Query 028761
Match_columns 204
No_of_seqs 166 out of 497
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 16:34:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028761.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028761hhsearch_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 2.5E-53 5.5E-58 359.6 15.0 150 55-204 55-209 (209)
2 PRK06369 nac nascent polypepti 100.0 1.5E-37 3.2E-42 245.1 11.6 106 64-204 5-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 8.8E-33 1.9E-37 219.3 8.3 113 64-204 6-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 1.7E-31 3.7E-36 210.7 11.2 101 67-204 12-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 3.5E-21 7.5E-26 134.6 6.0 58 66-123 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.7 7E-09 1.5E-13 86.5 3.6 64 63-126 38-101 (162)
7 PF00627 UBA: UBA/TS-N domain; 97.7 5.2E-05 1.1E-09 48.1 3.3 37 165-202 1-37 (37)
8 KOG3450 Huntingtin interacting 97.6 4.8E-05 1E-09 60.2 2.4 42 163-204 77-118 (119)
9 PF14555 UBA_4: UBA-like domai 95.5 0.02 4.4E-07 37.4 3.5 33 168-200 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.1 0.039 8.4E-07 34.5 3.7 32 170-202 5-36 (38)
11 smart00165 UBA Ubiquitin assoc 94.8 0.051 1.1E-06 33.8 3.7 28 175-202 9-36 (37)
12 COG4008 Predicted metal-bindin 86.0 1.1 2.4E-05 37.0 3.9 36 163-200 111-146 (153)
13 COG2103 Predicted sugar phosph 84.2 1.3 2.9E-05 40.5 4.0 39 164-202 231-269 (298)
14 PRK05441 murQ N-acetylmuramic 82.4 1.7 3.8E-05 39.1 4.0 38 165-202 234-271 (299)
15 PF10411 DsbC_N: Disulfide bon 79.2 4.4 9.5E-05 27.9 4.3 40 70-119 2-50 (57)
16 cd05007 SIS_Etherase N-acetylm 77.1 1.6 3.4E-05 38.5 2.0 36 165-200 221-256 (257)
17 PF02845 CUE: CUE domain; Int 76.7 3.9 8.5E-05 26.2 3.3 33 170-202 5-38 (42)
18 TIGR00274 N-acetylmuramic acid 76.7 3.4 7.3E-05 37.3 4.0 37 165-201 229-265 (291)
19 PF10446 DUF2457: Protein of u 76.7 1.7 3.8E-05 41.9 2.2 12 112-123 193-204 (458)
20 PRK12570 N-acetylmuramic acid- 72.3 4.9 0.00011 36.3 3.9 36 166-201 231-266 (296)
21 PF03474 DMA: DMRTA motif; In 68.3 6.2 0.00014 26.0 2.7 22 179-200 15-36 (39)
22 smart00546 CUE Domain that may 68.2 8.4 0.00018 24.7 3.4 34 169-202 5-39 (43)
23 PF14474 RTC4: RTC4-like domai 63.3 7.8 0.00017 30.9 3.0 26 166-191 89-114 (124)
24 PF05861 PhnI: Bacterial phosp 61.5 9.1 0.0002 36.1 3.5 33 170-202 45-78 (358)
25 PF11626 Rap1_C: TRF2-interact 60.9 13 0.00028 27.6 3.6 30 170-200 1-30 (87)
26 COG3626 PhnI Uncharacterized e 59.8 9 0.0002 35.5 3.1 33 170-202 45-78 (367)
27 TIGR00632 vsr DNA mismatch end 56.3 15 0.00032 29.4 3.4 35 58-92 16-56 (117)
28 PF06970 RepA_N: Replication i 56.0 12 0.00027 27.4 2.8 22 169-190 54-75 (76)
29 PF12244 DUF3606: Protein of u 54.3 25 0.00055 24.4 3.9 30 167-196 20-49 (57)
30 PRK10877 protein disulfide iso 54.2 36 0.00077 29.5 5.8 43 66-119 23-72 (232)
31 PF02796 HTH_7: Helix-turn-hel 51.9 11 0.00024 24.4 1.7 23 169-191 23-45 (45)
32 PF13730 HTH_36: Helix-turn-he 51.4 20 0.00044 23.4 3.0 22 169-190 27-48 (55)
33 PRK05441 murQ N-acetylmuramic 50.6 21 0.00046 32.2 3.9 32 170-201 266-297 (299)
34 TIGR00274 N-acetylmuramic acid 49.5 21 0.00046 32.2 3.8 30 170-199 261-290 (291)
35 PF08680 DUF1779: Protein of u 47.8 15 0.00033 31.0 2.4 53 66-119 131-197 (203)
36 PLN02150 terpene synthase/cycl 47.8 17 0.00038 27.6 2.5 25 166-190 6-30 (96)
37 COG4004 Uncharacterized protei 45.8 40 0.00086 26.3 4.2 34 65-98 13-56 (96)
38 KOG1071 Mitochondrial translat 44.5 28 0.0006 32.7 3.7 36 165-200 45-80 (340)
39 PF03861 ANTAR: ANTAR domain; 43.7 29 0.00064 23.5 2.9 21 170-190 19-39 (56)
40 PRK12570 N-acetylmuramic acid- 43.3 34 0.00074 30.9 4.1 30 170-199 262-291 (296)
41 PF06972 DUF1296: Protein of u 41.9 58 0.0012 23.4 4.2 33 170-202 9-42 (60)
42 COG1654 BirA Biotin operon rep 40.3 30 0.00066 25.7 2.7 25 171-195 23-50 (79)
43 PF00392 GntR: Bacterial regul 38.2 32 0.00068 23.5 2.4 21 170-190 27-47 (64)
44 PHA02608 67 prohead core prote 37.7 41 0.00089 25.4 3.1 13 19-31 45-57 (80)
45 PRK12702 mannosyl-3-phosphogly 36.2 1.7E+02 0.0036 27.1 7.4 29 163-191 119-147 (302)
46 KOG0944 Ubiquitin-specific pro 34.2 36 0.00078 35.0 2.9 26 174-199 642-667 (763)
47 KOG1832 HIV-1 Vpr-binding prot 33.3 19 0.00041 38.4 0.9 15 166-180 1489-1503(1516)
48 PF10975 DUF2802: Protein of u 32.9 36 0.00079 24.6 2.1 21 168-188 45-65 (70)
49 smart00400 ZnF_CHCC zinc finge 32.5 51 0.0011 22.1 2.7 20 169-188 35-54 (55)
50 COG2188 PhnF Transcriptional r 32.2 40 0.00086 29.0 2.6 19 172-190 36-54 (236)
51 PF11699 CENP-C_C: Mif2/CENP-C 31.3 61 0.0013 24.3 3.1 35 80-117 39-73 (85)
52 PF04871 Uso1_p115_C: Uso1 / p 30.6 34 0.00074 27.7 1.8 11 21-31 110-120 (136)
53 KOG0943 Predicted ubiquitin-pr 30.0 28 0.0006 38.6 1.5 6 97-102 1849-1854(3015)
54 smart00345 HTH_GNTR helix_turn 30.0 74 0.0016 20.2 3.1 22 169-190 22-43 (60)
55 PRK05564 DNA polymerase III su 30.0 2.9E+02 0.0064 24.4 7.8 47 66-121 75-133 (313)
56 PHA01748 hypothetical protein 29.3 73 0.0016 22.2 3.1 21 168-188 15-35 (60)
57 PRK14897 unknown domain/DNA-di 28.7 82 0.0018 31.2 4.3 27 67-93 330-356 (509)
58 COG0100 RpsK Ribosomal protein 28.7 44 0.00096 27.3 2.1 93 82-202 18-113 (129)
59 PF13276 HTH_21: HTH-like doma 28.4 49 0.0011 22.3 2.0 19 63-81 37-55 (60)
60 KOG3198 Signal recognition par 28.3 96 0.0021 26.1 4.1 41 62-102 42-95 (152)
61 cd07377 WHTH_GntR Winged helix 27.9 82 0.0018 20.4 3.1 22 169-190 27-48 (66)
62 smart00804 TAP_C C-terminal do 27.3 1.4E+02 0.0029 21.3 4.2 34 168-201 14-47 (63)
63 KOG3130 Uncharacterized conser 27.1 35 0.00075 33.2 1.4 12 178-189 501-512 (514)
64 PF13629 T2SS-T3SS_pil_N: Pilu 25.9 1.8E+02 0.0039 20.4 4.7 25 95-119 22-48 (72)
65 PHA01623 hypothetical protein 24.5 1E+02 0.0022 21.4 3.0 20 168-187 26-45 (56)
66 PF04239 DUF421: Protein of un 24.2 86 0.0019 23.8 2.9 39 63-102 26-64 (99)
67 PF03943 TAP_C: TAP C-terminal 24.0 41 0.00089 22.8 1.0 31 170-200 4-34 (51)
68 TIGR02325 C_P_lyase_phnF phosp 24.0 70 0.0015 26.7 2.7 19 172-190 37-55 (238)
69 PRK10079 phosphonate metabolis 23.6 71 0.0015 27.1 2.6 20 171-190 39-58 (241)
70 PF04931 DNA_pol_phi: DNA poly 23.5 46 0.001 33.8 1.7 13 66-78 701-714 (784)
71 PF01807 zf-CHC2: CHC2 zinc fi 22.8 96 0.0021 23.3 2.9 76 68-190 5-87 (97)
72 smart00411 BHL bacterial (prok 21.8 1E+02 0.0022 22.0 2.8 29 170-198 7-35 (90)
73 PF01978 TrmB: Sugar-specific 21.8 1.2E+02 0.0027 20.6 3.1 24 167-190 22-45 (68)
74 KOG3705 Glycoprotein 6-alpha-L 21.7 1.1E+02 0.0023 30.2 3.6 31 61-93 343-373 (580)
75 COG3636 Predicted transcriptio 21.7 90 0.002 24.6 2.6 31 171-201 53-83 (100)
76 PF12614 RRF_GI: Ribosome recy 21.5 79 0.0017 25.9 2.3 23 169-191 104-126 (128)
77 TIGR02404 trehalos_R_Bsub treh 21.5 84 0.0018 26.4 2.6 19 172-190 29-47 (233)
78 KOG3130 Uncharacterized conser 21.1 67 0.0014 31.3 2.1 10 22-31 268-277 (514)
79 cd02736 RNAP_III_Rpc1_C Larges 21.0 1.6E+02 0.0034 27.1 4.4 27 67-93 132-158 (300)
80 PF15652 Tox-SHH: HNH/Endo VII 20.7 91 0.002 24.5 2.4 17 174-190 78-94 (100)
81 cd00591 HU_IHF Integration hos 20.6 1.1E+02 0.0024 21.7 2.8 29 170-198 6-34 (87)
82 COG5097 MED6 RNA polymerase II 20.5 1.7E+02 0.0037 25.6 4.2 42 61-102 39-88 (210)
83 PRK04984 fatty acid metabolism 20.2 93 0.002 26.1 2.7 19 172-190 36-54 (239)
84 PF00403 HMA: Heavy-metal-asso 20.1 2.4E+02 0.0053 18.4 4.3 28 66-98 13-40 (62)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=2.5e-53 Score=359.62 Aligned_cols=150 Identities=67% Similarity=0.924 Sum_probs=135.4
Q ss_pred CCCCCCcCCcCHHHHHHHHHHcCCcccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEeccceecchhhHHHHHHHH
Q 028761 55 EAGGRSKQSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSSQLQTQAAE 134 (204)
Q Consensus 55 ~~~~~~k~sr~eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfGeak~ed~~~q~q~~aae 134 (204)
.+.+++||||++||.||+|.||||++|+||+|||||+++|++|+|++|+|||+|+++||+|||+++++++++|+|.+|++
T Consensus 55 ~~~~~akqsrsekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q~~aae 134 (209)
T KOG2239|consen 55 EPVAKAKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQMQAAE 134 (209)
T ss_pred cchhhhhcchHHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCcccCCC----Ccc-ccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028761 135 QFKAPDLSHVVSKP----ESS-AMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 135 ~~~~~~~~~~~~~~----~~~-~~~~~~eevd~~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~Lt~ 204 (204)
+|+.+..++..... .++ .+.+++++||++||+.+||+|||+|+||||++||||||+|+||||||||+||+
T Consensus 135 ~fk~~~~~~~~~~~~~~~~~~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 135 RFKVPQEAPGLIQEDTSATPPAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred hccCCccccccccccccCCCccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 99987655543221 122 22355667999999999999999999999999999999999999999999985
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=1.5e-37 Score=245.06 Aligned_cols=106 Identities=31% Similarity=0.501 Sum_probs=97.5
Q ss_pred cCHHHHHHHHHHcCCc--ccCCceEEEEEecCceEEEEcCCeEE--eeCCCcEEEEeccceecchhhHHHHHHHHHhcCC
Q 028761 64 RSEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDVF--KSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAP 139 (204)
Q Consensus 64 r~eKK~rk~mkKLGlk--~v~gV~rVtI~k~~~~~fvI~~P~V~--ks~gs~tYvVfGeak~ed~~~q~q~~aae~~~~~ 139 (204)
-||||+|+||+||||+ +| ||.||+|++.+ ..|||++|+|| +++|++||||||+++.++++++.
T Consensus 5 ~nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~-~~~Vi~~P~V~~m~~~g~~tY~I~Ge~~~e~~~~~~----------- 71 (115)
T PRK06369 5 MNPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKEAEK----------- 71 (115)
T ss_pred CCHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEeccEEeeccccc-----------
Confidence 4689999999999999 99 99999999987 89999999999 78999999999999998764420
Q ss_pred CCCcccCCCCccccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028761 140 DLSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~eevd~~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~Lt~ 204 (204)
+++|+++||+|||+||||||++|++||++||||||+|||.|+.
T Consensus 72 ----------------------~~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 72 ----------------------EVEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred ----------------------cCCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 3589999999999999999999999999999999999999973
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.98 E-value=8.8e-33 Score=219.33 Aligned_cols=113 Identities=38% Similarity=0.613 Sum_probs=95.2
Q ss_pred cCHHHHHHHHHHcCCc--ccCCceEEEEEecCceEEEEcCCeEEe--eCCCcEEEEeccceecchhhHHHHHHHHHhcCC
Q 028761 64 RSEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDVFK--SPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAP 139 (204)
Q Consensus 64 r~eKK~rk~mkKLGlk--~v~gV~rVtI~k~~~~~fvI~~P~V~k--s~gs~tYvVfGeak~ed~~~q~q~~aae~~~~~ 139 (204)
-|+|+|+|+|++|||+ +|+||.||+|++.++. |+|++|.||. ++|+.||+|.|.+..+.
T Consensus 6 mnpr~l~k~mkqmGi~~eeld~v~~V~i~~kd~e-~vi~~P~V~~~~~~g~~~yqi~g~~~~~~---------------- 68 (122)
T COG1308 6 MNPRKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVMKAMGQKTYQISGDPSAKE---------------- 68 (122)
T ss_pred CCHHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcchhhhc----------------
Confidence 5689999999999955 8999999999998875 9999999976 58899999999964100
Q ss_pred CCCcccCCCCccccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028761 140 DLSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~eevd~~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~Lt~ 204 (204)
.....++..+++..|+++||+|||+||||||++|||||+++|||||+|||+||.
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 000112334667789999999999999999999999999999999999999984
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=1.7e-31 Score=210.72 Aligned_cols=101 Identities=34% Similarity=0.530 Sum_probs=87.9
Q ss_pred HHHHHHHHHcCCc--ccCCceEEEEEecCceEEEEcCCeE--EeeCCCcEEEEeccceecchhhHHHHHHHHHhcCCCCC
Q 028761 67 KKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDV--FKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPDLS 142 (204)
Q Consensus 67 KK~rk~mkKLGlk--~v~gV~rVtI~k~~~~~fvI~~P~V--~ks~gs~tYvVfGeak~ed~~~q~q~~aae~~~~~~~~ 142 (204)
|+||+||+||||+ ++. |.+|+|++.++ .++|++|.| |+++|+.||||||+++.+++..
T Consensus 12 ~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~~---------------- 73 (116)
T TIGR00264 12 KQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVEE---------------- 73 (116)
T ss_pred HHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeeccc----------------
Confidence 3999999999999 476 99999999764 577999988 6789999999999998754310
Q ss_pred cccCCCCccccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028761 143 HVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 143 ~~~~~~~~~~~~~~~eevd~~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~Lt~ 204 (204)
+.+|+++||+|||+||||||++|++||+++|||||+|||.|+.
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 0259999999999999999999999999999999999999973
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=99.84 E-value=3.5e-21 Score=134.59 Aligned_cols=58 Identities=52% Similarity=0.886 Sum_probs=48.2
Q ss_pred HHHHHHHHHHcCCcccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEeccceecc
Q 028761 66 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIED 123 (204)
Q Consensus 66 eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfGeak~ed 123 (204)
|||+|++|+||||++|+||.||+|++.+|.+|+|++|+||++++++||+|||++++++
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 6999999999999999999999999999999999999999999999999999998764
No 6
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=98.74 E-value=7e-09 Score=86.54 Aligned_cols=64 Identities=28% Similarity=0.512 Sum_probs=59.5
Q ss_pred CcCHHHHHHHHHHcCCcccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEeccceecchhh
Q 028761 63 SRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSS 126 (204)
Q Consensus 63 sr~eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfGeak~ed~~~ 126 (204)
...+||++.-|+||++.+|+||.+|.|++.++.+++|++|.|+++...|||.|+|.++.+.++.
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 4568999999999999999999999999999999999999999999999999999998876543
No 7
>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=97.65 E-value=5.2e-05 Score=48.13 Aligned_cols=37 Identities=30% Similarity=0.524 Sum_probs=31.9
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 165 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 165 v~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
|+++.|..+++. |+|++.|++||+.++||+-.||.-|
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 356788999999 9999999999999999999998754
No 8
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.55 E-value=4.8e-05 Score=60.20 Aligned_cols=42 Identities=33% Similarity=0.577 Sum_probs=39.1
Q ss_pred CCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028761 163 TGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 163 ~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~Lt~ 204 (204)
..|.++||+|+|...-+++.-|.+-|++++||+|.|+-.|++
T Consensus 77 V~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 77 VTIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 358899999999999999999999999999999999988864
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=95.49 E-value=0.02 Score=37.39 Aligned_cols=33 Identities=24% Similarity=0.351 Sum_probs=27.6
Q ss_pred ccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 168 KDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
+-|.-.|+-|||+++.|+..|+.+++||-.||=
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 357788999999999999999999999988873
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=95.06 E-value=0.039 Score=34.47 Aligned_cols=32 Identities=34% Similarity=0.521 Sum_probs=26.0
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
|..++ ..|.+++.|+.||+.++||+-.|+--|
T Consensus 5 v~~L~-~mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 5 LEQLL-EMGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHH-HcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 44444 469999999999999999999987544
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=94.79 E-value=0.051 Score=33.78 Aligned_cols=28 Identities=43% Similarity=0.580 Sum_probs=23.7
Q ss_pred HhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 175 TQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 175 ~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
...|.+++.|+.||+.++||+-.|+--|
T Consensus 9 ~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 9 LEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 3459999999999999999998887543
No 12
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=86.01 E-value=1.1 Score=36.98 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=28.7
Q ss_pred CCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 163 TGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 163 ~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
..++.+-++.+..-. ||.++|++||.+++ |+..|+-
T Consensus 111 s~~~~e~v~v~a~a~-v~~eeAr~aleeag-Dl~~A~k 146 (153)
T COG4008 111 SEPPVEEVEVLADAF-VTPEEAREALEEAG-DLRTAMK 146 (153)
T ss_pred CCCcHHHHHHHHHhc-CCHHHHHHHHHHcC-CHHHHHH
Confidence 445667777776655 99999999999996 9999853
No 13
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=84.20 E-value=1.3 Score=40.47 Aligned_cols=39 Identities=28% Similarity=0.439 Sum_probs=33.8
Q ss_pred CCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 164 GVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 164 gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
.+-+.-+..||+-|||+|++|..+|++++|++=-||+-+
T Consensus 231 KL~dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~ 269 (298)
T COG2103 231 KLRDRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVML 269 (298)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHH
Confidence 355677899999999999999999999999998887643
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=82.40 E-value=1.7 Score=39.13 Aligned_cols=38 Identities=39% Similarity=0.583 Sum_probs=30.7
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 165 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 165 v~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
+-..=+.+||+-+|||+++|.++|..++|.+=-||+-+
T Consensus 234 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 234 LVDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 34566778899999999999999999999987777643
No 15
>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=79.17 E-value=4.4 Score=27.92 Aligned_cols=40 Identities=33% Similarity=0.684 Sum_probs=24.2
Q ss_pred HHHHHHc--CCc-------ccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEeccc
Q 028761 70 RKAMLKL--GMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEA 119 (204)
Q Consensus 70 rk~mkKL--Glk-------~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfGea 119 (204)
++.|+++ |++ +++|+-+|++ ++.+ + +|.++. ..|+|+|..
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 4566666 665 6999999988 4333 3 234443 369999974
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=77.09 E-value=1.6 Score=38.47 Aligned_cols=36 Identities=42% Similarity=0.653 Sum_probs=31.1
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 165 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 165 v~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
+-..=+.+||+-+|||+++|.++|..++|++=-||+
T Consensus 221 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~~ 256 (257)
T cd05007 221 LRERAIRIVMEATGVSRDEAEAALEQAGGDVKTAIL 256 (257)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeeee
Confidence 445678889999999999999999999999876664
No 17
>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=76.75 E-value=3.9 Score=26.22 Aligned_cols=33 Identities=24% Similarity=0.343 Sum_probs=21.4
Q ss_pred HHHHHHhh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 170 IELVMTQA-GVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qa-gvSr~kAvkALke~~GDIV~AIM~L 202 (204)
|..+.+-. +++++....+|+.++|||-.||-.|
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 33444444 6788888888888888886665544
No 18
>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=76.73 E-value=3.4 Score=37.30 Aligned_cols=37 Identities=22% Similarity=0.328 Sum_probs=30.6
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028761 165 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 201 (204)
Q Consensus 165 v~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~ 201 (204)
+-..=+.+||+=+|||+++|.++|..++|.|=-||+-
T Consensus 229 l~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~ 265 (291)
T TIGR00274 229 LKARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVM 265 (291)
T ss_pred HHHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHH
Confidence 3455677899999999999999999999999888764
No 19
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=76.72 E-value=1.7 Score=41.92 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=7.5
Q ss_pred EEEEeccceecc
Q 028761 112 TYVIFGEAKIED 123 (204)
Q Consensus 112 tYvVfGeak~ed 123 (204)
|-.|-|...+..
T Consensus 193 TDFVCGTLDEDR 204 (458)
T PF10446_consen 193 TDFVCGTLDEDR 204 (458)
T ss_pred ccccCCCcCCcc
Confidence 556678776544
No 20
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=72.27 E-value=4.9 Score=36.29 Aligned_cols=36 Identities=31% Similarity=0.470 Sum_probs=28.6
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028761 166 EPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 201 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~ 201 (204)
-..=+.+||+=+|||+++|.++|..++|.|=-||+-
T Consensus 231 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~ 266 (296)
T PRK12570 231 VARAVRIVMQATGCSEDEAKELLKESDNDVKLAILM 266 (296)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHH
Confidence 345667788888888888888888888888777763
No 21
>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=68.26 E-value=6.2 Score=26.02 Aligned_cols=22 Identities=32% Similarity=0.406 Sum_probs=17.0
Q ss_pred CCHHHHHHHHHHcCCcHHHHHh
Q 028761 179 VSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 179 vSr~kAvkALke~~GDIV~AIM 200 (204)
-.|+.-.-.|+-++||+|.||=
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE 36 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIE 36 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHH
Confidence 3455556678999999999984
No 22
>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=68.24 E-value=8.4 Score=24.67 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=25.5
Q ss_pred cHHHHHHhh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 169 DIELVMTQA-GVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 169 DIeLVm~Qa-gvSr~kAvkALke~~GDIV~AIM~L 202 (204)
.|+.+.+=. ++++..++..|+.++|++-.||=.|
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 344444444 7889999999999999998887444
No 23
>PF14474 RTC4: RTC4-like domain
Probab=63.27 E-value=7.8 Score=30.89 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=23.2
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHHc
Q 028761 166 EPKDIELVMTQAGVSRAKAVKALKAA 191 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAvkALke~ 191 (204)
+|==|.|||+-.||++++|++-|+++
T Consensus 89 PEl~~~LI~EDm~v~~~~A~~il~eS 114 (124)
T PF14474_consen 89 PELAVRLIMEDMGVDDEEARQILEES 114 (124)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 34458999999999999999999997
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=61.48 E-value=9.1 Score=36.09 Aligned_cols=33 Identities=33% Similarity=0.526 Sum_probs=27.6
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028761 170 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAvkALke~~GDIV~AIM~L 202 (204)
|+-||+..+. .++=|--|||.+.||+++||+-|
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=60.88 E-value=13 Score=27.60 Aligned_cols=30 Identities=33% Similarity=0.269 Sum_probs=24.8
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
|+- |.++|.++.....||..+.||+..|.-
T Consensus 1 i~~-~~~~g~~~~~v~~aL~~tSgd~~~a~~ 30 (87)
T PF11626_consen 1 IKH-YEELGYSREFVTHALYATSGDPELARR 30 (87)
T ss_dssp -HH-HHHHTB-HHHHHHHHHHTTTBHHHHHH
T ss_pred Cch-HHHhCCCHHHHHHHHHHhCCCHHHHHH
Confidence 344 899999999999999999999988754
No 26
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=59.80 E-value=9 Score=35.49 Aligned_cols=33 Identities=45% Similarity=0.616 Sum_probs=26.4
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028761 170 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAvkALke~~GDIV~AIM~L 202 (204)
|+-||...++ .|+=|-=|||.+.||+++||+-|
T Consensus 45 VdRVM~EgslyDreLAALAikQa~GD~~EAIFLl 78 (367)
T COG3626 45 VDRVMTEGSLYDRELAALALKQASGDLVEAIFLL 78 (367)
T ss_pred HHHHhhccchhHHHHHHHHHHHhcchHHHHHHHH
Confidence 4456665553 68888999999999999999876
No 27
>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=56.25 E-value=15 Score=29.42 Aligned_cols=35 Identities=23% Similarity=0.459 Sum_probs=28.2
Q ss_pred CCCcCCcCHHHHHHHHHHcCCc------ccCCceEEEEEec
Q 028761 58 GRSKQSRSEKKSRKAMLKLGMK------PIPGVSRVTVKKS 92 (204)
Q Consensus 58 ~~~k~sr~eKK~rk~mkKLGlk------~v~gV~rVtI~k~ 92 (204)
-+++.++.|..++++|..+|++ .+||+--+.+.+-
T Consensus 16 iR~~~T~pE~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~ 56 (117)
T TIGR00632 16 IRTKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEY 56 (117)
T ss_pred HhcCCCHHHHHHHHHHHhCCCEEEEecCCCCCcccEEecCC
Confidence 4678889999999999999998 3777766666664
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=56.02 E-value=12 Score=27.41 Aligned_cols=22 Identities=32% Similarity=0.379 Sum_probs=19.8
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028761 169 DIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke 190 (204)
-|+-+|+-.|||+.++++++++
T Consensus 54 s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHHc
Confidence 4778899999999999999986
No 29
>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=54.30 E-value=25 Score=24.39 Aligned_cols=30 Identities=17% Similarity=0.304 Sum_probs=26.9
Q ss_pred cccHHHHHHhhCCCHHHHHHHHHHcCCcHH
Q 028761 167 PKDIELVMTQAGVSRAKAVKALKAADGDIV 196 (204)
Q Consensus 167 eeDIeLVm~QagvSr~kAvkALke~~GDIV 196 (204)
+-.|...+...|||.++...|.+..++++.
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 30
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=54.22 E-value=36 Score=29.51 Aligned_cols=43 Identities=19% Similarity=0.470 Sum_probs=28.8
Q ss_pred HHHHHHHHHHcCCc-------ccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEeccc
Q 028761 66 EKKSRKAMLKLGMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEA 119 (204)
Q Consensus 66 eKK~rk~mkKLGlk-------~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfGea 119 (204)
...+++.|.++|++ +|+|+-+|++ +.+ +| |-.+ ...|+|+|..
T Consensus 23 ~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~-i~-------Y~~~-dg~y~i~G~l 72 (232)
T PRK10877 23 DAAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESG-VL-------YITD-DGKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCe-EE-------EEcC-CCCEEEeeee
Confidence 36778888888876 6888888865 223 22 3333 3359999974
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=51.89 E-value=11 Score=24.45 Aligned_cols=23 Identities=30% Similarity=0.382 Sum_probs=17.8
Q ss_pred cHHHHHHhhCCCHHHHHHHHHHc
Q 028761 169 DIELVMTQAGVSRAKAVKALKAA 191 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke~ 191 (204)
-|.-|+.++||||.-..+.|.+|
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 37788999999999999988654
No 32
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.37 E-value=20 Score=23.42 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=19.7
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028761 169 DIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke 190 (204)
-++.++..+|+||...+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 6899999999999998888875
No 33
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=50.62 E-value=21 Score=32.18 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=28.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAIME 201 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AIM~ 201 (204)
+-+||--+|||..+|.+.|..++|.|-.||=.
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhh
Confidence 45789999999999999999999999998744
No 34
>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=49.49 E-value=21 Score=32.17 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=26.8
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAI 199 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AI 199 (204)
+-++|-.+||+..+|++.|..++|.|-.||
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l 290 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQAL 290 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhh
Confidence 457888999999999999999999998775
No 35
>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=47.79 E-value=15 Score=30.99 Aligned_cols=53 Identities=21% Similarity=0.370 Sum_probs=19.6
Q ss_pred HHHHHHHHHHcCCcccCCceEEEEE-----ec--CceEEEEcCCeE-------EeeCCCcEEEEeccc
Q 028761 66 EKKSRKAMLKLGMKPIPGVSRVTVK-----KS--KNILFVISKPDV-------FKSPTTDTYVIFGEA 119 (204)
Q Consensus 66 eKK~rk~mkKLGlk~v~gV~rVtI~-----k~--~~~~fvI~~P~V-------~ks~gs~tYvVfGea 119 (204)
.++++++|++||.++|+.+..-++. .+ ++ .+-+..-.+ +...+..||+++|.|
T Consensus 131 ~~~~~~~l~~l~A~~vE~~~~~~~vSvsaYt~~~~~-~i~~~~~k~NlqiAlr~~~~~~~T~I~iGTP 197 (203)
T PF08680_consen 131 EKIAERLLKKLGAKPVESLKDENFVSVSAYTPKWDD-SIQTGGKKMNLQIALRYNSYGGKTYITIGTP 197 (203)
T ss_dssp HHHHHHHHHHH---------BTTEEEEEE--TTSS---EEETTEEE-EEEEEE--------EEEEESS
T ss_pred HHHHHHHHHHcCCcEeeEEecccEEEEEEEccchhh-hhhcCCeEEEEEEEEEecCCCCCEEEEEEec
Confidence 5778899999999988766543321 11 11 111222222 223577899999987
No 36
>PLN02150 terpene synthase/cyclase family protein
Probab=47.77 E-value=17 Score=27.62 Aligned_cols=25 Identities=32% Similarity=0.469 Sum_probs=21.9
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHH
Q 028761 166 EPKDIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAvkALke 190 (204)
.+.-|+--|.|-|||.++|++.|+.
T Consensus 6 vaSsIeCYMke~g~seeeA~~~i~~ 30 (96)
T PLN02150 6 VANGVNCYMKQHGVTKEEAVSELKK 30 (96)
T ss_pred chHHHHHHhccCCCCHHHHHHHHHH
Confidence 3557899999999999999999876
No 37
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.77 E-value=40 Score=26.30 Aligned_cols=34 Identities=26% Similarity=0.541 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHcCCc----------ccCCceEEEEEecCceEEE
Q 028761 65 SEKKSRKAMLKLGMK----------PIPGVSRVTVKKSKNILFV 98 (204)
Q Consensus 65 ~eKK~rk~mkKLGlk----------~v~gV~rVtI~k~~~~~fv 98 (204)
.+-.+.++|..||.. .+||+++|.|+..++.++|
T Consensus 13 ~~dri~~~l~e~g~~v~~eGD~ivas~pgis~ieik~E~kkL~v 56 (96)
T COG4004 13 DPDRIMRGLSELGWTVSEEGDRIVASSPGISRIEIKPENKKLLV 56 (96)
T ss_pred CHHHHHHHHHHhCeeEeecccEEEEecCCceEEEEecccceEEE
Confidence 356788889999965 4788888888887766554
No 38
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=44.52 E-value=28 Score=32.68 Aligned_cols=36 Identities=25% Similarity=0.276 Sum_probs=32.9
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 165 VEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 165 v~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
++..+|+-.=+.||.|----++||.++|||++.|--
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~ 80 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEE 80 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHH
Confidence 568899999999999999999999999999998854
No 39
>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=43.73 E-value=29 Score=23.46 Aligned_cols=21 Identities=24% Similarity=0.425 Sum_probs=17.1
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke 190 (204)
+-++|.+.|||.++|.+.|+.
T Consensus 19 kgiLm~~~g~~e~~A~~~Lr~ 39 (56)
T PF03861_consen 19 KGILMARYGLSEDEAYRLLRR 39 (56)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHHHHHH
Confidence 468999999999999999987
No 40
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=43.28 E-value=34 Score=30.89 Aligned_cols=30 Identities=33% Similarity=0.451 Sum_probs=27.3
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAI 199 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AI 199 (204)
+-++|-.+|||.++|.+.|..++|.|-.||
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l 291 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAI 291 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHH
Confidence 567899999999999999999999998886
No 41
>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=41.94 E-value=58 Score=23.44 Aligned_cols=33 Identities=21% Similarity=0.257 Sum_probs=25.6
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028761 170 IELVMTQAGV-SRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAvkALke~~GDIV~AIM~L 202 (204)
|.-+=+-+|| |.++....|+++|.|.=+|.=.|
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 42
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=40.34 E-value=30 Score=25.75 Aligned_cols=25 Identities=32% Similarity=0.524 Sum_probs=20.1
Q ss_pred HHHHHhhCCCHH---HHHHHHHHcCCcH
Q 028761 171 ELVMTQAGVSRA---KAVKALKAADGDI 195 (204)
Q Consensus 171 eLVm~QagvSr~---kAvkALke~~GDI 195 (204)
+-+.+..||||. |.|++|++.+-+|
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 456789999994 7888999887765
No 43
>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=38.19 E-value=32 Score=23.46 Aligned_cols=21 Identities=29% Similarity=0.328 Sum_probs=17.2
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke 190 (204)
..-+++..||||.-+++||..
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 456899999999999999975
No 44
>PHA02608 67 prohead core protein; Provisional
Probab=37.74 E-value=41 Score=25.44 Aligned_cols=13 Identities=31% Similarity=0.795 Sum_probs=6.3
Q ss_pred cCCCCCccccCCC
Q 028761 19 IDDDKPVVEDDED 31 (204)
Q Consensus 19 ~~~~~~~~~~~~~ 31 (204)
++.++|-.+++++
T Consensus 45 iEGEe~ed~ddd~ 57 (80)
T PHA02608 45 IEGEEPEDDDDDE 57 (80)
T ss_pred hcCCCCccccchh
Confidence 4455555544433
No 45
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=36.21 E-value=1.7e+02 Score=27.13 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=25.5
Q ss_pred CCCCcccHHHHHHhhCCCHHHHHHHHHHc
Q 028761 163 TGVEPKDIELVMTQAGVSRAKAVKALKAA 191 (204)
Q Consensus 163 ~gv~eeDIeLVm~QagvSr~kAvkALke~ 191 (204)
.|+..=.++-|++-||.|.+.|..|.+-.
T Consensus 119 ~gF~d~t~~ei~~~TGL~~~~A~~A~~Re 147 (302)
T PRK12702 119 IGFGDWTASELAAATGIPLEEAERAQKRE 147 (302)
T ss_pred eehhhCCHHHHHHHhCcCHHHHHHHHhcc
Confidence 47888899999999999999999998753
No 46
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=34.16 E-value=36 Score=34.96 Aligned_cols=26 Identities=38% Similarity=0.634 Sum_probs=22.3
Q ss_pred HHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028761 174 MTQAGVSRAKAVKALKAADGDIVSAI 199 (204)
Q Consensus 174 m~QagvSr~kAvkALke~~GDIV~AI 199 (204)
+--.|.+|..||+||+.+||+|-.|.
T Consensus 642 i~smGf~~~qa~~aL~~~n~nverav 667 (763)
T KOG0944|consen 642 IVSMGFSRNQAIKALKATNNNVERAV 667 (763)
T ss_pred eeeecCcHHHHHHHHHhcCccHHHHH
Confidence 33469999999999999999997773
No 47
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=33.26 E-value=19 Score=38.42 Aligned_cols=15 Identities=20% Similarity=0.003 Sum_probs=11.2
Q ss_pred CcccHHHHHHhhCCC
Q 028761 166 EPKDIELVMTQAGVS 180 (204)
Q Consensus 166 ~eeDIeLVm~QagvS 180 (204)
..++.++||+-.+-|
T Consensus 1489 ~Dee~~~~~~d~~ss 1503 (1516)
T KOG1832|consen 1489 EDEEDDGEMQDFMSS 1503 (1516)
T ss_pred cchhhhhhhhcccCC
Confidence 456778888888766
No 48
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=32.89 E-value=36 Score=24.63 Aligned_cols=21 Identities=38% Similarity=0.514 Sum_probs=17.5
Q ss_pred ccHHHHHHhhCCCHHHHHHHH
Q 028761 168 KDIELVMTQAGVSRAKAVKAL 188 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAvkAL 188 (204)
-||+-||..+|.||++|.=.+
T Consensus 45 a~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999996443
No 49
>smart00400 ZnF_CHCC zinc finger.
Probab=32.46 E-value=51 Score=22.07 Aligned_cols=20 Identities=35% Similarity=0.353 Sum_probs=18.1
Q ss_pred cHHHHHHhhCCCHHHHHHHH
Q 028761 169 DIELVMTQAGVSRAKAVKAL 188 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkAL 188 (204)
=|++||..-|+|-.+|++-|
T Consensus 35 ~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 35 VISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred HHHHHHHHHCcCHHHHHHHh
Confidence 49999999999999999876
No 50
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=32.18 E-value=40 Score=28.98 Aligned_cols=19 Identities=42% Similarity=0.406 Sum_probs=16.8
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028761 172 LVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAvkALke 190 (204)
-.++|.||||-.++|||..
T Consensus 36 eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHHCCcHHHHHHHHHH
Confidence 3689999999999999975
No 51
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=31.30 E-value=61 Score=24.33 Aligned_cols=35 Identities=31% Similarity=0.493 Sum_probs=26.2
Q ss_pred ccCCceEEEEEecCceEEEEcCCeEEeeCCCcEEEEec
Q 028761 80 PIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFG 117 (204)
Q Consensus 80 ~v~gV~rVtI~k~~~~~fvI~~P~V~ks~gs~tYvVfG 117 (204)
-+.|..+|+|-. ..|++..-..+.+|..|+|-|--
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 477888888854 57999999999999999999864
No 52
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=30.56 E-value=34 Score=27.67 Aligned_cols=11 Identities=18% Similarity=0.380 Sum_probs=5.4
Q ss_pred CCCCccccCCC
Q 028761 21 DDKPVVEDDED 31 (204)
Q Consensus 21 ~~~~~~~~~~~ 31 (204)
--.+|.+++..
T Consensus 110 LG~eVSddE~~ 120 (136)
T PF04871_consen 110 LGEEVSDDEDS 120 (136)
T ss_pred cCCCccCCccc
Confidence 34556555433
No 53
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=30.05 E-value=28 Score=38.60 Aligned_cols=6 Identities=50% Similarity=1.209 Sum_probs=2.5
Q ss_pred EEEcCC
Q 028761 97 FVISKP 102 (204)
Q Consensus 97 fvI~~P 102 (204)
|+|..|
T Consensus 1849 Fmiad~ 1854 (3015)
T KOG0943|consen 1849 FMIADP 1854 (3015)
T ss_pred eeecCC
Confidence 444444
No 54
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.00 E-value=74 Score=20.22 Aligned_cols=22 Identities=32% Similarity=0.326 Sum_probs=18.9
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028761 169 DIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke 190 (204)
.+.-+++..||||.-+.++|+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5667899999999999998875
No 55
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=29.98 E-value=2.9e+02 Score=24.38 Aligned_cols=47 Identities=15% Similarity=0.357 Sum_probs=30.1
Q ss_pred HHHHHHHHHHcCCcccCCceEEEEEecCceEEEEcCCeEEe------------eCCCcEEEEecccee
Q 028761 66 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFK------------SPTTDTYVIFGEAKI 121 (204)
Q Consensus 66 eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI~~P~V~k------------s~gs~tYvVfGeak~ 121 (204)
=..+|.++.++...++.|=.| +++|.+++.+. -|..+||+|+.....
T Consensus 75 v~~ir~~~~~~~~~p~~~~~k---------v~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~ 133 (313)
T PRK05564 75 VDDIRNIIEEVNKKPYEGDKK---------VIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENL 133 (313)
T ss_pred HHHHHHHHHHHhcCcccCCce---------EEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence 456888888888877765334 45555555431 266788888876433
No 56
>PHA01748 hypothetical protein
Probab=29.26 E-value=73 Score=22.25 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=17.1
Q ss_pred ccHHHHHHhhCCCHHHHHHHH
Q 028761 168 KDIELVMTQAGVSRAKAVKAL 188 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAvkAL 188 (204)
+-++..+.+.|+||+++|+..
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 356778999999999998844
No 57
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=28.71 E-value=82 Score=31.18 Aligned_cols=27 Identities=22% Similarity=0.309 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCcccCCceEEEEEecC
Q 028761 67 KKSRKAMLKLGMKPIPGVSRVTVKKSK 93 (204)
Q Consensus 67 KK~rk~mkKLGlk~v~gV~rVtI~k~~ 93 (204)
+++++.+..+-++.+|||.||+|+..+
T Consensus 330 ~~l~~~l~~i~I~GipgI~r~~i~~~~ 356 (509)
T PRK14897 330 YLLAEKVKSLTIKGIKGIKRAIARKEN 356 (509)
T ss_pred HHHHHHhhccEEeCCCCccEEEEecCC
Confidence 444555666668899999999998653
No 58
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=28.66 E-value=44 Score=27.32 Aligned_cols=93 Identities=25% Similarity=0.365 Sum_probs=53.7
Q ss_pred CCceEEEEEec-CceEEEEcCCe--EEeeCCCcEEEEeccceecchhhHHHHHHHHHhcCCCCCcccCCCCccccccCcc
Q 028761 82 PGVSRVTVKKS-KNILFVISKPD--VFKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPDLSHVVSKPESSAMAQDDE 158 (204)
Q Consensus 82 ~gV~rVtI~k~-~~~~fvI~~P~--V~ks~gs~tYvVfGeak~ed~~~q~q~~aae~~~~~~~~~~~~~~~~~~~~~~~e 158 (204)
.|| +.|... +|+++.|.++. +.....+-+..++|..+.-+...|+.+..+.+-
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 355 555544 56777888874 333334455666777655555444433322221
Q ss_pred ccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028761 159 EVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 159 evd~~gv~eeDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~L 202 (204)
..+-||. .|++++.=.|--|+-|++||-.. |.-|.-|+..
T Consensus 74 -a~e~Gi~--~v~v~vkgpG~GreaAiraL~~a-g~~i~~I~Dv 113 (129)
T COG0100 74 -AKEHGIK--SVEVKVKGPGPGREAAIRALAAA-GLKITRIEDV 113 (129)
T ss_pred -HHHhCcc--EEEEEEECCCCcHHHHHHHHHHc-cceEEEEEEc
Confidence 1123444 67777777899999999999855 5444444433
No 59
>PF13276 HTH_21: HTH-like domain
Probab=28.35 E-value=49 Score=22.26 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=16.2
Q ss_pred CcCHHHHHHHHHHcCCccc
Q 028761 63 SRSEKKSRKAMLKLGMKPI 81 (204)
Q Consensus 63 sr~eKK~rk~mkKLGlk~v 81 (204)
.-|.|+++++|+.|||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 5678999999999999753
No 60
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.29 E-value=96 Score=26.09 Aligned_cols=41 Identities=27% Similarity=0.391 Sum_probs=31.1
Q ss_pred CCcCHHHHHHHHHHcCCcc-------------cCCceEEEEEecCceEEEEcCC
Q 028761 62 QSRSEKKSRKAMLKLGMKP-------------IPGVSRVTVKKSKNILFVISKP 102 (204)
Q Consensus 62 ~sr~eKK~rk~mkKLGlk~-------------v~gV~rVtI~k~~~~~fvI~~P 102 (204)
+|-.-+.++.+++.|||.- =+|=.||.|+..+|.+|++.-|
T Consensus 42 eNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG~l~~~~~~ 95 (152)
T KOG3198|consen 42 ENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDGTLYVIAFI 95 (152)
T ss_pred cCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCCcEEeecch
Confidence 3444488899999999982 2456788888888999887765
No 61
>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=27.90 E-value=82 Score=20.41 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=18.6
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028761 169 DIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke 190 (204)
-+.-++.+.|+||..+.++|+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4667899999999999988876
No 62
>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=27.34 E-value=1.4e+02 Score=21.30 Aligned_cols=34 Identities=15% Similarity=0.187 Sum_probs=28.9
Q ss_pred ccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028761 168 KDIELVMTQAGVSRAKAVKALKAADGDIVSAIME 201 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAvkALke~~GDIV~AIM~ 201 (204)
.=|..++.+||....=+.+.|..++-|.=.|+-.
T Consensus 14 ~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~ 47 (63)
T smart00804 14 EMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKN 47 (63)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHH
Confidence 4467788999999999999999999998887653
No 63
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.09 E-value=35 Score=33.23 Aligned_cols=12 Identities=33% Similarity=0.337 Sum_probs=7.5
Q ss_pred CCCHHHHHHHHH
Q 028761 178 GVSRAKAVKALK 189 (204)
Q Consensus 178 gvSr~kAvkALk 189 (204)
-|||=||-++|-
T Consensus 501 rvs~fk~~r~~~ 512 (514)
T KOG3130|consen 501 RVSKFKAARLQQ 512 (514)
T ss_pred hHHHHHHHHHhc
Confidence 366767766663
No 64
>PF13629 T2SS-T3SS_pil_N: Pilus formation protein N terminal region
Probab=25.91 E-value=1.8e+02 Score=20.43 Aligned_cols=25 Identities=12% Similarity=0.268 Sum_probs=17.5
Q ss_pred eEEEEcCCeEE--eeCCCcEEEEeccc
Q 028761 95 ILFVISKPDVF--KSPTTDTYVIFGEA 119 (204)
Q Consensus 95 ~~fvI~~P~V~--ks~gs~tYvVfGea 119 (204)
..+.|.+|.|- ...+.++++|||..
T Consensus 22 ~rV~v~dp~Iadv~~~~~~~v~i~gk~ 48 (72)
T PF13629_consen 22 TRVAVGDPEIADVTVLSPNEVYITGKK 48 (72)
T ss_pred EEEEECCCCEEEEEEeCCCEEEEEEeC
Confidence 45678888884 34566788888864
No 65
>PHA01623 hypothetical protein
Probab=24.51 E-value=1e+02 Score=21.37 Aligned_cols=20 Identities=5% Similarity=0.242 Sum_probs=17.2
Q ss_pred ccHHHHHHhhCCCHHHHHHH
Q 028761 168 KDIELVMTQAGVSRAKAVKA 187 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAvkA 187 (204)
.-++..+.+-|++|+++|+-
T Consensus 26 ~~Ld~y~~~~g~~rSe~Ire 45 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIEE 45 (56)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 46788999999999999883
No 66
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=24.18 E-value=86 Score=23.75 Aligned_cols=39 Identities=21% Similarity=0.282 Sum_probs=26.0
Q ss_pred CcCHHHHHHHHHHcCCcccCCceEEEEEecCceEEEEcCC
Q 028761 63 SRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKP 102 (204)
Q Consensus 63 sr~eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI~~P 102 (204)
.-+...+..+|++-|+..+.+|..+++..+ |.+.+|.+.
T Consensus 26 ~it~~dl~~~LR~~gi~~l~dV~~a~lE~~-G~lsv~~k~ 64 (99)
T PF04239_consen 26 RITEEDLLSALREQGIESLSDVKAAVLEPN-GQLSVIKKE 64 (99)
T ss_dssp T--HHHHHHHHHHTT--SGGGEEEEEE-TT-S-EEEEE-G
T ss_pred CCCHHHHHHHHHhhCCCCHHHcCEEEECCC-CCEEEEEcC
Confidence 344567888899999999999999999996 556666655
No 67
>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=24.04 E-value=41 Score=22.79 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=24.8
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSAIM 200 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~AIM 200 (204)
|.-++.|+|...+=+.+-|.+|+-|+=.|+-
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 5667899999999999999999999876653
No 68
>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=24.02 E-value=70 Score=26.72 Aligned_cols=19 Identities=26% Similarity=0.378 Sum_probs=17.1
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028761 172 LVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAvkALke 190 (204)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 69
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=23.64 E-value=71 Score=27.11 Aligned_cols=20 Identities=15% Similarity=0.228 Sum_probs=17.6
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 028761 171 ELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 171 eLVm~QagvSr~kAvkALke 190 (204)
.-.+++-||||..+++||..
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 45789999999999999976
No 70
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=23.47 E-value=46 Score=33.84 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=7.0
Q ss_pred HHHHHHHHHH-cCC
Q 028761 66 EKKSRKAMLK-LGM 78 (204)
Q Consensus 66 eKK~rk~mkK-LGl 78 (204)
.+.++..|.+ ||.
T Consensus 701 d~~~~~~l~~aL~~ 714 (784)
T PF04931_consen 701 DEEFRSALAKALGD 714 (784)
T ss_pred HHHHHHHHHHHhcc
Confidence 3456655444 665
No 71
>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=22.75 E-value=96 Score=23.27 Aligned_cols=76 Identities=21% Similarity=0.280 Sum_probs=43.8
Q ss_pred HHHHHHHHcCCcccCCceEEEEEecCceEEEE-------cCCeEEeeCCCcEEEEeccceecchhhHHHHHHHHHhcCCC
Q 028761 68 KSRKAMLKLGMKPIPGVSRVTVKKSKNILFVI-------SKPDVFKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFKAPD 140 (204)
Q Consensus 68 K~rk~mkKLGlk~v~gV~rVtI~k~~~~~fvI-------~~P~V~ks~gs~tYvVfGeak~ed~~~q~q~~aae~~~~~~ 140 (204)
.+..+.+++-|..|-.-- +.+++.++ .+.. .+|..+..+..++|.-||--.-
T Consensus 5 ~~~~i~~~~~i~~v~~~~-~~l~~~G~-~~~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~~------------------- 63 (97)
T PF01807_consen 5 FIEEIKSRIDIVDVIERY-IKLKRRGR-EYRCLCPFHDDKTPSFSINPDKNRFKCFGCGKG------------------- 63 (97)
T ss_dssp HHHHHHHCS-HHHHHCCC-S--EEETT-EEEE--SSS--SS--EEEETTTTEEEETTT--E-------------------
T ss_pred HHHHHHHhCCHHHHHHHh-ccccccCC-eEEEECcCCCCCCCceEEECCCCeEEECCCCCC-------------------
Confidence 344555566665442222 55666543 3555 4466666677788888875211
Q ss_pred CCcccCCCCccccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHH
Q 028761 141 LSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 141 ~~~~~~~~~~~~~~~~~eevd~~gv~eeDIeLVm~QagvSr~kAvkALke 190 (204)
| .=|.|||.--|||-.+|++-|.+
T Consensus 64 -----------------------G---d~i~~v~~~~~~~f~eAv~~l~~ 87 (97)
T PF01807_consen 64 -----------------------G---DVIDFVMKYEGCSFKEAVKWLAE 87 (97)
T ss_dssp -----------------------E----HHHHHHHHHT--HHHHHHHHHH
T ss_pred -----------------------C---cHHhHHHHHhCCCHHHHHHHHHH
Confidence 1 24999999999999999999976
No 72
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=21.81 E-value=1e+02 Score=22.05 Aligned_cols=29 Identities=31% Similarity=0.326 Sum_probs=21.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSA 198 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~A 198 (204)
|+.|.+++|+|+..+...|..--.=|.++
T Consensus 7 i~~ia~~~~~~~~~v~~vl~~l~~~i~~~ 35 (90)
T smart00411 7 IDAIAEKAGLSKKDAKAAVDAFLEIITEA 35 (90)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999998887653333333
No 73
>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=21.80 E-value=1.2e+02 Score=20.60 Aligned_cols=24 Identities=33% Similarity=0.559 Sum_probs=20.5
Q ss_pred cccHHHHHHhhCCCHHHHHHHHHH
Q 028761 167 PKDIELVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 167 eeDIeLVm~QagvSr~kAvkALke 190 (204)
+-.+.-++..+|+||..+.++|+.
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 74
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=21.71 E-value=1.1e+02 Score=30.19 Aligned_cols=31 Identities=29% Similarity=0.532 Sum_probs=24.1
Q ss_pred cCCcCHHHHHHHHHHcCCcccCCceEEEEEecC
Q 028761 61 KQSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSK 93 (204)
Q Consensus 61 k~sr~eKK~rk~mkKLGlk~v~gV~rVtI~k~~ 93 (204)
-|+.-.+++.++|++||++. | |.-|.+|+.|
T Consensus 343 pqp~t~~~l~~a~k~lg~~~-P-ivGvhvRRTD 373 (580)
T KOG3705|consen 343 PQPATQEKLDKALKSLGLDK-P-IVGVHVRRTD 373 (580)
T ss_pred CChhhHHHHHHHHHhCCCCC-c-eeeEEEEecc
Confidence 46777899999999999995 3 4567777654
No 75
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=21.71 E-value=90 Score=24.56 Aligned_cols=31 Identities=29% Similarity=0.373 Sum_probs=24.5
Q ss_pred HHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028761 171 ELVMTQAGVSRAKAVKALKAADGDIVSAIME 201 (204)
Q Consensus 171 eLVm~QagvSr~kAvkALke~~GDIV~AIM~ 201 (204)
--|..++|+||+--.|+|...+|=-...||.
T Consensus 53 sqvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 53 SQVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 3578899999999999999887755555543
No 76
>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=21.49 E-value=79 Score=25.88 Aligned_cols=23 Identities=22% Similarity=0.161 Sum_probs=19.6
Q ss_pred cHHHHHHhhCCCHHHHHHHHHHc
Q 028761 169 DIELVMTQAGVSRAKAVKALKAA 191 (204)
Q Consensus 169 DIeLVm~QagvSr~kAvkALke~ 191 (204)
.+--.|.++|||-.+|+.|.-+.
T Consensus 104 TlaELm~~T~Ctl~eAR~ARf~~ 126 (128)
T PF12614_consen 104 TLAELMAATHCTLAEARRARFEA 126 (128)
T ss_pred cHHHHHHHhCCcHHHHHHHhhhc
Confidence 56678999999999999997554
No 77
>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=21.48 E-value=84 Score=26.41 Aligned_cols=19 Identities=42% Similarity=0.436 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028761 172 LVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAvkALke 190 (204)
-.+++.||||...++||..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 78
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.07 E-value=67 Score=31.34 Aligned_cols=10 Identities=40% Similarity=0.611 Sum_probs=4.9
Q ss_pred CCCccccCCC
Q 028761 22 DKPVVEDDED 31 (204)
Q Consensus 22 ~~~~~~~~~~ 31 (204)
..+++++|+|
T Consensus 268 ~ss~~edD~D 277 (514)
T KOG3130|consen 268 SSSYHEDDDD 277 (514)
T ss_pred CCCccccccc
Confidence 3445555544
No 79
>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=20.98 E-value=1.6e+02 Score=27.07 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=19.2
Q ss_pred HHHHHHHHHcCCcccCCceEEEEEecC
Q 028761 67 KKSRKAMLKLGMKPIPGVSRVTVKKSK 93 (204)
Q Consensus 67 KK~rk~mkKLGlk~v~gV~rVtI~k~~ 93 (204)
+.++++|..+=++.+|||.|+.|...+
T Consensus 132 ~~l~~~l~~~~v~Gi~gI~r~~i~~~~ 158 (300)
T cd02736 132 QSLKRKLPDVVVSGIPEVKRAVINKDK 158 (300)
T ss_pred HHHHHHhccceEeCCCCceEEEEecCC
Confidence 344455555667799999999997643
No 80
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=20.74 E-value=91 Score=24.54 Aligned_cols=17 Identities=59% Similarity=0.597 Sum_probs=15.2
Q ss_pred HHhhCCCHHHHHHHHHH
Q 028761 174 MTQAGVSRAKAVKALKA 190 (204)
Q Consensus 174 m~QagvSr~kAvkALke 190 (204)
|-.||||++-+.++|+.
T Consensus 78 M~dAGV~~~~~~~~l~~ 94 (100)
T PF15652_consen 78 MFDAGVSKECRKKALKA 94 (100)
T ss_pred HHHcCCCHHHHHHHHHH
Confidence 55699999999999987
No 81
>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=20.57 E-value=1.1e+02 Score=21.67 Aligned_cols=29 Identities=31% Similarity=0.334 Sum_probs=21.7
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHH
Q 028761 170 IELVMTQAGVSRAKAVKALKAADGDIVSA 198 (204)
Q Consensus 170 IeLVm~QagvSr~kAvkALke~~GDIV~A 198 (204)
|+.|+..+|+|+..+...|..--.=|.++
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~~i~~~ 34 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLDVITEA 34 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999887653333333
No 82
>COG5097 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]
Probab=20.50 E-value=1.7e+02 Score=25.61 Aligned_cols=42 Identities=24% Similarity=0.270 Sum_probs=29.3
Q ss_pred cCCcC-HHHHHHHHHHcCCc-------ccCCceEEEEEecCceEEEEcCC
Q 028761 61 KQSRS-EKKSRKAMLKLGMK-------PIPGVSRVTVKKSKNILFVISKP 102 (204)
Q Consensus 61 k~sr~-eKK~rk~mkKLGlk-------~v~gV~rVtI~k~~~~~fvI~~P 102 (204)
|.|-+ --||+.....|.|- .+.|+..|.+--..-.++||.+-
T Consensus 39 k~sNNeilKMQ~QF~~LdL~ql~~~l~~l~g~~~V~ss~rep~lwVIrKq 88 (210)
T COG5097 39 KSSNNEILKMQTQFRGLDLGQLSKLLSMLGGFYEVESSNREPTLWVIRKQ 88 (210)
T ss_pred cccchHHHHHHHHhhccChHHHHHHHHhccCEEEEEecCCCCcEEEEehh
Confidence 33444 36888888877743 58888899887655678888764
No 83
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=20.20 E-value=93 Score=26.12 Aligned_cols=19 Identities=21% Similarity=0.265 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028761 172 LVMTQAGVSRAKAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAvkALke 190 (204)
-++++.||||.-.++||+.
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999975
No 84
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=20.13 E-value=2.4e+02 Score=18.43 Aligned_cols=28 Identities=39% Similarity=0.529 Sum_probs=19.2
Q ss_pred HHHHHHHHHHcCCcccCCceEEEEEecCceEEE
Q 028761 66 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFV 98 (204)
Q Consensus 66 eKK~rk~mkKLGlk~v~gV~rVtI~k~~~~~fv 98 (204)
.++++++|++ ++||..|.+-...+.+.+
T Consensus 13 ~~~v~~~l~~-----~~GV~~v~vd~~~~~v~v 40 (62)
T PF00403_consen 13 AKKVEKALSK-----LPGVKSVKVDLETKTVTV 40 (62)
T ss_dssp HHHHHHHHHT-----STTEEEEEEETTTTEEEE
T ss_pred HHHHHHHHhc-----CCCCcEEEEECCCCEEEE
Confidence 3566777664 588988888877665544
Done!