------cchh
Confidence 1236
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHhCCcccccChH-HHHHHHHHHHHHhCCChHHHhhcCcccccccc-cccchHHHHHHH
Q 007621 470 LQERFDCLVQAGLDSNVVRNIVKRAPMVLNQSKD-VLEKKIDYLKNYLCYPLESVVAFPAYLCYDMG-RINHRCKMYVWL 547 (595)
Q Consensus 470 l~~r~~~L~~~G~s~~ev~~mi~~~P~iL~~s~e-~L~~k~~fL~~~mg~~~~~l~~~P~~L~~sle-ri~pR~~~~~~L 547 (595)
++++++|+...|++..|+..|++++|+++.+|.+ .++.+.+|+.+.|+++.+.++.+|++++|++| |+.||+.++.++
T Consensus 329 l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~ 408 (413)
T KOG1267|consen 329 LKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKL 408 (413)
T ss_pred hhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHH
Confidence 7889999999999999999999999999999998 99999999999999999999999999999999 999999988777
Q ss_pred HHc
Q 007621 548 RER 550 (595)
Q Consensus 548 ~~k 550 (595)
..+
T Consensus 409 ~~~ 411 (413)
T KOG1267|consen 409 GVK 411 (413)
T ss_pred hcc
Confidence 554
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.81 E-value=1.2e-19 Score=196.60 Aligned_cols=241 Identities=21% Similarity=0.296 Sum_probs=201.6
Q ss_pred hhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHH
Q 007621 280 QVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGF 359 (595)
Q Consensus 280 ~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~f 359 (595)
+...++++|+++|+++.+|..++..+|.++..+.++-+.++..+|...|.+..++..++...|.+|..+.+.++.+.++|
T Consensus 90 ~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~ 169 (413)
T KOG1267|consen 90 NPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEF 169 (413)
T ss_pred CcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHH
Confidence 44568899999999999999999999999999999999999989999999999999999999999999998999999999
Q ss_pred HHHhC--CChhhHHHHHHhcCccccc-ccccchHHHHHhcCCChhHHHHHHHhCCcccccccccchhhcccccccCCCCc
Q 007621 360 LIEIG--MGMKDISNMVLMHAELMGS-CSLKGPKTVCSKLKVGRESLCQIIKDDPLKLFHLASKTEVKIDEQVDCQNPSK 436 (595)
Q Consensus 360 L~~~G--l~~~~I~~il~~~P~lL~~-s~lk~~i~~L~~lGv~~~~l~~lI~~~P~~L~~~~~~~~~~~~l~~s~~~~~~ 436 (595)
|+.++ .....+.+.+...|..... +.++ ++++++++|+.+..+..++..+|+.... ...
T Consensus 170 l~~~~~~~~~s~~~~~~~~~~~~~~~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~-----------------~~~ 231 (413)
T KOG1267|consen 170 LKSIPPELLSSVVERLLTPVPSFLLNENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLL-----------------YLK 231 (413)
T ss_pred hhccchhhhhhHHHHhccccccccccccccc-cchhhHHhCCCHHHHHHHHhcCccceee-----------------ehh
Confidence 99985 5555666666555543333 3456 9999999999999999999999999851 115
Q ss_pred hHHHHHHHHHcCCCCChhHHHHHHHHhhcChh-HHHHHHHHHHHhCCCHHHHHHHHHhCCcccccChHHHHHHHHHHHHH
Q 007621 437 DVEKTEFLLRLGYVENSEEVTKALKQFRGRGD-QLQERFDCLVQAGLDSNVVRNIVKRAPMVLNQSKDVLEKKIDYLKNY 515 (595)
Q Consensus 437 ~~~k~~fl~~lGf~~~~~~~~~al~~~~~~~~-~l~~r~~~L~~~G~s~~ev~~mi~~~P~iL~~s~e~L~~k~~fL~~~ 515 (595)
+..++.++..+||++.+.++++|...+.+..+ ++++++++|.+.||+.+||..|++++|++|++|++++..+++|+.+.
T Consensus 232 l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~ 311 (413)
T KOG1267|consen 232 LKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN 311 (413)
T ss_pred hhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc
Confidence 67788999999999999999999999877655 99999999999999999999999999999999999766666666664
Q ss_pred hCCChHHHhhcCcccccccccccchHH
Q 007621 516 LCYPLESVVAFPAYLCYDMGRINHRCK 542 (595)
Q Consensus 516 mg~~~~~l~~~P~~L~~sleri~pR~~ 542 (595)
.+++.++|++++++.+.+.+|+.
T Consensus 312 ----~~~~~k~p~~l~~s~~~l~~~ie 334 (413)
T KOG1267|consen 312 ----PKHILKFPQLLRSSEDKLKPRIE 334 (413)
T ss_pred ----chhhhhhhhhhhccchhhhhhHH
Confidence 22255666666555556666654
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.01 E-value=0.00061 Score=44.90 Aligned_cols=30 Identities=33% Similarity=0.617 Sum_probs=27.4
Q ss_pred HHHHhCCcccccChHHHHHHHHHHHHHhCCC
Q 007621 489 NIVKRAPMVLNQSKDVLEKKIDYLKNYLCYP 519 (595)
Q Consensus 489 ~mi~~~P~iL~~s~e~L~~k~~fL~~~mg~~ 519 (595)
.++.++|.+|++++++|+++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4789999999999999999999999 79975
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.58 E-value=0.0014 Score=43.08 Aligned_cols=28 Identities=39% Similarity=0.592 Sum_probs=17.0
Q ss_pred HHhhCCceeeccccccHHHHHHHHHHhCC
Q 007621 337 LFSQNPQILSSKFVKNLLQAVGFLIEIGM 365 (595)
Q Consensus 337 ~I~~~P~lL~~sle~~l~p~~~fL~~~Gl 365 (595)
++.++|.+|+++ ++++.|+++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 455666666666 5566666666666654
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=94.63 E-value=0.35 Score=51.13 Aligned_cols=236 Identities=14% Similarity=0.101 Sum_probs=131.3
Q ss_pred hcCCCHHHHHHHHHhCCCccccCch-------hhHHHHHHHHHH----c-CCChhHHHHHHhhCCceeeccccccHH-HH
Q 007621 290 KIGYNEVQLLNLFKTNPALVFEGSG-------QKVYVLFGRLLK----L-GLKMNEVYSLFSQNPQILSSKFVKNLL-QA 356 (595)
Q Consensus 290 ~lG~s~~~I~~lv~~~P~iL~~~~e-------~~l~~~v~fL~~----l-Gl~~~~i~~~I~~~P~lL~~sle~~l~-p~ 356 (595)
.+|+....+...+.++|.|+..... =.+-+...-|.. + .-...++..-+ =.+|..|.+++|. ..
T Consensus 46 ~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL---~KLLMMS~~~rlpL~k 122 (335)
T PF11955_consen 46 QLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERL---RKLLMMSKDRRLPLSK 122 (335)
T ss_pred hcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHH---HHHhccCCCCcccHHH
Confidence 5888778899999999999875320 012222222221 1 11122332222 3467777776653 23
Q ss_pred HHHH-HHhCCChhhHHHHHHhcCcccccccccch------HHHHHhcCCChhHHHHHHH----hCCcccccccccchhhc
Q 007621 357 VGFL-IEIGMGMKDISNMVLMHAELMGSCSLKGP------KTVCSKLKVGRESLCQIIK----DDPLKLFHLASKTEVKI 425 (595)
Q Consensus 357 ~~fL-~~~Gl~~~~I~~il~~~P~lL~~s~lk~~------i~~L~~lGv~~~~l~~lI~----~~P~~L~~~~~~~~~~~ 425 (595)
+..+ .++|++++-...++.+||..|........ +.+=-++.++.-+-..... ........++-- +.
T Consensus 123 i~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp--~~- 199 (335)
T PF11955_consen 123 IAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFP--VS- 199 (335)
T ss_pred HHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeee--ec-
Confidence 4556 58999999889999999998876321111 1111123332211111110 000000000000 00
Q ss_pred ccccccCCCCchHHHHHHHHHc----------CCCCChhHHH-HHHHHhhc-----Chh-HHHHHHHHHH-HhCCCHHHH
Q 007621 426 DEQVDCQNPSKDVEKTEFLLRL----------GYVENSEEVT-KALKQFRG-----RGD-QLQERFDCLV-QAGLDSNVV 487 (595)
Q Consensus 426 ~l~~s~~~~~~~~~k~~fl~~l----------Gf~~~~~~~~-~al~~~~~-----~~~-~l~~r~~~L~-~~G~s~~ev 487 (595)
.+....-.....++++-.+++ |+++++.++. +|+.+++- .++ ...+++..|+ ++|++ +.+
T Consensus 200 -fp~G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~ 277 (335)
T PF11955_consen 200 -FPKGFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKF 277 (335)
T ss_pred -CCCCccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHH
Confidence 111111223456667777765 5677777777 67777762 334 6788999999 99999 468
Q ss_pred HHHHHhCCcccccChHHHHHHHHHHHHHhCCChHH-HhhcCcccccccccccchHH
Q 007621 488 RNIVKRAPMVLNQSKDVLEKKIDYLKNYLCYPLES-VVAFPAYLCYDMGRINHRCK 542 (595)
Q Consensus 488 ~~mi~~~P~iL~~s~e~L~~k~~fL~~~mg~~~~~-l~~~P~~L~~sleri~pR~~ 542 (595)
..|+.++|.|+..|... ..-.=||++ +|...+ |..+|.+ .++-|+.
T Consensus 278 ~~~l~rHPgIFYvS~kg-~~~TVfLrE--AY~~~~Liek~Pl~------~~r~k~~ 324 (335)
T PF11955_consen 278 RRLLLRHPGIFYVSLKG-KRHTVFLRE--AYDGGELIEKHPLV------VIREKFL 324 (335)
T ss_pred HHHHHhCCCeEEEeccC-CceEEEEee--ccCCCCCCCCCchH------HHHHHHH
Confidence 99999999999999752 122235665 455555 4567877 6666663
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=83.36 E-value=5.8 Score=37.89 Aligned_cols=23 Identities=9% Similarity=0.241 Sum_probs=17.4
Q ss_pred hhHHHHHhhcCCCcchHHHHHHh
Q 007621 179 LDNFHVLCDYGIPRSKMGKMYVE 201 (595)
Q Consensus 179 ~p~~~~L~~~g~s~~~i~~~~k~ 201 (595)
+..+..|++.|++-+.|..++..
T Consensus 48 L~~I~~lr~~G~sL~eI~~ll~~ 70 (172)
T cd04790 48 LEQICAYRSAGVSLEDIRSLLQQ 70 (172)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhc
Confidence 34577788888888888887754
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=75.50 E-value=18 Score=34.46 Aligned_cols=113 Identities=13% Similarity=0.167 Sum_probs=61.8
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH----cCCChhHHHHHHhhCCceeeccccccHHHHHH
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK----LGLKMNEVYSLFSQNPQILSSKFVKNLLQAVG 358 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~----lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~ 358 (595)
..+..++++|++-++|..++..... .....+..+++.+.. +--....+..++...+..-....- .....++
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~~~~~~~~~~~V-~~~~w~~ 123 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQQRAIATLLKQPTLLKEQRLV-TKEKWVA 123 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccC-CHHHHHH
Confidence 4677889999999999999876543 112233333333332 111122333343333222111110 1233456
Q ss_pred HHHHhCCChhhHHHHHHhcCccccccccc--chHHHHHhcCCChhHHHHH
Q 007621 359 FLIEIGMGMKDISNMVLMHAELMGSCSLK--GPKTVCSKLKVGRESLCQI 406 (595)
Q Consensus 359 fL~~~Gl~~~~I~~il~~~P~lL~~s~lk--~~i~~L~~lGv~~~~l~~l 406 (595)
.++..|+++.+..+.=..+ .... .-.+||..+|++.+++..+
T Consensus 124 l~~~~g~~~~~m~~wh~~f------e~~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 124 ILKAAGMDEADMRRWHIEF------EKMEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHcCCChHHHHHHHHHH------HHhCcHHHHHHHHHcCCCHHHHHHH
Confidence 6788999888765442221 1222 3468999999999886654
No 12
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=69.60 E-value=4.5 Score=37.08 Aligned_cols=39 Identities=18% Similarity=0.270 Sum_probs=25.3
Q ss_pred hhCCceeeccccccHHHHHHHHHHhCCChhhHHHHHHhcCccc
Q 007621 339 SQNPQILSSKFVKNLLQAVGFLIEIGMGMKDISNMVLMHAELM 381 (595)
Q Consensus 339 ~~~P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL 381 (595)
..+|.+-..++ ..+++||+..|++++||...+.+.+.--
T Consensus 13 L~~p~V~~sp~----~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 13 LQDPKVRNSPL----EKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HCTTTCCCS-H----HHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred hCCcccccCCH----HHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 44566666554 3488999999999999999988765533
No 13
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=64.67 E-value=1.1e+02 Score=28.23 Aligned_cols=73 Identities=15% Similarity=0.053 Sum_probs=39.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHHHHH
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIE 362 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~ 362 (595)
....-|..-|++.+.|..++...+ .+-++.+. ..+.+ ++...-..+. +.-.-.+.+|..
T Consensus 80 ~I~~~L~~kGi~~~~I~~~l~~~~----~d~~e~a~---~~~~k-------------~~~~~~~~~~-~~k~Ki~~~L~r 138 (157)
T PRK00117 80 RIRQELRQKGVDREIIEEALAELD----IDWEELAR---ELARK-------------KFRRPLPDDA-KEKAKLVRFLAR 138 (157)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHcC----ccHHHHHH---HHHHH-------------HcCCCCCCCH-HHHHHHHHHHHH
Confidence 355677788999988888888764 12111111 11111 1111111111 112234578888
Q ss_pred hCCChhhHHHHHHh
Q 007621 363 IGMGMKDISNMVLM 376 (595)
Q Consensus 363 ~Gl~~~~I~~il~~ 376 (595)
.|++.+.|..++..
T Consensus 139 kGF~~~~I~~~l~~ 152 (157)
T PRK00117 139 RGFSMDVIQRVLRN 152 (157)
T ss_pred CCCCHHHHHHHHHh
Confidence 88888888877754
No 14
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=63.21 E-value=12 Score=34.21 Aligned_cols=31 Identities=19% Similarity=0.272 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHhCCccc
Q 007621 468 DQLQERFDCLVQAGLDSNVVRNIVKRAPMVL 498 (595)
Q Consensus 468 ~~l~~r~~~L~~~G~s~~ev~~mi~~~P~iL 498 (595)
..+.+|++||++-|++.+||..++.+.+.-=
T Consensus 21 sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 21 SPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp S-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 3799999999999999999999999987655
No 15
>PRK14135 recX recombination regulator RecX; Provisional
Probab=58.86 E-value=76 Score=32.19 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCChhhHHHHHHhc
Q 007621 355 QAVGFLIEIGMGMKDISNMVLMH 377 (595)
Q Consensus 355 p~~~fL~~~Gl~~~~I~~il~~~ 377 (595)
-...||..-|++.+.|..++...
T Consensus 237 K~~~~L~rrGF~~~~I~~~l~~~ 259 (263)
T PRK14135 237 KLKQALYRKGFSYDDIDSFLREY 259 (263)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHh
Confidence 34579999999999999888654
No 16
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=58.41 E-value=20 Score=32.41 Aligned_cols=104 Identities=10% Similarity=0.092 Sum_probs=63.6
Q ss_pred hHHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCC--ccccCchhhHHHHHHHHH
Q 007621 248 RFVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPA--LVFEGSGQKVYVLFGRLL 325 (595)
Q Consensus 248 ~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~--iL~~~~e~~l~~~v~fL~ 325 (595)
+.+...+||.+-|++.... -+.+-+++.+++..++.+.+. ++. ..+ +.....+ ..
T Consensus 13 t~RKA~~~L~~~gi~~~~~--------------------d~~~~p~t~~eL~~~l~~~g~~~lin-~~~-~~~r~l~-~~ 69 (126)
T TIGR01616 13 NNARQKAALKASGHDVEVQ--------------------DILKEPWHADTLRPYFGNKPVGSWFN-RAA-PRVKSGE-VN 69 (126)
T ss_pred HHHHHHHHHHHCCCCcEEE--------------------eccCCCcCHHHHHHHHHHcCHHHHHh-ccc-hHhhhCC-CC
Confidence 4677888999888876531 122467888888888887641 222 112 1211222 11
Q ss_pred HcCCChhHHHHHHhhCCceeeccccccHHHHHHHHHHhCCChhhHHHHHHhcCc
Q 007621 326 KLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIEIGMGMKDISNMVLMHAE 379 (595)
Q Consensus 326 ~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~il~~~P~ 379 (595)
...++.+++..++..+|.++.+.+-.. ..- ..+|++.+++..++...|.
T Consensus 70 ~~~ls~~e~i~lm~~~P~LIKRPIi~~--~~~---~~iGf~~e~~~~~l~~~~~ 118 (126)
T TIGR01616 70 PDSIDEASALALMVSDPLLIRRPLMDL--GGI---RCAGFDREPVLSWIGLQTQ 118 (126)
T ss_pred cccCCHHHHHHHHHhCcCeEeCCEEEE--CCE---EEEcCCHHHHHHHhCCCCC
Confidence 235677888899999999888775211 110 1268888888887765554
No 17
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=53.63 E-value=51 Score=35.99 Aligned_cols=44 Identities=14% Similarity=0.058 Sum_probs=25.9
Q ss_pred HHHHHHHHHcCCCCChhHHHHHHHHhhcChhHHHHHHHHHHHhCCCHHH
Q 007621 438 VEKTEFLLRLGYVENSEEVTKALKQFRGRGDQLQERFDCLVQAGLDSNV 486 (595)
Q Consensus 438 ~~k~~fl~~lGf~~~~~~~~~al~~~~~~~~~l~~r~~~L~~~G~s~~e 486 (595)
..++..|..|||++++.. .|+.+..+ +.+.-..+|..-+=+..+
T Consensus 430 ~~~la~Lv~mGF~e~~A~--~ALe~~gn---n~~~a~~~L~~s~~n~~~ 473 (568)
T KOG2561|consen 430 GISLAELVSMGFEEGKAR--SALEAGGN---NEDTAQRLLSASVANEGE 473 (568)
T ss_pred hhhHHHHHHhccccchHH--HHHHhcCC---cHHHHHHHHHHhCCCCcc
Confidence 457788999999988644 34544433 444445566633333333
No 18
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=53.46 E-value=45 Score=26.90 Aligned_cols=57 Identities=16% Similarity=0.248 Sum_probs=40.2
Q ss_pred HHHHHHHHHhCCChhhHHHHHHhcCcccccccccchHHHHHhcCCChhHHHHH---HHhCCcccc
Q 007621 354 LQAVGFLIEIGMGMKDISNMVLMHAELMGSCSLKGPKTVCSKLKVGRESLCQI---IKDDPLKLF 415 (595)
Q Consensus 354 ~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s~lk~~i~~L~~lGv~~~~l~~l---I~~~P~~L~ 415 (595)
-|.+..|++-.++++.|..+.+. |+.+++ .....+..+|++.+.+-.+ +..+|.++.
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~NPl-~AMa~i~qLGip~eKLQ~lm~~VMqnP~Lik 61 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQNPL-AAMATIQQLGIPQEKLQQLMAQVMQNPALIK 61 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----HhhCHH-HHHHHHHHcCCCHHHHHHHHHHHhcChHHHH
Confidence 47889999999999999887654 222322 1245678899999887654 667777663
No 19
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=51.22 E-value=56 Score=27.31 Aligned_cols=38 Identities=16% Similarity=0.260 Sum_probs=31.1
Q ss_pred HHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-C
Q 007621 287 FLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL-G 328 (595)
Q Consensus 287 ~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l-G 328 (595)
+-+.+|+++.+|..+-..+|. +..+.....+..+... |
T Consensus 19 laR~LGlse~~Id~i~~~~~~----~~~eq~~~mL~~W~~~~g 57 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR----NLREQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----CHHHHHHHHHHHHHHhHC
Confidence 556899999999999999995 4556888888877764 6
No 20
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=49.35 E-value=9.5 Score=30.79 Aligned_cols=34 Identities=18% Similarity=0.082 Sum_probs=30.1
Q ss_pred cccchhhHHHHHHHHHHHHHhcCCCCHHHHHHHh
Q 007621 78 SRVSRLARTEAQEVLFDYLHSTRSLGYMDAEHIS 111 (595)
Q Consensus 78 ~~~~~~~~~~a~~~~~~YL~~tcgLs~~~A~~~S 111 (595)
..|+++.+-..+-+-.+=|+.+||||.+.|+=+.
T Consensus 32 ~~Y~~A~klv~~Ga~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 32 PLYSQAIKLVRQGASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred chHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH
Confidence 5689999888999999999999999999998654
No 21
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.78 E-value=1e+02 Score=33.42 Aligned_cols=127 Identities=16% Similarity=0.265 Sum_probs=0.0
Q ss_pred chhhHHHHHHHHHHcCCChhHHHHHHhhCCceeeccccccHHHHHHHHHHhCCC--------------------------
Q 007621 313 SGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIEIGMG-------------------------- 366 (595)
Q Consensus 313 ~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~~Gl~-------------------------- 366 (595)
........|+-+.++|+++++|.+.+... -.|-..-++||- -|++
T Consensus 152 ~g~~~e~~I~~i~eMGf~R~qV~~ALRAa--------fNNPdRAVEYL~-tGIP~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (378)
T TIGR00601 152 VGSERETTIEEIMEMGYEREEVERALRAA--------FNNPDRAVEYLL-TGIPEDPEQPEPVQQTAASTAAATTETPQH 222 (378)
T ss_pred cchHHHHHHHHHHHhCCCHHHHHHHHHHH--------hCCHHHHHHHHH-hCCCccccccccCCCcccccccccCCCCCC
Q ss_pred ----------------------------------hhhHHHHHHhcCcccccccccchHHHHHhcCCChhHHHHHHHhCCc
Q 007621 367 ----------------------------------MKDISNMVLMHAELMGSCSLKGPKTVCSKLKVGRESLCQIIKDDPL 412 (595)
Q Consensus 367 ----------------------------------~~~I~~il~~~P~lL~~s~lk~~i~~L~~lGv~~~~l~~lI~~~P~ 412 (595)
-.++..+|+.+|.+|-. +|+.+|-..-++.++|..+|+
T Consensus 223 ~~lf~~a~~~~~~~~~~~~~~g~~~l~~Lr~~pqf~~lR~~vq~NP~~L~~--------lLqql~~~nP~l~q~I~~n~e 294 (378)
T TIGR00601 223 GSVFEQAAQGGTEQPATEAAQGGNPLEFLRNQPQFQQLRQVVQQNPQLLPP--------LLQQIGQENPQLLQQISQHPE 294 (378)
T ss_pred cchhhhhhcccccccccccccCCchHHHhhcCHHHHHHHHHHHHCHHHHHH--------HHHHHHhhCHHHHHHHHHCHH
Q ss_pred ccccccccchhhcccccccCCCCchHHHHHHHHHcCCCCChhHHHHHHHH-----------------------hhcChhH
Q 007621 413 KLFHLASKTEVKIDEQVDCQNPSKDVEKTEFLLRLGYVENSEEVTKALKQ-----------------------FRGRGDQ 469 (595)
Q Consensus 413 ~L~~~~~~~~~~~~l~~s~~~~~~~~~k~~fl~~lGf~~~~~~~~~al~~-----------------------~~~~~~~ 469 (595)
.+. .++.....- ......+
T Consensus 295 ~Fl--------------------------------------~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~lT~e 336 (378)
T TIGR00601 295 QFL--------------------------------------QMLNEPVGELAGESDMEGGVGAIAEAGLPQMNQIQVTPE 336 (378)
T ss_pred HHH--------------------------------------HHhcCcccccccccccccccccccccCcccccccccCHH
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHhC
Q 007621 470 LQERFDCLVQAGLDSNVVRNIVKRA 494 (595)
Q Consensus 470 l~~r~~~L~~~G~s~~ev~~mi~~~ 494 (595)
=++-|+-|+.+||+++.|.+....|
T Consensus 337 E~~AIeRL~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 337 EKEAIERLCALGFDRGLVIQAYFAC 361 (378)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhc
No 22
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=46.31 E-value=26 Score=31.56 Aligned_cols=72 Identities=22% Similarity=0.238 Sum_probs=39.5
Q ss_pred hhhHHHHHHHHHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHH--cCCCCcccccccCCCCCCChhhhHHHHHHH
Q 007621 211 GVLASKLWAYENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKE--LGFKNDWIGRYLPGKGSYNWDQVSETLDFL 288 (595)
Q Consensus 211 ~~l~~~l~~L~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~--lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l 288 (595)
+.+---.++|+ .|++.++|..+..-.|+.|..= . ++...=+.|++ -+++ .+.+.-.
T Consensus 11 ~Rlf~i~eAlr-rG~sveeI~e~T~ID~wFL~~i-~-~Iv~~e~~L~~~~~~~~-------------------~~~L~~a 68 (123)
T PF02787_consen 11 ERLFAIAEALR-RGYSVEEIHELTKIDPWFLEQI-K-NIVDMEKELKEYLNELD-------------------PELLRKA 68 (123)
T ss_dssp THHHHHHHHHH-TTB-HHHHHHHH---HHHHHHH-H-HHHHHHHHHHHHGGG---------------------HHHHHHH
T ss_pred cHHHHHHHHHH-cCCCHHHHHHHHCccHHHHHHH-H-HHHHHHHHHHHhhccch-------------------HHHHHHH
Confidence 34444445554 4999999999998899988631 1 13333333443 1111 2356677
Q ss_pred HhcCCCHHHHHHHHHh
Q 007621 289 YKIGYNEVQLLNLFKT 304 (595)
Q Consensus 289 ~~lG~s~~~I~~lv~~ 304 (595)
+.+|||+.+|+++...
T Consensus 69 K~~GFsD~~IA~l~~~ 84 (123)
T PF02787_consen 69 KRLGFSDRQIARLWGV 84 (123)
T ss_dssp HHTT--HHHHHHHHTS
T ss_pred HHcCCCHHHHHhccCC
Confidence 8899999999998643
No 23
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=45.91 E-value=49 Score=22.73 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhC
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKTN 305 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~~ 305 (595)
+.++-|.++||++++..+++.++
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 45677778899998888888774
No 24
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=43.96 E-value=50 Score=28.01 Aligned_cols=66 Identities=24% Similarity=0.315 Sum_probs=38.1
Q ss_pred hhhhHHHHHhhcCCCcchHHHHHHhcccccccCchhhHHHHHHHHHCCCChHHHHHHHHhCCcceecCcc-chHHHHHHH
Q 007621 177 VLLDNFHVLCDYGIPRSKMGKMYVEATEIFRHDRGVLASKLWAYENLGLSKNTVIKLVSCCPSLLIGGVD-SRFVKVLEK 255 (595)
Q Consensus 177 ~l~p~~~~L~~~g~s~~~i~~~~k~~p~ll~~~~~~l~~~l~~L~~lGls~~~I~klv~~~P~lL~~~~~-~~l~~~v~~ 255 (595)
.+...+.+|..+|++...+.++++.+ | ++....+..+|..|..++. -.|+.+=+.
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~y---------------------g---~~ai~~l~~nPY~L~~~i~gi~F~~aD~i 62 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKY---------------------G---DDAIEILKENPYRLIEDIDGIGFKTADKI 62 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-------------------------TTHHHHHHH-STCCCB-SSSSBHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH---------------------h---HHHHHHHHHChHHHHHHccCCCHHHHHHH
Confidence 34556788999999988888887652 2 1344677889999998543 236555555
Q ss_pred HHHcCCCCccc
Q 007621 256 LKELGFKNDWI 266 (595)
Q Consensus 256 L~~lGv~~~~~ 266 (595)
..++|+++++.
T Consensus 63 A~~~g~~~~d~ 73 (94)
T PF14490_consen 63 ALKLGIEPDDP 73 (94)
T ss_dssp HHTTT--TT-H
T ss_pred HHHcCCCCCCH
Confidence 56677776653
No 25
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=42.51 E-value=41 Score=23.17 Aligned_cols=21 Identities=14% Similarity=0.398 Sum_probs=10.2
Q ss_pred HHHHHHHhCCCHHHHHHHHHh
Q 007621 473 RFDCLVQAGLDSNVVRNIVKR 493 (595)
Q Consensus 473 r~~~L~~~G~s~~ev~~mi~~ 493 (595)
.++-|+++||+.+++...+..
T Consensus 5 ~v~~L~~mGf~~~~~~~AL~~ 25 (37)
T PF00627_consen 5 KVQQLMEMGFSREQAREALRA 25 (37)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 344455555555555555443
No 26
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=41.97 E-value=46 Score=34.09 Aligned_cols=64 Identities=20% Similarity=0.305 Sum_probs=47.5
Q ss_pred HHHHHHHHHH-HhCC-CHHHHHHHHHhCCcccccChHHHHHHHHHHHHHhCCChH-HHhhcCccccc
Q 007621 469 QLQERFDCLV-QAGL-DSNVVRNIVKRAPMVLNQSKDVLEKKIDYLKNYLCYPLE-SVVAFPAYLCY 532 (595)
Q Consensus 469 ~l~~r~~~L~-~~G~-s~~ev~~mi~~~P~iL~~s~e~L~~k~~fL~~~mg~~~~-~l~~~P~~L~~ 532 (595)
+|+.++-|-. ..|+ +.-.|.+=|.-.|.++.++.++++.|.+-|.+-+|++++ +.-+||.=|+=
T Consensus 72 ~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLSG 138 (309)
T COG1125 72 ELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELSG 138 (309)
T ss_pred HHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcCc
Confidence 5666666655 5554 334455667789999999999999999999999999874 55566655543
No 27
>PRK09875 putative hydrolase; Provisional
Probab=41.92 E-value=1.7e+02 Score=30.52 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=18.9
Q ss_pred HHHHHHHHHHcCCChhHHHHHHhhCCc
Q 007621 317 VYVLFGRLLKLGLKMNEVYSLFSQNPQ 343 (595)
Q Consensus 317 l~~~v~fL~~lGl~~~~i~~~I~~~P~ 343 (595)
+...+..|...|++.++|.+++..||.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 444555666678888888888887774
No 28
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=41.25 E-value=2.1e+02 Score=27.40 Aligned_cols=23 Identities=9% Similarity=0.075 Sum_probs=15.6
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHh
Q 007621 282 SETLDFLYKIGYNEVQLLNLFKT 304 (595)
Q Consensus 282 ~~~l~~l~~lG~s~~~I~~lv~~ 304 (595)
....+-|...|++++.|..++..
T Consensus 88 ~rl~qeL~qkGi~~~~Ie~aL~~ 110 (174)
T COG2137 88 ARLKQELKQKGIDDEIIEEALEL 110 (174)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhc
Confidence 34556677778887777777763
No 29
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=40.17 E-value=44 Score=22.72 Aligned_cols=19 Identities=16% Similarity=0.359 Sum_probs=8.5
Q ss_pred HHHHHHhCCCHHHHHHHHH
Q 007621 474 FDCLVQAGLDSNVVRNIVK 492 (595)
Q Consensus 474 ~~~L~~~G~s~~ev~~mi~ 492 (595)
++-|.++|++.+++...+.
T Consensus 5 v~~L~~mGf~~~~a~~aL~ 23 (37)
T smart00165 5 IDQLLEMGFSREEALKALR 23 (37)
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3344444444444444443
No 30
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=39.76 E-value=77 Score=26.81 Aligned_cols=22 Identities=27% Similarity=0.502 Sum_probs=10.4
Q ss_pred HHHHHHHhcCCCHHHHHHHHHh
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKT 304 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~ 304 (595)
+.+.+|..+|++.....++++.
T Consensus 10 ~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 10 ELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp HHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHH
Confidence 3455555566555555555444
No 31
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=39.31 E-value=44 Score=24.49 Aligned_cols=24 Identities=17% Similarity=0.369 Sum_probs=19.1
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHhC
Q 007621 282 SETLDFLYKIGYNEVQLLNLFKTN 305 (595)
Q Consensus 282 ~~~l~~l~~lG~s~~~I~~lv~~~ 305 (595)
.+.++-|.++||++.++.+++.+-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 357788889999999999988875
No 32
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=38.44 E-value=48 Score=22.65 Aligned_cols=20 Identities=15% Similarity=0.484 Sum_probs=9.8
Q ss_pred HHHHHHHhCCCHHHHHHHHH
Q 007621 473 RFDCLVQAGLDSNVVRNIVK 492 (595)
Q Consensus 473 r~~~L~~~G~s~~ev~~mi~ 492 (595)
+++-|.++|++.+++...+.
T Consensus 4 ~v~~L~~mGf~~~~~~~AL~ 23 (38)
T cd00194 4 KLEQLLEMGFSREEARKALR 23 (38)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34444455555555544444
No 33
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=37.80 E-value=71 Score=28.77 Aligned_cols=80 Identities=11% Similarity=0.209 Sum_probs=53.4
Q ss_pred CCCHHHHHHHHHhCCCc--cc--cCchhhHHHHHHHHHHc-CCC--hhHHH---HHHhhCCceeeccccccHHHHHHHHH
Q 007621 292 GYNEVQLLNLFKTNPAL--VF--EGSGQKVYVLFGRLLKL-GLK--MNEVY---SLFSQNPQILSSKFVKNLLQAVGFLI 361 (595)
Q Consensus 292 G~s~~~I~~lv~~~P~i--L~--~~~e~~l~~~v~fL~~l-Gl~--~~~i~---~~I~~~P~lL~~sle~~l~p~~~fL~ 361 (595)
-=|..||-.++.+||.+ +. .+-..++-..++-|..+ |++ ..|++ +=|-. .|.++..+..++.-|+
T Consensus 27 RPSN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinE-----Yy~i~~~vi~~I~el~ 101 (131)
T PF08004_consen 27 RPSNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINE-----YYEIPESVIERIKELK 101 (131)
T ss_pred cCcchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCcc-----cccCCHHHHHHHHHHH
Confidence 34778999999999987 22 23346676777766654 765 22222 11111 1445677888999999
Q ss_pred HhCCChhhHHHHHHh
Q 007621 362 EIGMGMKDISNMVLM 376 (595)
Q Consensus 362 ~~Gl~~~~I~~il~~ 376 (595)
.-|.+.++|..-+.+
T Consensus 102 ~eG~s~eei~~ki~~ 116 (131)
T PF08004_consen 102 SEGKSEEEIAEKISR 116 (131)
T ss_pred HcCCCHHHHHHHHHH
Confidence 999999999887765
No 34
>PRK09875 putative hydrolase; Provisional
Probab=37.18 E-value=4.2e+02 Score=27.52 Aligned_cols=29 Identities=7% Similarity=0.161 Sum_probs=19.9
Q ss_pred ccchHHHHHhcCCChhHHHHHHHhCCccc
Q 007621 386 LKGPKTVCSKLKVGRESLCQIIKDDPLKL 414 (595)
Q Consensus 386 lk~~i~~L~~lGv~~~~l~~lI~~~P~~L 414 (595)
++..+..|++.|++.++|.+|+..||.-+
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~r~ 290 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPSQF 290 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHHHH
Confidence 34445567777777777777777777654
No 35
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=36.81 E-value=60 Score=34.45 Aligned_cols=113 Identities=17% Similarity=0.122 Sum_probs=67.6
Q ss_pred HHHHHHHhCCCccccCchhhHHHHHHHHH-HcCCChhHHHHHHhhCCceeeccc-cc------cHHHHHHHH--HHhCCC
Q 007621 297 QLLNLFKTNPALVFEGSGQKVYVLFGRLL-KLGLKMNEVYSLFSQNPQILSSKF-VK------NLLQAVGFL--IEIGMG 366 (595)
Q Consensus 297 ~I~~lv~~~P~iL~~~~e~~l~~~v~fL~-~lGl~~~~i~~~I~~~P~lL~~sl-e~------~l~p~~~fL--~~~Gl~ 366 (595)
.+..++..+|.=.. +- . .++-+. .+|+....+...|.++|.++.... .. ++.|...-| +|..+-
T Consensus 22 ~l~~~i~~~p~~~~--pl---~-~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~ 95 (335)
T PF11955_consen 22 RLKDLILSQPSHSL--PL---R-DLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVR 95 (335)
T ss_pred HHHHHHHcCCCCcc--cH---H-HHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHH
Confidence 45677888886221 11 1 222233 468876889999999999998643 11 233333333 233222
Q ss_pred hhhHHHHHHhcCccccccc---c-cchHHHHH-hcCCChhHHHHHHHhCCcccc
Q 007621 367 MKDISNMVLMHAELMGSCS---L-KGPKTVCS-KLKVGRESLCQIIKDDPLKLF 415 (595)
Q Consensus 367 ~~~I~~il~~~P~lL~~s~---l-k~~i~~L~-~lGv~~~~l~~lI~~~P~~L~ 415 (595)
.+.-..++.+--.+|.++. + -..+..++ ++|+|.+=...++.++|+.+.
T Consensus 96 ~~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Fr 149 (335)
T PF11955_consen 96 EEMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFR 149 (335)
T ss_pred HhChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcE
Confidence 2111333334445666653 2 24566665 699999988999999999984
No 36
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=36.47 E-value=53 Score=22.32 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=18.2
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhC
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKTN 305 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~~ 305 (595)
++++-|.++||+++++..++.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777788899988888888775
No 37
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=34.39 E-value=42 Score=29.18 Aligned_cols=79 Identities=25% Similarity=0.348 Sum_probs=39.7
Q ss_pred HHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCC----CccccCchhhHHHHHHHH
Q 007621 249 FVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNP----ALVFEGSGQKVYVLFGRL 324 (595)
Q Consensus 249 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P----~iL~~~~e~~l~~~v~fL 324 (595)
-+.+.++|++-|++...+- +.+-+++.+++..++.... .++.. .. +....+.-+
T Consensus 9 ~rka~~~L~~~gi~~~~~d--------------------~~k~p~s~~el~~~l~~~~~~~~~lin~-~~-~~~k~l~~~ 66 (110)
T PF03960_consen 9 CRKALKWLEENGIEYEFID--------------------YKKEPLSREELRELLSKLGNGPDDLINT-RS-KTYKELGKL 66 (110)
T ss_dssp HHHHHHHHHHTT--EEEEE--------------------TTTS---HHHHHHHHHHHTSSGGGGB-T-TS-HHHHHTTHH
T ss_pred HHHHHHHHHHcCCCeEeeh--------------------hhhCCCCHHHHHHHHHHhcccHHHHhcC-cc-chHhhhhhh
Confidence 4567788888776654311 1124567777777777655 23321 12 222222212
Q ss_pred HHcCCChhHHHHHHhhCCceeeccc
Q 007621 325 LKLGLKMNEVYSLFSQNPQILSSKF 349 (595)
Q Consensus 325 ~~lGl~~~~i~~~I~~~P~lL~~sl 349 (595)
....++.+++..++..+|.++.+.+
T Consensus 67 ~~~~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 67 KKDDLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp HCTTSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhhhhHHHHHHHHhChhheeCCE
Confidence 2235777777777777777776654
No 38
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=34.30 E-value=1.1e+02 Score=32.27 Aligned_cols=116 Identities=13% Similarity=0.203 Sum_probs=68.7
Q ss_pred HHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHcCCChhHHHHHHhhCCceeec------------c--
Q 007621 283 ETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKLGLKMNEVYSLFSQNPQILSS------------K-- 348 (595)
Q Consensus 283 ~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~~~~i~~~I~~~P~lL~~------------s-- 348 (595)
..+.-+-++||.++++.++++.. -++=.+.++||.+ |++...-.......|..-.. .
T Consensus 137 ~~V~~Im~MGy~re~V~~AlRAa--------fNNPeRAVEYLl~-GIP~~~~~~~~~~~~~~~~~~p~~~~p~~~~~~~~ 207 (340)
T KOG0011|consen 137 QTVQQIMEMGYDREEVERALRAA--------FNNPERAVEYLLN-GIPEDAEVPEPEKSTAAAAELPANAQPLDLFPQGA 207 (340)
T ss_pred HHHHHHHHhCccHHHHHHHHHHh--------hCChhhhHHHHhc-CCcccccCCcccCCcccCCCCCCCCChhhcCCccc
Confidence 34556667999999999988763 2345577888874 33321000000111111111 1
Q ss_pred ccccHHHHHHHHHHhCCChhhHHHHHHhcCcccccccccchHHHHHhcCCChhHHHHHHHhCCccccc
Q 007621 349 FVKNLLQAVGFLIEIGMGMKDISNMVLMHAELMGSCSLKGPKTVCSKLKVGRESLCQIIKDDPLKLFH 416 (595)
Q Consensus 349 le~~l~p~~~fL~~~Gl~~~~I~~il~~~P~lL~~s~lk~~i~~L~~lGv~~~~l~~lI~~~P~~L~~ 416 (595)
++..-.+.++||+.. -.-..+..+|..+|.+|. ..|+++|-..-++.++|..++..++.
T Consensus 208 ~~~~~~~~l~fLr~~-~qf~~lR~~iqqNP~ll~--------~~Lqqlg~~nP~L~q~Iq~nqe~Fl~ 266 (340)
T KOG0011|consen 208 VEASGGDPLEFLRNQ-PQFQQLRQMIQQNPELLH--------PLLQQLGKQNPQLLQLIQENQEAFLQ 266 (340)
T ss_pred hhhhcCCchhhhhcc-HHHHHHHHHHhhCHHHHH--------HHHHHHhhhCHHHHHHHHHHHHHHHH
Confidence 112222446777542 122367788888888775 36788888888899999999888863
No 39
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=33.37 E-value=3.1e+02 Score=23.54 Aligned_cols=41 Identities=20% Similarity=0.256 Sum_probs=31.9
Q ss_pred HHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH-cCCC
Q 007621 286 DFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK-LGLK 330 (595)
Q Consensus 286 ~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~-lGl~ 330 (595)
+|-+.+|+|+.+|..+-..+|.=. .+.....+.-|.. .|-.
T Consensus 25 ~faR~lglse~~Id~I~~~~~~d~----~Eq~~qmL~~W~~~~G~~ 66 (97)
T cd08316 25 KFVRKSGLSEPKIDEIKLDNPQDT----AEQKVQLLRAWYQSHGKT 66 (97)
T ss_pred HHHHHcCCCHHHHHHHHHcCCCCh----HHHHHHHHHHHHHHhCCC
Confidence 477899999999999999999843 4566667776665 4765
No 40
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=31.37 E-value=44 Score=29.59 Aligned_cols=20 Identities=10% Similarity=0.064 Sum_probs=12.0
Q ss_pred HHHHHHhcCCCHHHHHHHHH
Q 007621 284 TLDFLYKIGYNEVQLLNLFK 303 (595)
Q Consensus 284 ~l~~l~~lG~s~~~I~~lv~ 303 (595)
...-|+.-|++.+.|..++.
T Consensus 48 I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 48 IRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 44556667777777777776
No 41
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=30.83 E-value=62 Score=23.77 Aligned_cols=39 Identities=28% Similarity=0.515 Sum_probs=25.2
Q ss_pred HHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCCCC
Q 007621 221 ENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKN 263 (595)
Q Consensus 221 ~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~ 263 (595)
+.+|+|...+.+++...|.+ +++ .-+.+.+.++++|..|
T Consensus 7 ~~agvS~~TVSr~ln~~~~v---s~~-tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPPRV---SEE-TRERILEAAEELGYRP 45 (46)
T ss_dssp HHHTSSHHHHHHHHTTCSSS---THH-HHHHHHHHHHHHTB-S
T ss_pred HHHCcCHHHHHHHHhCCCCC---CHH-HHHHHHHHHHHHCCCC
Confidence 56799999999988777544 222 2445556666776654
No 42
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=30.65 E-value=81 Score=29.17 Aligned_cols=48 Identities=17% Similarity=0.269 Sum_probs=32.2
Q ss_pred HHHHHHcCCCCChhHHHHHHHHhhcChhHHHHHHHHHHHhCCCHHHHH
Q 007621 441 TEFLLRLGYVENSEEVTKALKQFRGRGDQLQERFDCLVQAGLDSNVVR 488 (595)
Q Consensus 441 ~~fl~~lGf~~~~~~~~~al~~~~~~~~~l~~r~~~L~~~G~s~~ev~ 488 (595)
++.|+.+||++=......++....+...+.+.|-.-|...|++.+++.
T Consensus 73 ~KALe~LgF~eYiee~~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL~ 120 (156)
T KOG0871|consen 73 IKALENLGFGEYIEEAEEVLENCKEEAKKRRRKSSKFEKSGIPEEELL 120 (156)
T ss_pred HHHHHHcchHHHHHHHHHHHHHHHHHHHHhhhhhhhHHhcCCCHHHHH
Confidence 478899999854444444444333333456777778888999999874
No 43
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=29.96 E-value=3.2e+02 Score=23.96 Aligned_cols=56 Identities=11% Similarity=0.174 Sum_probs=27.7
Q ss_pred hhhhHHHHHhhcC-CCcchHHHHHHhcccc-cccCchhhHHHHHHHHHCCCChHHHHHHHH
Q 007621 177 VLLDNFHVLCDYG-IPRSKMGKMYVEATEI-FRHDRGVLASKLWAYENLGLSKNTVIKLVS 235 (595)
Q Consensus 177 ~l~p~~~~L~~~g-~s~~~i~~~~k~~p~l-l~~~~~~l~~~l~~L~~lGls~~~I~klv~ 235 (595)
.+...++.|...| +++......+.+.-.- =.+++..+ ..-|.+-|++...|...+.
T Consensus 10 ~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I---~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 10 AIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRI---RQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHH---HHHHHHTT--HHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHH---HHHHHHHCCChHHHHHHHH
Confidence 3455567777766 3555555555442221 12222222 3456777888877777765
No 44
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=28.29 E-value=1.9e+02 Score=24.72 Aligned_cols=39 Identities=13% Similarity=0.239 Sum_probs=31.9
Q ss_pred HHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH-cCCC
Q 007621 287 FLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK-LGLK 330 (595)
Q Consensus 287 ~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~-lGl~ 330 (595)
+.+.+|+|+.+|..+-..+|. + .+.....+.-|.. .|-.
T Consensus 25 laR~LGLse~~I~~i~~~~~~----~-~eq~~qmL~~W~~~~G~~ 64 (96)
T cd08315 25 LMRQLGLSENEIDVAKANERV----T-REQLYQMLLTWVNKTGRK 64 (96)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----C-HHHHHHHHHHHHHhhCCC
Confidence 678999999999999999997 3 5578888887776 4654
No 45
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=28.18 E-value=1.1e+02 Score=21.89 Aligned_cols=30 Identities=20% Similarity=0.338 Sum_probs=22.5
Q ss_pred HHHHHHHHHH-HhCCCHHHHHHHHHhCCccc
Q 007621 469 QLQERFDCLV-QAGLDSNVVRNIVKRAPMVL 498 (595)
Q Consensus 469 ~l~~r~~~L~-~~G~s~~ev~~mi~~~P~iL 498 (595)
++-.....|. ++|++..+..++|..+|.+-
T Consensus 7 k~H~n~~~L~~~f~ip~~vAk~IV~~C~~Cq 37 (40)
T PF02022_consen 7 KYHSNAKALRHKFGIPRLVAKQIVNQCPKCQ 37 (40)
T ss_dssp HHHH-HHHHHHHHT--HHHHHHHHHHSCCHH
T ss_pred HHccCHHHHHHHHccCHHHHHHHHHHCHHHh
Confidence 4556677888 99999999999999999763
No 46
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=27.84 E-value=1.9e+02 Score=24.12 Aligned_cols=42 Identities=14% Similarity=0.393 Sum_probs=33.2
Q ss_pred ChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-C
Q 007621 277 NWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL-G 328 (595)
Q Consensus 277 ~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l-G 328 (595)
.|++ +-+.+|+++.+|..+-..+|. +..+.+...+.-+++- |
T Consensus 15 ~W~~------Lar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~r~G 57 (83)
T cd08319 15 EWEQ------VLLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQRFG 57 (83)
T ss_pred hHHH------HHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhcC
Confidence 4776 446899999999999999997 4556787777777764 6
No 47
>PRK14136 recX recombination regulator RecX; Provisional
Probab=27.27 E-value=6.4e+02 Score=26.45 Aligned_cols=74 Identities=12% Similarity=0.075 Sum_probs=40.7
Q ss_pred HHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH-cCCChhHHHHHHhhCCceeeccccccHHHHHHHHHH
Q 007621 284 TLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK-LGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIE 362 (595)
Q Consensus 284 ~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~-lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~ 362 (595)
...-|+.-|++.+.|..++... .++.+......+.+ ++- .|. . .+...-.+.||..
T Consensus 231 IrqELrQKGId~eLIEqALeei-------eEDE~E~A~~L~eKK~~~-----------~~~----d-~kek~K~iRfL~r 287 (309)
T PRK14136 231 IVSELKRHAVGDALVESVGAQL-------RETEFERAQAVWRKKFGA-----------LPQ----T-PAERAKQARFLAA 287 (309)
T ss_pred HHHHHHHcCCCHHHHHHHHHhc-------cHhHHHHHHHHHHHHhcc-----------cCc----C-HHHHHHHHHHHHH
Confidence 4566777888888888777643 12223322233322 111 111 1 0112234688888
Q ss_pred hCCChhhHHHHHHhcCcc
Q 007621 363 IGMGMKDISNMVLMHAEL 380 (595)
Q Consensus 363 ~Gl~~~~I~~il~~~P~l 380 (595)
.|++.+.|..+|..+-..
T Consensus 288 RGFS~D~I~~vLk~~~de 305 (309)
T PRK14136 288 RGFSSATIVKLLKVGDDE 305 (309)
T ss_pred CCCCHHHHHHHHHhchhc
Confidence 888888888888665443
No 48
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=26.88 E-value=1.7e+02 Score=25.37 Aligned_cols=75 Identities=15% Similarity=0.112 Sum_probs=41.1
Q ss_pred HHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-
Q 007621 249 FVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL- 327 (595)
Q Consensus 249 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l- 327 (595)
-+.+.++|.+-|++....- +.+-+++.+++..++.+.. .++-+..+=..++++
T Consensus 12 crka~~~L~~~~i~~~~~d--------------------i~~~p~s~~eL~~~l~~~g------~~~li~~~~~~yk~l~ 65 (105)
T cd03035 12 VKKARKWLEARGVAYTFHD--------------------YRKDGLDAATLERWLAKVG------WETLLNKRGTTWRKLD 65 (105)
T ss_pred HHHHHHHHHHcCCCeEEEe--------------------cccCCCCHHHHHHHHHHhC------hHHHHccCchHHHhCC
Confidence 3456677777776654211 1124666677776666543 111122222222222
Q ss_pred -----CCChhHHHHHHhhCCceeeccc
Q 007621 328 -----GLKMNEVYSLFSQNPQILSSKF 349 (595)
Q Consensus 328 -----Gl~~~~i~~~I~~~P~lL~~sl 349 (595)
.++.+++..++..+|.++...+
T Consensus 66 l~~~~~~s~~e~~~~l~~~p~LikRPI 92 (105)
T cd03035 66 DAQKAALDAAKAIALMLEHPSLIKRPV 92 (105)
T ss_pred hhhhccCCHHHHHHHHHhCcCeeecce
Confidence 3556777788888888877654
No 49
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=24.97 E-value=2.5e+02 Score=26.70 Aligned_cols=82 Identities=11% Similarity=0.218 Sum_probs=48.2
Q ss_pred HHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHH-H
Q 007621 221 ENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQL-L 299 (595)
Q Consensus 221 ~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I-~ 299 (595)
.++|+++.++++..- + -+|.++.+..-.++|. ..++.+.++.|.+.- +..| +
T Consensus 15 k~LGitQ~dLA~~aG---------V---SQ~~IArlE~G~vdPr-------------lSt~k~Il~aL~e~e--~~~ita 67 (187)
T COG3620 15 KELGITQKDLARRAG---------V---SQPYIARLEAGKVDPR-------------LSTVKRILEALEEAE--KTRITA 67 (187)
T ss_pred HHcCCCHHHHHHHcC---------c---cHHHHHHHhcCCCCcc-------------HHHHHHHHHHHHHhh--cceEeH
Confidence 357888877776531 1 2345555544444443 233444555555421 1222 3
Q ss_pred HHHHhCCCccccCchhhHHHHHHHHHHcCCC
Q 007621 300 NLFKTNPALVFEGSGQKVYVLFGRLLKLGLK 330 (595)
Q Consensus 300 ~lv~~~P~iL~~~~e~~l~~~v~fL~~lGl~ 330 (595)
+-+...|-+.. ++++.+...++.+++.|++
T Consensus 68 ~~iM~spvv~v-~pdDsi~~vv~lM~~~g~S 97 (187)
T COG3620 68 KTIMHSPVVSV-SPDDSISDVVNLMRDKGIS 97 (187)
T ss_pred hhhccCCeeEE-CchhhHHHHHHHHHHcCCc
Confidence 44555666555 7899999999999999987
No 50
>PRK14134 recX recombination regulator RecX; Provisional
Probab=24.57 E-value=7.9e+02 Score=25.34 Aligned_cols=22 Identities=5% Similarity=-0.020 Sum_probs=18.0
Q ss_pred chHHHHHhcCCChhHHHHHHHh
Q 007621 388 GPKTVCSKLKVGRESLCQIIKD 409 (595)
Q Consensus 388 ~~i~~L~~lGv~~~~l~~lI~~ 409 (595)
....||..-|++.+.|..++..
T Consensus 257 Kl~~~L~rkGf~~e~I~~vl~~ 278 (283)
T PRK14134 257 RLSNYLLRRGYSWEEVKKSLNE 278 (283)
T ss_pred HHHHHHHhCCCCHHHHHHHHHH
Confidence 4468999999999998888754
No 51
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.79 E-value=1.1e+02 Score=22.22 Aligned_cols=42 Identities=24% Similarity=0.380 Sum_probs=27.6
Q ss_pred HHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCCCCccc
Q 007621 221 ENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKNDWI 266 (595)
Q Consensus 221 ~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~~~ 266 (595)
+.+|++...|..++...|.+ +++ ....+.+.++++|..+++.
T Consensus 5 ~~~gvs~~tvs~~l~g~~~v---s~~-~~~~i~~~~~~l~~~~~~~ 46 (52)
T cd01392 5 RAAGVSVATVSRVLNGKPRV---SEE-TRERVLAAAEELGYRPNAA 46 (52)
T ss_pred HHHCcCHHHHHHHHcCCCCC---CHH-HHHHHHHHHHHhCCCCCHH
Confidence 46789999998888766532 222 2555666777777776653
No 52
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.74 E-value=3e+02 Score=22.93 Aligned_cols=37 Identities=8% Similarity=0.102 Sum_probs=30.3
Q ss_pred HHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc
Q 007621 287 FLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL 327 (595)
Q Consensus 287 ~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l 327 (595)
+-+.+|+++.+|..+-..||. +..+.+...+..+...
T Consensus 19 lar~LGlse~~Id~Ie~~~~~----dl~eq~~~mL~~W~~~ 55 (86)
T cd08779 19 IGLHLGLSYRELQRIKYNNRD----DLDEQIFDMLFSWAQR 55 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCcc----CHHHHHHHHHHHHHHh
Confidence 556899999999999999996 4456888888888764
No 53
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=23.59 E-value=5.8e+02 Score=23.42 Aligned_cols=25 Identities=16% Similarity=0.236 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHhh
Q 007621 316 KVYVLFGRLLKLGLKMNEVYSLFSQ 340 (595)
Q Consensus 316 ~l~~~v~fL~~lGl~~~~i~~~I~~ 340 (595)
.-...+.+|..-|++.+.|.+++..
T Consensus 128 ~k~Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 128 EKAKLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4456667888888888887766654
No 54
>PRK10026 arsenate reductase; Provisional
Probab=23.55 E-value=2.3e+02 Score=26.10 Aligned_cols=77 Identities=12% Similarity=0.122 Sum_probs=38.2
Q ss_pred HHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-
Q 007621 249 FVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL- 327 (595)
Q Consensus 249 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l- 327 (595)
-+.+.+||.+-|++....- +.+-+++.+++..++.+.+. ..++-+..+=..+.++
T Consensus 15 ~RKA~~wL~~~gi~~~~~d--------------------~~~~ppt~~eL~~~l~~~g~----~~~~lint~~~~yr~L~ 70 (141)
T PRK10026 15 SRNTLEMIRNSGTEPTIIH--------------------YLETPPTRDELVKLIADMGI----SVRALLRKNVEPYEELG 70 (141)
T ss_pred HHHHHHHHHHCCCCcEEEe--------------------eeCCCcCHHHHHHHHHhCCC----CHHHHHHcCCchHHHcC
Confidence 5677778887776654211 11245566666666665431 1111122221222222
Q ss_pred ----CCChhHHHHHHhhCCceeeccc
Q 007621 328 ----GLKMNEVYSLFSQNPQILSSKF 349 (595)
Q Consensus 328 ----Gl~~~~i~~~I~~~P~lL~~sl 349 (595)
+++.+++..++..+|.++...+
T Consensus 71 ~~~~~ls~~e~l~ll~~~P~LIKRPI 96 (141)
T PRK10026 71 LAEDKFTDDQLIDFMLQHPILINRPI 96 (141)
T ss_pred CCccCCCHHHHHHHHHhCccceeCcE
Confidence 3455566666666666666554
No 55
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=23.32 E-value=74 Score=25.52 Aligned_cols=23 Identities=30% Similarity=0.462 Sum_probs=18.4
Q ss_pred HHHHHHHHhcCCCCHHHHHHHhcc
Q 007621 90 EVLFDYLHSTRSLGYMDAEHISKN 113 (595)
Q Consensus 90 ~~~~~YL~~tcgLs~~~A~~~Sk~ 113 (595)
+-+.||||.. |+|+-+|-++...
T Consensus 5 TdlAD~LVr~-GipFR~AH~iVg~ 27 (70)
T PF14698_consen 5 TDLADYLVRK-GIPFREAHHIVGR 27 (70)
T ss_dssp HHHHHHHHHT-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHH
Confidence 4578999999 9999999998654
No 56
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=22.96 E-value=2.6e+02 Score=33.01 Aligned_cols=74 Identities=20% Similarity=0.231 Sum_probs=45.1
Q ss_pred HHHHhh---cCCCcchHHHHHHhcccccccC-chhhHHHHHHHHHC-CCChHHHHHHHHhCCcceecCccchHHHHHHHH
Q 007621 182 FHVLCD---YGIPRSKMGKMYVEATEIFRHD-RGVLASKLWAYENL-GLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKL 256 (595)
Q Consensus 182 ~~~L~~---~g~s~~~i~~~~k~~p~ll~~~-~~~l~~~l~~L~~l-Gls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L 256 (595)
+.||.+ -|+......+++.. |+.+ -+.+....+.|.+. |+++.....+...... ......++.+|
T Consensus 81 ~~yL~s~~~~GIG~~~A~~iv~~----fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~~~~~L 150 (720)
T TIGR01448 81 VAYLSSRSIKGVGKKLAQRIVKT----FGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERRLLAGL 150 (720)
T ss_pred HHHHhcCCCCCcCHHHHHHHHHH----hCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHHHHHHH
Confidence 456664 25555555566544 3333 35555556666665 8888887777765421 12366777888
Q ss_pred HHcCCCCcc
Q 007621 257 KELGFKNDW 265 (595)
Q Consensus 257 ~~lGv~~~~ 265 (595)
.++|+++..
T Consensus 151 ~~~gi~~~~ 159 (720)
T TIGR01448 151 QGLGIGIKL 159 (720)
T ss_pred HHcCCCHHH
Confidence 888887764
No 57
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=22.62 E-value=3.1e+02 Score=22.92 Aligned_cols=42 Identities=12% Similarity=0.280 Sum_probs=31.9
Q ss_pred ChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-C
Q 007621 277 NWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL-G 328 (595)
Q Consensus 277 ~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l-G 328 (595)
.|.+ +-+.+|+++.+|..+-..+|. +..+.....+..+.+. |
T Consensus 17 dW~~------Lar~L~vs~~dI~~I~~e~p~----~l~~Q~~~~L~~W~~r~g 59 (84)
T cd08805 17 SWAE------LARELQFSVEDINRIRVENPN----SLLEQSTALLNLWVDREG 59 (84)
T ss_pred hHHH------HHHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHHhcC
Confidence 5765 456899999999999999996 3445666777777764 5
No 58
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=22.13 E-value=3.2e+02 Score=22.68 Aligned_cols=38 Identities=18% Similarity=0.280 Sum_probs=30.1
Q ss_pred HHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHHc-C
Q 007621 287 FLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLKL-G 328 (595)
Q Consensus 287 ~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~l-G 328 (595)
+-+.+||++.+|..+-..+|. +..+.....+..+... |
T Consensus 21 LAr~Lg~se~dI~~i~~~~~~----~~~eq~~~mL~~W~~r~g 59 (84)
T cd08804 21 LARELDFTEEQIHQIRIENPN----SLQDQSHALLKYWLERDG 59 (84)
T ss_pred HHHHcCCCHHHHHHHHHHCcc----cHHHHHHHHHHHHHHccC
Confidence 446899999999999999996 3455777777877764 5
No 59
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=21.65 E-value=2.7e+02 Score=24.22 Aligned_cols=77 Identities=13% Similarity=0.130 Sum_probs=39.7
Q ss_pred HHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH--
Q 007621 249 FVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK-- 326 (595)
Q Consensus 249 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~-- 326 (595)
-+.+.+||++-|++...+- +.+-+++.+++..++...+. ..++-+..+=..+.+
T Consensus 12 ~rkA~~~L~~~~i~~~~~d--------------------i~~~~~t~~el~~~l~~~~~----~~~~lin~~~~~y~~l~ 67 (112)
T cd03034 12 SRNALALLEEAGIEPEIVE--------------------YLKTPPTAAELRELLAKLGI----SPRDLLRTKEAPYKELG 67 (112)
T ss_pred HHHHHHHHHHCCCCeEEEe--------------------cccCCcCHHHHHHHHHHcCC----CHHHHHhcCCchHHHcC
Confidence 4567778887766544210 12356666676666666541 111111111112222
Q ss_pred ---cCCChhHHHHHHhhCCceeeccc
Q 007621 327 ---LGLKMNEVYSLFSQNPQILSSKF 349 (595)
Q Consensus 327 ---lGl~~~~i~~~I~~~P~lL~~sl 349 (595)
.+++.+++..++..+|.++.+.+
T Consensus 68 ~~~~~ls~~e~i~ll~~~P~LikRPI 93 (112)
T cd03034 68 LADPELSDEELIDAMAAHPILIERPI 93 (112)
T ss_pred CCccCCCHHHHHHHHHhCcCcccCCE
Confidence 24566666677777777766654
No 60
>PRK14135 recX recombination regulator RecX; Provisional
Probab=21.55 E-value=4.6e+02 Score=26.41 Aligned_cols=23 Identities=4% Similarity=0.062 Sum_probs=18.9
Q ss_pred chHHHHHhcCCChhHHHHHHHhC
Q 007621 388 GPKTVCSKLKVGRESLCQIIKDD 410 (595)
Q Consensus 388 ~~i~~L~~lGv~~~~l~~lI~~~ 410 (595)
....+|..-|++.+.|..++...
T Consensus 237 K~~~~L~rrGF~~~~I~~~l~~~ 259 (263)
T PRK14135 237 KLKQALYRKGFSYDDIDSFLREY 259 (263)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHh
Confidence 45679999999999998888653
No 61
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=21.51 E-value=1.6e+02 Score=34.73 Aligned_cols=82 Identities=16% Similarity=0.205 Sum_probs=39.3
Q ss_pred HHHHHHHHH---CCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHc-CCCCcccccccCCCCCCChh---hhHHHHH
Q 007621 214 ASKLWAYEN---LGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKEL-GFKNDWIGRYLPGKGSYNWD---QVSETLD 286 (595)
Q Consensus 214 ~~~l~~L~~---lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~l-Gv~~~~~~~~l~~~~~~~~~---~~~~~l~ 286 (595)
..-+.||.+ -|+.+..-.+++..+..=...- +..--+.|.++ |+.+....... ..|. ...+.+.
T Consensus 78 ~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~----i~~~~~~L~~v~gi~~~~~~~i~-----~~~~~~~~~~~~~~ 148 (720)
T TIGR01448 78 EGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDV----LDDDPEKLLEVPGISKANLEKFV-----SQWSQQGDERRLLA 148 (720)
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHH----HHhCHHHHhcCCCCCHHHHHHHH-----HHHHHhHHHHHHHH
Confidence 344567764 3777777777776664211111 11112223332 33333322111 1232 2345666
Q ss_pred HHHhcCCCHHHHHHHHHh
Q 007621 287 FLYKIGYNEVQLLNLFKT 304 (595)
Q Consensus 287 ~l~~lG~s~~~I~~lv~~ 304 (595)
+|.++|++.....++...
T Consensus 149 ~L~~~gi~~~~a~ki~~~ 166 (720)
T TIGR01448 149 GLQGLGIGIKLAQRIYKF 166 (720)
T ss_pred HHHHcCCCHHHHHHHHHH
Confidence 777777776666555554
No 62
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=21.17 E-value=1.3e+02 Score=23.78 Aligned_cols=40 Identities=28% Similarity=0.383 Sum_probs=25.8
Q ss_pred HHCCCChHHHHHHHHhCCcceecCccchHHHHHHHHHHcCCCCc
Q 007621 221 ENLGLSKNTVIKLVSCCPSLLIGGVDSRFVKVLEKLKELGFKND 264 (595)
Q Consensus 221 ~~lGls~~~I~klv~~~P~lL~~~~~~~l~~~v~~L~~lGv~~~ 264 (595)
+.+|++...|..++...|.+ +++ .-..+.+.++++|..+.
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v---~~~-t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV---SEE-TREKVLAAMEELGYIPN 47 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC---CHH-HHHHHHHHHHHhCCCCC
Confidence 45788888888887766665 333 24455566666666554
No 63
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=20.47 E-value=4.4e+02 Score=23.12 Aligned_cols=94 Identities=14% Similarity=0.164 Sum_probs=51.2
Q ss_pred HHHHHHHHHHcCCCCcccccccCCCCCCChhhhHHHHHHHHhcCCCHHHHHHHHHhCCCccccCchhhHHHHHHHHHH--
Q 007621 249 FVKVLEKLKELGFKNDWIGRYLPGKGSYNWDQVSETLDFLYKIGYNEVQLLNLFKTNPALVFEGSGQKVYVLFGRLLK-- 326 (595)
Q Consensus 249 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~l~~l~~lG~s~~~I~~lv~~~P~iL~~~~e~~l~~~v~fL~~-- 326 (595)
-+.+.+||++-|++.... + +.+-+.+.+++..++...+. ++-+..+-..+++
T Consensus 13 crkA~~~L~~~gi~~~~~-------------------d-~~~~p~s~~eL~~~l~~~g~------~~l~n~~~~~~r~~~ 66 (113)
T cd03033 13 NARQKALLEAAGHEVEVR-------------------D-LLTEPWTAETLRPFFGDLPV------AEWFNPAAPRVKSGE 66 (113)
T ss_pred HHHHHHHHHHcCCCcEEe-------------------e-hhcCCCCHHHHHHHHHHcCH------HHHHhcccHHHHhcC
Confidence 456677788777665421 1 12356777777777776541 1122222222332
Q ss_pred ---cCCChhHHHHHHhhCCceeeccccccHHHHHHHHHHhCCChhhHHHH
Q 007621 327 ---LGLKMNEVYSLFSQNPQILSSKFVKNLLQAVGFLIEIGMGMKDISNM 373 (595)
Q Consensus 327 ---lGl~~~~i~~~I~~~P~lL~~sle~~l~p~~~fL~~~Gl~~~~I~~i 373 (595)
..++.+++..++..+|.++...+-.. .. - -.+|++.+++..+
T Consensus 67 ~~~~~ls~~e~~~ll~~~P~LikRPIv~~--~~--~-~~vG~~~e~~~~~ 111 (113)
T cd03033 67 VVPEALDEEEALALMIADPLLIRRPLMQV--GD--R-RMVGFDTARVDAW 111 (113)
T ss_pred CCccCCCHHHHHHHHHhCcceeeCCeEEE--CC--E-EEecCCHHHHHHH
Confidence 24566777888888888877665210 00 0 1156666666554
No 64
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=20.45 E-value=1.8e+02 Score=21.22 Aligned_cols=26 Identities=12% Similarity=0.289 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHhCCc
Q 007621 471 QERFDCLVQAGLDSNVVRNIVKRAPM 496 (595)
Q Consensus 471 ~~r~~~L~~~G~s~~ev~~mi~~~P~ 496 (595)
.+-++-|..+||+..++..++.+...
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~ 29 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLE 29 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhc
Confidence 44456677888888888877776543
No 65
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=20.38 E-value=44 Score=31.52 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHH
Q 007621 85 RTEAQEVLFDYLHSTRSLGYMDAEH 109 (595)
Q Consensus 85 ~~~a~~~~~~YL~~tcgLs~~~A~~ 109 (595)
..+-+.++++||.++.||.++.++.
T Consensus 52 s~eer~avVkYLAd~~GLap~Et~~ 76 (167)
T PF09098_consen 52 SPEERRAVVKYLADTQGLAPSETAP 76 (167)
T ss_dssp -HHHHHHHHHHHHHHT---CGGCTT
T ss_pred CHHHHHHHHHHHHHccCCCchhhcc
Confidence 4556788999999999999988764
No 66
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=20.07 E-value=1.7e+02 Score=23.26 Aligned_cols=42 Identities=17% Similarity=0.196 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHhcc-----CchHHHHHHhcCC
Q 007621 85 RTEAQEVLFDYLHSTRSLGYMDAEHISKN-----SPDFVLNLLSKID 126 (595)
Q Consensus 85 ~~~a~~~~~~YL~~tcgLs~~~A~~~Sk~-----sP~~v~~lL~~~~ 126 (595)
.-..+..+..||+...|++.+.|..-+-. ||..+..+-.-++
T Consensus 11 i~~rH~~le~fl~~~lgv~~~~a~~~A~~iEH~is~e~~~~l~~~l~ 57 (71)
T PF02742_consen 11 ILRRHRILEEFLVEVLGVDEEEAEEEACRIEHVISPETIERLCKFLG 57 (71)
T ss_dssp HHHHHHHHHHHHHHTTT--HHHHHHHHHHHGCCS-HHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHccCCHHHHHHHHHHhc
Confidence 45678899999999999999999888775 7777766555443
Done!