Query 030484
Match_columns 176
No_of_seqs 117 out of 458
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 14:24:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030484.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030484hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2239 Transcription factor c 100.0 3.7E-48 8.1E-53 320.1 14.3 149 28-176 56-209 (209)
2 PRK06369 nac nascent polypepti 100.0 4.2E-37 9.1E-42 236.5 12.3 105 37-176 6-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 8.4E-32 1.8E-36 208.4 8.1 111 38-176 8-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 5.7E-31 1.2E-35 202.6 11.8 103 37-176 10-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 4.4E-21 9.6E-26 130.8 5.9 58 38-95 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.5 8.6E-08 1.9E-12 78.0 2.9 64 35-98 38-101 (162)
7 KOG3450 Huntingtin interacting 97.8 1.3E-05 2.8E-10 61.7 2.6 43 134-176 76-118 (119)
8 PF00627 UBA: UBA/TS-N domain; 97.7 4.1E-05 9E-10 47.4 3.5 37 137-174 1-37 (37)
9 PF14555 UBA_4: UBA-like domai 95.9 0.012 2.6E-07 37.4 3.7 33 140-172 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.5 0.029 6.3E-07 34.1 3.9 33 141-174 4-36 (38)
11 smart00165 UBA Ubiquitin assoc 95.4 0.03 6.5E-07 33.9 3.9 33 141-174 4-36 (37)
12 COG4008 Predicted metal-bindin 91.6 0.28 6E-06 39.3 4.0 38 133-172 109-146 (153)
13 COG2103 Predicted sugar phosph 86.2 1 2.2E-05 40.1 4.0 39 136-174 231-269 (298)
14 PRK05441 murQ N-acetylmuramic 84.2 1.4 3.1E-05 38.7 4.1 38 137-174 234-271 (299)
15 PF02845 CUE: CUE domain; Int 80.6 3.7 7.9E-05 25.6 3.9 34 141-174 4-38 (42)
16 cd05007 SIS_Etherase N-acetylm 79.2 1.3 2.8E-05 38.0 2.0 36 137-172 221-256 (257)
17 TIGR00274 N-acetylmuramic acid 78.6 2.9 6.4E-05 36.7 4.1 37 137-173 229-265 (291)
18 PF10411 DsbC_N: Disulfide bon 75.9 8.6 0.00019 25.7 4.9 40 42-91 2-50 (57)
19 PRK12570 N-acetylmuramic acid- 74.7 4.2 9.2E-05 35.7 4.0 37 137-173 230-266 (296)
20 PF14474 RTC4: RTC4-like domai 73.4 4 8.6E-05 31.7 3.1 27 137-163 88-114 (124)
21 smart00546 CUE Domain that may 72.1 9.9 0.00021 23.6 4.2 35 140-174 4-39 (43)
22 PF03474 DMA: DMRTA motif; In 71.6 5 0.00011 25.7 2.7 22 152-173 16-37 (39)
23 PF12244 DUF3606: Protein of u 68.5 8.2 0.00018 26.1 3.5 30 139-168 20-49 (57)
24 PF05861 PhnI: Bacterial phosp 63.4 8.3 0.00018 35.4 3.5 33 142-174 45-78 (358)
25 PF11626 Rap1_C: TRF2-interact 62.2 12 0.00027 26.9 3.6 27 146-172 4-30 (87)
26 KOG1071 Mitochondrial translat 60.6 12 0.00026 34.1 3.9 37 136-172 44-80 (340)
27 PF06972 DUF1296: Protein of u 58.4 23 0.00051 24.7 4.2 33 142-174 9-42 (60)
28 PF06970 RepA_N: Replication i 57.7 12 0.00025 26.8 2.8 22 141-162 54-75 (76)
29 COG3626 PhnI Uncharacterized e 57.2 11 0.00024 34.0 3.1 33 142-174 45-78 (367)
30 PF13730 HTH_36: Helix-turn-he 56.4 16 0.00034 23.3 3.1 22 141-162 27-48 (55)
31 PF02796 HTH_7: Helix-turn-hel 54.8 9.6 0.00021 24.0 1.8 23 141-163 23-45 (45)
32 PRK05441 murQ N-acetylmuramic 54.4 18 0.00038 31.8 3.9 32 142-173 266-297 (299)
33 TIGR00274 N-acetylmuramic acid 53.8 17 0.00037 31.9 3.8 30 142-171 261-290 (291)
34 PRK10877 protein disulfide iso 52.4 39 0.00084 28.5 5.6 43 38-91 23-72 (232)
35 COG1654 BirA Biotin operon rep 52.3 17 0.00036 26.4 2.9 25 143-167 23-50 (79)
36 PF03861 ANTAR: ANTAR domain; 52.0 19 0.00041 23.7 3.0 22 142-163 19-40 (56)
37 PLN02150 terpene synthase/cycl 51.7 14 0.00031 27.3 2.5 25 139-163 7-31 (96)
38 PRK12570 N-acetylmuramic acid- 48.6 24 0.00051 31.1 3.8 30 142-171 262-291 (296)
39 TIGR00632 vsr DNA mismatch end 48.2 33 0.00072 26.7 4.2 34 31-64 17-56 (117)
40 COG0100 RpsK Ribosomal protein 43.5 30 0.00064 27.5 3.3 87 54-168 18-107 (129)
41 PF02845 CUE: CUE domain; Int 42.7 39 0.00084 20.9 3.1 28 136-163 14-41 (42)
42 PF00392 GntR: Bacterial regul 38.5 34 0.00075 22.6 2.6 21 142-162 27-47 (64)
43 PRK14897 unknown domain/DNA-di 38.4 49 0.0011 31.8 4.4 27 39-65 330-356 (509)
44 COG2188 PhnF Transcriptional r 35.4 34 0.00073 28.6 2.6 19 144-162 36-54 (236)
45 PF08680 DUF1779: Protein of u 34.3 58 0.0013 26.7 3.8 53 38-91 131-197 (203)
46 KOG0944 Ubiquitin-specific pro 33.3 39 0.00084 33.8 2.9 24 148-171 644-667 (763)
47 TIGR02389 RNA_pol_rpoA2 DNA-di 33.0 79 0.0017 29.0 4.7 25 39-63 196-220 (367)
48 PF10975 DUF2802: Protein of u 32.1 39 0.00086 23.7 2.1 21 140-160 45-65 (70)
49 COG3636 Predicted transcriptio 30.7 52 0.0011 25.1 2.7 30 144-173 54-83 (100)
50 PRK05564 DNA polymerase III su 30.4 3.5E+02 0.0076 23.2 8.3 42 40-90 77-130 (313)
51 smart00804 TAP_C C-terminal do 30.1 1.2E+02 0.0026 20.9 4.2 35 139-173 13-47 (63)
52 smart00345 HTH_GNTR helix_turn 29.9 78 0.0017 19.5 3.1 22 141-162 22-43 (60)
53 smart00400 ZnF_CHCC zinc finge 29.6 64 0.0014 21.0 2.7 20 141-160 35-54 (55)
54 cd02736 RNAP_III_Rpc1_C Larges 29.5 89 0.0019 27.8 4.4 25 41-65 134-158 (300)
55 cd06528 RNAP_A'' A'' subunit o 29.2 78 0.0017 29.0 4.1 24 42-65 194-217 (363)
56 PHA01748 hypothetical protein 28.4 73 0.0016 21.6 2.9 21 140-160 15-35 (60)
57 COG4004 Uncharacterized protei 28.4 1E+02 0.0022 23.3 3.9 30 40-69 16-55 (96)
58 PF08383 Maf_N: Maf N-terminal 28.1 45 0.00098 20.9 1.6 14 149-162 21-34 (35)
59 smart00411 BHL bacterial (prok 27.7 71 0.0015 22.3 2.9 29 142-170 7-35 (90)
60 cd07377 WHTH_GntR Winged helix 27.5 89 0.0019 19.7 3.1 22 141-162 27-48 (66)
61 KOG3198 Signal recognition par 27.4 88 0.0019 25.6 3.6 45 30-74 38-95 (152)
62 PF03943 TAP_C: TAP C-terminal 26.7 39 0.00085 22.2 1.3 31 142-172 4-34 (51)
63 PRK11426 hypothetical protein; 25.9 70 0.0015 25.5 2.8 28 136-163 69-96 (132)
64 PF13629 T2SS-T3SS_pil_N: Pilu 25.9 83 0.0018 21.6 2.9 23 68-90 23-47 (72)
65 PF12614 RRF_GI: Ribosome recy 25.7 54 0.0012 26.1 2.1 23 141-163 104-126 (128)
66 PRK10079 phosphonate metabolis 25.2 66 0.0014 26.6 2.7 20 143-162 39-58 (241)
67 TIGR02325 C_P_lyase_phnF phosp 25.1 67 0.0015 26.1 2.7 19 144-162 37-55 (238)
68 PF00216 Bac_DNA_binding: Bact 24.5 81 0.0018 21.9 2.7 30 142-171 7-36 (90)
69 PF03333 PapB: Adhesin biosynt 23.8 71 0.0015 23.8 2.3 30 134-163 20-49 (91)
70 cd00591 HU_IHF Integration hos 23.2 94 0.002 21.4 2.8 29 142-170 6-34 (87)
71 PF01978 TrmB: Sugar-specific 22.5 1.2E+02 0.0026 20.0 3.2 24 139-162 22-45 (68)
72 PF01807 zf-CHC2: CHC2 zinc fi 22.1 1.1E+02 0.0023 22.4 3.0 23 141-163 66-88 (97)
73 PRK04984 fatty acid metabolism 22.0 83 0.0018 25.7 2.7 19 144-162 36-54 (239)
74 TIGR02404 trehalos_R_Bsub treh 22.0 83 0.0018 25.7 2.7 19 144-162 29-47 (233)
75 PF08503 DapH_N: Tetrahydrodip 21.9 1.6E+02 0.0035 21.6 3.8 33 57-93 19-52 (83)
76 PHA01623 hypothetical protein 21.7 1.3E+02 0.0028 20.2 3.1 23 140-162 26-49 (56)
77 PF11699 CENP-C_C: Mif2/CENP-C 21.3 1.8E+02 0.0039 21.2 4.0 35 52-89 39-73 (85)
78 PF00356 LacI: Bacterial regul 20.9 1.1E+02 0.0024 19.6 2.6 22 142-163 2-23 (46)
79 cd00687 Terpene_cyclase_nonpla 20.8 99 0.0021 26.1 2.9 28 139-166 229-256 (303)
80 TIGR00987 himA integration hos 20.4 1.1E+02 0.0024 22.0 2.8 29 142-170 8-36 (96)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=3.7e-48 Score=320.05 Aligned_cols=149 Identities=67% Similarity=0.930 Sum_probs=133.0
Q ss_pred CCCCCcCChhHHHHHHHHHHcCCcccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEeccceecchhhHHHHHHHHh
Q 030484 28 AGGRSKQSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQ 107 (176)
Q Consensus 28 ~~~~~~~sr~eKK~rk~LkKLGlk~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfGe~k~~d~~~~~~~~a~e~ 107 (176)
+..++++||+|||.|++|.||||++|+||+||+|++.+|++|+|++|+||++|+++||+|||+++.+|+++|++.+++++
T Consensus 56 ~~~~akqsrsekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q~~aae~ 135 (209)
T KOG2239|consen 56 PVAKAKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQMQAAER 135 (209)
T ss_pred chhhhhcchHHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhHHHHHHHHHHh
Confidence 45688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCcccCCCC-----ccccccCccccccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 030484 108 FKAPDLSHVVSKPE-----SSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 176 (176)
Q Consensus 108 ~~~~~~~~~~~~~~-----~~~~~~~~eevd~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L~~ 176 (176)
|..+..+....... +..+++++++||++|++++||+|||.|+||||++||+||++|+||||||||+||.
T Consensus 136 fk~~~~~~~~~~~~~~~~~~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 136 FKVPQEAPGLIQEDTSATPPAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred ccCCccccccccccccCCCccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 98776543332211 1122345667999999999999999999999999999999999999999999984
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=4.2e-37 Score=236.49 Aligned_cols=105 Identities=31% Similarity=0.519 Sum_probs=96.5
Q ss_pred hHHHHHHHHHHcCCc--ccCCceEEEEEecCeEEEEecCCeEE--ecCCCCeEEEeccceecchhhHHHHHHHHhccCCC
Q 030484 37 SEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDVF--KSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPD 112 (176)
Q Consensus 37 ~eKK~rk~LkKLGlk--~I~gV~rV~I~k~~~~~fvI~~PeV~--k~~gs~tyvVfGe~k~~d~~~~~~~~a~e~~~~~~ 112 (176)
++|++|+||+||||+ +| ||+||+|++++ ..|+|++|+|| +++|++||||||++++++++++
T Consensus 6 nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~-~~~Vi~~P~V~~m~~~g~~tY~I~Ge~~~e~~~~~------------- 70 (115)
T PRK06369 6 NPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKEAE------------- 70 (115)
T ss_pred CHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEeccEEeecccc-------------
Confidence 579999999999999 99 99999999987 89999999998 7999999999999999876432
Q ss_pred CCcccCCCCccccccCccccccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 030484 113 LSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 176 (176)
Q Consensus 113 ~~~~~~~~~~~~~~~~~eevd~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L~~ 176 (176)
.+.+|+++||+|||+||||||++|++||+++||||++|||.|+.
T Consensus 71 --------------------~~~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 71 --------------------KEVEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred --------------------ccCCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 13589999999999999999999999999999999999999973
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.97 E-value=8.4e-32 Score=208.42 Aligned_cols=111 Identities=40% Similarity=0.641 Sum_probs=92.2
Q ss_pred HHHHHHHHHHcC--CcccCCceEEEEEecCeEEEEecCCeEE--ecCCCCeEEEeccceecchhhHHHHHHHHhccCCCC
Q 030484 38 EKKSRKAMLKLG--MKPIPGVSRVTVKKSKNILFVISKPDVF--KSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPDL 113 (176)
Q Consensus 38 eKK~rk~LkKLG--lk~I~gV~rV~I~k~~~~~fvI~~PeV~--k~~gs~tyvVfGe~k~~d~~~~~~~~a~e~~~~~~~ 113 (176)
=++++++|++|| +++++||+||+|+..++. |+|++|.|| +++|+.+|+|.|.+....
T Consensus 8 pr~l~k~mkqmGi~~eeld~v~~V~i~~kd~e-~vi~~P~V~~~~~~g~~~yqi~g~~~~~~------------------ 68 (122)
T COG1308 8 PRKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVMKAMGQKTYQISGDPSAKE------------------ 68 (122)
T ss_pred HHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcchhhhc------------------
Confidence 478889999999 558999999999998775 899999997 578999999999753100
Q ss_pred CcccCCCCccccccCccccccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 030484 114 SHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 176 (176)
Q Consensus 114 ~~~~~~~~~~~~~~~~eevd~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L~~ 176 (176)
....+++..+++..|+++||+|||+||||||++||+||++++||||+|||+|+.
T Consensus 69 ---------~~~~~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 69 ---------AVKKPEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred ---------ccccchhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 000112334667789999999999999999999999999999999999999974
No 4
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=99.97 E-value=5.7e-31 Score=202.56 Aligned_cols=103 Identities=33% Similarity=0.506 Sum_probs=88.2
Q ss_pred hHHHHHHHHHHcCCc--ccCCceEEEEEecCeEEEEecCCeE--EecCCCCeEEEeccceecchhhHHHHHHHHhccCCC
Q 030484 37 SEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDV--FKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPD 112 (176)
Q Consensus 37 ~eKK~rk~LkKLGlk--~I~gV~rV~I~k~~~~~fvI~~PeV--~k~~gs~tyvVfGe~k~~d~~~~~~~~a~e~~~~~~ 112 (176)
.=|++|+||++|||+ +++ |.+|+|+++++ .++|++|+| |+++|+.||||||++++++...
T Consensus 10 ~~~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~~-------------- 73 (116)
T TIGR00264 10 MLKQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVEE-------------- 73 (116)
T ss_pred cHHHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeeccc--------------
Confidence 345999999999999 465 99999999754 447888888 7899999999999998753210
Q ss_pred CCcccCCCCccccccCccccccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 030484 113 LSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 176 (176)
Q Consensus 113 ~~~~~~~~~~~~~~~~~eevd~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L~~ 176 (176)
+.+|+++||+|||+||||||++|++||+++|||||+|||.|+.
T Consensus 74 ---------------------~~~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~~ 116 (116)
T TIGR00264 74 ---------------------EEEITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLEE 116 (116)
T ss_pred ---------------------ccCCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhhC
Confidence 1259999999999999999999999999999999999999973
No 5
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=99.83 E-value=4.4e-21 Score=130.83 Aligned_cols=58 Identities=52% Similarity=0.886 Sum_probs=48.3
Q ss_pred HHHHHHHHHHcCCcccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEeccceecc
Q 030484 38 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIED 95 (176)
Q Consensus 38 eKK~rk~LkKLGlk~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfGe~k~~d 95 (176)
|||+|++|+||||++|+||+||+|++.++.+|+|++|+||+++|++||+|||+++++|
T Consensus 1 ekk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~~~~P~V~~~~~~~tyvV~G~~~~~~ 58 (58)
T PF01849_consen 1 EKKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFVFNNPEVQKSPGSNTYVVFGEAEEED 58 (58)
T ss_dssp -------GHHCT-EEETTEEEEEEEETTTEEEEEESEEEEEETTCCEEEEESEEEEEE
T ss_pred CHHHHHHHHHcCCcccCCcEEEEEEECCceEEEEcCCeEEEcCCCCEEEEEeeeEEcC
Confidence 6999999999999999999999999999899999999999999999999999998864
No 6
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=98.48 E-value=8.6e-08 Score=78.00 Aligned_cols=64 Identities=28% Similarity=0.512 Sum_probs=59.8
Q ss_pred ChhHHHHHHHHHHcCCcccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEeccceecchhh
Q 030484 35 SRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSS 98 (176)
Q Consensus 35 sr~eKK~rk~LkKLGlk~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfGe~k~~d~~~ 98 (176)
+.++||++.-|++|++..|+||.+|.|++.++.+++|++|.|..+...|||.|+|.++.+.++.
T Consensus 38 ~~ddkKlqs~lkkl~v~~i~~i~evn~~k~~g~Vihf~~~~vqasl~~nTf~ItG~~~~k~l~E 101 (162)
T KOG2240|consen 38 TADDKKLQSSLKKLGVNNIPGIEEVNMFKNDGTVIHFNNPKVQASLAANTFTITGHAETKQLTE 101 (162)
T ss_pred CcccchhhhhhhhhccccccchhHhhhccccceeEecCCccccccccCCeEEEecCCcccchhh
Confidence 6679999999999999999999999999999999999999999999999999999999886544
No 7
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.81 E-value=1.3e-05 Score=61.68 Aligned_cols=43 Identities=33% Similarity=0.573 Sum_probs=40.0
Q ss_pred cCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 030484 134 ETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 176 (176)
Q Consensus 134 ~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L~~ 176 (176)
...|..+||+|||...-+++..|.+-|++++||+|.|+-.|++
T Consensus 76 kV~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 76 KVTIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 3578999999999999999999999999999999999998864
No 8
>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=97.72 E-value=4.1e-05 Score=47.35 Aligned_cols=37 Identities=30% Similarity=0.524 Sum_probs=32.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L 174 (176)
++++.|+.+++. |+|++.|++||+.++||+-.|+--|
T Consensus 1 i~~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 1 IDEEKVQQLMEM-GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp SHHHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 467889999999 9999999999999999999998644
No 9
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.95 E-value=0.012 Score=37.44 Aligned_cols=33 Identities=24% Similarity=0.351 Sum_probs=27.9
Q ss_pred ccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 140 KDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 140 eDIeLVmeQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
+.|.-.|+=|||+++.|+..|..+++||-.||=
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~ 34 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVN 34 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHH
Confidence 467888999999999999999999999988874
No 10
>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=95.45 E-value=0.029 Score=34.13 Aligned_cols=33 Identities=33% Similarity=0.492 Sum_probs=26.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 141 DIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L 174 (176)
.|+.+++ .|.+++.++.||+.++||+-.|+--|
T Consensus 4 ~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 4 KLEQLLE-MGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4444444 69999999999999999999887544
No 11
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=95.40 E-value=0.03 Score=33.93 Aligned_cols=33 Identities=39% Similarity=0.609 Sum_probs=25.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 141 DIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L 174 (176)
.|..++ ..|.+++.|+.||+.++||+-.|+--|
T Consensus 4 ~v~~L~-~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQLL-EMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHH-HcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 344444 349999999999999999998886443
No 12
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=91.58 E-value=0.28 Score=39.32 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=30.8
Q ss_pred ccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 133 DETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 133 d~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
+...++.+.++++..-. ||.++|++||.+++ |+..|.-
T Consensus 109 ~~s~~~~e~v~v~a~a~-v~~eeAr~aleeag-Dl~~A~k 146 (153)
T COG4008 109 GHSEPPVEEVEVLADAF-VTPEEAREALEEAG-DLRTAMK 146 (153)
T ss_pred ccCCCcHHHHHHHHHhc-CCHHHHHHHHHHcC-CHHHHHH
Confidence 34456778888887655 99999999999995 9999853
No 13
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=86.18 E-value=1 Score=40.14 Aligned_cols=39 Identities=28% Similarity=0.439 Sum_probs=33.8
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 136 GVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 136 ~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L 174 (176)
.+-+--+..||+-|||+|++|..+|++++|++=-||+-+
T Consensus 231 KL~dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~ 269 (298)
T COG2103 231 KLRDRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVML 269 (298)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHH
Confidence 455778899999999999999999999999997777643
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=84.21 E-value=1.4 Score=38.67 Aligned_cols=38 Identities=39% Similarity=0.583 Sum_probs=30.9
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~L 174 (176)
+-.-=+.+|++-+|||+++|.++|.+++|++=-||+-+
T Consensus 234 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 234 LVDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 34556778999999999999999999999997777643
No 15
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=80.56 E-value=3.7 Score=25.63 Aligned_cols=34 Identities=24% Similarity=0.303 Sum_probs=22.5
Q ss_pred cHHHHHHHh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 141 DIELVMTQA-GVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 141 DIeLVmeQa-gvSr~kAikALke~~GDiv~Ai~~L 174 (176)
.|+-+.+-. +++++....+|+.++||+-.||-.|
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 445555554 7788888888888888886665443
No 16
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=79.21 E-value=1.3 Score=37.98 Aligned_cols=36 Identities=42% Similarity=0.653 Sum_probs=30.6
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
+-+-=+..|++-+|||+++|.++|..++|++=-||+
T Consensus 221 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~~ 256 (257)
T cd05007 221 LRERAIRIVMEATGVSRDEAEAALEQAGGDVKTAIL 256 (257)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeeee
Confidence 345567889999999999999999999999866654
No 17
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=78.59 E-value=2.9 Score=36.70 Aligned_cols=37 Identities=22% Similarity=0.328 Sum_probs=30.7
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhh
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~ 173 (176)
+-+-=+.+|++=+|||+++|.++|.+++|++=-||+-
T Consensus 229 l~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~ 265 (291)
T TIGR00274 229 LKARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVM 265 (291)
T ss_pred HHHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHH
Confidence 3355677899999999999999999999999888763
No 18
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=75.88 E-value=8.6 Score=25.70 Aligned_cols=40 Identities=33% Similarity=0.684 Sum_probs=24.2
Q ss_pred HHHHHHc--CCc-------ccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEeccc
Q 030484 42 RKAMLKL--GMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEA 91 (176)
Q Consensus 42 rk~LkKL--Glk-------~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfGe~ 91 (176)
++.|++. |++ +++|+-+|++ .+++ + +|-.+. ..|+|+|+.
T Consensus 2 ~~~l~~~~p~~~v~~v~~spi~GlyeV~~-~~~~-i-------~Y~~~d-g~yli~G~l 50 (57)
T PF10411_consen 2 KQALKKAFPGLKVESVSPSPIPGLYEVVL-KGGG-I-------LYVDED-GRYLIQGQL 50 (57)
T ss_dssp HHHHHCT--T-TCEEEEE-SSTTEEEEEE--TTE-E-------EEEETT-SSEEEES-E
T ss_pred hhHHHhhcCCCceeEEEcCCCCCeEEEEE-CCCe-E-------EEEcCC-CCEEEEeEE
Confidence 4556666 555 6899999998 4444 3 344443 368999964
No 19
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=74.71 E-value=4.2 Score=35.74 Aligned_cols=37 Identities=30% Similarity=0.473 Sum_probs=29.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhh
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~ 173 (176)
+-+--+.+|++=+|||+++|.++|.+++|++=-||+-
T Consensus 230 l~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~ 266 (296)
T PRK12570 230 LVARAVRIVMQATGCSEDEAKELLKESDNDVKLAILM 266 (296)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHH
Confidence 3345567788888999999999999988888777763
No 20
>PF14474 RTC4: RTC4-like domain
Probab=73.41 E-value=4 Score=31.69 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=24.1
Q ss_pred CCcccHHHHHHHhCCCHHHHHHHHHHc
Q 030484 137 VEPKDIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 137 ~~eeDIeLVmeQagvSr~kAikALke~ 163 (176)
++|==|.|||+-.||+.++|++.|+++
T Consensus 88 vPEl~~~LI~EDm~v~~~~A~~il~eS 114 (124)
T PF14474_consen 88 VPELAVRLIMEDMGVDDEEARQILEES 114 (124)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 455569999999999999999999997
No 21
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=72.13 E-value=9.9 Score=23.65 Aligned_cols=35 Identities=14% Similarity=0.228 Sum_probs=26.6
Q ss_pred ccHHHHHHHh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 030484 140 KDIELVMTQA-GVSRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 140 eDIeLVmeQa-gvSr~kAikALke~~GDiv~Ai~~L 174 (176)
+.|+.+.+=. ++++..++..|+.++||+-.||=.|
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 3455555555 7899999999999999998877444
No 22
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=71.59 E-value=5 Score=25.72 Aligned_cols=22 Identities=32% Similarity=0.454 Sum_probs=16.5
Q ss_pred CHHHHHHHHHHcCCcHHHHHhh
Q 030484 152 SRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 152 Sr~kAikALke~~GDiv~Ai~~ 173 (176)
.|..-.-.|.-++||+|.||-.
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE~ 37 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIEQ 37 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHHH
Confidence 3444555788899999999854
No 23
>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=68.49 E-value=8.2 Score=26.10 Aligned_cols=30 Identities=17% Similarity=0.304 Sum_probs=26.9
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHcCCcHH
Q 030484 139 PKDIELVMTQAGVSRAKAVKALKAADGDIV 168 (176)
Q Consensus 139 eeDIeLVmeQagvSr~kAikALke~~GDiv 168 (176)
+-+|...+...|||.++...|.+..++++.
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~ 49 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLREAVRAVGNSRA 49 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHCcCHH
Confidence 578999999999999999999999977753
No 24
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=63.35 E-value=8.3 Score=35.39 Aligned_cols=33 Identities=33% Similarity=0.526 Sum_probs=27.3
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 030484 142 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 142 IeLVmeQagv-Sr~kAikALke~~GDiv~Ai~~L 174 (176)
|+-||...+. +++=|--|||.+.||+++||+-|
T Consensus 45 vdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 45 VDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 3457777764 78889999999999999999876
No 25
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=62.23 E-value=12 Score=26.93 Aligned_cols=27 Identities=33% Similarity=0.258 Sum_probs=23.7
Q ss_pred HHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 146 MTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 146 meQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
++++|.++.....||..+.||+..|..
T Consensus 4 ~~~~g~~~~~v~~aL~~tSgd~~~a~~ 30 (87)
T PF11626_consen 4 YEELGYSREFVTHALYATSGDPELARR 30 (87)
T ss_dssp HHHHTB-HHHHHHHHHHTTTBHHHHHH
T ss_pred HHHhCCCHHHHHHHHHHhCCCHHHHHH
Confidence 889999999999999999999987754
No 26
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=60.64 E-value=12 Score=34.12 Aligned_cols=37 Identities=24% Similarity=0.273 Sum_probs=33.6
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 136 GVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 136 ~~~eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
.++.++|+-.=+.||.|-.-.++||.+++||++.|--
T Consensus 44 ~~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~ 80 (340)
T KOG1071|consen 44 ASSKALLKKLREKTGASMVNCKKALEECGGDLVLAEE 80 (340)
T ss_pred cccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHH
Confidence 4678899999999999999999999999999998853
No 27
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=58.36 E-value=23 Score=24.67 Aligned_cols=33 Identities=21% Similarity=0.257 Sum_probs=25.1
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 030484 142 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 142 IeLVmeQagv-Sr~kAikALke~~GDiv~Ai~~L 174 (176)
|.-+=+-+|| |.++....|++++.|.=.|.=+|
T Consensus 9 VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrL 42 (60)
T PF06972_consen 9 VQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRL 42 (60)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 3444556788 99999999999999987776554
No 28
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=57.67 E-value=12 Score=26.77 Aligned_cols=22 Identities=32% Similarity=0.379 Sum_probs=19.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 030484 141 DIELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke 162 (176)
-++-+|+-.|||+.+++++++|
T Consensus 54 s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHHc
Confidence 4777899999999999999986
No 29
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=57.23 E-value=11 Score=34.03 Aligned_cols=33 Identities=45% Similarity=0.616 Sum_probs=25.3
Q ss_pred HHHHHHHhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 030484 142 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 174 (176)
Q Consensus 142 IeLVmeQagv-Sr~kAikALke~~GDiv~Ai~~L 174 (176)
|+-||...++ +|+=|-=|||.+.||+++||+-|
T Consensus 45 VdRVM~EgslyDreLAALAikQa~GD~~EAIFLl 78 (367)
T COG3626 45 VDRVMTEGSLYDRELAALALKQASGDLVEAIFLL 78 (367)
T ss_pred HHHHhhccchhHHHHHHHHHHHhcchHHHHHHHH
Confidence 3445554443 67888889999999999999876
No 30
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.39 E-value=16 Score=23.30 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=19.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 030484 141 DIELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke 162 (176)
-++-+++.+|+|+...+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 6899999999999999888876
No 31
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=54.79 E-value=9.6 Score=24.03 Aligned_cols=23 Identities=30% Similarity=0.382 Sum_probs=17.7
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 030484 141 DIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke~ 163 (176)
-|.-|+.++||||....+.|.++
T Consensus 23 si~~IA~~~gvsr~TvyR~l~~~ 45 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYRYLNKN 45 (45)
T ss_dssp -HHHHHHHTTS-HHHHHHHHCC-
T ss_pred CHHHHHHHHCcCHHHHHHHHhcC
Confidence 47778999999999999988653
No 32
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=54.45 E-value=18 Score=31.83 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=28.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhh
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~Ai~~ 173 (176)
+-++|--+|||.++|.+.|..++|.|-.||-.
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhh
Confidence 44688889999999999999999999998744
No 33
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=53.83 E-value=17 Score=31.91 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=26.4
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSAI 171 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~Ai 171 (176)
+-++|--+|||.++|++.|..++|.|-.||
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l 290 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQAL 290 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhh
Confidence 446788899999999999999999998775
No 34
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=52.40 E-value=39 Score=28.48 Aligned_cols=43 Identities=19% Similarity=0.468 Sum_probs=28.4
Q ss_pred HHHHHHHHHHcCCc-------ccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEeccc
Q 030484 38 EKKSRKAMLKLGMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEA 91 (176)
Q Consensus 38 eKK~rk~LkKLGlk-------~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfGe~ 91 (176)
+..+++.|.++|++ +++|+-+|++ +++ + +|-.+ ...|+|+|+.
T Consensus 23 ~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~-i-------~Y~~~-dg~y~i~G~l 72 (232)
T PRK10877 23 DAAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESG-V-------LYITD-DGKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCe-E-------EEEcC-CCCEEEeeee
Confidence 36778888888876 5788888865 223 3 24333 3458999964
No 35
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=52.31 E-value=17 Score=26.40 Aligned_cols=25 Identities=32% Similarity=0.468 Sum_probs=20.3
Q ss_pred HHHHHHhCCCH---HHHHHHHHHcCCcH
Q 030484 143 ELVMTQAGVSR---AKAVKALKAADGDI 167 (176)
Q Consensus 143 eLVmeQagvSr---~kAikALke~~GDi 167 (176)
+-+.++.|||| .|.|+.|++.+-||
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 34678999999 57899999987775
No 36
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=52.05 E-value=19 Score=23.71 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCHHHHHHHHHHc
Q 030484 142 IELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~ 163 (176)
+-++|.+.|||.++|.+.|+..
T Consensus 19 kgiLm~~~g~~e~~A~~~Lr~~ 40 (56)
T PF03861_consen 19 KGILMARYGLSEDEAYRLLRRQ 40 (56)
T ss_dssp HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHHHHHHH
Confidence 4679999999999999999873
No 37
>PLN02150 terpene synthase/cyclase family protein
Probab=51.75 E-value=14 Score=27.34 Aligned_cols=25 Identities=32% Similarity=0.485 Sum_probs=21.6
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHc
Q 030484 139 PKDIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 139 eeDIeLVmeQagvSr~kAikALke~ 163 (176)
..-|+--|.|-|||.++|++.|++-
T Consensus 7 aSsIeCYMke~g~seeeA~~~i~~l 31 (96)
T PLN02150 7 ANGVNCYMKQHGVTKEEAVSELKKM 31 (96)
T ss_pred hHHHHHHhccCCCCHHHHHHHHHHH
Confidence 4468899999999999999998763
No 38
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=48.59 E-value=24 Score=31.07 Aligned_cols=30 Identities=33% Similarity=0.451 Sum_probs=27.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSAI 171 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~Ai 171 (176)
+-++|-.+|||.++|.+.|.+++|.|-.||
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l 291 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAI 291 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHH
Confidence 457888899999999999999999998886
No 39
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=48.24 E-value=33 Score=26.65 Aligned_cols=34 Identities=24% Similarity=0.516 Sum_probs=26.4
Q ss_pred CCcCChhHHHHHHHHHHcCCc------ccCCceEEEEEec
Q 030484 31 RSKQSRSEKKSRKAMLKLGMK------PIPGVSRVTVKKS 64 (176)
Q Consensus 31 ~~~~sr~eKK~rk~LkKLGlk------~I~gV~rV~I~k~ 64 (176)
+++.++.|..++++|..+|++ .+||+--+++.+.
T Consensus 17 R~~~T~pE~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~ 56 (117)
T TIGR00632 17 RTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEY 56 (117)
T ss_pred hcCCCHHHHHHHHHHHhCCCEEEEecCCCCCcccEEecCC
Confidence 455688899999999999997 3677766666664
No 40
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=43.49 E-value=30 Score=27.52 Aligned_cols=87 Identities=24% Similarity=0.336 Sum_probs=50.5
Q ss_pred CCceEEEEEec-CeEEEEecCCeE--EecCCCCeEEEeccceecchhhHHHHHHHHhccCCCCCcccCCCCccccccCcc
Q 030484 54 PGVSRVTVKKS-KNILFVISKPDV--FKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPDLSHVVSKPESSAMAQDDE 130 (176)
Q Consensus 54 ~gV~rV~I~k~-~~~~fvI~~PeV--~k~~gs~tyvVfGe~k~~d~~~~~~~~a~e~~~~~~~~~~~~~~~~~~~~~~~e 130 (176)
.|| +.|... +|++++|.+++= .-...+.+..+.|.-+.-+.+.++++..+++-
T Consensus 18 ~Gv--ahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~---------------------- 73 (129)
T COG0100 18 DGV--AHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKK---------------------- 73 (129)
T ss_pred cce--EEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHH----------------------
Confidence 345 666655 788888888752 22223334566676655555444433322211
Q ss_pred ccccCCCCcccHHHHHHHhCCCHHHHHHHHHHcCCcHH
Q 030484 131 EVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIV 168 (176)
Q Consensus 131 evd~~~~~eeDIeLVmeQagvSr~kAikALke~~GDiv 168 (176)
..+-|+. +|++++.=.|--|+.||+||--. |.-+
T Consensus 74 -a~e~Gi~--~v~v~vkgpG~GreaAiraL~~a-g~~i 107 (129)
T COG0100 74 -AKEHGIK--SVEVKVKGPGPGREAAIRALAAA-GLKI 107 (129)
T ss_pred -HHHhCcc--EEEEEEECCCCcHHHHHHHHHHc-cceE
Confidence 1123444 66666666899999999999854 4433
No 41
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=42.75 E-value=39 Score=20.88 Aligned_cols=28 Identities=21% Similarity=0.227 Sum_probs=24.6
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHc
Q 030484 136 GVEPKDIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 136 ~~~eeDIeLVmeQagvSr~kAikALke~ 163 (176)
.++++.|+.+..+.+-+-+.|+.+|-+.
T Consensus 14 ~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 14 DLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp SS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 5789999999999999999999998763
No 42
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=38.50 E-value=34 Score=22.62 Aligned_cols=21 Identities=29% Similarity=0.328 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCHHHHHHHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke 162 (176)
..-++++.||||.-+++||..
T Consensus 27 ~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHhccCCcHHHHHHHH
Confidence 456799999999999999975
No 43
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=38.41 E-value=49 Score=31.85 Aligned_cols=27 Identities=22% Similarity=0.309 Sum_probs=19.6
Q ss_pred HHHHHHHHHcCCcccCCceEEEEEecC
Q 030484 39 KKSRKAMLKLGMKPIPGVSRVTVKKSK 65 (176)
Q Consensus 39 KK~rk~LkKLGlk~I~gV~rV~I~k~~ 65 (176)
+++++.+..+-++.+|||.||+|+..+
T Consensus 330 ~~l~~~l~~i~I~GipgI~r~~i~~~~ 356 (509)
T PRK14897 330 YLLAEKVKSLTIKGIKGIKRAIARKEN 356 (509)
T ss_pred HHHHHHhhccEEeCCCCccEEEEecCC
Confidence 334455556667899999999998653
No 44
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=35.37 E-value=34 Score=28.64 Aligned_cols=19 Identities=42% Similarity=0.406 Sum_probs=16.8
Q ss_pred HHHHHhCCCHHHHHHHHHH
Q 030484 144 LVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 144 LVmeQagvSr~kAikALke 162 (176)
-.++|.||||-.+++||.+
T Consensus 36 eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHHCCcHHHHHHHHHH
Confidence 3688999999999999976
No 45
>PF08680 DUF1779: Protein of unknown function (DUF1779); InterPro: IPR014794 This entry represents uncharacterised proteins. The structure of the YwmB protein from Bacillus subtilis has shown it to adopt an alpha/beta fold. ; PDB: 2FPN_A.
Probab=34.30 E-value=58 Score=26.73 Aligned_cols=53 Identities=23% Similarity=0.421 Sum_probs=19.7
Q ss_pred HHHHHHHHHHcCCcccCCceE-----EEEEec--CeEEEEecCC----eE---EecCCCCeEEEeccc
Q 030484 38 EKKSRKAMLKLGMKPIPGVSR-----VTVKKS--KNILFVISKP----DV---FKSPTTDTYVIFGEA 91 (176)
Q Consensus 38 eKK~rk~LkKLGlk~I~gV~r-----V~I~k~--~~~~fvI~~P----eV---~k~~gs~tyvVfGe~ 91 (176)
++.+.++|+.||.++|+.+.. |+=..+ ++. +-+.+- +| |..-++.||+++|.|
T Consensus 131 ~~~~~~~l~~l~A~~vE~~~~~~~vSvsaYt~~~~~~-i~~~~~k~NlqiAlr~~~~~~~T~I~iGTP 197 (203)
T PF08680_consen 131 EKIAERLLKKLGAKPVESLKDENFVSVSAYTPKWDDS-IQTGGKKMNLQIALRYNSYGGKTYITIGTP 197 (203)
T ss_dssp HHHHHHHHHHH---------BTTEEEEEE--TTSS---EEETTEEE-EEEEEE--------EEEEESS
T ss_pred HHHHHHHHHHcCCcEeeEEecccEEEEEEEccchhhh-hhcCCeEEEEEEEEEecCCCCCEEEEEEec
Confidence 677889999999998765543 222222 221 122222 22 234578899999987
No 46
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=33.29 E-value=39 Score=33.82 Aligned_cols=24 Identities=42% Similarity=0.652 Sum_probs=21.3
Q ss_pred HhCCCHHHHHHHHHHcCCcHHHHH
Q 030484 148 QAGVSRAKAVKALKAADGDIVSAI 171 (176)
Q Consensus 148 QagvSr~kAikALke~~GDiv~Ai 171 (176)
--|.++..||+||+.+||+|-.|.
T Consensus 644 smGf~~~qa~~aL~~~n~nverav 667 (763)
T KOG0944|consen 644 SMGFSRNQAIKALKATNNNVERAV 667 (763)
T ss_pred eecCcHHHHHHHHHhcCccHHHHH
Confidence 469999999999999999997763
No 47
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=33.00 E-value=79 Score=29.04 Aligned_cols=25 Identities=32% Similarity=0.607 Sum_probs=18.5
Q ss_pred HHHHHHHHHcCCcccCCceEEEEEe
Q 030484 39 KKSRKAMLKLGMKPIPGVSRVTVKK 63 (176)
Q Consensus 39 KK~rk~LkKLGlk~I~gV~rV~I~k 63 (176)
+++++.|..+-++.+|||.||.|..
T Consensus 196 ~~l~~~l~~~~v~Gi~gI~r~~i~~ 220 (367)
T TIGR02389 196 RKLKEKIKNLHIKGIKGIKRVVIRK 220 (367)
T ss_pred HHHHHHhhhceEeCCCCceEEEEEC
Confidence 4444556666677999999999974
No 48
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=32.12 E-value=39 Score=23.74 Aligned_cols=21 Identities=38% Similarity=0.514 Sum_probs=17.5
Q ss_pred ccHHHHHHHhCCCHHHHHHHH
Q 030484 140 KDIELVMTQAGVSRAKAVKAL 160 (176)
Q Consensus 140 eDIeLVmeQagvSr~kAikAL 160 (176)
-||+-||+.+|.||.+|.=.+
T Consensus 45 a~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999996443
No 49
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=30.73 E-value=52 Score=25.13 Aligned_cols=30 Identities=30% Similarity=0.384 Sum_probs=25.0
Q ss_pred HHHHHhCCCHHHHHHHHHHcCCcHHHHHhh
Q 030484 144 LVMTQAGVSRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 144 LVmeQagvSr~kAikALke~~GDiv~Ai~~ 173 (176)
-|.+++|.||+--.|+|...+|=-...|++
T Consensus 54 qvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 54 QVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 477899999999999999988766666654
No 50
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=30.38 E-value=3.5e+02 Score=23.21 Aligned_cols=42 Identities=17% Similarity=0.358 Sum_probs=24.9
Q ss_pred HHHHHHHHcCCcccCCceEEEEEecCeEEEEecCCeEE------------ecCCCCeEEEecc
Q 030484 40 KSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVF------------KSPTTDTYVIFGE 90 (176)
Q Consensus 40 K~rk~LkKLGlk~I~gV~rV~I~k~~~~~fvI~~PeV~------------k~~gs~tyvVfGe 90 (176)
.+|.+...+...+..+= ..+++|.+++.+ .-|..+||+|+..
T Consensus 77 ~ir~~~~~~~~~p~~~~---------~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~ 130 (313)
T PRK05564 77 DIRNIIEEVNKKPYEGD---------KKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLC 130 (313)
T ss_pred HHHHHHHHHhcCcccCC---------ceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEe
Confidence 47777777766666542 334555555553 2356677888765
No 51
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=30.14 E-value=1.2e+02 Score=20.94 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=29.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHhh
Q 030484 139 PKDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 173 (176)
Q Consensus 139 eeDIeLVmeQagvSr~kAikALke~~GDiv~Ai~~ 173 (176)
+.=|..+..+||...+=+.+.|.+++-|.=.|+-.
T Consensus 13 ~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~ 47 (63)
T smart00804 13 QEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKN 47 (63)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHH
Confidence 34577788999999999999999999999887654
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.85 E-value=78 Score=19.55 Aligned_cols=22 Identities=32% Similarity=0.326 Sum_probs=18.8
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 030484 141 DIELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke 162 (176)
.+.-+++..|||+..+.++|..
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5666899999999999998876
No 53
>smart00400 ZnF_CHCC zinc finger.
Probab=29.59 E-value=64 Score=20.97 Aligned_cols=20 Identities=35% Similarity=0.353 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHH
Q 030484 141 DIELVMTQAGVSRAKAVKAL 160 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikAL 160 (176)
=|++||..-|+|-.+|.+-|
T Consensus 35 ~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 35 VISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred HHHHHHHHHCcCHHHHHHHh
Confidence 49999999999999998876
No 54
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=29.50 E-value=89 Score=27.84 Aligned_cols=25 Identities=24% Similarity=0.433 Sum_probs=18.0
Q ss_pred HHHHHHHcCCcccCCceEEEEEecC
Q 030484 41 SRKAMLKLGMKPIPGVSRVTVKKSK 65 (176)
Q Consensus 41 ~rk~LkKLGlk~I~gV~rV~I~k~~ 65 (176)
+++.|...-++.+|||.|+.|...+
T Consensus 134 l~~~l~~~~v~Gi~gI~r~~i~~~~ 158 (300)
T cd02736 134 LKRKLPDVVVSGIPEVKRAVINKDK 158 (300)
T ss_pred HHHHhccceEeCCCCceEEEEecCC
Confidence 3445555667789999999997643
No 55
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=29.20 E-value=78 Score=28.96 Aligned_cols=24 Identities=33% Similarity=0.565 Sum_probs=17.4
Q ss_pred HHHHHHcCCcccCCceEEEEEecC
Q 030484 42 RKAMLKLGMKPIPGVSRVTVKKSK 65 (176)
Q Consensus 42 rk~LkKLGlk~I~gV~rV~I~k~~ 65 (176)
+..|...-++.+|||.||.|...+
T Consensus 194 ~~~l~~~~v~Gi~gI~r~~i~~~~ 217 (363)
T cd06528 194 AEKILNTKIKGIKGIKRVIVRKEE 217 (363)
T ss_pred HHhhcccEEeCCCCceEEEEecCC
Confidence 334445557789999999998653
No 56
>PHA01748 hypothetical protein
Probab=28.42 E-value=73 Score=21.58 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=17.2
Q ss_pred ccHHHHHHHhCCCHHHHHHHH
Q 030484 140 KDIELVMTQAGVSRAKAVKAL 160 (176)
Q Consensus 140 eDIeLVmeQagvSr~kAikAL 160 (176)
+.++..+.+.|+||.++|+..
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 457778999999999998844
No 57
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.40 E-value=1e+02 Score=23.35 Aligned_cols=30 Identities=27% Similarity=0.570 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCc----------ccCCceEEEEEecCeEEE
Q 030484 40 KSRKAMLKLGMK----------PIPGVSRVTVKKSKNILF 69 (176)
Q Consensus 40 K~rk~LkKLGlk----------~I~gV~rV~I~k~~~~~f 69 (176)
.+.+.|..||.. .+||+++|.|+..++.++
T Consensus 16 ri~~~l~e~g~~v~~eGD~ivas~pgis~ieik~E~kkL~ 55 (96)
T COG4004 16 RIMRGLSELGWTVSEEGDRIVASSPGISRIEIKPENKKLL 55 (96)
T ss_pred HHHHHHHHhCeeEeecccEEEEecCCceEEEEecccceEE
Confidence 356778888865 358888888888765553
No 58
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=28.15 E-value=45 Score=20.90 Aligned_cols=14 Identities=36% Similarity=0.480 Sum_probs=11.0
Q ss_pred hCCCHHHHHHHHHH
Q 030484 149 AGVSRAKAVKALKA 162 (176)
Q Consensus 149 agvSr~kAikALke 162 (176)
.|.|.+.|++||..
T Consensus 21 l~LtpEDAvEaLi~ 34 (35)
T PF08383_consen 21 LGLTPEDAVEALIG 34 (35)
T ss_pred cCCCHHHHHHHHhc
Confidence 47788889998864
No 59
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=27.72 E-value=71 Score=22.28 Aligned_cols=29 Identities=31% Similarity=0.326 Sum_probs=22.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSA 170 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~A 170 (176)
|+.|.+++|+|+..+...|..--.-|.++
T Consensus 7 i~~ia~~~~~~~~~v~~vl~~l~~~i~~~ 35 (90)
T smart00411 7 IDAIAEKAGLSKKDAKAAVDAFLEIITEA 35 (90)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999998887754444444
No 60
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=27.47 E-value=89 Score=19.69 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHH
Q 030484 141 DIELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke 162 (176)
.+.-++++.|+|+..+.++|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999999988876
No 61
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.37 E-value=88 Score=25.58 Aligned_cols=45 Identities=24% Similarity=0.408 Sum_probs=34.6
Q ss_pred CCCcCChhHHHHHHHHHHcCCccc-------------CCceEEEEEecCeEEEEecCC
Q 030484 30 GRSKQSRSEKKSRKAMLKLGMKPI-------------PGVSRVTVKKSKNILFVISKP 74 (176)
Q Consensus 30 ~~~~~sr~eKK~rk~LkKLGlk~I-------------~gV~rV~I~k~~~~~fvI~~P 74 (176)
..+..|..=+.++..++.|||.-+ +|=.||.|+..++.+|+++-|
T Consensus 38 e~aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG~l~~~~~~ 95 (152)
T KOG3198|consen 38 EKAVENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDGTLYVIAFI 95 (152)
T ss_pred HHhhcCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCCcEEeecch
Confidence 344567777899999999999821 456688888888888888764
No 62
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=26.72 E-value=39 Score=22.22 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=24.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHHHh
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSAIM 172 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~Ai~ 172 (176)
|.-++.|||...+=+.+-|.+++-|+=.|+-
T Consensus 4 v~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~ 34 (51)
T PF03943_consen 4 VQQFSQQTGMNLEWSQKCLEENNWDYERALQ 34 (51)
T ss_dssp HHHHHHHCSS-CCHHHHHHHHTTT-CCHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHcCCCHHHHHH
Confidence 5667899999999999999999999877754
No 63
>PRK11426 hypothetical protein; Provisional
Probab=25.90 E-value=70 Score=25.47 Aligned_cols=28 Identities=14% Similarity=0.183 Sum_probs=24.6
Q ss_pred CCCcccHHHHHHHhCCCHHHHHHHHHHc
Q 030484 136 GVEPKDIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 136 ~~~eeDIeLVmeQagvSr~kAikALke~ 163 (176)
-+.++.|.-+.+|+|+|+++|...|-+.
T Consensus 69 ~lG~d~i~~lA~q~Gl~~~~~~~~LA~~ 96 (132)
T PRK11426 69 ALGTNAVSDLGQKLGVDTSTASSLLAEQ 96 (132)
T ss_pred HhChHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 3667899999999999999999998764
No 64
>PF13629 T2SS-T3SS_pil_N: Pilus formation protein N terminal region
Probab=25.89 E-value=83 Score=21.57 Aligned_cols=23 Identities=13% Similarity=0.306 Sum_probs=16.0
Q ss_pred EEEecCCeEE--ecCCCCeEEEecc
Q 030484 68 LFVISKPDVF--KSPTTDTYVIFGE 90 (176)
Q Consensus 68 ~fvI~~PeV~--k~~gs~tyvVfGe 90 (176)
.+.|.||+|- .....++++|||.
T Consensus 23 rV~v~dp~Iadv~~~~~~~v~i~gk 47 (72)
T PF13629_consen 23 RVAVGDPEIADVTVLSPNEVYITGK 47 (72)
T ss_pred EEEECCCCEEEEEEeCCCEEEEEEe
Confidence 3468888883 4456678888884
No 65
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=25.70 E-value=54 Score=26.07 Aligned_cols=23 Identities=22% Similarity=0.161 Sum_probs=19.5
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 030484 141 DIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke~ 163 (176)
.+--.|++||||-.+|+.|.-+.
T Consensus 104 TlaELm~~T~Ctl~eAR~ARf~~ 126 (128)
T PF12614_consen 104 TLAELMAATHCTLAEARRARFEA 126 (128)
T ss_pred cHHHHHHHhCCcHHHHHHHhhhc
Confidence 56678999999999999997554
No 66
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=25.21 E-value=66 Score=26.60 Aligned_cols=20 Identities=15% Similarity=0.228 Sum_probs=17.6
Q ss_pred HHHHHHhCCCHHHHHHHHHH
Q 030484 143 ELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 143 eLVmeQagvSr~kAikALke 162 (176)
.-.+++-||||..+++||.+
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999986
No 67
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=25.08 E-value=67 Score=26.13 Aligned_cols=19 Identities=26% Similarity=0.378 Sum_probs=17.0
Q ss_pred HHHHHhCCCHHHHHHHHHH
Q 030484 144 LVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 144 LVmeQagvSr~kAikALke 162 (176)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999976
No 68
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=24.54 E-value=81 Score=21.86 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSAI 171 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~Ai 171 (176)
|+.|.+++|+|+.++..+|..--.-|.+++
T Consensus 7 i~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 36 (90)
T PF00216_consen 7 IKRIAEKTGLSKKDVEAVLDALFDVIKEAL 36 (90)
T ss_dssp HHHHHHHHTSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 678889999999999998887644444443
No 69
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=23.82 E-value=71 Score=23.82 Aligned_cols=30 Identities=17% Similarity=0.241 Sum_probs=21.8
Q ss_pred cCCCCcccHHHHHHHhCCCHHHHHHHHHHc
Q 030484 134 ETGVEPKDIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 134 ~~~~~eeDIeLVmeQagvSr~kAikALke~ 163 (176)
...++++...|.++=+++.-++.|.||+++
T Consensus 20 pG~vs~e~F~lLl~ls~IrS~kiI~AL~dy 49 (91)
T PF03333_consen 20 PGKVSEEHFWLLLELSSIRSEKIIAALRDY 49 (91)
T ss_dssp TT-S-HHHHHHHHHHS----HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHHHCCCCcHHHHHHHHHH
Confidence 346899999999999999999999999985
No 70
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=23.24 E-value=94 Score=21.43 Aligned_cols=29 Identities=31% Similarity=0.334 Sum_probs=21.7
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSA 170 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~A 170 (176)
|+.|++.+|+|+.++...|..--.=|.++
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~~i~~~ 34 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLDVITEA 34 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999998887753333333
No 71
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=22.53 E-value=1.2e+02 Score=20.03 Aligned_cols=24 Identities=33% Similarity=0.559 Sum_probs=20.5
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHH
Q 030484 139 PKDIELVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 139 eeDIeLVmeQagvSr~kAikALke 162 (176)
+-.+.-+.+.+|+||..+.++|+.
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 346777899999999999999976
No 72
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=22.09 E-value=1.1e+02 Score=22.40 Aligned_cols=23 Identities=39% Similarity=0.397 Sum_probs=18.6
Q ss_pred cHHHHHHHhCCCHHHHHHHHHHc
Q 030484 141 DIELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 141 DIeLVmeQagvSr~kAikALke~ 163 (176)
=|++||.--|||-.+|++-|.+-
T Consensus 66 ~i~~v~~~~~~~f~eAv~~l~~~ 88 (97)
T PF01807_consen 66 VIDFVMKYEGCSFKEAVKWLAEE 88 (97)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHH
T ss_pred HHhHHHHHhCCCHHHHHHHHHHH
Confidence 49999999999999999998763
No 73
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=22.04 E-value=83 Score=25.72 Aligned_cols=19 Identities=21% Similarity=0.265 Sum_probs=17.1
Q ss_pred HHHHHhCCCHHHHHHHHHH
Q 030484 144 LVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 144 LVmeQagvSr~kAikALke 162 (176)
-++++.||||.-.++||..
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999976
No 74
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=22.02 E-value=83 Score=25.73 Aligned_cols=19 Identities=42% Similarity=0.436 Sum_probs=16.9
Q ss_pred HHHHHhCCCHHHHHHHHHH
Q 030484 144 LVMTQAGVSRAKAVKALKA 162 (176)
Q Consensus 144 LVmeQagvSr~kAikALke 162 (176)
-.+++.||||-..++||.+
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999976
No 75
>PF08503 DapH_N: Tetrahydrodipicolinate succinyltransferase N-terminal; InterPro: IPR013710 This domain is found at the N terminus of tetrahydrodipicolinate N-acetyltransferase (DapH) which catalyses the acylation of L-2-amino-6-oxopimelate to 2-N-acetyl-6-oxopimelate in the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants []. The N-terminal domain as defined here contains three alpha-helices and two twisted hairpin loops []. ; GO: 0047200 tetrahydrodipicolinate N-acetyltransferase activity; PDB: 3CJ8_A 3BV8_A 3R8Y_F.
Probab=21.88 E-value=1.6e+02 Score=21.64 Aligned_cols=33 Identities=30% Similarity=0.346 Sum_probs=21.9
Q ss_pred eEEEEEec-CeEEEEecCCeEEecCCCCeEEEecccee
Q 030484 57 SRVTVKKS-KNILFVISKPDVFKSPTTDTYVIFGEAKI 93 (176)
Q Consensus 57 ~rV~I~k~-~~~~fvI~~PeV~k~~gs~tyvVfGe~k~ 93 (176)
.+|.++.. .+. .+.+-++|.. .++++|||+...
T Consensus 19 VKvYv~G~l~~~--~~~~~~~fg~--~~~~vvfGd~~~ 52 (83)
T PF08503_consen 19 VKVYVKGDLAGI--DFEDVKVFGS--GNFGVVFGDWDE 52 (83)
T ss_dssp EEEEEEESCTC-----TTSEEEEE--SSEEEEEEEHHH
T ss_pred EEEEEeeeecCC--ChhheEEEeC--CCcEEEEecHHH
Confidence 36777776 454 4588888864 468999998754
No 76
>PHA01623 hypothetical protein
Probab=21.69 E-value=1.3e+02 Score=20.20 Aligned_cols=23 Identities=13% Similarity=0.332 Sum_probs=18.5
Q ss_pred ccHHHHHHHhCCCHHHHHH-HHHH
Q 030484 140 KDIELVMTQAGVSRAKAVK-ALKA 162 (176)
Q Consensus 140 eDIeLVmeQagvSr~kAik-ALke 162 (176)
+-++..+.+-|++|.++|+ |+++
T Consensus 26 ~~Ld~y~~~~g~~rSe~IreAI~~ 49 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIEEAIKE 49 (56)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4678889999999999987 4443
No 77
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=21.29 E-value=1.8e+02 Score=21.16 Aligned_cols=35 Identities=31% Similarity=0.493 Sum_probs=25.4
Q ss_pred ccCCceEEEEEecCeEEEEecCCeEEecCCCCeEEEec
Q 030484 52 PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFG 89 (176)
Q Consensus 52 ~I~gV~rV~I~k~~~~~fvI~~PeV~k~~gs~tyvVfG 89 (176)
-+.|..+|+|-. .-|++..-..+.+|..|.|-|--
T Consensus 39 V~~G~v~Vti~~---~~f~v~~G~~F~VP~gN~Y~i~N 73 (85)
T PF11699_consen 39 VIKGKVEVTIHE---TSFVVTKGGSFQVPRGNYYSIKN 73 (85)
T ss_dssp EEESEEEEEETT---EEEEEETT-EEEE-TT-EEEEEE
T ss_pred EEeCEEEEEEcC---cEEEEeCCCEEEECCCCEEEEEE
Confidence 457888888844 57789999999999999998864
No 78
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=20.88 E-value=1.1e+02 Score=19.62 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHHc
Q 030484 142 IELVMTQAGVSRAKAVKALKAA 163 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~ 163 (176)
|+-|...+|||....-++|-..
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHHCcCHHHHHHHHhCC
Confidence 5678899999999999999765
No 79
>cd00687 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in
Probab=20.83 E-value=99 Score=26.13 Aligned_cols=28 Identities=11% Similarity=0.311 Sum_probs=22.8
Q ss_pred cccHHHHHHHhCCCHHHHHHHHHHcCCc
Q 030484 139 PKDIELVMTQAGVSRAKAVKALKAADGD 166 (176)
Q Consensus 139 eeDIeLVmeQagvSr~kAikALke~~GD 166 (176)
-.=|.++|.+.|+|.++|+..+.+--.+
T Consensus 229 ~N~V~vl~~~~g~s~~eA~~~~~~~~~~ 256 (303)
T cd00687 229 HNLVKVLAEEHGLSLEEAISVVRDMHNE 256 (303)
T ss_pred chHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4568899999999999999988765333
No 80
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=20.37 E-value=1.1e+02 Score=22.02 Aligned_cols=29 Identities=21% Similarity=0.248 Sum_probs=21.7
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHH
Q 030484 142 IELVMTQAGVSRAKAVKALKAADGDIVSA 170 (176)
Q Consensus 142 IeLVmeQagvSr~kAikALke~~GDiv~A 170 (176)
|+.|.+.+|+|+..+..+|..--.-|.++
T Consensus 8 i~~ia~~~~~s~~~v~~vv~~~~~~i~~~ 36 (96)
T TIGR00987 8 SEYLFDELGLSKREAKELVELFFEEIRRA 36 (96)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 78899999999999998887653333333
Done!