Query 011168
Match_columns 492
No_of_seqs 292 out of 1347
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:52:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011168.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011168hhsearch_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 5.9E-57 1.3E-61 479.4 26.1 385 60-478 52-451 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 4.6E-45 9.9E-50 375.3 7.2 330 129-464 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 8E-43 1.7E-47 371.2 19.7 344 121-477 60-419 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 3.3E-34 7.2E-39 294.7 -1.0 312 74-415 2-326 (345)
5 KOG1267 Mitochondrial transcri 99.9 1.5E-26 3.2E-31 243.6 12.2 343 69-448 59-411 (413)
6 KOG1267 Mitochondrial transcri 99.8 3.5E-20 7.5E-25 195.4 13.0 265 173-446 73-340 (413)
7 smart00733 Mterf Mitochondrial 96.5 0.0019 4E-08 41.4 2.3 11 401-411 16-26 (31)
8 smart00733 Mterf Mitochondrial 96.5 0.0015 3.3E-08 41.8 1.9 30 350-380 2-31 (31)
9 PF11955 PORR: Plant organelle 92.7 0.36 7.8E-06 49.7 7.5 202 195-399 40-292 (335)
10 cd04790 HTH_Cfa-like_unk Helix 80.4 4.4 9.5E-05 37.6 6.1 115 193-318 49-167 (172)
11 cd04790 HTH_Cfa-like_unk Helix 75.9 8.4 0.00018 35.8 6.6 22 229-250 49-70 (172)
12 PF04695 Pex14_N: Peroxisomal 75.5 4 8.6E-05 36.4 4.2 48 331-394 3-50 (136)
13 PF11955 PORR: Plant organelle 67.9 14 0.0003 38.2 6.6 118 207-329 22-151 (335)
14 PF11212 DUF2999: Protein of u 61.7 23 0.0005 27.8 5.1 48 228-283 2-49 (82)
15 PF10975 DUF2802: Protein of u 58.0 5.8 0.00013 31.2 1.4 20 70-89 45-64 (70)
16 PRK00117 recX recombination re 51.3 1.3E+02 0.0028 27.0 9.4 22 370-391 132-153 (157)
17 PF02631 RecX: RecX family; I 46.3 68 0.0015 27.5 6.4 108 261-390 9-118 (121)
18 PF00627 UBA: UBA/TS-N domain; 44.0 37 0.00079 22.8 3.4 23 300-322 4-26 (37)
19 PF13560 HTH_31: Helix-turn-he 43.1 47 0.001 24.9 4.4 55 72-140 6-60 (64)
20 PF14490 HHH_4: Helix-hairpin- 40.9 1E+02 0.0022 25.4 6.3 71 190-285 7-78 (94)
21 PF09388 SpoOE-like: Spo0E lik 38.6 84 0.0018 22.2 4.7 37 62-102 3-39 (45)
22 PTZ00217 flap endonuclease-1; 37.6 4.3E+02 0.0093 27.9 11.9 25 297-321 304-329 (393)
23 PF04695 Pex14_N: Peroxisomal 37.1 39 0.00084 30.1 3.5 38 286-326 14-51 (136)
24 TIGR03070 couple_hipB transcri 35.2 1.1E+02 0.0024 21.7 5.2 31 72-102 7-37 (58)
25 cd03211 GST_C_Metaxin2 GST_C f 35.2 1.8E+02 0.0038 25.2 7.3 89 55-152 24-118 (126)
26 PRK14136 recX recombination re 34.8 3.9E+02 0.0085 27.3 10.4 23 369-391 280-302 (309)
27 PRK09726 antitoxin HipB; Provi 32.6 1.1E+02 0.0024 24.7 5.2 52 72-138 17-68 (88)
28 TIGR00601 rad23 UV excision re 30.8 2.1E+02 0.0045 30.2 8.1 43 189-240 154-196 (378)
29 cd01392 HTH_LacI Helix-turn-he 30.5 92 0.002 22.0 4.0 41 271-314 5-45 (52)
30 COG3747 Phage terminase, small 30.1 32 0.00069 31.0 1.7 99 243-349 32-133 (160)
31 PF13744 HTH_37: Helix-turn-he 28.7 1.7E+02 0.0037 23.1 5.6 52 71-137 22-74 (80)
32 COG1125 OpuBA ABC-type proline 28.5 1.4E+02 0.003 30.0 5.9 41 320-361 97-138 (309)
33 smart00165 UBA Ubiquitin assoc 27.5 1.8E+02 0.004 19.0 5.0 23 193-215 3-25 (37)
34 smart00354 HTH_LACI helix_turn 27.4 1.2E+02 0.0026 23.3 4.4 42 271-315 8-49 (70)
35 PF00356 LacI: Bacterial regul 27.0 1E+02 0.0023 22.0 3.6 38 271-311 7-44 (46)
36 cd00194 UBA Ubiquitin Associat 26.8 1.9E+02 0.0042 19.0 5.0 23 193-215 3-25 (38)
37 KOG0369 Pyruvate carboxylase [ 25.6 1E+02 0.0022 34.7 4.8 68 72-176 914-987 (1176)
38 PF11212 DUF2999: Protein of u 25.5 1.9E+02 0.0042 22.8 5.0 48 264-318 2-49 (82)
39 smart00530 HTH_XRE Helix-turn- 25.3 2E+02 0.0044 19.0 5.0 30 73-102 3-32 (56)
40 cd00128 XPG Xeroderma pigmento 25.1 5.1E+02 0.011 26.2 9.7 32 118-154 145-176 (316)
41 COG2511 GatE Archaeal Glu-tRNA 24.6 3.2E+02 0.007 30.1 8.2 29 121-151 453-482 (631)
42 PRK00116 ruvA Holliday junctio 24.1 2E+02 0.0044 27.0 6.1 25 298-322 149-173 (192)
43 PF12844 HTH_19: Helix-turn-he 24.0 2.6E+02 0.0056 20.6 5.6 52 72-138 4-55 (64)
44 PF13543 KSR1-SAM: SAM like do 23.6 88 0.0019 27.7 3.2 52 266-320 69-123 (129)
45 TIGR01448 recD_rel helicase, p 23.3 1.9E+02 0.004 33.2 6.7 84 188-281 74-161 (720)
46 PF02742 Fe_dep_repr_C: Iron d 22.9 86 0.0019 24.3 2.8 37 62-102 8-45 (71)
47 cd08319 Death_RAIDD Death doma 22.6 2.2E+02 0.0048 23.1 5.2 35 234-272 20-54 (83)
48 PRK03980 flap endonuclease-1; 22.1 6.5E+02 0.014 25.4 9.7 25 297-321 250-275 (292)
49 KOG2629 Peroxisomal membrane a 22.1 1.2E+02 0.0026 30.5 4.2 25 366-390 21-45 (300)
50 PF07499 RuvA_C: RuvA, C-termi 22.0 1.4E+02 0.003 21.3 3.5 24 192-215 4-27 (47)
51 PF08671 SinI: Anti-repressor 21.9 1.2E+02 0.0025 19.9 2.7 24 367-390 5-28 (30)
52 COG2137 OraA Uncharacterized p 20.8 4.5E+02 0.0097 24.5 7.5 25 366-390 138-163 (174)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=5.9e-57 Score=479.40 Aligned_cols=385 Identities=25% Similarity=0.452 Sum_probs=346.9
Q ss_pred HHHHHHHHH--HHHHHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhh
Q 011168 60 LLAAEKEEA--KAVLTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEE 137 (492)
Q Consensus 60 ~~~~~~~~a--~~~~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls 137 (492)
+.+++++++ ++.+.+||..-|+....+.+.-. |.-++++++ ++.||.++|++
T Consensus 52 ~~~~~~~~~~~~~~~~~~L~~lgi~~~~l~~~~~--p~~~~~~~~------------------------~l~~L~s~G~~ 105 (487)
T PLN03196 52 LLEMKKEKLVNREKVLDFLRGIGIDPDELDGLEL--PSTVDVMRE------------------------RVEFLHKLGLT 105 (487)
T ss_pred HHHhhhhhhhhHHHHHHHHHHcCCCchhhhccCC--CccHHHHHH------------------------HHHHHHHcCCC
Confidence 777766655 88899999999999998866422 223444444 45788888888
Q ss_pred hhhhHHHHHhcCCCCCCcccccCccCCCCCcCCCChHHHHhc-------cccccCCCCCChHHHHHHHHhCCCCHHHHHH
Q 011168 138 YGNVLVDLVENFPNAPPPAKQKAVAPVSPPVSTLDSKKLKAI-------SRVSELDSSGDLRPQILYLIELGMDLEKIKL 210 (492)
Q Consensus 138 ~~~~ia~~V~~~P~lL~~~~~~~~~~~~~~l~~~~~~~~~~~-------~r~l~~~~~~~l~~~l~~L~~lG~s~~~i~~ 210 (492)
.++ |+ ++|.+|.+++++++.|++.+|..+|++..+ + ++++..+.+.++.|+++||+++|++.++|.+
T Consensus 106 ~~~-i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~-i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~ 179 (487)
T PLN03196 106 IED-IN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSS-LPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPR 179 (487)
T ss_pred hHH-hc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHH-HHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 866 65 688888888888888888888877777654 3 3455555577899999999999999999999
Q ss_pred HHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChhhHHHHHHhCCcc
Q 011168 211 ITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKTQWAKVIQRFPAV 290 (492)
Q Consensus 211 ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~~i~kll~~~P~i 290 (492)
++.++|.+|++++++.+.|+++||.++|++.++|++++.++|++|+++++++++|+++||+++|++.+++.+++.++|++
T Consensus 180 ~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~i 259 (487)
T PLN03196 180 VLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYI 259 (487)
T ss_pred HHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCce
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccch-hhhhHHHHHHHcCCChHhHhhhhhcCcceeeccchhhhhhhHHHHH-hhCCCcch---hhhccccccccccch
Q 011168 291 LTYSRQ-KVKQTVDFLYEMGLSAESIGKVLTRCPNIISYSIEEKLRPTAEYFR-SLGVDVSV---LLQRCPQSLGCSIEA 365 (492)
Q Consensus 291 L~~s~e-kl~~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v~fL~-~lGl~~~~---il~r~P~iL~~sle~ 365 (492)
++++.+ ++++++++|.++|++++++..++.++|.+++++.++++.++++||. ++|++... ++.++|+++++| ++
T Consensus 260 L~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lS-e~ 338 (487)
T PLN03196 260 LGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLN-RN 338 (487)
T ss_pred eEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhccc-HH
Confidence 999988 7999999999999999999999999999999998889999999996 79998754 678999999999 57
Q ss_pred hhhHHHHHHHHcCCCHHHHHHHHhhccceeeecccccHHHHHHHHH-HcCCChHHHhhcCcccccCcccccHhHHHHHHH
Q 011168 366 NLKPVTEFFLERGFTVEEIGTMISRFGALYTFSLTENLIPKWEFFL-TMDYDKSELVKFPQYFGYSLEERIKPRYARVKV 444 (492)
Q Consensus 366 ~L~~r~~fL~~~Gls~~ev~~mi~~~P~lL~~sle~~L~~k~~fL~-~~G~~~~~i~~~P~lL~~Sle~rIkpR~~~L~~ 444 (492)
++.++++||+++|++.+++..|+.++|++|++| .++|++|++||+ +||++.++|++||++|+||+|+||+|||++|+.
T Consensus 339 kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S-~~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~ 417 (487)
T PLN03196 339 VALKHVEFLRGRGFSAQDVAKMVVRCPQILALN-LEIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAK 417 (487)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhCCceeecc-HHHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHH
Confidence 899999999999999999999999999999999 599999999999 899999999999999999999999999999999
Q ss_pred hccccChhhhhcCChHhHHHHHHHHHHHhccCCC
Q 011168 445 HGVKLLLNQVLSLSGSNFENVLKKKIEKALSDGG 478 (492)
Q Consensus 445 lg~~~~l~~~L~~Sd~~F~~~~~~~~~~l~~~~~ 478 (492)
.|.++++.++|.+||++|+++|+.+|.|...-+.
T Consensus 418 kGl~~sL~~~L~~sd~~F~~r~v~~y~e~~~~~~ 451 (487)
T PLN03196 418 KGIKCSLAWFLNCSDDKFEQRMSGDFIEGEEMEP 451 (487)
T ss_pred cCCCCCHHHHhccCHHHHHHHHhhhcccccccCC
Confidence 9999999999999999999999999988666554
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=4.6e-45 Score=375.30 Aligned_cols=330 Identities=34% Similarity=0.572 Sum_probs=235.8
Q ss_pred HHHHHhhhhhhhhHHHHHhcCCCCCCcccccCccCCCCCcCCCChHHHHhccc-------cccCCCCCChHHHHHHHHhC
Q 011168 129 PYLESLLEEYGNVLVDLVENFPNAPPPAKQKAVAPVSPPVSTLDSKKLKAISR-------VSELDSSGDLRPQILYLIEL 201 (492)
Q Consensus 129 afLe~lGls~~~~ia~~V~~~P~lL~~~~~~~~~~~~~~l~~~~~~~~~~~~r-------~l~~~~~~~l~~~l~~L~~l 201 (492)
++|+.+|++..+ |..+++++|.+|.+++++++.|...++..+|++..+ +++ ++..+.+.++.|.++||.++
T Consensus 2 ~~~~~~gf~~~~-i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~-i~~il~~~P~il~~s~~~~i~p~~~~L~~~ 79 (345)
T PF02536_consen 2 DLLKNHGFSDSQ-ISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSD-IAKILSKNPQILSRSLEKNIIPVFDFLKSI 79 (345)
T ss_dssp HHHHHHHHHTS--HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHH-HHHHHHH-GGGGGS--HHHHHHHHHHHTTT
T ss_pred hHHHHcCCCHHH-HHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHH-HHHHHHhChHHHhccchhhHHHHHHHHHHH
Confidence 689999999966 999999999999999888888888888877777554 333 44444467788888999998
Q ss_pred CCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChhhHH
Q 011168 202 GMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKTQWA 281 (492)
Q Consensus 202 G~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~~i~ 281 (492)
|++++++.+++.++|.++..+.++++.+++++|+++|++.+.+.+++...|.++... +++.+.++++.++|++++++.
T Consensus 80 ~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~ 157 (345)
T PF02536_consen 80 GLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIG 157 (345)
T ss_dssp SS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHC
T ss_pred cCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhc
Confidence 888888999888889888887766788899999999998877888888888766544 678888888888899998888
Q ss_pred HHHHhCCccccc-cchhhhhHHHHHHHcCCChHhHhhhhhcCcceeeccchhhhhhhHHHHHhhCCCcchhhhccccccc
Q 011168 282 KVIQRFPAVLTY-SRQKVKQTVDFLYEMGLSAESIGKVLTRCPNIISYSIEEKLRPTAEYFRSLGVDVSVLLQRCPQSLG 360 (492)
Q Consensus 282 kll~~~P~iL~~-s~ekl~~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v~fL~~lGl~~~~il~r~P~iL~ 360 (492)
+++..+|.++.. +.+.++++++||+++|++.+++.+++.++|.++..+.++.+++...++...|.....++.++|.++.
T Consensus 158 ~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~ 237 (345)
T PF02536_consen 158 RVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILS 237 (345)
T ss_dssp CCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------T
T ss_pred ccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccc
Confidence 888888865554 4456889999998899999999999999999998887666666555555566555577888899998
Q ss_pred cccchhhhHHHHHHHHcCCCHHHHHHHHhhccceeeecccccHHHHHHHHH-HcCCChHHHhhcCcccccCcccccHhHH
Q 011168 361 CSIEANLKPVTEFFLERGFTVEEIGTMISRFGALYTFSLTENLIPKWEFFL-TMDYDKSELVKFPQYFGYSLEERIKPRY 439 (492)
Q Consensus 361 ~sle~~L~~r~~fL~~~Gls~~ev~~mi~~~P~lL~~sle~~L~~k~~fL~-~~G~~~~~i~~~P~lL~~Sle~rIkpR~ 439 (492)
++ ++++.++++||+++|++.+|+.+|+.++|.+|++|. +++++|++||. +||++.++|+++|++|+||+|+||+|||
T Consensus 238 ~~-~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~-e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~ 315 (345)
T PF02536_consen 238 LS-EEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSI-EKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRY 315 (345)
T ss_dssp HH-HHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-H-HHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHH
T ss_pred cc-hHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcch-hhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHH
Confidence 88 568999999999999999999999999999999995 67999999999 7999999999999999999999999995
Q ss_pred ---HHHHHhc--cccChhhhhcCChHhHHH
Q 011168 440 ---ARVKVHG--VKLLLNQVLSLSGSNFEN 464 (492)
Q Consensus 440 ---~~L~~lg--~~~~l~~~L~~Sd~~F~~ 464 (492)
++++..| .++++.+||.+||++|++
T Consensus 316 ~~~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 316 EVLKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HHHHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 5555667 667889999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=8e-43 Score=371.24 Aligned_cols=344 Identities=22% Similarity=0.396 Sum_probs=300.3
Q ss_pred hHHhHhHHHHHHHhhhhhhhhHHHHHhcCCCCCCcccccCccCCCCCcCCCChHHHH--hccccccCCCCCChHHHHHHH
Q 011168 121 LEIRDALTPYLESLLEEYGNVLVDLVENFPNAPPPAKQKAVAPVSPPVSTLDSKKLK--AISRVSELDSSGDLRPQILYL 198 (492)
Q Consensus 121 ~~~~davlafLe~lGls~~~~ia~~V~~~P~lL~~~~~~~~~~~~~~l~~~~~~~~~--~~~r~l~~~~~~~l~~~l~~L 198 (492)
..++..|+.||+++|+...+ +.++. +.++++ .+.+++.+|..+|++..+ .-+.++..+...++.|+++||
T Consensus 60 ~~~~~~~~~~L~~lgi~~~~-l~~~~------~p~~~~-~~~~~l~~L~s~G~~~~~i~~~P~iL~~~v~~~l~Pvl~fL 131 (487)
T PLN03196 60 LVNREKVLDFLRGIGIDPDE-LDGLE------LPSTVD-VMRERVEFLHKLGLTIEDINEYPLVLGCSVKKNMIPVLDYL 131 (487)
T ss_pred hhhHHHHHHHHHHcCCCchh-hhccC------CCccHH-HHHHHHHHHHHcCCChHHhccCcHHhhcCHhhhhHHHHHHH
Confidence 55677899999999999755 54432 123333 345666677767766554 225566677789999999999
Q ss_pred HhCCCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChh
Q 011168 199 IELGMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKT 278 (492)
Q Consensus 199 ~~lG~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~ 278 (492)
.++|++..+|.+++.++|.+|.+++++++.|+++||+++|++.++|++++.++|++|+++++.++.++++||+++|++++
T Consensus 132 ~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~ 211 (487)
T PLN03196 132 EKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPR 211 (487)
T ss_pred HHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHH
Confidence 99999999999999999999999999999999999999999999999999999999999998899999999999999999
Q ss_pred hHHHHHHhCCccccccch-hhhhHHHHHHHcCCChHhHhhhhhcCcceeeccchhhhhhhHHHHHhhCCCc---chhhhc
Q 011168 279 QWAKVIQRFPAVLTYSRQ-KVKQTVDFLYEMGLSAESIGKVLTRCPNIISYSIEEKLRPTAEYFRSLGVDV---SVLLQR 354 (492)
Q Consensus 279 ~i~kll~~~P~iL~~s~e-kl~~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v~fL~~lGl~~---~~il~r 354 (492)
++++++.++|++|+++.+ ++.++++||+++|++.++|.+++.++|++|+++++++++++++||.++|++. ..++.+
T Consensus 212 ~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~ 291 (487)
T PLN03196 212 DIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQ 291 (487)
T ss_pred HHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 999999999999999988 5999999999999999999999999999999999889999999999999985 567889
Q ss_pred cccccccccchhhhHHHHHHH-HcCCCHHHHHHHHhhccceeeecccccHHHHHHHHHHcCCChHHH----hhcCccccc
Q 011168 355 CPQSLGCSIEANLKPVTEFFL-ERGFTVEEIGTMISRFGALYTFSLTENLIPKWEFFLTMDYDKSEL----VKFPQYFGY 429 (492)
Q Consensus 355 ~P~iL~~sle~~L~~r~~fL~-~~Gls~~ev~~mi~~~P~lL~~sle~~L~~k~~fL~~~G~~~~~i----~~~P~lL~~ 429 (492)
+|.++++++++++.++++||. ++|++.+++..++.++|.++++| ++++++|++||.++|++.++| .++|++|+|
T Consensus 292 ~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lS-e~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~ 370 (487)
T PLN03196 292 YPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLN-RNVALKHVEFLRGRGFSAQDVAKMVVRCPQILAL 370 (487)
T ss_pred CCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhccc-HHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeec
Confidence 999999999999999999996 79999999999999999999999 799999999999999999997 699999999
Q ss_pred CcccccHhHHHHHHH-hcccc----ChhhhhcCChHhHHHHHHHHHHHhccCC
Q 011168 430 SLEERIKPRYARVKV-HGVKL----LLNQVLSLSGSNFENVLKKKIEKALSDG 477 (492)
Q Consensus 430 Sle~rIkpR~~~L~~-lg~~~----~l~~~L~~Sd~~F~~~~~~~~~~l~~~~ 477 (492)
|. +.|+++++|+.. +|... ...++++.|= .+++..||+-+.++|
T Consensus 371 S~-~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySL---EkRI~PR~~~L~~kG 419 (487)
T PLN03196 371 NL-EIMKPSLEFFKKEMKRPLKELVEFPAYFTYGL---ESRIKPRYERVAKKG 419 (487)
T ss_pred cH-HHHHHHHHHHHHHhCCCHHHHHhChHHhccCh---hhhhHHHHHHHHHcC
Confidence 98 599999999874 55542 1234666552 267788888777655
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=99.97 E-value=3.3e-34 Score=294.71 Aligned_cols=312 Identities=28% Similarity=0.450 Sum_probs=222.5
Q ss_pred HHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhhhhhhHHHHHhcCCCCC
Q 011168 74 LFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEEYGNVLVDLVENFPNAP 153 (492)
Q Consensus 74 ~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls~~~~ia~~V~~~P~lL 153 (492)
.++++.|.+.+|-.++.++.|..+.. + . -..-.-.++||.++|+|..| |+.+|.++|.+|
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~--~-~----------------~~~l~pk~~fl~s~G~s~~~-i~~il~~~P~il 61 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLC--D-P----------------EKTLLPKLEFLRSLGFSSSD-IAKILSKNPQIL 61 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT----S----------------S-HHHHHHHHHHHTT--HHH-HHHHHHH-GGGG
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEe--c-C----------------ccchhHHHHHHHHCCCCHHH-HHHHHHhChHHH
Confidence 46778899999999998886666311 1 0 12233356799999999978 999999999999
Q ss_pred CcccccCccCCCCCcCCCChHHHHhc------cccccCCCCCChHHHHHHHHhCCCCHHHHHHHHHhCCceeecCcCCCH
Q 011168 154 PPAKQKAVAPVSPPVSTLDSKKLKAI------SRVSELDSSGDLRPQILYLIELGMDLEKIKLITRRFPAFSYYSLEGKI 227 (492)
Q Consensus 154 ~~~~~~~~~~~~~~l~~~~~~~~~~~------~r~l~~~~~~~l~~~l~~L~~lG~s~~~i~~ll~~~P~lL~~~le~~l 227 (492)
+.+.+..+.|+...+.+++.+..+.+ ++++..+...++.++++||.++|++.+.+.+++...|..+... +.+
T Consensus 62 ~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~ 139 (345)
T PF02536_consen 62 SRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKI 139 (345)
T ss_dssp GS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHH
T ss_pred hccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHH
Confidence 99989999999999998887755422 2233344455899999999999999998889998888765554 589
Q ss_pred HHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHH
Q 011168 228 KPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYE 307 (492)
Q Consensus 228 kp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~ 307 (492)
++.++++.++|++.+++.+++..+|+++..+.++++++++++|+++|++.+++.+++.++|.++..+.+++.+.+.++.+
T Consensus 140 ~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~ 219 (345)
T PF02536_consen 140 KERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLS 219 (345)
T ss_dssp HCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC----------
T ss_pred HHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccc
Confidence 99999999999999999999999998888788899999999999999999999999999999999999986556666654
Q ss_pred cCCChHhHhhhhhcCcceeeccchhhhhhhHHHHHhhCCC---cchhhhccccccccccchhhhHHHHHHH-HcCCCHHH
Q 011168 308 MGLSAESIGKVLTRCPNIISYSIEEKLRPTAEYFRSLGVD---VSVLLQRCPQSLGCSIEANLKPVTEFFL-ERGFTVEE 383 (492)
Q Consensus 308 lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v~fL~~lGl~---~~~il~r~P~iL~~sle~~L~~r~~fL~-~~Gls~~e 383 (492)
.|...++ .++.++|.++.++ ++++.++++||+++|++ +..|+.++|++|+++.+. ++++++||. ++|++.++
T Consensus 220 ~~~~~~~--~~i~~~p~il~~~-~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~-l~~k~~fl~~~m~~~~~~ 295 (345)
T PF02536_consen 220 SGGVEEE--RVIKKFPQILSLS-EEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEK-LKPKFEFLVKEMGLPLEE 295 (345)
T ss_dssp -------------------THH-HHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHH-HHHHHHHHHHCCT--HHH
T ss_pred ccccccc--ccccccccccccc-hHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhh-hhHHHHHHHHHhCcCHHH
Confidence 4444434 7889999999999 57999999999999997 466889999999999765 999999998 59999999
Q ss_pred HHHHHhhccceeeecccccHHHHHHHHH---HcCC
Q 011168 384 IGTMISRFGALYTFSLTENLIPKWEFFL---TMDY 415 (492)
Q Consensus 384 v~~mi~~~P~lL~~sle~~L~~k~~fL~---~~G~ 415 (492)
+. ++|.+|+||+|++|+||++++. +.|.
T Consensus 296 i~----~~P~~l~~sLe~ri~PR~~~~~~l~~~g~ 326 (345)
T PF02536_consen 296 IV----EFPQYLSYSLEKRIKPRYEVLKVLKSKGL 326 (345)
T ss_dssp HH----HSCHHHCS-HHHHHHHHHHHHHTT--TTT
T ss_pred Hh----hCCceeEechhhhhhhHHHHHHHHHHCcC
Confidence 87 9999999999999999965554 6773
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.94 E-value=1.5e-26 Score=243.61 Aligned_cols=343 Identities=26% Similarity=0.416 Sum_probs=281.8
Q ss_pred HHHHHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhhhhhhHHHHHhc
Q 011168 69 KAVLTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEEYGNVLVDLVEN 148 (492)
Q Consensus 69 ~~~~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls~~~~ia~~V~~ 148 (492)
+-..+|++.++|++...|..+++. + ...+ ..+|+.++.+|+++|++. ++|..++..
T Consensus 59 ~f~~s~~~~s~~~~~~~~~~~~~~----~-~~~~------------------~~~p~s~~~~l~s~g~~~-~~i~s~i~~ 114 (413)
T KOG1267|consen 59 NFESSYLVDSLGLSIKLARKLSRE----V-SSED------------------SVNPSSVLSSLRSLGFTD-SQISSIILS 114 (413)
T ss_pred CcceeeeccccccchhhHHHHHHH----H-Hhhh------------------ccCcHHHHHHHHhcCCch-hhccccccc
Confidence 556788889999888888888776 2 2222 669999999999999998 559999999
Q ss_pred CCCCCCcccccCccCCCCCcCCCChHHHH------hccccccCCCCCChHHHHHHHHhCC--CCHHHHHHHHHhCCceee
Q 011168 149 FPNAPPPAKQKAVAPVSPPVSTLDSKKLK------AISRVSELDSSGDLRPQILYLIELG--MDLEKIKLITRRFPAFSY 220 (492)
Q Consensus 149 ~P~lL~~~~~~~~~~~~~~l~~~~~~~~~------~~~r~l~~~~~~~l~~~l~~L~~lG--~s~~~i~~ll~~~P~lL~ 220 (492)
+|++|.++.+..+.+....+...|.+... .++.++......++.+.++|+.+++ .....+.+++...|..
T Consensus 115 ~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~-- 192 (413)
T KOG1267|consen 115 SPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSF-- 192 (413)
T ss_pred CchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccc--
Confidence 99999998888777777554443332221 1223443344578899999999974 7777777776555532
Q ss_pred cCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChhhHHHHHHhCCccccccch-hhh
Q 011168 221 YSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKTQWAKVIQRFPAVLTYSRQ-KVK 299 (492)
Q Consensus 221 ~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~~i~kll~~~P~iL~~s~e-kl~ 299 (492)
...+..+. ++++++++|....++..++..+|+...... .+...+.++.++|+.+.. +++.+.|.++.++.+ ++.
T Consensus 193 ~~~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~ 267 (413)
T KOG1267|consen 193 LLNENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLE 267 (413)
T ss_pred cccccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHH
Confidence 22234566 899999999999999999999999876542 678888999999987776 578888999988666 699
Q ss_pred hHHHHHHHcCCChHhHhhhhhcCcceeeccchhhhhhhHHHHHhhCCCcchhhhccccccccccchhhhHHHHHHHHcCC
Q 011168 300 QTVDFLYEMGLSAESIGKVLTRCPNIISYSIEEKLRPTAEYFRSLGVDVSVLLQRCPQSLGCSIEANLKPVTEFFLERGF 379 (492)
Q Consensus 300 ~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v~fL~~lGl~~~~il~r~P~iL~~sle~~L~~r~~fL~~~Gl 379 (492)
+++++|+.+|++.+|+..+++++|++|+++. +++..+++|+.+. ..+ +.++|+++.++ +..+.++++|+...|+
T Consensus 268 ~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~-~~~~~~~~~~~~~---~~~-~~k~p~~l~~s-~~~l~~~ie~l~~~g~ 341 (413)
T KOG1267|consen 268 PKVEVLKSLGFSREEIWKMVKKCPQILGYSV-KKNLKTTEYLLKN---PKH-ILKFPQLLRSS-EDKLKPRIEFLLSLGF 341 (413)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCchheEeeh-hhhhHHHHHHHhc---chh-hhhhhhhhhcc-chhhhhhHHHHHHcCC
Confidence 9999999999999999999999999999996 5677888888765 333 77889999666 7899999999999999
Q ss_pred CHHHHHHHHhhccceeeecccccHHHHHHHHH-HcCCChHHHhhcCcccccCcccccHhHHHHHHHhccc
Q 011168 380 TVEEIGTMISRFGALYTFSLTENLIPKWEFFL-TMDYDKSELVKFPQYFGYSLEERIKPRYARVKVHGVK 448 (492)
Q Consensus 380 s~~ev~~mi~~~P~lL~~sle~~L~~k~~fL~-~~G~~~~~i~~~P~lL~~Sle~rIkpR~~~L~~lg~~ 448 (492)
+..++..|++++|+++.+|+++.++.+.+|+. .|+++.+.++.+|.++.|++|+|+.||+....+++.+
T Consensus 342 ~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 342 SDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred cHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 99999999999999999997558889999998 7999999999999999999999999999999988765
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.82 E-value=3.5e-20 Score=195.35 Aligned_cols=265 Identities=24% Similarity=0.384 Sum_probs=210.0
Q ss_pred hHHHHhccccccCCCCCChHHHHHHHHhCCCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCC
Q 011168 173 SKKLKAISRVSELDSSGDLRPQILYLIELGMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRP 252 (492)
Q Consensus 173 ~~~~~~~~r~l~~~~~~~l~~~l~~L~~lG~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P 252 (492)
......+.+-+......+..+.+++|+++|++..+|.+++..+|.++..+.++.+.|+..+|+..|++...+.+++...|
T Consensus 73 ~~~~~~~~~~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~ 152 (413)
T KOG1267|consen 73 IKLARKLSREVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVP 152 (413)
T ss_pred hhhHHHHHHHHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccH
Confidence 33333344555566678899999999999999999999999999999999999999999999999999999999999989
Q ss_pred ccccCCccCchHHHHHHHHHhC--CChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHhHhhhhhcCcceeeccc
Q 011168 253 QLCGISLSENLIPTMTFLENLG--VDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAESIGKVLTRCPNIISYSI 330 (492)
Q Consensus 253 ~lL~~s~e~~l~~~v~~L~~lG--v~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~ 330 (492)
.+|+.+..+++.+.++|+++++ .....+.+++...|.. ......+. +++++.++|+.+.++..++...|.++....
T Consensus 153 ~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~-~~~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~ 230 (413)
T KOG1267|consen 153 KILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSF-LLNENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL 230 (413)
T ss_pred HHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccc-cccccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh
Confidence 9999888789999999999985 5555555444444322 12233566 899999999999999999999999998773
Q ss_pred hhhhhhhHHHHHhhCCCcc-hhhhccccccccccchhhhHHHHHHHHcCCCHHHHHHHHhhccceeeecccccHHHHHHH
Q 011168 331 EEKLRPTAEYFRSLGVDVS-VLLQRCPQSLGCSIEANLKPVTEFFLERGFTVEEIGTMISRFGALYTFSLTENLIPKWEF 409 (492)
Q Consensus 331 e~~L~~~v~fL~~lGl~~~-~il~r~P~iL~~sle~~L~~r~~fL~~~Gls~~ev~~mi~~~P~lL~~sle~~L~~k~~f 409 (492)
.+...+.++..+|+++. .++.+.|.++.++.++++++++++|++.||+.+|+..|++++|.++++| ++++..+++|
T Consensus 231 --~l~~~~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s-~~~~~~~~~~ 307 (413)
T KOG1267|consen 231 --KLKARLPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYS-VKKNLKTTEY 307 (413)
T ss_pred --hhhhhhhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEee-hhhhhHHHHH
Confidence 78888899999998864 5777889999999999999999999999999999999999999999999 5665455555
Q ss_pred HHHcCCChHHHhhcCcccccCcccccHhHHHHHHHhc
Q 011168 410 FLTMDYDKSELVKFPQYFGYSLEERIKPRYARVKVHG 446 (492)
Q Consensus 410 L~~~G~~~~~i~~~P~lL~~Sle~rIkpR~~~L~~lg 446 (492)
+.+. .+++.++|+++.++ +..+.+|++++...|
T Consensus 308 ~~~~---~~~~~k~p~~l~~s-~~~l~~~ie~l~~~g 340 (413)
T KOG1267|consen 308 LLKN---PKHILKFPQLLRSS-EDKLKPRIEFLLSLG 340 (413)
T ss_pred HHhc---chhhhhhhhhhhcc-chhhhhhHHHHHHcC
Confidence 5422 22255555555444 235555555555444
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=96.53 E-value=0.0019 Score=41.39 Aligned_cols=11 Identities=45% Similarity=0.685 Sum_probs=4.1
Q ss_pred ccHHHHHHHHH
Q 011168 401 ENLIPKWEFFL 411 (492)
Q Consensus 401 ~~L~~k~~fL~ 411 (492)
++++++++||.
T Consensus 16 ~~l~~~~~~l~ 26 (31)
T smart00733 16 KKLKPKVEFLK 26 (31)
T ss_pred HHhhHHHHHHH
Confidence 33333333333
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=96.53 E-value=0.0015 Score=41.81 Aligned_cols=30 Identities=50% Similarity=0.815 Sum_probs=23.8
Q ss_pred hhhhccccccccccchhhhHHHHHHHHcCCC
Q 011168 350 VLLQRCPQSLGCSIEANLKPVTEFFLERGFT 380 (492)
Q Consensus 350 ~il~r~P~iL~~sle~~L~~r~~fL~~~Gls 380 (492)
.++.++|.+++++ +++++++++||+++|++
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGFS 31 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCCC
Confidence 4677788888888 77888888888888864
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=92.67 E-value=0.36 Score=49.71 Aligned_cols=202 Identities=18% Similarity=0.269 Sum_probs=109.5
Q ss_pred HHHHHh-CCCCHHHHHHHHHhCCceeecCc---CC----CHHHHHHHH-H-hCCCCCCcHHHHHhhCCccccCCccCch-
Q 011168 195 ILYLIE-LGMDLEKIKLITRRFPAFSYYSL---EG----KIKPVVEFL-L-DLGIPKAQIPTILGKRPQLCGISLSENL- 263 (492)
Q Consensus 195 l~~L~~-lG~s~~~i~~ll~~~P~lL~~~l---e~----~lkp~v~fL-~-~~Gls~~~I~~li~~~P~lL~~s~e~~l- 263 (492)
+.-+.. +|+....+...+.+||.++..-. .. .+-|...-| . +..+-.+.-..++.+=-.+|.++.+.++
T Consensus 40 l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlp 119 (335)
T PF11955_consen 40 LSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLP 119 (335)
T ss_pred HHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCccc
Confidence 444444 79977899999999999886422 00 011222222 1 2211111112333333346767775554
Q ss_pred HHHHHHHH-HhCCChhhHHHHHHhCCccccccc-h---hhhhHHHHHHHcCCChHhHhhhh-----------------hc
Q 011168 264 IPTMTFLE-NLGVDKTQWAKVIQRFPAVLTYSR-Q---KVKQTVDFLYEMGLSAESIGKVL-----------------TR 321 (492)
Q Consensus 264 ~~~v~~L~-~lGv~~~~i~kll~~~P~iL~~s~-e---kl~~~v~fL~~lG~s~~ei~~~v-----------------~~ 321 (492)
..++..++ ++|+|++-...++.+||..|.... + ..-+-+.+=.++.++.-|-.... .+
T Consensus 120 L~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~ 199 (335)
T PF11955_consen 120 LSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVS 199 (335)
T ss_pred HHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeec
Confidence 44666665 799999999899999999887633 1 11111121112333332222221 12
Q ss_pred CcceeeccchhhhhhhHHHHHhhCC----------Ccch------hhhccccccccccchhh-hHHHHHHH-HcCCCHHH
Q 011168 322 CPNIISYSIEEKLRPTAEYFRSLGV----------DVSV------LLQRCPQSLGCSIEANL-KPVTEFFL-ERGFTVEE 383 (492)
Q Consensus 322 ~P~iL~~s~e~~L~~~v~fL~~lGl----------~~~~------il~r~P~iL~~sle~~L-~~r~~fL~-~~Gls~~e 383 (492)
+|.=+.. ..+.+..++-++++-+ ++++ .+.-.-.+|++.+|+++ ..++..|+ ++|++ +.
T Consensus 200 fp~G~~l--~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k 276 (335)
T PF11955_consen 200 FPKGFRL--KKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QK 276 (335)
T ss_pred CCCCccc--cHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HH
Confidence 2222222 2455666666665532 2111 01001236677766553 34566666 68998 67
Q ss_pred HHHHHhhccceeeecc
Q 011168 384 IGTMISRFGALYTFSL 399 (492)
Q Consensus 384 v~~mi~~~P~lL~~sl 399 (492)
+..|+.+||.|+-.|.
T Consensus 277 ~~~~l~rHPgIFYvS~ 292 (335)
T PF11955_consen 277 FRRLLLRHPGIFYVSL 292 (335)
T ss_pred HHHHHHhCCCeEEEec
Confidence 8889999999999994
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=80.39 E-value=4.4 Score=37.65 Aligned_cols=115 Identities=17% Similarity=0.225 Sum_probs=58.4
Q ss_pred HHHHHHHhCCCCHHHHHHHHHhCCc----eeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHH
Q 011168 193 PQILYLIELGMDLEKIKLITRRFPA----FSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMT 268 (492)
Q Consensus 193 ~~l~~L~~lG~s~~~i~~ll~~~P~----lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~ 268 (492)
..+..|+++|++-++|..++..... ++...+ ..+...++-|+.. ...|..++...+.. .....-+....++
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~~~~-~~l~~ei~~L~~~---~~~l~~ll~~~~~~-~~~~~V~~~~w~~ 123 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRL-AELNREIQRLRQQ---QRAIATLLKQPTLL-KEQRLVTKEKWVA 123 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCChhHHHHHHHHH-HHHHHHHHHHHHH---HHHHHHHHHHHhhc-cccccCCHHHHHH
Confidence 3467788999999999998865432 011011 1122222222221 22344444322222 1111122345566
Q ss_pred HHHHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHhHhhh
Q 011168 269 FLENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAESIGKV 318 (492)
Q Consensus 269 ~L~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei~~~ 318 (492)
.++..|+++++..+.=.. |. ...=..-.+||.++|++++++..+
T Consensus 124 l~~~~g~~~~~m~~wh~~----fe--~~~p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 124 ILKAAGMDEADMRRWHIE----FE--KMEPEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHcCCChHHHHHHHHH----HH--HhCcHHHHHHHHHcCCCHHHHHHH
Confidence 667788887775332111 11 112234468899999999887643
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=75.92 E-value=8.4 Score=35.78 Aligned_cols=22 Identities=14% Similarity=0.209 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCCCCcHHHHHhh
Q 011168 229 PVVEFLLDLGIPKAQIPTILGK 250 (492)
Q Consensus 229 p~v~fL~~~Gls~~~I~~li~~ 250 (492)
..+..|++.|++-.+|..++..
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~ 70 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQ 70 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhc
Confidence 4567778899998888887754
No 12
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=75.51 E-value=4 Score=36.43 Aligned_cols=48 Identities=23% Similarity=0.467 Sum_probs=31.8
Q ss_pred hhhhhhhHHHHHhhCCCcchhhhccccccccccchhhhHHHHHHHHcCCCHHHHHHHHhhccce
Q 011168 331 EEKLRPTAEYFRSLGVDVSVLLQRCPQSLGCSIEANLKPVTEFFLERGFTVEEIGTMISRFGAL 394 (492)
Q Consensus 331 e~~L~~~v~fL~~lGl~~~~il~r~P~iL~~sle~~L~~r~~fL~~~Gls~~ev~~mi~~~P~l 394 (492)
|+.++..+.||++ |.+-.-+ +..|++||+++|++.+||...+.+.+.-
T Consensus 3 e~li~~A~~FL~~------------p~V~~sp----~~~k~~FL~sKGLt~~EI~~al~~a~~~ 50 (136)
T PF04695_consen 3 EDLIEQAVKFLQD------------PKVRNSP----LEKKIAFLESKGLTEEEIDEALGRAGSP 50 (136)
T ss_dssp HHHHHHHHHHHCT------------TTCCCS-----HHHHHHHHHHCT--HHHHHHHHHHHT--
T ss_pred HHHHHHHHHHhCC------------cccccCC----HHHHHHHHHcCCCCHHHHHHHHHhcCCc
Confidence 3566666777763 4433333 5578999999999999999999887644
No 13
>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=67.95 E-value=14 Score=38.17 Aligned_cols=118 Identities=15% Similarity=0.280 Sum_probs=73.2
Q ss_pred HHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCc-------cCchHHHHHHH-H-HhCCCh
Q 011168 207 KIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISL-------SENLIPTMTFL-E-NLGVDK 277 (492)
Q Consensus 207 ~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~-------e~~l~~~v~~L-~-~lGv~~ 277 (492)
++.+++.+.|. -..+ +...-..-..+|+....+...+.++|.++.... --.+.+...-+ . +..+-.
T Consensus 22 ~l~~~i~~~p~-~~~p----l~~l~k~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~ 96 (335)
T PF11955_consen 22 RLKDLILSQPS-HSLP----LRDLSKLRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVRE 96 (335)
T ss_pred HHHHHHHcCCC-Cccc----HHHHHHHHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHH
Confidence 55666767764 1111 211122335789977899999999999986422 11233333322 1 222211
Q ss_pred hhHHHHHHhCCccccccchh--hhhHHHHHH-HcCCChHhHhhhhhcCcceeecc
Q 011168 278 TQWAKVIQRFPAVLTYSRQK--VKQTVDFLY-EMGLSAESIGKVLTRCPNIISYS 329 (492)
Q Consensus 278 ~~i~kll~~~P~iL~~s~ek--l~~~v~fL~-~lG~s~~ei~~~v~~~P~iL~~s 329 (492)
+.-..++.+.-.+|.+|.++ --.++..++ ++|++++-...++.++|..|...
T Consensus 97 ~~e~~~v~rL~KLLMMS~~~rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv 151 (335)
T PF11955_consen 97 EMEPDLVERLRKLLMMSKDRRLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVV 151 (335)
T ss_pred hChHHHHHHHHHHhccCCCCcccHHHHHHHHHHcCCChhhccchhhhCCCCcEEe
Confidence 11123444555678888875 367788887 89999999999999999999764
No 14
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=61.70 E-value=23 Score=27.84 Aligned_cols=48 Identities=17% Similarity=0.434 Sum_probs=30.4
Q ss_pred HHHHHHHHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHHhCCChhhHHHH
Q 011168 228 KPVVEFLLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLENLGVDKTQWAKV 283 (492)
Q Consensus 228 kp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lGv~~~~i~kl 283 (492)
.|.++.|++..+|+++|..+... |+ ++--..+.....+|++++.+-.+
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT----~NPl~AMa~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LT----QNPLAAMATIQQLGIPQEKLQQL 49 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----Hh----hCHHHHHHHHHHcCCCHHHHHHH
Confidence 36777788888887777776642 22 22234556677788887765443
No 15
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=57.99 E-value=5.8 Score=31.21 Aligned_cols=20 Identities=25% Similarity=0.303 Sum_probs=17.2
Q ss_pred HHHHHHHHHcCCChHHHhhh
Q 011168 70 AVLTLFLKKQGLSKGVAART 89 (492)
Q Consensus 70 ~~~~~~l~t~GLt~~~A~~~ 89 (492)
+.++++..+||||.++|.=+
T Consensus 45 a~~~el~~~CgL~~aEAeLl 64 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELL 64 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHH
Confidence 56999999999999999643
No 16
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=51.29 E-value=1.3e+02 Score=27.00 Aligned_cols=22 Identities=23% Similarity=0.570 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHhhc
Q 011168 370 VTEFFLERGFTVEEIGTMISRF 391 (492)
Q Consensus 370 r~~fL~~~Gls~~ev~~mi~~~ 391 (492)
.+.+|...||+.+.+...+...
T Consensus 132 i~~~L~rkGF~~~~I~~~l~~~ 153 (157)
T PRK00117 132 LVRFLARRGFSMDVIQRVLRNA 153 (157)
T ss_pred HHHHHHHCCCCHHHHHHHHHhh
Confidence 4788889999999998777653
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=46.34 E-value=68 Score=27.55 Aligned_cols=108 Identities=22% Similarity=0.295 Sum_probs=50.9
Q ss_pred CchHHHHHHHHHhCC-ChhhHHHHHHhCCc-cccccchhhhhHHHHHHHcCCChHhHhhhhhcCcceeeccchhhhhhhH
Q 011168 261 ENLIPTMTFLENLGV-DKTQWAKVIQRFPA-VLTYSRQKVKQTVDFLYEMGLSAESIGKVLTRCPNIISYSIEEKLRPTA 338 (492)
Q Consensus 261 ~~l~~~v~~L~~lGv-~~~~i~kll~~~P~-iL~~s~ekl~~~v~fL~~lG~s~~ei~~~v~~~P~iL~~s~e~~L~~~v 338 (492)
+.+...++.|.+.|. ++...+..+.+.-. .-..++ .....-|+.-|++.+.|..++.. .+..+. ..
T Consensus 9 e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~---~~I~~~L~~kGi~~~~i~~~l~~------~~~~e~---a~ 76 (121)
T PF02631_consen 9 EAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGP---RRIRQKLKQKGIDREIIEEALEE------YDEEEE---AL 76 (121)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--H---HHHHHHHHHTT--HHHHHHHHTC------S-HHHH---HH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccH---HHHHHHHHHHCCChHHHHHHHHH------hhHHHH---HH
Confidence 567777888888874 55555444333111 112222 33346677789998888777662 111111 11
Q ss_pred HHHHhhCCCcchhhhccccccccccchhhhHHHHHHHHcCCCHHHHHHHHhh
Q 011168 339 EYFRSLGVDVSVLLQRCPQSLGCSIEANLKPVTEFFLERGFTVEEIGTMISR 390 (492)
Q Consensus 339 ~fL~~lGl~~~~il~r~P~iL~~sle~~L~~r~~fL~~~Gls~~ev~~mi~~ 390 (492)
+... .++...-..+-....+..+.+|...||+.+.+...+..
T Consensus 77 ~~~~----------kk~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 77 ELAE----------KKYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHH----------HHHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHH----------HHHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 1111 01111111111223333478899999999999877653
No 18
>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=43.98 E-value=37 Score=22.78 Aligned_cols=23 Identities=39% Similarity=0.629 Sum_probs=14.4
Q ss_pred hHHHHHHHcCCChHhHhhhhhcC
Q 011168 300 QTVDFLYEMGLSAESIGKVLTRC 322 (492)
Q Consensus 300 ~~v~fL~~lG~s~~ei~~~v~~~ 322 (492)
..++-|.++|+++++...++..+
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 34566667777777777666543
No 19
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=43.14 E-value=47 Score=24.94 Aligned_cols=55 Identities=20% Similarity=0.207 Sum_probs=35.4
Q ss_pred HHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhhhhh
Q 011168 72 LTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEEYGN 140 (492)
Q Consensus 72 ~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls~~~ 140 (492)
+.++-..+|+|.++.++...-|+.+++++-. |+ .+.-.++.+.++.+.+|++..+
T Consensus 6 lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~------------G~--~~~p~~~~l~~l~~~l~~~~~~ 60 (64)
T PF13560_consen 6 LRRLRERAGLSQAQLADRLGVSQSTVSRIER------------GR--RPRPSPDTLQRLARALGVPPDE 60 (64)
T ss_dssp HHHHHHCHTS-HHHHHHHHTS-HHHHHHHHT------------TS--SSS-BHHHHHHHHHHTT--HHH
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC------------CC--CCCCCHHHHHHHHHHHCcCHHH
Confidence 4444557899999999999998888888776 11 1111345677888999998643
No 20
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=40.86 E-value=1e+02 Score=25.39 Aligned_cols=71 Identities=14% Similarity=0.203 Sum_probs=39.6
Q ss_pred ChHHHHHHHHhCCCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCCCCcHHHHHhhCCccccCCcc-CchHHHHH
Q 011168 190 DLRPQILYLIELGMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIPKAQIPTILGKRPQLCGISLS-ENLIPTMT 268 (492)
Q Consensus 190 ~l~~~l~~L~~lG~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls~~~I~~li~~~P~lL~~s~e-~~l~~~v~ 268 (492)
.+...+.+|..+|++.....++...+. ++...+|..+|..|..+.. -..+..=+
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg-------------------------~~ai~~l~~nPY~L~~~i~gi~F~~aD~ 61 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYG-------------------------DDAIEILKENPYRLIEDIDGIGFKTADK 61 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH--------------------------TTHHHHHHH-STCCCB-SSSSBHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHh-------------------------HHHHHHHHHChHHHHHHccCCCHHHHHH
Confidence 456778899999999888888766541 1233667788888776332 22344444
Q ss_pred HHHHhCCChhhHHHHHH
Q 011168 269 FLENLGVDKTQWAKVIQ 285 (492)
Q Consensus 269 ~L~~lGv~~~~i~kll~ 285 (492)
..+++|++.++-.++-.
T Consensus 62 iA~~~g~~~~d~~Ri~A 78 (94)
T PF14490_consen 62 IALKLGIEPDDPRRIRA 78 (94)
T ss_dssp HHHTTT--TT-HHHHHH
T ss_pred HHHHcCCCCCCHHHHHH
Confidence 55678888777665543
No 21
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=38.58 E-value=84 Score=22.16 Aligned_cols=37 Identities=24% Similarity=0.349 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCChHHHhhhhccChHHHHHHHH
Q 011168 62 AAEKEEAKAVLTLFLKKQGLSKGVAARTINKSDLFIDHLVS 102 (492)
Q Consensus 62 ~~~~~~a~~~~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s 102 (492)
..++++.|.-+..+....|++-+...++|.. |++|.-
T Consensus 3 ~~~Ie~~R~~L~~~~~~~~l~~~~vl~~Sq~----LD~lI~ 39 (45)
T PF09388_consen 3 LEEIEELRQELNELAEKKGLTDPEVLELSQE----LDKLIN 39 (45)
T ss_dssp HHHHHHHHHHHHHHHHHCCTTCHHHHHHHHH----HHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH----HHHHHH
Confidence 4578889999999999889999999999999 887764
No 22
>PTZ00217 flap endonuclease-1; Provisional
Probab=37.63 E-value=4.3e+02 Score=27.92 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=19.2
Q ss_pred hhhhHHHHHH-HcCCChHhHhhhhhc
Q 011168 297 KVKQTVDFLY-EMGLSAESIGKVLTR 321 (492)
Q Consensus 297 kl~~~v~fL~-~lG~s~~ei~~~v~~ 321 (492)
......+||. +.||+++.+...+.+
T Consensus 304 D~~~l~~fl~~e~~f~~~rv~~~i~r 329 (393)
T PTZ00217 304 DEEGLKKFLVKEKNFNEERVEKYIER 329 (393)
T ss_pred CHHHHHHHHHhccCCCHHHHHHHHHH
Confidence 4677788995 899999998776543
No 23
>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=37.12 E-value=39 Score=30.06 Aligned_cols=38 Identities=26% Similarity=0.364 Sum_probs=24.6
Q ss_pred hCCccccccchhhhhHHHHHHHcCCChHhHhhhhhcCccee
Q 011168 286 RFPAVLTYSRQKVKQTVDFLYEMGLSAESIGKVLTRCPNII 326 (492)
Q Consensus 286 ~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei~~~v~~~P~iL 326 (492)
.+|.|-.. -+..+++||++-|++++||..++.+.+.--
T Consensus 14 ~~p~V~~s---p~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 14 QDPKVRNS---PLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp CTTTCCCS----HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred CCcccccC---CHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 35555443 267888999999999999998888765443
No 24
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=35.21 E-value=1.1e+02 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.120 Sum_probs=25.2
Q ss_pred HHHHHHHcCCChHHHhhhhccChHHHHHHHH
Q 011168 72 LTLFLKKQGLSKGVAARTINKSDLFIDHLVS 102 (492)
Q Consensus 72 ~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s 102 (492)
+..+-...|+|..+.++...-|+..++++..
T Consensus 7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4444557899999999999988888888876
No 25
>cd03211 GST_C_Metaxin2 GST_C family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury.
Probab=35.16 E-value=1.8e+02 Score=25.22 Aligned_cols=89 Identities=20% Similarity=0.200 Sum_probs=54.5
Q ss_pred ccChhHHHHHHHHHHHHHHHHHHHcCC---ChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHH-HH
Q 011168 55 VVPSTLLAAEKEEAKAVLTLFLKKQGL---SKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALT-PY 130 (492)
Q Consensus 55 ~~~~~~~~~~~~~a~~~~~~~l~t~GL---t~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davl-af 130 (492)
.+|+.+...-...++..+...+...|+ +.++....+.++ +..|-..|.+ ..|+-|++ |+..||.+ +|
T Consensus 24 ~~p~~l~~~~~~~~r~~~~~~l~~~G~gr~~~ee~~~~~~~~---l~aLs~~Lg~---~~~l~Gd~---pT~~Da~vf~~ 94 (126)
T cd03211 24 PYPWPLNHILPYQKQREARRKLKAIGWDDKTLDQVIEEVDQC---CQALSQRLGT---QPYFFGDQ---PTELDALVFGH 94 (126)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH---HHHHHHHHCC---CCCCCCCC---CcHHHHHHHHH
Confidence 478888877777888888888888887 555555555553 4444444433 23455544 45678876 46
Q ss_pred HHHhh-h-hhhhhHHHHHhcCCCC
Q 011168 131 LESLL-E-EYGNVLVDLVENFPNA 152 (492)
Q Consensus 131 Le~lG-l-s~~~~ia~~V~~~P~l 152 (492)
|..+- . .....+...++.+|.|
T Consensus 95 la~~~~~~~~~~~l~~~~~~~pnL 118 (126)
T cd03211 95 LFTILTTQLPNDELAEKVKKYSNL 118 (126)
T ss_pred HHHHHhcCCCChHHHHHHHhCcHH
Confidence 65543 2 1112366678888874
No 26
>PRK14136 recX recombination regulator RecX; Provisional
Probab=34.83 E-value=3.9e+02 Score=27.29 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHhhc
Q 011168 369 PVTEFFLERGFTVEEIGTMISRF 391 (492)
Q Consensus 369 ~r~~fL~~~Gls~~ev~~mi~~~ 391 (492)
..+.||...||+.+.|..+|..+
T Consensus 280 K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 280 KQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred HHHHHHHHCCCCHHHHHHHHHhc
Confidence 34789999999999998887654
No 27
>PRK09726 antitoxin HipB; Provisional
Probab=32.57 E-value=1.1e+02 Score=24.70 Aligned_cols=52 Identities=15% Similarity=0.174 Sum_probs=38.3
Q ss_pred HHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhhh
Q 011168 72 LTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEEY 138 (492)
Q Consensus 72 ~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls~ 138 (492)
+..+....|+|.+++++...-|+..++++.. +-..| ..+.+..+...+|.+-
T Consensus 17 lk~~R~~~gltq~elA~~~gvs~~tis~~e~--------------g~~~p-s~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 17 MKLVRQQNGWTQSELAKKIGIKQATISNFEN--------------NPDNT-TLTTFFKILQSLELSM 68 (88)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC--------------CCCCC-CHHHHHHHHHHcCCCc
Confidence 4445567899999999998888888888877 11223 3456777888888874
No 28
>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=30.82 E-value=2.1e+02 Score=30.19 Aligned_cols=43 Identities=28% Similarity=0.495 Sum_probs=33.2
Q ss_pred CChHHHHHHHHhCCCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhCCCC
Q 011168 189 GDLRPQILYLIELGMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDLGIP 240 (492)
Q Consensus 189 ~~l~~~l~~L~~lG~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~Gls 240 (492)
......|+-+.+.|++++++.+.++.. . ++-..-|+||.. |++
T Consensus 154 ~~~e~~I~~i~eMGf~R~qV~~ALRAa-------f-NNPdRAVEYL~t-GIP 196 (378)
T TIGR00601 154 SERETTIEEIMEMGYEREEVERALRAA-------F-NNPDRAVEYLLT-GIP 196 (378)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHHH-------h-CCHHHHHHHHHh-CCC
Confidence 456788999999999999999998763 2 355677888875 455
No 29
>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=30.51 E-value=92 Score=21.98 Aligned_cols=41 Identities=17% Similarity=0.277 Sum_probs=19.6
Q ss_pred HHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHh
Q 011168 271 ENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAES 314 (492)
Q Consensus 271 ~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~e 314 (492)
+.+|++...+.+++...+ ..+.+......+..+.+|+..+.
T Consensus 5 ~~~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~~ 45 (52)
T cd01392 5 RAAGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPNA 45 (52)
T ss_pred HHHCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCCH
Confidence 345666666655554433 12233334444444555555443
No 30
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=30.15 E-value=32 Score=31.05 Aligned_cols=99 Identities=15% Similarity=0.217 Sum_probs=55.8
Q ss_pred cHHHHHhhCCccccCCccCchHHHHHHHHHhC-CChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHhH-hhhhh
Q 011168 243 QIPTILGKRPQLCGISLSENLIPTMTFLENLG-VDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAESI-GKVLT 320 (492)
Q Consensus 243 ~I~~li~~~P~lL~~s~e~~l~~~v~~L~~lG-v~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei-~~~v~ 320 (492)
.+.+..-+.|.-|.---.+.++..+-+|.+++ +.+.++. ++. +.|...+.....++.++..|+....- ...+.
T Consensus 32 ~~~r~~pkaPdwLd~~A~~~Wrrvvp~L~e~~ll~~~D~~-~Le----~YC~~ysiY~~av~~lkk~G~ii~~~~~g~~k 106 (160)
T COG3747 32 KFGRLAPKAPDWLDPTAKKEWRRVVPFLEELKLLKPADLT-LLE----LYCVAYSIYRNAVAHLKKHGFIITNQFSGRVK 106 (160)
T ss_pred cccccCCCCccccCHHHHHHHHHHHHHHHHhccCCHHHHH-HHH----HHHHHHHHHHHHHHHHHHcceeeeccccceec
Confidence 34444455666554332356777778888776 5666664 332 23444555666777777777765432 22367
Q ss_pred cCcceeeccchhhhhhhHHHH-HhhCCCcc
Q 011168 321 RCPNIISYSIEEKLRPTAEYF-RSLGVDVS 349 (492)
Q Consensus 321 ~~P~iL~~s~e~~L~~~v~fL-~~lGl~~~ 349 (492)
++|.+=.+|- -+ ..+--| .++|+++.
T Consensus 107 rNPav~~~sd--A~-~~l~klaSeLGltP~ 133 (160)
T COG3747 107 RNPAVQAASD--AI-RNLLKLASELGLTPS 133 (160)
T ss_pred CChHHHHHHH--HH-HHHHHHHHHhCCChH
Confidence 7787766662 22 223233 35777753
No 31
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=28.73 E-value=1.7e+02 Score=23.14 Aligned_cols=52 Identities=21% Similarity=0.338 Sum_probs=34.8
Q ss_pred HHHHHHHHcCCChHHHhhhhccChHHHHHHHH-HhHhhhhhcccccccccchHHhHhHHHHHHHhhhh
Q 011168 71 VLTLFLKKQGLSKGVAARTINKSDLFIDHLVS-RLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEE 137 (492)
Q Consensus 71 ~~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s-~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls 137 (492)
++..+....|+|.+++++.-.-+.--+|+|.. +.+ .+ --|.++.|++.+|..
T Consensus 22 ~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~-----------~~----sl~~L~~~l~aLG~~ 74 (80)
T PF13744_consen 22 AIRELREERGLTQAELAERLGISQPRVSRLENGKID-----------DF----SLDTLLRYLEALGGR 74 (80)
T ss_dssp HHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GC-----------C------HHHHHHHHHHTTEE
T ss_pred HHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCccc-----------CC----CHHHHHHHHHHcCCe
Confidence 36667779999999999998888778888886 111 11 235677888888864
No 32
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=28.55 E-value=1.4e+02 Score=30.01 Aligned_cols=41 Identities=22% Similarity=0.465 Sum_probs=18.8
Q ss_pred hcCcceeeccchhhhhhhHHHHH-hhCCCcchhhhcccccccc
Q 011168 320 TRCPNIISYSIEEKLRPTAEYFR-SLGVDVSVLLQRCPQSLGC 361 (492)
Q Consensus 320 ~~~P~iL~~s~e~~L~~~v~fL~-~lGl~~~~il~r~P~iL~~ 361 (492)
.-.|.++.++. ++++.+++-|. -+|+++.....|+|.=|+-
T Consensus 97 a~VP~L~~w~k-~~i~~r~~ELl~lvgL~p~~~~~RyP~eLSG 138 (309)
T COG1125 97 ATVPKLLGWDK-ERIKKRADELLDLVGLDPSEYADRYPHELSG 138 (309)
T ss_pred HhhhhhcCCCH-HHHHHHHHHHHHHhCCCHHHHhhcCchhcCc
Confidence 33444444442 34444444443 2455555555555554433
No 33
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=27.50 E-value=1.8e+02 Score=19.01 Aligned_cols=23 Identities=26% Similarity=0.270 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCHHHHHHHHHhC
Q 011168 193 PQILYLIELGMDLEKIKLITRRF 215 (492)
Q Consensus 193 ~~l~~L~~lG~s~~~i~~ll~~~ 215 (492)
..++.|.+.||+.+++...+...
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45777888888888888877664
No 34
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=27.37 E-value=1.2e+02 Score=23.29 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=24.6
Q ss_pred HHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHhH
Q 011168 271 ENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAESI 315 (492)
Q Consensus 271 ~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei 315 (492)
+..|++...+.+++...+.+ +++......+.++++|+.+...
T Consensus 8 ~~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~~~ 49 (70)
T smart00354 8 RLAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPNRV 49 (70)
T ss_pred HHHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCCHH
Confidence 45677777776666554444 3445555556666677655543
No 35
>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=27.02 E-value=1e+02 Score=21.96 Aligned_cols=38 Identities=24% Similarity=0.392 Sum_probs=17.8
Q ss_pred HHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCC
Q 011168 271 ENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLS 311 (492)
Q Consensus 271 ~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s 311 (492)
+..|++...+.++|...+.+ +++.-+...+..+++|+.
T Consensus 7 ~~agvS~~TVSr~ln~~~~v---s~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 7 REAGVSKSTVSRVLNGPPRV---SEETRERILEAAEELGYR 44 (46)
T ss_dssp HHHTSSHHHHHHHHTTCSSS---THHHHHHHHHHHHHHTB-
T ss_pred HHHCcCHHHHHHHHhCCCCC---CHHHHHHHHHHHHHHCCC
Confidence 44566666666555544322 333334444444455543
No 36
>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=26.79 E-value=1.9e+02 Score=19.00 Aligned_cols=23 Identities=22% Similarity=0.340 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCHHHHHHHHHhC
Q 011168 193 PQILYLIELGMDLEKIKLITRRF 215 (492)
Q Consensus 193 ~~l~~L~~lG~s~~~i~~ll~~~ 215 (492)
..++-|.+.|++.+++...+...
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46778888999988888887664
No 37
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=25.56 E-value=1e+02 Score=34.68 Aligned_cols=68 Identities=15% Similarity=0.342 Sum_probs=42.1
Q ss_pred HHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHH-hhhhhh----hhHHHHH
Q 011168 72 LTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLES-LLEEYG----NVLVDLV 146 (492)
Q Consensus 72 ~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~-lGls~~----~~ia~~V 146 (492)
+..|....+||++++..-+.. .++|+.|+.|++| +|..++ .--..|+
T Consensus 914 LAQFMVqN~Lt~~~~~~rA~~----------------------------LsFP~SVvdf~qG~iGqP~gGFPEPlRs~VL 965 (1176)
T KOG0369|consen 914 LAQFMVQNKLTRDDVERRAEE----------------------------LSFPKSVVDFFQGLIGQPYGGFPEPLRSKVL 965 (1176)
T ss_pred HHHHHHhcCCCHHHHHHHhhh----------------------------cCCcHHHHHHHhcccCCCCCCCCchhHHHHh
Confidence 445566778888777655444 7899999999998 454432 2125666
Q ss_pred hcCCCCCCcccccCccCCC-CCcCCCChHHH
Q 011168 147 ENFPNAPPPAKQKAVAPVS-PPVSTLDSKKL 176 (492)
Q Consensus 147 ~~~P~lL~~~~~~~~~~~~-~~l~~~~~~~~ 176 (492)
..-|++ .+++ .+|-++|+++.
T Consensus 966 k~~~r~---------~gRPG~~l~p~Dldai 987 (1176)
T KOG0369|consen 966 KGKPRL---------TGRPGAELPPLDLDAI 987 (1176)
T ss_pred cCCCcc---------CCCCCCcCCccCHHHH
Confidence 666763 2333 33556676654
No 38
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.53 E-value=1.9e+02 Score=22.84 Aligned_cols=48 Identities=19% Similarity=0.342 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCCChhhHHHHHHhCCccccccchhhhhHHHHHHHcCCChHhHhhh
Q 011168 264 IPTMTFLENLGVDKTQWAKVIQRFPAVLTYSRQKVKQTVDFLYEMGLSAESIGKV 318 (492)
Q Consensus 264 ~~~v~~L~~lGv~~~~i~kll~~~P~iL~~s~ekl~~~v~fL~~lG~s~~ei~~~ 318 (492)
.|.++.|++..++++.+..++.. ++. +--..+.....+|++++.+..+
T Consensus 2 NPIia~LKehnvsd~qi~elFq~----lT~---NPl~AMa~i~qLGip~eKLQ~l 49 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA----LTQ---NPLAAMATIQQLGIPQEKLQQL 49 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH----Hhh---CHHHHHHHHHHcCCCHHHHHHH
Confidence 35778888888888888777654 222 2233456677889988876544
No 39
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.32 E-value=2e+02 Score=19.04 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=22.7
Q ss_pred HHHHHHcCCChHHHhhhhccChHHHHHHHH
Q 011168 73 TLFLKKQGLSKGVAARTINKSDLFIDHLVS 102 (492)
Q Consensus 73 ~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s 102 (492)
..+....|+|..+.++...-++..++++..
T Consensus 3 ~~~~~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 3 KELREEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 345667899998888888777777777665
No 40
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=25.12 E-value=5.1e+02 Score=26.17 Aligned_cols=32 Identities=9% Similarity=-0.012 Sum_probs=20.6
Q ss_pred ccchHHhHhHHHHHHHhhhhhhhhHHHHHhcCCCCCC
Q 011168 118 LTTLEIRDALTPYLESLLEEYGNVLVDLVENFPNAPP 154 (492)
Q Consensus 118 l~~~~~~davlafLe~lGls~~~~ia~~V~~~P~lL~ 154 (492)
+.+|.-+||.+|+|+..|. +.+++..|-.+|.
T Consensus 145 i~ap~EAdaq~a~l~~~g~-----v~~i~S~DsD~l~ 176 (316)
T cd00128 145 IVAPYEAEAQCAYLAKKGL-----VDAIITEDSDLLL 176 (316)
T ss_pred EECCcCHHHHHHHHHhCCC-----eeEEEecCCCeee
Confidence 3457789999999988774 2345555544433
No 41
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=24.61 E-value=3.2e+02 Score=30.07 Aligned_cols=29 Identities=14% Similarity=0.202 Sum_probs=22.5
Q ss_pred hHHhHhHHH-HHHHhhhhhhhhHHHHHhcCCC
Q 011168 121 LEIRDALTP-YLESLLEEYGNVLVDLVENFPN 151 (492)
Q Consensus 121 ~~~~davla-fLe~lGls~~~~ia~~V~~~P~ 151 (492)
|..|+.... |-..+|+|. + +|.-++.+|.
T Consensus 453 Pe~~~ek~~r~~~eygLs~-~-LA~~~~~~~~ 482 (631)
T COG2511 453 PELPEEKVERYVKEYGLSK-E-LAEQLASDPR 482 (631)
T ss_pred CCCHHHHHHHHHHHhCCCH-H-HHHHHHhhhh
Confidence 666766664 667899995 5 9999999887
No 42
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.08 E-value=2e+02 Score=27.01 Aligned_cols=25 Identities=16% Similarity=0.373 Sum_probs=18.3
Q ss_pred hhhHHHHHHHcCCChHhHhhhhhcC
Q 011168 298 VKQTVDFLYEMGLSAESIGKVLTRC 322 (492)
Q Consensus 298 l~~~v~fL~~lG~s~~ei~~~v~~~ 322 (492)
+...+.+|..+|+++.++.+++.+.
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5666777777888877777777654
No 43
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.99 E-value=2.6e+02 Score=20.58 Aligned_cols=52 Identities=19% Similarity=0.209 Sum_probs=33.6
Q ss_pred HHHHHHHcCCChHHHhhhhccChHHHHHHHHHhHhhhhhcccccccccchHHhHhHHHHHHHhhhhh
Q 011168 72 LTLFLKKQGLSKGVAARTINKSDLFIDHLVSRLHSVHKSRYLVGRELTTLEIRDALTPYLESLLEEY 138 (492)
Q Consensus 72 ~~~~l~t~GLt~~~A~~~s~~s~~~l~~l~s~~~~~~~~~~~~~~~l~~~~~~davlafLe~lGls~ 138 (492)
+..+...+|+|..+.++...-++..++++.+ |+ +.|+ ++.+..+.+.+|++.
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~------------g~--~~~~-~~~l~~i~~~~~v~~ 55 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKIEN------------GK--RKPS-VSTLKKIAEALGVSL 55 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHHHT------------TS--S--B-HHHHHHHHHHHTS-H
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC------------CC--cCCC-HHHHHHHHHHhCCCH
Confidence 4556678999999999988888778888777 21 1232 556677888888875
No 44
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=23.62 E-value=88 Score=27.71 Aligned_cols=52 Identities=17% Similarity=0.343 Sum_probs=33.2
Q ss_pred HHHHHHHhCCChhhHHHHHHh---CCccccccchhhhhHHHHHHHcCCChHhHhhhhh
Q 011168 266 TMTFLENLGVDKTQWAKVIQR---FPAVLTYSRQKVKQTVDFLYEMGLSAESIGKVLT 320 (492)
Q Consensus 266 ~v~~L~~lGv~~~~i~kll~~---~P~iL~~s~ekl~~~v~fL~~lG~s~~ei~~~v~ 320 (492)
.-.||+-+|++++.+..++.+ ...++.++.+.+. +.|.++|...+|.+++..
T Consensus 69 l~~WL~vVgl~~~~i~~i~~~~~tLe~Llemsd~el~---~~l~~~g~~~EE~rRL~~ 123 (129)
T PF13543_consen 69 LRQWLRVVGLRPESIQAILSKVLTLEALLEMSDEELK---EILNRCGAREEECRRLCR 123 (129)
T ss_pred HHHHhhhcCCCHHHHHHHHHhhcCHHHHHhCCHHHHH---HHHHHhCCCHHHHHHHHH
Confidence 346888889999888766543 2234444444444 445568888888876654
No 45
>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=23.27 E-value=1.9e+02 Score=33.23 Aligned_cols=84 Identities=19% Similarity=0.244 Sum_probs=47.9
Q ss_pred CCChHHHHHHHHh--C-CCCHHHHHHHHHhCCceeecCcCCCHHHHHHHHHhC-CCCCCcHHHHHhhCCccccCCccCch
Q 011168 188 SGDLRPQILYLIE--L-GMDLEKIKLITRRFPAFSYYSLEGKIKPVVEFLLDL-GIPKAQIPTILGKRPQLCGISLSENL 263 (492)
Q Consensus 188 ~~~l~~~l~~L~~--l-G~s~~~i~~ll~~~P~lL~~~le~~lkp~v~fL~~~-Gls~~~I~~li~~~P~lL~~s~e~~l 263 (492)
+.+....+.||.+ + |+-+....+++..++. +.-+.+....+-|.++ |++...+..+...... ....
T Consensus 74 p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~----~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~------~~~~ 143 (720)
T TIGR01448 74 PTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGE----AAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ------QGDE 143 (720)
T ss_pred CCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCH----hHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH------hHHH
Confidence 3455667778875 3 7777777777766542 2112333344455554 7776666666553311 1235
Q ss_pred HHHHHHHHHhCCChhhHH
Q 011168 264 IPTMTFLENLGVDKTQWA 281 (492)
Q Consensus 264 ~~~v~~L~~lGv~~~~i~ 281 (492)
...+.||.++|++.....
T Consensus 144 ~~~~~~L~~~gi~~~~a~ 161 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQ 161 (720)
T ss_pred HHHHHHHHHcCCCHHHHH
Confidence 566677777777764443
No 46
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=22.93 E-value=86 Score=24.30 Aligned_cols=37 Identities=24% Similarity=0.369 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHH-HHcCCChHHHhhhhccChHHHHHHHH
Q 011168 62 AAEKEEAKAVLTLFL-KKQGLSKGVAARTINKSDLFIDHLVS 102 (492)
Q Consensus 62 ~~~~~~a~~~~~~~l-~t~GLt~~~A~~~s~~s~~~l~~l~s 102 (492)
+...-+.-..+..|+ ...|++..+|.+-+.. +.|..|
T Consensus 8 A~~i~~rH~~le~fl~~~lgv~~~~a~~~A~~----iEH~is 45 (71)
T PF02742_consen 8 AERILRRHRILEEFLVEVLGVDEEEAEEEACR----IEHVIS 45 (71)
T ss_dssp HHHHHHHHHHHHHHHHHTTT--HHHHHHHHHH----HGCCS-
T ss_pred HHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHH----HHccCC
Confidence 344445567788999 5899999999999998 888877
No 47
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=22.65 E-value=2.2e+02 Score=23.08 Aligned_cols=35 Identities=20% Similarity=0.440 Sum_probs=21.8
Q ss_pred HHhCCCCCCcHHHHHhhCCccccCCccCchHHHHHHHHH
Q 011168 234 LLDLGIPKAQIPTILGKRPQLCGISLSENLIPTMTFLEN 272 (492)
Q Consensus 234 L~~~Gls~~~I~~li~~~P~lL~~s~e~~l~~~v~~L~~ 272 (492)
-+.+|++..+|..+-..+|. ++.+.+..++..+++
T Consensus 20 ar~Lgls~~~I~~i~~~~p~----~l~eQv~~mL~~W~~ 54 (83)
T cd08319 20 LLDLGLSQTDIYRCKENHPH----NVQSQIVEALVKWRQ 54 (83)
T ss_pred HHHcCCCHHHHHHHHHhCCC----CHHHHHHHHHHHHHH
Confidence 46777777777777776674 444555555555543
No 48
>PRK03980 flap endonuclease-1; Provisional
Probab=22.09 E-value=6.5e+02 Score=25.38 Aligned_cols=25 Identities=32% Similarity=0.507 Sum_probs=19.5
Q ss_pred hhhhHHHHHH-HcCCChHhHhhhhhc
Q 011168 297 KVKQTVDFLY-EMGLSAESIGKVLTR 321 (492)
Q Consensus 297 kl~~~v~fL~-~lG~s~~ei~~~v~~ 321 (492)
+....++||- +.||+++.|...+.+
T Consensus 250 d~~~l~~fl~~e~~f~~~rv~~~~~~ 275 (292)
T PRK03980 250 DKEGIIEFLVEEHDFSEERVKKALER 275 (292)
T ss_pred CHHHHHHHHhccCCCCHHHHHHHHHH
Confidence 4677789995 899999998776543
No 49
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.07 E-value=1.2e+02 Score=30.47 Aligned_cols=25 Identities=36% Similarity=0.485 Sum_probs=20.5
Q ss_pred hhhHHHHHHHHcCCCHHHHHHHHhh
Q 011168 366 NLKPVTEFFLERGFTVEEIGTMISR 390 (492)
Q Consensus 366 ~L~~r~~fL~~~Gls~~ev~~mi~~ 390 (492)
-+..+.+||+..|++.+||...+++
T Consensus 21 Pli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 21 PLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred hHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 3556789999999999999777765
No 50
>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=22.02 E-value=1.4e+02 Score=21.26 Aligned_cols=24 Identities=17% Similarity=0.249 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHHHhC
Q 011168 192 RPQILYLIELGMDLEKIKLITRRF 215 (492)
Q Consensus 192 ~~~l~~L~~lG~s~~~i~~ll~~~ 215 (492)
...++.|.++|++..++.+++..-
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 456778888999998888887663
No 51
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=21.94 E-value=1.2e+02 Score=19.85 Aligned_cols=24 Identities=21% Similarity=0.203 Sum_probs=13.9
Q ss_pred hhHHHHHHHHcCCCHHHHHHHHhh
Q 011168 367 LKPVTEFFLERGFTVEEIGTMISR 390 (492)
Q Consensus 367 L~~r~~fL~~~Gls~~ev~~mi~~ 390 (492)
+..-+.--++.|++.+|+...+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 333444455789999998866653
No 52
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=20.84 E-value=4.5e+02 Score=24.51 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=17.8
Q ss_pred hhhHH-HHHHHHcCCCHHHHHHHHhh
Q 011168 366 NLKPV-TEFFLERGFTVEEIGTMISR 390 (492)
Q Consensus 366 ~L~~r-~~fL~~~Gls~~ev~~mi~~ 390 (492)
..+.+ ..+|...||+.+.+...+..
T Consensus 138 ~~k~Ki~r~L~~rGFs~~~i~~~l~~ 163 (174)
T COG2137 138 KEKAKIQRFLLRRGFSYEVIKEALNE 163 (174)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34444 56778899999988876653
Done!