Query 023626
Match_columns 279
No_of_seqs 179 out of 1288
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 05:26:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023626hhsearch_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 9.3E-46 2E-50 353.7 17.8 239 38-279 158-440 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 2.3E-39 5E-44 298.7 3.6 234 38-276 103-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.4E-34 3.1E-39 276.7 15.9 216 39-259 91-317 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 3.4E-29 7.4E-34 231.0 6.7 212 45-260 2-292 (345)
5 KOG1267 Mitochondrial transcri 99.8 3E-21 6.5E-26 182.5 10.2 181 70-260 231-411 (413)
6 KOG1267 Mitochondrial transcri 99.7 1.9E-17 4.1E-22 156.6 12.8 181 37-223 88-310 (413)
7 smart00733 Mterf Mitochondrial 97.3 0.0002 4.4E-09 41.4 2.6 28 129-157 3-30 (31)
8 smart00733 Mterf Mitochondrial 97.2 0.00027 5.8E-09 40.9 2.5 30 197-228 2-31 (31)
9 cd04790 HTH_Cfa-like_unk Helix 92.3 2.1 4.6E-05 35.7 10.4 142 43-198 17-167 (172)
10 PF11955 PORR: Plant organelle 85.7 0.6 1.3E-05 43.2 2.6 177 69-259 117-331 (335)
11 PF04695 Pex14_N: Peroxisomal 78.6 2.1 4.6E-05 34.2 3.0 29 71-99 23-51 (136)
12 PF14490 HHH_4: Helix-hairpin- 74.0 14 0.0003 27.3 6.2 59 70-129 7-76 (94)
13 PF04695 Pex14_N: Peroxisomal 73.1 5.9 0.00013 31.7 4.2 41 91-137 11-51 (136)
14 PF00627 UBA: UBA/TS-N domain; 73.0 5.3 0.00012 24.1 3.0 24 179-202 3-26 (37)
15 PF11955 PORR: Plant organelle 72.8 7.2 0.00016 36.1 5.2 30 179-208 120-150 (335)
16 PRK08561 rps15p 30S ribosomal 70.2 31 0.00068 28.1 7.6 70 50-122 9-81 (151)
17 smart00165 UBA Ubiquitin assoc 68.0 8.1 0.00017 23.1 3.1 24 179-202 2-25 (37)
18 COG1125 OpuBA ABC-type proline 67.3 16 0.00034 32.9 5.8 67 170-237 65-134 (309)
19 PF02022 Integrase_Zn: Integra 66.3 11 0.00023 23.6 3.3 30 176-205 6-36 (40)
20 COG4669 EscJ Type III secretor 65.7 12 0.00026 32.9 4.7 96 37-142 30-130 (246)
21 cd00194 UBA Ubiquitin Associat 65.1 9.8 0.00021 22.8 3.1 23 180-202 3-25 (38)
22 PF08069 Ribosomal_S13_N: Ribo 63.0 12 0.00026 25.6 3.4 45 51-95 10-57 (60)
23 PF07499 RuvA_C: RuvA, C-termi 61.8 6.6 0.00014 25.2 1.9 26 178-203 3-28 (47)
24 PF07499 RuvA_C: RuvA, C-termi 61.6 15 0.00031 23.6 3.5 26 71-96 3-28 (47)
25 PTZ00072 40S ribosomal protein 58.0 58 0.0013 26.4 7.0 70 50-122 6-78 (148)
26 PRK09875 putative hydrolase; P 57.8 28 0.00061 31.6 6.0 92 42-135 167-288 (292)
27 PF08069 Ribosomal_S13_N: Ribo 54.4 12 0.00027 25.5 2.3 38 165-202 20-57 (60)
28 PF11212 DUF2999: Protein of u 54.3 60 0.0013 23.0 5.7 56 73-138 3-61 (82)
29 PF03960 ArsC: ArsC family; I 53.2 38 0.00083 25.6 5.3 23 119-141 69-91 (110)
30 cd08306 Death_FADD Fas-associa 44.5 54 0.0012 23.8 4.6 39 77-120 19-57 (86)
31 cd08315 Death_TRAILR_DR4_DR5 D 43.8 57 0.0012 24.3 4.8 40 75-120 23-62 (96)
32 cd08313 Death_TNFR1 Death doma 42.3 66 0.0014 23.2 4.7 50 74-129 14-63 (80)
33 smart00657 RPOL4c DNA-directed 40.7 81 0.0017 24.4 5.4 58 66-131 52-109 (118)
34 KOG0400 40S ribosomal protein 40.5 51 0.0011 26.2 4.1 69 60-131 20-93 (151)
35 KOG0995 Centromere-associated 39.1 1.7E+02 0.0037 29.0 8.3 82 50-140 51-146 (581)
36 PF02787 CPSase_L_D3: Carbamoy 38.1 34 0.00074 26.8 2.9 59 69-130 11-82 (123)
37 PRK11613 folP dihydropteroate 36.6 54 0.0012 29.6 4.3 24 66-89 35-58 (282)
38 cd04784 HTH_CadR-PbrR Helix-Tu 36.0 1.6E+02 0.0034 22.8 6.4 49 43-94 16-69 (127)
39 cd08784 Death_DRs Death Domain 34.8 1E+02 0.0022 21.9 4.7 40 75-120 15-54 (79)
40 cd08316 Death_FAS_TNFRSF6 Deat 33.7 1.8E+02 0.004 21.7 6.1 43 73-120 22-64 (97)
41 PF09288 UBA_3: Fungal ubiquit 32.7 57 0.0012 21.9 2.8 21 181-201 12-32 (55)
42 PRK09875 putative hydrolase; P 32.4 40 0.00087 30.6 2.8 27 178-204 262-288 (292)
43 PF03874 RNA_pol_Rpb4: RNA pol 31.5 58 0.0013 24.8 3.2 57 66-130 54-110 (117)
44 cd01773 Faf1_like1_UBX Faf1 ik 30.2 29 0.00063 25.2 1.2 60 24-86 12-73 (82)
45 PRK00116 ruvA Holliday junctio 30.1 1.9E+02 0.0041 24.4 6.4 55 77-133 109-173 (192)
46 PF08671 SinI: Anti-repressor 28.5 70 0.0015 18.6 2.4 24 71-94 5-28 (30)
47 TIGR00601 rad23 UV excision re 28.0 1.1E+02 0.0024 28.9 4.9 43 176-228 154-196 (378)
48 PF13720 Acetyltransf_11: Udp 27.9 97 0.0021 22.4 3.7 38 77-117 22-59 (83)
49 PF08004 DUF1699: Protein of u 25.5 3.4E+02 0.0074 21.5 7.0 80 122-201 29-116 (131)
50 cd01109 HTH_YyaN Helix-Turn-He 25.4 2.6E+02 0.0057 21.0 5.9 23 179-201 47-69 (113)
51 PF07223 DUF1421: Protein of u 25.1 69 0.0015 30.0 3.0 24 178-201 321-344 (358)
52 PHA02591 hypothetical protein; 24.9 1E+02 0.0022 22.3 3.1 30 64-93 41-70 (83)
53 PF12244 DUF3606: Protein of u 24.9 77 0.0017 21.2 2.5 22 181-202 22-44 (57)
54 PF09278 MerR-DNA-bind: MerR, 24.7 85 0.0018 20.9 2.8 19 181-199 6-24 (65)
55 cd08805 Death_ank1 Death domai 24.0 2.6E+02 0.0057 20.3 5.3 38 78-120 22-59 (84)
56 cd08319 Death_RAIDD Death doma 23.7 2.1E+02 0.0045 20.7 4.7 44 78-127 20-63 (83)
57 PRK08561 rps15p 30S ribosomal 23.7 1.3E+02 0.0028 24.6 3.9 39 165-203 20-58 (151)
58 cd04769 HTH_MerR2 Helix-Turn-H 23.6 2.9E+02 0.0063 20.9 5.9 56 146-202 14-69 (116)
59 cd04787 HTH_HMRTR_unk Helix-Tu 23.2 2.6E+02 0.0057 21.8 5.7 55 148-202 16-70 (133)
60 PF13443 HTH_26: Cro/C1-type H 23.0 1.2E+02 0.0027 19.8 3.3 45 184-235 15-60 (63)
61 PRK06361 hypothetical protein; 22.0 1.3E+02 0.0028 25.4 4.0 31 70-100 178-208 (212)
62 PF13411 MerR_1: MerR HTH fami 21.0 2.6E+02 0.0057 18.5 4.9 23 178-200 45-67 (69)
63 PRK14601 ruvA Holliday junctio 20.3 2.1E+02 0.0046 24.0 4.8 40 178-220 142-181 (183)
64 PRK14487 cbb3-type cytochrome 20.2 75 0.0016 27.5 2.1 28 132-159 137-165 (217)
65 PRK14136 recX recombination re 20.1 3.2E+02 0.007 25.0 6.2 112 64-202 189-302 (309)
66 cd04777 HTH_MerR-like_sg1 Heli 20.0 3.7E+02 0.0079 20.0 5.7 51 147-201 15-67 (107)
67 cd08777 Death_RIP1 Death Domai 20.0 2.3E+02 0.0051 20.5 4.4 48 77-128 19-66 (86)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=9.3e-46 Score=353.72 Aligned_cols=239 Identities=23% Similarity=0.407 Sum_probs=189.2
Q ss_pred CCchhhHHHHHhCCCCCC--CCccccCC--Ccchh-hhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHH
Q 023626 38 TSHRENLRYLRAIGVIDP--STKPHKLP--SPEVV-SQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVF 112 (279)
Q Consensus 38 ~~~~~~l~~L~~~Gls~~--~~ii~~~P--l~~~~-~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v 112 (279)
.++.|+++||+++|+++. .+++.++| +..+. .++.++++||+++|++.++|++++.++|++|+++++ ++++|++
T Consensus 158 ~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve-~~i~P~v 236 (487)
T PLN03196 158 VDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVG-NNIKPKV 236 (487)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChh-hhHHHHH
Confidence 344555555555555433 24455555 44444 356666666666666666666666677777777776 6777777
Q ss_pred HHHHHhcCCChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCCCC--Cc----------------------------
Q 023626 113 DFLITDLHASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVKKL--NV---------------------------- 162 (279)
Q Consensus 113 ~fL~~~lGls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~~~--~~---------------------------- 162 (279)
+||+ ++|++.++|.+++.++|++|+++++++++|++++|+++|++.. ..
T Consensus 237 ~fL~-~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~l 315 (487)
T PLN03196 237 DYLE-SLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKL 315 (487)
T ss_pred HHHH-HcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhh
Confidence 7777 5777777777777777777777777777777777777777641 11
Q ss_pred ---------chhcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChHHHh
Q 023626 163 ---------PSTLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLEELK 233 (279)
Q Consensus 163 ---------li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~~i~ 233 (279)
++.++|++++.+.++++++++||+++||+.+++..|+.++|++|++|. ++|++|++||.++||++.++|+
T Consensus 316 G~s~e~i~~~v~k~P~il~lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~Iv 394 (487)
T PLN03196 316 KIDPEDFGRVIEKLPQIVSLNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKELV 394 (487)
T ss_pred CCCHHHHHHHHHhcchhhcccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHHHH
Confidence 234567777777788999999999999999999999999999999998 7999999999999999999999
Q ss_pred hCCceeecccCCchHHHHHHHHHCCCCCChhhhhccchhHHHHhhC
Q 023626 234 EFPQYFGFSLGKRIAPRHWHLKQRNVRIKLNKMLLWSDNRFYTKWK 279 (279)
Q Consensus 234 ~~P~~L~~sl~~ri~pR~~~L~~~G~~~~l~~~l~~s~~~F~~~~~ 279 (279)
++|.+|+||+|+||+|||++|+++|+++++.+++++||++|+++|.
T Consensus 395 ~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r~v 440 (487)
T PLN03196 395 EFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQRMS 440 (487)
T ss_pred hChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999984
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=2.3e-39 Score=298.72 Aligned_cols=234 Identities=34% Similarity=0.532 Sum_probs=173.2
Q ss_pred CCchhhHHHHHhCCCCCCC--CccccCC--CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHH
Q 023626 38 TSHRENLRYLRAIGVIDPS--TKPHKLP--SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFD 113 (279)
Q Consensus 38 ~~~~~~l~~L~~~Gls~~~--~ii~~~P--l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~ 113 (279)
.++.+++++|+++|+++.. +.+...| .... +.+.+.++++.++|++++++++++.++|.++..+.+ ++++++++
T Consensus 103 ~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~-~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~-~~~~~~v~ 180 (345)
T PF02536_consen 103 ENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS-EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSE-SELKPKVE 180 (345)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS--HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCC-CCCHHHHH
T ss_pred hhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch-hHHHHHHHHHHHhCCCchhhcccccccchhhccccH-HHHHHHHH
Confidence 3577889999999996431 3455556 2333 899999999999999999999999999988888877 79999999
Q ss_pred HHHHhcCCChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChH
Q 023626 114 FLITDLHASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRR 193 (279)
Q Consensus 114 fL~~~lGls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~ 193 (279)
||+ ++|++.+++.+++.++|++|+.+.++.+++...++...|..+. .++.++|.++..+.+++.++++||+++||+++
T Consensus 181 ~L~-~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~-~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ 258 (345)
T PF02536_consen 181 FLR-SLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEE-RVIKKFPQILSLSEEKLKPKIEFLQSLGFSEE 258 (345)
T ss_dssp HHH-HCTT-GHHHHHHHHHTTTGGGCGCHC----------------------------THHHHHHHHHHHHHHTTT--HH
T ss_pred HHH-hhcccchhhhHHhhcccceeccccccccccccccccccccccc-ccccccccccccchHhHHHHHHHHHHhcCcHH
Confidence 999 6999999999999999999999988777766666665666555 88889999999999999999999999999999
Q ss_pred HHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChHHHhhCCceeecccCCchHHH---HHHHHHCC--CCCChhhhhc
Q 023626 194 EAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLEELKEFPQYFGFSLGKRIAPR---HWHLKQRN--VRIKLNKMLL 268 (279)
Q Consensus 194 ~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~~i~~~P~~L~~sl~~ri~pR---~~~L~~~G--~~~~l~~~l~ 268 (279)
++++|+.++|++|++|. +++++|++||.++||++.++|+++|.+|+||+|+||+|| +++|+++| .++++.+++.
T Consensus 259 ei~~mv~~~P~iL~~s~-e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~~~~l~~~g~~~~~sl~~~l~ 337 (345)
T PF02536_consen 259 EIAKMVRRFPQILSYSI-EKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEVLKVLKSKGLIINPSLSSMLS 337 (345)
T ss_dssp HHHHHHHHSGGGGGS-H-HHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHHHHTT--TTTGGGGGS-HHHH
T ss_pred HHHHHHHhCcchhhcch-hhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHHHHHHHHCcCCCCCCHHHHhh
Confidence 99999999999999999 579999999999999999999999999999999999999 66688999 7899999999
Q ss_pred cchhHHHH
Q 023626 269 WSDNRFYT 276 (279)
Q Consensus 269 ~s~~~F~~ 276 (279)
+||++|++
T Consensus 338 ~s~~~F~~ 345 (345)
T PF02536_consen 338 CSDEEFLK 345 (345)
T ss_dssp HHHHHHT-
T ss_pred ccHHHhcC
Confidence 99999974
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.4e-34 Score=276.73 Aligned_cols=216 Identities=21% Similarity=0.429 Sum_probs=157.4
Q ss_pred CchhhHHHHHhCCCCCCCCccccCC--Ccchh-hhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHH
Q 023626 39 SHRENLRYLRAIGVIDPSTKPHKLP--SPEVV-SQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFL 115 (279)
Q Consensus 39 ~~~~~l~~L~~~Gls~~~~ii~~~P--l~~~~-~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL 115 (279)
.++++++||+++|+++++ +.++| +..++ +++.++++||+++|+++.+|++++.++|.+|.++++ +++.|+++||
T Consensus 91 ~~~~~l~~L~s~G~~~~~--i~~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve-~~L~P~v~fL 167 (487)
T PLN03196 91 VMRERVEFLHKLGLTIED--INEYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVV-VDLAPVVKYL 167 (487)
T ss_pred HHHHHHHHHHHcCCChHH--hccCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHH-HHHHHHHHHH
Confidence 444667788888885433 23677 55555 677778888877888888888888888888877777 7777888888
Q ss_pred HHhcCCChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCCC--CCcchhcccccccccHHH-HHHHHHHHHHccCCh
Q 023626 116 ITDLHASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVKK--LNVPSTLNARLLNTRVER-LRETLRFLRSIGLNR 192 (279)
Q Consensus 116 ~~~lGls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~~--~~~li~~~P~ll~~s~~~-l~~~v~~L~~~G~s~ 192 (279)
+ .+|++.++|.+++.++|++|++++++++.++++||+++|++. ...++.++|++|+++.++ ++++++||.++|++.
T Consensus 168 ~-~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~ 246 (487)
T PLN03196 168 Q-GLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPR 246 (487)
T ss_pred H-HcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCH
Confidence 7 577777777777777777777777777777777777777764 446777777777777664 777777777777777
Q ss_pred HHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChHH----HhhCCceeecccCCchHHHHHHH-HHCCC
Q 023626 193 REAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLEE----LKEFPQYFGFSLGKRIAPRHWHL-KQRNV 259 (279)
Q Consensus 193 ~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~~----i~~~P~~L~~sl~~ri~pR~~~L-~~~G~ 259 (279)
+++++++.++|++|++|+|++++++++||.+ +|++.+. |.++|.++++++++++.++.++| ++.|+
T Consensus 247 ~~I~~il~~~P~iL~~sle~~lkp~v~~L~e-lGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~ 317 (487)
T PLN03196 247 LAVARILEKRPYILGFDLEETVKPNVECLLE-FGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKI 317 (487)
T ss_pred HHHHHHHHhCCceeEcCHHHhHHHHHHHHHH-cCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCC
Confidence 7777777777777777776677777777773 6776554 34677777777777777777776 35565
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.95 E-value=3.4e-29 Score=230.99 Aligned_cols=212 Identities=27% Similarity=0.498 Sum_probs=135.8
Q ss_pred HHHHhCCCCCCC--CccccCC---CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhc
Q 023626 45 RYLRAIGVIDPS--TKPHKLP---SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDL 119 (279)
Q Consensus 45 ~~L~~~Gls~~~--~ii~~~P---l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~l 119 (279)
++|+++|+++++ ++++++| +....+++.++++||++.|++..++++++.++|.++..+.+ +++.|.++||+ ++
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~-~~i~p~~~~L~-~~ 79 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLE-KNIIPVFDFLK-SI 79 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--H-HHHHHHHHHHT-TT
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccch-hhHHHHHHHHH-HH
Confidence 355666665443 4555566 23333666666666666666666666666666666666655 56666666666 46
Q ss_pred CCChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCCC------------------------------------CCcc
Q 023626 120 HASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVKK------------------------------------LNVP 163 (279)
Q Consensus 120 Gls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~~------------------------------------~~~l 163 (279)
|++++++.+++.++|++|+.+.+.++.+++.+|+++|+++ ...+
T Consensus 80 ~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~~~~~~~v~~l~~lG~~~~~~~~v 159 (345)
T PF02536_consen 80 GLSDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSSEKIKERVEFLKELGFDPEKIGRV 159 (345)
T ss_dssp SS-HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS-HHHHCHHHHHCCCTSSHHHHCCC
T ss_pred cCCHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccchhHHHHHHHHHHHhCCCchhhccc
Confidence 6666666666666666666555555666666666666643 2345
Q ss_pred hhccccc-ccccHHHHHHHHHHHHHccCChHHHHHHHhcCCcccccChhh------------------------------
Q 023626 164 STLNARL-LNTRVERLRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEH------------------------------ 212 (279)
Q Consensus 164 i~~~P~l-l~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~------------------------------ 212 (279)
+.++|.+ +..+.+.++++++||+++|++.+++.+++.++|.++..|.++
T Consensus 160 i~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~ 239 (345)
T PF02536_consen 160 IAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLS 239 (345)
T ss_dssp HHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THH
T ss_pred ccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccc
Confidence 6788854 445556799999999999999999999999999999999854
Q ss_pred --hHHHHHHHHHHHhCCChHHH----hhCCceeecccCCchHHHHHHHH-HCCCC
Q 023626 213 --HLKIKFEFLAVEMERSLEEL----KEFPQYFGFSLGKRIAPRHWHLK-QRNVR 260 (279)
Q Consensus 213 --~i~~k~~fL~~~mg~~~~~i----~~~P~~L~~sl~~ri~pR~~~L~-~~G~~ 260 (279)
+++++++||.+ +|++.++| .++|.+|++|.+ +++++++||. ++|++
T Consensus 240 ~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~ 292 (345)
T PF02536_consen 240 EEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLP 292 (345)
T ss_dssp HHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT--
T ss_pred hHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcC
Confidence 58999999997 99997775 689999999999 6999999986 47773
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.85 E-value=3e-21 Score=182.49 Aligned_cols=181 Identities=30% Similarity=0.486 Sum_probs=152.4
Q ss_pred hHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHHHhCCcccccChhhhhHhHH
Q 023626 70 QILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLIIGCPQMLSSNVEYCLKPTL 149 (279)
Q Consensus 70 ~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll~~~P~iL~~s~~~~l~~~i 149 (279)
.+...+.++..+|+.+.. +++.++|.++.++.+ +.+++++++|+ .+|++.++|..++.++|++|+++.+ ++..++
T Consensus 231 ~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~-~~i~~kv~~l~-~~Gf~~~di~~~~~k~P~~l~~s~~-~~~~~~ 305 (413)
T KOG1267|consen 231 KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSE-KTLEPKVEVLK-SLGFSREEIWKMVKKCPQILGYSVK-KNLKTT 305 (413)
T ss_pred hhhhhhhhHHHhccCCch--hHHHhhhhhhccccc-ccHHHHHHHHH-HcCCCHHHHHHHHHhCchheEeehh-hhhHHH
Confidence 333344444444444333 555556666666788 89999999999 6999999999999999999999966 477777
Q ss_pred HHHHHhCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCCh
Q 023626 150 DYLTKLGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSL 229 (279)
Q Consensus 150 ~~L~~lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~ 229 (279)
+++.+. .+. +.++|+++..+...+.++++|+..+|++..|+..++.++|+++.+|+|+.++.+.+|+.+.|+++.
T Consensus 306 ~~~~~~--~~~---~~k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~ 380 (413)
T KOG1267|consen 306 EYLLKN--PKH---ILKFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPL 380 (413)
T ss_pred HHHHhc--chh---hhhhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchH
Confidence 777776 222 889999999999999999999999999999999999999999999995599999999999999999
Q ss_pred HHHhhCCceeecccCCchHHHHHHHHHCCCC
Q 023626 230 EELKEFPQYFGFSLGKRIAPRHWHLKQRNVR 260 (279)
Q Consensus 230 ~~i~~~P~~L~~sl~~ri~pR~~~L~~~G~~ 260 (279)
+.++.+|.+++|++++|+.||+......|.+
T Consensus 381 ~~~~~~p~~~~y~le~ri~pr~~~~~~~~~~ 411 (413)
T KOG1267|consen 381 SALVSFPAFFGYSLEKRIRPRFNVIKKLGVK 411 (413)
T ss_pred HHHhccchhhccchhhcchhHHHHHHHHhcc
Confidence 9999999999999999999999998877653
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.74 E-value=1.9e-17 Score=156.64 Aligned_cols=181 Identities=20% Similarity=0.310 Sum_probs=130.9
Q ss_pred CCCchhhHHHHHhCCCCCC--CCccccCC---CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhH
Q 023626 37 KTSHRENLRYLRAIGVIDP--STKPHKLP---SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPV 111 (279)
Q Consensus 37 ~~~~~~~l~~L~~~Gls~~--~~ii~~~P---l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~ 111 (279)
..+.+..+++|++.|++++ ++++...| ...+...+.++..+|...|++..++.+++...|.+|..+.+ .++.+.
T Consensus 88 ~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~-~~~~~~ 166 (413)
T KOG1267|consen 88 SVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKG-ESLSTF 166 (413)
T ss_pred ccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcC-CchhhH
Confidence 3455567999999999766 46788888 35556888888889999999999999999999999998877 789999
Q ss_pred HHHHHHhcC--CChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCC-------------------------------
Q 023626 112 FDFLITDLH--ASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVK------------------------------- 158 (279)
Q Consensus 112 v~fL~~~lG--ls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~------------------------------- 158 (279)
++|++ .++ .....+.+++...|...... ..+. ++++++++|..
T Consensus 167 ~~~l~-~~~~~~~~s~~~~~~~~~~~~~~~~--~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~~l~~~~~~i~~~ 242 (413)
T KOG1267|consen 167 IEFLK-SIPPELLSSVVERLLTPVPSFLLNE--NSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYLKLKARLPFLLTL 242 (413)
T ss_pred HHHhh-ccchhhhhhHHHHhccccccccccc--cccc-cchhhHHhCCCHHHHHHHHhcCccceeeehhhhhhhhhHHHh
Confidence 99998 463 55555555555555322221 1233 55555555554
Q ss_pred ---CCCcchhccccccccc-HHHHHHHHHHHHHccCChHHHHHHHhcCCcccccChhhhHHHHHHHHHH
Q 023626 159 ---KLNVPSTLNARLLNTR-VERLRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAV 223 (279)
Q Consensus 159 ---~~~~li~~~P~ll~~s-~~~l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~ 223 (279)
....++.+.|.++.++ .+.+++++++|+++||+.+|+++|+.++|++|+++. +++..+++|+.+
T Consensus 243 g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~-~~~~~~~~~~~~ 310 (413)
T KOG1267|consen 243 GFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSV-KKNLKTTEYLLK 310 (413)
T ss_pred ccCCchhHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeeh-hhhhHHHHHHHh
Confidence 2223334455555544 456999999999999999999999999999999998 554444444433
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=97.31 E-value=0.0002 Score=41.43 Aligned_cols=28 Identities=36% Similarity=0.679 Sum_probs=14.4
Q ss_pred HHHhCCcccccChhhhhHhHHHHHHHhCC
Q 023626 129 LIIGCPQMLSSNVEYCLKPTLDYLTKLGV 157 (279)
Q Consensus 129 ll~~~P~iL~~s~~~~l~~~i~~L~~lG~ 157 (279)
++.++|++|+.+ +++++++++||+++|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 344555555555 4445555555555554
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=97.23 E-value=0.00027 Score=40.87 Aligned_cols=30 Identities=40% Similarity=0.650 Sum_probs=21.8
Q ss_pred HHHhcCCcccccChhhhHHHHHHHHHHHhCCC
Q 023626 197 EFCARMPAIFGYNIEHHLKIKFEFLAVEMERS 228 (279)
Q Consensus 197 ~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~ 228 (279)
+++.++|.+++++. ++++++++||. ++|++
T Consensus 2 ~~~~~~P~il~~~~-~~l~~~~~~l~-~~g~~ 31 (31)
T smart00733 2 KILKKFPQILGYSE-KKLKPKVEFLK-ELGFS 31 (31)
T ss_pred chhhhCcCcccccH-HHhhHHHHHHH-HcCCC
Confidence 35677888888884 68888888887 57753
No 9
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=92.25 E-value=2.1 Score=35.65 Aligned_cols=142 Identities=15% Similarity=0.186 Sum_probs=74.4
Q ss_pred hHHHHHhCCCCCCCCccccCC---CcchhhhH--HHHHHHHhhCCCChhHHHHHHhhCCc----cccccccCCchhhHHH
Q 023626 43 NLRYLRAIGVIDPSTKPHKLP---SPEVVSQI--LSTIDFFKSKGLTNGHFSRLAYLCPQ----FFSINFDPSEIEPVFD 113 (279)
Q Consensus 43 ~l~~L~~~Gls~~~~ii~~~P---l~~~~~~l--~~~i~~L~~~G~s~~~i~~li~~~P~----lL~~~~e~~~l~~~v~ 113 (279)
.+.|....|+=.+.. +.+ ..++.+.+ ...+..|+++|++-++|..++..... ++....+ .+...++
T Consensus 17 tLRyYe~~GLl~p~~---r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~~~~~--~l~~ei~ 91 (172)
T cd04790 17 TLLYYERIGLLSPSA---RSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLRRRLA--ELNREIQ 91 (172)
T ss_pred HHHHHHHCCCCCCCc---cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhHHHHHHHHHH--HHHHHHH
Confidence 477888888832221 222 34444332 26677889999999999999876543 1111111 3333333
Q ss_pred HHHHhcCCChHHHHHHHHhCCcccccChhhhhHhHHHHHHHhCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChH
Q 023626 114 FLITDLHASVEERRGLIIGCPQMLSSNVEYCLKPTLDYLTKLGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRR 193 (279)
Q Consensus 114 fL~~~lGls~~~i~~ll~~~P~iL~~s~~~~l~~~i~~L~~lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~ 193 (279)
-|+. ....+..++...+..-.... -+....++.++.+|+++...- ..+- .+....=....+||.++|++++
T Consensus 92 ~L~~----~~~~l~~ll~~~~~~~~~~~-V~~~~w~~l~~~~g~~~~~m~-~wh~---~fe~~~p~~h~~~l~~~g~~~~ 162 (172)
T cd04790 92 RLRQ----QQRAIATLLKQPTLLKEQRL-VTKEKWVAILKAAGMDEADMR-RWHI---EFEKMEPEAHQEFLQSLGIPED 162 (172)
T ss_pred HHHH----HHHHHHHHHHHHhhcccccc-CCHHHHHHHHHHcCCChHHHH-HHHH---HHHHhCcHHHHHHHHHcCCCHH
Confidence 3331 23444444443333322221 123556677777887653200 0000 0000112456789999999999
Q ss_pred HHHHH
Q 023626 194 EAAEF 198 (279)
Q Consensus 194 ~v~~~ 198 (279)
++..+
T Consensus 163 ~~~~i 167 (172)
T cd04790 163 EIERI 167 (172)
T ss_pred HHHHH
Confidence 88654
No 10
>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=85.70 E-value=0.6 Score=43.19 Aligned_cols=177 Identities=20% Similarity=0.231 Sum_probs=95.4
Q ss_pred hhHHHHHHHHh-hCCCChhHHHHHHhhCCcccccccc--CCchhhHHHHHHHhcCCChHHHHHHH---------------
Q 023626 69 SQILSTIDFFK-SKGLTNGHFSRLAYLCPQFFSINFD--PSEIEPVFDFLITDLHASVEERRGLI--------------- 130 (279)
Q Consensus 69 ~~l~~~i~~L~-~~G~s~~~i~~li~~~P~lL~~~~e--~~~l~~~v~fL~~~lGls~~~i~~ll--------------- 130 (279)
.-...+++.++ ++|++++=...++.++|..|..... ....-..+.+=- ++.++.-+-....
T Consensus 117 rlpL~ki~~l~~dLGLP~Df~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~-~LAvs~~E~~~~~~~~~~~~~~~~~~~~ 195 (335)
T PF11955_consen 117 RLPLSKIAHLRRDLGLPDDFRDSLVPKYPDYFRVVDLEDGGRYLELVSWDP-ELAVSALEKRAEKEYREKREDGFDRPLA 195 (335)
T ss_pred cccHHHHHHHHHHcCCChhhccchhhhCCCCcEEeecCCCCCEEEEeecCC-ccCcCccchhhhhccccccccccCCcee
Confidence 34456667666 6888887777888888887765320 011111222211 3333332222211
Q ss_pred --HhCCcccccChhhhhHhHHHHHHHhCCC----CCCcc-----------hhcccccccccHHH--HHHHHHHHH-HccC
Q 023626 131 --IGCPQMLSSNVEYCLKPTLDYLTKLGVK----KLNVP-----------STLNARLLNTRVER--LRETLRFLR-SIGL 190 (279)
Q Consensus 131 --~~~P~iL~~s~~~~l~~~i~~L~~lG~~----~~~~l-----------i~~~P~ll~~s~~~--l~~~v~~L~-~~G~ 190 (279)
.++|.= +.+++.....++-++++-+. +...+ +.-.=.+|+..+++ ...++..|+ ++|+
T Consensus 196 Fp~~fp~G--~~l~k~~~~~l~~fQ~lPy~SPYed~~~l~~~s~~~EKRaVaVlHElLSLTveKr~~~~~L~~fr~ef~l 273 (335)
T PF11955_consen 196 FPVSFPKG--FRLKKKFREWLEEFQKLPYISPYEDASHLDPGSDEAEKRAVAVLHELLSLTVEKRTEVDHLTHFRKEFGL 273 (335)
T ss_pred eeecCCCC--ccccHHHHHHHHHHhcCCCCCCCCCccCCCCCChHHHhHHHHHHHHHHHhhhhhhccHHHHHHHHHHhCC
Confidence 122322 22335566666666665542 11111 11111345555554 456677777 8899
Q ss_pred ChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChHHHhhCCceeecccCCchHHHHHHHHHCCC
Q 023626 191 NRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLEELKEFPQYFGFSLGKRIAPRHWHLKQRNV 259 (279)
Q Consensus 191 s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~~i~~~P~~L~~sl~~ri~pR~~~L~~~G~ 259 (279)
+ ..+..++.+||.|+..|. +-+.-.=||.+....+ +-|-++|.+ .++-|+.-|...|.
T Consensus 274 p-~k~~~~l~rHPgIFYvS~--kg~~~TVfLrEAY~~~-~Liek~Pl~-------~~r~k~~~Lm~~~~ 331 (335)
T PF11955_consen 274 P-QKFRRLLLRHPGIFYVSL--KGKRHTVFLREAYDGG-ELIEKHPLV-------VIREKFLELMQEGR 331 (335)
T ss_pred c-HHHHHHHHhCCCeEEEec--cCCceEEEEeeccCCC-CCCCCCchH-------HHHHHHHHHHhhcc
Confidence 7 678899999999999986 4455555666543332 224566652 55666666665553
No 11
>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=78.60 E-value=2.1 Score=34.23 Aligned_cols=29 Identities=24% Similarity=0.208 Sum_probs=21.0
Q ss_pred HHHHHHHHhhCCCChhHHHHHHhhCCccc
Q 023626 71 ILSTIDFFKSKGLTNGHFSRLAYLCPQFF 99 (279)
Q Consensus 71 l~~~i~~L~~~G~s~~~i~~li~~~P~lL 99 (279)
+..+++||++.|++++||..++.+.+.--
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 67788999999999999999888876654
No 12
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=74.04 E-value=14 Score=27.33 Aligned_cols=59 Identities=14% Similarity=0.100 Sum_probs=26.2
Q ss_pred hHHHHHHHHhhCCCChhHHH-----------HHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHH
Q 023626 70 QILSTIDFFKSKGLTNGHFS-----------RLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGL 129 (279)
Q Consensus 70 ~l~~~i~~L~~~G~s~~~i~-----------~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~l 129 (279)
.+...+.||..+|++..... .++..+|..|..++. .-=-..++-+-..+|++..+-.++
T Consensus 7 ~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~-gi~F~~aD~iA~~~g~~~~d~~Ri 76 (94)
T PF14490_consen 7 GLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDID-GIGFKTADKIALKLGIEPDDPRRI 76 (94)
T ss_dssp --HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SS-SSBHHHHHHHHHTTT--TT-HHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHcc-CCCHHHHHHHHHHcCCCCCCHHHH
Confidence 34445555666666554444 455667777766443 333444444444566655544433
No 13
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=73.13 E-value=5.9 Score=31.67 Aligned_cols=41 Identities=15% Similarity=-0.013 Sum_probs=28.3
Q ss_pred HHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHHHhCCccc
Q 023626 91 LAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLIIGCPQML 137 (279)
Q Consensus 91 li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll~~~P~iL 137 (279)
-+..+|.+-.. .+..+++||+ ..|+++++|...+.+.+.--
T Consensus 11 ~FL~~p~V~~s-----p~~~k~~FL~-sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 11 KFLQDPKVRNS-----PLEKKIAFLE-SKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHCTTTCCCS------HHHHHHHHH-HCT--HHHHHHHHHHHT--S
T ss_pred HHhCCcccccC-----CHHHHHHHHH-cCCCCHHHHHHHHHhcCCcc
Confidence 34457777655 4678999999 69999999999998766544
No 14
>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=72.96 E-value=5.3 Score=24.09 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=18.0
Q ss_pred HHHHHHHHHccCChHHHHHHHhcC
Q 023626 179 RETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 179 ~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
++.++-|.++||+.++..+.+..+
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHc
Confidence 356777888999999988887754
No 15
>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=72.79 E-value=7.2 Score=36.12 Aligned_cols=30 Identities=20% Similarity=0.368 Sum_probs=17.5
Q ss_pred HHHHHHHH-HccCChHHHHHHHhcCCccccc
Q 023626 179 RETLRFLR-SIGLNRREAAEFCARMPAIFGY 208 (279)
Q Consensus 179 ~~~v~~L~-~~G~s~~~v~~~l~~~P~iL~~ 208 (279)
-.++..++ ++|++.+-...++.+||..+..
T Consensus 120 L~ki~~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 120 LSKIAHLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HHHHHHHHHHcCCChhhccchhhhCCCCcEE
Confidence 34455555 6666666666666666665543
No 16
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=70.16 E-value=31 Score=28.08 Aligned_cols=70 Identities=7% Similarity=-0.014 Sum_probs=47.2
Q ss_pred CCCCCCCCccccC-C--CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCC
Q 023626 50 IGVIDPSTKPHKL-P--SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHAS 122 (279)
Q Consensus 50 ~Gls~~~~ii~~~-P--l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls 122 (279)
-|.|.+..-.+.. | +..+.+.+.+.+--|..-|.++++|+-++...-.+=....- .=.....+|+ +.|+.
T Consensus 9 kG~S~S~~P~~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~v--tG~ki~~iLk-~~gl~ 81 (151)
T PRK08561 9 RGKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLI--TGKKITEILE-ENGLA 81 (151)
T ss_pred CCCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeee--ccchHHHHHH-HcCCC
Confidence 4666444333444 4 78888999999999999999999999988766443322211 1234556777 57764
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=68.02 E-value=8.1 Score=23.05 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=19.0
Q ss_pred HHHHHHHHHccCChHHHHHHHhcC
Q 023626 179 RETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 179 ~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
..+++-|.++||+++++...+.++
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 356777889999999988877755
No 18
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=67.26 E-value=16 Score=32.86 Aligned_cols=67 Identities=18% Similarity=0.306 Sum_probs=41.6
Q ss_pred cccccHHHHHHHHHHHH-Hcc-CChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChH-HHhhCCc
Q 023626 170 LLNTRVERLRETLRFLR-SIG-LNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLE-ELKEFPQ 237 (279)
Q Consensus 170 ll~~s~~~l~~~v~~L~-~~G-~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~-~i~~~P~ 237 (279)
+-.++.-.+++++.|.. ..| |+.-.+.+=+.-.|.++.++. ++++.|.+-|.+.+|+++. ..-+||.
T Consensus 65 i~~~d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k-~~i~~r~~ELl~lvgL~p~~~~~RyP~ 134 (309)
T COG1125 65 ISDLDPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDK-ERIKKRADELLDLVGLDPSEYADRYPH 134 (309)
T ss_pred cccCCHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCH-HHHHHHHHHHHHHhCCCHHHHhhcCch
Confidence 33445556777777765 666 333445666667777777776 5777777777776777653 2334444
No 19
>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=66.26 E-value=11 Score=23.60 Aligned_cols=30 Identities=23% Similarity=0.410 Sum_probs=23.4
Q ss_pred HHHHHHHHHHH-HccCChHHHHHHHhcCCcc
Q 023626 176 ERLRETLRFLR-SIGLNRREAAEFCARMPAI 205 (279)
Q Consensus 176 ~~l~~~v~~L~-~~G~s~~~v~~~l~~~P~i 205 (279)
+++..+...|. ++|++....++++..||.+
T Consensus 6 ~k~H~n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 6 EKYHSNAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp HHHHH-HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred HHHccCHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 45777888999 9999999999999999975
No 20
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=65.70 E-value=12 Score=32.87 Aligned_cols=96 Identities=16% Similarity=0.239 Sum_probs=67.3
Q ss_pred CCCchhhHHHHHhCCCCCCCCccccCC---CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCc--cccccccCCchhhH
Q 023626 37 KTSHRENLRYLRAIGVIDPSTKPHKLP---SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQ--FFSINFDPSEIEPV 111 (279)
Q Consensus 37 ~~~~~~~l~~L~~~Gls~~~~ii~~~P---l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~--lL~~~~e~~~l~~~ 111 (279)
+.+..+.++.|.+.|+ +++|...+.= +.-.....-..+++|...|++......+-.-+|. +.....+ =+.+
T Consensus 30 e~eANemlAlL~~~gI-~A~K~~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~e---EkaR 105 (246)
T COG4669 30 EKEANEMLALLMSHGI-NAEKKADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTE---EKAR 105 (246)
T ss_pred HhHHHHHHHHHHHcCC-cceeeccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHH---HHHH
Confidence 4566788999999999 5655433332 4445578888999999999998777766666663 4444332 3555
Q ss_pred HHHHHHhcCCChHHHHHHHHhCCcccccChh
Q 023626 112 FDFLITDLHASVEERRGLIIGCPQMLSSNVE 142 (279)
Q Consensus 112 v~fL~~~lGls~~~i~~ll~~~P~iL~~s~~ 142 (279)
+.|.. ++++.+.+.+-..++..++.
T Consensus 106 ~~~~~------eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 106 LNYAK------EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHH------HHHHHHHHHhcCceEEEEEE
Confidence 66655 67888899988888887753
No 21
>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=65.12 E-value=9.8 Score=22.78 Aligned_cols=23 Identities=30% Similarity=0.372 Sum_probs=18.2
Q ss_pred HHHHHHHHccCChHHHHHHHhcC
Q 023626 180 ETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 180 ~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
.+++-|.++||+++++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 56777889999999888776644
No 22
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=62.99 E-value=12 Score=25.60 Aligned_cols=45 Identities=16% Similarity=0.128 Sum_probs=26.9
Q ss_pred CCCCCCCccccC-C--CcchhhhHHHHHHHHhhCCCChhHHHHHHhhC
Q 023626 51 GVIDPSTKPHKL-P--SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLC 95 (279)
Q Consensus 51 Gls~~~~ii~~~-P--l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~ 95 (279)
|.|.+..-.++. | +..+.+.+++.+--|.+-|+++++|+-++...
T Consensus 10 G~S~S~~P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~ 57 (60)
T PF08069_consen 10 GISGSTRPYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQ 57 (60)
T ss_dssp --------S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHS
T ss_pred CccCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhc
Confidence 555443323333 5 78888999999999999999999999888653
No 23
>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=61.80 E-value=6.6 Score=25.19 Aligned_cols=26 Identities=27% Similarity=0.450 Sum_probs=20.1
Q ss_pred HHHHHHHHHHccCChHHHHHHHhcCC
Q 023626 178 LRETLRFLRSIGLNRREAAEFCARMP 203 (279)
Q Consensus 178 l~~~v~~L~~~G~s~~~v~~~l~~~P 203 (279)
+.+-+.-|..+||++.++.+++.+-.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 45677788999999999988888653
No 24
>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=61.63 E-value=15 Score=23.56 Aligned_cols=26 Identities=8% Similarity=0.077 Sum_probs=17.8
Q ss_pred HHHHHHHHhhCCCChhHHHHHHhhCC
Q 023626 71 ILSTIDFFKSKGLTNGHFSRLAYLCP 96 (279)
Q Consensus 71 l~~~i~~L~~~G~s~~~i~~li~~~P 96 (279)
..+.++.|.++|+++.++.+++.+-.
T Consensus 3 ~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 3 LEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 45667777788888888877776543
No 25
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=57.95 E-value=58 Score=26.38 Aligned_cols=70 Identities=13% Similarity=0.054 Sum_probs=45.4
Q ss_pred CCCCCCCCccccC-C--CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCC
Q 023626 50 IGVIDPSTKPHKL-P--SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHAS 122 (279)
Q Consensus 50 ~Gls~~~~ii~~~-P--l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls 122 (279)
-|.|.+..-.++. | +..+.+.+.+.+--|..-|+++++|+-++...-.+-....- .=.....+|+ +.|+.
T Consensus 6 kG~S~S~~P~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~v--tG~kI~rILk-~~Gla 78 (148)
T PTZ00072 6 KGISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNV--TGSKILRILK-KNGLA 78 (148)
T ss_pred CCCCCCCCCCCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeec--cchHHHHHHH-hcCCC
Confidence 4665444333443 4 67888999999999999999999999888765433222111 1233556777 57753
No 26
>PRK09875 putative hydrolase; Provisional
Probab=57.76 E-value=28 Score=31.56 Aligned_cols=92 Identities=18% Similarity=0.163 Sum_probs=50.1
Q ss_pred hhHHHHHhCCCCCCCCccccCC-CcchhhhHHHHHH---HHh--hCCC----ChhHHHHHHh----hC---Ccccccccc
Q 023626 42 ENLRYLRAIGVIDPSTKPHKLP-SPEVVSQILSTID---FFK--SKGL----TNGHFSRLAY----LC---PQFFSINFD 104 (279)
Q Consensus 42 ~~l~~L~~~Gls~~~~ii~~~P-l~~~~~~l~~~i~---~L~--~~G~----s~~~i~~li~----~~---P~lL~~~~e 104 (279)
+.++.|++.|+ ++++++-.++ ...+.+.+.+.++ |+. .+|. +.++..+++. +- --+|+.+..
T Consensus 167 e~l~il~e~Gv-d~~rvvi~H~d~~~d~~~~~~l~~~G~~l~fD~~g~~~~~pd~~r~~~i~~L~~~Gy~drilLS~D~~ 245 (292)
T PRK09875 167 EQLALLQAHGV-DLSRVTVGHCDLKDNLDNILKMIDLGAYVQFDTIGKNSYYPDEKRIAMLHALRDRGLLNRVMLSMDIT 245 (292)
T ss_pred HHHHHHHHcCc-CcceEEEeCCCCCCCHHHHHHHHHcCCEEEeccCCCcccCCHHHHHHHHHHHHhcCCCCeEEEeCCCC
Confidence 45889999999 6777666665 4444444444432 111 1121 2222222221 11 123444432
Q ss_pred C-------------CchhhHHHHHHHhcCCChHHHHHHHHhCCc
Q 023626 105 P-------------SEIEPVFDFLITDLHASVEERRGLIIGCPQ 135 (279)
Q Consensus 105 ~-------------~~l~~~v~fL~~~lGls~~~i~~ll~~~P~ 135 (279)
+ .-+...+-.|+ +.|+++++|.+++..||.
T Consensus 246 ~~~~~~~~gg~G~~~i~~~~ip~L~-~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 246 RRSHLKANGGYGYDYLLTTFIPQLR-QSGFSQADVDVMLRENPS 288 (292)
T ss_pred CcccccccCCCChhHHHHHHHHHHH-HcCCCHHHHHHHHHHCHH
Confidence 0 11445566677 689999999999999885
No 27
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=54.43 E-value=12 Score=25.50 Aligned_cols=38 Identities=16% Similarity=0.104 Sum_probs=29.0
Q ss_pred hcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcC
Q 023626 165 TLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 165 ~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
...|..+..+.+.+++.|--|.+-|++..+|.-+++..
T Consensus 20 ~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~ 57 (60)
T PF08069_consen 20 RSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQ 57 (60)
T ss_dssp SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHS
T ss_pred CCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhc
Confidence 45688999999999999999999999999999888753
No 28
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=54.31 E-value=60 Score=22.97 Aligned_cols=56 Identities=13% Similarity=0.236 Sum_probs=36.3
Q ss_pred HHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHH---HhCCcccc
Q 023626 73 STIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLI---IGCPQMLS 138 (279)
Q Consensus 73 ~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll---~~~P~iL~ 138 (279)
|.+..|++..+|+++|..++.. |+. +-......+. .+|++.+.+..++ ..+|.++.
T Consensus 3 PIia~LKehnvsd~qi~elFq~----lT~-----NPl~AMa~i~-qLGip~eKLQ~lm~~VMqnP~Lik 61 (82)
T PF11212_consen 3 PIIAILKEHNVSDEQINELFQA----LTQ-----NPLAAMATIQ-QLGIPQEKLQQLMAQVMQNPALIK 61 (82)
T ss_pred hHHHHHHHcCCCHHHHHHHHHH----Hhh-----CHHHHHHHHH-HcCCCHHHHHHHHHHHhcChHHHH
Confidence 5677888888888888887762 332 3344556676 6888887775544 35555443
No 29
>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=53.25 E-value=38 Score=25.55 Aligned_cols=23 Identities=22% Similarity=0.293 Sum_probs=18.9
Q ss_pred cCCChHHHHHHHHhCCcccccCh
Q 023626 119 LHASVEERRGLIIGCPQMLSSNV 141 (279)
Q Consensus 119 lGls~~~i~~ll~~~P~iL~~s~ 141 (279)
..++.+++..++..+|.++..++
T Consensus 69 ~~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 69 DDLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp TTSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhhHHHHHHHHhChhheeCCE
Confidence 45789999999999999988775
No 30
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=44.45 E-value=54 Score=23.83 Aligned_cols=39 Identities=10% Similarity=0.174 Sum_probs=26.9
Q ss_pred HHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcC
Q 023626 77 FFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLH 120 (279)
Q Consensus 77 ~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lG 120 (279)
+-+.+|+++.+|..+-..+|. +.. +.....+..+++..|
T Consensus 19 laR~LGlse~~Id~i~~~~~~----~~~-eq~~~mL~~W~~~~g 57 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR----NLR-EQVRQSLREWKKIKK 57 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC----CHH-HHHHHHHHHHHHhHC
Confidence 445688888888888888884 232 367777776665455
No 31
>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=43.82 E-value=57 Score=24.34 Aligned_cols=40 Identities=5% Similarity=-0.023 Sum_probs=29.8
Q ss_pred HHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcC
Q 023626 75 IDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLH 120 (279)
Q Consensus 75 i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lG 120 (279)
-++.+.+|++..+|..+-..+|.- . +.....+.-+++..|
T Consensus 23 k~laR~LGLse~~I~~i~~~~~~~----~--eq~~qmL~~W~~~~G 62 (96)
T cd08315 23 NRLMRQLGLSENEIDVAKANERVT----R--EQLYQMLLTWVNKTG 62 (96)
T ss_pred HHHHHHcCCCHHHHHHHHHHCCCC----H--HHHHHHHHHHHHhhC
Confidence 345678899999999999888863 2 367777777776566
No 32
>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=42.34 E-value=66 Score=23.23 Aligned_cols=50 Identities=10% Similarity=0.082 Sum_probs=31.8
Q ss_pred HHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHH
Q 023626 74 TIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGL 129 (279)
Q Consensus 74 ~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~l 129 (279)
--+|.+.+|+++.+|..+-..+| ... +...+.+.-+++..|-.+..+..+
T Consensus 14 wk~~~R~LGlse~~Id~ie~~~~---~~~---Eq~yqmL~~W~~~~g~~~At~~~L 63 (80)
T cd08313 14 WKEFVRRLGLSDNEIERVELDHR---RCR---DAQYQMLKVWKERGPRPYATLQHL 63 (80)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCC---ChH---HHHHHHHHHHHHhcCCCcchHHHH
Confidence 34567788999999998888887 211 366667777765556423333333
No 33
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=40.72 E-value=81 Score=24.37 Aligned_cols=58 Identities=21% Similarity=0.174 Sum_probs=41.5
Q ss_pred chhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHHH
Q 023626 66 EVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLII 131 (279)
Q Consensus 66 ~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll~ 131 (279)
.+.+.+......|...|+.+.++..++.-+|.= .+ .+...+.-+.+. ++++++.+++.
T Consensus 52 ~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s----~~--E~~~lI~sl~~r--~~ee~l~~iL~ 109 (118)
T smart00657 52 KNREIVRAVRTLLKSKKLHKFEIAQLGNLRPET----AE--EAQLLIPSLEER--IDEEELEELLD 109 (118)
T ss_pred CCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCC----HH--HHHHHhhhhhcc--CCHHHHHHHHH
Confidence 456778888888888899999999888877763 32 566666666532 67777766654
No 34
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=40.51 E-value=51 Score=26.21 Aligned_cols=69 Identities=16% Similarity=0.123 Sum_probs=46.7
Q ss_pred ccCC--CcchhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCCh---HHHHHHHH
Q 023626 60 HKLP--SPEVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASV---EERRGLII 131 (279)
Q Consensus 60 ~~~P--l~~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~---~~i~~ll~ 131 (279)
+..| +..+.+.+.+-+--|.+.|+++.||+-++...-.+=....- .=...+.+|+ ..|+-+ +|+-.++.
T Consensus 20 r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v--~G~kI~Rilk-~~Gl~PeiPeDLy~lik 93 (151)
T KOG0400|consen 20 RSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFV--TGNKILRILK-SNGLAPEIPEDLYHLIK 93 (151)
T ss_pred cCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhhee--chhHHHHHHH-HcCCCCCCcHHHHHHHH
Confidence 4456 77778888888888899999999999887766655444432 2344566777 577753 44444443
No 35
>KOG0995 consensus Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning]
Probab=39.12 E-value=1.7e+02 Score=29.03 Aligned_cols=82 Identities=18% Similarity=0.294 Sum_probs=49.8
Q ss_pred CCCCCCCCccccCC--Ccc---hhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHH----hcC
Q 023626 50 IGVIDPSTKPHKLP--SPE---VVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLIT----DLH 120 (279)
Q Consensus 50 ~Gls~~~~ii~~~P--l~~---~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~----~lG 120 (279)
+|...+ ....+.| +.. --+.+....+||...|++ ..+.-=+...|.. ++....+.||.+ .++
T Consensus 51 ~~~~~~-~~s~~dpRpl~dk~~~s~c~~~I~~fL~engf~-~~iS~k~l~~PS~-------KdF~~iFkfLY~~Ldp~y~ 121 (581)
T KOG0995|consen 51 LSSFNT-SNSIRDPRPLSDKRYRSQCIRQIYNFLVENGFS-HPISIKLLMKPSV-------KDFIAIFKFLYGFLDPDYE 121 (581)
T ss_pred ccccCc-hhccCCCCCcccHHHHHHHHHHHHHHHHHcCCC-CChhhhhcCCCcc-------ccHHHHHHHHHhccCCCcc
Confidence 666433 2334445 433 347788889999999998 3343333344433 467778888874 244
Q ss_pred CC---hHHHHHHHH--hCCcccccC
Q 023626 121 AS---VEERRGLII--GCPQMLSSN 140 (279)
Q Consensus 121 ls---~~~i~~ll~--~~P~iL~~s 140 (279)
++ +++|..++. +||..++.+
T Consensus 122 f~~r~EeEV~~ilK~L~YPf~~siS 146 (581)
T KOG0995|consen 122 FPERIEEEVVQILKNLKYPFLLSIS 146 (581)
T ss_pred cchhHHHHHHHHHHhCCCCcccchh
Confidence 42 467777775 678777644
No 36
>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=38.14 E-value=34 Score=26.80 Aligned_cols=59 Identities=14% Similarity=0.231 Sum_probs=33.5
Q ss_pred hhHHHHHHHHhhCCCChhHHHHHHhhCCccccc-----cccCCch--------hhHHHHHHHhcCCChHHHHHHH
Q 023626 69 SQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSI-----NFDPSEI--------EPVFDFLITDLHASVEERRGLI 130 (279)
Q Consensus 69 ~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~-----~~e~~~l--------~~~v~fL~~~lGls~~~i~~ll 130 (279)
+++....+.|+. |++.++|..+=.-.|+.|.. +.| +.+ ...+.-.+ .+|+|+..|+++.
T Consensus 11 ~Rlf~i~eAlrr-G~sveeI~e~T~ID~wFL~~i~~Iv~~e-~~L~~~~~~~~~~~L~~aK-~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 11 ERLFAIAEALRR-GYSVEEIHELTKIDPWFLEQIKNIVDME-KELKEYLNELDPELLRKAK-RLGFSDRQIARLW 82 (123)
T ss_dssp THHHHHHHHHHT-TB-HHHHHHHH---HHHHHHHHHHHHHH-HHHHHHGGG--HHHHHHHH-HTT--HHHHHHHH
T ss_pred cHHHHHHHHHHc-CCCHHHHHHHHCccHHHHHHHHHHHHHH-HHHHHhhccchHHHHHHHH-HcCCCHHHHHhcc
Confidence 556666666644 99999999988888888752 111 111 22333444 6899999998875
No 37
>PRK11613 folP dihydropteroate synthase; Provisional
Probab=36.59 E-value=54 Score=29.62 Aligned_cols=24 Identities=8% Similarity=0.093 Sum_probs=16.4
Q ss_pred chhhhHHHHHHHHhhCCCChhHHH
Q 023626 66 EVVSQILSTIDFFKSKGLTNGHFS 89 (279)
Q Consensus 66 ~~~~~l~~~i~~L~~~G~s~~~i~ 89 (279)
.+.+.+..+...+.+-|.+--||+
T Consensus 35 ~~~~~a~~~a~~~~~~GAdIIDIG 58 (282)
T PRK11613 35 NSLIDAVKHANLMINAGATIIDVG 58 (282)
T ss_pred CCHHHHHHHHHHHHHCCCcEEEEC
Confidence 456777777777777776666665
No 38
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.98 E-value=1.6e+02 Score=22.83 Aligned_cols=49 Identities=14% Similarity=0.149 Sum_probs=34.1
Q ss_pred hHHHHHhCCCCCCCCccccCC---CcchhhhHH--HHHHHHhhCCCChhHHHHHHhh
Q 023626 43 NLRYLRAIGVIDPSTKPHKLP---SPEVVSQIL--STIDFFKSKGLTNGHFSRLAYL 94 (279)
Q Consensus 43 ~l~~L~~~Gls~~~~ii~~~P---l~~~~~~l~--~~i~~L~~~G~s~~~i~~li~~ 94 (279)
.+.|....|+=.+. .+.+ ..++.+.+. ..+..|+++||+-++|..++..
T Consensus 16 tLRyYe~~GLl~p~---~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 16 TIRYYEKEGLLPAP---ARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred HHHHHHHCCCCCCC---CcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 47788888882211 1122 456665554 5678889999999999998874
No 39
>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=34.76 E-value=1e+02 Score=21.93 Aligned_cols=40 Identities=15% Similarity=0.239 Sum_probs=30.5
Q ss_pred HHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcC
Q 023626 75 IDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLH 120 (279)
Q Consensus 75 i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lG 120 (279)
-++.+.+|+++.+|..+-..+|. .. +...+.+.-+++..|
T Consensus 15 k~laR~LGls~~~I~~ie~~~~~-~~-----eq~~~mL~~W~~k~G 54 (79)
T cd08784 15 KRFFRKLGLSDNEIKVAELDNPQ-HR-----DRVYELLRIWRNKEG 54 (79)
T ss_pred HHHHHHcCCCHHHHHHHHHcCCc-hH-----HHHHHHHHHHHhccC
Confidence 34667899999999999999998 32 367777777775566
No 40
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=33.70 E-value=1.8e+02 Score=21.73 Aligned_cols=43 Identities=12% Similarity=0.148 Sum_probs=28.7
Q ss_pred HHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcC
Q 023626 73 STIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLH 120 (279)
Q Consensus 73 ~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lG 120 (279)
..-+|-+.+|+++.+|..+-..+|.=.. ++..+.+.-+.+..|
T Consensus 22 ~wK~faR~lglse~~Id~I~~~~~~d~~-----Eq~~qmL~~W~~~~G 64 (97)
T cd08316 22 DVKKFVRKSGLSEPKIDEIKLDNPQDTA-----EQKVQLLRAWYQSHG 64 (97)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCCCChH-----HHHHHHHHHHHHHhC
Confidence 3445667888888888888888886531 255566666654455
No 41
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=32.68 E-value=57 Score=21.86 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=14.4
Q ss_pred HHHHHHHccCChHHHHHHHhc
Q 023626 181 TLRFLRSIGLNRREAAEFCAR 201 (279)
Q Consensus 181 ~v~~L~~~G~s~~~v~~~l~~ 201 (279)
.++-+..+||+.+.+..++++
T Consensus 12 lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHcCCcHHHHHHHHHH
Confidence 455588899999888877765
No 42
>PRK09875 putative hydrolase; Provisional
Probab=32.44 E-value=40 Score=30.57 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=23.8
Q ss_pred HHHHHHHHHHccCChHHHHHHHhcCCc
Q 023626 178 LRETLRFLRSIGLNRREAAEFCARMPA 204 (279)
Q Consensus 178 l~~~v~~L~~~G~s~~~v~~~l~~~P~ 204 (279)
+..-+-.|++.|+++++|.+|+..||+
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 566677788899999999999999997
No 43
>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=31.55 E-value=58 Score=24.81 Aligned_cols=57 Identities=19% Similarity=0.164 Sum_probs=35.8
Q ss_pred chhhhHHHHHHHHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHH
Q 023626 66 EVVSQILSTIDFFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLI 130 (279)
Q Consensus 66 ~~~~~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll 130 (279)
.+.+.+...++.|.+.|+++.++.+++.-+|.= .+ .+...+.-+. -.++++++.+++
T Consensus 54 ~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~~----~~--El~~ii~~~~--~r~~ee~l~~iL 110 (117)
T PF03874_consen 54 QNPESIKELREELKKFGLTEFEILQIINLRPTT----AV--ELRAIIESLE--SRFSEEDLEEIL 110 (117)
T ss_dssp SSHHHHHHHHHHHTTSTS-HHHHHHHHHH--SS----HH--HHHHHSTTGT--TTSTHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcccCCHHHHHHHhcCCCCC----HH--HHHHHHHHhc--cCCCHHHHHHHH
Confidence 445778888888889999999999999888842 22 3444444443 235677776665
No 44
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.19 E-value=29 Score=25.24 Aligned_cols=60 Identities=10% Similarity=0.071 Sum_probs=37.1
Q ss_pred CCCCCCCCCcccCCCCchhhHHHHHhCCCCCCC-CccccCC-CcchhhhHHHHHHHHhhCCCChh
Q 023626 24 FSSSQNPPLYLKFKTSHRENLRYLRAIGVIDPS-TKPHKLP-SPEVVSQILSTIDFFKSKGLTNG 86 (279)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~l~~L~~~Gls~~~-~ii~~~P-l~~~~~~l~~~i~~L~~~G~s~~ 86 (279)
++.-...-++++..+.++....|..+.|..... +++..+| ...+.+.+. .-|+++|+-+.
T Consensus 12 lP~G~r~~rrF~~~~~L~~v~~fv~~~g~~~~~f~L~t~FPRr~~~~~d~~---~TL~e~GL~P~ 73 (82)
T cd01773 12 YPDGKREQIALPEQAKLLALVRHVQSKGYPNERFELLTNFPRRKLSHLDYD---ITLQEAGLCPQ 73 (82)
T ss_pred CCCCCEEEEEeCCCCcHHHHHHHHHhcCCCCCCEEEecCCCCcccCCcccC---CCHHHcCCCCC
Confidence 344445556777778888888888888874222 6888888 333333332 25567777654
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=30.10 E-value=1.9e+02 Score=24.35 Aligned_cols=55 Identities=13% Similarity=0.112 Sum_probs=32.3
Q ss_pred HHhhC-CCChhHHHHHHhhCCcccc---------ccccCCchhhHHHHHHHhcCCChHHHHHHHHhC
Q 023626 77 FFKSK-GLTNGHFSRLAYLCPQFFS---------INFDPSEIEPVFDFLITDLHASVEERRGLIIGC 133 (279)
Q Consensus 77 ~L~~~-G~s~~~i~~li~~~P~lL~---------~~~e~~~l~~~v~fL~~~lGls~~~i~~ll~~~ 133 (279)
.|..+ |++.....+++...-.-+. .... ..+...+.+|. .+|++..++.+++...
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~-~~~~ev~~aL~-~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAAS-SALEEAVSALV-ALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHHhhccccccccccccc-chHHHHHHHHH-HcCCCHHHHHHHHHHH
Confidence 45554 7776666666644332221 0111 13567778887 5888888888777765
No 46
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=28.48 E-value=70 Score=18.60 Aligned_cols=24 Identities=17% Similarity=0.203 Sum_probs=12.5
Q ss_pred HHHHHHHHhhCCCChhHHHHHHhh
Q 023626 71 ILSTIDFFKSKGLTNGHFSRLAYL 94 (279)
Q Consensus 71 l~~~i~~L~~~G~s~~~i~~li~~ 94 (279)
+...+.--+..|++.+++.+.+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 344444455667777777666543
No 47
>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=27.96 E-value=1.1e+02 Score=28.90 Aligned_cols=43 Identities=14% Similarity=0.183 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHccCChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCC
Q 023626 176 ERLRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERS 228 (279)
Q Consensus 176 ~~l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~ 228 (279)
+..+..|+-+.+|||.+++|.+.++. +. .+=.+-++||.. |++
T Consensus 154 ~~~e~~I~~i~eMGf~R~qV~~ALRA-------af-NNPdRAVEYL~t--GIP 196 (378)
T TIGR00601 154 SERETTIEEIMEMGYEREEVERALRA-------AF-NNPDRAVEYLLT--GIP 196 (378)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHH-------Hh-CCHHHHHHHHHh--CCC
Confidence 35788999999999999999988772 22 233588999984 776
No 48
>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=27.89 E-value=97 Score=22.37 Aligned_cols=38 Identities=16% Similarity=0.224 Sum_probs=24.8
Q ss_pred HHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHH
Q 023626 77 FFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLIT 117 (279)
Q Consensus 77 ~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~ 117 (279)
=|+..|+++++|..+=..+-.++..+ ..+...++-+.+
T Consensus 22 GLrR~Gfs~~~i~~l~~ayr~l~~~~---~~~~~a~~~l~~ 59 (83)
T PF13720_consen 22 GLRRRGFSKEEISALRRAYRILFRSG---LTLEEALEELEE 59 (83)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHHHTSS---S-HHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhCC---CCHHHHHHHHHH
Confidence 46778888888887777666666544 256777777763
No 49
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=25.54 E-value=3.4e+02 Score=21.48 Aligned_cols=80 Identities=20% Similarity=0.245 Sum_probs=46.2
Q ss_pred ChHHHHHHHHhCCcccccChh----hhhHhHHHHHHH-hCCCCC-Ccchhccccccccc--HHHHHHHHHHHHHccCChH
Q 023626 122 SVEERRGLIIGCPQMLSSNVE----YCLKPTLDYLTK-LGVKKL-NVPSTLNARLLNTR--VERLRETLRFLRSIGLNRR 193 (279)
Q Consensus 122 s~~~i~~ll~~~P~iL~~s~~----~~l~~~i~~L~~-lG~~~~-~~li~~~P~ll~~s--~~~l~~~v~~L~~~G~s~~ 193 (279)
|..|+-.++.+||.+=...+. +++...++.+-+ -|+.=. +.+....-.+=.+. .+.+-+++.-|.+-|.+.+
T Consensus 29 SN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinEYy~i~~~vi~~I~el~~eG~s~e 108 (131)
T PF08004_consen 29 SNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINEYYEIPESVIERIKELKSEGKSEE 108 (131)
T ss_pred cchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCcccccCCHHHHHHHHHHHHcCCCHH
Confidence 678889999999987664433 334444443333 455421 11111111111111 3457888899998999999
Q ss_pred HHHHHHhc
Q 023626 194 EAAEFCAR 201 (279)
Q Consensus 194 ~v~~~l~~ 201 (279)
++..-+.+
T Consensus 109 ei~~ki~~ 116 (131)
T PF08004_consen 109 EIAEKISR 116 (131)
T ss_pred HHHHHHHH
Confidence 98766554
No 50
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, 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 domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.42 E-value=2.6e+02 Score=21.02 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=19.0
Q ss_pred HHHHHHHHHccCChHHHHHHHhc
Q 023626 179 RETLRFLRSIGLNRREAAEFCAR 201 (279)
Q Consensus 179 ~~~v~~L~~~G~s~~~v~~~l~~ 201 (279)
-..|..|+++||+.++|..++..
T Consensus 47 l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 47 LEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 35677888999999999988764
No 51
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=25.06 E-value=69 Score=29.98 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.9
Q ss_pred HHHHHHHHHHccCChHHHHHHHhc
Q 023626 178 LRETLRFLRSIGLNRREAAEFCAR 201 (279)
Q Consensus 178 l~~~v~~L~~~G~s~~~v~~~l~~ 201 (279)
+.+.||-+..|||++|.|+.+|+|
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v~r 344 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATVRR 344 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHH
Confidence 567777788999999999888875
No 52
>PHA02591 hypothetical protein; Provisional
Probab=24.90 E-value=1e+02 Score=22.29 Aligned_cols=30 Identities=20% Similarity=0.171 Sum_probs=24.7
Q ss_pred CcchhhhHHHHHHHHhhCCCChhHHHHHHh
Q 023626 64 SPEVVSQILSTIDFFKSKGLTNGHFSRLAY 93 (279)
Q Consensus 64 l~~~~~~l~~~i~~L~~~G~s~~~i~~li~ 93 (279)
...+.+.+.....-|.+.|++.++|++.+.
T Consensus 41 fi~~~dd~~~vA~eL~eqGlSqeqIA~~LG 70 (83)
T PHA02591 41 FVESEDDLISVTHELARKGFTVEKIASLLG 70 (83)
T ss_pred EEeccchHHHHHHHHHHcCCCHHHHHHHhC
Confidence 345678888899999999999999998653
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=24.89 E-value=77 Score=21.22 Aligned_cols=22 Identities=14% Similarity=0.339 Sum_probs=17.2
Q ss_pred HHHHHH-HccCChHHHHHHHhcC
Q 023626 181 TLRFLR-SIGLNRREAAEFCARM 202 (279)
Q Consensus 181 ~v~~L~-~~G~s~~~v~~~l~~~ 202 (279)
-+.|.. ++|++.+++..+|...
T Consensus 22 ev~ywa~~~gvt~~~L~~AV~~v 44 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQLREAVRAV 44 (57)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHH
Confidence 456666 8999999999888753
No 54
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=24.72 E-value=85 Score=20.92 Aligned_cols=19 Identities=32% Similarity=0.488 Sum_probs=13.7
Q ss_pred HHHHHHHccCChHHHHHHH
Q 023626 181 TLRFLRSIGLNRREAAEFC 199 (279)
Q Consensus 181 ~v~~L~~~G~s~~~v~~~l 199 (279)
-|..++.+|||-+++..++
T Consensus 6 ~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3455668999999999998
No 55
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=23.96 E-value=2.6e+02 Score=20.27 Aligned_cols=38 Identities=5% Similarity=0.117 Sum_probs=26.2
Q ss_pred HhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcC
Q 023626 78 FKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLH 120 (279)
Q Consensus 78 L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lG 120 (279)
-+.+|++..+|..+-..||.=+. ++....+..+++.-|
T Consensus 22 ar~L~vs~~dI~~I~~e~p~~l~-----~Q~~~~L~~W~~r~g 59 (84)
T cd08805 22 ARELQFSVEDINRIRVENPNSLL-----EQSTALLNLWVDREG 59 (84)
T ss_pred HHHcCCCHHHHHHHHHhCCCCHH-----HHHHHHHHHHHHhcC
Confidence 35799999999999999996322 245555555554334
No 56
>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=23.71 E-value=2.1e+02 Score=20.74 Aligned_cols=44 Identities=14% Similarity=0.066 Sum_probs=29.7
Q ss_pred HhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHH
Q 023626 78 FKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERR 127 (279)
Q Consensus 78 L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~ 127 (279)
.+.+|++..+|..+-..+|.=+ . +++...+--+++..| ..+.+.
T Consensus 20 ar~Lgls~~~I~~i~~~~p~~l----~-eQv~~mL~~W~~r~G-~~ATv~ 63 (83)
T cd08319 20 LLDLGLSQTDIYRCKENHPHNV----Q-SQIVEALVKWRQRFG-KKATVQ 63 (83)
T ss_pred HHHcCCCHHHHHHHHHhCCCCH----H-HHHHHHHHHHHHhcC-CCCcHH
Confidence 3579999999999999989633 2 366666666665455 343333
No 57
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=23.68 E-value=1.3e+02 Score=24.58 Aligned_cols=39 Identities=13% Similarity=0.018 Sum_probs=33.7
Q ss_pred hcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcCC
Q 023626 165 TLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARMP 203 (279)
Q Consensus 165 ~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~P 203 (279)
...|..+.++.+.+++.|.-|.+-|.+.++|+-+++..=
T Consensus 20 ~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~ 58 (151)
T PRK08561 20 TEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQY 58 (151)
T ss_pred CCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhcc
Confidence 456778999999999999999999999999998887664
No 58
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.60 E-value=2.9e+02 Score=20.93 Aligned_cols=56 Identities=14% Similarity=0.125 Sum_probs=0.0
Q ss_pred HhHHHHHHHhCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcC
Q 023626 146 KPTLDYLTKLGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 146 ~~~i~~L~~lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
...+.|+.+.|+=....--. .-+.++.+--..-..+..|+++|++.++|..++..+
T Consensus 14 ~~tLryYe~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (116)
T cd04769 14 IKAIRLYEEKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGH 69 (116)
T ss_pred HHHHHHHHHCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
No 59
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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 two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=23.25 E-value=2.6e+02 Score=21.80 Aligned_cols=55 Identities=15% Similarity=0.227 Sum_probs=32.2
Q ss_pred HHHHHHHhCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcC
Q 023626 148 TLDYLTKLGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 148 ~i~~L~~lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
.+.|+.+.|+=...+-=...-+.++.+.-..-..|..|+++||+.++|..++...
T Consensus 16 TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (133)
T cd04787 16 TVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHA 70 (133)
T ss_pred HHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhh
Confidence 5677777776321110001112333322234567888899999999999988743
No 60
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.00 E-value=1.2e+02 Score=19.84 Aligned_cols=45 Identities=24% Similarity=0.274 Sum_probs=23.8
Q ss_pred HHH-HccCChHHHHHHHhcCCcccccChhhhHHHHHHHHHHHhCCChHHHhhC
Q 023626 184 FLR-SIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEFLAVEMERSLEELKEF 235 (279)
Q Consensus 184 ~L~-~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~fL~~~mg~~~~~i~~~ 235 (279)
.|. ..|++...+.+++...+.- .+. ..+.-+...+|++++++..+
T Consensus 15 ~La~~~gis~~tl~~~~~~~~~~--~~~-----~~l~~ia~~l~~~~~el~~~ 60 (63)
T PF13443_consen 15 DLARKTGISRSTLSRILNGKPSN--PSL-----DTLEKIAKALNCSPEELFEY 60 (63)
T ss_dssp HHHHHHT--HHHHHHHHTTT-------H-----HHHHHHHHHHT--HHHCTEC
T ss_pred HHHHHHCcCHHHHHHHHhccccc--ccH-----HHHHHHHHHcCCCHHHHhhc
Confidence 344 7899999999888866432 222 22444555678888887653
No 61
>PRK06361 hypothetical protein; Provisional
Probab=22.05 E-value=1.3e+02 Score=25.37 Aligned_cols=31 Identities=13% Similarity=0.057 Sum_probs=18.6
Q ss_pred hHHHHHHHHhhCCCChhHHHHHHhhCCcccc
Q 023626 70 QILSTIDFFKSKGLTNGHFSRLAYLCPQFFS 100 (279)
Q Consensus 70 ~l~~~i~~L~~~G~s~~~i~~li~~~P~lL~ 100 (279)
.......+.++.|++++++.++++.+|..+.
T Consensus 178 ~~~~~~~i~~~~gl~~~~v~~~~~~~~~~~~ 208 (212)
T PRK06361 178 TYEFARKVALGAGLTEKELEEALENNPKLLL 208 (212)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHhHHHHH
Confidence 3444455555666666666666666666543
No 62
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.04 E-value=2.6e+02 Score=18.52 Aligned_cols=23 Identities=17% Similarity=0.242 Sum_probs=17.8
Q ss_pred HHHHHHHHHHccCChHHHHHHHh
Q 023626 178 LRETLRFLRSIGLNRREAAEFCA 200 (279)
Q Consensus 178 l~~~v~~L~~~G~s~~~v~~~l~ 200 (279)
.-..+..|.+.|++.++|.+++.
T Consensus 45 ~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 45 RLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHHHHHHHTTTHHHHHHHHH-
T ss_pred HHHHHHHHHHCcCCHHHHHHHHc
Confidence 44567777789999999998875
No 63
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.30 E-value=2.1e+02 Score=24.00 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=29.2
Q ss_pred HHHHHHHHHHccCChHHHHHHHhcCCcccccChhhhHHHHHHH
Q 023626 178 LRETLRFLRSIGLNRREAAEFCARMPAIFGYNIEHHLKIKFEF 220 (279)
Q Consensus 178 l~~~v~~L~~~G~s~~~v~~~l~~~P~iL~~s~e~~i~~k~~f 220 (279)
..+-++-|..+||++.++.+++..-. ..+.|+-|+.-+..
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~~---~~~~eelir~aLk~ 181 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASCQ---STGTSELIKEALKK 181 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhcc---cCCHHHHHHHHHHh
Confidence 46778889999999999999998764 34555555554443
No 64
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=20.24 E-value=75 Score=27.52 Aligned_cols=28 Identities=14% Similarity=0.227 Sum_probs=16.1
Q ss_pred hCCcccccChh-hhhHhHHHHHHHhCCCC
Q 023626 132 GCPQMLSSNVE-YCLKPTLDYLTKLGVKK 159 (279)
Q Consensus 132 ~~P~iL~~s~~-~~l~~~i~~L~~lG~~~ 159 (279)
.+|+++...++ ..+...+.-|+.+|++.
T Consensus 137 ay~~L~~~~ld~~~~~~~l~~l~~~gvPY 165 (217)
T PRK14487 137 AYPWLAENDLDGTDTAEKMTALRVVGVPY 165 (217)
T ss_pred CCcccccccCCHHHHHHHHHHhhhcCCCC
Confidence 34555554444 34666666666677764
No 65
>PRK14136 recX recombination regulator RecX; Provisional
Probab=20.05 E-value=3.2e+02 Score=25.03 Aligned_cols=112 Identities=10% Similarity=0.073 Sum_probs=67.1
Q ss_pred CcchhhhHHHHHHHHhhCCC-ChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHHHHHhCCcccccChh
Q 023626 64 SPEVVSQILSTIDFFKSKGL-TNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRGLIIGCPQMLSSNVE 142 (279)
Q Consensus 64 l~~~~~~l~~~i~~L~~~G~-s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ll~~~P~iL~~s~~ 142 (279)
...+.+.+..+|+.|++.|+ ++...+..+.+. ..-.. . . .....-|+ ..|++.+.|...+... . +
T Consensus 189 kG~~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~~kk--G--p-~rIrqELr-QKGId~eLIEqALeei------e-E 254 (309)
T PRK14136 189 YADESDSVEPLLDALEREGWLSDARFAESLVHR-RASRV--G--S-ARIVSELK-RHAVGDALVESVGAQL------R-E 254 (309)
T ss_pred cCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-Hhhch--h--H-HHHHHHHH-HcCCCHHHHHHHHHhc------c-H
Confidence 45667888999999998765 566677766643 11111 1 1 22345666 6999999998877633 1 1
Q ss_pred hhhHhHHHHHHH-hCCCCCCcchhcccccccccHHHHHHHHHHHHHccCChHHHHHHHhcC
Q 023626 143 YCLKPTLDYLTK-LGVKKLNVPSTLNARLLNTRVERLRETLRFLRSIGLNRREAAEFCARM 202 (279)
Q Consensus 143 ~~l~~~i~~L~~-lG~~~~~~li~~~P~ll~~s~~~l~~~v~~L~~~G~s~~~v~~~l~~~ 202 (279)
..+......++. ++- .| .........+.||..-||+.+.|..++..+
T Consensus 255 DE~E~A~~L~eKK~~~---------~~----~d~kek~K~iRfL~rRGFS~D~I~~vLk~~ 302 (309)
T PRK14136 255 TEFERAQAVWRKKFGA---------LP----QTPAERAKQARFLAARGFSSATIVKLLKVG 302 (309)
T ss_pred hHHHHHHHHHHHHhcc---------cC----cCHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 122222333322 211 01 112334556899999999999998887643
No 66
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, 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 two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.03 E-value=3.7e+02 Score=19.97 Aligned_cols=51 Identities=14% Similarity=0.047 Sum_probs=31.5
Q ss_pred hHHHHHHHhCCCCCCcchhcccccccccHHH--HHHHHHHHHHccCChHHHHHHHhc
Q 023626 147 PTLDYLTKLGVKKLNVPSTLNARLLNTRVER--LRETLRFLRSIGLNRREAAEFCAR 201 (279)
Q Consensus 147 ~~i~~L~~lG~~~~~~li~~~P~ll~~s~~~--l~~~v~~L~~~G~s~~~v~~~l~~ 201 (279)
..+.|+.+.|+=.... ...-.. ++.+. .-..|..++++||+.++|..++..
T Consensus 15 ~tlRyYe~~GLl~p~~--~~g~r~--Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 15 DTVRHYIDLGLLIPEK--KGGQYF--FDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHHCCCcCCcc--CCCccc--cCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3577888888721111 111122 34444 455677788999999999998863
No 67
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=20.03 E-value=2.3e+02 Score=20.51 Aligned_cols=48 Identities=4% Similarity=-0.003 Sum_probs=27.6
Q ss_pred HHhhCCCChhHHHHHHhhCCccccccccCCchhhHHHHHHHhcCCChHHHHH
Q 023626 77 FFKSKGLTNGHFSRLAYLCPQFFSINFDPSEIEPVFDFLITDLHASVEERRG 128 (279)
Q Consensus 77 ~L~~~G~s~~~i~~li~~~P~lL~~~~e~~~l~~~v~fL~~~lGls~~~i~~ 128 (279)
+.+.+|++..+|..+-..++.- +.. +.....+..++...|-....+.+
T Consensus 19 lar~LG~s~~eI~~ie~~~~r~---~~~-eq~~~mL~~W~~r~g~~~ATv~~ 66 (86)
T cd08777 19 CARKLGFTESEIEEIDHDYERD---GLK-EKVHQMLHKWKMKEGSKGATVGK 66 (86)
T ss_pred HHHHcCCCHHHHHHHHHhcccC---CHH-HHHHHHHHHHHHccCCCCcHHHH
Confidence 4457899999999876554332 111 35666666666445532333333
Done!