Query 013135
Match_columns 449
No_of_seqs 256 out of 1258
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 00:45:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013135.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013135hhsearch_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 2E-67 4.3E-72 544.7 31.4 370 46-429 66-445 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 4.8E-56 1E-60 446.6 9.2 337 81-421 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 4.9E-47 1.1E-51 392.7 25.9 332 47-390 96-439 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 4.9E-39 1.1E-43 323.2 7.8 304 50-362 3-323 (345)
5 KOG1267 Mitochondrial transcri 100.0 1.4E-33 3E-38 289.5 20.8 349 38-399 53-411 (413)
6 KOG1267 Mitochondrial transcri 99.9 9.8E-23 2.1E-27 209.3 15.2 247 138-393 88-336 (413)
7 smart00733 Mterf Mitochondrial 97.3 0.00018 3.9E-09 44.8 2.6 30 337-367 2-31 (31)
8 smart00733 Mterf Mitochondrial 97.0 0.00052 1.1E-08 42.7 2.1 29 160-189 2-30 (31)
9 PF11955 PORR: Plant organelle 94.1 0.39 8.4E-06 48.0 10.3 68 283-351 209-293 (335)
10 cd04790 HTH_Cfa-like_unk Helix 89.2 2.7 6E-05 37.8 9.0 23 179-201 49-71 (172)
11 cd04790 HTH_Cfa-like_unk Helix 88.1 1.8 3.9E-05 39.0 7.0 143 45-197 16-167 (172)
12 PF11955 PORR: Plant organelle 86.3 3.4 7.3E-05 41.4 8.4 200 82-282 43-293 (335)
13 PRK00117 recX recombination re 86.0 19 0.0004 31.7 12.3 126 74-237 26-153 (157)
14 PF02631 RecX: RecX family; I 84.3 5.2 0.00011 33.6 7.6 24 140-163 44-67 (121)
15 COG2137 OraA Uncharacterized p 79.4 44 0.00095 30.2 12.0 72 76-163 37-109 (174)
16 PF04695 Pex14_N: Peroxisomal 79.0 1.5 3.4E-05 37.8 2.4 32 315-346 20-51 (136)
17 PHA01351 putative minor struct 78.7 91 0.002 34.1 15.5 159 45-203 500-717 (1070)
18 PF04695 Pex14_N: Peroxisomal 77.2 2.7 5.8E-05 36.4 3.4 26 178-203 24-49 (136)
19 PRK14136 recX recombination re 75.6 41 0.0009 33.1 11.3 128 73-239 176-304 (309)
20 PF00356 LacI: Bacterial regul 74.9 7.2 0.00016 26.9 4.4 42 255-299 5-46 (46)
21 PF11212 DUF2999: Protein of u 74.0 9.9 0.00022 28.7 5.1 23 77-99 2-24 (82)
22 PRK14135 recX recombination re 71.4 86 0.0019 30.0 12.7 167 74-272 72-258 (263)
23 PRK14137 recX recombination re 69.0 43 0.00093 30.8 9.5 144 54-237 31-179 (195)
24 PF00627 UBA: UBA/TS-N domain; 65.5 9.3 0.0002 24.8 3.2 23 320-342 4-26 (37)
25 PF14490 HHH_4: Helix-hairpin- 64.8 16 0.00036 29.2 5.2 25 75-99 7-31 (94)
26 PF14490 HHH_4: Helix-hairpin- 64.6 27 0.00059 27.9 6.4 46 108-174 7-52 (94)
27 PRK14605 ruvA Holliday junctio 62.7 93 0.002 28.6 10.4 64 54-130 61-125 (194)
28 PRK14136 recX recombination re 62.7 1.6E+02 0.0036 29.0 14.0 130 183-342 171-302 (309)
29 PHA02591 hypothetical protein; 61.2 26 0.00057 27.0 5.2 43 54-96 22-68 (83)
30 smart00165 UBA Ubiquitin assoc 60.7 13 0.00028 23.9 3.2 23 320-342 3-25 (37)
31 PRK14601 ruvA Holliday junctio 58.4 1.1E+02 0.0023 27.9 9.9 65 54-131 61-126 (183)
32 cd00194 UBA Ubiquitin Associat 58.1 15 0.00033 23.7 3.2 23 320-342 3-25 (38)
33 TIGR01448 recD_rel helicase, p 56.1 72 0.0016 35.6 10.0 111 72-210 73-187 (720)
34 PF00356 LacI: Bacterial regul 55.3 13 0.00028 25.7 2.6 42 48-89 3-44 (46)
35 PF07499 RuvA_C: RuvA, C-termi 54.7 19 0.00041 24.8 3.4 24 76-99 3-26 (47)
36 PF11181 YflT: Heat induced st 53.9 49 0.0011 26.8 6.4 76 249-337 12-89 (103)
37 COG1125 OpuBA ABC-type proline 53.2 22 0.00048 34.3 4.6 65 315-379 70-137 (309)
38 PRK14135 recX recombination re 52.9 96 0.0021 29.7 9.2 23 143-165 180-202 (263)
39 PF02022 Integrase_Zn: Integra 51.9 25 0.00055 23.5 3.5 31 316-346 6-37 (40)
40 PRK14134 recX recombination re 51.8 2.4E+02 0.0052 27.5 17.5 76 73-165 75-151 (283)
41 smart00354 HTH_LACI helix_turn 50.9 30 0.00065 25.9 4.3 49 47-95 3-51 (70)
42 smart00354 HTH_LACI helix_turn 50.7 36 0.00078 25.4 4.7 42 256-300 7-48 (70)
43 smart00342 HTH_ARAC helix_turn 50.6 64 0.0014 23.9 6.3 25 44-68 1-25 (84)
44 cd08319 Death_RAIDD Death doma 50.1 92 0.002 24.4 7.0 21 81-101 18-38 (83)
45 PRK14606 ruvA Holliday junctio 49.4 1.8E+02 0.0039 26.5 9.9 64 54-130 61-125 (188)
46 KOG0011 Nucleotide excision re 46.7 1E+02 0.0022 30.6 8.1 99 179-299 214-313 (340)
47 cd01392 HTH_LacI Helix-turn-he 44.0 49 0.0011 22.6 4.3 41 257-300 5-45 (52)
48 COG2511 GatE Archaeal Glu-tRNA 43.3 1.8E+02 0.0039 31.0 9.6 53 143-199 527-579 (631)
49 PF07499 RuvA_C: RuvA, C-termi 41.5 47 0.001 22.8 3.7 25 318-342 3-27 (47)
50 PRK14604 ruvA Holliday junctio 40.2 2.5E+02 0.0055 25.7 9.4 131 54-220 61-192 (195)
51 PF02631 RecX: RecX family; I 39.7 1.4E+02 0.0031 24.7 7.2 21 143-163 97-117 (121)
52 PRK13901 ruvA Holliday junctio 39.0 2.8E+02 0.0061 25.5 9.4 108 54-201 60-168 (196)
53 PF12244 DUF3606: Protein of u 38.6 40 0.00087 24.4 3.1 29 40-68 16-44 (57)
54 TIGR01448 recD_rel helicase, p 37.4 84 0.0018 35.1 6.9 85 46-133 80-167 (720)
55 PRK14600 ruvA Holliday junctio 37.3 2E+02 0.0044 26.2 8.2 44 54-99 61-104 (186)
56 PF11212 DUF2999: Protein of u 35.3 2E+02 0.0043 21.9 7.1 48 215-270 3-50 (82)
57 cd01392 HTH_LacI Helix-turn-he 35.1 61 0.0013 22.1 3.6 42 52-93 5-46 (52)
58 PHA01351 putative minor struct 34.8 6.7E+02 0.015 27.8 19.0 193 76-278 595-861 (1070)
59 COG1393 ArsC Arsenate reductas 33.6 27 0.00057 29.4 1.7 41 153-198 75-115 (117)
60 PF03960 ArsC: ArsC family; I 33.5 74 0.0016 26.0 4.4 20 189-208 71-90 (110)
61 PRK00116 ruvA Holliday junctio 33.0 1.1E+02 0.0023 28.0 5.8 25 177-201 149-173 (192)
62 COG1378 Predicted transcriptio 32.7 1.9E+02 0.0041 27.7 7.6 88 322-436 6-95 (247)
63 KOG0400 40S ribosomal protein 32.4 40 0.00087 28.7 2.5 66 235-301 20-85 (151)
64 PRK14603 ruvA Holliday junctio 31.5 3.9E+02 0.0084 24.6 9.2 117 53-201 59-176 (197)
65 cd08313 Death_TNFR1 Death doma 30.8 1.6E+02 0.0034 22.9 5.5 44 76-121 11-55 (80)
66 PF00165 HTH_AraC: Bacterial r 30.6 1.1E+02 0.0024 20.0 4.1 26 42-67 6-31 (42)
67 KOG2629 Peroxisomal membrane a 30.5 70 0.0015 31.1 4.1 27 315-341 19-45 (300)
68 PF02787 CPSase_L_D3: Carbamoy 30.4 34 0.00073 29.0 1.8 19 144-162 64-82 (123)
69 PRK14605 ruvA Holliday junctio 30.4 2.8E+02 0.0061 25.4 8.1 24 178-201 149-172 (194)
70 cd08316 Death_FAS_TNFRSF6 Deat 29.8 3E+02 0.0065 22.2 7.8 56 251-308 22-77 (97)
71 PF03874 RNA_pol_Rpb4: RNA pol 29.0 2.1E+02 0.0046 23.4 6.5 29 73-101 56-84 (117)
72 PRK14602 ruvA Holliday junctio 28.4 4.8E+02 0.01 24.1 9.4 118 53-201 61-179 (203)
73 cd08315 Death_TRAILR_DR4_DR5 D 27.6 3.2E+02 0.007 21.9 7.8 53 253-309 23-76 (96)
74 TIGR00084 ruvA Holliday juncti 27.3 4.8E+02 0.01 23.8 9.8 43 54-98 60-102 (191)
75 PRK07562 ribonucleotide-diphos 26.6 1.1E+02 0.0024 35.9 5.6 41 327-367 1031-1077(1220)
76 cd01421 IMPCH Inosine monophos 26.5 56 0.0012 29.8 2.6 39 141-181 30-68 (187)
77 TIGR00601 rad23 UV excision re 26.0 1.1E+02 0.0023 31.3 4.9 44 315-367 153-196 (378)
78 PRK09562 mazG nucleoside triph 25.7 1.6E+02 0.0034 28.5 5.7 70 87-156 83-162 (262)
79 PF13331 DUF4093: Domain of un 25.4 3.4E+02 0.0074 21.4 6.7 80 260-340 6-87 (87)
80 PRK00116 ruvA Holliday junctio 24.2 1.3E+02 0.0027 27.6 4.6 25 109-133 149-173 (192)
81 PF13543 KSR1-SAM: SAM like do 23.8 1.9E+02 0.0041 24.8 5.2 22 142-163 102-123 (129)
82 KOG2561 Adaptor protein NUB1, 23.6 6.6E+02 0.014 26.3 9.7 179 104-300 260-445 (568)
83 cd08318 Death_NMPP84 Death dom 23.2 2.6E+02 0.0056 21.9 5.6 36 80-117 22-57 (86)
84 PHA02591 hypothetical protein; 23.2 1.6E+02 0.0035 22.8 4.1 25 105-129 44-68 (83)
85 cd04752 Commd4 COMM_Domain con 22.7 3.5E+02 0.0076 24.2 7.1 44 118-161 33-82 (174)
86 PF14117 DUF4287: Domain of un 22.6 2.5E+02 0.0053 20.7 4.9 42 223-270 13-55 (61)
87 PF11264 ThylakoidFormat: Thyl 22.4 3.8E+02 0.0082 25.1 7.3 56 42-97 66-124 (216)
88 PLN03060 inositol phosphatase- 22.3 1.4E+02 0.0031 27.7 4.4 58 42-99 69-128 (206)
89 PRK09570 rpoH DNA-directed RNA 21.9 35 0.00076 26.5 0.4 27 75-101 19-45 (79)
90 PF13720 Acetyltransf_11: Udp 21.8 1E+02 0.0022 24.1 3.0 14 52-65 24-37 (83)
91 cd08324 CARD_NOD1_CARD4 Caspas 21.7 1.4E+02 0.0031 23.5 3.6 52 241-297 10-61 (85)
92 PRK13503 transcriptional activ 21.7 3.1E+02 0.0067 25.9 7.1 26 43-68 186-211 (278)
93 cd08784 Death_DRs Death Domain 21.5 2.4E+02 0.0053 21.6 5.1 38 77-116 12-49 (79)
94 PRK08561 rps15p 30S ribosomal 21.4 2E+02 0.0044 25.2 4.9 35 237-272 22-56 (151)
95 PHA01976 helix-turn-helix prot 21.2 91 0.002 22.6 2.5 25 320-344 5-30 (67)
96 smart00422 HTH_MERR helix_turn 20.8 2.8E+02 0.006 20.0 5.2 21 46-66 2-22 (70)
97 cd03035 ArsC_Yffb Arsenate Red 20.8 2E+02 0.0042 23.4 4.6 18 191-208 74-91 (105)
98 PRK11613 folP dihydropteroate 20.5 1.7E+02 0.0038 28.5 4.9 66 353-426 165-230 (282)
99 cd08315 Death_TRAILR_DR4_DR5 D 20.2 4.6E+02 0.0099 21.0 7.0 39 76-116 19-57 (96)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=2e-67 Score=544.70 Aligned_cols=370 Identities=19% Similarity=0.336 Sum_probs=347.6
Q ss_pred hHHHHHHhcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCC---CCCCChhhHHHHHHHcCCC
Q 013135 46 TVSDLQKSCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSG---DLGDTLEPNLKLFKSLGIT 122 (449)
Q Consensus 46 ~v~~L~~~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l---~~~~~l~~~l~~L~~lG~~ 122 (449)
.++|| +++|++..++.++.. + .+-+.+.++++||+++||++++|. ++|.+ ++++++.|+++||+++|++
T Consensus 66 ~~~~L-~~lgi~~~~l~~~~~--p-~~~~~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s 137 (487)
T PLN03196 66 VLDFL-RGIGIDPDELDGLEL--P-STVDVMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVT 137 (487)
T ss_pred HHHHH-HHcCCCchhhhccCC--C-ccHHHHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCC
Confidence 34788 689999999986532 1 344678899999999999999997 69999 6789999999999999999
Q ss_pred hHHHHHHHHhhhhhhccc----hhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHH
Q 013135 123 GANLAEMLNKEHRVLESD----AYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFL 198 (449)
Q Consensus 123 ~~~l~~~i~~~P~lL~~~----l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il 198 (449)
..+++++|.++|.+|..+ +.++++||+++|++.++|++++.++|++|+++++++|.|+++||.++|++.+++++++
T Consensus 138 ~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il 217 (487)
T PLN03196 138 RSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPML 217 (487)
T ss_pred HHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 999999999999999864 6789999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCcceeccccccchHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccce
Q 013135 199 SSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLL 278 (449)
Q Consensus 199 ~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~ 278 (449)
.++|++|+++++++++|+++||+++|++.+++.+++.++|++|+++++++++|++++|+++|++++.++.++..+|.+++
T Consensus 218 ~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~ 297 (487)
T PLN03196 218 TRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILG 297 (487)
T ss_pred HhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeE
Confidence 99999999999999999999999999999999999999999999999988999999999999999999999999999999
Q ss_pred ecch-HHHHHHHHH-HhcCCCCChhH-HHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHhcCCcccccChHHHHh
Q 013135 279 QSTA-RLNKIIDEV-KKLGFDPTNLL-FVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISK 355 (449)
Q Consensus 279 ~s~~-~l~~~v~~l-~~lG~~~~~~~-~~~a~~~i~~~s~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL~~S~e~l~~ 355 (449)
++.+ ++.++++++ +++|+++++.. ++.+.+.++++|+++|++|++||+++||+.++|..||+++|++|++|+++|++
T Consensus 298 ~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~ 377 (487)
T PLN03196 298 LDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKP 377 (487)
T ss_pred ecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHH
Confidence 9865 799999998 59999999864 66778889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCChHHHhhCCceeccCCCCcchhHHHHHHHHHHCCCCCCCcchhhhccccHHHHHHHHhhcCCC
Q 013135 356 LMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFSLTYMFKMTEKQFIERIVKKYEH 429 (449)
Q Consensus 356 k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~se~~F~~~~v~~~~~ 429 (449)
|++||+++||++.++|+++|+||+||||+||+|||++ |+++|+ ++++.++|++||++|+++||.+|.|
T Consensus 378 k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~---L~~kGl---~~sL~~~L~~sd~~F~~r~v~~y~e 445 (487)
T PLN03196 378 SLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYER---VAKKGI---KCSLAWFLNCSDDKFEQRMSGDFIE 445 (487)
T ss_pred HHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHH---HHHcCC---CCCHHHHhccCHHHHHHHHhhhccc
Confidence 9999999999999999999999999999999999975 568998 6899999999999999999999987
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=4.8e-56 Score=446.58 Aligned_cols=337 Identities=26% Similarity=0.421 Sum_probs=269.6
Q ss_pred HHHHhCCCCHHHHHHHHhhCCCC---CCCCChhhHHHHHHHcCCChHHHHHHHHhhhhhhccc----hhhHHHHHHHCCC
Q 013135 81 KLLRTHGLTRSQINNFVTKRPSG---DLGDTLEPNLKLFKSLGITGANLAEMLNKEHRVLESD----AYATVEFFRTNGF 153 (449)
Q Consensus 81 ~~L~~~G~~~~~i~~il~~~P~l---~~~~~l~~~l~~L~~lG~~~~~l~~~i~~~P~lL~~~----l~~~l~fL~~lGl 153 (449)
++|+++||++++|.++++++|.+ ++++++.|+++||.++|++..++++++.++|.+|..+ +.+.++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 57899999999999999999999 8899999999999999999999999999999999865 6789999999999
Q ss_pred ChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceeccccccchHHHHHHHHhcCChHHHHHH
Q 013135 154 SDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKA 233 (449)
Q Consensus 154 ~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~ 233 (449)
+++|+.+++.++|++|..+.++++.+.++||+++|++.+.+.+++..+|.++... +++.+.++++.++|++++++.++
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~v 159 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRV 159 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCC
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhccc
Confidence 9999999999999999999888999999999999999998899999999876665 58999999999999999999999
Q ss_pred HHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCChhHHHHHHHHHHhc
Q 013135 234 IRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNLLFVLAIRSMAVM 313 (449)
Q Consensus 234 l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~~~~~~a~~~i~~~ 313 (449)
+.++|+++..+.+++++++++||+++|++.+++.+++.++|.++..+.++..+...++.+.|...++ .++.+.+.++..
T Consensus 160 i~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~-~~i~~~p~il~~ 238 (345)
T PF02536_consen 160 IAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE-RVIKKFPQILSL 238 (345)
T ss_dssp HHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC----------------------------TH
T ss_pred ccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccc-cccccccccccc
Confidence 9999988888877779999999999999999999999999999999998866677766655555555 777777888888
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHhcCCcccccChHHHHhHHHHHHHhcCCChHHHhhCCceeccCCCCcchhHHHHH
Q 013135 314 SKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVL 393 (449)
Q Consensus 314 s~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l 393 (449)
+.++++++++||+++|||.+|+++|++++|++|++|.|++++|++||+++||++.++|+++|++|+||||+||+|||+++
T Consensus 239 ~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~ 318 (345)
T PF02536_consen 239 SEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVL 318 (345)
T ss_dssp HHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHH
T ss_pred chHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCCCCCCcchhhhccccHHHHHH
Q 013135 394 QLLMSNKVITEDFSLTYMFKMTEKQFIE 421 (449)
Q Consensus 394 ~~L~~~Gl~~~~~~l~~~l~~se~~F~~ 421 (449)
++|+++|+ ..++++.+++.+||++|++
T Consensus 319 ~~l~~~g~-~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 319 KVLKSKGL-IINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HTT--TTT-GGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHCcC-CCCCCHHHHhhccHHHhcC
Confidence 99999997 7789999999999999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=4.9e-47 Score=392.74 Aligned_cols=332 Identities=18% Similarity=0.285 Sum_probs=299.1
Q ss_pred HHHHHHhcCCCHHHHHHhhcccccCC-CcCHHHHHHHHHhCCCCHHHHHHHHhhCCCC---CCCCChhhHHHHHHHcCCC
Q 013135 47 VSDLQKSCGFSLESAVSASEKLRVDT-TDKIDSVLKLLRTHGLTRSQINNFVTKRPSG---DLGDTLEPNLKLFKSLGIT 122 (449)
Q Consensus 47 v~~L~~~~Gls~~~~~~~~~~~~~~s-~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l---~~~~~l~~~l~~L~~lG~~ 122 (449)
|+|| +++|++.+++.+ .+++...+ ..++.++++||+++|+++++|++++.++|.+ +++.++.|+++||+++|++
T Consensus 96 l~~L-~s~G~~~~~i~~-~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs 173 (487)
T PLN03196 96 VEFL-HKLGLTIEDINE-YPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVK 173 (487)
T ss_pred HHHH-HHcCCChHHhcc-CcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCC
Confidence 3566 789999999983 23333333 4779999999999999999999999999999 7789999999999999999
Q ss_pred hHHHHHHHHhhhhhhccc----hhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHH
Q 013135 123 GANLAEMLNKEHRVLESD----AYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFL 198 (449)
Q Consensus 123 ~~~l~~~i~~~P~lL~~~----l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il 198 (449)
.+++++++.++|.+|+.+ +.++++||.++|++.++|++++.++|++|++++++++.|+++||+++|++.+++++++
T Consensus 174 ~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il 253 (487)
T PLN03196 174 RQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARIL 253 (487)
T ss_pred HHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHH
Confidence 999999999999999865 5688999999999999999999999999999999999999999999999999999999
Q ss_pred HhCCcceeccccccchHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHH-hCCCChHHHHHHHhhcCccc
Q 013135 199 SSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILV-NHGVPKSLVVKLMLIQPRTL 277 (449)
Q Consensus 199 ~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~-~lGv~~~~i~~li~~~P~lL 277 (449)
.++|++|++|++++++|+++||+++|++.+++..++.++|.+++.++++++.+++.|+. ++|++++++..++.++|.++
T Consensus 254 ~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il 333 (487)
T PLN03196 254 EKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIV 333 (487)
T ss_pred HhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhh
Confidence 99999999999999999999999999999999999999999999999988999999995 59999999999999999999
Q ss_pred eecchHHHHHHHHHHhcCCCCChh-HHHHHHHHHHhcCHHHHHHHHHHHH-HcCCCHHHHHHHHhcCCcccccChH-HHH
Q 013135 278 LQSTARLNKIIDEVKKLGFDPTNL-LFVLAIRSMAVMSKALWEKKLEAYM-NFGLTKDEVYSAFRRQPMFMIVSEQ-KIS 354 (449)
Q Consensus 278 ~~s~~~l~~~v~~l~~lG~~~~~~-~~~~a~~~i~~~s~~~l~~k~~~l~-~lG~s~~ev~~~v~~~P~iL~~S~e-~l~ 354 (449)
+++.+++.++++|++++|++.++. .++...|.+++.|.+++++|++||. +|||+.++|. ++|++|+||.| +|+
T Consensus 334 ~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~~~l~~k~dFlvneMg~~~~~Iv----~fP~~LsySLEkRI~ 409 (487)
T PLN03196 334 SLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNLEIMKPSLEFFKKEMKRPLKELV----EFPAYFTYGLESRIK 409 (487)
T ss_pred cccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccHHHHHHHHHHHHHHhCCCHHHHH----hChHHhccChhhhhH
Confidence 999999999999999999999985 4666677888999999999999999 8999999988 89999999998 899
Q ss_pred hHHHHHHHhcCCChHHHhhCCceeccCCCCcchhHH
Q 013135 355 KLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRC 390 (449)
Q Consensus 355 ~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~ 390 (449)
+++++|.++ |+.. .-..+|.+| |++..-|+
T Consensus 410 PR~~~L~~k-Gl~~----sL~~~L~~s-d~~F~~r~ 439 (487)
T PLN03196 410 PRYERVAKK-GIKC----SLAWFLNCS-DDKFEQRM 439 (487)
T ss_pred HHHHHHHHc-CCCC----CHHHHhccC-HHHHHHHH
Confidence 999998864 7632 122445555 44665555
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=4.9e-39 Score=323.17 Aligned_cols=304 Identities=25% Similarity=0.434 Sum_probs=233.4
Q ss_pred HHHhcCCCHHHHHHhhcccc----cCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCC---CCCCChhhHHHHHHHcCCC
Q 013135 50 LQKSCGFSLESAVSASEKLR----VDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSG---DLGDTLEPNLKLFKSLGIT 122 (449)
Q Consensus 50 L~~~~Gls~~~~~~~~~~~~----~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l---~~~~~l~~~l~~L~~lG~~ 122 (449)
+++++|++..++.++.++.+ .....++.++++||++.|++..++++++.++|.+ +.++++.|.+++|+++|++
T Consensus 3 ~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s 82 (345)
T PF02536_consen 3 LLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLS 82 (345)
T ss_dssp HHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-
T ss_pred HHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCC
Confidence 56899999999999976532 3455779999999999999999999999999999 5589999999999999999
Q ss_pred hHHHHHHHHhhhhhhcc----chhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHH
Q 013135 123 GANLAEMLNKEHRVLES----DAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFL 198 (449)
Q Consensus 123 ~~~l~~~i~~~P~lL~~----~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il 198 (449)
++++.+++.++|.+|.. ++.+.++||+++|++.+.+.+++..+|.++... +++.+.++++.++|++++++++++
T Consensus 83 ~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi 160 (345)
T PF02536_consen 83 DEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVI 160 (345)
T ss_dssp HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCH
T ss_pred HHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccc
Confidence 99999999999999874 477899999999999998999999999877666 679999999999999999999999
Q ss_pred HhCCcceeccccccchHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccce
Q 013135 199 SSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLL 278 (449)
Q Consensus 199 ~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~ 278 (449)
.++|+++..+.+++++|+++||+++|++.+++.+++.++|+++..+.++.+++...++...|...+ .++.++|.++.
T Consensus 161 ~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~---~~i~~~p~il~ 237 (345)
T PF02536_consen 161 AKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE---RVIKKFPQILS 237 (345)
T ss_dssp HHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC------------------------------T
T ss_pred cccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccc---ccccccccccc
Confidence 999998888888899999999999999999999999999999999999856554444444444444 88899999999
Q ss_pred ecchHHHHHHHHHHhcCCCCChh-HHHHHHHHHHhcCHHHHHHHHHHHH-HcCCCHHHHHHHHhcCCcccccChH-HHHh
Q 013135 279 QSTARLNKIIDEVKKLGFDPTNL-LFVLAIRSMAVMSKALWEKKLEAYM-NFGLTKDEVYSAFRRQPMFMIVSEQ-KISK 355 (449)
Q Consensus 279 ~s~~~l~~~v~~l~~lG~~~~~~-~~~~a~~~i~~~s~~~l~~k~~~l~-~lG~s~~ev~~~v~~~P~iL~~S~e-~l~~ 355 (449)
++.+++.++++++.++||+.++. .++...|.+++.+.+++++|++|+. ++|++.++|. ++|++|+||.| +|++
T Consensus 238 ~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e~l~~k~~fl~~~m~~~~~~i~----~~P~~l~~sLe~ri~P 313 (345)
T PF02536_consen 238 LSEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSIEKLKPKFEFLVKEMGLPLEEIV----EFPQYLSYSLEKRIKP 313 (345)
T ss_dssp HHHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-HHHHHHHHHHHHHCCT--HHHHH----HSCHHHCS-HHHHHHH
T ss_pred cchHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcchhhhhHHHHHHHHHhCcCHHHHh----hCCceeEechhhhhhh
Confidence 99999999999999999999885 4777778889999999999999998 7999999987 89999999998 6999
Q ss_pred H---HHHHHH
Q 013135 356 L---MDCYVN 362 (449)
Q Consensus 356 k---~~fL~~ 362 (449)
+ +++|.+
T Consensus 314 R~~~~~~l~~ 323 (345)
T PF02536_consen 314 RYEVLKVLKS 323 (345)
T ss_dssp HHHHHHTT--
T ss_pred HHHHHHHHHH
Confidence 9 555555
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=100.00 E-value=1.4e-33 Score=289.52 Aligned_cols=349 Identities=21% Similarity=0.319 Sum_probs=312.2
Q ss_pred ccCCCCCchHHHHHHhcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCC---CCCCChhhHHH
Q 013135 38 KITCTQPLTVSDLQKSCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSG---DLGDTLEPNLK 114 (449)
Q Consensus 38 ~~~~~~~~~v~~L~~~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l---~~~~~l~~~l~ 114 (449)
...+..++++.|+++++|++...+..+++.+......++++++++|+++|++.++|.+++..+|.+ +.+..+.+.+.
T Consensus 53 ~~~~~~~f~~s~~~~s~~~~~~~~~~~~~~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~ 132 (413)
T KOG1267|consen 53 LELKGSNFESSYLVDSLGLSIKLARKLSREVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLR 132 (413)
T ss_pred ccccCCCcceeeeccccccchhhHHHHHHHHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhh
Confidence 344555899999999999999999999998888889999999999999999999999999999999 67888999998
Q ss_pred HHHHcCCChHHHHHHHHhhhhhhcc----chhhHHHHHHHCC--CChhhHhhHhhhCCceeecCcccchhhHHHHHHHcC
Q 013135 115 LFKSLGITGANLAEMLNKEHRVLES----DAYATVEFFRTNG--FSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLG 188 (449)
Q Consensus 115 ~L~~lG~~~~~l~~~i~~~P~lL~~----~l~~~l~fL~~lG--l~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG 188 (449)
+|...|++..++.+++...|.+|.. ++...++|+.+.+ +....+.+++...|..... +..+. ++++++++|
T Consensus 133 ~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~--~~~v~-~~~~~~~lg 209 (413)
T KOG1267|consen 133 LLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLN--ENSVE-RLDIRRELG 209 (413)
T ss_pred hhhccCccccccchhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhcccccccccc--ccccc-cchhhHHhC
Confidence 9999999999999999999999873 6778999999984 8888888888888754443 23355 899999999
Q ss_pred CChHHHHHHHHhCCcceeccccccchHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHH
Q 013135 189 FAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVK 268 (449)
Q Consensus 189 ~s~~~i~~il~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~ 268 (449)
....++...+..+|..+.... .+...+.++...|+.+.. +++.+.|.++.++.++.+++++++|+++|++.++|..
T Consensus 210 ~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~ 285 (413)
T KOG1267|consen 210 VKPRLLKSLLESQPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWK 285 (413)
T ss_pred CCHHHHHHHHhcCccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHH
Confidence 999999999999999887653 577888888888876554 7888899999999999999999999999999999999
Q ss_pred HHhhcCccceecchHHHHHHHHHHhcCCCCChhHHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHhcCCccccc
Q 013135 269 LMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIV 348 (449)
Q Consensus 269 li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~~~~~~a~~~i~~~s~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL~~ 348 (449)
|+.++|.+|+++.+++..+++++.+. .++ +...++++..++..++++++|+..+|++..|+..|++++|+++.+
T Consensus 286 ~~~k~P~~l~~s~~~~~~~~~~~~~~--~~~----~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~ 359 (413)
T KOG1267|consen 286 MVKKCPQILGYSVKKNLKTTEYLLKN--PKH----ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSF 359 (413)
T ss_pred HHHhCchheEeehhhhhHHHHHHHhc--chh----hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhh
Confidence 99999999999999999999998766 222 556677778999999999999999999999999999999999999
Q ss_pred ChH-HHHhHHHHHHHhcCCChHHHhhCCceeccCCCCcchhHHHHHHHHHHC
Q 013135 349 SEQ-KISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSN 399 (449)
Q Consensus 349 S~e-~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~ 399 (449)
|.+ .++.+.+|+.+.|+++.+.++.+|.++.|++|+|+.||+.+..++..+
T Consensus 360 s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 360 SLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred hHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 999 899999999999999999999999999999999999999998876544
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.89 E-value=9.8e-23 Score=209.32 Aligned_cols=247 Identities=28% Similarity=0.386 Sum_probs=211.6
Q ss_pred ccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceeccccccchHHH
Q 013135 138 ESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCI 217 (449)
Q Consensus 138 ~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p~v 217 (449)
..+++.++++|++.|++..+|.+++..+|+++..+.++.+.|+..+|.+.|++..++++++...|.+|+.+.+.++.+.+
T Consensus 88 ~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~~~~ 167 (413)
T KOG1267|consen 88 SVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLSTFI 167 (413)
T ss_pred ccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchhhHH
Confidence 46788999999999999999999999999999999999999999999999999999999999999999988888999999
Q ss_pred HHHHHhc--CChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcC
Q 013135 218 EILRRVL--DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLG 295 (449)
Q Consensus 218 ~fL~~~g--~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG 295 (449)
+|+++++ .....+.+.+...|.... .+..++ ++++++++|+.+..+..++..+|....... .+...+.++..+|
T Consensus 168 ~~l~~~~~~~~~s~~~~~~~~~~~~~~--~~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~-~l~~~~~~i~~~g 243 (413)
T KOG1267|consen 168 EFLKSIPPELLSSVVERLLTPVPSFLL--NENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL-KLKARLPFLLTLG 243 (413)
T ss_pred HHhhccchhhhhhHHHHhccccccccc--cccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh-hhhhhhhhHHHhc
Confidence 9999986 445445555544442221 222265 899999999999999999999999876654 8999999999999
Q ss_pred CCCChhHHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHhcCCcccccChHHHHhHHHHHHHhcCCChHHHhhCC
Q 013135 296 FDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHP 375 (449)
Q Consensus 296 ~~~~~~~~~~a~~~i~~~s~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~~~~i~~~P 375 (449)
|++.+.++++|+..+...+++++++|+++|.++||+.+||..|++++|++|++|++++..+++|+++. .+++.++|
T Consensus 244 ~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~----~~~~~k~p 319 (413)
T KOG1267|consen 244 FDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKN----PKHILKFP 319 (413)
T ss_pred cCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhc----chhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999877777777775 33377777
Q ss_pred ceeccCCCCcchhHHHHH
Q 013135 376 YLLLFSLEKRILPRCSVL 393 (449)
Q Consensus 376 ~~L~~Sle~ri~pR~~~l 393 (449)
+++.+|.+ .+.||+.++
T Consensus 320 ~~l~~s~~-~l~~~ie~l 336 (413)
T KOG1267|consen 320 QLLRSSED-KLKPRIEFL 336 (413)
T ss_pred hhhhccch-hhhhhHHHH
Confidence 77755544 677777444
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.32 E-value=0.00018 Score=44.82 Aligned_cols=30 Identities=17% Similarity=0.321 Sum_probs=26.8
Q ss_pred HHHhcCCcccccChHHHHhHHHHHHHhcCCC
Q 013135 337 SAFRRQPMFMIVSEQKISKLMDCYVNKLSME 367 (449)
Q Consensus 337 ~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~ 367 (449)
.++.++|.++++|.++|+++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSEKKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccHHHhhHHHHHHH-HcCCC
Confidence 4678999999999889999999999 78874
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=96.96 E-value=0.00052 Score=42.67 Aligned_cols=29 Identities=48% Similarity=0.809 Sum_probs=18.7
Q ss_pred hHhhhCCceeecCcccchhhHHHHHHHcCC
Q 013135 160 SITVKRPKFYVYNLKKCMKPKLEFFKSLGF 189 (449)
Q Consensus 160 ~il~~~P~lL~~~~e~~l~pkl~fL~~lG~ 189 (449)
+++.++|+++.++ ++++.++++||+++|+
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 3556666666666 4566666666666665
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=94.15 E-value=0.39 Score=48.02 Aligned_cols=68 Identities=22% Similarity=0.341 Sum_probs=42.9
Q ss_pred HHHHHHHHHHhc----------CCCCChhHHH-HHH---HHHHhcC--HHHHHHHHHHHH-HcCCCHHHHHHHHhcCCcc
Q 013135 283 RLNKIIDEVKKL----------GFDPTNLLFV-LAI---RSMAVMS--KALWEKKLEAYM-NFGLTKDEVYSAFRRQPMF 345 (449)
Q Consensus 283 ~l~~~v~~l~~l----------G~~~~~~~~~-~a~---~~i~~~s--~~~l~~k~~~l~-~lG~s~~ev~~~v~~~P~i 345 (449)
+..+.++..+++ |+++++..+- +|. .=+++++ ......++..|+ ++|++ +.+..++.+||.|
T Consensus 209 ~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp-~k~~~~l~rHPgI 287 (335)
T PF11955_consen 209 KFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLP-QKFRRLLLRHPGI 287 (335)
T ss_pred HHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCc-HHHHHHHHhCCCe
Confidence 455555554443 5556654433 222 2234444 334466777887 79998 5788899999999
Q ss_pred cccChH
Q 013135 346 MIVSEQ 351 (449)
Q Consensus 346 L~~S~e 351 (449)
+..|..
T Consensus 288 FYvS~k 293 (335)
T PF11955_consen 288 FYVSLK 293 (335)
T ss_pred EEEecc
Confidence 999876
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=89.20 E-value=2.7 Score=37.84 Aligned_cols=23 Identities=13% Similarity=0.271 Sum_probs=16.9
Q ss_pred hHHHHHHHcCCChHHHHHHHHhC
Q 013135 179 PKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 179 pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
..+..++++|++-++|..++...
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Confidence 45667778888888888877643
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=88.09 E-value=1.8 Score=39.03 Aligned_cols=143 Identities=18% Similarity=0.280 Sum_probs=66.0
Q ss_pred chHHHHHHhcCCCHHHHHHhhcccccCCCcCHH--HHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHH----
Q 013135 45 LTVSDLQKSCGFSLESAVSASEKLRVDTTDKID--SVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKS---- 118 (449)
Q Consensus 45 ~~v~~L~~~~Gls~~~~~~~~~~~~~~s~~~~~--~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~---- 118 (449)
-|+.|. ...|+=+...+.- ...+.-+...+. ..+..|++.||+-++|..++..... +....+...++.+..
T Consensus 16 ~tLRyY-e~~GLl~p~~r~~-~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~-~~~~~L~~~~~~l~~ei~~ 92 (172)
T cd04790 16 STLLYY-ERIGLLSPSARSE-SNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGD-DATDVLRRRLAELNREIQR 92 (172)
T ss_pred HHHHHH-HHCCCCCCCccCC-CCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCh-hHHHHHHHHHHHHHHHHHH
Confidence 356666 4567755433221 222222222222 3456677888888888887765321 111112222222211
Q ss_pred cCCChHHHHHHHHhhhhhhc---cchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHH
Q 013135 119 LGITGANLAEMLNKEHRVLE---SDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMA 195 (449)
Q Consensus 119 lG~~~~~l~~~i~~~P~lL~---~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~ 195 (449)
+--....+..++...+..-. .+-+..++-++..|++++++.+.=..+=+ ..+ ..-.+||.++|++.+++.
T Consensus 93 L~~~~~~l~~ll~~~~~~~~~~~V~~~~w~~l~~~~g~~~~~m~~wh~~fe~---~~p----~~h~~~l~~~g~~~~~~~ 165 (172)
T cd04790 93 LRQQQRAIATLLKQPTLLKEQRLVTKEKWVAILKAAGMDEADMRRWHIEFEK---MEP----EAHQEFLQSLGIPEDEIE 165 (172)
T ss_pred HHHHHHHHHHHHHHHhhccccccCCHHHHHHHHHHcCCChHHHHHHHHHHHH---hCc----HHHHHHHHHcCCCHHHHH
Confidence 22222333333322222211 12345566677777777776443222111 111 123467777888777776
Q ss_pred HH
Q 013135 196 KF 197 (449)
Q Consensus 196 ~i 197 (449)
.|
T Consensus 166 ~i 167 (172)
T cd04790 166 RI 167 (172)
T ss_pred HH
Confidence 54
No 12
>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=86.32 E-value=3.4 Score=41.38 Aligned_cols=200 Identities=17% Similarity=0.230 Sum_probs=107.9
Q ss_pred HHHhCCCCHHHHHHHHhhCCCC-CC---------CCChhhHHHHHHH--cCCChHHHHHHHHhhhhhhccc-----hhhH
Q 013135 82 LLRTHGLTRSQINNFVTKRPSG-DL---------GDTLEPNLKLFKS--LGITGANLAEMLNKEHRVLESD-----AYAT 144 (449)
Q Consensus 82 ~L~~~G~~~~~i~~il~~~P~l-~~---------~~~l~~~l~~L~~--lG~~~~~l~~~i~~~P~lL~~~-----l~~~ 144 (449)
+-..+|+....+...+.++|.+ .. .-.+.+...-|.+ ..+-.+.-..++.+--.+|-.+ +-.+
T Consensus 43 ~~~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~k 122 (335)
T PF11955_consen 43 LRRQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSK 122 (335)
T ss_pred HHHhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHH
Confidence 4457999778999999999999 21 1245555554422 2221111123333333344221 2356
Q ss_pred HHHHH-HCCCChhhHhhHhhhCCceeecCc---ccchhhHHHHHHHcCCChHHHHHHH---------HhCCcce------
Q 013135 145 VEFFR-TNGFSDSQIKSITVKRPKFYVYNL---KKCMKPKLEFFKSLGFAELQMAKFL---------SSQPYIL------ 205 (449)
Q Consensus 145 l~fL~-~lGl~~~~i~~il~~~P~lL~~~~---e~~l~pkl~fL~~lG~s~~~i~~il---------~~~P~iL------ 205 (449)
+..++ ++|++.+-..+++.++|..+...- ......-+.+=-++.+|.-|-.... ...|.-|
T Consensus 123 i~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~~~~~~~~~~~~~~~~~~Fp~~fp~ 202 (335)
T PF11955_consen 123 IAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRAEKEYREKREDGFDRPLAFPVSFPK 202 (335)
T ss_pred HHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhhhhccccccccccCCceeeeecCCC
Confidence 77776 899999999999999999876632 1111111122113444433332221 0111111
Q ss_pred eccccccchHHHHHHHHhc----------C---ChHHHHHHHHhCCcccccchhhhh-HHHHHHHHh-CCCChHHHHHHH
Q 013135 206 ERSLENHIIPCIEILRRVL----------D---TDENVLKAIRAGCLVLEYDIEKVL-EPNIAILVN-HGVPKSLVVKLM 270 (449)
Q Consensus 206 ~~s~~~~l~p~v~fL~~~g----------~---~~~~v~~~l~~~P~iL~~s~e~~l-~~~v~~L~~-lGv~~~~i~~li 270 (449)
++.+++.....++-|+++- . +++.=.+++.-.-.+|+..+++.+ ..++..+++ +|++. .+..++
T Consensus 203 G~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~lp~-k~~~~l 281 (335)
T PF11955_consen 203 GFRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGLPQ-KFRRLL 281 (335)
T ss_pred CccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCCcH-HHHHHH
Confidence 2223334555555555431 1 111112233333457777776643 345566664 99985 468899
Q ss_pred hhcCccceecch
Q 013135 271 LIQPRTLLQSTA 282 (449)
Q Consensus 271 ~~~P~lL~~s~~ 282 (449)
.++|.|+..|..
T Consensus 282 ~rHPgIFYvS~k 293 (335)
T PF11955_consen 282 LRHPGIFYVSLK 293 (335)
T ss_pred HhCCCeEEEecc
Confidence 999999998753
No 13
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=86.04 E-value=19 Score=31.68 Aligned_cols=126 Identities=11% Similarity=0.114 Sum_probs=72.3
Q ss_pred cCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcC-CChHHHHHHHHhhhhhhccchhhHHHHHHHCC
Q 013135 74 DKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLG-ITGANLAEMLNKEHRVLESDAYATVEFFRTNG 152 (449)
Q Consensus 74 ~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG-~~~~~l~~~i~~~P~lL~~~l~~~l~fL~~lG 152 (449)
..-..+.+.|.+.|++++.|..+|.. |.+.| ++...++....+.-.--........+-|...|
T Consensus 26 ~s~~el~~kL~~kg~~~~~i~~vl~~----------------l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kG 89 (157)
T PRK00117 26 HSRAELRRKLAAKGFSEEVIEAVLDR----------------LKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKG 89 (157)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHH----------------HHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcC
Confidence 44566778888889988888776554 55665 34444444333222111223445678888999
Q ss_pred CChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHh-CCcceeccccccchHHHHHHHHhcCChHHHH
Q 013135 153 FSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSS-QPYILERSLENHIIPCIEILRRVLDTDENVL 231 (449)
Q Consensus 153 l~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~-~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~ 231 (449)
++.+.|..++...+ .+. . +.+.+++.+ +...-..+. ..-...+.+|.+-|++.+.|.
T Consensus 90 i~~~~I~~~l~~~~----~d~---~--------------e~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~ 147 (157)
T PRK00117 90 VDREIIEEALAELD----IDW---E--------------ELARELARKKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQ 147 (157)
T ss_pred CCHHHHHHHHHHcC----ccH---H--------------HHHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHH
Confidence 99999998887654 111 1 111112221 222212221 223455678888888888888
Q ss_pred HHHHhC
Q 013135 232 KAIRAG 237 (449)
Q Consensus 232 ~~l~~~ 237 (449)
+++...
T Consensus 148 ~~l~~~ 153 (157)
T PRK00117 148 RVLRNA 153 (157)
T ss_pred HHHHhh
Confidence 777653
No 14
>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=84.29 E-value=5.2 Score=33.57 Aligned_cols=24 Identities=8% Similarity=0.097 Sum_probs=15.6
Q ss_pred chhhHHHHHHHCCCChhhHhhHhh
Q 013135 140 DAYATVEFFRTNGFSDSQIKSITV 163 (449)
Q Consensus 140 ~l~~~l~fL~~lGl~~~~i~~il~ 163 (449)
......+-|+..|++.+.|...+.
T Consensus 44 G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 44 GPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHT
T ss_pred cHHHHHHHHHHHCCChHHHHHHHH
Confidence 345566777888888888887776
No 15
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=79.41 E-value=44 Score=30.19 Aligned_cols=72 Identities=11% Similarity=0.157 Sum_probs=40.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcC-CChHHHHHHHHhhhhhhccchhhHHHHHHHCCCC
Q 013135 76 IDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLG-ITGANLAEMLNKEHRVLESDAYATVEFFRTNGFS 154 (449)
Q Consensus 76 ~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG-~~~~~l~~~i~~~P~lL~~~l~~~l~fL~~lGl~ 154 (449)
-..+-..|...|+++..|..+ +++|...| ++...++....+.-.--.......-+-|...|++
T Consensus 37 e~ELr~kL~k~~~~~~~Ie~V----------------i~~l~~~~~ldD~~fAe~~i~~r~~~g~G~~rl~qeL~qkGi~ 100 (174)
T COG2137 37 EKELRRKLAKKEFSEEIIEEV----------------IDRLAEEGYLDDTRFAEAYIRSRSRKGKGPARLKQELKQKGID 100 (174)
T ss_pred HHHHHHHHHhccCCHHHHHHH----------------HHHHHHcCcccHHHHHHHHHHHHHhcccChHHHHHHHHHcCCC
Confidence 445566666777766555443 44555555 3444444444333333333344556667777777
Q ss_pred hhhHhhHhh
Q 013135 155 DSQIKSITV 163 (449)
Q Consensus 155 ~~~i~~il~ 163 (449)
++.|..++.
T Consensus 101 ~~~Ie~aL~ 109 (174)
T COG2137 101 DEIIEEALE 109 (174)
T ss_pred HHHHHHHHh
Confidence 777777665
No 16
>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=78.95 E-value=1.5 Score=37.84 Aligned_cols=32 Identities=28% Similarity=0.260 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhcCCccc
Q 013135 315 KALWEKKLEAYMNFGLTKDEVYSAFRRQPMFM 346 (449)
Q Consensus 315 ~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL 346 (449)
...+.+|++||++-|++.+||..++.+.+.--
T Consensus 20 ~sp~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 20 NSPLEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp CS-HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred cCCHHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 44578999999999999999999999877655
No 17
>PHA01351 putative minor structural protein
Probab=78.68 E-value=91 Score=34.10 Aligned_cols=159 Identities=13% Similarity=0.118 Sum_probs=98.0
Q ss_pred chHHHHHHhcCCCHHHHHHhhcccc----cCC------------CcCHHHHHHHHHhCCCCHHHHHHHHhhCCCC-----
Q 013135 45 LTVSDLQKSCGFSLESAVSASEKLR----VDT------------TDKIDSVLKLLRTHGLTRSQINNFVTKRPSG----- 103 (449)
Q Consensus 45 ~~v~~L~~~~Gls~~~~~~~~~~~~----~~s------------~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l----- 103 (449)
-++.-+++++|+..+.+..+..... ..+ -=.+...-.-|+.+|++++=+..++..+=..
T Consensus 500 kkIke~LKa~gfnks~~d~~L~~~~n~a~iesqIK~LQ~qL~nF~IS~QD~EkELKkLg~s~alIqaiI~EyftepL~Kl 579 (1070)
T PHA01351 500 KKIKEELKANKFNEQVALQILESELQFAQLQNQLKEYQFKLNNFLISPQDLEKDLKHLGFDSAIISALIYENQVEQLIKF 579 (1070)
T ss_pred HHHHHHHHhcCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 3566677888888777765543211 000 0123333456678899888887777664333
Q ss_pred --CCCC--------ChhhHHHHHHHcCCChHHHHHHHHhhhhhhcc----------------chhhHHHHHHHCCCChhh
Q 013135 104 --DLGD--------TLEPNLKLFKSLGITGANLAEMLNKEHRVLES----------------DAYATVEFFRTNGFSDSQ 157 (449)
Q Consensus 104 --~~~~--------~l~~~l~~L~~lG~~~~~l~~~i~~~P~lL~~----------------~l~~~l~fL~~lGl~~~~ 157 (449)
+.-+ +....-.-|+.+|.+..-+.+++.-+-+++.- +.+....-|+.+|++++-
T Consensus 580 QLnvyEsLakKGY~d~qq~ksElk~LGidKe~i~klin~Y~ql~qt~~eIkYIqe~LK~f~IspkeAitELKKL~ISdaL 659 (1070)
T PHA01351 580 QLNNIESLAKKGYLSLDEIKKQFKAIGIIKEYEDAFINFYNQELQISAFLTILKSQLRQFQIDPKEAETELKKLNINEYL 659 (1070)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHcCchHHH
Confidence 1111 22333345677898888888888777776531 345678889999999988
Q ss_pred HhhHhhhC---Cceee-cCcccc--------hhhHHHHHHHcCCChHHHHHHHHhCCc
Q 013135 158 IKSITVKR---PKFYV-YNLKKC--------MKPKLEFFKSLGFAELQMAKFLSSQPY 203 (449)
Q Consensus 158 i~~il~~~---P~lL~-~~~e~~--------l~pkl~fL~~lG~s~~~i~~il~~~P~ 203 (449)
+..++..+ |-+-. .++-++ .......|+.+|++.+.+.-++..+-.
T Consensus 660 An~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~yy~ 717 (1070)
T PHA01351 660 ANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKFYY 717 (1070)
T ss_pred HHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 88888776 43211 111111 223446788999999988887776543
No 18
>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=77.17 E-value=2.7 Score=36.37 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=12.7
Q ss_pred hhHHHHHHHcCCChHHHHHHHHhCCc
Q 013135 178 KPKLEFFKSLGFAELQMAKFLSSQPY 203 (449)
Q Consensus 178 ~pkl~fL~~lG~s~~~i~~il~~~P~ 203 (449)
..|++||++.|++.+||...+.+.+.
T Consensus 24 ~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 24 EKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp HHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred HHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 34555555555555555555555443
No 19
>PRK14136 recX recombination regulator RecX; Provisional
Probab=75.56 E-value=41 Score=33.09 Aligned_cols=128 Identities=12% Similarity=0.133 Sum_probs=74.5
Q ss_pred CcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcC-CChHHHHHHHHhhhhhhccchhhHHHHHHHC
Q 013135 73 TDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLG-ITGANLAEMLNKEHRVLESDAYATVEFFRTN 151 (449)
Q Consensus 73 ~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG-~~~~~l~~~i~~~P~lL~~~l~~~l~fL~~l 151 (449)
...-.++.+.|+..|++++.|..+ +++|.+.| ++...+....... ..-..-......-|+..
T Consensus 176 eRSe~ELr~KL~kkG~~ee~IE~V----------------IerLke~gYLDDeRFAesyVr~-R~~kkGp~rIrqELrQK 238 (309)
T PRK14136 176 EYSRAELARKLAPYADESDSVEPL----------------LDALEREGWLSDARFAESLVHR-RASRVGSARIVSELKRH 238 (309)
T ss_pred cccHHHHHHHHHHcCCCHHHHHHH----------------HHHHHHcCCcCHHHHHHHHHHH-HhhchhHHHHHHHHHHc
Confidence 355667888888889988877765 45588877 4556666555433 11112234456778889
Q ss_pred CCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceeccccccchHHHHHHHHhcCChHHHH
Q 013135 152 GFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVL 231 (449)
Q Consensus 152 Gl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~ 231 (449)
|++.+.|..++.... +..+..-...+. + ++..+ ... .......+.||..-|++.+.|.
T Consensus 239 GId~eLIEqALeeie-------EDE~E~A~~L~e----------K---K~~~~-~~d-~kek~K~iRfL~rRGFS~D~I~ 296 (309)
T PRK14136 239 AVGDALVESVGAQLR-------ETEFERAQAVWR----------K---KFGAL-PQT-PAERAKQARFLAARGFSSATIV 296 (309)
T ss_pred CCCHHHHHHHHHhcc-------HhHHHHHHHHHH----------H---Hhccc-CcC-HHHHHHHHHHHHHCCCCHHHHH
Confidence 999999988876331 111111111111 1 11111 011 1123344788999999988888
Q ss_pred HHHHhCCc
Q 013135 232 KAIRAGCL 239 (449)
Q Consensus 232 ~~l~~~P~ 239 (449)
.+|..+-.
T Consensus 297 ~vLk~~~d 304 (309)
T PRK14136 297 KLLKVGDD 304 (309)
T ss_pred HHHHhchh
Confidence 88876543
No 20
>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=74.89 E-value=7.2 Score=26.92 Aligned_cols=42 Identities=29% Similarity=0.478 Sum_probs=30.7
Q ss_pred HHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCC
Q 013135 255 ILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPT 299 (449)
Q Consensus 255 ~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~ 299 (449)
.-+.+|++...+.+.+...| ..+++.-+...+.++++||.++
T Consensus 5 IA~~agvS~~TVSr~ln~~~---~vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 5 IAREAGVSKSTVSRVLNGPP---RVSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHTSSHHHHHHHHTTCS---SSTHHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHCCCCC
Confidence 34568999999999887765 3466666667777788998775
No 21
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=73.96 E-value=9.9 Score=28.65 Aligned_cols=23 Identities=22% Similarity=0.583 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhh
Q 013135 77 DSVLKLLRTHGLTRSQINNFVTK 99 (449)
Q Consensus 77 ~~v~~~L~~~G~~~~~i~~il~~ 99 (449)
+++++.|+++.+|+++|..++..
T Consensus 2 NPIia~LKehnvsd~qi~elFq~ 24 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQA 24 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHH
Confidence 46778888888888888877654
No 22
>PRK14135 recX recombination regulator RecX; Provisional
Probab=71.41 E-value=86 Score=30.01 Aligned_cols=167 Identities=16% Similarity=0.141 Sum_probs=79.5
Q ss_pred cCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcCC-ChHHHHHHHHhhhhhh-ccchhhHHHHHHHC
Q 013135 74 DKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLGI-TGANLAEMLNKEHRVL-ESDAYATVEFFRTN 151 (449)
Q Consensus 74 ~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG~-~~~~l~~~i~~~P~lL-~~~l~~~l~fL~~l 151 (449)
..-..+.+-|...|++++.|..+|.. |...|. +...++......-.-. .........-|...
T Consensus 72 ~s~~el~~kL~~kg~~~~~Ie~vl~~----------------l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~k 135 (263)
T PRK14135 72 RTEKEVRDYLKKHEISEEIISEVIDK----------------LKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQK 135 (263)
T ss_pred ccHHHHHHHHHHCCCCHHHHHHHHHH----------------HHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHc
Confidence 44467777888888888777776554 555552 3323322222110000 11233344555666
Q ss_pred CCChhhHhhHhhhCCce--------e---------ecCcccchhhH-HHHHHHcCCChHHHHHHHHhCCcceeccccccc
Q 013135 152 GFSDSQIKSITVKRPKF--------Y---------VYNLKKCMKPK-LEFFKSLGFAELQMAKFLSSQPYILERSLENHI 213 (449)
Q Consensus 152 Gl~~~~i~~il~~~P~l--------L---------~~~~e~~l~pk-l~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l 213 (449)
|++.+.|..++.....- + ..+ ......+ ..+|..-|++.+.|..++.... ...+ -
T Consensus 136 Gi~~~~Ie~~l~~l~~~~~~d~a~~~~~k~~~~~~~~~-~~~~k~Ki~~~L~rkGf~~~~I~~~l~~~~----~e~d--~ 208 (263)
T PRK14135 136 GIEDEIIEEALSEYTEEDQIEVAQKLAEKLLKKYQKLP-FKALKQKIIQSLLTKGFSYEVIKAALEELD----LEQD--E 208 (263)
T ss_pred CCCHHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHhCCCCHHHHHHHHHHcc----cCCC--h
Confidence 66666666665543110 0 000 0112223 3677777888777777766431 0000 0
Q ss_pred hHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhh
Q 013135 214 IPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 272 (449)
Q Consensus 214 ~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~ 272 (449)
..-.+-+.. .+.+...++. ..+..+.-.....||..-|++.+.|..++..
T Consensus 209 ~~e~e~l~~------~~~k~~~k~~---~~~~~k~k~K~~~~L~rrGF~~~~I~~~l~~ 258 (263)
T PRK14135 209 EEEQELLQK------ELEKAYRKYS---KYDGYELKQKLKQALYRKGFSYDDIDSFLRE 258 (263)
T ss_pred HHHHHHHHH------HHHHHHHHHh---cCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 000000000 0111122221 1122232345557899999999999888754
No 23
>PRK14137 recX recombination regulator RecX; Provisional
Probab=69.04 E-value=43 Score=30.82 Aligned_cols=144 Identities=13% Similarity=0.102 Sum_probs=80.6
Q ss_pred cCCCHHHHHHhhccc--cc--CCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcCC-ChHHHHH
Q 013135 54 CGFSLESAVSASEKL--RV--DTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLGI-TGANLAE 128 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~--~~--~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG~-~~~~l~~ 128 (449)
-+++++++..-.... .+ .-...-..+.+.|...|++++.|..+|. .|.+.|+ +...+..
T Consensus 31 ~~~~~~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~----------------rL~e~gyLDD~rfAe 94 (195)
T PRK14137 31 TPPTPDEAREALLAYAFRALAARAMTAAELRAKLERRSEDEALVTEVLE----------------RVQELGYQDDAQVAR 94 (195)
T ss_pred CCCCHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHH----------------HHHHcCCCCHHHHHH
Confidence 345555555433221 11 2235567888899999999988887654 5777774 5566665
Q ss_pred HHHhhhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceecc
Q 013135 129 MLNKEHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERS 208 (449)
Q Consensus 129 ~i~~~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s 208 (449)
..... =.......-+-|+..|++.+.|...+... +.+..+..-...+.. +++.+-. .
T Consensus 95 ~~~~~---k~~Gp~rI~~eL~qKGI~~~lI~~al~~~------d~ede~e~a~~l~~K-------------K~~~~~~-~ 151 (195)
T PRK14137 95 AENSR---RGVGALRVRQTLRRRGVEETLIEETLAAR------DPQEEQQEARNLLER-------------RWSSFAR-K 151 (195)
T ss_pred HHHHh---cCchHHHHHHHHHHcCCCHHHHHHHHHhc------CchhHHHHHHHHHHH-------------hccccCc-c
Confidence 43110 01123345677889999999998888643 211112221222221 1111110 0
Q ss_pred ccccchHHHHHHHHhcCChHHHHHHHHhC
Q 013135 209 LENHIIPCIEILRRVLDTDENVLKAIRAG 237 (449)
Q Consensus 209 ~~~~l~p~v~fL~~~g~~~~~v~~~l~~~ 237 (449)
...-...+.||..-|++.+.|..++...
T Consensus 152 -~~~k~K~~~~L~rRGFs~~~I~~al~~~ 179 (195)
T PRK14137 152 -RDPRASAYAFLARRGFSGAVIWPAIREV 179 (195)
T ss_pred -hhHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence 1112345678888899888887777653
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=65.49 E-value=9.3 Score=24.77 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 013135 320 KKLEAYMNFGLTKDEVYSAFRRQ 342 (449)
Q Consensus 320 ~k~~~l~~lG~s~~ev~~~v~~~ 342 (449)
.+++-|+.+||+.+++..++..+
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 45666777788888887776654
No 25
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=64.83 E-value=16 Score=29.17 Aligned_cols=25 Identities=16% Similarity=0.304 Sum_probs=12.8
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHHhh
Q 013135 75 KIDSVLKLLRTHGLTRSQINNFVTK 99 (449)
Q Consensus 75 ~~~~v~~~L~~~G~~~~~i~~il~~ 99 (449)
....++.+|.++|++.....++...
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3455566666666666666665554
No 26
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=64.56 E-value=27 Score=27.89 Aligned_cols=46 Identities=11% Similarity=0.184 Sum_probs=22.6
Q ss_pred ChhhHHHHHHHcCCChHHHHHHHHhhhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcc
Q 013135 108 TLEPNLKLFKSLGITGANLAEMLNKEHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLK 174 (449)
Q Consensus 108 ~l~~~l~~L~~lG~~~~~l~~~i~~~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e 174 (449)
.....+.+|...|++.....++...+. ++.-.+|..+|-.|..++.
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg---------------------~~ai~~l~~nPY~L~~~i~ 52 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYG---------------------DDAIEILKENPYRLIEDID 52 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH----------------------TTHHHHHHH-STCCCB-SS
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHh---------------------HHHHHHHHHChHHHHHHcc
Confidence 345556666667766666666554431 1333556667777666543
No 27
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.73 E-value=93 Score=28.56 Aligned_cols=64 Identities=17% Similarity=0.208 Sum_probs=36.4
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHH
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEML 130 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i 130 (449)
+||...+=+.+++.+..-+.-.+..-+..|..+| .+++...+... -.+.|..+ |+.++...+++
T Consensus 61 yGF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~--~~~l~~aI~~~-----------D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 61 FGFATTEELSLFETLIDVSGIGPKLGLAMLSAMN--AEALASAIISG-----------NAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred eCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCC--HHHHHHHHHhC-----------CHHHHHhCCCCCHHHHHHHH
Confidence 7888888888877654334444555556666544 55655555321 12344443 66666665554
No 28
>PRK14136 recX recombination regulator RecX; Provisional
Probab=62.65 E-value=1.6e+02 Score=29.01 Aligned_cols=130 Identities=13% Similarity=0.167 Sum_probs=74.0
Q ss_pred HHHHcCCChHHHHHHHHhCCcceeccccccchHHHHHHHHhc-CChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCC
Q 013135 183 FFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVL-DTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGV 261 (449)
Q Consensus 183 fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p~v~fL~~~g-~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv 261 (449)
||..---+..||.+-|.+. +++ ++.|...|++|++.| +++....+.+.+. +.-.... ...-.-|+.-||
T Consensus 171 lLSrReRSe~ELr~KL~kk----G~~-ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kkGp----~rIrqELrQKGI 240 (309)
T PRK14136 171 YLSRREYSRAELARKLAPY----ADE-SDSVEPLLDALEREGWLSDARFAESLVHR-RASRVGS----ARIVSELKRHAV 240 (309)
T ss_pred HhhcccccHHHHHHHHHHc----CCC-HHHHHHHHHHHHHcCCcCHHHHHHHHHHH-HhhchhH----HHHHHHHHHcCC
Confidence 3333455777777666654 333 336788899999987 5666666666643 1111111 112245788999
Q ss_pred ChHHHHHHHhhcCccceecchHHHHHHHHHH-hcCCCCChhHHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHHHHh
Q 013135 262 PKSLVVKLMLIQPRTLLQSTARLNKIIDEVK-KLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYSAFR 340 (449)
Q Consensus 262 ~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~-~lG~~~~~~~~~~a~~~i~~~s~~~l~~k~~~l~~lG~s~~ev~~~v~ 340 (449)
+.+.|...+... ..+.++.....+. +++-.+. ......+.+.||..-||+.+.|..++.
T Consensus 241 d~eLIEqALeei------eEDE~E~A~~L~eKK~~~~~~--------------d~kek~K~iRfL~rRGFS~D~I~~vLk 300 (309)
T PRK14136 241 GDALVESVGAQL------RETEFERAQAVWRKKFGALPQ--------------TPAERAKQARFLAARGFSSATIVKLLK 300 (309)
T ss_pred CHHHHHHHHHhc------cHhHHHHHHHHHHHHhcccCc--------------CHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 999888776532 1122222222222 3321111 122334446888899999999998876
Q ss_pred cC
Q 013135 341 RQ 342 (449)
Q Consensus 341 ~~ 342 (449)
.+
T Consensus 301 ~~ 302 (309)
T PRK14136 301 VG 302 (309)
T ss_pred hc
Confidence 53
No 29
>PHA02591 hypothetical protein; Provisional
Probab=61.18 E-value=26 Score=26.99 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=29.9
Q ss_pred cCCCHHHHHHhhc----ccccCCCcCHHHHHHHHHhCCCCHHHHHHH
Q 013135 54 CGFSLESAVSASE----KLRVDTTDKIDSVLKLLRTHGLTRSQINNF 96 (449)
Q Consensus 54 ~Gls~~~~~~~~~----~~~~~s~~~~~~v~~~L~~~G~~~~~i~~i 96 (449)
|-++.....++.. +.-..+.+...++..-|.+.|++.++|+..
T Consensus 22 ~~~~~~~m~k~vqv~~~ryfi~~~dd~~~vA~eL~eqGlSqeqIA~~ 68 (83)
T PHA02591 22 CYIGEKKMQKVVQVGQTRYFVESEDDLISVTHELARKGFTVEKIASL 68 (83)
T ss_pred EEhhhHhHHHhheeCCEEEEEeccchHHHHHHHHHHcCCCHHHHHHH
Confidence 3344455555532 122467788889999999999999999885
No 30
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=60.73 E-value=13 Score=23.85 Aligned_cols=23 Identities=22% Similarity=0.618 Sum_probs=15.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 013135 320 KKLEAYMNFGLTKDEVYSAFRRQ 342 (449)
Q Consensus 320 ~k~~~l~~lG~s~~ev~~~v~~~ 342 (449)
++++-+.++|++++++..++.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45566667777777777666544
No 31
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.44 E-value=1.1e+02 Score=27.92 Aligned_cols=65 Identities=12% Similarity=0.139 Sum_probs=36.6
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHH
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLN 131 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~ 131 (449)
+||...+=+.+++.+..-+.-.+..-+..|.. ++.+++..++... -...|..+ |+.++...+++.
T Consensus 61 yGF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~--~~~~el~~aI~~~-----------D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 61 YGFLDKDEQKMFEMLLKVNGIGANTAMAVCSS--LDVNSFYKALSLG-----------DESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred eCCCCHHHHHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhC-----------CHHHHhhCCCCCHHHHHHHHH
Confidence 78888887777765543333344444445544 4666777766652 23344443 666665555543
No 32
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=58.12 E-value=15 Score=23.67 Aligned_cols=23 Identities=30% Similarity=0.625 Sum_probs=15.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Q 013135 320 KKLEAYMNFGLTKDEVYSAFRRQ 342 (449)
Q Consensus 320 ~k~~~l~~lG~s~~ev~~~v~~~ 342 (449)
++++-|.++||+.+++..++..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 45566667777777777666543
No 33
>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=56.14 E-value=72 Score=35.61 Aligned_cols=111 Identities=14% Similarity=0.219 Sum_probs=66.2
Q ss_pred CCcCHHHHHHHHHh---CCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHHhhhhhhccchhhHHHH
Q 013135 72 TTDKIDSVLKLLRT---HGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLNKEHRVLESDAYATVEF 147 (449)
Q Consensus 72 s~~~~~~v~~~L~~---~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~~~P~lL~~~l~~~l~f 147 (449)
.|...+.++.||.+ -|+.+..-.+++.+...= .-+.+....+-|.++ |++++.+..+...+... ......+.|
T Consensus 73 ~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~-~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~~--~~~~~~~~~ 149 (720)
T TIGR01448 73 APTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEA-AFDVLDDDPEKLLEVPGISKANLEKFVSQWSQQ--GDERRLLAG 149 (720)
T ss_pred CCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHh-HHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHHh--HHHHHHHHH
Confidence 35677888999975 467777777777664321 011111112345454 77777766666654221 125566777
Q ss_pred HHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceecccc
Q 013135 148 FRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLE 210 (449)
Q Consensus 148 L~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~ 210 (449)
|.++|++.....++...+ .++...+|..||+.|..++.
T Consensus 150 L~~~gi~~~~a~ki~~~y-------------------------g~~~~~~i~~nPY~L~~~i~ 187 (720)
T TIGR01448 150 LQGLGIGIKLAQRIYKFY-------------------------QADTLDRVEKDPYLLAEDVK 187 (720)
T ss_pred HHHcCCCHHHHHHHHHHH-------------------------hHHHHHHHHhCchhhhhhcC
Confidence 777777776666655432 13556778888887776544
No 34
>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=55.28 E-value=13 Score=25.66 Aligned_cols=42 Identities=12% Similarity=0.184 Sum_probs=28.2
Q ss_pred HHHHHhcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCC
Q 013135 48 SDLQKSCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLT 89 (449)
Q Consensus 48 ~~L~~~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~ 89 (449)
.-+-+.+|+|.+.+.++...-..-+++.-+.+.+..+++|+.
T Consensus 3 ~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 3 KDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYR 44 (46)
T ss_dssp HHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-
T ss_pred HHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCC
Confidence 344567888888888887654444556667777777777764
No 35
>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=54.71 E-value=19 Score=24.81 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=18.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhh
Q 013135 76 IDSVLKLLRTHGLTRSQINNFVTK 99 (449)
Q Consensus 76 ~~~v~~~L~~~G~~~~~i~~il~~ 99 (449)
.+.+++.|.++||++.++.+++.+
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHH
Confidence 356778888888888888887766
No 36
>PF11181 YflT: Heat induced stress protein YflT
Probab=53.89 E-value=49 Score=26.83 Aligned_cols=76 Identities=18% Similarity=0.238 Sum_probs=44.4
Q ss_pred hHHHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHH--HhcCCCCChhHHHHHHHHHHhcCHHHHHHHHHHHH
Q 013135 249 LEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEV--KKLGFDPTNLLFVLAIRSMAVMSKALWEKKLEAYM 326 (449)
Q Consensus 249 l~~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l--~~lG~~~~~~~~~~a~~~i~~~s~~~l~~k~~~l~ 326 (449)
+...|+-|+.-|+..++| .++..+.++....-+.- ...|.+. ..|...+..+.....+.++.++ .
T Consensus 12 ~~~~I~~L~~~Gy~~ddI--------~Vva~d~~~~~~l~~~t~~~~~~~~~--~~~~d~~~~~f~~~~d~~~~~l---~ 78 (103)
T PF11181_consen 12 ALSAIEELKAQGYSEDDI--------YVVAKDKDRTERLADQTDTNTVGASE--ESFWDKIKNFFTSGGDELRSKL---E 78 (103)
T ss_pred HHHHHHHHHHcCCCcccE--------EEEEcCchHHHHHHHhcCCceecccc--ccHHHHHHHhccCCcHHHHHHH---H
Confidence 777888888899988885 24444443333222221 1223333 3444555555554566666555 5
Q ss_pred HcCCCHHHHHH
Q 013135 327 NFGLTKDEVYS 337 (449)
Q Consensus 327 ~lG~s~~ev~~ 337 (449)
++|++.+++..
T Consensus 79 ~lGl~~~ea~~ 89 (103)
T PF11181_consen 79 SLGLSEDEAER 89 (103)
T ss_pred HcCCCHHHHHH
Confidence 89999988763
No 37
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=53.21 E-value=22 Score=34.28 Aligned_cols=65 Identities=17% Similarity=0.227 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHH-HcCCCH-HHHHHHHhcCCcccccChHHHHhHHHHHHHhcCCChH-HHhhCCceec
Q 013135 315 KALWEKKLEAYM-NFGLTK-DEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPL-IISKHPYLLL 379 (449)
Q Consensus 315 ~~~l~~k~~~l~-~lG~s~-~ev~~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~~~-~i~~~P~~L~ 379 (449)
.-.+++++.|.. ..|+=+ -.|.+=+...|.++.++.++++.+.+-|.+-+|++++ +.-+||.=|+
T Consensus 70 ~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~i~~r~~ELl~lvgL~p~~~~~RyP~eLS 137 (309)
T COG1125 70 PVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKERIKKRADELLDLVGLDPSEYADRYPHELS 137 (309)
T ss_pred HHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHHHHHHHHHHHHHhCCCHHHHhhcCchhcC
Confidence 334455555443 444322 2334444467888888888888888888888888774 5566666554
No 38
>PRK14135 recX recombination regulator RecX; Provisional
Probab=52.90 E-value=96 Score=29.69 Aligned_cols=23 Identities=26% Similarity=0.278 Sum_probs=19.5
Q ss_pred hHHHHHHHCCCChhhHhhHhhhC
Q 013135 143 ATVEFFRTNGFSDSQIKSITVKR 165 (449)
Q Consensus 143 ~~l~fL~~lGl~~~~i~~il~~~ 165 (449)
....+|..-|++.+.|..++...
T Consensus 180 Ki~~~L~rkGf~~~~I~~~l~~~ 202 (263)
T PRK14135 180 KIIQSLLTKGFSYEVIKAALEEL 202 (263)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHc
Confidence 35788999999999999998764
No 39
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=51.89 E-value=25 Score=23.48 Aligned_cols=31 Identities=13% Similarity=0.210 Sum_probs=23.2
Q ss_pred HHHHHHHHHHH-HcCCCHHHHHHHHhcCCccc
Q 013135 316 ALWEKKLEAYM-NFGLTKDEVYSAFRRQPMFM 346 (449)
Q Consensus 316 ~~l~~k~~~l~-~lG~s~~ev~~~v~~~P~iL 346 (449)
+++-.....|. ++|++..+..++|..+|.+-
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~Cq 37 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKCQ 37 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCHH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHHh
Confidence 45566677888 89999999999999999863
No 40
>PRK14134 recX recombination regulator RecX; Provisional
Probab=51.82 E-value=2.4e+02 Score=27.53 Aligned_cols=76 Identities=11% Similarity=0.110 Sum_probs=50.1
Q ss_pred CcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcC-CChHHHHHHHHhhhhhhccchhhHHHHHHHC
Q 013135 73 TDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLG-ITGANLAEMLNKEHRVLESDAYATVEFFRTN 151 (449)
Q Consensus 73 ~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG-~~~~~l~~~i~~~P~lL~~~l~~~l~fL~~l 151 (449)
...-..+.+.|...|++++.|..+ +++|.+.| ++...++....+.-. -.......-.-|+..
T Consensus 75 ~rSe~Elr~KL~~k~~~~~~Ie~v----------------I~~L~e~~yldD~ryA~~yv~~~~-~~~G~~~I~~eL~qK 137 (283)
T PRK14134 75 YKTEKQIKEKLYLKEYDEDAVNRV----------------IRFLKEYNFIDDDKYCDMYIREKI-NSYGRNKIKYTLLNK 137 (283)
T ss_pred cchHHHHHHHHHhCCCCHHHHHHH----------------HHHHHHCCCCCHHHHHHHHHHHHH-HhhhHHHHHHHHHHC
Confidence 466678888888889998888775 44577777 455566555443211 012234455677788
Q ss_pred CCChhhHhhHhhhC
Q 013135 152 GFSDSQIKSITVKR 165 (449)
Q Consensus 152 Gl~~~~i~~il~~~ 165 (449)
|++.+.|..++...
T Consensus 138 GI~~~iIe~al~~~ 151 (283)
T PRK14134 138 GIKENIIIEKINNI 151 (283)
T ss_pred CCCHHHHHHHHHhC
Confidence 88888888777654
No 41
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=50.85 E-value=30 Score=25.86 Aligned_cols=49 Identities=12% Similarity=0.199 Sum_probs=35.4
Q ss_pred HHHHHHhcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHH
Q 013135 47 VSDLQKSCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINN 95 (449)
Q Consensus 47 v~~L~~~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~ 95 (449)
...+-+.+|+|.+.+.++.+.-..-+++..+.+.+.++++|........
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~~~~~ 51 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNRVAR 51 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCHHHH
Confidence 4456678899999998887644333566778888888888887665544
No 42
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=50.71 E-value=36 Score=25.43 Aligned_cols=42 Identities=24% Similarity=0.367 Sum_probs=29.9
Q ss_pred HHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCCh
Q 013135 256 LVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTN 300 (449)
Q Consensus 256 L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~ 300 (449)
-+.+|++...|.+++...+.+ +++.-+...+.++++|+.++.
T Consensus 7 A~~~gvS~~TVSr~ln~~~~v---~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 7 ARLAGVSKATVSRVLNGNGRV---SEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred HHHHCCCHHHHHHHHCCCCCC---CHHHHHHHHHHHHHhCCCCCH
Confidence 345788888888887766654 556666667777888887663
No 43
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=50.60 E-value=64 Score=23.89 Aligned_cols=25 Identities=32% Similarity=0.380 Sum_probs=19.6
Q ss_pred CchHHHHHHhcCCCHHHHHHhhccc
Q 013135 44 PLTVSDLQKSCGFSLESAVSASEKL 68 (449)
Q Consensus 44 ~~~v~~L~~~~Gls~~~~~~~~~~~ 68 (449)
+.++..+.+.+|++...+.++.+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3578888889999999888876643
No 44
>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=50.11 E-value=92 Score=24.41 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=16.3
Q ss_pred HHHHhCCCCHHHHHHHHhhCC
Q 013135 81 KLLRTHGLTRSQINNFVTKRP 101 (449)
Q Consensus 81 ~~L~~~G~~~~~i~~il~~~P 101 (449)
.+.+.+|++..+|..+-..||
T Consensus 18 ~Lar~Lgls~~~I~~i~~~~p 38 (83)
T cd08319 18 QVLLDLGLSQTDIYRCKENHP 38 (83)
T ss_pred HHHHHcCCCHHHHHHHHHhCC
Confidence 345788888888888877777
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.39 E-value=1.8e+02 Score=26.54 Aligned_cols=64 Identities=16% Similarity=0.218 Sum_probs=35.7
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHH
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEML 130 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i 130 (449)
+||...+=+.+++.+..-+.-.+..-+..|.. ++.+++..++... -.+.|..+ |+.++...+++
T Consensus 61 yGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~-----------D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 61 YGFSNERKKELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQ-----------DVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred eCCCCHHHHHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhC-----------CHHHHhhCCCCCHHHHHHHH
Confidence 78888877777765543333444444555544 3556777666552 13344443 56555555554
No 46
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=46.68 E-value=1e+02 Score=30.58 Aligned_cols=99 Identities=16% Similarity=0.260 Sum_probs=53.9
Q ss_pred hHHHHHHHcCCChHHHHHHHHhCCcceeccccccchHHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHh
Q 013135 179 PKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIPCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVN 258 (449)
Q Consensus 179 pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~ 258 (449)
.-++||++.- .-.+++.+|..||.+|. ..|+.+|-....+.+.|..|+.-|..=+..-+.. .+
T Consensus 214 ~~l~fLr~~~-qf~~lR~~iqqNP~ll~-----------~~Lqqlg~~nP~L~q~Iq~nqe~Fl~mlnep~~~-----~~ 276 (340)
T KOG0011|consen 214 DPLEFLRNQP-QFQQLRQMIQQNPELLH-----------PLLQQLGKQNPQLLQLIQENQEAFLQLLNEPVEG-----GD 276 (340)
T ss_pred CchhhhhccH-HHHHHHHHHhhCHHHHH-----------HHHHHHhhhCHHHHHHHHHHHHHHHHHhhccccc-----cc
Confidence 4477777531 12467888999988764 2466778777888888887765432111100110 01
Q ss_pred CCCChHHHHHHHhhcC-ccceecchHHHHHHHHHHhcCCCCC
Q 013135 259 HGVPKSLVVKLMLIQP-RTLLQSTARLNKIIDEVKKLGFDPT 299 (449)
Q Consensus 259 lGv~~~~i~~li~~~P-~lL~~s~~~l~~~v~~l~~lG~~~~ 299 (449)
-|... .+=..-| ..+.+.++ =++.+++|+.|||++.
T Consensus 277 ~~~~~----~~~~~~~~~~I~vtpe-e~eAIeRL~alGF~ra 313 (340)
T KOG0011|consen 277 GGGTG----APAAEGPGHQIQVTPE-EKEAIERLEALGFPRA 313 (340)
T ss_pred ccccc----cccccCCcceEecCHH-HHHHHHHHHHhCCcHH
Confidence 11111 1111223 23444443 3577889999999764
No 47
>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=43.97 E-value=49 Score=22.63 Aligned_cols=41 Identities=20% Similarity=0.388 Sum_probs=27.3
Q ss_pred HhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCCh
Q 013135 257 VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTN 300 (449)
Q Consensus 257 ~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~ 300 (449)
+.+|++...|.+++...+ ..+++......+.+.++|+.++.
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 457888888888777655 23445555566666777877653
No 48
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=43.25 E-value=1.8e+02 Score=31.00 Aligned_cols=53 Identities=13% Similarity=0.081 Sum_probs=23.1
Q ss_pred hHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHH
Q 013135 143 ATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLS 199 (449)
Q Consensus 143 ~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~ 199 (449)
..+..+.+--+.+..+..++. .|..+.+.+....++-+.-..++.+++.+++.
T Consensus 527 ~~~~~~~~g~iake~iee~l~----~l~~~p~~~~~e~~~~~gL~~ls~eEve~iI~ 579 (631)
T COG2511 527 ELLRLVSEGKIAKEAIEEILK----ALAENPGKDAAEIAEKLGLKELSEEEVEKIID 579 (631)
T ss_pred HHHHHHhcccchHHHHHHHHH----HHHhCCCCCHHHHHHHhccccCCHHHHHHHHH
Confidence 334444444555555544433 12222223333333322223456777776654
No 49
>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=41.54 E-value=47 Score=22.82 Aligned_cols=25 Identities=32% Similarity=0.466 Sum_probs=17.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHhcC
Q 013135 318 WEKKLEAYMNFGLTKDEVYSAFRRQ 342 (449)
Q Consensus 318 l~~k~~~l~~lG~s~~ev~~~v~~~ 342 (449)
+.+-++-|..+||+..|+.+++.+-
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~ 27 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKL 27 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3445566778888888888777654
No 50
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.21 E-value=2.5e+02 Score=25.74 Aligned_cols=131 Identities=17% Similarity=0.202 Sum_probs=68.9
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHHh
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLNK 132 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~~ 132 (449)
+||...+=+.+++.+..-+.-.+..-+..|.. ++.+++..++... -...|..+ |+.+....+++..
T Consensus 61 yGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~--~~~~el~~aI~~~-----------D~~~L~kvpGIGkKtAerIilE 127 (195)
T PRK14604 61 YGFSTPAQRQLFELLIGVSGVGPKAALNLLSS--GTPDELQLAIAGG-----------DVARLARVPGIGKKTAERIVLE 127 (195)
T ss_pred eCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhC-----------CHHHHhhCCCCCHHHHHHHHHH
Confidence 88888888888776644444445555566653 4667777776652 23445443 6666665555432
Q ss_pred hhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhCCcceecccccc
Q 013135 133 EHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQPYILERSLENH 212 (449)
Q Consensus 133 ~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~ 212 (449)
++.++.. .++.... .+ ...+....-++-|.++|+++.++.+++.+--.-=..++++-
T Consensus 128 --------Lk~K~~~---~~~~~~~-------~~-----~~~~~~~e~~~aL~~LGy~~~ea~~ai~~i~~~~~~~~~~~ 184 (195)
T PRK14604 128 --------LKGKIDV---RQLSGST-------SP-----AVSALDRELSEILISLGYSAAEAAAAIAALPSDAPPDLEER 184 (195)
T ss_pred --------HHHHhcc---ccccccc-------cc-----cccccHHHHHHHHHHcCCCHHHHHHHHHHHhhcCCCCHHHH
Confidence 2222210 0111000 00 01111345667777888888888777765410002355555
Q ss_pred chHHHHHH
Q 013135 213 IIPCIEIL 220 (449)
Q Consensus 213 l~p~v~fL 220 (449)
++..+.+|
T Consensus 185 ir~aLk~l 192 (195)
T PRK14604 185 LRLALRYF 192 (195)
T ss_pred HHHHHHHh
Confidence 55555554
No 51
>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=39.69 E-value=1.4e+02 Score=24.66 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=12.3
Q ss_pred hHHHHHHHCCCChhhHhhHhh
Q 013135 143 ATVEFFRTNGFSDSQIKSITV 163 (449)
Q Consensus 143 ~~l~fL~~lGl~~~~i~~il~ 163 (449)
..++||..-|++.+.|.+++.
T Consensus 97 K~~~~L~rrGF~~~~i~~vi~ 117 (121)
T PF02631_consen 97 KLIRFLMRRGFSYDVIRRVIS 117 (121)
T ss_dssp HHHHHHHHTT--HHHHHHHCH
T ss_pred HHHHHHHHCCCCHHHHHHHHh
Confidence 456666777777776666654
No 52
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.99 E-value=2.8e+02 Score=25.55 Aligned_cols=108 Identities=13% Similarity=0.108 Sum_probs=61.4
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHHh
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLNK 132 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~~ 132 (449)
+||...+=+.++..+..-+.-.+..-+..|..+ +.+++..+|... -.+.|..+ |+.++...+++..
T Consensus 60 YGF~t~~Er~lF~~LisVsGIGPK~ALaILs~~--~~~el~~aI~~~-----------D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 60 FGFLNSSEREVFEELIGVDGIGPRAALRVLSGI--KYNEFRDAIDRE-----------DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred eCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCC--CHHHHHHHHHhC-----------CHHHHhhCCCCCHHHHHHHHHH
Confidence 788888888887766444445555556666553 566777776652 23445443 6666666665532
Q ss_pred hhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhC
Q 013135 133 EHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 133 ~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
+..++... . .+. .....+..-++-|.++|+++.++.+++...
T Consensus 127 --------LkdKl~~~-----~----------~~~----~~~~~~~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 127 --------LRGKLVKN-----D----------ELE----SSLFKFKELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred --------HHHhhccc-----c----------ccc----cCcccHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 11111100 0 000 001224566788888888888888877754
No 53
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=38.58 E-value=40 Score=24.36 Aligned_cols=29 Identities=21% Similarity=0.235 Sum_probs=24.2
Q ss_pred CCCCCchHHHHHHhcCCCHHHHHHhhccc
Q 013135 40 TCTQPLTVSDLQKSCGFSLESAVSASEKL 68 (449)
Q Consensus 40 ~~~~~~~v~~L~~~~Gls~~~~~~~~~~~ 68 (449)
.-.++..|.|+.+.+|+|++++..+.+.+
T Consensus 16 ~~~e~~ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 16 DLSEPYEVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 44677789999999999999999887654
No 54
>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=37.43 E-value=84 Score=35.08 Aligned_cols=85 Identities=16% Similarity=0.151 Sum_probs=52.9
Q ss_pred hHHHHHH--hcCCCHHHHHHhhcccccCCCcCHHHHHHHHHh-CCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHcCCC
Q 013135 46 TVSDLQK--SCGFSLESAVSASEKLRVDTTDKIDSVLKLLRT-HGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSLGIT 122 (449)
Q Consensus 46 ~v~~L~~--~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~-~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~lG~~ 122 (449)
-+.||.+ =-|+-+..|.++...+.-+..+.++.--+-|.+ -|+++....++...... .......+.||.+.|++
T Consensus 80 i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~---~~~~~~~~~~L~~~gi~ 156 (720)
T TIGR01448 80 IVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWSQ---QGDERRLLAGLQGLGIG 156 (720)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHHH---hHHHHHHHHHHHHcCCC
Confidence 3478843 257888889888766532221222222233444 38888887777765421 22366778899999999
Q ss_pred hHHHHHHHHhh
Q 013135 123 GANLAEMLNKE 133 (449)
Q Consensus 123 ~~~l~~~i~~~ 133 (449)
.+...++...|
T Consensus 157 ~~~a~ki~~~y 167 (720)
T TIGR01448 157 IKLAQRIYKFY 167 (720)
T ss_pred HHHHHHHHHHH
Confidence 88877776644
No 55
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.34 E-value=2e+02 Score=26.18 Aligned_cols=44 Identities=14% Similarity=0.127 Sum_probs=29.8
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhh
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTK 99 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~ 99 (449)
+||...+=+.+++.+..-+.-.+..-+..|..+ +.+++..++..
T Consensus 61 yGF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~--~~~~l~~aI~~ 104 (186)
T PRK14600 61 YGFLNREEQDCLRMLVKVSGVNYKTAMSILSKL--TPEQLFSAIVN 104 (186)
T ss_pred eCCCCHHHHHHHHHHhCcCCcCHHHHHHHHccC--CHHHHHHHHHc
Confidence 899888888888766544445555556666654 56677777665
No 56
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=35.33 E-value=2e+02 Score=21.86 Aligned_cols=48 Identities=27% Similarity=0.415 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHH
Q 013135 215 PCIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLM 270 (449)
Q Consensus 215 p~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li 270 (449)
|-+..|++..++++.+..+... |+.++ -.......++|++++.+..+.
T Consensus 3 PIia~LKehnvsd~qi~elFq~----lT~NP----l~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQA----LTQNP----LAAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHH----HhhCH----HHHHHHHHHcCCCHHHHHHHH
Confidence 5666777777777766665543 12222 123345566777777665543
No 57
>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=35.07 E-value=61 Score=22.15 Aligned_cols=42 Identities=12% Similarity=0.145 Sum_probs=22.4
Q ss_pred HhcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHH
Q 013135 52 KSCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQI 93 (449)
Q Consensus 52 ~~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i 93 (449)
+.+|++.+.+.++.+.-..-++.....+.+..+.+|+....+
T Consensus 5 ~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~~~ 46 (52)
T cd01392 5 RAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAA 46 (52)
T ss_pred HHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCHH
Confidence 456777776666654322223344555555666666655443
No 58
>PHA01351 putative minor structural protein
Probab=34.85 E-value=6.7e+02 Score=27.81 Aligned_cols=193 Identities=14% Similarity=0.163 Sum_probs=110.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhCCCC-CCCC--------------ChhhHHHHHHHcCCChHHHHHHHHhh---hhhh
Q 013135 76 IDSVLKLLRTHGLTRSQINNFVTKRPSG-DLGD--------------TLEPNLKLFKSLGITGANLAEMLNKE---HRVL 137 (449)
Q Consensus 76 ~~~v~~~L~~~G~~~~~i~~il~~~P~l-~~~~--------------~l~~~l~~L~~lG~~~~~l~~~i~~~---P~lL 137 (449)
.+..-.-|..+|.+++-+.+++.-+-.. ..+. +=+....-|+.||++++-...++..+ |.+-
T Consensus 595 ~qq~ksElk~LGidKe~i~klin~Y~ql~qt~~eIkYIqe~LK~f~IspkeAitELKKL~ISdaLAn~IV~eYf~iP~l~ 674 (1070)
T PHA01351 595 LDEIKKQFKAIGIIKEYEDAFINFYNQELQISAFLTILKSQLRQFQIDPKEAETELKKLNINEYLANQIIQEEYNINIAK 674 (1070)
T ss_pred HHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHcCchHHHHHHHHHHHhcchHHH
Confidence 3445566778888888777776655443 1111 11233456778888888777777777 4432
Q ss_pred c-------------cchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHH-H---HHHcCC--ChHHHHHHH
Q 013135 138 E-------------SDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLE-F---FKSLGF--AELQMAKFL 198 (449)
Q Consensus 138 ~-------------~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~-f---L~~lG~--s~~~i~~il 198 (449)
. .+.+....-|+.+|+++.++.-++..+=. .-+.||+. + +.+.|. +.+++.+.+
T Consensus 675 ~q~TViEnIikgvpint~~~~~ELKKL~IpdSqInil~t~yy~-------~~~~~kls~~~~sl~~~g~l~~~s~i~e~~ 747 (1070)
T PHA01351 675 LQLSVLETIAKTLYYDQQQLSGELKKIHKDKTALELYITKFYY-------EYIYPKISNYHLQLARHGILSDISKLPKEV 747 (1070)
T ss_pred HHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHhcCchhhHHHhhHHH
Confidence 1 24567788999999999999988876643 22455552 2 224565 334555555
Q ss_pred HhC---Ccceeccc-------cc-----cchH--HHHHHHHhcCChHHHHHHHHh-C-Ccccccchhhhh----------
Q 013135 199 SSQ---PYILERSL-------EN-----HIIP--CIEILRRVLDTDENVLKAIRA-G-CLVLEYDIEKVL---------- 249 (449)
Q Consensus 199 ~~~---P~iL~~s~-------~~-----~l~p--~v~fL~~~g~~~~~v~~~l~~-~-P~iL~~s~e~~l---------- 249 (449)
..+ |.+..+-. ++ .+.| .+.-|+.+|+++ ++++++.. + |.+. |+...+
T Consensus 748 ~~y~~~~a~~~y~~~~ei~yi~~~lkdl~i~~k~a~~el~kl~~s~-~i~~~iv~~~~p~~~--s~~t~~q~iieg~ly~ 824 (1070)
T PHA01351 748 NDYEYKPAVLTYQTTLEIEYIKESLKDLEIKPKTAINELEKLGMQK-DIAQLIVNTYIPTFY--SPHTIIQNIIEGQLYK 824 (1070)
T ss_pred HhccchhHHHhhhHHHHHHHHHHHHhhcccCchhHHHHHHHcCchH-HHHHHHHhhcCCccc--cHHHHHHHHhhhhhee
Confidence 544 33333210 00 1222 345677778864 45555543 2 4433 222211
Q ss_pred --------HHHHHHHHhCCCChHHHHHHHhhcCccce
Q 013135 250 --------EPNIAILVNHGVPKSLVVKLMLIQPRTLL 278 (449)
Q Consensus 250 --------~~~v~~L~~lGv~~~~i~~li~~~P~lL~ 278 (449)
.....-|+.+|++.++|..++-.+-.-+.
T Consensus 825 i~kvpv~~~~~~~elkkl~ipdsqin~lidq~~s~~~ 861 (1070)
T PHA01351 825 IGKVPINLGNAESELRKLGIPDSQIKALLDQYESTFG 861 (1070)
T ss_pred ccccccchhhhHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 12334577888888888877766555444
No 59
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=33.58 E-value=27 Score=29.35 Aligned_cols=41 Identities=22% Similarity=0.397 Sum_probs=19.7
Q ss_pred CChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHH
Q 013135 153 FSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFL 198 (449)
Q Consensus 153 l~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il 198 (449)
++.+++...+..+|.++...+- +.++- ..+|++++++..++
T Consensus 75 ~~~~~~~~~i~~~~~LikRPiv--v~~~~---~~iG~~~e~~~~~l 115 (117)
T COG1393 75 LSDEELIEALLENPSLIKRPIV--VDNKK---LRVGFNEEEIRAFL 115 (117)
T ss_pred cChHHHHHHHHhChhhccCCeE--EeCCc---eEecCCHHHHHHHh
Confidence 3445555666666655444431 11111 23566666665544
No 60
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=33.53 E-value=74 Score=25.98 Aligned_cols=20 Identities=15% Similarity=0.502 Sum_probs=10.1
Q ss_pred CChHHHHHHHHhCCcceecc
Q 013135 189 FAELQMAKFLSSQPYILERS 208 (449)
Q Consensus 189 ~s~~~i~~il~~~P~iL~~s 208 (449)
++.+++..++..+|.++.+.
T Consensus 71 ~s~~e~i~~l~~~p~LikRP 90 (110)
T PF03960_consen 71 LSDEELIELLLENPKLIKRP 90 (110)
T ss_dssp SBHHHHHHHHHHSGGGB-SS
T ss_pred hhhHHHHHHHHhChhheeCC
Confidence 45555555555555555544
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.01 E-value=1.1e+02 Score=28.02 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=15.0
Q ss_pred hhhHHHHHHHcCCChHHHHHHHHhC
Q 013135 177 MKPKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 177 l~pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
+...+.+|.++|+++.++.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4455566666666666666665544
No 62
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=32.73 E-value=1.9e+02 Score=27.65 Aligned_cols=88 Identities=17% Similarity=0.107 Sum_probs=50.4
Q ss_pred HHHHHHcCCCHHHHHHHHhcCCcccccChHHHHhHHHHHHHhcCCChHHHhhCCceeccCCCCcchhH-HHHHHHHHHCC
Q 013135 322 LEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPR-CSVLQLLMSNK 400 (449)
Q Consensus 322 ~~~l~~lG~s~~ev~~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR-~~~l~~L~~~G 400 (449)
++.|+++|+|..|+. .+-.|+..-..+..+|.+.-. -=+|| |.|++-|.+||
T Consensus 6 ~~~L~~lGlt~yEa~-------------------vY~aLl~~g~~tA~eis~~sg--------vP~~kvY~vl~sLe~kG 58 (247)
T COG1378 6 EENLQKLGLTEYEAK-------------------VYLALLCLGEATAKEISEASG--------VPRPKVYDVLRSLEKKG 58 (247)
T ss_pred HHHHHHcCCCHHHHH-------------------HHHHHHHhCCccHHHHHHHcC--------CCchhHHHHHHHHHHCC
Confidence 467789999999988 566677654556677765311 11233 67888889999
Q ss_pred CCCCC-cchhhhccccHHHHHHHHhhcCCCchhHHHH
Q 013135 401 VITED-FSLTYMFKMTEKQFIERIVKKYEHKVPKVVK 436 (449)
Q Consensus 401 l~~~~-~~l~~~l~~se~~F~~~~v~~~~~~~p~l~~ 436 (449)
++... .+....-..+-+...++.-....+...++.+
T Consensus 59 ~v~~~~g~P~~y~av~p~~~i~~~~~~~~~~~~~~~~ 95 (247)
T COG1378 59 LVEVIEGRPKKYRAVPPEELIERIKEELQELLRELES 95 (247)
T ss_pred CEEeeCCCCceEEeCCHHHHHHHHHHHHHHHHHHHHH
Confidence 97531 1222222223333555554444443444333
No 63
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=32.42 E-value=40 Score=28.67 Aligned_cols=66 Identities=18% Similarity=0.125 Sum_probs=43.6
Q ss_pred HhCCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCChh
Q 013135 235 RAGCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNL 301 (449)
Q Consensus 235 ~~~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~~ 301 (449)
+..|..+..+.+. +++-+--+-.-|+++++|.-+++..-.+=..+.-.=+..+.+++.-|+-++-.
T Consensus 20 r~~PtWlK~~~dd-vkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl~PeiP 85 (151)
T KOG0400|consen 20 RSVPTWLKLTADD-VKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGLAPEIP 85 (151)
T ss_pred cCCcHHHhcCHHH-HHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCCCCCCc
Confidence 4568888888887 88888778888999998876655433332222111234556678888887753
No 64
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.51 E-value=3.9e+02 Score=24.58 Aligned_cols=117 Identities=16% Similarity=0.095 Sum_probs=63.1
Q ss_pred hcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHH
Q 013135 53 SCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLN 131 (449)
Q Consensus 53 ~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~ 131 (449)
=+||...+=+.+++.+..-+.-.+..-+..|.. ++.+++..+|... -...|..+ |+.++...+++.
T Consensus 59 LyGF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~--~~~~~l~~aI~~~-----------D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 59 LYGFPDEDSLELFELLLGVSGVGPKLALALLSA--LPPALLARALLEG-----------DARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred eeCcCCHHHHHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhC-----------CHHHHhhCCCCCHHHHHHHHH
Confidence 388888888888776543344445555556654 4566777776652 23445443 666666666654
Q ss_pred hhhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhC
Q 013135 132 KEHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 132 ~~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
. ++.++.-+. ...... ...+. ........-++-|.++|+++.++.+++.+-
T Consensus 126 E--------LkdK~~~~~-~~~~~~------~~~~~----~~~~~~~ea~~AL~~LGy~~~ea~~al~~i 176 (197)
T PRK14603 126 E--------LKGKVPEHL-LAGPAG------GGGTK----VSSTAAEDAVLALLALGFREAQVRSVVAEL 176 (197)
T ss_pred H--------HHHHhhhhc-cccccc------ccccc----cCCccHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3 222221000 000000 00000 011124567788889999999988888764
No 65
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=30.76 E-value=1.6e+02 Score=22.93 Aligned_cols=44 Identities=18% Similarity=0.153 Sum_probs=28.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHH-cCC
Q 013135 76 IDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKS-LGI 121 (449)
Q Consensus 76 ~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~-lG~ 121 (449)
+..+-+|.+.+|+++.+|..+-..+| +..+.....+..|.. -|-
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~--~~~Eq~yqmL~~W~~~~g~ 55 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHR--RCRDAQYQMLKVWKERGPR 55 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCC--ChHHHHHHHHHHHHHhcCC
Confidence 44566777888888888888877776 444444555554433 443
No 66
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=30.59 E-value=1.1e+02 Score=20.04 Aligned_cols=26 Identities=31% Similarity=0.367 Sum_probs=17.7
Q ss_pred CCCchHHHHHHhcCCCHHHHHHhhcc
Q 013135 42 TQPLTVSDLQKSCGFSLESAVSASEK 67 (449)
Q Consensus 42 ~~~~~v~~L~~~~Gls~~~~~~~~~~ 67 (449)
..+++|.-+.+.+|+|+....++.++
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKK 31 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45688988889999988888877653
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=30.53 E-value=70 Score=31.11 Aligned_cols=27 Identities=41% Similarity=0.469 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhc
Q 013135 315 KALWEKKLEAYMNFGLTKDEVYSAFRR 341 (449)
Q Consensus 315 ~~~l~~k~~~l~~lG~s~~ev~~~v~~ 341 (449)
...+..|.+||++-|++.+||..++++
T Consensus 19 ~aPli~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 19 DAPLIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred cchHHHHHHHHHhcCCCHHHHHHHHHh
Confidence 456778999999999999999999987
No 68
>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=30.42 E-value=34 Score=29.01 Aligned_cols=19 Identities=32% Similarity=0.361 Sum_probs=11.7
Q ss_pred HHHHHHHCCCChhhHhhHh
Q 013135 144 TVEFFRTNGFSDSQIKSIT 162 (449)
Q Consensus 144 ~l~fL~~lGl~~~~i~~il 162 (449)
.+.-.+.+|||+.+|+++.
T Consensus 64 ~L~~aK~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 64 LLRKAKRLGFSDRQIARLW 82 (123)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHhcc
Confidence 4455567888888888774
No 69
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.38 E-value=2.8e+02 Score=25.36 Aligned_cols=24 Identities=29% Similarity=0.378 Sum_probs=14.2
Q ss_pred hhHHHHHHHcCCChHHHHHHHHhC
Q 013135 178 KPKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 178 ~pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
..-+..|.++|++..++.+++...
T Consensus 149 ~e~~~aL~~LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 149 SDILATLTALGYSSSEAAKAISSL 172 (194)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 344566666666666666665544
No 70
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=29.83 E-value=3e+02 Score=22.22 Aligned_cols=56 Identities=9% Similarity=0.137 Sum_probs=31.1
Q ss_pred HHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCChhHHHHHHH
Q 013135 251 PNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTNLLFVLAIR 308 (449)
Q Consensus 251 ~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~~~~~~a~~ 308 (449)
..-.|.+++|++..+|-.+-..+|+=. .+...+---.|.+..|-.......+.++.
T Consensus 22 ~wK~faR~lglse~~Id~I~~~~~~d~--~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr 77 (97)
T cd08316 22 DVKKFVRKSGLSEPKIDEIKLDNPQDT--AEQKVQLLRAWYQSHGKTGAYRTLIKTLR 77 (97)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCCCCh--HHHHHHHHHHHHHHhCCCchHHHHHHHHH
Confidence 344566788888888888877777532 12222222234445566655444444443
No 71
>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=28.96 E-value=2.1e+02 Score=23.44 Aligned_cols=29 Identities=28% Similarity=0.474 Sum_probs=20.5
Q ss_pred CcCHHHHHHHHHhCCCCHHHHHHHHhhCC
Q 013135 73 TDKIDSVLKLLRTHGLTRSQINNFVTKRP 101 (449)
Q Consensus 73 ~~~~~~v~~~L~~~G~~~~~i~~il~~~P 101 (449)
+..+...++.|.++|+++.++..++--+|
T Consensus 56 ~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P 84 (117)
T PF03874_consen 56 PESIKELREELKKFGLTEFEILQIINLRP 84 (117)
T ss_dssp HHHHHHHHHHHTTSTS-HHHHHHHHHH--
T ss_pred HHHHHHHHHHHhcccCCHHHHHHHhcCCC
Confidence 34466777888888899988888888877
No 72
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.36 E-value=4.8e+02 Score=24.08 Aligned_cols=118 Identities=12% Similarity=0.146 Sum_probs=64.2
Q ss_pred hcCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHHHc-CCChHHHHHHHH
Q 013135 53 SCGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFKSL-GITGANLAEMLN 131 (449)
Q Consensus 53 ~~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~~l-G~~~~~l~~~i~ 131 (449)
=+||...+=+.++..+..-+.-.+..-+..|..+ +.+++..+|... -.+.|..+ |+.++...+++.
T Consensus 61 LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~--~~~~l~~aI~~~-----------D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 61 LFGFATWDERQTFIVLISISKVGAKTALAILSQF--RPDDLRRLVAEE-----------DVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred eeCCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhC--CHHHHHHHHHhC-----------CHHHHhcCCCcCHHHHHHHHH
Confidence 3888888888887765444445555556666654 555777666552 23445443 666666666553
Q ss_pred hhhhhhccchhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHHHHHHHcCCChHHHHHHHHhC
Q 013135 132 KEHRVLESDAYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKLEFFKSLGFAELQMAKFLSSQ 201 (449)
Q Consensus 132 ~~P~lL~~~l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl~fL~~lG~s~~~i~~il~~~ 201 (449)
. ++.++.. .+++.... .+.. .....+.+..-++-|.++|+++.++.+.+.+.
T Consensus 128 E--------LkdK~~~---~~~~~~~~------~~~~-~~~~~~~~~ea~~AL~~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 128 E--------LKYKLKV---EGLPAAAV------LAGT-GAVPGSVFRDALAGLANLGYGEEEARPVLKEV 179 (203)
T ss_pred H--------HHHhhcc---cccccccc------cccc-ccCCCchHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 2 2222211 01111000 0000 00011224667788889999999988888764
No 73
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.61 E-value=3.2e+02 Score=21.89 Aligned_cols=53 Identities=11% Similarity=0.090 Sum_probs=31.0
Q ss_pred HHHHHhCCCChHHHHHHHhhcCccceecchH-HHHHHHHHHhcCCCCChhHHHHHHHH
Q 013135 253 IAILVNHGVPKSLVVKLMLIQPRTLLQSTAR-LNKIIDEVKKLGFDPTNLLFVLAIRS 309 (449)
Q Consensus 253 v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~-l~~~v~~l~~lG~~~~~~~~~~a~~~ 309 (449)
-.+.+++|++..+|..+-..+|.- .+. .+--..|..+.|-...-...+.|+..
T Consensus 23 k~laR~LGLse~~I~~i~~~~~~~----~eq~~qmL~~W~~~~G~~At~~~L~~aL~~ 76 (96)
T cd08315 23 NRLMRQLGLSENEIDVAKANERVT----REQLYQMLLTWVNKTGRKASVNTLLDALEA 76 (96)
T ss_pred HHHHHHcCCCHHHHHHHHHHCCCC----HHHHHHHHHHHHHhhCCCcHHHHHHHHHHH
Confidence 346678888888888888887752 233 33333345566665443344444443
No 74
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=27.34 E-value=4.8e+02 Score=23.78 Aligned_cols=43 Identities=12% Similarity=0.071 Sum_probs=24.4
Q ss_pred cCCCHHHHHHhhcccccCCCcCHHHHHHHHHhCCCCHHHHHHHHh
Q 013135 54 CGFSLESAVSASEKLRVDTTDKIDSVLKLLRTHGLTRSQINNFVT 98 (449)
Q Consensus 54 ~Gls~~~~~~~~~~~~~~s~~~~~~v~~~L~~~G~~~~~i~~il~ 98 (449)
+||...+=+.++..+.--+.-.+...+..|.. ++.+++..++.
T Consensus 60 yGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~--~~~~el~~aI~ 102 (191)
T TIGR00084 60 FGFNTLEERELFKELIKVNGVGPKLALAILSN--MSPEEFVYAIE 102 (191)
T ss_pred eCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhc--CCHHHHHHHHH
Confidence 78888877777765533333344444445443 34556666555
No 75
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.65 E-value=1.1e+02 Score=35.87 Aligned_cols=41 Identities=22% Similarity=0.451 Sum_probs=25.6
Q ss_pred HcCCCHHHHHHHHhc---CCcccccChHHHH---hHHHHHHHhcCCC
Q 013135 327 NFGLTKDEVYSAFRR---QPMFMIVSEQKIS---KLMDCYVNKLSME 367 (449)
Q Consensus 327 ~lG~s~~ev~~~v~~---~P~iL~~S~e~l~---~k~~fL~~~mg~~ 367 (449)
.-|.+.+++...++- -|.=+....+.|+ .-+||+..+++++
T Consensus 1031 qyGVplee~Vd~f~~trFEPaG~v~g~d~Ik~atSilDyifr~l~~~ 1077 (1220)
T PRK07562 1031 QYGVPLEEYVDAFTFTRFEPAGMVQGNDAIKNATSILDYVFRELAVS 1077 (1220)
T ss_pred HcCCCHHHHHHHhccCcccCCcccCCCcccchhhhHHHHHHHHHHHH
Confidence 568888888877642 2554444334343 5688888777654
No 76
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=26.54 E-value=56 Score=29.83 Aligned_cols=39 Identities=18% Similarity=0.367 Sum_probs=31.0
Q ss_pred hhhHHHHHHHCCCChhhHhhHhhhCCceeecCcccchhhHH
Q 013135 141 AYATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCMKPKL 181 (449)
Q Consensus 141 l~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l~pkl 181 (449)
-..+-+||++.|++-..|.+ ++.+|.+|.-.+ ++|-|++
T Consensus 30 T~GTAk~L~e~GI~v~~V~k-~TgfpE~l~GRV-KTLHP~i 68 (187)
T cd01421 30 TGGTAKFLKEAGIPVTDVSD-ITGFPEILGGRV-KTLHPKI 68 (187)
T ss_pred ccHHHHHHHHcCCeEEEhhh-ccCCcHhhCCcc-ccCChhh
Confidence 34578888888888777765 456999999888 7899887
No 77
>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=25.97 E-value=1.1e+02 Score=31.32 Aligned_cols=44 Identities=18% Similarity=0.333 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHhcCCcccccChHHHHhHHHHHHHhcCCC
Q 013135 315 KALWEKKLEAYMNFGLTKDEVYSAFRRQPMFMIVSEQKISKLMDCYVNKLSME 367 (449)
Q Consensus 315 ~~~l~~k~~~l~~lG~s~~ev~~~v~~~P~iL~~S~e~l~~k~~fL~~~mg~~ 367 (449)
.+..+..|+-+.+|||++++|.++++ -+-.+=.+-++||.+ |++
T Consensus 153 g~~~e~~I~~i~eMGf~R~qV~~ALR-------AafNNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 153 GSERETTIEEIMEMGYEREEVERALR-------AAFNNPDRAVEYLLT--GIP 196 (378)
T ss_pred chHHHHHHHHHHHhCCCHHHHHHHHH-------HHhCCHHHHHHHHHh--CCC
Confidence 45667777778888888888887665 233444567888885 676
No 78
>PRK09562 mazG nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=25.74 E-value=1.6e+02 Score=28.49 Aligned_cols=70 Identities=16% Similarity=0.244 Sum_probs=35.3
Q ss_pred CCCHHHH-----HHHHhhCCCC--CC-CCChhhHHHHHHHcCCChHHHHHHHHhhhhhhcc--chhhHHHHHHHCCCChh
Q 013135 87 GLTRSQI-----NNFVTKRPSG--DL-GDTLEPNLKLFKSLGITGANLAEMLNKEHRVLES--DAYATVEFFRTNGFSDS 156 (449)
Q Consensus 87 G~~~~~i-----~~il~~~P~l--~~-~~~l~~~l~~L~~lG~~~~~l~~~i~~~P~lL~~--~l~~~l~fL~~lGl~~~ 156 (449)
||+.+++ .|++.++|.+ .. ..++......|+..--.+..=.+++..-|.-|.. ........-...|++-.
T Consensus 83 ~~d~e~vl~~~~~K~~~R~p~vf~~~~~~s~~e~~~~We~~K~~ek~~~s~l~~ip~~lPaL~~a~KiqkrAa~~Gf~w~ 162 (262)
T PRK09562 83 AFDFADVVEAISDKLIRRHPHVFGDVEAESSEEVLANWEQIKAEERAESSVLDGIPRGLPALMRAYKIQKKAARVGFDWE 162 (262)
T ss_pred CCCHHHHHHHHHHHHhhhchhhccCCCCCCHHHHHHHHHHHHHHHHhccCchhcCcccCCHHHHHHHHHHHHHhcCCCCC
Confidence 4777664 4788999999 32 4456666666655321111101233333333321 22233444456777644
No 79
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=25.45 E-value=3.4e+02 Score=21.42 Aligned_cols=80 Identities=11% Similarity=0.093 Sum_probs=0.0
Q ss_pred CCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCC--CChhHHHHHHHHHHhcCHHHHHHHHHHHHHcCCCHHHHHH
Q 013135 260 GVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFD--PTNLLFVLAIRSMAVMSKALWEKKLEAYMNFGLTKDEVYS 337 (449)
Q Consensus 260 Gv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~--~~~~~~~~a~~~i~~~s~~~l~~k~~~l~~lG~s~~ev~~ 337 (449)
+.++++|...+...-.......+. .=..+.|.++|+. +++..-+..+...++....+=+.=++.|-.+|+|.+|+..
T Consensus 6 ~A~~e~I~~AL~~~~~~~~~~~~~-~it~~dL~~~GL~g~~~s~~rR~~l~~~L~iGy~N~KqllkrLN~f~it~~e~~~ 84 (87)
T PF13331_consen 6 HASPEAIREALENARTEDEEPKES-EITWEDLIELGLIGGPDSKERREKLGEYLGIGYGNAKQLLKRLNMFGITREEFEE 84 (87)
T ss_pred CCCHHHHHHHHHHhCccccCCccC-cCCHHHHHHCCCCCCccHHHHHHHHHHHHCCCCCCHHHHHHHHHHcCCCHHHHHH
Q ss_pred HHh
Q 013135 338 AFR 340 (449)
Q Consensus 338 ~v~ 340 (449)
+++
T Consensus 85 alk 87 (87)
T PF13331_consen 85 ALK 87 (87)
T ss_pred HhC
No 80
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=24.21 E-value=1.3e+02 Score=27.57 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=19.3
Q ss_pred hhhHHHHHHHcCCChHHHHHHHHhh
Q 013135 109 LEPNLKLFKSLGITGANLAEMLNKE 133 (449)
Q Consensus 109 l~~~l~~L~~lG~~~~~l~~~i~~~ 133 (449)
....+.+|.++|+++.++.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 5677778888888888888877766
No 81
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=23.84 E-value=1.9e+02 Score=24.78 Aligned_cols=22 Identities=9% Similarity=0.148 Sum_probs=12.9
Q ss_pred hhHHHHHHHCCCChhhHhhHhh
Q 013135 142 YATVEFFRTNGFSDSQIKSITV 163 (449)
Q Consensus 142 ~~~l~fL~~lGl~~~~i~~il~ 163 (449)
++.-+.|.+.|.+.++.+++..
T Consensus 102 ~el~~~l~~~g~~~EE~rRL~~ 123 (129)
T PF13543_consen 102 EELKEILNRCGAREEECRRLCR 123 (129)
T ss_pred HHHHHHHHHhCCCHHHHHHHHH
Confidence 3445555566666666666554
No 82
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=23.65 E-value=6.6e+02 Score=26.32 Aligned_cols=179 Identities=13% Similarity=0.081 Sum_probs=0.0
Q ss_pred CCCCChhhHHHHHHH-----cCCChHHHHHHHHhhhhhhccch-hhHHHHHHHCCCChhhHhhHhhhCCceeecCcccch
Q 013135 104 DLGDTLEPNLKLFKS-----LGITGANLAEMLNKEHRVLESDA-YATVEFFRTNGFSDSQIKSITVKRPKFYVYNLKKCM 177 (449)
Q Consensus 104 ~~~~~l~~~l~~L~~-----lG~~~~~l~~~i~~~P~lL~~~l-~~~l~fL~~lGl~~~~i~~il~~~P~lL~~~~e~~l 177 (449)
+++.-+.=++..|+. -|-....+..+=..+-.++...+ +.++..+.++|+.+.+-+..+..+-.-+...+ .-|
T Consensus 260 spEraL~lRL~LLQGV~~yHqg~~deAye~le~a~~~l~elki~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~Av-qfI 338 (568)
T KOG2561|consen 260 SPERALILRLELLQGVVAYHQGQRDEAYEALESAHAKLLELKINDETLSLLVGMGFEESDARLALRSCNGDVDSAV-QFI 338 (568)
T ss_pred ChhHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHeeccchHHHHHHHcCCCchHHHHHHHhccccHHHHH-HHH
Q ss_pred hhHHHHHHHcCCChHHHHHHHHhCCcceeccccccchH-HHHHHHHhcCChHHHHHHHHhCCcccccchhhhhHHHHHHH
Q 013135 178 KPKLEFFKSLGFAELQMAKFLSSQPYILERSLENHIIP-CIEILRRVLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAIL 256 (449)
Q Consensus 178 ~pkl~fL~~lG~s~~~i~~il~~~P~iL~~s~~~~l~p-~v~fL~~~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L 256 (449)
..+-+-+...-.....-.+-+.+.-..=+....+.+.| .+.+|.++|.+..-...++.++ -.+...+|
T Consensus 339 ~erre~laq~R~k~~a~Ere~~~r~k~~n~~~~~wvn~rs~~rL~~mGyer~la~eaL~r~-----------~Ndi~~al 407 (568)
T KOG2561|consen 339 IERREKLAQKREKDLAREREILERKKYGNTPMKKWVNPRSLERLVSMGYERELAAEALRRN-----------ENDIQKAL 407 (568)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCcccccCHHHHHHHHhcchHhHHHHHHHHhc-----------cCcHHHHH
Q ss_pred HhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCCCCh
Q 013135 257 VNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFDPTN 300 (449)
Q Consensus 257 ~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~~~~ 300 (449)
.-+.=..+++..-..+.|.-+.-. ++..|..|||++.+
T Consensus 408 dllq~esdel~~n~~~~p~~vd~~------~la~Lv~mGF~e~~ 445 (568)
T KOG2561|consen 408 DLLQDESDELESNKPKRPEQVDGI------SLAELVSMGFEEGK 445 (568)
T ss_pred HhcCCcchhhhccCCCCCcccchh------hHHHHHHhccccch
No 83
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. 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 (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.22 E-value=2.6e+02 Score=21.85 Aligned_cols=36 Identities=8% Similarity=0.075 Sum_probs=22.3
Q ss_pred HHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHHH
Q 013135 80 LKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLFK 117 (449)
Q Consensus 80 ~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L~ 117 (449)
-++-+.+||++.+|..+-..+|. ..+.....+..|+
T Consensus 22 k~Lar~LGls~~dI~~i~~~~~~--~~eq~~~mL~~W~ 57 (86)
T cd08318 22 KTLAPHLEMKDKEIRAIESDSED--IKMQAKQLLVAWQ 57 (86)
T ss_pred HHHHHHcCCCHHHHHHHHhcCCC--HHHHHHHHHHHHH
Confidence 34557899999999887666552 2334444454443
No 84
>PHA02591 hypothetical protein; Provisional
Probab=23.19 E-value=1.6e+02 Score=22.77 Aligned_cols=25 Identities=20% Similarity=0.174 Sum_probs=16.0
Q ss_pred CCCChhhHHHHHHHcCCChHHHHHH
Q 013135 105 LGDTLEPNLKLFKSLGITGANLAEM 129 (449)
Q Consensus 105 ~~~~l~~~l~~L~~lG~~~~~l~~~ 129 (449)
.++++.....-|.++|++..+++..
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~ 68 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASL 68 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHH
Confidence 4556666666677777776666643
No 85
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.66 E-value=3.5e+02 Score=24.20 Aligned_cols=44 Identities=7% Similarity=0.101 Sum_probs=24.6
Q ss_pred HcCCChHHHHHHHHhhhhhhc----cc--hhhHHHHHHHCCCChhhHhhH
Q 013135 118 SLGITGANLAEMLNKEHRVLE----SD--AYATVEFFRTNGFSDSQIKSI 161 (449)
Q Consensus 118 ~lG~~~~~l~~~i~~~P~lL~----~~--l~~~l~fL~~lGl~~~~i~~i 161 (449)
+.|++..++..++..--.+|. .+ .+...+-|.++|++++.+..+
T Consensus 33 ~~~~~~~~lk~~va~l~fiL~~A~k~n~~~~~l~~eL~~lglp~e~~~~l 82 (174)
T cd04752 33 DAKFESGDVKASIAVLSFILSSAAKYNVDGESLSSELQQLGLPKEHATSL 82 (174)
T ss_pred HhCCCHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHH
Confidence 356666666666655555553 22 233455667777777555443
No 86
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=22.56 E-value=2.5e+02 Score=20.70 Aligned_cols=42 Identities=21% Similarity=0.222 Sum_probs=27.3
Q ss_pred hcCChHHHHHHHHhCCcccccchhhhhHHHHHHHHh-CCCChHHHHHHH
Q 013135 223 VLDTDENVLKAIRAGCLVLEYDIEKVLEPNIAILVN-HGVPKSLVVKLM 270 (449)
Q Consensus 223 ~g~~~~~v~~~l~~~P~iL~~s~e~~l~~~v~~L~~-lGv~~~~i~~li 270 (449)
.|-+.++..+++...| +..+ -.+.++||++ .|+.......++
T Consensus 13 TGk~~~~W~~~~~~~~-----~~~k-~~e~v~WLK~ehgLghGhA~Aiv 55 (61)
T PF14117_consen 13 TGKTLDEWLALAREGG-----PLTK-HGEIVAWLKDEHGLGHGHANAIV 55 (61)
T ss_pred HCcCHHHHHHHHHHhC-----CCCc-HHHHHHHHHHHHCCChHHHHHHH
Confidence 4677777777777776 2233 5677778875 777776644443
No 87
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=22.42 E-value=3.8e+02 Score=25.11 Aligned_cols=56 Identities=20% Similarity=0.283 Sum_probs=38.8
Q ss_pred CCCchH-HHHHHhcCCCHHHHHHhhcccc-cCCCcCHHHHHHHHHh-CCCCHHHHHHHH
Q 013135 42 TQPLTV-SDLQKSCGFSLESAVSASEKLR-VDTTDKIDSVLKLLRT-HGLTRSQINNFV 97 (449)
Q Consensus 42 ~~~~~v-~~L~~~~Gls~~~~~~~~~~~~-~~s~~~~~~v~~~L~~-~G~~~~~i~~il 97 (449)
++..++ ..|++++|+++++.++-+..+. .....+...+.+||.+ -|-.+..+.+++
T Consensus 66 ~~~~~If~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~~l~~~~ 124 (216)
T PF11264_consen 66 EDKDSIFNALCQALGFDPEQYRQDAEKLEEWAKGKSIEDLLSWLSQKGGEGDNPLAAIL 124 (216)
T ss_pred hHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHhccccccchHHHHHH
Confidence 444555 7899999999999998876643 3455678888888865 334444555544
No 88
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=22.27 E-value=1.4e+02 Score=27.69 Aligned_cols=58 Identities=9% Similarity=0.147 Sum_probs=41.6
Q ss_pred CCCchH-HHHHHhcCCCHHHHHHhhcccc-cCCCcCHHHHHHHHHhCCCCHHHHHHHHhh
Q 013135 42 TQPLTV-SDLQKSCGFSLESAVSASEKLR-VDTTDKIDSVLKLLRTHGLTRSQINNFVTK 99 (449)
Q Consensus 42 ~~~~~v-~~L~~~~Gls~~~~~~~~~~~~-~~s~~~~~~v~~~L~~~G~~~~~i~~il~~ 99 (449)
++..+. ..|++++|+++++.++-+..+. .......+.+.+||..-|-.+..+..++.+
T Consensus 69 e~~~~IF~Alc~a~~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~~~~ 128 (206)
T PLN03060 69 TDRDAIFKAYIEALGEDPDQYRKDAKKLEEWASSQSASGIADFNSGDGEVEAVLKDIAER 128 (206)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcccccchHHHHHHHH
Confidence 444445 7899999999999998876643 445677888888888777555566665443
No 89
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=21.87 E-value=35 Score=26.52 Aligned_cols=27 Identities=22% Similarity=0.389 Sum_probs=21.6
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHHhhCC
Q 013135 75 KIDSVLKLLRTHGLTRSQINNFVTKRP 101 (449)
Q Consensus 75 ~~~~v~~~L~~~G~~~~~i~~il~~~P 101 (449)
+.++.-++|+++++..+++.+|....|
T Consensus 19 s~eE~~~lL~~y~i~~~qLP~I~~~DP 45 (79)
T PRK09570 19 SEEEAKKLLKEYGIKPEQLPKIKASDP 45 (79)
T ss_pred CHHHHHHHHHHcCCCHHHCCceeccCh
Confidence 456777888889999988888877766
No 90
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=21.76 E-value=1e+02 Score=24.09 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=7.9
Q ss_pred HhcCCCHHHHHHhh
Q 013135 52 KSCGFSLESAVSAS 65 (449)
Q Consensus 52 ~~~Gls~~~~~~~~ 65 (449)
+..|++.+++..+.
T Consensus 24 rR~Gfs~~~i~~l~ 37 (83)
T PF13720_consen 24 RRRGFSKEEISALR 37 (83)
T ss_dssp HHTTS-HHHHHHHH
T ss_pred HHcCCCHHHHHHHH
Confidence 45666666666553
No 91
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. 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 hom
Probab=21.73 E-value=1.4e+02 Score=23.47 Aligned_cols=52 Identities=17% Similarity=0.209 Sum_probs=30.8
Q ss_pred cccchhhhhHHHHHHHHhCCCChHHHHHHHhhcCccceecchHHHHHHHHHHhcCCC
Q 013135 241 LEYDIEKVLEPNIAILVNHGVPKSLVVKLMLIQPRTLLQSTARLNKIIDEVKKLGFD 297 (449)
Q Consensus 241 L~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~~P~lL~~s~~~l~~~v~~l~~lG~~ 297 (449)
|...+.. ++|.++-|.+.|+=..+=...++.+|. +.++++..+++++..|-.
T Consensus 10 LV~rI~~-v~plLD~Ll~n~~it~E~y~~V~a~~T----~qdkmRkLld~v~akG~~ 61 (85)
T cd08324 10 LVTHIRN-TQCLVDNLLKNDYFSTEDAEIVCACPT----QPDKVRKILDLVQSKGEE 61 (85)
T ss_pred HHHHHHh-hHHHHHHHhccCCccHHHHHHHHhCCC----CHHHHHHHHHHHHhcCch
Confidence 3333443 777777777776544443455555553 456777777776665544
No 92
>PRK13503 transcriptional activator RhaS; Provisional
Probab=21.66 E-value=3.1e+02 Score=25.94 Aligned_cols=26 Identities=12% Similarity=0.135 Sum_probs=16.4
Q ss_pred CCchHHHHHHhcCCCHHHHHHhhccc
Q 013135 43 QPLTVSDLQKSCGFSLESAVSASEKL 68 (449)
Q Consensus 43 ~~~~v~~L~~~~Gls~~~~~~~~~~~ 68 (449)
++.||+.+.+.+|+|+....++.++.
T Consensus 186 ~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 186 EEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45666666666666666666665543
No 93
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.52 E-value=2.4e+02 Score=21.59 Aligned_cols=38 Identities=21% Similarity=0.359 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHH
Q 013135 77 DSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLF 116 (449)
Q Consensus 77 ~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L 116 (449)
+..-.+.+.+||++.+|..+-..+|. ..+.....+.-|
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~--~~eq~~~mL~~W 49 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQ--HRDRVYELLRIW 49 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCc--hHHHHHHHHHHH
Confidence 44556777888888888888777775 333344444444
No 94
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=21.36 E-value=2e+02 Score=25.24 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=22.9
Q ss_pred CCcccccchhhhhHHHHHHHHhCCCChHHHHHHHhh
Q 013135 237 GCLVLEYDIEKVLEPNIAILVNHGVPKSLVVKLMLI 272 (449)
Q Consensus 237 ~P~iL~~s~e~~l~~~v~~L~~lGv~~~~i~~li~~ 272 (449)
.|..+.++.+. ++..+.-|..-|+++++|.-+++.
T Consensus 22 ~P~W~~~~~ee-ve~~I~~lakkG~~pSqIG~~LRD 56 (151)
T PRK08561 22 PPEWVDYSPEE-IEELVVELAKQGYSPSMIGIILRD 56 (151)
T ss_pred CCccccCCHHH-HHHHHHHHHHCCCCHHHhhhhHhh
Confidence 35566666666 666666666677777777666654
No 95
>PHA01976 helix-turn-helix protein
Probab=21.19 E-value=91 Score=22.59 Aligned_cols=25 Identities=8% Similarity=-0.137 Sum_probs=14.2
Q ss_pred HHHHHHH-HcCCCHHHHHHHHhcCCc
Q 013135 320 KKLEAYM-NFGLTKDEVYSAFRRQPM 344 (449)
Q Consensus 320 ~k~~~l~-~lG~s~~ev~~~v~~~P~ 344 (449)
.++..++ ..|+|.++++..+.-.++
T Consensus 5 ~rl~~~R~~~glt~~~lA~~~gvs~~ 30 (67)
T PHA01976 5 IQLIKARNARAWSAPELSRRAGVRHS 30 (67)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHH
Confidence 4455555 567777776665544433
No 96
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.79 E-value=2.8e+02 Score=19.99 Aligned_cols=21 Identities=19% Similarity=0.284 Sum_probs=13.3
Q ss_pred hHHHHHHhcCCCHHHHHHhhc
Q 013135 46 TVSDLQKSCGFSLESAVSASE 66 (449)
Q Consensus 46 ~v~~L~~~~Gls~~~~~~~~~ 66 (449)
++.-+.+-+|+++..++...+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 344455667888877776643
No 97
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=20.76 E-value=2e+02 Score=23.43 Aligned_cols=18 Identities=11% Similarity=0.373 Sum_probs=9.4
Q ss_pred hHHHHHHHHhCCcceecc
Q 013135 191 ELQMAKFLSSQPYILERS 208 (449)
Q Consensus 191 ~~~i~~il~~~P~iL~~s 208 (449)
.+++..++..+|.++.+.
T Consensus 74 ~~e~~~~l~~~p~LikRP 91 (105)
T cd03035 74 AAKAIALMLEHPSLIKRP 91 (105)
T ss_pred HHHHHHHHHhCcCeeecc
Confidence 344555555555555544
No 98
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=20.49 E-value=1.7e+02 Score=28.53 Aligned_cols=66 Identities=15% Similarity=0.209 Sum_probs=42.2
Q ss_pred HHhHHHHHHHhcCCChHHHhhCCceeccCCCCcchhHHHHHHHHHHCCCCCCCcchhhhccccHHHHHHHHhhc
Q 013135 353 ISKLMDCYVNKLSMEPLIISKHPYLLLFSLEKRILPRCSVLQLLMSNKVITEDFSLTYMFKMTEKQFIERIVKK 426 (449)
Q Consensus 353 l~~k~~fL~~~mg~~~~~i~~~P~~L~~Sle~ri~pR~~~l~~L~~~Gl~~~~~~l~~~l~~se~~F~~~~v~~ 426 (449)
++.+++.+.+ .|++.+.|+-=|- ++|. +....-+.+++.|..- +...+..++..|.|.|...+.+.
T Consensus 165 l~~~i~~a~~-~GI~~~~IilDPG-iGF~--k~~~~n~~ll~~l~~l----~~lg~Pilvg~SRKsfig~~~~~ 230 (282)
T PRK11613 165 FIEQIARCEA-AGIAKEKLLLDPG-FGFG--KNLSHNYQLLARLAEF----HHFNLPLLVGMSRKSMIGQLLNV 230 (282)
T ss_pred HHHHHHHHHH-cCCChhhEEEeCC-CCcC--CCHHHHHHHHHHHHHH----HhCCCCEEEEecccHHHHhhcCC
Confidence 4556666554 6999888888885 4543 4445555555554332 12345567888999999887653
No 99
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.23 E-value=4.6e+02 Score=21.00 Aligned_cols=39 Identities=23% Similarity=0.286 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhCCCCCCCCChhhHHHHH
Q 013135 76 IDSVLKLLRTHGLTRSQINNFVTKRPSGDLGDTLEPNLKLF 116 (449)
Q Consensus 76 ~~~v~~~L~~~G~~~~~i~~il~~~P~l~~~~~l~~~l~~L 116 (449)
.+.+-++.+.+|+++.+|..+-..+|.- .+.....+..|
T Consensus 19 ~~~Wk~laR~LGLse~~I~~i~~~~~~~--~eq~~qmL~~W 57 (96)
T cd08315 19 FDSWNRLMRQLGLSENEIDVAKANERVT--REQLYQMLLTW 57 (96)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCCCC--HHHHHHHHHHH
Confidence 3566677789999999998888887742 33344444444
Done!