Query 007270
Match_columns 610
No_of_seqs 344 out of 1343
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 21:17:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007270.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007270hhsearch_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 1.4E-60 3.1E-65 524.4 33.3 349 243-607 94-446 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 1.4E-52 2.9E-57 446.0 10.6 332 261-598 7-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.6E-45 3.6E-50 405.2 33.5 311 241-575 124-441 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.9E-37 1.3E-41 326.0 9.7 285 243-548 35-325 (345)
5 KOG1267 Mitochondrial transcri 100.0 9.6E-32 2.1E-36 292.8 15.5 314 244-582 94-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 1E-20 2.2E-25 206.4 14.0 327 155-546 78-408 (413)
7 smart00733 Mterf Mitochondrial 96.4 0.0017 3.8E-08 43.1 1.7 28 520-549 3-30 (31)
8 smart00733 Mterf Mitochondrial 96.2 0.0043 9.4E-08 41.1 2.6 30 483-513 2-31 (31)
9 cd04790 HTH_Cfa-like_unk Helix 88.7 1.6 3.6E-05 42.0 7.7 20 428-447 118-137 (172)
10 cd04790 HTH_Cfa-like_unk Helix 88.1 3 6.6E-05 40.2 9.0 50 393-448 118-167 (172)
11 PF11212 DUF2999: Protein of u 79.9 12 0.00027 30.4 7.5 55 359-420 2-59 (82)
12 PRK14135 recX recombination re 75.3 1E+02 0.0022 31.5 15.5 112 293-417 36-149 (263)
13 PF04695 Pex14_N: Peroxisomal 74.1 4.9 0.00011 37.2 4.5 29 499-527 22-50 (136)
14 PF11955 PORR: Plant organelle 73.4 37 0.0008 36.4 11.5 66 488-558 247-315 (335)
15 PF14490 HHH_4: Helix-hairpin- 65.9 17 0.00038 31.2 5.9 46 285-354 6-51 (94)
16 PRK14136 recX recombination re 64.5 1.1E+02 0.0024 32.3 12.4 22 502-523 280-301 (309)
17 PF02631 RecX: RecX family; I 63.7 20 0.00043 32.1 6.1 13 358-370 11-23 (121)
18 PRK14135 recX recombination re 61.6 1.9E+02 0.0042 29.4 16.2 223 253-524 32-259 (263)
19 PF14490 HHH_4: Helix-hairpin- 60.6 18 0.0004 31.0 5.1 22 393-414 8-29 (94)
20 PF14698 ASL_C2: Argininosucci 54.8 11 0.00023 30.8 2.5 23 89-111 5-27 (70)
21 PHA01351 putative minor struct 52.7 2.8E+02 0.006 32.6 13.6 22 431-452 694-715 (1070)
22 TIGR01448 recD_rel helicase, p 52.7 79 0.0017 37.5 10.2 86 287-382 77-167 (720)
23 COG1393 ArsC Arsenate reductas 50.7 20 0.00044 32.3 3.8 39 478-521 77-115 (117)
24 PF00627 UBA: UBA/TS-N domain; 50.6 26 0.00056 24.5 3.6 21 431-451 5-25 (37)
25 PF02631 RecX: RecX family; I 47.3 2E+02 0.0043 25.5 9.9 109 391-523 9-118 (121)
26 PF00627 UBA: UBA/TS-N domain; 46.2 52 0.0011 23.0 4.6 23 395-417 4-26 (37)
27 PF11955 PORR: Plant organelle 45.9 33 0.00072 36.7 5.2 40 491-530 109-150 (335)
28 PRK09875 putative hydrolase; P 45.6 1.7E+02 0.0038 30.6 10.4 131 271-419 149-288 (292)
29 PRK14134 recX recombination re 44.7 3.9E+02 0.0084 27.9 14.0 108 296-417 43-151 (283)
30 PRK00117 recX recombination re 44.6 2.7E+02 0.0058 26.0 14.6 21 503-523 132-152 (157)
31 TIGR01448 recD_rel helicase, p 43.1 2.5E+02 0.0053 33.5 12.3 76 261-345 90-166 (720)
32 PRK00116 ruvA Holliday junctio 42.3 1E+02 0.0022 30.1 7.7 25 428-452 149-173 (192)
33 TIGR00601 rad23 UV excision re 40.9 1.3E+02 0.0028 32.8 8.8 42 357-406 155-196 (378)
34 COG3620 Predicted transcriptio 39.9 1.1E+02 0.0024 29.3 6.9 51 391-442 48-98 (187)
35 PF04695 Pex14_N: Peroxisomal 39.8 55 0.0012 30.2 5.1 37 344-384 13-49 (136)
36 PF11212 DUF2999: Protein of u 39.8 74 0.0016 26.1 4.9 50 394-450 2-51 (82)
37 TIGR00601 rad23 UV excision re 39.1 2.4E+02 0.0053 30.7 10.6 42 286-335 155-196 (378)
38 PRK00117 recX recombination re 38.8 2.3E+02 0.0049 26.4 9.2 22 395-416 131-152 (157)
39 PF07499 RuvA_C: RuvA, C-termi 38.5 30 0.00064 25.8 2.5 23 429-451 4-26 (47)
40 cd00194 UBA Ubiquitin Associat 38.1 44 0.00096 23.2 3.2 24 502-525 3-26 (38)
41 KOG0400 40S ribosomal protein 37.9 39 0.00084 30.9 3.5 70 382-451 22-94 (151)
42 smart00165 UBA Ubiquitin assoc 37.5 46 0.001 22.9 3.2 23 502-524 3-25 (37)
43 COG2137 OraA Uncharacterized p 36.2 3.1E+02 0.0068 26.5 9.7 56 358-416 54-110 (174)
44 PF00356 LacI: Bacterial regul 35.8 67 0.0015 23.9 4.0 37 402-441 8-44 (46)
45 PF14117 DUF4287: Domain of un 35.3 1.3E+02 0.0029 23.9 5.8 51 246-308 4-55 (61)
46 PF08004 DUF1699: Protein of u 32.5 1.1E+02 0.0023 28.1 5.3 80 442-523 30-116 (131)
47 PHA01351 putative minor struct 31.7 5.8E+02 0.013 30.1 12.0 53 259-311 651-715 (1070)
48 PF06089 Asparaginase_II: L-as 30.8 63 0.0014 34.4 4.3 52 243-304 48-99 (324)
49 PRK14134 recX recombination re 28.2 7E+02 0.015 26.0 16.3 221 261-523 44-278 (283)
50 PRK08561 rps15p 30S ribosomal 28.0 1.8E+02 0.004 27.4 6.3 30 386-415 26-55 (151)
51 PRK00116 ruvA Holliday junctio 27.7 2.3E+02 0.005 27.6 7.5 88 327-417 73-173 (192)
52 cd01392 HTH_LacI Helix-turn-he 26.9 1.4E+02 0.003 21.9 4.6 13 368-380 7-19 (52)
53 cd08808 CARD_CARD11_CARMA1 Cas 26.5 62 0.0013 27.5 2.7 24 164-187 59-82 (86)
54 PF02787 CPSase_L_D3: Carbamoy 26.4 2.1E+02 0.0045 26.0 6.3 78 350-449 5-82 (123)
55 PTZ00072 40S ribosomal protein 26.1 2E+02 0.0043 27.0 6.1 35 383-417 20-54 (148)
56 PF07499 RuvA_C: RuvA, C-termi 25.4 68 0.0015 23.8 2.5 18 326-343 7-24 (47)
57 smart00354 HTH_LACI helix_turn 25.3 1.8E+02 0.0038 23.3 5.2 39 403-444 10-48 (70)
58 smart00354 HTH_LACI helix_turn 24.1 1.6E+02 0.0036 23.5 4.8 43 367-412 9-51 (70)
59 smart00657 RPOL4c DNA-directed 23.9 4.4E+02 0.0095 23.5 8.0 26 358-383 57-82 (118)
60 cd01392 HTH_LacI Helix-turn-he 23.7 1.8E+02 0.0039 21.3 4.7 43 401-446 5-47 (52)
61 KOG0400 40S ribosomal protein 23.3 62 0.0013 29.7 2.2 50 262-313 10-59 (151)
62 cd08785 CARD_CARD9-like Caspas 22.8 1.1E+02 0.0023 26.1 3.5 21 91-111 21-42 (86)
63 smart00657 RPOL4c DNA-directed 22.6 4.2E+02 0.0091 23.7 7.6 56 389-449 53-108 (118)
64 PF02330 MAM33: Mitochondrial 22.4 77 0.0017 31.2 3.0 29 85-113 158-186 (204)
65 PHA02591 hypothetical protein; 22.4 1.9E+02 0.0041 24.3 4.6 22 357-378 47-68 (83)
66 KOG4168 Predicted RNA polymera 21.4 6.9E+02 0.015 23.5 9.4 29 391-419 70-98 (149)
67 KOG2629 Peroxisomal membrane a 21.1 1.3E+02 0.0029 31.3 4.4 25 499-523 21-45 (300)
68 PF03874 RNA_pol_Rpb4: RNA pol 20.9 2.2E+02 0.0047 25.1 5.4 26 358-383 59-84 (117)
69 COG1135 AbcC ABC-type metal io 20.5 78 0.0017 33.6 2.7 33 409-441 151-194 (339)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.4e-60 Score=524.43 Aligned_cols=349 Identities=23% Similarity=0.468 Sum_probs=337.4
Q ss_pred hhhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCH-HH
Q 007270 243 QTLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNI-KA 321 (610)
Q Consensus 243 ~vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~-~~ 321 (610)
+++.||++ +|+++++|. ++|.+|.+++++++.|+++||.++|++..+|++++.++|.+|.++. .+
T Consensus 94 ~~l~~L~s----------~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~ 159 (487)
T PLN03196 94 ERVEFLHK----------LGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVD 159 (487)
T ss_pred HHHHHHHH----------cCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHH
Confidence 45788887 699999996 6999999999999999999999999999999999999999999998 68
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCCh-hHHHHHHHHH
Q 007270 322 IRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCST-SKLKLMLDQL 400 (610)
Q Consensus 322 L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~-~~l~~~l~~L 400 (610)
+.|+++||+++|++++++.+++.++|++|+.++++.+.+.++||+++|++.++|++++.++|++|+++. +++++.+++|
T Consensus 160 L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL 239 (487)
T PLN03196 160 LAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYL 239 (487)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999998 7899999999
Q ss_pred HHcCCChhHHHHHHHhCCcccccCch-hHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHHHHH-HcCCCC
Q 007270 401 GELGVENKKLGQVIAKSPQLLLRKPQ-EFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKIDFLI-GIGISK 478 (610)
Q Consensus 401 ~elG~~~~~l~~il~~~P~lL~~s~~-~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL~-~lGls~ 478 (610)
+++|++.+.+++++.++|++|..+.+ ++.+++++|+++|++++++..+++++|.++..++++++.++++||. ++|++.
T Consensus 240 ~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~ 319 (487)
T PLN03196 240 ESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDP 319 (487)
T ss_pred HHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCH
Confidence 99999999999999999999999987 7999999999999999999999999999999999999999999996 699999
Q ss_pred CcHHHHHhhCCccccccccccchhHHHHHHHhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHHcCCChhHHhhcC
Q 007270 479 DHLPRTIKKYPELLVSDVDRTLLPRIKYLMEMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNTMEKSLQDVVAYP 558 (610)
Q Consensus 479 ~~i~~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~~~~~Iv~~P 558 (610)
+++.+++.++|.+++.|. ++|++|++||+++||+.++|..||+++|+||++|.+ +|++|++||+++||++.++|+++|
T Consensus 320 e~i~~~v~k~P~il~lSe-~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~-~l~~k~dFlvneMg~~~~~Iv~fP 397 (487)
T PLN03196 320 EDFGRVIEKLPQIVSLNR-NVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLE-IMKPSLEFFKKEMKRPLKELVEFP 397 (487)
T ss_pred HHHHHHHHhcchhhcccH-HHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHH-HHHHHHHHHHHHhCCCHHHHHhCh
Confidence 999999999999999995 589999999999999999999999999999999997 599999999999999999999999
Q ss_pred ccccccccchHHhHHHHHHhcCCCCChHHhhcCChHHHHhhccccCCCC
Q 007270 559 RYFSYSLEKKIKPRFWVLKGRNIECSLEEMLGKNDDEFATEFLLAPSAH 607 (610)
Q Consensus 559 ~~L~ySlekRI~pR~~vL~~~Gl~~sl~~vL~~sdk~F~~~yV~~y~~~ 607 (610)
+||+||+|+||+|||++|+++|++++|.++|.|||++|+++||.+|.|-
T Consensus 398 ~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r~v~~y~e~ 446 (487)
T PLN03196 398 AYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQRMSGDFIEG 446 (487)
T ss_pred HHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHHHhhhcccc
Confidence 9999999999999999999999999999999999999999999999873
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=1.4e-52 Score=446.03 Aligned_cols=332 Identities=37% Similarity=0.649 Sum_probs=261.4
Q ss_pred CCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecC-HHHHHHHHHHHHHhCCChHHH
Q 007270 261 LGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWN-IKAIRTKALAFEEIGAVDNDV 339 (610)
Q Consensus 261 lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s-~~~L~~~l~~L~~lG~s~~~v 339 (610)
+||++++|.++++++|.+|.+++++++.|+++||++.|++..+|++++..+|.|+.++ .+.+.+.+++|+++|++++++
T Consensus 7 ~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~ 86 (345)
T PF02536_consen 7 HGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDI 86 (345)
T ss_dssp HHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHH
T ss_pred cCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHH
Confidence 6999999999999999999999999999999999999999999999999999999999 489999999999999999999
Q ss_pred HHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhCCc
Q 007270 340 GKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQ 419 (610)
Q Consensus 340 ~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~P~ 419 (610)
++++.++|++|..+.+.++.+++++|+++|++.+.+..++..+|..+... +++++.++++.++|++++.+++++..+|.
T Consensus 87 ~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~-~~~~~~v~~l~~lG~~~~~~~~vi~~~P~ 165 (345)
T PF02536_consen 87 VKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS-EKIKERVEFLKELGFDPEKIGRVIAKNPR 165 (345)
T ss_dssp HHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS--HHHHCHHHHHCCCTSSHHHHCCCHHHHHH
T ss_pred HHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch-hHHHHHHHHHHHhCCCchhhcccccccch
Confidence 99999999999998888999999999999999998999999998866655 89999999999999999999999999996
Q ss_pred ccccC-chhHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHHHHHHcCCCCCcHHHHHhhCCccccccccc
Q 007270 420 LLLRK-PQEFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKIDFLIGIGISKDHLPRTIKKYPELLVSDVDR 498 (610)
Q Consensus 420 lL~~s-~~~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL~~lGls~~~i~~~I~~~P~iL~~sle~ 498 (610)
++... .+.+.++++||+++|++.+++.+++.++|.++..+.++.++....++...|...+ +++.++|.++.++. +
T Consensus 166 ~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~---~~i~~~p~il~~~~-~ 241 (345)
T PF02536_consen 166 LLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE---RVIKKFPQILSLSE-E 241 (345)
T ss_dssp HHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC------------------------------THHH-H
T ss_pred hhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccc---ccccccccccccch-H
Confidence 66555 4579999999999999999999999999999999988666665555544554444 89999999999995 5
Q ss_pred cchhHHHHHHHhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHHcCCChhHHhhcCccccccccchHHhHHHH---
Q 007270 499 TLLPRIKYLMEMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNTMEKSLQDVVAYPRYFSYSLEKKIKPRFWV--- 575 (610)
Q Consensus 499 ~L~~kv~~L~~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~~~~~Iv~~P~~L~ySlekRI~pR~~v--- 575 (610)
++.+++++|.++|++.+++..|++++|++|++|.|+ +++|++||+++||++.++|+++|++|+||+|+||+|||++
T Consensus 242 ~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~ 320 (345)
T PF02536_consen 242 KLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKV 320 (345)
T ss_dssp HHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHH
Confidence 899999999999999999999999999999999997 9999999999999999999999999999999999999655
Q ss_pred HHhcC--CCCChHHhhcCChHHHHh
Q 007270 576 LKGRN--IECSLEEMLGKNDDEFAT 598 (610)
Q Consensus 576 L~~~G--l~~sl~~vL~~sdk~F~~ 598 (610)
|+.+| ..+++.+|+.+||++|++
T Consensus 321 l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 321 LKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp T--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred HHHCcCCCCCCHHHHhhccHHHhcC
Confidence 55678 689999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.6e-45 Score=405.22 Aligned_cols=311 Identities=23% Similarity=0.452 Sum_probs=288.4
Q ss_pred hhhhhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCH-
Q 007270 241 VQQTLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNI- 319 (610)
Q Consensus 241 a~~vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~- 319 (610)
..+++.||++ +|+++++|+++|.++|++|.+++++++.|+++||+++|++.++|++++.++|++|.++.
T Consensus 124 l~Pvl~fL~~----------lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e 193 (487)
T PLN03196 124 MIPVLDYLEK----------LGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLE 193 (487)
T ss_pred hHHHHHHHHH----------cCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHH
Confidence 3457899987 69999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCCh-hHHHHHHH
Q 007270 320 KAIRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCST-SKLKLMLD 398 (610)
Q Consensus 320 ~~L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~-~~l~~~l~ 398 (610)
+.+.++++||+++|++.+++.+++.++|++|+.+++++++|+++||+++|++.++|++++.++|++++++. +++++.++
T Consensus 194 ~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~ 273 (487)
T PLN03196 194 GTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVE 273 (487)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHH
Confidence 67999999999999999999999999999999999999999999999999999999999999999999998 59999999
Q ss_pred HHHHcCCChhHHHHHHHhCCcccccCch-hHHHHHHHH-HHcCCChhhHHHHHhccCcccccchhhHHHhHHHHHHHcCC
Q 007270 399 QLGELGVENKKLGQVIAKSPQLLLRKPQ-EFRQVVSFL-EDVGFDRENVGRILGRCPELFASNIERTLMKKIDFLIGIGI 476 (610)
Q Consensus 399 ~L~elG~~~~~l~~il~~~P~lL~~s~~-~i~~kv~fL-~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL~~lGl 476 (610)
+|+++|++++.+++++.++|.++..+.+ ++.++++|+ +++|++++++..++.++|++++.+. ++++++++||+++|+
T Consensus 274 ~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe-~kl~~kvefL~~~Gl 352 (487)
T PLN03196 274 CLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNR-NVALKHVEFLRGRGF 352 (487)
T ss_pred HHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccH-HHHHHHHHHHHHcCC
Confidence 9999999999999999999999998876 688999999 5899999999999999999999994 589999999999999
Q ss_pred CCCcHHHHHhhCCccccccccccchhHHHHHH-HhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHHcCC--ChhH
Q 007270 477 SKDHLPRTIKKYPELLVSDVDRTLLPRIKYLM-EMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNTMEK--SLQD 553 (610)
Q Consensus 477 s~~~i~~~I~~~P~iL~~sle~~L~~kv~~L~-~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~--~~~~ 553 (610)
+.++|.+|++++|++|++|. +.|++|++||. ++|++.++| .++|++|+||.|++|+||+.+|.+ -|+ ++..
T Consensus 353 s~edI~~mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~I----v~fP~~LsySLEkRI~PR~~~L~~-kGl~~sL~~ 426 (487)
T PLN03196 353 SAQDVAKMVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKEL----VEFPAYFTYGLESRIKPRYERVAK-KGIKCSLAW 426 (487)
T ss_pred CHHHHHHHHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHHH----HhChHHhccChhhhhHHHHHHHHH-cCCCCCHHH
Confidence 99999999999999999997 69999999999 599999987 999999999999899999999985 464 3444
Q ss_pred HhhcCccccccccchHHhHHHH
Q 007270 554 VVAYPRYFSYSLEKKIKPRFWV 575 (610)
Q Consensus 554 Iv~~P~~L~ySlekRI~pR~~v 575 (610)
++.++ |+++.-|+..
T Consensus 427 ~L~~s-------d~~F~~r~v~ 441 (487)
T PLN03196 427 FLNCS-------DDKFEQRMSG 441 (487)
T ss_pred HhccC-------HHHHHHHHhh
Confidence 44444 6788877743
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=5.9e-37 Score=325.99 Aligned_cols=285 Identities=25% Similarity=0.495 Sum_probs=217.3
Q ss_pred hhhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCH-HH
Q 007270 243 QTLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNI-KA 321 (610)
Q Consensus 243 ~vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~-~~ 321 (610)
+++.||.+ .|++.++|++++.++|.+|..+.++++.|.+++|+++|.+++++++++.++|++|..+. +.
T Consensus 35 pk~~fl~s----------~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~ 104 (345)
T PF02536_consen 35 PKLEFLRS----------LGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEEN 104 (345)
T ss_dssp HHHHHHHH----------TT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HH
T ss_pred HHHHHHHH----------CCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhh
Confidence 35889988 49999999999999999999998899999999999999999999999999999998766 57
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCCh-hHHHHHHHHH
Q 007270 322 IRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCST-SKLKLMLDQL 400 (610)
Q Consensus 322 L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~-~~l~~~l~~L 400 (610)
+.+++.+|+++|++.+.+.+++...|.++... +.+.+.+++|.++|++.+++.+++..+|+++.+.. +.+++.+++|
T Consensus 105 l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L 182 (345)
T PF02536_consen 105 LSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFL 182 (345)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHH
T ss_pred hhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHH
Confidence 99999999999999998889998888866555 67999999999999999999999999997666554 8999999999
Q ss_pred HHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHHHHHHcCCCCCc
Q 007270 401 GELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKIDFLIGIGISKDH 480 (610)
Q Consensus 401 ~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL~~lGls~~~ 480 (610)
+++|++.+++.+++.++|.++..+.+++.+.+.++...|...++ .++.++|.++..+. .+++++++||.++|++.++
T Consensus 183 ~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~--~~i~~~p~il~~~~-~~l~~~i~~L~~lG~s~~e 259 (345)
T PF02536_consen 183 RSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE--RVIKKFPQILSLSE-EKLKPKIEFLQSLGFSEEE 259 (345)
T ss_dssp HHCTT-GHHHHHHHHHTTTGGGCGCHC-----------------------------THHH-HHHHHHHHHHHTTT--HHH
T ss_pred HhhcccchhhhHHhhcccceeccccccccccccccccccccccc--ccccccccccccch-HhHHHHHHHHHHhcCcHHH
Confidence 99999999999999999999999998866666666655555544 88999999999984 5899999999999999999
Q ss_pred HHHHHhhCCccccccccccchhHHHHHH-HhCCCHHHHHHHHHhcCcccccChhhhHHHH---HHHHHHHcC
Q 007270 481 LPRTIKKYPELLVSDVDRTLLPRIKYLM-EMGLSKRDIAFMVRRFSPLLGYSIDEVFRPK---LAFLLNTME 548 (610)
Q Consensus 481 i~~~I~~~P~iL~~sle~~L~~kv~~L~-~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~k---i~fL~~~mG 548 (610)
|.+|+.++|.+|++|.+ .+++|++||. ++|++.++| .++|++|+||.|++|+|| +.+|.+ .|
T Consensus 260 i~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~~~~i----~~~P~~l~~sLe~ri~PR~~~~~~l~~-~g 325 (345)
T PF02536_consen 260 IAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLPLEEI----VEFPQYLSYSLEKRIKPRYEVLKVLKS-KG 325 (345)
T ss_dssp HHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT--HHHH----HHSCHHHCS-HHHHHHHHHHHHHTT---TT
T ss_pred HHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcCHHHH----hhCCceeEechhhhhhhHHHHHHHHHH-Cc
Confidence 99999999999999987 5999999998 599999998 899999999999899999 555554 45
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.97 E-value=9.6e-32 Score=292.75 Aligned_cols=314 Identities=29% Similarity=0.533 Sum_probs=275.4
Q ss_pred hhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCH-HHH
Q 007270 244 TLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNI-KAI 322 (610)
Q Consensus 244 vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~-~~L 322 (610)
++.++++ +|+++++|.+++..+|.++.++.++.+.+++.+|++.|++.+.++++++..|.+|..+. ..+
T Consensus 94 ~~~~l~s----------~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~ 163 (413)
T KOG1267|consen 94 VLSSLRS----------LGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESL 163 (413)
T ss_pred HHHHHHh----------cCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCch
Confidence 5888887 69999999999999999999999999999999999999999999999999899888554 689
Q ss_pred HHHHHHHHHhC--CChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHH
Q 007270 323 RTKALAFEEIG--AVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQL 400 (610)
Q Consensus 323 ~~~l~~L~~lG--~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L 400 (610)
...++|+.+++ .....+.+++...|... ...+-.+++++++++|+...++...+..+|....... .+...+.++
T Consensus 164 ~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~---~~~~~v~~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i 239 (413)
T KOG1267|consen 164 STFIEFLKSIPPELLSSVVERLLTPVPSFL---LNENSVERLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFL 239 (413)
T ss_pred hhHHHHhhccchhhhhhHHHHhcccccccc---ccccccccchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhH
Confidence 99999999985 66666666655555322 2223334899999999999999999999998765432 788889999
Q ss_pred HHcCCChhHHHHHHHhCCcccccCch-hHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHHHHHHcCCCCC
Q 007270 401 GELGVENKKLGQVIAKSPQLLLRKPQ-EFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKIDFLIGIGISKD 479 (610)
Q Consensus 401 ~elG~~~~~l~~il~~~P~lL~~s~~-~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL~~lGls~~ 479 (610)
.++|+++.. +++...|.++..+.+ ++++++++|+.+||+.+||+.+++++|+++..+.+ ++..+++++.+. .+
T Consensus 240 ~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~-~~~~~~~~~~~~---~~ 313 (413)
T KOG1267|consen 240 LTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVK-KNLKTTEYLLKN---PK 313 (413)
T ss_pred HHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehh-hhhHHHHHHHhc---ch
Confidence 999998887 788888888887765 79999999999999999999999999999999965 778888888876 22
Q ss_pred cHHHHHhhCCccccccccccchhHHHHHHHhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHHcCCChhHHhhcCc
Q 007270 480 HLPRTIKKYPELLVSDVDRTLLPRIKYLMEMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNTMEKSLQDVVAYPR 559 (610)
Q Consensus 480 ~i~~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~~~~~Iv~~P~ 559 (610)
+ +.++|+++.++ +..+.++++|+...|++.+++.+|++++|+|+.++.++.++.+.+|+++.|+++.++++.+|+
T Consensus 314 ~----~~k~p~~l~~s-~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~ 388 (413)
T KOG1267|consen 314 H----ILKFPQLLRSS-EDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPA 388 (413)
T ss_pred h----hhhhhhhhhcc-chhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccch
Confidence 2 88999999777 578999999999999999999999999999999999966899999999999999999999999
Q ss_pred cccccccchHHhHHHHHHhcCCC
Q 007270 560 YFSYSLEKKIKPRFWVLKGRNIE 582 (610)
Q Consensus 560 ~L~ySlekRI~pR~~vL~~~Gl~ 582 (610)
++.|++|+|++||+.++..++..
T Consensus 389 ~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 389 FFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred hhccchhhcchhHHHHHHHHhcc
Confidence 99999999999999998886643
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.84 E-value=1e-20 Score=206.38 Aligned_cols=327 Identities=20% Similarity=0.356 Sum_probs=265.8
Q ss_pred chHHHHHHHHhhcCCCccchhhhccCCCcchhhhhhhhcCCCCChhhhhhhhhhhhhhccCCCccccccchhhhhhhcCC
Q 007270 155 GFKEKVVRMAKEKGDNGKVAFLESLGLSLSSAISIARSLSGEPLPPLIHKVKYMKEIFFSGSNTERTLGKNGRRMMKHLS 234 (610)
Q Consensus 155 ~~~~~~~~~~~~~p~n~~~~f~EslG~~~s~~~~~a~~~~~~~L~~l~~kv~fl~~~~~~~~d~~~~l~~~~~~~l~~~~ 234 (610)
.....+..+...+|++.+. +++|+|++.+++.++.. .-| ++.++ +++..+..
T Consensus 78 ~~~~~~~~~~~~~p~s~~~-~l~s~g~~~~~i~s~i~-----~~p----~ll~~--------~~~~~l~~---------- 129 (413)
T KOG1267|consen 78 KLSREVSSEDSVNPSSVLS-SLRSLGFTDSQISSIIL-----SSP----KLLYL--------SSENILKP---------- 129 (413)
T ss_pred HHHHHHHhhhccCcHHHHH-HHHhcCCchhhcccccc-----cCc----hhhhc--------cchhhhhh----------
Confidence 4556677888899999655 99999999999887333 112 22222 22111111
Q ss_pred CCCChhhhhhhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcC--CChHHHHHHHhhCC
Q 007270 235 IPIDEDVQQTLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVG--VPKDCMGNVLLLFP 312 (610)
Q Consensus 235 ~~~~~da~~vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slG--is~~~I~~il~~~P 312 (610)
.+.++.+ .|++.+.+..++...|.+|....+.++.+.+++|.+.+ .....+.++....|
T Consensus 130 ---------~~~~l~~----------~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~ 190 (413)
T KOG1267|consen 130 ---------KLRLLDS----------LGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVP 190 (413)
T ss_pred ---------hhhhhhc----------cCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccc
Confidence 1234443 49999999999999888888777788999999999985 88888888877776
Q ss_pred CceecCHHHHHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCCh-h
Q 007270 313 PLIFWNIKAIRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCST-S 391 (610)
Q Consensus 313 ~IL~~s~~~L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~-~ 391 (610)
.-.. ....+. +++++..+|...+++..++..+|....... .+...+.++.+.|+.+.. +.+...|.+++++. +
T Consensus 191 ~~~~-~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~ 264 (413)
T KOG1267|consen 191 SFLL-NENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEK 264 (413)
T ss_pred cccc-cccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccc
Confidence 4322 123444 899999999999999999999999886643 467778888889976665 77788899998876 8
Q ss_pred HHHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHHHH
Q 007270 392 KLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKIDFL 471 (610)
Q Consensus 392 ~l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~fL 471 (610)
.+++.++++.++||+.+++..++.++|.++..+.+++..+++++.+. .++ +.++|+++..+ +..+.++++||
T Consensus 265 ~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~---~~~----~~k~p~~l~~s-~~~l~~~ie~l 336 (413)
T KOG1267|consen 265 TLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN---PKH----ILKFPQLLRSS-EDKLKPRIEFL 336 (413)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc---chh----hhhhhhhhhcc-chhhhhhHHHH
Confidence 99999999999999999999999999999999999999999999877 333 78999999666 67999999999
Q ss_pred HHcCCCCCcHHHHHhhCCccccccccccchhHHHHHH-HhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHH
Q 007270 472 IGIGISKDHLPRTIKKYPELLVSDVDRTLLPRIKYLM-EMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNT 546 (610)
Q Consensus 472 ~~lGls~~~i~~~I~~~P~iL~~sle~~L~~kv~~L~-~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~ 546 (610)
..+|++..++.++++++|+++++++++.++.+.+++. .++++.+++ ..+|.+++|+.|+.+.+|....+..
T Consensus 337 ~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~----~~~p~~~~y~le~ri~pr~~~~~~~ 408 (413)
T KOG1267|consen 337 LSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSAL----VSFPAFFGYSLEKRIRPRFNVIKKL 408 (413)
T ss_pred HHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHH----hccchhhccchhhcchhHHHHHHHH
Confidence 9999999999999999999999999777888899998 599996655 8999999999999999999988753
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=96.41 E-value=0.0017 Score=43.10 Aligned_cols=28 Identities=32% Similarity=0.729 Sum_probs=15.3
Q ss_pred HHHhcCcccccChhhhHHHHHHHHHHHcCC
Q 007270 520 MVRRFSPLLGYSIDEVFRPKLAFLLNTMEK 549 (610)
Q Consensus 520 mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~ 549 (610)
++.++|.+|+++.+ .|+++++||. ++|+
T Consensus 3 ~~~~~P~il~~~~~-~l~~~~~~l~-~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYSEK-KLKPKVEFLK-ELGF 30 (31)
T ss_pred hhhhCcCcccccHH-HhhHHHHHHH-HcCC
Confidence 44555665555533 3555666555 4554
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=96.18 E-value=0.0043 Score=41.11 Aligned_cols=30 Identities=33% Similarity=0.830 Sum_probs=25.4
Q ss_pred HHHhhCCccccccccccchhHHHHHHHhCCC
Q 007270 483 RTIKKYPELLVSDVDRTLLPRIKYLMEMGLS 513 (610)
Q Consensus 483 ~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s 513 (610)
+++.++|.+|+++ +++++++++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 5788899999998 67899999999988874
No 9
>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=88.73 E-value=1.6 Score=42.00 Aligned_cols=20 Identities=25% Similarity=0.456 Sum_probs=12.4
Q ss_pred HHHHHHHHHHcCCChhhHHH
Q 007270 428 FRQVVSFLEDVGFDRENVGR 447 (610)
Q Consensus 428 i~~kv~fL~~lG~s~~~i~~ 447 (610)
....++.++..|++++++..
T Consensus 118 ~~~w~~l~~~~g~~~~~m~~ 137 (172)
T cd04790 118 KEKWVAILKAAGMDEADMRR 137 (172)
T ss_pred HHHHHHHHHHcCCChHHHHH
Confidence 34556666777777766543
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=88.11 E-value=3 Score=40.17 Aligned_cols=50 Identities=16% Similarity=0.247 Sum_probs=30.2
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHH
Q 007270 393 LKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRI 448 (610)
Q Consensus 393 l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~l 448 (610)
....++.++..|+++..+.+.=..+- ...-..-.+||.++|++++++..+
T Consensus 118 ~~~w~~l~~~~g~~~~~m~~wh~~fe------~~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 118 KEKWVAILKAAGMDEADMRRWHIEFE------KMEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHHHHHHHcCCChHHHHHHHHHHH------HhCcHHHHHHHHHcCCCHHHHHHH
Confidence 34556666777877766533322210 112235678899999998888654
No 11
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=79.95 E-value=12 Score=30.42 Aligned_cols=55 Identities=20% Similarity=0.439 Sum_probs=37.6
Q ss_pred HHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHH---hCCcc
Q 007270 359 EEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIA---KSPQL 420 (610)
Q Consensus 359 ~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~---~~P~l 420 (610)
.|+++.|++..+++++|..++... + ++--..+..+..+|++++.+..++. .+|.+
T Consensus 2 NPIia~LKehnvsd~qi~elFq~l----T---~NPl~AMa~i~qLGip~eKLQ~lm~~VMqnP~L 59 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQAL----T---QNPLAAMATIQQLGIPQEKLQQLMAQVMQNPAL 59 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHH----h---hCHHHHHHHHHHcCCCHHHHHHHHHHHhcChHH
Confidence 467889999999999988776543 1 1223345677889999987665544 45554
No 12
>PRK14135 recX recombination regulator RecX; Provisional
Probab=75.30 E-value=1e+02 Score=31.52 Aligned_cols=112 Identities=12% Similarity=0.123 Sum_probs=61.0
Q ss_pred HHHhcCCChHHHHHHHhhCCCceecCH-HHHHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCC-
Q 007270 293 FLEIVGVPKDCMGNVLLLFPPLIFWNI-KAIRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKV- 370 (610)
Q Consensus 293 ~L~slGis~~~I~~il~~~P~IL~~s~-~~L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl- 370 (610)
.-.+.-++.+++..|+.. ... ......+.+|..-.-+..++..-|.+. +.+ ...+..+++.|.+.|.
T Consensus 36 L~~g~~l~~~~~~~i~~~------~~~~~a~~~Al~~L~~r~~s~~el~~kL~~k----g~~-~~~Ie~vl~~l~~~~~l 104 (263)
T PRK14135 36 LKKGKELDEEDLEEIQYA------DQVSKGKNLALYYLSYQMRTEKEVRDYLKKH----EIS-EEIISEVIDKLKEEKYI 104 (263)
T ss_pred CcCCCcCCHHHHHHHHHH------HHHHHHHHHHHHHhhhccccHHHHHHHHHHC----CCC-HHHHHHHHHHHHHcCCC
Confidence 334555677777766643 111 223333555555556666666555543 222 4567888899988884
Q ss_pred ChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhC
Q 007270 371 PKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKS 417 (610)
Q Consensus 371 ~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~ 417 (610)
.....+...... .+......-..+...|+.-|++.+.+..++...
T Consensus 105 dD~~~a~~~~~~--~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l 149 (263)
T PRK14135 105 DDKEYAESYVRT--NINTGDKGPRVIKQKLLQKGIEDEIIEEALSEY 149 (263)
T ss_pred CHHHHHHHHHHH--HHhccccchHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 443444333221 111111122334456777899988888888754
No 13
>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=74.14 E-value=4.9 Score=37.23 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=21.2
Q ss_pred cchhHHHHHHHhCCCHHHHHHHHHhcCcc
Q 007270 499 TLLPRIKYLMEMGLSKRDIAFMVRRFSPL 527 (610)
Q Consensus 499 ~L~~kv~~L~~lG~s~~ev~~mi~r~P~i 527 (610)
-+..|++||++.|++.+||..++.+.+.-
T Consensus 22 p~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 22 PLEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp -HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred CHHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 35679999999999999999999887753
No 14
>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=73.37 E-value=37 Score=36.38 Aligned_cols=66 Identities=18% Similarity=0.279 Sum_probs=41.5
Q ss_pred CCcccccccccc-chhHHHHHH-HhCCCHHHHHHHHHhcCcccccChhhhHHHHHHHHHHHcCCChhH-HhhcC
Q 007270 488 YPELLVSDVDRT-LLPRIKYLM-EMGLSKRDIAFMVRRFSPLLGYSIDEVFRPKLAFLLNTMEKSLQD-VVAYP 558 (610)
Q Consensus 488 ~P~iL~~sle~~-L~~kv~~L~-~lG~s~~ev~~mi~r~P~iL~~s~e~~Lk~ki~fL~~~mG~~~~~-Iv~~P 558 (610)
.=.+|+..+|++ ..+++..|+ ++|++ ..+..|+.+||.|+..|... +.-.-||.+. |.-.. |.++|
T Consensus 247 lHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~rHPgIFYvS~kg--~~~TVfLrEA--Y~~~~Liek~P 315 (335)
T PF11955_consen 247 LHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLLRHPGIFYVSLKG--KRHTVFLREA--YDGGELIEKHP 315 (335)
T ss_pred HHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHHhCCCeEEEeccC--CceEEEEeec--cCCCCCCCCCc
Confidence 344555555543 355677787 58988 66888999999999888752 2333366553 33333 45566
No 15
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=65.92 E-value=17 Score=31.18 Aligned_cols=46 Identities=17% Similarity=0.314 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCChHHHHHHHHhCCcccccCh
Q 007270 285 SHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDNDVGKMLLKYPWILSTSI 354 (610)
Q Consensus 285 ~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~ 354 (610)
..+...+.+|..+|++.....+|+..+. ++....|..+|+.|..++
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~yg------------------------~~ai~~l~~nPY~L~~~i 51 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKYG------------------------DDAIEILKENPYRLIEDI 51 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH-------------------------TTHHHHHHH-STCCCB-S
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHh------------------------HHHHHHHHHChHHHHHHc
Confidence 3466778899999999888877776532 134567788999888754
No 16
>PRK14136 recX recombination regulator RecX; Provisional
Probab=64.54 E-value=1.1e+02 Score=32.28 Aligned_cols=22 Identities=18% Similarity=0.394 Sum_probs=16.1
Q ss_pred hHHHHHHHhCCCHHHHHHHHHh
Q 007270 502 PRIKYLMEMGLSKRDIAFMVRR 523 (610)
Q Consensus 502 ~kv~~L~~lG~s~~ev~~mi~r 523 (610)
..+.||...||+.+.|..+++.
T Consensus 280 K~iRfL~rRGFS~D~I~~vLk~ 301 (309)
T PRK14136 280 KQARFLAARGFSSATIVKLLKV 301 (309)
T ss_pred HHHHHHHHCCCCHHHHHHHHHh
Confidence 3477888888888887777654
No 17
>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=63.74 E-value=20 Score=32.15 Aligned_cols=13 Identities=23% Similarity=0.317 Sum_probs=7.0
Q ss_pred HHHHHHHHHhCCC
Q 007270 358 YEEILSVFNEEKV 370 (610)
Q Consensus 358 l~~~v~fL~~~Gl 370 (610)
+..+|+.|.+.|+
T Consensus 11 I~~vi~~l~~~gy 23 (121)
T PF02631_consen 11 IEEVIDRLKELGY 23 (121)
T ss_dssp HHHHHHHHHHTTS
T ss_pred HHHHHHHHHHcCC
Confidence 4455555555553
No 18
>PRK14135 recX recombination regulator RecX; Provisional
Probab=61.61 E-value=1.9e+02 Score=29.45 Aligned_cols=223 Identities=12% Similarity=0.103 Sum_probs=115.3
Q ss_pred hhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHh
Q 007270 253 ARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEI 332 (610)
Q Consensus 253 ~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~l 332 (610)
.+++-....-++..++..++... .........+.+|..-.-+..+|.+=+... +++.+.+...++.|...
T Consensus 32 ~~~~L~~g~~l~~~~~~~i~~~~------~~~~a~~~Al~~L~~r~~s~~el~~kL~~k----g~~~~~Ie~vl~~l~~~ 101 (263)
T PRK14135 32 VKFMLKKGKELDEEDLEEIQYAD------QVSKGKNLALYYLSYQMRTEKEVRDYLKKH----EISEEIISEVIDKLKEE 101 (263)
T ss_pred HHhcCcCCCcCCHHHHHHHHHHH------HHHHHHHHHHHHhhhccccHHHHHHHHHHC----CCCHHHHHHHHHHHHHc
Confidence 34333344578888888887552 122223334556666666777776666544 44557778888888888
Q ss_pred CC-ChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHH
Q 007270 333 GA-VDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLG 411 (610)
Q Consensus 333 G~-s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~ 411 (610)
|. ++...+....+.- +... ...-..+..-|+.-|++.+.|..++..... . +-+.....+ ..
T Consensus 102 ~~ldD~~~a~~~~~~~--~~~~-~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~---~--~~~d~a~~~----------~~ 163 (263)
T PRK14135 102 KYIDDKEYAESYVRTN--INTG-DKGPRVIKQKLLQKGIEDEIIEEALSEYTE---E--DQIEVAQKL----------AE 163 (263)
T ss_pred CCCCHHHHHHHHHHHH--Hhcc-ccchHHHHHHHHHcCCCHHHHHHHHHhCCh---h--hHHHHHHHH----------HH
Confidence 75 4434443333211 1000 112345667788999999999998875411 0 111111111 11
Q ss_pred HHHHhCCcccccCchh-HHHHHHHHHHcCCChhhHHHHHhccCcccccchhh---HHHhHHHHHHHcCCCCCcHHHHHhh
Q 007270 412 QVIAKSPQLLLRKPQE-FRQVVSFLEDVGFDRENVGRILGRCPELFASNIER---TLMKKIDFLIGIGISKDHLPRTIKK 487 (610)
Q Consensus 412 ~il~~~P~lL~~s~~~-i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~---~L~~k~~fL~~lGls~~~i~~~I~~ 487 (610)
+....... .+... -.....+|..-||+.+.|..++.... ...+.+. .+...++ +..++
T Consensus 164 k~~~~~~~---~~~~~~k~Ki~~~L~rkGf~~~~I~~~l~~~~--~e~d~~~e~e~l~~~~~-------------k~~~k 225 (263)
T PRK14135 164 KLLKKYQK---LPFKALKQKIIQSLLTKGFSYEVIKAALEELD--LEQDEEEEQELLQKELE-------------KAYRK 225 (263)
T ss_pred HHHHHhcC---CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHcc--cCCChHHHHHHHHHHHH-------------HHHHH
Confidence 11111110 11112 23456788899999999998887631 0001110 1111111 01111
Q ss_pred CCccccccccccchhHHHHHHHhCCCHHHHHHHHHhc
Q 007270 488 YPELLVSDVDRTLLPRIKYLMEMGLSKRDIAFMVRRF 524 (610)
Q Consensus 488 ~P~iL~~sle~~L~~kv~~L~~lG~s~~ev~~mi~r~ 524 (610)
+.. ..-.+.-+.-+.||...||+.+.|..++...
T Consensus 226 ~~~---~~~~k~k~K~~~~L~rrGF~~~~I~~~l~~~ 259 (263)
T PRK14135 226 YSK---YDGYELKQKLKQALYRKGFSYDDIDSFLREY 259 (263)
T ss_pred Hhc---CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 110 0001122334678889999999998887653
No 19
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=60.61 E-value=18 Score=31.03 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=8.8
Q ss_pred HHHHHHHHHHcCCChhHHHHHH
Q 007270 393 LKLMLDQLGELGVENKKLGQVI 414 (610)
Q Consensus 393 l~~~l~~L~elG~~~~~l~~il 414 (610)
++..+.+|.++|++.....++.
T Consensus 8 ~~~~~~~L~~~gl~~~~a~kl~ 29 (94)
T PF14490_consen 8 LRELMAFLQEYGLSPKLAMKLY 29 (94)
T ss_dssp -HHHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHH
Confidence 3444455555555544444433
No 20
>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=54.82 E-value=11 Score=30.80 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=18.1
Q ss_pred HHHHHHHHHcCCChhhHhHHhhC
Q 007270 89 QAIYDYLSELGISQEDCAFISSN 111 (610)
Q Consensus 89 ~a~~~yl~~~~~~~~~a~~i~~~ 111 (610)
.-|+|||+.+|+||-+|-+|..+
T Consensus 5 TdlAD~LVr~GipFR~AH~iVg~ 27 (70)
T PF14698_consen 5 TDLADYLVRKGIPFREAHHIVGR 27 (70)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 45899996669999999988754
No 21
>PHA01351 putative minor structural protein
Probab=52.72 E-value=2.8e+02 Score=32.56 Aligned_cols=22 Identities=9% Similarity=0.155 Sum_probs=15.5
Q ss_pred HHHHHHHcCCChhhHHHHHhcc
Q 007270 431 VVSFLEDVGFDRENVGRILGRC 452 (610)
Q Consensus 431 kv~fL~~lG~s~~~i~~ll~k~ 452 (610)
.-.-|+++|.+.+++..++..+
T Consensus 694 ~~~ELKKL~IpdSqInil~t~y 715 (1070)
T PHA01351 694 LSGELKKIHKDKTALELYITKF 715 (1070)
T ss_pred HHHHHHHcCCCHHHHHHHHHHH
Confidence 4456778888888777766654
No 22
>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=52.68 E-value=79 Score=37.54 Aligned_cols=86 Identities=14% Similarity=0.201 Sum_probs=52.3
Q ss_pred HHHHHHHHHh---cCCChHHHHHHHhhCCCceecCH-HHHHHHHHHHHHh-CCChHHHHHHHHhCCcccccChhhhHHHH
Q 007270 287 VKPVVDFLEI---VGVPKDCMGNVLLLFPPLIFWNI-KAIRTKALAFEEI-GAVDNDVGKMLLKYPWILSTSIQENYEEI 361 (610)
Q Consensus 287 l~p~l~~L~s---lGis~~~I~~il~~~P~IL~~s~-~~L~~~l~~L~~l-G~s~~~v~kll~~~P~lL~~s~~~~l~~~ 361 (610)
....+.||.+ -|+-+..-.+|+...+ .+. +.|...-+.|.++ |++++.+.++...+.. .......
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv~~fg----~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~~~~ 146 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIVKTFG----EAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDERRL 146 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHhC----HhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHHHHH
Confidence 4456678875 4776666666775543 222 5555555666666 7777776666554321 2235677
Q ss_pred HHHHHhCCCChHHHHHHHHhC
Q 007270 362 LSVFNEEKVPKLSVDRAIRSW 382 (610)
Q Consensus 362 v~fL~~~Gl~~~~I~~il~~~ 382 (610)
+.||.++|++...+.++...+
T Consensus 147 ~~~L~~~gi~~~~a~ki~~~y 167 (720)
T TIGR01448 147 LAGLQGLGIGIKLAQRIYKFY 167 (720)
T ss_pred HHHHHHcCCCHHHHHHHHHHH
Confidence 778888888776666665543
No 23
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=50.68 E-value=20 Score=32.30 Aligned_cols=39 Identities=13% Similarity=0.362 Sum_probs=21.9
Q ss_pred CCcHHHHHhhCCccccccccccchhHHHHHHHhCCCHHHHHHHH
Q 007270 478 KDHLPRTIKKYPELLVSDVDRTLLPRIKYLMEMGLSKRDIAFMV 521 (610)
Q Consensus 478 ~~~i~~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s~~ev~~mi 521 (610)
.+++...|..+|.++...+ .+.++- ...|++.+++..++
T Consensus 77 ~~~~~~~i~~~~~LikRPi--vv~~~~---~~iG~~~e~~~~~l 115 (117)
T COG1393 77 DEELIEALLENPSLIKRPI--VVDNKK---LRVGFNEEEIRAFL 115 (117)
T ss_pred hHHHHHHHHhChhhccCCe--EEeCCc---eEecCCHHHHHHHh
Confidence 3445666677775555543 121221 34788888876654
No 24
>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=50.55 E-value=26 Score=24.53 Aligned_cols=21 Identities=33% Similarity=0.474 Sum_probs=11.6
Q ss_pred HHHHHHHcCCChhhHHHHHhc
Q 007270 431 VVSFLEDVGFDRENVGRILGR 451 (610)
Q Consensus 431 kv~fL~~lG~s~~~i~~ll~k 451 (610)
.++-|.++||+.++....+..
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 455555666666666655544
No 25
>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=47.28 E-value=2e+02 Score=25.54 Aligned_cols=109 Identities=24% Similarity=0.352 Sum_probs=49.3
Q ss_pred hHHHHHHHHHHHcCC-ChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHHHhccCcccccchhhHHHhHHH
Q 007270 391 SKLKLMLDQLGELGV-ENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILGRCPELFASNIERTLMKKID 469 (610)
Q Consensus 391 ~~l~~~l~~L~elG~-~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~s~e~~L~~k~~ 469 (610)
+.+..+++.|.+.|+ ++..++......-.- .....-.....-|+.-|++.+.|..++...+. ... ..+
T Consensus 9 e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~--~~~~G~~~I~~~L~~kGi~~~~i~~~l~~~~~------~e~---a~~ 77 (121)
T PF02631_consen 9 EAIEEVIDRLKELGYIDDERYAESYVRSRLR--RKGKGPRRIRQKLKQKGIDREIIEEALEEYDE------EEE---ALE 77 (121)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH--HTT--HHHHHHHHHHTT--HHHHHHHHTCS-H------HHH---HHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHhcc--cccccHHHHHHHHHHHCCChHHHHHHHHHhhH------HHH---HHH
Confidence 456666777777775 444444443332110 01112233445566778888888877662111 111 111
Q ss_pred HHHHcCCCCCcHHHHHhhCCccccccccccchhHHHHHHHhCCCHHHHHHHHHh
Q 007270 470 FLIGIGISKDHLPRTIKKYPELLVSDVDRTLLPRIKYLMEMGLSKRDIAFMVRR 523 (610)
Q Consensus 470 fL~~lGls~~~i~~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s~~ev~~mi~r 523 (610)
... +++...-..+-.+..+.-+.+|...||+.+.|..++..
T Consensus 78 ~~~-------------kk~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 78 LAE-------------KKYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHH-------------HHHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHH-------------HHHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 111 11111101111122333478888999999998777654
No 26
>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=46.23 E-value=52 Score=22.96 Aligned_cols=23 Identities=17% Similarity=0.284 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCChhHHHHHHHhC
Q 007270 395 LMLDQLGELGVENKKLGQVIAKS 417 (610)
Q Consensus 395 ~~l~~L~elG~~~~~l~~il~~~ 417 (610)
..++.|.++||+.+...+.+..+
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 45667777888888777776654
No 27
>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=45.85 E-value=33 Score=36.72 Aligned_cols=40 Identities=28% Similarity=0.421 Sum_probs=26.0
Q ss_pred cccccccccc-hhHHHHHH-HhCCCHHHHHHHHHhcCccccc
Q 007270 491 LLVSDVDRTL-LPRIKYLM-EMGLSKRDIAFMVRRFSPLLGY 530 (610)
Q Consensus 491 iL~~sle~~L-~~kv~~L~-~lG~s~~ev~~mi~r~P~iL~~ 530 (610)
+|+.|.+++| ..++..++ .+|++.+-...++.++|..+..
T Consensus 109 LLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 109 LLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 4444444333 34577776 5888887777778888876655
No 28
>PRK09875 putative hydrolase; Provisional
Probab=45.63 E-value=1.7e+02 Score=30.63 Aligned_cols=131 Identities=18% Similarity=0.181 Sum_probs=65.3
Q ss_pred HHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCChH--HHHHHHHhCCc
Q 007270 271 LVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDN--DVGKMLLKYPW 348 (610)
Q Consensus 271 iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s~~--~v~kll~~~P~ 348 (610)
.-.-.|-.........-...++.|++.|++.+++ +..+... ..+.+.+...++ .|.--+ .+.+- ..+|
T Consensus 149 ~~TG~pi~~Ht~~~~~g~e~l~il~e~Gvd~~rv---vi~H~d~-~~d~~~~~~l~~----~G~~l~fD~~g~~-~~~p- 218 (292)
T PRK09875 149 NQTGRPISTHTSFSTMGLEQLALLQAHGVDLSRV---TVGHCDL-KDNLDNILKMID----LGAYVQFDTIGKN-SYYP- 218 (292)
T ss_pred HHHCCcEEEcCCCccchHHHHHHHHHcCcCcceE---EEeCCCC-CCCHHHHHHHHH----cCCEEEeccCCCc-ccCC-
Confidence 3445577666555545667789999999976543 3333321 123333322221 122111 00000 0011
Q ss_pred ccccChhhhHHHHHHHHHhCCCCh-----HHHHHHHHhCCcccc-CCh-hHHHHHHHHHHHcCCChhHHHHHHHhCCc
Q 007270 349 ILSTSIQENYEEILSVFNEEKVPK-----LSVDRAIRSWPHLLG-CST-SKLKLMLDQLGELGVENKKLGQVIAKSPQ 419 (610)
Q Consensus 349 lL~~s~~~~l~~~v~fL~~~Gl~~-----~~I~~il~~~P~lL~-~s~-~~l~~~l~~L~elG~~~~~l~~il~~~P~ 419 (610)
.......+..|.+.|... .|+.+- .++.-.+ ... .-+...+-.|++.|+++++|.+++..||.
T Consensus 219 ------d~~r~~~i~~L~~~Gy~drilLS~D~~~~--~~~~~~gg~G~~~i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 219 ------DEKRIAMLHALRDRGLLNRVMLSMDITRR--SHLKANGGYGYDYLLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred ------HHHHHHHHHHHHhcCCCCeEEEeCCCCCc--ccccccCCCChhHHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 123456666666666222 111110 0100000 011 34666777888899999999999999997
No 29
>PRK14134 recX recombination regulator RecX; Provisional
Probab=44.71 E-value=3.9e+02 Score=27.89 Aligned_cols=108 Identities=8% Similarity=0.022 Sum_probs=62.4
Q ss_pred hcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCChHHHHHHHHhCCcccccChhhhHHHHHHHHHhCCC-ChHH
Q 007270 296 IVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDNDVGKMLLKYPWILSTSIQENYEEILSVFNEEKV-PKLS 374 (610)
Q Consensus 296 slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s~~~v~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl-~~~~ 374 (610)
+.-++..++..|+... .+ .......+.+|..---+..++..-|.+. ..+ +..+..+|+.|++.|. ....
T Consensus 43 G~eld~e~~~ei~~~~----~~-~~a~~~AL~~Ls~r~rSe~Elr~KL~~k----~~~-~~~Ie~vI~~L~e~~yldD~r 112 (283)
T PRK14134 43 GKVIDVNSLNDIIKED----NY-IKCKGYALKYIEKSYKTEKQIKEKLYLK----EYD-EDAVNRVIRFLKEYNFIDDDK 112 (283)
T ss_pred CCCcCHHHHHHHHHHH----HH-HHHHHHHHHHhccCcchHHHHHHHHHhC----CCC-HHHHHHHHHHHHHCCCCCHHH
Confidence 3445667777666432 00 1333444445544455666776665543 223 4568889999999884 5555
Q ss_pred HHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhC
Q 007270 375 VDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKS 417 (610)
Q Consensus 375 I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~ 417 (610)
.+....+.- .-..++.+ +-..|+.-|+++..|..++...
T Consensus 113 yA~~yv~~~-~~~~G~~~---I~~eL~qKGI~~~iIe~al~~~ 151 (283)
T PRK14134 113 YCDMYIREK-INSYGRNK---IKYTLLNKGIKENIIIEKINNI 151 (283)
T ss_pred HHHHHHHHH-HHhhhHHH---HHHHHHHCCCCHHHHHHHHHhC
Confidence 555544321 11122222 3456778999999998888764
No 30
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=44.58 E-value=2.7e+02 Score=25.96 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHh
Q 007270 503 RIKYLMEMGLSKRDIAFMVRR 523 (610)
Q Consensus 503 kv~~L~~lG~s~~ev~~mi~r 523 (610)
-+.+|...||+.+.|..++..
T Consensus 132 i~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 132 LVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHCCCCHHHHHHHHHh
Confidence 367888899999888777654
No 31
>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=43.07 E-value=2.5e+02 Score=33.47 Aligned_cols=76 Identities=12% Similarity=0.098 Sum_probs=46.0
Q ss_pred CCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhc-CCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCChHHH
Q 007270 261 LGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIV-GVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAVDNDV 339 (610)
Q Consensus 261 lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~sl-Gis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s~~~v 339 (610)
-|+.+..-.+|+..|+.=.. ..+...-+.|.++ |++......|..... ........+.+|.++|++...+
T Consensus 90 ~GIG~~~A~~iv~~fg~~~~----~~i~~~~~~L~~v~gi~~~~~~~i~~~~~-----~~~~~~~~~~~L~~~gi~~~~a 160 (720)
T TIGR01448 90 KGVGKKLAQRIVKTFGEAAF----DVLDDDPEKLLEVPGISKANLEKFVSQWS-----QQGDERRLLAGLQGLGIGIKLA 160 (720)
T ss_pred CCcCHHHHHHHHHHhCHhHH----HHHHhCHHHHhcCCCCCHHHHHHHHHHHH-----HhHHHHHHHHHHHHcCCCHHHH
Confidence 36666666777766642111 1122333455554 888877777765431 1234667778889999998887
Q ss_pred HHHHHh
Q 007270 340 GKMLLK 345 (610)
Q Consensus 340 ~kll~~ 345 (610)
.++...
T Consensus 161 ~ki~~~ 166 (720)
T TIGR01448 161 QRIYKF 166 (720)
T ss_pred HHHHHH
Confidence 776544
No 32
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=42.31 E-value=1e+02 Score=30.12 Aligned_cols=25 Identities=16% Similarity=0.412 Sum_probs=18.8
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhcc
Q 007270 428 FRQVVSFLEDVGFDRENVGRILGRC 452 (610)
Q Consensus 428 i~~kv~fL~~lG~s~~~i~~ll~k~ 452 (610)
..+.+.+|..+|++..++.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5667777788888888877777764
No 33
>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=40.86 E-value=1.3e+02 Score=32.85 Aligned_cols=42 Identities=19% Similarity=0.194 Sum_probs=26.8
Q ss_pred hHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCC
Q 007270 357 NYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVE 406 (610)
Q Consensus 357 ~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~ 406 (610)
.+...|.-+-++|++++++.+.++.. ..+-...|+||- .|++
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAa-------fNNPdRAVEYL~-tGIP 196 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAA-------FNNPDRAVEYLL-TGIP 196 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHH-------hCCHHHHHHHHH-hCCC
Confidence 46667777777788777777776642 235556666664 3555
No 34
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=39.94 E-value=1.1e+02 Score=29.30 Aligned_cols=51 Identities=24% Similarity=0.390 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCCh
Q 007270 391 SKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDR 442 (610)
Q Consensus 391 ~~l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~ 442 (610)
.+++.+++.|.+.-= ..-.++-|...|.+.....+.+...++.++.-|++.
T Consensus 48 St~k~Il~aL~e~e~-~~ita~~iM~spvv~v~pdDsi~~vv~lM~~~g~SQ 98 (187)
T COG3620 48 STVKRILEALEEAEK-TRITAKTIMHSPVVSVSPDDSISDVVNLMRDKGISQ 98 (187)
T ss_pred HHHHHHHHHHHHhhc-ceEeHhhhccCCeeEECchhhHHHHHHHHHHcCCcc
Confidence 466666666655211 112345566677766666667888888888888773
No 35
>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=39.83 E-value=55 Score=30.20 Aligned_cols=37 Identities=14% Similarity=0.251 Sum_probs=22.6
Q ss_pred HhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCc
Q 007270 344 LKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPH 384 (610)
Q Consensus 344 ~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~ 384 (610)
++.|.+-... ....++||++-|++.++|..++.+.+.
T Consensus 13 L~~p~V~~sp----~~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 13 LQDPKVRNSP----LEKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp HCTTTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred hCCcccccCC----HHHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 3456655544 456778888888888888887776543
No 36
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=39.77 E-value=74 Score=26.09 Aligned_cols=50 Identities=12% Similarity=0.312 Sum_probs=35.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHHHh
Q 007270 394 KLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRILG 450 (610)
Q Consensus 394 ~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~ll~ 450 (610)
.++++.|++..++++++..++... .++-...+.....+|+.++.+..++.
T Consensus 2 NPIia~LKehnvsd~qi~elFq~l-------T~NPl~AMa~i~qLGip~eKLQ~lm~ 51 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQAL-------TQNPLAAMATIQQLGIPQEKLQQLMA 51 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHH-------hhCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 467889999999999888776542 12333456677789999987765543
No 37
>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=39.14 E-value=2.4e+02 Score=30.75 Aligned_cols=42 Identities=7% Similarity=0.037 Sum_probs=32.4
Q ss_pred CHHHHHHHHHhcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCC
Q 007270 286 HVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAV 335 (610)
Q Consensus 286 ~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s 335 (610)
.+...++-+.+.|++++++.+.++.. .+.-.+.|+||.. |+.
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAa-------fNNPdRAVEYL~t-GIP 196 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAA-------FNNPDRAVEYLLT-GIP 196 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHH-------hCCHHHHHHHHHh-CCC
Confidence 46778899999999999999888754 3345667888875 565
No 38
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=38.79 E-value=2.3e+02 Score=26.44 Aligned_cols=22 Identities=14% Similarity=0.237 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCChhHHHHHHHh
Q 007270 395 LMLDQLGELGVENKKLGQVIAK 416 (610)
Q Consensus 395 ~~l~~L~elG~~~~~l~~il~~ 416 (610)
.+..+|..-||+...|..++..
T Consensus 131 Ki~~~L~rkGF~~~~I~~~l~~ 152 (157)
T PRK00117 131 KLVRFLARRGFSMDVIQRVLRN 152 (157)
T ss_pred HHHHHHHHCCCCHHHHHHHHHh
Confidence 3445566666666666655543
No 39
>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=38.52 E-value=30 Score=25.76 Aligned_cols=23 Identities=9% Similarity=0.384 Sum_probs=14.5
Q ss_pred HHHHHHHHHcCCChhhHHHHHhc
Q 007270 429 RQVVSFLEDVGFDRENVGRILGR 451 (610)
Q Consensus 429 ~~kv~fL~~lG~s~~~i~~ll~k 451 (610)
.+.++-|..+||++.++.+++.+
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 34566667777777777766665
No 40
>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=38.06 E-value=44 Score=23.17 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=19.2
Q ss_pred hHHHHHHHhCCCHHHHHHHHHhcC
Q 007270 502 PRIKYLMEMGLSKRDIAFMVRRFS 525 (610)
Q Consensus 502 ~kv~~L~~lG~s~~ev~~mi~r~P 525 (610)
.+++-|.++||+++++...+..+=
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~~ 26 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRATN 26 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhC
Confidence 467888899999999888877643
No 41
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=37.88 E-value=39 Score=30.92 Aligned_cols=70 Identities=14% Similarity=0.260 Sum_probs=40.5
Q ss_pred CCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCCh---hhHHHHHhc
Q 007270 382 WPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDR---ENVGRILGR 451 (610)
Q Consensus 382 ~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~---~~i~~ll~k 451 (610)
.|.-+..+.+.+++-+-.+..-|+++.+|+-+++....+=....-.=...+.+|++-|+.+ +|+..++.+
T Consensus 22 ~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~PeiPeDLy~likk 94 (151)
T KOG0400|consen 22 VPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPEIPEDLYHLIKK 94 (151)
T ss_pred CcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCCCcHHHHHHHHH
Confidence 4555556666777777777777777777776666554432221112234566777777654 455555544
No 42
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=37.49 E-value=46 Score=22.94 Aligned_cols=23 Identities=30% Similarity=0.492 Sum_probs=18.9
Q ss_pred hHHHHHHHhCCCHHHHHHHHHhc
Q 007270 502 PRIKYLMEMGLSKRDIAFMVRRF 524 (610)
Q Consensus 502 ~kv~~L~~lG~s~~ev~~mi~r~ 524 (610)
.+++-|.++||+.+++...+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46788889999999988887765
No 43
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=36.21 E-value=3.1e+02 Score=26.52 Aligned_cols=56 Identities=16% Similarity=0.256 Sum_probs=31.2
Q ss_pred HHHHHHHHHhCC-CChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHh
Q 007270 358 YEEILSVFNEEK-VPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAK 416 (610)
Q Consensus 358 l~~~v~fL~~~G-l~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~ 416 (610)
+..+|.+|.+.| ++....+....+.-.--+.++.++ ...|...|++++.|..++..
T Consensus 54 Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g~G~~rl---~qeL~qkGi~~~~Ie~aL~~ 110 (174)
T COG2137 54 IEEVIDRLAEEGYLDDTRFAEAYIRSRSRKGKGPARL---KQELKQKGIDDEIIEEALEL 110 (174)
T ss_pred HHHHHHHHHHcCcccHHHHHHHHHHHHHhcccChHHH---HHHHHHcCCCHHHHHHHHhc
Confidence 667777777777 355555544333222222333333 34566678888777777763
No 44
>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=35.82 E-value=67 Score=23.90 Aligned_cols=37 Identities=19% Similarity=0.491 Sum_probs=17.5
Q ss_pred HcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCC
Q 007270 402 ELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFD 441 (610)
Q Consensus 402 elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s 441 (610)
..|++...+.++|...+.+ +++.-+...+..+++|+.
T Consensus 8 ~agvS~~TVSr~ln~~~~v---s~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 8 EAGVSKSTVSRVLNGPPRV---SEETRERILEAAEELGYR 44 (46)
T ss_dssp HHTSSHHHHHHHHTTCSSS---THHHHHHHHHHHHHHTB-
T ss_pred HHCcCHHHHHHHHhCCCCC---CHHHHHHHHHHHHHHCCC
Confidence 3555555555555555432 333344444444555543
No 45
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=35.29 E-value=1.3e+02 Score=23.89 Aligned_cols=51 Identities=14% Similarity=0.231 Sum_probs=39.6
Q ss_pred hhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHH-hcCCChHHHHHHH
Q 007270 246 AFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLE-IVGVPKDCMGNVL 308 (610)
Q Consensus 246 ~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~-slGis~~~I~~il 308 (610)
+++++|..+ .|-+.++...++...| +...-.+.+.||+ +.|+....-.-|+
T Consensus 4 sy~~~Ie~k------TGk~~~~W~~~~~~~~------~~~k~~e~v~WLK~ehgLghGhA~Aiv 55 (61)
T PF14117_consen 4 SYLPNIEKK------TGKTLDEWLALAREGG------PLTKHGEIVAWLKDEHGLGHGHANAIV 55 (61)
T ss_pred HHHhHhHHH------HCcCHHHHHHHHHHhC------CCCcHHHHHHHHHHHHCCChHHHHHHH
Confidence 577777777 6999999999999988 2345778999998 5888876654444
No 46
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=32.50 E-value=1.1e+02 Score=28.07 Aligned_cols=80 Identities=28% Similarity=0.401 Sum_probs=44.3
Q ss_pred hhhHHHHHhccCccccc----chhhHHHhHHHHHHH-cCC--CCCcHHHHHhhCCccccccccccchhHHHHHHHhCCCH
Q 007270 442 RENVGRILGRCPELFAS----NIERTLMKKIDFLIG-IGI--SKDHLPRTIKKYPELLVSDVDRTLLPRIKYLMEMGLSK 514 (610)
Q Consensus 442 ~~~i~~ll~k~P~iL~~----s~e~~L~~k~~fL~~-lGl--s~~~i~~~I~~~P~iL~~sle~~L~~kv~~L~~lG~s~ 514 (610)
..++..++.+||.+=.. |--+++-..++-+.+ -|+ -+.||+.-=+--... +.+.+.+-.|++-|+.-|.+.
T Consensus 30 N~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinEY--y~i~~~vi~~I~el~~eG~s~ 107 (131)
T PF08004_consen 30 NKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINEY--YEIPESVIERIKELKSEGKSE 107 (131)
T ss_pred chHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCccc--ccCCHHHHHHHHHHHHcCCCH
Confidence 35666677777766332 223345555554443 233 334443111111111 123456888999999999999
Q ss_pred HHHHHHHHh
Q 007270 515 RDIAFMVRR 523 (610)
Q Consensus 515 ~ev~~mi~r 523 (610)
+++..-+.+
T Consensus 108 eei~~ki~~ 116 (131)
T PF08004_consen 108 EEIAEKISR 116 (131)
T ss_pred HHHHHHHHH
Confidence 998776655
No 47
>PHA01351 putative minor structural protein
Probab=31.72 E-value=5.8e+02 Score=30.10 Aligned_cols=53 Identities=11% Similarity=0.039 Sum_probs=34.9
Q ss_pred ccCCCCHHHHHHHHHhC---CCeee-c--------CccCCHHHHHHHHHhcCCChHHHHHHHhhC
Q 007270 259 DMLGSSDASFRYLVESF---PRLLL-L--------SAESHVKPVVDFLEIVGVPKDCMGNVLLLF 311 (610)
Q Consensus 259 ~~lGls~s~I~~iv~~~---P~LL~-~--------~~~~~l~p~l~~L~slGis~~~I~~il~~~ 311 (610)
+.||+|++=...+|..+ |.+-. . .+--+....-..|+.+|++.+++.-++..+
T Consensus 651 KKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~y 715 (1070)
T PHA01351 651 KKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKF 715 (1070)
T ss_pred HHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34699998888888777 54211 0 111223445678999999999988777654
No 48
>PF06089 Asparaginase_II: L-asparaginase II; InterPro: IPR010349 This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (3.5.1.1 from EC) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source [].
Probab=30.80 E-value=63 Score=34.44 Aligned_cols=52 Identities=23% Similarity=0.418 Sum_probs=41.2
Q ss_pred hhhhhhhhhHhhhCCcccCCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHH
Q 007270 243 QTLAFFEKIEARRGGLDMLGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCM 304 (610)
Q Consensus 243 ~vl~fl~sL~~kl~gl~~lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I 304 (610)
|.++++++ ++.+.+||++++++-++.++ ...+.++.-+-.+|..+|++.+++
T Consensus 48 QAlp~l~s-----Ga~e~~~l~~~elAl~cASH-----~Ge~~H~~~v~~~L~k~gL~e~~L 99 (324)
T PF06089_consen 48 QALPLLES-----GAAEAFGLTDEELALACASH-----SGEPEHVEAVRSMLAKAGLSEEDL 99 (324)
T ss_pred HHHHHHHc-----CchhhcCCCHHHHHHHhhcc-----cChHHHHHHHHHHHHHcCCCHHHc
Confidence 56788887 45566899999999999887 333456777778999999999886
No 49
>PRK14134 recX recombination regulator RecX; Provisional
Probab=28.16 E-value=7e+02 Score=25.96 Aligned_cols=221 Identities=14% Similarity=0.152 Sum_probs=112.3
Q ss_pred CCCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCCceecCHHHHHHHHHHHHHhCCC-hHHH
Q 007270 261 LGSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPPLIFWNIKAIRTKALAFEEIGAV-DNDV 339 (610)
Q Consensus 261 lGls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~IL~~s~~~L~~~l~~L~~lG~s-~~~v 339 (610)
.-++..++..|+... ...+-....+.+|..---+..+|.+=+... .++.+.+...|+.|++.|.= +...
T Consensus 44 ~eld~e~~~ei~~~~------~~~~a~~~AL~~Ls~r~rSe~Elr~KL~~k----~~~~~~Ie~vI~~L~e~~yldD~ry 113 (283)
T PRK14134 44 KVIDVNSLNDIIKED------NYIKCKGYALKYIEKSYKTEKQIKEKLYLK----EYDEDAVNRVIRFLKEYNFIDDDKY 113 (283)
T ss_pred CCcCHHHHHHHHHHH------HHHHHHHHHHHHhccCcchHHHHHHHHHhC----CCCHHHHHHHHHHHHHCCCCCHHHH
Confidence 466788887777442 111112233444444444556665555443 34456677777888888664 4444
Q ss_pred HHHHHhCCcccccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhCCc
Q 007270 340 GKMLLKYPWILSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQ 419 (610)
Q Consensus 340 ~kll~~~P~lL~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~P~ 419 (610)
+....+.- +- . ..-..+..-|+.-|++.+.|..++...+. . +........+.. +.+.
T Consensus 114 A~~yv~~~-~~--~--~G~~~I~~eL~qKGI~~~iIe~al~~~~~----e-~e~e~a~~l~~K-------------k~~~ 170 (283)
T PRK14134 114 CDMYIREK-IN--S--YGRNKIKYTLLNKGIKENIIIEKINNIDE----E-KEKKVAYKLAEK-------------KYKI 170 (283)
T ss_pred HHHHHHHH-HH--h--hhHHHHHHHHHHCCCCHHHHHHHHHhCCh----h-hHHHHHHHHHHH-------------hhcc
Confidence 44443321 10 1 12345567789999999999988875421 0 112222222211 1111
Q ss_pred cccc--Cc-hhHHHHHHHHHHcCCChhhHHHHHhccCccccc---chhh---HHHhHHHHHHHcCCCCCcH-HHH-HhhC
Q 007270 420 LLLR--KP-QEFRQVVSFLEDVGFDRENVGRILGRCPELFAS---NIER---TLMKKIDFLIGIGISKDHL-PRT-IKKY 488 (610)
Q Consensus 420 lL~~--s~-~~i~~kv~fL~~lG~s~~~i~~ll~k~P~iL~~---s~e~---~L~~k~~fL~~lGls~~~i-~~~-I~~~ 488 (610)
.-.. +. ........||..-||+.+.|..++.. ++.. +.+. ++.++. ..+.-+. ..+ -+++
T Consensus 171 ~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~---~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~a~kr~ 241 (283)
T PRK14134 171 LILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNE---LIKNEALYKDNNSQNIENNI------KDENIEELHNLARKRY 241 (283)
T ss_pred cccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHH---HHhHhhhhhhccccchhhcc------ccChHHHHHHHHHHHH
Confidence 1001 11 12345678899999999999988876 2221 1010 111111 1111111 111 1233
Q ss_pred Ccccccccc-ccchhH-HHHHHHhCCCHHHHHHHHHh
Q 007270 489 PELLVSDVD-RTLLPR-IKYLMEMGLSKRDIAFMVRR 523 (610)
Q Consensus 489 P~iL~~sle-~~L~~k-v~~L~~lG~s~~ev~~mi~r 523 (610)
+.+.....+ ..+..| +.||.+.||+.+.|..++..
T Consensus 242 ~~~~~~e~d~~k~~~Kl~~~L~rkGf~~e~I~~vl~~ 278 (283)
T PRK14134 242 DIIIKSEDDKNKIYRRLSNYLLRRGYSWEEVKKSLNE 278 (283)
T ss_pred hhhhcccccHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 333221111 134455 78889999999999988764
No 50
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=28.02 E-value=1.8e+02 Score=27.40 Aligned_cols=30 Identities=13% Similarity=0.336 Sum_probs=14.0
Q ss_pred ccCChhHHHHHHHHHHHcCCChhHHHHHHH
Q 007270 386 LGCSTSKLKLMLDQLGELGVENKKLGQVIA 415 (610)
Q Consensus 386 L~~s~~~l~~~l~~L~elG~~~~~l~~il~ 415 (610)
+.++++.++..+-.|..-|+++.+|+-+++
T Consensus 26 ~~~~~eeve~~I~~lakkG~~pSqIG~~LR 55 (151)
T PRK08561 26 VDYSPEEIEELVVELAKQGYSPSMIGIILR 55 (151)
T ss_pred ccCCHHHHHHHHHHHHHCCCCHHHhhhhHh
Confidence 334444444444444444444444444444
No 51
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=27.72 E-value=2.3e+02 Score=27.65 Aligned_cols=88 Identities=15% Similarity=0.145 Sum_probs=40.0
Q ss_pred HHHHHh-CCChHHHHHHHHhCCcccccChhhhHH-HHHHHHHhC-CCChHHHHHHHHhCCcccc---------CC-hhHH
Q 007270 327 LAFEEI-GAVDNDVGKMLLKYPWILSTSIQENYE-EILSVFNEE-KVPKLSVDRAIRSWPHLLG---------CS-TSKL 393 (610)
Q Consensus 327 ~~L~~l-G~s~~~v~kll~~~P~lL~~s~~~~l~-~~v~fL~~~-Gl~~~~I~~il~~~P~lL~---------~s-~~~l 393 (610)
..|..+ |+.+....+++..+.. ..+.+.+. ...+.|.++ |++.+...+++..+-.-+. .. ...+
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg~---~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~ 149 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLSP---EELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSAL 149 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCCH---HHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchH
Confidence 344455 7777776666554431 00111111 123344443 6666666555544322111 00 0124
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhC
Q 007270 394 KLMLDQLGELGVENKKLGQVIAKS 417 (610)
Q Consensus 394 ~~~l~~L~elG~~~~~l~~il~~~ 417 (610)
.+.+..|..+|+++.++.+++...
T Consensus 150 ~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 150 EEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 555555556666655555555443
No 52
>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=26.90 E-value=1.4e+02 Score=21.89 Aligned_cols=13 Identities=23% Similarity=0.337 Sum_probs=5.9
Q ss_pred CCCChHHHHHHHH
Q 007270 368 EKVPKLSVDRAIR 380 (610)
Q Consensus 368 ~Gl~~~~I~~il~ 380 (610)
+|++...|.+++.
T Consensus 7 ~gvs~~tvs~~l~ 19 (52)
T cd01392 7 AGVSVATVSRVLN 19 (52)
T ss_pred HCcCHHHHHHHHc
Confidence 3444444444444
No 53
>cd08808 CARD_CARD11_CARMA1 Caspase activation and recruitment domain of CARD11-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD11, also known as caspase recruitment domain-containing membrane-associated guanylate kinase protein 1 (CARMA1). CARMA1, together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), form the L-CBM signalosome (CBM complex in lymphoid immune cells) which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARMA1 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 as
Probab=26.54 E-value=62 Score=27.50 Aligned_cols=24 Identities=38% Similarity=0.516 Sum_probs=18.6
Q ss_pred HhhcCCCccchhhhccCCCcchhh
Q 007270 164 AKEKGDNGKVAFLESLGLSLSSAI 187 (610)
Q Consensus 164 ~~~~p~n~~~~f~EslG~~~s~~~ 187 (610)
+.-++.+.|++|+|||-+......
T Consensus 59 L~trG~~af~aFLeSLe~~yP~l~ 82 (86)
T cd08808 59 LHTKGQRGYVVFLESLEFYYPELY 82 (86)
T ss_pred HHhcCchHHHHHHHHHHhhCHHHH
Confidence 456788889999999987766554
No 54
>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=26.36 E-value=2.1e+02 Score=26.02 Aligned_cols=78 Identities=15% Similarity=0.233 Sum_probs=0.0
Q ss_pred cccChhhhHHHHHHHHHhCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHH
Q 007270 350 LSTSIQENYEEILSVFNEEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFR 429 (610)
Q Consensus 350 L~~s~~~~l~~~v~fL~~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~ 429 (610)
|.......+--+.+.|+. |++.++|..+-.-.|+.|. +++.+++. ++.+... ..+.-.
T Consensus 5 L~~Ptd~Rlf~i~eAlrr-G~sveeI~e~T~ID~wFL~----~i~~Iv~~-------e~~L~~~----------~~~~~~ 62 (123)
T PF02787_consen 5 LRHPTDERLFAIAEALRR-GYSVEEIHELTKIDPWFLE----QIKNIVDM-------EKELKEY----------LNELDP 62 (123)
T ss_dssp HHSTBTTHHHHHHHHHHT-TB-HHHHHHHH---HHHHH----HHHHHHHH-------HHHHHHH----------GGG--H
T ss_pred hCCCCCcHHHHHHHHHHc-CCCHHHHHHHHCccHHHHH----HHHHHHHH-------HHHHHHh----------hccchH
Q ss_pred HHHHHHHHcCCChhhHHHHH
Q 007270 430 QVVSFLEDVGFDRENVGRIL 449 (610)
Q Consensus 430 ~kv~fL~~lG~s~~~i~~ll 449 (610)
+.+.-.+++||++.+|+.+.
T Consensus 63 ~~L~~aK~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 63 ELLRKAKRLGFSDRQIARLW 82 (123)
T ss_dssp HHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHhcc
No 55
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=26.14 E-value=2e+02 Score=27.04 Aligned_cols=35 Identities=23% Similarity=0.409 Sum_probs=18.9
Q ss_pred CccccCChhHHHHHHHHHHHcCCChhHHHHHHHhC
Q 007270 383 PHLLGCSTSKLKLMLDQLGELGVENKKLGQVIAKS 417 (610)
Q Consensus 383 P~lL~~s~~~l~~~l~~L~elG~~~~~l~~il~~~ 417 (610)
|.-+..+++.+++.+-.|..-|+++.+|+-+++..
T Consensus 20 P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 20 PSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred CchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 33344445555555555555566566665555543
No 56
>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=25.35 E-value=68 Score=23.80 Aligned_cols=18 Identities=17% Similarity=0.195 Sum_probs=7.3
Q ss_pred HHHHHHhCCChHHHHHHH
Q 007270 326 ALAFEEIGAVDNDVGKML 343 (610)
Q Consensus 326 l~~L~~lG~s~~~v~kll 343 (610)
++.|..||+++.++.+++
T Consensus 7 ~~AL~~LGy~~~e~~~av 24 (47)
T PF07499_consen 7 LEALISLGYSKAEAQKAV 24 (47)
T ss_dssp HHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 344444444444444333
No 57
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.33 E-value=1.8e+02 Score=23.31 Aligned_cols=39 Identities=15% Similarity=0.374 Sum_probs=20.1
Q ss_pred cCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhh
Q 007270 403 LGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDREN 444 (610)
Q Consensus 403 lG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~ 444 (610)
+|++...+.+++...+.+ +++......+.++++|+.++.
T Consensus 10 ~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 10 AGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred HCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCCH
Confidence 555555555555544442 334444455555555655443
No 58
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=24.07 E-value=1.6e+02 Score=23.48 Aligned_cols=43 Identities=21% Similarity=0.281 Sum_probs=28.4
Q ss_pred hCCCChHHHHHHHHhCCccccCChhHHHHHHHHHHHcCCChhHHHH
Q 007270 367 EEKVPKLSVDRAIRSWPHLLGCSTSKLKLMLDQLGELGVENKKLGQ 412 (610)
Q Consensus 367 ~~Gl~~~~I~~il~~~P~lL~~s~~~l~~~l~~L~elG~~~~~l~~ 412 (610)
.+|++..-|.+++...+.+ +++..+.+.+.++++|+.+.....
T Consensus 9 ~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~~~~~ 51 (70)
T smart00354 9 LAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPNRVAR 51 (70)
T ss_pred HHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCCHHHH
Confidence 4677777777777665543 345666667777788887665443
No 59
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=23.90 E-value=4.4e+02 Score=23.55 Aligned_cols=26 Identities=12% Similarity=0.256 Sum_probs=13.0
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhCC
Q 007270 358 YEEILSVFNEEKVPKLSVDRAIRSWP 383 (610)
Q Consensus 358 l~~~v~fL~~~Gl~~~~I~~il~~~P 383 (610)
+......|...|+...++..++.-+|
T Consensus 57 i~~~~~~L~~~~L~k~E~~~i~Nl~P 82 (118)
T smart00657 57 VRAVRTLLKSKKLHKFEIAQLGNLRP 82 (118)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCC
Confidence 44444445555555555555544444
No 60
>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=23.69 E-value=1.8e+02 Score=21.26 Aligned_cols=43 Identities=16% Similarity=0.340 Sum_probs=26.1
Q ss_pred HHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHH
Q 007270 401 GELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVG 446 (610)
Q Consensus 401 ~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~ 446 (610)
+.+|++...+.+++...+. .+++......+....+|+..+.+.
T Consensus 5 ~~~gvs~~tvs~~l~g~~~---vs~~~~~~i~~~~~~l~~~~~~~~ 47 (52)
T cd01392 5 RAAGVSVATVSRVLNGKPR---VSEETRERVLAAAEELGYRPNAAA 47 (52)
T ss_pred HHHCcCHHHHHHHHcCCCC---CCHHHHHHHHHHHHHhCCCCCHHH
Confidence 3467777777777766653 234445555666667777665543
No 61
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=23.34 E-value=62 Score=29.66 Aligned_cols=50 Identities=28% Similarity=0.325 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHhCCCeeecCccCCHHHHHHHHHhcCCChHHHHHHHhhCCC
Q 007270 262 GSSDASFRYLVESFPRLLLLSAESHVKPVVDFLEIVGVPKDCMGNVLLLFPP 313 (610)
Q Consensus 262 Gls~s~I~~iv~~~P~LL~~~~~~~l~p~l~~L~slGis~~~I~~il~~~P~ 313 (610)
|++.+.++.- .+.|..|..++|. +.+-+--|-..|++.+|||-++...-.
T Consensus 10 Gis~SAlPY~-r~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLRDshG 59 (151)
T KOG0400|consen 10 GISGSALPYR-RSVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILRDSHG 59 (151)
T ss_pred ccccCccccc-cCCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeeecccC
Confidence 4555554443 3458888888864 888888888999999999977765433
No 62
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=22.76 E-value=1.1e+02 Score=26.13 Aligned_cols=21 Identities=19% Similarity=0.199 Sum_probs=17.4
Q ss_pred HHHHH-HHcCCChhhHhHHhhC
Q 007270 91 IYDYL-SELGISQEDCAFISSN 111 (610)
Q Consensus 91 ~~~yl-~~~~~~~~~a~~i~~~ 111 (610)
+++|| ...=++..|+|.|...
T Consensus 21 l~d~L~q~~VLt~~d~EeI~~~ 42 (86)
T cd08785 21 LTPYLRQCKVLDEQDEEEVLSS 42 (86)
T ss_pred HHHHHHhcCCCCHHHHHHHhCC
Confidence 89999 7777899999988763
No 63
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=22.60 E-value=4.2e+02 Score=23.68 Aligned_cols=56 Identities=16% Similarity=0.261 Sum_probs=35.3
Q ss_pred ChhHHHHHHHHHHHcCCChhHHHHHHHhCCcccccCchhHHHHHHHHHHcCCChhhHHHHH
Q 007270 389 STSKLKLMLDQLGELGVENKKLGQVIAKSPQLLLRKPQEFRQVVSFLEDVGFDRENVGRIL 449 (610)
Q Consensus 389 s~~~l~~~l~~L~elG~~~~~l~~il~~~P~lL~~s~~~i~~kv~fL~~lG~s~~~i~~ll 449 (610)
+.+.+....+.|...|+.+..+..++..+|. +.+.+...+.-+.+- ++++++..++
T Consensus 53 ~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~----s~~E~~~lI~sl~~r-~~ee~l~~iL 108 (118)
T smart00657 53 NREIVRAVRTLLKSKKLHKFEIAQLGNLRPE----TAEEAQLLIPSLEER-IDEEELEELL 108 (118)
T ss_pred CHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC----CHHHHHHHhhhhhcc-CCHHHHHHHH
Confidence 4577778888888888888888888877776 334444444444321 5555555444
No 64
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=22.37 E-value=77 Score=31.19 Aligned_cols=29 Identities=34% Similarity=0.479 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHcCCChhhHhHHhhCCH
Q 007270 85 TLTQQAIYDYLSELGISQEDCAFISSNSP 113 (610)
Q Consensus 85 ~~a~~a~~~yl~~~~~~~~~a~~i~~~sp 113 (610)
..=|.++.+||.+|||...-|+.|..-|-
T Consensus 158 e~Lq~~~~~yLeeRGId~~la~fl~~y~~ 186 (204)
T PF02330_consen 158 ENLQDAFMNYLEERGIDEELANFLHDYST 186 (204)
T ss_dssp HHHHHHHHHHHHHTT-SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45689999999999999999988765443
No 65
>PHA02591 hypothetical protein; Provisional
Probab=22.36 E-value=1.9e+02 Score=24.26 Aligned_cols=22 Identities=0% Similarity=-0.016 Sum_probs=11.8
Q ss_pred hHHHHHHHHHhCCCChHHHHHH
Q 007270 357 NYEEILSVFNEEKVPKLSVDRA 378 (610)
Q Consensus 357 ~l~~~v~fL~~~Gl~~~~I~~i 378 (610)
++..+..-|.+.|++..+|+..
T Consensus 47 d~~~vA~eL~eqGlSqeqIA~~ 68 (83)
T PHA02591 47 DLISVTHELARKGFTVEKIASL 68 (83)
T ss_pred hHHHHHHHHHHcCCCHHHHHHH
Confidence 3445555555666665555443
No 66
>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]
Probab=21.40 E-value=6.9e+02 Score=23.47 Aligned_cols=29 Identities=14% Similarity=0.300 Sum_probs=14.7
Q ss_pred hHHHHHHHHHHHcCCChhHHHHHHHhCCc
Q 007270 391 SKLKLMLDQLGELGVENKKLGQVIAKSPQ 419 (610)
Q Consensus 391 ~~l~~~l~~L~elG~~~~~l~~il~~~P~ 419 (610)
+.+...+..+.++|+.+..+..++...|.
T Consensus 70 E~i~el~~k~~~fkLtKAE~LqiiN~rPs 98 (149)
T KOG4168|consen 70 ESIIELITKLKSFKLTKAEILQIINLRPS 98 (149)
T ss_pred HHHHHHHHHhccccchHHHHHHHhccCcc
Confidence 44444444555555555555555554444
No 67
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.14 E-value=1.3e+02 Score=31.32 Aligned_cols=25 Identities=24% Similarity=0.499 Sum_probs=18.1
Q ss_pred cchhHHHHHHHhCCCHHHHHHHHHh
Q 007270 499 TLLPRIKYLMEMGLSKRDIAFMVRR 523 (610)
Q Consensus 499 ~L~~kv~~L~~lG~s~~ev~~mi~r 523 (610)
-+..|.+||++.|++.+||..++++
T Consensus 21 Pli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 21 PLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred hHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 3556777777777777777777775
No 68
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=20.90 E-value=2.2e+02 Score=25.12 Aligned_cols=26 Identities=12% Similarity=0.198 Sum_probs=12.2
Q ss_pred HHHHHHHHHhCCCChHHHHHHHHhCC
Q 007270 358 YEEILSVFNEEKVPKLSVDRAIRSWP 383 (610)
Q Consensus 358 l~~~v~fL~~~Gl~~~~I~~il~~~P 383 (610)
+...++.|..+|++..++.+++.-+|
T Consensus 59 ~~~l~~~L~~~~L~~~E~~qi~Nl~P 84 (117)
T PF03874_consen 59 IKELREELKKFGLTEFEILQIINLRP 84 (117)
T ss_dssp HHHHHHHHTTSTS-HHHHHHHHHH--
T ss_pred HHHHHHHHhcccCCHHHHHHHhcCCC
Confidence 44445555555555555555555554
No 69
>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=20.46 E-value=78 Score=33.59 Aligned_cols=33 Identities=21% Similarity=0.644 Sum_probs=22.6
Q ss_pred HHHHHHHhCCccccc-------CchhHHHHHHHHH----HcCCC
Q 007270 409 KLGQVIAKSPQLLLR-------KPQEFRQVVSFLE----DVGFD 441 (610)
Q Consensus 409 ~l~~il~~~P~lL~~-------s~~~i~~kv~fL~----~lG~s 441 (610)
.|+++++.+|.+|.+ +|++....++.|+ ++|++
T Consensus 151 aIARALa~~P~iLL~DEaTSALDP~TT~sIL~LL~~In~~lglT 194 (339)
T COG1135 151 AIARALANNPKILLCDEATSALDPETTQSILELLKDINRELGLT 194 (339)
T ss_pred HHHHHHhcCCCEEEecCccccCChHHHHHHHHHHHHHHHHcCCE
Confidence 378888899998875 3445556667665 46654
Done!