Query 028762
Match_columns 204
No_of_seqs 171 out of 489
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 16:35:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028762hhsearch_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 6.1E-55 1.3E-59 369.6 15.3 150 53-204 55-209 (209)
2 PRK06369 nac nascent polypepti 100.0 1.7E-38 3.7E-43 250.4 11.9 106 62-204 5-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 6.7E-33 1.5E-37 220.0 8.2 113 62-204 6-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 8E-32 1.7E-36 212.6 11.2 104 62-204 6-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 1.2E-21 2.6E-26 136.9 6.0 58 64-121 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.5 7.9E-08 1.7E-12 80.3 3.0 64 61-124 38-101 (162)
7 PF00627 UBA: UBA/TS-N domain; 97.7 4.5E-05 9.7E-10 48.4 3.3 37 165-202 1-37 (37)
8 KOG3450 Huntingtin interacting 97.6 4.2E-05 9.1E-10 60.5 2.4 42 163-204 77-118 (119)
9 PF14555 UBA_4: UBA-like domai 95.5 0.019 4.1E-07 37.6 3.5 33 168-200 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.1 0.038 8.2E-07 34.5 3.7 32 170-202 5-36 (38)
11 smart00165 UBA Ubiquitin assoc 94.8 0.049 1.1E-06 33.9 3.7 28 175-202 9-36 (37)
12 COG4008 Predicted metal-bindin 85.7 1.1 2.5E-05 36.9 3.9 34 164-199 112-145 (153)
13 COG2103 Predicted sugar phosph 85.1 1.1 2.4E-05 40.9 3.9 39 164-202 231-269 (298)
14 PRK05441 murQ N-acetylmuramic 83.4 1.5 3.2E-05 39.6 4.0 38 165-202 234-271 (299)
15 PF10411 DsbC_N: Disulfide bon 83.4 2.5 5.3E-05 29.2 4.2 40 68-117 2-50 (57)
16 cd05007 SIS_Etherase N-acetylm 78.4 1.4 3E-05 38.8 2.0 36 165-200 221-256 (257)
17 TIGR00274 N-acetylmuramic acid 77.9 3 6.4E-05 37.7 4.0 37 165-201 229-265 (291)
18 PF02845 CUE: CUE domain; Int 76.8 3.7 8.1E-05 26.3 3.2 33 170-202 5-38 (42)
19 PRK12570 N-acetylmuramic acid- 73.7 4.3 9.4E-05 36.6 3.9 37 165-201 230-266 (296)
20 PF03474 DMA: DMRTA motif; In 70.4 5.2 0.00011 26.4 2.7 21 180-200 16-36 (39)
21 smart00546 CUE Domain that may 69.5 7.5 0.00016 24.9 3.3 34 169-202 5-39 (43)
22 PF10446 DUF2457: Protein of u 68.6 3.9 8.4E-05 39.6 2.5 10 110-119 193-202 (458)
23 PF14474 RTC4: RTC4-like domai 65.5 6.6 0.00014 31.3 2.9 26 166-191 89-114 (124)
24 PF05861 PhnI: Bacterial phosp 60.7 9.6 0.00021 35.9 3.5 33 170-202 45-78 (358)
25 COG3626 PhnI Uncharacterized e 59.3 9.3 0.0002 35.4 3.1 33 170-202 45-78 (367)
26 PF11626 Rap1_C: TRF2-interact 59.3 14 0.00029 27.5 3.5 30 170-200 1-30 (87)
27 PRK10877 protein disulfide iso 58.6 28 0.00061 30.2 5.8 43 64-117 23-72 (232)
28 PF06970 RepA_N: Replication i 57.7 11 0.00024 27.7 2.7 22 169-190 54-75 (76)
29 PF12244 DUF3606: Protein of u 55.6 23 0.00051 24.6 4.0 31 166-196 19-49 (57)
30 PF02796 HTH_7: Helix-turn-hel 52.5 10 0.00023 24.6 1.7 23 169-191 23-45 (45)
31 PRK05441 murQ N-acetylmuramic 52.5 19 0.0004 32.6 3.9 32 170-201 266-297 (299)
32 PF13730 HTH_36: Helix-turn-he 52.2 19 0.00041 23.6 3.0 22 169-190 27-48 (55)
33 KOG1071 Mitochondrial translat 52.2 18 0.00039 33.9 3.7 36 165-200 45-80 (340)
34 TIGR00632 vsr DNA mismatch end 52.2 19 0.0004 28.9 3.4 35 56-90 16-56 (117)
35 TIGR00274 N-acetylmuramic acid 51.6 19 0.0004 32.6 3.7 30 170-199 261-290 (291)
36 COG4004 Uncharacterized protei 49.2 35 0.00075 26.6 4.3 34 63-96 13-56 (96)
37 PLN02150 terpene synthase/cycl 49.2 17 0.00036 27.8 2.6 25 166-190 6-30 (96)
38 PF06972 DUF1296: Protein of u 47.3 41 0.00089 24.2 4.1 33 170-202 9-42 (60)
39 PRK12570 N-acetylmuramic acid- 45.7 26 0.00057 31.6 3.7 30 170-199 262-291 (296)
40 PF03861 ANTAR: ANTAR domain; 43.3 29 0.00064 23.5 2.9 21 170-190 19-39 (56)
41 COG1654 BirA Biotin operon rep 42.2 28 0.0006 26.0 2.8 25 171-195 23-50 (79)
42 PF08680 DUF1779: Protein of u 41.7 22 0.00048 30.0 2.5 54 64-117 131-197 (203)
43 PF00392 GntR: Bacterial regul 39.0 29 0.00063 23.6 2.4 21 170-190 27-47 (64)
44 COG0100 RpsK Ribosomal protein 38.0 21 0.00045 29.2 1.7 93 80-202 18-113 (129)
45 PF11699 CENP-C_C: Mif2/CENP-C 37.9 39 0.00085 25.4 3.0 34 78-114 39-72 (85)
46 COG2188 PhnF Transcriptional r 35.0 33 0.00071 29.5 2.5 19 172-190 36-54 (236)
47 KOG0944 Ubiquitin-specific pro 33.3 37 0.00081 34.8 2.9 26 174-199 642-667 (763)
48 smart00400 ZnF_CHCC zinc finge 32.9 49 0.0011 22.2 2.6 20 169-188 35-54 (55)
49 PRK05564 DNA polymerase III su 32.1 2.5E+02 0.0054 24.8 7.7 45 64-117 75-131 (313)
50 PF10975 DUF2802: Protein of u 31.6 39 0.00084 24.5 2.1 20 169-188 46-65 (70)
51 PF13629 T2SS-T3SS_pil_N: Pilu 31.5 1.3E+02 0.0028 21.2 4.8 25 93-117 22-48 (72)
52 smart00345 HTH_GNTR helix_turn 31.1 67 0.0015 20.4 3.0 22 169-190 22-43 (60)
53 PRK14897 unknown domain/DNA-di 30.0 77 0.0017 31.4 4.4 27 65-91 330-356 (509)
54 PF04871 Uso1_p115_C: Uso1 / p 29.4 45 0.00097 27.0 2.3 9 21-29 110-118 (136)
55 cd07377 WHTH_GntR Winged helix 28.8 76 0.0017 20.6 3.0 22 169-190 27-48 (66)
56 PHA01748 hypothetical protein 28.7 74 0.0016 22.2 3.0 20 169-188 16-35 (60)
57 smart00804 TAP_C C-terminal do 28.3 1.2E+02 0.0026 21.5 4.1 34 168-201 14-47 (63)
58 KOG3198 Signal recognition par 28.1 1.1E+02 0.0023 25.8 4.4 42 59-100 41-95 (152)
59 KOG3130 Uncharacterized conser 27.9 33 0.00072 33.3 1.5 12 178-189 501-512 (514)
60 PF03943 TAP_C: TAP C-terminal 27.3 39 0.00085 22.9 1.4 31 170-200 4-34 (51)
61 PRK12702 mannosyl-3-phosphogly 27.1 4.6E+02 0.0099 24.3 8.6 29 163-191 119-147 (302)
62 TIGR02325 C_P_lyase_phnF phosp 26.0 60 0.0013 27.1 2.6 19 172-190 37-55 (238)
63 PRK10079 phosphonate metabolis 25.6 61 0.0013 27.5 2.6 20 171-190 39-58 (241)
64 PRK00523 hypothetical protein; 25.3 57 0.0012 24.2 2.0 17 62-78 40-56 (72)
65 PF13276 HTH_21: HTH-like doma 24.1 65 0.0014 21.6 2.0 19 61-79 37-55 (60)
66 PHA01623 hypothetical protein 23.7 1E+02 0.0023 21.3 3.0 22 168-189 26-48 (56)
67 TIGR02404 trehalos_R_Bsub treh 23.4 72 0.0016 26.8 2.6 19 172-190 29-47 (233)
68 smart00411 BHL bacterial (prok 23.3 91 0.002 22.3 2.8 29 170-198 7-35 (90)
69 PRK01844 hypothetical protein; 22.8 68 0.0015 23.8 2.0 17 62-78 39-55 (72)
70 PF01807 zf-CHC2: CHC2 zinc fi 22.5 95 0.0021 23.3 2.9 76 66-190 5-87 (97)
71 PRK10361 DNA recombination pro 22.3 1.6E+02 0.0035 28.9 5.0 54 57-113 200-255 (475)
72 PF04931 DNA_pol_phi: DNA poly 22.2 1.2E+02 0.0025 31.0 4.2 13 64-76 701-714 (784)
73 PF12614 RRF_GI: Ribosome recy 22.1 73 0.0016 26.1 2.3 23 169-191 104-126 (128)
74 KOG3705 Glycoprotein 6-alpha-L 22.0 98 0.0021 30.4 3.4 31 59-91 343-373 (580)
75 KOG0943 Predicted ubiquitin-pr 22.0 54 0.0012 36.6 1.8 6 95-100 1849-1854(3015)
76 PF01978 TrmB: Sugar-specific 21.8 1.2E+02 0.0026 20.7 3.1 23 168-190 23-45 (68)
77 cd00591 HU_IHF Integration hos 21.7 1E+02 0.0022 21.9 2.7 29 170-198 6-34 (87)
78 PF03672 UPF0154: Uncharacteri 21.6 75 0.0016 23.0 2.0 17 62-78 32-48 (64)
79 PF15652 Tox-SHH: HNH/Endo VII 21.5 85 0.0018 24.7 2.4 17 174-190 78-94 (100)
80 COG3636 Predicted transcriptio 21.3 93 0.002 24.5 2.6 30 172-201 54-83 (100)
81 PF08503 DapH_N: Tetrahydrodip 21.2 2.1E+02 0.0045 21.7 4.4 32 83-118 19-51 (83)
82 PRK11402 DNA-binding transcrip 20.6 88 0.0019 26.5 2.6 19 172-190 38-56 (241)
83 PRK04984 fatty acid metabolism 20.6 89 0.0019 26.2 2.6 19 172-190 36-54 (239)
84 PF04239 DUF421: Protein of un 20.3 1.2E+02 0.0025 23.1 2.9 40 60-100 25-64 (99)
85 cd06528 RNAP_A'' A'' subunit o 20.2 1E+02 0.0022 29.0 3.1 27 66-92 192-218 (363)
86 PF00403 HMA: Heavy-metal-asso 20.0 2.4E+02 0.0053 18.4 4.2 31 64-99 13-43 (62)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=6.1e-55 Score=369.56 Aligned_cols=150 Identities=67% Similarity=0.926 Sum_probs=133.1
Q ss_pred CCCCCcccCcCHHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEeccceecchhhHHHHHHHH
Q 028762 53 DGSGRSKQSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIEDLSSQLQTQAAE 132 (204)
Q Consensus 53 ~~~~~~k~sr~eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVFGEak~~d~s~~~q~~aae 132 (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 HcCCCCCCCCCCCC----CCCCcc-cccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028762 133 QFKVPPPNTGNVAS----KPESSA-MAQDDEEVDETGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 133 ~~~~~~~~~~~~~~----~~~~~~-~~~~~eevd~~gi~eeDIeLVm~QagvSr~kAikALke~~GDIV~AIM~Lt~ 204 (204)
+|+.. ..+.... ...++. +.+++++||++||+.+||+|||+|+||||++|||||++|+||||||||+||+
T Consensus 135 ~fk~~--~~~~~~~~~~~~~~~~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 135 RFKVP--QEAPGLIQEDTSATPPAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred hccCC--ccccccccccccCCCccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 99983 3322221 111222 2255667999999999999999999999999999999999999999999985
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=1.7e-38 Score=250.43 Aligned_cols=106 Identities=29% Similarity=0.490 Sum_probs=97.7
Q ss_pred cCHHHHHHHHHHcCCc--cCCCceEEEEEecCceEEEEcCCeEE--eeCCCCeEEEeccceecchhhHHHHHHHHHcCCC
Q 028762 62 RSEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDVF--KSPTSDTYIVFGEAKIEDLSSQLQTQAAEQFKVP 137 (204)
Q Consensus 62 r~eKK~rk~mkKLGlk--~I~gV~rVtIrk~~~~~fvI~~PdVy--Ks~gs~tyvVFGEak~~d~s~~~q~~aae~~~~~ 137 (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 4699999999999999 99 99999999987 89999999999 79999999999999988765420
Q ss_pred CCCCCCCCCCCCCcccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028762 138 PPNTGNVASKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~eevd~~gi~eeDIeLVm~QagvSr~kAikALke~~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 3479999999999999999999999999999999999999974
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.98 E-value=6.7e-33 Score=220.03 Aligned_cols=113 Identities=38% Similarity=0.611 Sum_probs=95.2
Q ss_pred cCHHHHHHHHHHcCCc--cCCCceEEEEEecCceEEEEcCCeEEe--eCCCCeEEEeccceecchhhHHHHHHHHHcCCC
Q 028762 62 RSEKKSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDVFK--SPTSDTYIVFGEAKIEDLSSQLQTQAAEQFKVP 137 (204)
Q Consensus 62 r~eKK~rk~mkKLGlk--~I~gV~rVtIrk~~~~~fvI~~PdVyK--s~gs~tyvVFGEak~~d~s~~~q~~aae~~~~~ 137 (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-YVIENPQVTVMKAMGQKTYQISGDPS-----------AKE----- 68 (122)
T ss_pred CCHHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcchh-----------hhc-----
Confidence 5789999999999954 9999999999998875 9999999986 68999999999752 000
Q ss_pred CCCCCCCCCCCCCcccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028762 138 PPNTGNVASKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~eevd~~gi~eeDIeLVm~QagvSr~kAikALke~~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 000122344677789999999999999999999999999999999999999984
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=8e-32 Score=212.61 Aligned_cols=104 Identities=31% Similarity=0.495 Sum_probs=89.2
Q ss_pred cCHH---HHHHHHHHcCCc--cCCCceEEEEEecCceEEEEcCCeE--EeeCCCCeEEEeccceecchhhHHHHHHHHHc
Q 028762 62 RSEK---KSRKAMLKLGMK--PIPGVSRVTVKKSKNILFVISKPDV--FKSPTSDTYIVFGEAKIEDLSSQLQTQAAEQF 134 (204)
Q Consensus 62 r~eK---K~rk~mkKLGlk--~I~gV~rVtIrk~~~~~fvI~~PdV--yKs~gs~tyvVFGEak~~d~s~~~q~~aae~~ 134 (204)
-||| +||+||+||||+ ++. |.+|+|++.++ .|+|++|.| |+++|+.||+|||+++.+++.+
T Consensus 6 ~nPr~~~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~~---------- 73 (116)
T TIGR00264 6 MNPKMLKQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVEE---------- 73 (116)
T ss_pred CCcccHHHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeeccc----------
Confidence 3456 999999999999 476 99999999764 677999987 6789999999999998643210
Q ss_pred CCCCCCCCCCCCCCCCcccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028762 135 KVPPPNTGNVASKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~eevd~~gi~eeDIeLVm~QagvSr~kAikALke~~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=99.85 E-value=1.2e-21 Score=136.94 Aligned_cols=58 Identities=53% Similarity=0.890 Sum_probs=48.2
Q ss_pred HHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEeccceecc
Q 028762 64 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIED 121 (204)
Q Consensus 64 eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVFGEak~~d 121 (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=98.48 E-value=7.9e-08 Score=80.28 Aligned_cols=64 Identities=27% Similarity=0.507 Sum_probs=60.3
Q ss_pred CcCHHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEeccceecchhh
Q 028762 61 SRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEAKIEDLSS 124 (204)
Q Consensus 61 sr~eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVFGEak~~d~s~ 124 (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 6789999999999999999999999999999999999999999999999999999999887654
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=97.68 E-value=4.5e-05 Score=48.44 Aligned_cols=37 Identities=27% Similarity=0.510 Sum_probs=31.9
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~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 356789999999 9999999999999999999998654
No 8
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.58 E-value=4.2e-05 Score=60.54 Aligned_cols=42 Identities=29% Similarity=0.551 Sum_probs=39.2
Q ss_pred CCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhhcC
Q 028762 163 TGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMELTN 204 (204)
Q Consensus 163 ~gi~eeDIeLVm~QagvSr~kAikALke~~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=95.55 E-value=0.019 Score=37.56 Aligned_cols=33 Identities=24% Similarity=0.344 Sum_probs=27.6
Q ss_pred ccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028762 168 KDIELVMTQAGVPRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAikALke~~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=95.10 E-value=0.038 Score=34.53 Aligned_cols=32 Identities=31% Similarity=0.496 Sum_probs=26.0
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~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=94.82 E-value=0.049 Score=33.87 Aligned_cols=28 Identities=39% Similarity=0.552 Sum_probs=23.7
Q ss_pred HhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 175 TQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 175 ~QagvSr~kAikALke~~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=85.74 E-value=1.1 Score=36.86 Aligned_cols=34 Identities=24% Similarity=0.324 Sum_probs=27.7
Q ss_pred CCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028762 164 GVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAI 199 (204)
Q Consensus 164 gi~eeDIeLVm~QagvSr~kAikALke~~GDIV~AI 199 (204)
.++.+-++.+..-. ||.++|++||.+++ |+..|+
T Consensus 112 ~~~~e~v~v~a~a~-v~~eeAr~aleeag-Dl~~A~ 145 (153)
T COG4008 112 EPPVEEVEVLADAF-VTPEEAREALEEAG-DLRTAM 145 (153)
T ss_pred CCcHHHHHHHHHhc-CCHHHHHHHHHHcC-CHHHHH
Confidence 45666777776655 99999999999996 999985
No 13
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=85.13 E-value=1.1 Score=40.93 Aligned_cols=39 Identities=26% Similarity=0.418 Sum_probs=34.0
Q ss_pred CCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 164 GVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 164 gi~eeDIeLVm~QagvSr~kAikALke~~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 355677899999999999999999999999998887644
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=83.42 E-value=1.5 Score=39.56 Aligned_cols=38 Identities=37% Similarity=0.562 Sum_probs=31.6
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~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 44566788999999999999999999999998887643
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=83.38 E-value=2.5 Score=29.18 Aligned_cols=40 Identities=30% Similarity=0.687 Sum_probs=24.5
Q ss_pred HHHHHHc--CCc-------cCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEeccc
Q 028762 68 RKAMLKL--GMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEA 117 (204)
Q Consensus 68 rk~mkKL--Glk-------~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVFGEa 117 (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-IL-------YVDED-GRYLIQGQL 50 (57)
T ss_dssp HHHHHCT--T-TCEEEEE-SSTTEEEEEE--TTE-EE-------EEETT-SSEEEES-E
T ss_pred hhHHHhhcCCCceeEEEcCCCCCeEEEEE-CCCe-EE-------EEcCC-CCEEEEeEE
Confidence 4566666 665 6999999988 4433 32 44443 469999974
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=78.40 E-value=1.4 Score=38.83 Aligned_cols=36 Identities=39% Similarity=0.637 Sum_probs=31.2
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~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 445678889999999999999999999999877664
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=77.88 E-value=3 Score=37.66 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=31.3
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIME 201 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~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 4456677899999999999999999999999888764
No 18
>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=76.84 E-value=3.7 Score=26.34 Aligned_cols=33 Identities=24% Similarity=0.330 Sum_probs=22.6
Q ss_pred HHHHHHhh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 170 IELVMTQA-GVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qa-gvSr~kAikALke~~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 44444444 7888888889999999986666544
No 19
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=73.70 E-value=4.3 Score=36.64 Aligned_cols=37 Identities=27% Similarity=0.457 Sum_probs=30.2
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIME 201 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~GDIV~AIM~ 201 (204)
+-..=+.+||+=+|||+++|.++|..++|.|=-||+-
T Consensus 230 l~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~ 266 (296)
T PRK12570 230 LVARAVRIVMQATGCSEDEAKELLKESDNDVKLAILM 266 (296)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHH
Confidence 3455677888889999999999999999998888764
No 20
>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=70.35 E-value=5.2 Score=26.39 Aligned_cols=21 Identities=38% Similarity=0.450 Sum_probs=16.5
Q ss_pred CHHHHHHHHHHcCCcHHHHHh
Q 028762 180 PRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 180 Sr~kAikALke~~GDIV~AIM 200 (204)
.|+.---.|+-++||+|.||=
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE 36 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIE 36 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHH
Confidence 455555678999999999984
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=69.47 E-value=7.5 Score=24.89 Aligned_cols=34 Identities=15% Similarity=0.210 Sum_probs=25.9
Q ss_pred cHHHHHHhh-CCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 169 DIELVMTQA-GVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 169 DIeLVm~Qa-gvSr~kAikALke~~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 7899999999999999998887444
No 22
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=68.58 E-value=3.9 Score=39.62 Aligned_cols=10 Identities=30% Similarity=0.215 Sum_probs=5.1
Q ss_pred eEEEecccee
Q 028762 110 TYIVFGEAKI 119 (204)
Q Consensus 110 tyvVFGEak~ 119 (204)
|-.|-|..-+
T Consensus 193 TDFVCGTLDE 202 (458)
T PF10446_consen 193 TDFVCGTLDE 202 (458)
T ss_pred ccccCCCcCC
Confidence 4445565543
No 23
>PF14474 RTC4: RTC4-like domain
Probab=65.46 E-value=6.6 Score=31.30 Aligned_cols=26 Identities=23% Similarity=0.368 Sum_probs=23.2
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHHc
Q 028762 166 EPKDIELVMTQAGVPRSRAVKALKAA 191 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAikALke~ 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 44458999999999999999999997
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=60.75 E-value=9.6 Score=35.94 Aligned_cols=33 Identities=33% Similarity=0.515 Sum_probs=27.7
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028762 170 IELVMTQAGV-PRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAikALke~~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
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=59.29 E-value=9.3 Score=35.41 Aligned_cols=33 Identities=45% Similarity=0.605 Sum_probs=26.5
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028762 170 IELVMTQAGV-PRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAikALke~~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 4456665543 68889999999999999999876
No 26
>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=59.27 E-value=14 Score=27.45 Aligned_cols=30 Identities=30% Similarity=0.253 Sum_probs=24.9
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~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 27
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=58.62 E-value=28 Score=30.16 Aligned_cols=43 Identities=19% Similarity=0.474 Sum_probs=29.1
Q ss_pred HHHHHHHHHHcCCc-------cCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEeccc
Q 028762 64 EKKSRKAMLKLGMK-------PIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVFGEA 117 (204)
Q Consensus 64 eKK~rk~mkKLGlk-------~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVFGEa 117 (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 222 22 3344 3469999974
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=57.70 E-value=11 Score=27.71 Aligned_cols=22 Identities=32% Similarity=0.363 Sum_probs=19.8
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke 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=55.65 E-value=23 Score=24.56 Aligned_cols=31 Identities=19% Similarity=0.320 Sum_probs=27.1
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHHcCCcHH
Q 028762 166 EPKDIELVMTQAGVPRSRAVKALKAADGDIV 196 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAikALke~~GDIV 196 (204)
++-.|...+...|||.++.+.|.+..++++.
T Consensus 19 e~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~ 49 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLREAVRAVGNSRA 49 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHHCcCHH
Confidence 3568999999999999999999999977753
No 30
>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=52.53 E-value=10 Score=24.56 Aligned_cols=23 Identities=30% Similarity=0.368 Sum_probs=17.8
Q ss_pred cHHHHHHhhCCCHHHHHHHHHHc
Q 028762 169 DIELVMTQAGVPRSRAVKALKAA 191 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke~ 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 37778999999999999988654
No 31
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=52.51 E-value=19 Score=32.56 Aligned_cols=32 Identities=25% Similarity=0.343 Sum_probs=28.5
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAIME 201 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~GDIV~AIM~ 201 (204)
+-+||--+|||..+|.+.|..++|.|-.||=.
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhh
Confidence 45788999999999999999999999998744
No 32
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.23 E-value=19 Score=23.58 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=19.6
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke 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 5899999999999998888875
No 33
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=52.21 E-value=18 Score=33.89 Aligned_cols=36 Identities=22% Similarity=0.244 Sum_probs=33.0
Q ss_pred CCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028762 165 VEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 165 i~eeDIeLVm~QagvSr~kAikALke~~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 577899999999999999999999999999998854
No 34
>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=52.21 E-value=19 Score=28.85 Aligned_cols=35 Identities=23% Similarity=0.459 Sum_probs=28.1
Q ss_pred CCcccCcCHHHHHHHHHHcCCc------cCCCceEEEEEec
Q 028762 56 GRSKQSRSEKKSRKAMLKLGMK------PIPGVSRVTVKKS 90 (204)
Q Consensus 56 ~~~k~sr~eKK~rk~mkKLGlk------~I~gV~rVtIrk~ 90 (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 4678899999999999999998 3777766666664
No 35
>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=51.55 E-value=19 Score=32.56 Aligned_cols=30 Identities=23% Similarity=0.275 Sum_probs=26.8
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAI 199 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~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 36
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.18 E-value=35 Score=26.64 Aligned_cols=34 Identities=26% Similarity=0.541 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHcCCc----------cCCCceEEEEEecCceEEE
Q 028762 63 SEKKSRKAMLKLGMK----------PIPGVSRVTVKKSKNILFV 96 (204)
Q Consensus 63 ~eKK~rk~mkKLGlk----------~I~gV~rVtIrk~~~~~fv 96 (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 456777889999976 4899999999998765554
No 37
>PLN02150 terpene synthase/cyclase family protein
Probab=49.17 E-value=17 Score=27.75 Aligned_cols=25 Identities=32% Similarity=0.442 Sum_probs=21.8
Q ss_pred CcccHHHHHHhhCCCHHHHHHHHHH
Q 028762 166 EPKDIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 166 ~eeDIeLVm~QagvSr~kAikALke 190 (204)
.+.-|+--|.|-|||.++|++.|++
T Consensus 6 vaSsIeCYMke~g~seeeA~~~i~~ 30 (96)
T PLN02150 6 VANGVNCYMKQHGVTKEEAVSELKK 30 (96)
T ss_pred chHHHHHHhccCCCCHHHHHHHHHH
Confidence 3456899999999999999999876
No 38
>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=47.34 E-value=41 Score=24.19 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=26.2
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHcCCcHHHHHhhh
Q 028762 170 IELVMTQAGV-PRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 170 IeLVm~Qagv-Sr~kAikALke~~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 4444566788 99999999999999997776555
No 39
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=45.71 E-value=26 Score=31.64 Aligned_cols=30 Identities=33% Similarity=0.440 Sum_probs=27.3
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAI 199 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~GDIV~AI 199 (204)
+-++|-.+|||.++|++.|..++|.|-.||
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l 291 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAI 291 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHH
Confidence 567889999999999999999999998886
No 40
>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=43.31 E-value=29 Score=23.47 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=17.0
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke 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 457999999999999999987
No 41
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.15 E-value=28 Score=25.98 Aligned_cols=25 Identities=24% Similarity=0.441 Sum_probs=20.2
Q ss_pred HHHHHhhCCCH---HHHHHHHHHcCCcH
Q 028762 171 ELVMTQAGVPR---SRAVKALKAADGDI 195 (204)
Q Consensus 171 eLVm~QagvSr---~kAikALke~~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 45678999999 47889999987765
No 42
>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=41.72 E-value=22 Score=30.01 Aligned_cols=54 Identities=22% Similarity=0.314 Sum_probs=19.0
Q ss_pred HHHHHHHHHHcCCccCCCceEEEE-----Eec--------CceEEEEcCCeEEeeCCCCeEEEeccc
Q 028762 64 EKKSRKAMLKLGMKPIPGVSRVTV-----KKS--------KNILFVISKPDVFKSPTSDTYIVFGEA 117 (204)
Q Consensus 64 eKK~rk~mkKLGlk~I~gV~rVtI-----rk~--------~~~~fvI~~PdVyKs~gs~tyvVFGEa 117 (204)
.++++++|++||.++|..+..-++ ..+ ++..+.+.=.-=|..-++.|||++|.|
T Consensus 131 ~~~~~~~l~~l~A~~vE~~~~~~~vSvsaYt~~~~~~i~~~~~k~NlqiAlr~~~~~~~T~I~iGTP 197 (203)
T PF08680_consen 131 EKIAERLLKKLGAKPVESLKDENFVSVSAYTPKWDDSIQTGGKKMNLQIALRYNSYGGKTYITIGTP 197 (203)
T ss_dssp HHHHHHHHHHH---------BTTEEEEEE--TTSS--EEETTEEE-EEEEEE--------EEEEESS
T ss_pred HHHHHHHHHHcCCcEeeEEecccEEEEEEEccchhhhhhcCCeEEEEEEEEEecCCCCCEEEEEEec
Confidence 577889999999998776553222 111 111122111111334578899999987
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=39.01 E-value=29 Score=23.63 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=17.2
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke 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
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=37.98 E-value=21 Score=29.22 Aligned_cols=93 Identities=26% Similarity=0.343 Sum_probs=55.2
Q ss_pred CCceEEEEEec-CceEEEEcCCe--EEeeCCCCeEEEeccceecchhhHHHHHHHHHcCCCCCCCCCCCCCCCCcccccC
Q 028762 80 PGVSRVTVKKS-KNILFVISKPD--VFKSPTSDTYIVFGEAKIEDLSSQLQTQAAEQFKVPPPNTGNVASKPESSAMAQD 156 (204)
Q Consensus 80 ~gV~rVtIrk~-~~~~fvI~~Pd--VyKs~gs~tyvVFGEak~~d~s~~~q~~aae~~~~~~~~~~~~~~~~~~~~~~~~ 156 (204)
.|| +.|... +|+++.|.++. +.-...+-+..++|..+.-..+.|+.+..+.+-..
T Consensus 18 ~Gv--ahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~-------------------- 75 (129)
T COG0100 18 DGV--AHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAK-------------------- 75 (129)
T ss_pred cce--EEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHHHH--------------------
Confidence 355 555544 57788888884 33333344567778775555555444433332111
Q ss_pred ccccccCCCCcccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhhh
Q 028762 157 DEEVDETGVEPKDIELVMTQAGVPRSRAVKALKAADGDIVSAIMEL 202 (204)
Q Consensus 157 ~eevd~~gi~eeDIeLVm~QagvSr~kAikALke~~GDIV~AIM~L 202 (204)
+-||. .|++++.=.|--|+-|++||... |.-|.-|+..
T Consensus 76 -----e~Gi~--~v~v~vkgpG~GreaAiraL~~a-g~~i~~I~Dv 113 (129)
T COG0100 76 -----EHGIK--SVEVKVKGPGPGREAAIRALAAA-GLKITRIEDV 113 (129)
T ss_pred -----HhCcc--EEEEEEECCCCcHHHHHHHHHHc-cceEEEEEEc
Confidence 23443 66777777899999999999855 5444444433
No 45
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=37.87 E-value=39 Score=25.37 Aligned_cols=34 Identities=29% Similarity=0.502 Sum_probs=26.3
Q ss_pred cCCCceEEEEEecCceEEEEcCCeEEeeCCCCeEEEe
Q 028762 78 PIPGVSRVTVKKSKNILFVISKPDVFKSPTSDTYIVF 114 (204)
Q Consensus 78 ~I~gV~rVtIrk~~~~~fvI~~PdVyKs~gs~tyvVF 114 (204)
-+.|..+|+|-. ..|++..-..|.+|..|+|-|-
T Consensus 39 V~~G~v~Vti~~---~~f~v~~G~~F~VP~gN~Y~i~ 72 (85)
T PF11699_consen 39 VIKGKVEVTIHE---TSFVVTKGGSFQVPRGNYYSIK 72 (85)
T ss_dssp EEESEEEEEETT---EEEEEETT-EEEE-TT-EEEEE
T ss_pred EEeCEEEEEEcC---cEEEEeCCCEEEECCCCEEEEE
Confidence 477888998854 5799999999999999999885
No 46
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=34.99 E-value=33 Score=29.49 Aligned_cols=19 Identities=37% Similarity=0.358 Sum_probs=16.8
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028762 172 LVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAikALke 190 (204)
-.++|.||||-.++|||..
T Consensus 36 eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHHCCcHHHHHHHHHH
Confidence 3689999999999999975
No 47
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=33.33 E-value=37 Score=34.85 Aligned_cols=26 Identities=35% Similarity=0.626 Sum_probs=22.3
Q ss_pred HHhhCCCHHHHHHHHHHcCCcHHHHH
Q 028762 174 MTQAGVPRSRAVKALKAADGDIVSAI 199 (204)
Q Consensus 174 m~QagvSr~kAikALke~~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 34469999999999999999997763
No 48
>smart00400 ZnF_CHCC zinc finger.
Probab=32.93 E-value=49 Score=22.19 Aligned_cols=20 Identities=30% Similarity=0.291 Sum_probs=18.1
Q ss_pred cHHHHHHhhCCCHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKAL 188 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikAL 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 49
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=32.08 E-value=2.5e+02 Score=24.82 Aligned_cols=45 Identities=16% Similarity=0.311 Sum_probs=29.8
Q ss_pred HHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcCCeEEe------------eCCCCeEEEeccc
Q 028762 64 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFK------------SPTSDTYIVFGEA 117 (204)
Q Consensus 64 eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~PdVyK------------s~gs~tyvVFGEa 117 (204)
=..+|.++.++...+..|=. .+++|.+++.+. -|...||+||...
T Consensus 75 v~~ir~~~~~~~~~p~~~~~---------kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~ 131 (313)
T PRK05564 75 VDDIRNIIEEVNKKPYEGDK---------KVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCE 131 (313)
T ss_pred HHHHHHHHHHHhcCcccCCc---------eEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeC
Confidence 45688888888887776533 455555555531 2667889988763
No 50
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=31.57 E-value=39 Score=24.48 Aligned_cols=20 Identities=30% Similarity=0.481 Sum_probs=17.1
Q ss_pred cHHHHHHhhCCCHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKAL 188 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikAL 188 (204)
||+-||..+|.||++|.=.+
T Consensus 46 ~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 46 SVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CHHHHHHHcCCCHHHHHHHH
Confidence 78899999999999996443
No 51
>PF13629 T2SS-T3SS_pil_N: Pilus formation protein N terminal region
Probab=31.47 E-value=1.3e+02 Score=21.19 Aligned_cols=25 Identities=8% Similarity=0.266 Sum_probs=17.2
Q ss_pred eEEEEcCCeEE--eeCCCCeEEEeccc
Q 028762 93 ILFVISKPDVF--KSPTSDTYIVFGEA 117 (204)
Q Consensus 93 ~~fvI~~PdVy--Ks~gs~tyvVFGEa 117 (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 45678888873 44566788888854
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.10 E-value=67 Score=20.42 Aligned_cols=22 Identities=27% Similarity=0.308 Sum_probs=18.9
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke 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 53
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=29.96 E-value=77 Score=31.38 Aligned_cols=27 Identities=22% Similarity=0.309 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCccCCCceEEEEEecC
Q 028762 65 KKSRKAMLKLGMKPIPGVSRVTVKKSK 91 (204)
Q Consensus 65 KK~rk~mkKLGlk~I~gV~rVtIrk~~ 91 (204)
+++++.+.++-++.+|||.||+|++.+
T Consensus 330 ~~l~~~l~~i~I~GipgI~r~~i~~~~ 356 (509)
T PRK14897 330 YLLAEKVKSLTIKGIKGIKRAIARKEN 356 (509)
T ss_pred HHHHHHhhccEEeCCCCccEEEEecCC
Confidence 444555666678899999999998653
No 54
>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=29.36 E-value=45 Score=27.00 Aligned_cols=9 Identities=33% Similarity=0.497 Sum_probs=4.6
Q ss_pred CCCCcccCC
Q 028762 21 PDEPVVEDD 29 (204)
Q Consensus 21 ~~~~~~~~~ 29 (204)
--.+|.+|+
T Consensus 110 LG~eVSddE 118 (136)
T PF04871_consen 110 LGEEVSDDE 118 (136)
T ss_pred cCCCccCCc
Confidence 445555554
No 55
>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=28.76 E-value=76 Score=20.59 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=18.6
Q ss_pred cHHHHHHhhCCCHHHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke 190 (204)
-+.-++.+.|+||..+.++|+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999999988876
No 56
>PHA01748 hypothetical protein
Probab=28.72 E-value=74 Score=22.22 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=16.7
Q ss_pred cHHHHHHhhCCCHHHHHHHH
Q 028762 169 DIELVMTQAGVPRSRAVKAL 188 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikAL 188 (204)
-++..+.+.|+||+++|+..
T Consensus 16 eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 16 LLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHhCCCHHHHHHHH
Confidence 56778999999999998844
No 57
>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=28.30 E-value=1.2e+02 Score=21.53 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=29.0
Q ss_pred ccHHHHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028762 168 KDIELVMTQAGVPRSRAVKALKAADGDIVSAIME 201 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAikALke~~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 4567788999999999999999999999888754
No 58
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.14 E-value=1.1e+02 Score=25.80 Aligned_cols=42 Identities=26% Similarity=0.369 Sum_probs=32.9
Q ss_pred ccCcCHHHHHHHHHHcCCcc-------------CCCceEEEEEecCceEEEEcCC
Q 028762 59 KQSRSEKKSRKAMLKLGMKP-------------IPGVSRVTVKKSKNILFVISKP 100 (204)
Q Consensus 59 k~sr~eKK~rk~mkKLGlk~-------------I~gV~rVtIrk~~~~~fvI~~P 100 (204)
.+|-.-+.++.+++.|||+- =+|=.||.++..+|.+|+|.-|
T Consensus 41 VeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG~l~~~~~~ 95 (152)
T KOG3198|consen 41 VENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDGTLYVIAFI 95 (152)
T ss_pred hcCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCCcEEeecch
Confidence 45556688899999999982 2466788888889999998765
No 59
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.86 E-value=33 Score=33.33 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=7.5
Q ss_pred CCCHHHHHHHHH
Q 028762 178 GVPRSRAVKALK 189 (204)
Q Consensus 178 gvSr~kAikALk 189 (204)
-|||=||-++|-
T Consensus 501 rvs~fk~~r~~~ 512 (514)
T KOG3130|consen 501 RVSKFKAARLQQ 512 (514)
T ss_pred hHHHHHHHHHhc
Confidence 366666666663
No 60
>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=27.27 E-value=39 Score=22.90 Aligned_cols=31 Identities=19% Similarity=0.232 Sum_probs=25.0
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHHHh
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSAIM 200 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~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 5667899999999999999999999877764
No 61
>PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=27.11 E-value=4.6e+02 Score=24.33 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=25.1
Q ss_pred CCCCcccHHHHHHhhCCCHHHHHHHHHHc
Q 028762 163 TGVEPKDIELVMTQAGVPRSRAVKALKAA 191 (204)
Q Consensus 163 ~gi~eeDIeLVm~QagvSr~kAikALke~ 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 46788889999999999999999998753
No 62
>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=26.05 E-value=60 Score=27.14 Aligned_cols=19 Identities=26% Similarity=0.352 Sum_probs=17.1
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028762 172 LVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAikALke 190 (204)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 63
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=25.58 E-value=61 Score=27.52 Aligned_cols=20 Identities=15% Similarity=0.204 Sum_probs=17.6
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 028762 171 ELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 171 eLVm~QagvSr~kAikALke 190 (204)
.-.+++-||||..+++||..
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 35789999999999999976
No 64
>PRK00523 hypothetical protein; Provisional
Probab=25.29 E-value=57 Score=24.25 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.6
Q ss_pred cCHHHHHHHHHHcCCcc
Q 028762 62 RSEKKSRKAMLKLGMKP 78 (204)
Q Consensus 62 r~eKK~rk~mkKLGlk~ 78 (204)
-+|+.+|.||.+||-||
T Consensus 40 ine~mir~M~~QMGqKP 56 (72)
T PRK00523 40 ITENMIRAMYMQMGRKP 56 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
No 65
>PF13276 HTH_21: HTH-like domain
Probab=24.11 E-value=65 Score=21.62 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=16.2
Q ss_pred CcCHHHHHHHHHHcCCccC
Q 028762 61 SRSEKKSRKAMLKLGMKPI 79 (204)
Q Consensus 61 sr~eKK~rk~mkKLGlk~I 79 (204)
.-|.|+.+++|+++||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 5678999999999999753
No 66
>PHA01623 hypothetical protein
Probab=23.65 E-value=1e+02 Score=21.27 Aligned_cols=22 Identities=14% Similarity=0.354 Sum_probs=18.0
Q ss_pred ccHHHHHHhhCCCHHHHHH-HHH
Q 028762 168 KDIELVMTQAGVPRSRAVK-ALK 189 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAik-ALk 189 (204)
.-++..+.+-|++|.++|+ ||+
T Consensus 26 ~~Ld~y~~~~g~~rSe~IreAI~ 48 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIEEAIK 48 (56)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 4678899999999999988 443
No 67
>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=23.41 E-value=72 Score=26.83 Aligned_cols=19 Identities=37% Similarity=0.403 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028762 172 LVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAikALke 190 (204)
-.+++.||||...++||..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999976
No 68
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.35 E-value=91 Score=22.34 Aligned_cols=29 Identities=28% Similarity=0.302 Sum_probs=21.9
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSA 198 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~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 67889999999999999887654434443
No 69
>PRK01844 hypothetical protein; Provisional
Probab=22.76 E-value=68 Score=23.84 Aligned_cols=17 Identities=29% Similarity=0.559 Sum_probs=14.5
Q ss_pred cCHHHHHHHHHHcCCcc
Q 028762 62 RSEKKSRKAMLKLGMKP 78 (204)
Q Consensus 62 r~eKK~rk~mkKLGlk~ 78 (204)
-+|+.+|.||.+||-||
T Consensus 39 ine~mir~Mm~QMGqkP 55 (72)
T PRK01844 39 INEQMLKMMMMQMGQKP 55 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
No 70
>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=22.52 E-value=95 Score=23.30 Aligned_cols=76 Identities=20% Similarity=0.288 Sum_probs=44.6
Q ss_pred HHHHHHHHcCCccCCCceEEEEEecCceEEEE-------cCCeEEeeCCCCeEEEeccceecchhhHHHHHHHHHcCCCC
Q 028762 66 KSRKAMLKLGMKPIPGVSRVTVKKSKNILFVI-------SKPDVFKSPTSDTYIVFGEAKIEDLSSQLQTQAAEQFKVPP 138 (204)
Q Consensus 66 K~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI-------~~PdVyKs~gs~tyvVFGEak~~d~s~~~q~~aae~~~~~~ 138 (204)
.+..+.+++-|..|-.-- +.+++.++ .+.. .+|..+-.+..++|-.||--.
T Consensus 5 ~~~~i~~~~~i~~v~~~~-~~l~~~G~-~~~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~-------------------- 62 (97)
T PF01807_consen 5 FIEEIKSRIDIVDVIERY-IKLKRRGR-EYRCLCPFHDDKTPSFSINPDKNRFKCFGCGK-------------------- 62 (97)
T ss_dssp HHHHHHHCS-HHHHHCCC-S--EEETT-EEEE--SSS--SS--EEEETTTTEEEETTT----------------------
T ss_pred HHHHHHHhCCHHHHHHHh-ccccccCC-eEEEECcCCCCCCCceEEECCCCeEEECCCCC--------------------
Confidence 344455556665432222 55666544 3555 457667778888999997421
Q ss_pred CCCCCCCCCCCCcccccCccccccCCCCcccHHHHHHhhCCCHHHHHHHHHH
Q 028762 139 PNTGNVASKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 139 ~~~~~~~~~~~~~~~~~~~eevd~~gi~eeDIeLVm~QagvSr~kAikALke 190 (204)
.| .=|.|||.--|||.-+|++-|.+
T Consensus 63 ------------------------~G---d~i~~v~~~~~~~f~eAv~~l~~ 87 (97)
T PF01807_consen 63 ------------------------GG---DVIDFVMKYEGCSFKEAVKWLAE 87 (97)
T ss_dssp ------------------------EE----HHHHHHHHHT--HHHHHHHHHH
T ss_pred ------------------------CC---cHHhHHHHHhCCCHHHHHHHHHH
Confidence 01 24999999999999999999976
No 71
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=22.29 E-value=1.6e+02 Score=28.93 Aligned_cols=54 Identities=13% Similarity=0.289 Sum_probs=40.0
Q ss_pred CcccCcCHHHHHHHHHHcCCcc-CCCceEEEEEecCceEEEEcCCeE-EeeCCCCeEEE
Q 028762 57 RSKQSRSEKKSRKAMLKLGMKP-IPGVSRVTVKKSKNILFVISKPDV-FKSPTSDTYIV 113 (204)
Q Consensus 57 ~~k~sr~eKK~rk~mkKLGlk~-I~gV~rVtIrk~~~~~fvI~~PdV-yKs~gs~tyvV 113 (204)
+.+-+++|-.+++.|...||.+ ..=.+.++++..+|.. -.||| .+.||....||
T Consensus 200 K~rG~WGE~qLerILE~sGL~~~~~y~~Q~~~~~~~g~~---~rPDviV~LP~~k~ivI 255 (475)
T PRK10361 200 KTQGNWGEVVLTRVLEASGLREGYEYETQVSIENDARSR---MQPDVIVRLPQGKDVVI 255 (475)
T ss_pred CcCcchHHHHHHHHHHHhCCCcCCcceeeeeccCCCCCe---eCCeEEEECCCCCCceE
Confidence 4456899999999999999984 3334677777765543 37997 57899887666
No 72
>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=22.15 E-value=1.2e+02 Score=31.01 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=7.3
Q ss_pred HHHHHHHHHH-cCC
Q 028762 64 EKKSRKAMLK-LGM 76 (204)
Q Consensus 64 eKK~rk~mkK-LGl 76 (204)
.+.++..|.+ ||.
T Consensus 701 d~~~~~~l~~aL~~ 714 (784)
T PF04931_consen 701 DEEFRSALAKALGD 714 (784)
T ss_pred HHHHHHHHHHHhcc
Confidence 3556665554 665
No 73
>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=22.14 E-value=73 Score=26.06 Aligned_cols=23 Identities=17% Similarity=0.111 Sum_probs=19.5
Q ss_pred cHHHHHHhhCCCHHHHHHHHHHc
Q 028762 169 DIELVMTQAGVPRSRAVKALKAA 191 (204)
Q Consensus 169 DIeLVm~QagvSr~kAikALke~ 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 74
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=21.99 E-value=98 Score=30.43 Aligned_cols=31 Identities=29% Similarity=0.532 Sum_probs=24.3
Q ss_pred ccCcCHHHHHHHHHHcCCccCCCceEEEEEecC
Q 028762 59 KQSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSK 91 (204)
Q Consensus 59 k~sr~eKK~rk~mkKLGlk~I~gV~rVtIrk~~ 91 (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 46778899999999999995 2 4567777654
No 75
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.96 E-value=54 Score=36.55 Aligned_cols=6 Identities=50% Similarity=1.209 Sum_probs=2.9
Q ss_pred EEEcCC
Q 028762 95 FVISKP 100 (204)
Q Consensus 95 fvI~~P 100 (204)
|+|..|
T Consensus 1849 Fmiad~ 1854 (3015)
T KOG0943|consen 1849 FMIADP 1854 (3015)
T ss_pred eeecCC
Confidence 444444
No 76
>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=21.84 E-value=1.2e+02 Score=20.67 Aligned_cols=23 Identities=30% Similarity=0.459 Sum_probs=20.0
Q ss_pred ccHHHHHHhhCCCHHHHHHHHHH
Q 028762 168 KDIELVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 168 eDIeLVm~QagvSr~kAikALke 190 (204)
-.+.-+...+|+||..+.++|+.
T Consensus 23 ~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35677899999999999999976
No 77
>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=21.73 E-value=1e+02 Score=21.91 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=21.9
Q ss_pred HHHHHHhhCCCHHHHHHHHHHcCCcHHHH
Q 028762 170 IELVMTQAGVPRSRAVKALKAADGDIVSA 198 (204)
Q Consensus 170 IeLVm~QagvSr~kAikALke~~GDIV~A 198 (204)
|+.|+..+|+|+..+...|..--.=|.++
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~~i~~~ 34 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLDVITEA 34 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999887654333333
No 78
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=21.63 E-value=75 Score=23.05 Aligned_cols=17 Identities=41% Similarity=0.643 Sum_probs=14.6
Q ss_pred cCHHHHHHHHHHcCCcc
Q 028762 62 RSEKKSRKAMLKLGMKP 78 (204)
Q Consensus 62 r~eKK~rk~mkKLGlk~ 78 (204)
-+|+.+|.|+.+||-++
T Consensus 32 ine~mir~M~~QMG~kp 48 (64)
T PF03672_consen 32 INEKMIRAMMMQMGRKP 48 (64)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
No 79
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=21.48 E-value=85 Score=24.71 Aligned_cols=17 Identities=53% Similarity=0.577 Sum_probs=15.3
Q ss_pred HHhhCCCHHHHHHHHHH
Q 028762 174 MTQAGVPRSRAVKALKA 190 (204)
Q Consensus 174 m~QagvSr~kAikALke 190 (204)
|-.||||+.-+.++|+.
T Consensus 78 M~dAGV~~~~~~~~l~~ 94 (100)
T PF15652_consen 78 MFDAGVSKECRKKALKA 94 (100)
T ss_pred HHHcCCCHHHHHHHHHH
Confidence 55699999999999987
No 80
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=21.34 E-value=93 Score=24.50 Aligned_cols=30 Identities=27% Similarity=0.367 Sum_probs=24.0
Q ss_pred HHHHhhCCCHHHHHHHHHHcCCcHHHHHhh
Q 028762 172 LVMTQAGVPRSRAVKALKAADGDIVSAIME 201 (204)
Q Consensus 172 LVm~QagvSr~kAikALke~~GDIV~AIM~ 201 (204)
-|..++|+||+--.|||...++=-...||.
T Consensus 54 qvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 54 QVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 477899999999999999887755555543
No 81
>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=21.16 E-value=2.1e+02 Score=21.65 Aligned_cols=32 Identities=28% Similarity=0.369 Sum_probs=21.3
Q ss_pred eEEEEEec-CceEEEEcCCeEEeeCCCCeEEEeccce
Q 028762 83 SRVTVKKS-KNILFVISKPDVFKSPTSDTYIVFGEAK 118 (204)
Q Consensus 83 ~rVtIrk~-~~~~fvI~~PdVyKs~gs~tyvVFGEak 118 (204)
.+|.++-. .+ +.+..-.+|-. .++++|||+..
T Consensus 19 VKvYv~G~l~~--~~~~~~~~fg~--~~~~vvfGd~~ 51 (83)
T PF08503_consen 19 VKVYVKGDLAG--IDFEDVKVFGS--GNFGVVFGDWD 51 (83)
T ss_dssp EEEEEEESCTC-----TTSEEEEE--SSEEEEEEEHH
T ss_pred EEEEEeeeecC--CChhheEEEeC--CCcEEEEecHH
Confidence 36777765 44 34577788875 47899999874
No 82
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=20.59 E-value=88 Score=26.49 Aligned_cols=19 Identities=32% Similarity=0.237 Sum_probs=16.9
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028762 172 LVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAikALke 190 (204)
-.+++-||||..+++||..
T Consensus 38 eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 38 ELCTQYNVSRITIRKAISD 56 (241)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 83
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=20.57 E-value=89 Score=26.25 Aligned_cols=19 Identities=21% Similarity=0.251 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 028762 172 LVMTQAGVPRSRAVKALKA 190 (204)
Q Consensus 172 LVm~QagvSr~kAikALke 190 (204)
-++++.||||.-.++||+.
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 84
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=20.29 E-value=1.2e+02 Score=23.06 Aligned_cols=40 Identities=20% Similarity=0.273 Sum_probs=26.3
Q ss_pred cCcCHHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcCC
Q 028762 60 QSRSEKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISKP 100 (204)
Q Consensus 60 ~sr~eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~P 100 (204)
..-+...+..+|++-|+..+.+|..+++..+ |.+.||.+.
T Consensus 25 ~~it~~dl~~~LR~~gi~~l~dV~~a~lE~~-G~lsv~~k~ 64 (99)
T PF04239_consen 25 ARITEEDLLSALREQGIESLSDVKAAVLEPN-GQLSVIKKE 64 (99)
T ss_dssp TT--HHHHHHHHHHTT--SGGGEEEEEE-TT-S-EEEEE-G
T ss_pred cCCCHHHHHHHHHhhCCCCHHHcCEEEECCC-CCEEEEEcC
Confidence 3345567888899999999999999999996 446666655
No 85
>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=20.22 E-value=1e+02 Score=29.00 Aligned_cols=27 Identities=33% Similarity=0.543 Sum_probs=19.2
Q ss_pred HHHHHHHHcCCccCCCceEEEEEecCc
Q 028762 66 KSRKAMLKLGMKPIPGVSRVTVKKSKN 92 (204)
Q Consensus 66 K~rk~mkKLGlk~I~gV~rVtIrk~~~ 92 (204)
+++..|..+-++.+|||.||.|.+.++
T Consensus 192 ~l~~~l~~~~v~Gi~gI~r~~i~~~~~ 218 (363)
T cd06528 192 KLAEKILNTKIKGIKGIKRVIVRKEED 218 (363)
T ss_pred HHHHhhcccEEeCCCCceEEEEecCCc
Confidence 344445556677999999999987543
No 86
>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=20.04 E-value=2.4e+02 Score=18.42 Aligned_cols=31 Identities=32% Similarity=0.416 Sum_probs=20.4
Q ss_pred HHHHHHHHHHcCCccCCCceEEEEEecCceEEEEcC
Q 028762 64 EKKSRKAMLKLGMKPIPGVSRVTVKKSKNILFVISK 99 (204)
Q Consensus 64 eKK~rk~mkKLGlk~I~gV~rVtIrk~~~~~fvI~~ 99 (204)
.++++++|+ .++||..|.+-...+.+-+.-+
T Consensus 13 ~~~v~~~l~-----~~~GV~~v~vd~~~~~v~v~~~ 43 (62)
T PF00403_consen 13 AKKVEKALS-----KLPGVKSVKVDLETKTVTVTYD 43 (62)
T ss_dssp HHHHHHHHH-----TSTTEEEEEEETTTTEEEEEES
T ss_pred HHHHHHHHh-----cCCCCcEEEEECCCCEEEEEEe
Confidence 356666665 4589998988877665544333
Done!