Query 028148
Match_columns 213
No_of_seqs 158 out of 480
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:59:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028148hhsearch_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 1.7E-56 3.7E-61 382.1 16.6 155 58-213 55-209 (209)
2 PRK06369 nac nascent polypepti 100.0 1.2E-38 2.6E-43 253.3 11.4 106 67-213 5-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 5.4E-33 1.2E-37 222.4 8.2 113 67-213 6-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 1.1E-31 2.5E-36 213.5 11.0 102 69-213 11-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 1.9E-21 4.2E-26 136.9 6.6 58 69-126 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.2 1.3E-06 2.7E-11 73.8 3.7 64 66-129 38-101 (162)
7 PF00627 UBA: UBA/TS-N domain; 97.7 3.9E-05 8.5E-10 49.1 3.1 37 174-211 1-37 (37)
8 KOG3450 Huntingtin interacting 97.6 4.1E-05 8.9E-10 61.2 2.3 41 173-213 78-118 (119)
9 PF14555 UBA_4: UBA-like domai 95.5 0.025 5.3E-07 37.3 4.0 33 177-209 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.3 0.03 6.6E-07 35.3 3.8 32 179-211 5-36 (38)
11 smart00165 UBA Ubiquitin assoc 95.0 0.04 8.7E-07 34.6 3.7 27 185-211 10-36 (37)
12 COG2103 Predicted sugar phosph 86.3 0.88 1.9E-05 42.0 3.9 38 174-211 232-269 (298)
13 COG4008 Predicted metal-bindin 86.1 1 2.2E-05 37.5 3.8 36 171-208 110-145 (153)
14 PRK05441 murQ N-acetylmuramic 84.3 1.3 2.7E-05 40.3 4.0 37 175-211 235-271 (299)
15 PF10411 DsbC_N: Disulfide bon 83.2 2.9 6.3E-05 29.1 4.6 40 73-122 2-50 (57)
16 cd05007 SIS_Etherase N-acetylm 78.9 1.2 2.6E-05 39.5 1.8 35 175-209 222-256 (257)
17 TIGR00274 N-acetylmuramic acid 78.9 2.6 5.6E-05 38.4 3.9 36 176-211 231-266 (291)
18 PF02845 CUE: CUE domain; Int 77.5 3.6 7.9E-05 26.6 3.3 33 179-211 5-38 (42)
19 PRK12570 N-acetylmuramic acid- 74.5 3.9 8.4E-05 37.2 3.8 36 176-211 232-267 (296)
20 PF10446 DUF2457: Protein of u 73.8 1.6 3.5E-05 42.5 1.2 11 115-125 193-203 (458)
21 smart00546 CUE Domain that may 71.3 6.6 0.00014 25.4 3.4 34 178-211 5-39 (43)
22 PF14474 RTC4: RTC4-like domai 70.9 4.4 9.5E-05 32.6 2.9 30 176-206 90-119 (124)
23 PF03474 DMA: DMRTA motif; In 67.9 6.3 0.00014 26.3 2.7 21 189-209 16-36 (39)
24 PF11626 Rap1_C: TRF2-interact 61.2 12 0.00026 28.0 3.5 30 179-209 1-30 (87)
25 PF05861 PhnI: Bacterial phosp 60.3 9.9 0.00021 36.2 3.5 33 179-211 45-78 (358)
26 PF06970 RepA_N: Replication i 59.9 9.4 0.0002 28.3 2.7 22 178-199 54-75 (76)
27 PRK10877 protein disulfide iso 59.0 26 0.00056 30.6 5.7 43 69-122 23-72 (232)
28 COG3626 PhnI Uncharacterized e 58.6 9.7 0.00021 35.7 3.1 33 179-211 45-78 (367)
29 PF12244 DUF3606: Protein of u 58.4 18 0.00039 25.4 3.8 30 176-205 20-49 (57)
30 PF02796 HTH_7: Helix-turn-hel 57.9 7.9 0.00017 25.4 1.8 23 178-200 23-45 (45)
31 TIGR00632 vsr DNA mismatch end 57.0 14 0.00031 29.8 3.5 35 61-95 16-56 (117)
32 PRK05441 murQ N-acetylmuramic 55.7 15 0.00033 33.4 3.8 33 179-211 266-298 (299)
33 TIGR00274 N-acetylmuramic acid 54.9 15 0.00032 33.4 3.7 30 179-208 261-290 (291)
34 PF13730 HTH_36: Helix-turn-he 54.3 16 0.00034 24.2 2.9 22 178-199 27-48 (55)
35 PRK12570 N-acetylmuramic acid- 48.6 24 0.00052 32.2 3.9 30 179-208 262-291 (296)
36 PLN02150 terpene synthase/cycl 48.2 17 0.00037 28.0 2.5 25 176-200 7-31 (96)
37 KOG3130 Uncharacterized conser 47.3 13 0.00027 36.4 2.0 21 178-198 489-512 (514)
38 COG1654 BirA Biotin operon rep 46.5 20 0.00044 27.0 2.6 25 180-204 23-50 (79)
39 PF03861 ANTAR: ANTAR domain; 44.8 26 0.00055 24.0 2.8 22 179-200 19-40 (56)
40 KOG1071 Mitochondrial translat 44.4 24 0.00052 33.4 3.3 36 174-209 45-80 (340)
41 PF06972 DUF1296: Protein of u 43.7 49 0.0011 24.1 4.1 33 179-211 9-42 (60)
42 PF00392 GntR: Bacterial regul 42.8 23 0.0005 24.4 2.3 21 179-199 27-47 (64)
43 PF04931 DNA_pol_phi: DNA poly 42.4 45 0.00098 34.2 5.2 13 69-81 701-714 (784)
44 PF11699 CENP-C_C: Mif2/CENP-C 38.5 47 0.001 25.2 3.6 35 83-120 39-73 (85)
45 COG2188 PhnF Transcriptional r 37.5 28 0.0006 30.2 2.5 18 182-199 37-54 (236)
46 COG4004 Uncharacterized protei 37.0 72 0.0016 25.2 4.4 34 68-101 13-56 (96)
47 PRK05564 DNA polymerase III su 35.5 2E+02 0.0044 25.6 7.8 48 69-125 75-134 (313)
48 PF10975 DUF2802: Protein of u 35.2 30 0.00066 25.3 2.0 21 177-197 45-65 (70)
49 KOG3198 Signal recognition par 35.0 62 0.0013 27.5 4.1 42 64-105 41-95 (152)
50 smart00345 HTH_GNTR helix_turn 33.9 54 0.0012 21.1 2.9 22 178-199 22-43 (60)
51 PHA01748 hypothetical protein 33.7 51 0.0011 23.3 2.9 21 177-197 15-35 (60)
52 PRK07993 DNA polymerase III su 33.5 2.6E+02 0.0056 25.9 8.3 104 65-208 86-202 (334)
53 smart00804 TAP_C C-terminal do 33.3 86 0.0019 22.5 4.1 35 177-211 14-48 (63)
54 smart00400 ZnF_CHCC zinc finge 33.0 46 0.001 22.5 2.6 20 178-197 35-54 (55)
55 KOG3130 Uncharacterized conser 32.5 26 0.00057 34.3 1.7 21 23-43 267-287 (514)
56 PF04931 DNA_pol_phi: DNA poly 32.3 30 0.00065 35.5 2.1 12 70-81 706-717 (784)
57 PHA01623 hypothetical protein 32.2 56 0.0012 22.9 2.9 20 177-196 26-45 (56)
58 KOG0944 Ubiquitin-specific pro 31.4 42 0.00091 34.8 2.9 24 184-207 643-666 (763)
59 cd07377 WHTH_GntR Winged helix 30.7 64 0.0014 21.1 2.9 22 178-199 27-48 (66)
60 PF08680 DUF1779: Protein of u 30.3 40 0.00088 28.6 2.3 54 69-122 131-197 (203)
61 TIGR02325 C_P_lyase_phnF phosp 29.3 47 0.001 28.0 2.5 19 181-199 37-55 (238)
62 PRK10079 phosphonate metabolis 28.9 48 0.001 28.4 2.5 19 181-199 40-58 (241)
63 PF04239 DUF421: Protein of un 28.1 89 0.0019 23.9 3.7 39 66-105 26-64 (99)
64 PF13276 HTH_21: HTH-like doma 27.7 51 0.0011 22.4 2.0 19 66-84 37-55 (60)
65 PF12614 RRF_GI: Ribosome recy 27.7 44 0.00096 27.6 2.0 23 178-200 104-126 (128)
66 TIGR02404 trehalos_R_Bsub treh 26.4 57 0.0012 27.7 2.5 19 181-199 29-47 (233)
67 PF03943 TAP_C: TAP C-terminal 26.4 33 0.00072 23.5 0.9 31 179-209 4-34 (51)
68 KOG1832 HIV-1 Vpr-binding prot 25.9 55 0.0012 35.5 2.7 14 176-189 1490-1503(1516)
69 COG0100 RpsK Ribosomal protein 24.6 69 0.0015 26.5 2.6 93 85-211 18-113 (129)
70 PRK04984 fatty acid metabolism 23.9 68 0.0015 27.2 2.5 19 181-199 36-54 (239)
71 PF01978 TrmB: Sugar-specific 23.9 97 0.0021 21.3 3.0 23 177-199 23-45 (68)
72 smart00411 BHL bacterial (prok 23.6 84 0.0018 22.7 2.7 29 179-207 7-35 (90)
73 PRK11402 DNA-binding transcrip 23.2 71 0.0015 27.3 2.5 19 181-199 38-56 (241)
74 PF01807 zf-CHC2: CHC2 zinc fi 23.2 86 0.0019 23.7 2.8 76 71-199 5-87 (97)
75 PRK00523 hypothetical protein; 22.5 66 0.0014 24.2 1.9 17 67-83 40-56 (72)
76 PRK14999 histidine utilization 22.5 74 0.0016 27.2 2.5 20 180-199 40-59 (241)
77 PF08503 DapH_N: Tetrahydrodip 22.2 1.9E+02 0.0042 22.1 4.5 33 88-124 19-52 (83)
78 PF00403 HMA: Heavy-metal-asso 22.0 2.2E+02 0.0048 18.8 4.4 32 69-105 13-44 (62)
79 COG3636 Predicted transcriptio 22.0 91 0.002 24.8 2.7 32 179-210 52-83 (100)
80 cd00591 HU_IHF Integration hos 21.9 92 0.002 22.3 2.6 29 179-207 6-34 (87)
81 KOG3705 Glycoprotein 6-alpha-L 21.8 97 0.0021 30.7 3.4 60 64-125 343-438 (580)
82 PF00356 LacI: Bacterial regul 21.3 1E+02 0.0022 20.6 2.5 22 179-200 2-23 (46)
83 KOG0943 Predicted ubiquitin-pr 21.1 52 0.0011 37.0 1.5 26 29-54 1739-1764(3015)
84 PRK10361 DNA recombination pro 20.8 1.8E+02 0.0039 28.8 5.0 54 62-118 200-255 (475)
85 PF07717 OB_NTP_bind: Oligonuc 20.8 2.4E+02 0.0052 21.0 4.8 30 95-124 54-90 (114)
86 COG2103 Predicted sugar phosph 20.4 1.2E+02 0.0026 28.3 3.6 32 179-210 264-295 (298)
87 PF08002 DUF1697: Protein of u 20.2 86 0.0019 25.4 2.3 28 69-101 21-48 (137)
88 PRK01844 hypothetical protein; 20.1 79 0.0017 23.7 1.9 17 67-83 39-55 (72)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=1.7e-56 Score=382.13 Aligned_cols=155 Identities=65% Similarity=0.918 Sum_probs=138.0
Q ss_pred CCCCCCccCcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecchhhHHHHHHHH
Q 028148 58 AQGGSSKQSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLSTQLQTQAAQ 137 (213)
Q Consensus 58 ~~~~~~k~sr~eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFGEak~eD~s~q~q~~aae 137 (213)
.+.+++||||++||.||+|.||||++|+||+||||||++|++|+|++|+|||+|+++||||||+++++|+++|+|.+|++
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 46778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCCCCCCCcchhhccCCCCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028148 138 QFRMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~Lt~ 213 (213)
+|+.+..+........++.. ...+++++++||++||+.+||+|||+|+||||++||+|||+|+||||||||+||+
T Consensus 135 ~fk~~~~~~~~~~~~~~~~~-~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 135 RFKVPQEAPGLIQEDTSATP-PAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred hccCCccccccccccccCCC-ccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 99987766544443333211 1133345667999999999999999999999999999999999999999999985
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=1.2e-38 Score=253.31 Aligned_cols=106 Identities=30% Similarity=0.487 Sum_probs=97.5
Q ss_pred cCHHHHHHHHHHcCCe--ecCCceEEEEEecCceEEEecCCeEE--eeCCCceEEEeccceecchhhHHHHHHHHhhcCC
Q 028148 67 RSEKKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDVF--KSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 142 (213)
Q Consensus 67 r~eKK~rK~mkKLGlk--~V~gV~rVtIrk~dn~lfvI~~PdVy--KspgsdTYvVFGEak~eD~s~q~q~~aae~~~~~ 142 (213)
=|||||||||+||||+ +| ||.||+||+++ .+|||++|+|| ++||++||+|||+++.++++++.
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 99999999997 89999999999 78999999999999998765310
Q ss_pred CCCCCCCCCCcchhhccCCCCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028148 143 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~Lt~ 213 (213)
+++|+++||+|||+||||||++|++||++||||||+|||.|+.
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 3579999999999999999999999999999999999999973
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.98 E-value=5.4e-33 Score=222.44 Aligned_cols=113 Identities=40% Similarity=0.606 Sum_probs=96.0
Q ss_pred cCHHHHHHHHHHcCC--eecCCceEEEEEecCceEEEecCCeEEe--eCCCceEEEeccceecchhhHHHHHHHHhhcCC
Q 028148 67 RSEKKSRKAMLKLGM--KPVTGVSRVTIKRTKNILFFISKPDVFK--SPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 142 (213)
Q Consensus 67 r~eKK~rK~mkKLGl--k~V~gV~rVtIrk~dn~lfvI~~PdVyK--spgsdTYvVFGEak~eD~s~q~q~~aae~~~~~ 142 (213)
=|+|+|+|+|++||| ++|+||.||+|++.++. ++|++|.||. ++|..||+|.|.+.. .++
T Consensus 6 mnpr~l~k~mkqmGi~~eeld~v~~V~i~~kd~e-~vi~~P~V~~~~~~g~~~yqi~g~~~~---------~~~------ 69 (122)
T COG1308 6 MNPRKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVMKAMGQKTYQISGDPSA---------KEA------ 69 (122)
T ss_pred CCHHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcchhh---------hcc------
Confidence 478999999999995 48999999999999886 9999999986 589999999997530 000
Q ss_pred CCCCCCCCCCcchhhccCCCCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028148 143 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~Lt~ 213 (213)
....++..+++.+|+++||+|||+||||||++||+||+++|||||+|||+|+.
T Consensus 70 ------------------~~~~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 70 ------------------VKKPEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred ------------------cccchhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 11123455777889999999999999999999999999999999999999984
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=1.1e-31 Score=213.48 Aligned_cols=102 Identities=33% Similarity=0.499 Sum_probs=87.5
Q ss_pred HHHHHHHHHHcCCe--ecCCceEEEEEecCceEEEecCCeE--EeeCCCceEEEeccceecchhhHHHHHHHHhhcCCCC
Q 028148 69 EKKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDV--FKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPDM 144 (213)
Q Consensus 69 eKK~rK~mkKLGlk--~V~gV~rVtIrk~dn~lfvI~~PdV--yKspgsdTYvVFGEak~eD~s~q~q~~aae~~~~~~~ 144 (213)
-|+|||||+||||+ ++. |.+|+|++.++ .++|++|+| |+++|+.||+|||+++.+++.+
T Consensus 11 ~~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~~--------------- 73 (116)
T TIGR00264 11 LKQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVEE--------------- 73 (116)
T ss_pred HHHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeeccc---------------
Confidence 34999999999999 466 99999999764 567888876 7789999999999998743210
Q ss_pred CCCCCCCCcchhhccCCCCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028148 145 GSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~Lt~ 213 (213)
..+|+++||+|||+||||||++|++||++||||||+|||.|+.
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=1.9e-21 Score=136.87 Aligned_cols=58 Identities=48% Similarity=0.824 Sum_probs=48.4
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecc
Q 028148 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIED 126 (213)
Q Consensus 69 eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFGEak~eD 126 (213)
|||||++|+||||++|+||.||+|++.+|.+|+|++|+||+++|++||+|||+++.++
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 6999999999999999999999999999999999999999999999999999998864
No 6
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=98.19 E-value=1.3e-06 Score=73.80 Aligned_cols=64 Identities=23% Similarity=0.468 Sum_probs=60.1
Q ss_pred CcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecchhh
Q 028148 66 SRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLST 129 (213)
Q Consensus 66 sr~eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFGEak~eD~s~ 129 (213)
....||++--|+||++..|+||.+|.|.+.++.++.|++|.|.++...+||.|.|.++..-++.
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 6778999999999999999999999999999999999999999999999999999999876644
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=97.69 E-value=3.9e-05 Score=49.12 Aligned_cols=37 Identities=30% Similarity=0.494 Sum_probs=31.9
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 174 v~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
|+++.|..+++. |+|++.|++||+.++||+-.||.-|
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 346788999999 9999999999999999999998754
No 8
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.57 E-value=4.1e-05 Score=61.17 Aligned_cols=41 Identities=32% Similarity=0.632 Sum_probs=38.6
Q ss_pred CCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028148 173 GVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 173 gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~Lt~ 213 (213)
.|..+||+|||...-+++.-|.+-|++|+||+|.|+-.|++
T Consensus 78 ~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 78 TIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 58899999999999999999999999999999999988863
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=95.50 E-value=0.025 Score=37.33 Aligned_cols=33 Identities=24% Similarity=0.361 Sum_probs=27.5
Q ss_pred cchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028148 177 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkALke~nGDIV~AIM 209 (213)
+-|.-.|+=|||+++.|+..|+.+|+||-.||=
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=95.30 E-value=0.03 Score=35.26 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=26.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
|..++ ..|.+++.|+.||+.++||+-.|+--|
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 34444 469999999999999999999987554
No 11
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=95.03 E-value=0.04 Score=34.56 Aligned_cols=27 Identities=41% Similarity=0.578 Sum_probs=23.4
Q ss_pred hhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 185 QAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 185 QagvSRekAvkALke~nGDIV~AIM~L 211 (213)
..|.+++.|++||+.++||+-.|+--|
T Consensus 10 ~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 10 EMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 459999999999999999998887543
No 12
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=86.31 E-value=0.88 Score=41.99 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=33.2
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 174 v~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
+-..-+.+||+-|||+|++|.++|++++|++=-||+-+
T Consensus 232 L~dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~ 269 (298)
T COG2103 232 LRDRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVML 269 (298)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHH
Confidence 34567899999999999999999999999998887654
No 13
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=86.11 E-value=1 Score=37.49 Aligned_cols=36 Identities=17% Similarity=0.274 Sum_probs=28.2
Q ss_pred cCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028148 171 ETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 171 e~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AI 208 (213)
...++.+-++.+..- +||.++|++||.++| |+..|+
T Consensus 110 ~s~~~~e~v~v~a~a-~v~~eeAr~aleeag-Dl~~A~ 145 (153)
T COG4008 110 HSEPPVEEVEVLADA-FVTPEEAREALEEAG-DLRTAM 145 (153)
T ss_pred cCCCcHHHHHHHHHh-cCCHHHHHHHHHHcC-CHHHHH
Confidence 344556677766655 599999999999995 999985
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=84.30 E-value=1.3 Score=40.33 Aligned_cols=37 Identities=35% Similarity=0.529 Sum_probs=30.4
Q ss_pred CccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 175 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 175 ~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
-..=+.+||+-+|||+++|.++|.+++|.+=-||+-+
T Consensus 235 ~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 235 VDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 3456778999999999999999999999988887644
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=83.22 E-value=2.9 Score=29.09 Aligned_cols=40 Identities=25% Similarity=0.627 Sum_probs=25.0
Q ss_pred HHHHHHc--CCe-------ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccc
Q 028148 73 RKAMLKL--GMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 122 (213)
Q Consensus 73 rK~mkKL--Glk-------~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFGEa 122 (213)
|+.|+++ |++ +++|+-+|++ +..+ + +|-++.+ .|+|+|..
T Consensus 2 ~~~l~~~~p~~~v~~v~~spi~GlyeV~~-~~~~-i-------~Y~~~dg-~yli~G~l 50 (57)
T PF10411_consen 2 KQALKKAFPGLKVESVSPSPIPGLYEVVL-KGGG-I-------LYVDEDG-RYLIQGQL 50 (57)
T ss_dssp HHHHHCT--T-TCEEEEE-SSTTEEEEEE--TTE-E-------EEEETTS-SEEEES-E
T ss_pred hhHHHhhcCCCceeEEEcCCCCCeEEEEE-CCCe-E-------EEEcCCC-CEEEEeEE
Confidence 5567776 665 6899999988 3333 3 3555544 69999963
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=78.92 E-value=1.2 Score=39.52 Aligned_cols=35 Identities=43% Similarity=0.649 Sum_probs=30.5
Q ss_pred CccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028148 175 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 175 ~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM 209 (213)
-..=+.+||+-+|||+++|.++|..++|++=-||+
T Consensus 222 ~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~~ 256 (257)
T cd05007 222 RERAIRIVMEATGVSRDEAEAALEQAGGDVKTAIL 256 (257)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeeee
Confidence 34668889999999999999999999999877664
No 17
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=78.92 E-value=2.6 Score=38.36 Aligned_cols=36 Identities=17% Similarity=0.279 Sum_probs=30.0
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 176 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 176 eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
..=+.+||+=+|||+++|.++|..++|.+=-||+-+
T Consensus 231 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~ 266 (291)
T TIGR00274 231 ARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMI 266 (291)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 456778999999999999999999999998887643
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=77.52 E-value=3.6 Score=26.63 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=22.3
Q ss_pred hHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQa-gvSRekAvkALke~nGDIV~AIM~L 211 (213)
|..+.+-. +++++....+|+.++||+-.||-.|
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 6788888888989999986666554
No 19
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=74.49 E-value=3.9 Score=37.23 Aligned_cols=36 Identities=31% Similarity=0.496 Sum_probs=28.5
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 176 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 176 eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
..=+.+||+=+|||+++|.++|..++|.|=-||+-+
T Consensus 232 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~ 267 (296)
T PRK12570 232 ARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMI 267 (296)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHH
Confidence 355677888888888888888888888887777643
No 20
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=73.75 E-value=1.6 Score=42.54 Aligned_cols=11 Identities=18% Similarity=0.241 Sum_probs=6.3
Q ss_pred eEEEeccceec
Q 028148 115 TYVIFGEAKIE 125 (213)
Q Consensus 115 TYvVFGEak~e 125 (213)
|-.|-|..-..
T Consensus 193 TDFVCGTLDED 203 (458)
T PF10446_consen 193 TDFVCGTLDED 203 (458)
T ss_pred ccccCCCcCCc
Confidence 45566765553
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=71.26 E-value=6.6 Score=25.40 Aligned_cols=34 Identities=15% Similarity=0.237 Sum_probs=25.8
Q ss_pred chHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 178 DIDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 178 DIeLVmeQa-gvSRekAvkALke~nGDIV~AIM~L 211 (213)
.|+.+.+=. .+++..++..|+.++|++-.||=.|
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 7899999999999999998888554
No 22
>PF14474 RTC4: RTC4-like domain
Probab=70.91 E-value=4.4 Score=32.61 Aligned_cols=30 Identities=20% Similarity=0.315 Sum_probs=24.7
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHH
Q 028148 176 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVS 206 (213)
Q Consensus 176 eeDIeLVmeQagvSRekAvkALke~nGDIV~ 206 (213)
|==|.|||+-.||++++|++.|+++ .++-.
T Consensus 90 El~~~LI~EDm~v~~~~A~~il~eS-~~~G~ 119 (124)
T PF14474_consen 90 ELAVRLIMEDMGVDDEEARQILEES-SEYGE 119 (124)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHH-HHHHH
Confidence 3458999999999999999999998 34433
No 23
>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=67.94 E-value=6.3 Score=26.30 Aligned_cols=21 Identities=43% Similarity=0.469 Sum_probs=16.8
Q ss_pred CHHHHHHHHHhcCCcHHHHHh
Q 028148 189 SRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 189 SRekAvkALke~nGDIV~AIM 209 (213)
.|+.---.|+-+|||+|.||=
T Consensus 16 kr~~Le~iL~~C~GDvv~AIE 36 (39)
T PF03474_consen 16 KRSVLELILQRCNGDVVQAIE 36 (39)
T ss_pred ChHHHHHHHHHcCCcHHHHHH
Confidence 455556689999999999984
No 24
>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=61.23 E-value=12 Score=28.03 Aligned_cols=30 Identities=30% Similarity=0.238 Sum_probs=24.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM 209 (213)
|+- |.++|.++.-...||..+.||+..|.-
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 25
>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=60.33 E-value=9.9 Score=36.19 Aligned_cols=33 Identities=33% Similarity=0.524 Sum_probs=27.9
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQagv-SRekAvkALke~nGDIV~AIM~L 211 (213)
|+-||+..+. .++=|--|||.+.||+++||.-|
T Consensus 45 vdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 45 VDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 4457777764 78889999999999999999876
No 26
>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=59.85 E-value=9.4 Score=28.34 Aligned_cols=22 Identities=32% Similarity=0.380 Sum_probs=19.7
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028148 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke 199 (213)
-|+-+|+-.|||+.++++++++
T Consensus 54 s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHHc
Confidence 3777899999999999999986
No 27
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=59.03 E-value=26 Score=30.59 Aligned_cols=43 Identities=21% Similarity=0.473 Sum_probs=29.3
Q ss_pred HHHHHHHHHHcCCe-------ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccc
Q 028148 69 EKKSRKAMLKLGMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 122 (213)
Q Consensus 69 eKK~rK~mkKLGlk-------~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFGEa 122 (213)
...+++.|.++|++ +++|+-+|++. .+ + +|-++ ...|+|+|..
T Consensus 23 ~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~~--~~-i-------~Y~~~-dg~y~i~G~l 72 (232)
T PRK10877 23 DAAIQQTLAKLGIQSADIQPSPVAGMKTVLTE--SG-V-------LYITD-DGKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHHcCCceeEEccCCCCCeEEEEEC--Ce-E-------EEEcC-CCCEEEeeee
Confidence 36788889998886 58888888652 22 3 34444 3469999963
No 28
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=58.58 E-value=9.7 Score=35.65 Aligned_cols=33 Identities=45% Similarity=0.612 Sum_probs=27.0
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQagv-SRekAvkALke~nGDIV~AIM~L 211 (213)
|+-||...++ .|+=|-=|||.+.||+++||+-|
T Consensus 45 VdRVM~EgslyDreLAALAikQa~GD~~EAIFLl 78 (367)
T COG3626 45 VDRVMTEGSLYDRELAALALKQASGDLVEAIFLL 78 (367)
T ss_pred HHHHhhccchhHHHHHHHHHHHhcchHHHHHHHH
Confidence 4556666654 68889999999999999999876
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=58.43 E-value=18 Score=25.37 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=26.7
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHH
Q 028148 176 PRDIDLVMTQAGVSRSKAVKALKTHNGDIV 205 (213)
Q Consensus 176 eeDIeLVmeQagvSRekAvkALke~nGDIV 205 (213)
+-.|...+...|||.++.+.|.+..++++.
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~ 49 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLREAVRAVGNSRA 49 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHCcCHH
Confidence 568999999999999999999999977743
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=57.86 E-value=7.9 Score=25.40 Aligned_cols=23 Identities=35% Similarity=0.423 Sum_probs=17.9
Q ss_pred chHHHHhhhCCCHHHHHHHHHhc
Q 028148 178 DIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke~ 200 (213)
-|.-|+.++||||....+.|++|
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 47788999999999999988764
No 31
>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=56.98 E-value=14 Score=29.81 Aligned_cols=35 Identities=17% Similarity=0.333 Sum_probs=28.6
Q ss_pred CCCccCcCHHHHHHHHHHcCCe------ecCCceEEEEEec
Q 028148 61 GSSKQSRSEKKSRKAMLKLGMK------PVTGVSRVTIKRT 95 (213)
Q Consensus 61 ~~~k~sr~eKK~rK~mkKLGlk------~V~gV~rVtIrk~ 95 (213)
-+++.++.|..++++|..+|++ .++|+--+++.+.
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 4578889999999999999997 2688777777765
No 32
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=55.66 E-value=15 Score=33.37 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=29.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
+-+||--+||+.++|.+.|..++|.|-.||=.+
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence 457899999999999999999999999987443
No 33
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=54.88 E-value=15 Score=33.43 Aligned_cols=30 Identities=30% Similarity=0.383 Sum_probs=26.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AI 208 (213)
+-++|-.+||+..+|++.|..++|.|-.||
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l 290 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQAL 290 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhh
Confidence 457889999999999999999999998775
No 34
>PF13730 HTH_36: Helix-turn-helix domain
Probab=54.32 E-value=16 Score=24.17 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=19.4
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028148 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke 199 (213)
-++-++..+|+||...+++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 6889999999999988888765
No 35
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=48.65 E-value=24 Score=32.16 Aligned_cols=30 Identities=27% Similarity=0.392 Sum_probs=27.4
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AI 208 (213)
+-++|-.+|||.++|.+.|..++|.|-.||
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l 291 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAI 291 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHH
Confidence 567899999999999999999999998886
No 36
>PLN02150 terpene synthase/cyclase family protein
Probab=48.22 E-value=17 Score=27.96 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=21.6
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhc
Q 028148 176 PRDIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 176 eeDIeLVmeQagvSRekAvkALke~ 200 (213)
+.-|+--|.|-|||.++|++.|++-
T Consensus 7 aSsIeCYMke~g~seeeA~~~i~~l 31 (96)
T PLN02150 7 ANGVNCYMKQHGVTKEEAVSELKKM 31 (96)
T ss_pred hHHHHHHhccCCCCHHHHHHHHHHH
Confidence 4568999999999999999988763
No 37
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.32 E-value=13 Score=36.44 Aligned_cols=21 Identities=24% Similarity=0.287 Sum_probs=11.6
Q ss_pred chHHHHhhh---CCCHHHHHHHHH
Q 028148 178 DIDLVMTQA---GVSRSKAVKALK 198 (213)
Q Consensus 178 DIeLVmeQa---gvSRekAvkALk 198 (213)
-+.|+.+.+ -|||=||-+||-
T Consensus 489 ~~~~~~s~~~~krvs~fk~~r~~~ 512 (514)
T KOG3130|consen 489 EVLLEASEETGKRVSKFKAARLQQ 512 (514)
T ss_pred cceeecccccchhHHHHHHHHHhc
Confidence 344444443 467777776663
No 38
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=46.48 E-value=20 Score=26.97 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=20.4
Q ss_pred HHHHhhhCCCH---HHHHHHHHhcCCcH
Q 028148 180 DLVMTQAGVSR---SKAVKALKTHNGDI 204 (213)
Q Consensus 180 eLVmeQagvSR---ekAvkALke~nGDI 204 (213)
+-+.+..|||| .|.|++|++.+-+|
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 34678999999 48899999987765
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=44.77 E-value=26 Score=24.00 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=17.5
Q ss_pred hHHHHhhhCCCHHHHHHHHHhc
Q 028148 179 IDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~ 200 (213)
+-++|.+.|||.++|.+.|+..
T Consensus 19 kgiLm~~~g~~e~~A~~~Lr~~ 40 (56)
T PF03861_consen 19 KGILMARYGLSEDEAYRLLRRQ 40 (56)
T ss_dssp HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHHHHHHH
Confidence 5689999999999999999863
No 40
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=44.38 E-value=24 Score=33.38 Aligned_cols=36 Identities=25% Similarity=0.243 Sum_probs=32.5
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028148 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 174 v~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM 209 (213)
++...|+-.=+.||.|----++||.++|||++.|--
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~ 80 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEE 80 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHH
Confidence 567889999999999999999999999999998853
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=43.72 E-value=49 Score=24.07 Aligned_cols=33 Identities=24% Similarity=0.248 Sum_probs=26.1
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028148 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVmeQagv-SRekAvkALke~nGDIV~AIM~L 211 (213)
|.-+=+=+|| |.++....|+++|.|.=.|.=+|
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 99999999999999987776555
No 42
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=42.80 E-value=23 Score=24.35 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHh
Q 028148 179 IDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke 199 (213)
..-++++.||||.-+++||..
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 355899999999999999974
No 43
>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=42.43 E-value=45 Score=34.17 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=7.4
Q ss_pred HHHHHHHHHH-cCC
Q 028148 69 EKKSRKAMLK-LGM 81 (213)
Q Consensus 69 eKK~rK~mkK-LGl 81 (213)
.+++|..|.+ ||.
T Consensus 701 d~~~~~~l~~aL~~ 714 (784)
T PF04931_consen 701 DEEFRSALAKALGD 714 (784)
T ss_pred HHHHHHHHHHHhcc
Confidence 3556666554 665
No 44
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=38.45 E-value=47 Score=25.19 Aligned_cols=35 Identities=29% Similarity=0.472 Sum_probs=27.2
Q ss_pred ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEec
Q 028148 83 PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFG 120 (213)
Q Consensus 83 ~V~gV~rVtIrk~dn~lfvI~~PdVyKspgsdTYvVFG 120 (213)
-+.|..+|+|- +.-|++..-..|..|.+++|-|--
T Consensus 39 V~~G~v~Vti~---~~~f~v~~G~~F~VP~gN~Y~i~N 73 (85)
T PF11699_consen 39 VIKGKVEVTIH---ETSFVVTKGGSFQVPRGNYYSIKN 73 (85)
T ss_dssp EEESEEEEEET---TEEEEEETT-EEEE-TT-EEEEEE
T ss_pred EEeCEEEEEEc---CcEEEEeCCCEEEECCCCEEEEEE
Confidence 47899999996 458999999999999999998853
No 45
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=37.54 E-value=28 Score=30.19 Aligned_cols=18 Identities=44% Similarity=0.466 Sum_probs=16.3
Q ss_pred HHhhhCCCHHHHHHHHHh
Q 028148 182 VMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 182 VmeQagvSRekAvkALke 199 (213)
.++|.||||-.++|||..
T Consensus 37 La~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 37 LAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHCCcHHHHHHHHHH
Confidence 689999999999999965
No 46
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.98 E-value=72 Score=25.17 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHcCCe----------ecCCceEEEEEecCceEEE
Q 028148 68 SEKKSRKAMLKLGMK----------PVTGVSRVTIKRTKNILFF 101 (213)
Q Consensus 68 ~eKK~rK~mkKLGlk----------~V~gV~rVtIrk~dn~lfv 101 (213)
.+-.+.++|..||.. -+||+++|.|+..++.++|
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 356778889999975 3799999999988776554
No 47
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=35.49 E-value=2e+02 Score=25.57 Aligned_cols=48 Identities=17% Similarity=0.342 Sum_probs=31.9
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEe------------eCCCceEEEeccceec
Q 028148 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFK------------SPNSETYVIFGEAKIE 125 (213)
Q Consensus 69 eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~PdVyK------------spgsdTYvVFGEak~e 125 (213)
=..+|.++.++...++.| +..+++|.+++.+. -|..+||+||......
T Consensus 75 v~~ir~~~~~~~~~p~~~---------~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~ 134 (313)
T PRK05564 75 VDDIRNIIEEVNKKPYEG---------DKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE 134 (313)
T ss_pred HHHHHHHHHHHhcCcccC---------CceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence 456888898888877754 33456666665542 2667899999764433
No 48
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=35.22 E-value=30 Score=25.30 Aligned_cols=21 Identities=29% Similarity=0.476 Sum_probs=17.7
Q ss_pred cchHHHHhhhCCCHHHHHHHH
Q 028148 177 RDIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkAL 197 (213)
-||+-||..+|.||++|.=.+
T Consensus 45 a~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999996444
No 49
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.02 E-value=62 Score=27.49 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=33.3
Q ss_pred ccCcCHHHHHHHHHHcCCee-------------cCCceEEEEEecCceEEEecCC
Q 028148 64 KQSRSEKKSRKAMLKLGMKP-------------VTGVSRVTIKRTKNILFFISKP 105 (213)
Q Consensus 64 k~sr~eKK~rK~mkKLGlk~-------------V~gV~rVtIrk~dn~lfvI~~P 105 (213)
..|=.-+.++.+++.|||+- =+|=.||.|++.+|.+|+|.-|
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 44556688999999999982 2466789999889999998875
No 50
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.92 E-value=54 Score=21.08 Aligned_cols=22 Identities=32% Similarity=0.335 Sum_probs=18.6
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028148 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke 199 (213)
.+.-+++..||||.-+.++|+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999999888865
No 51
>PHA01748 hypothetical protein
Probab=33.66 E-value=51 Score=23.26 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.3
Q ss_pred cchHHHHhhhCCCHHHHHHHH
Q 028148 177 RDIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkAL 197 (213)
+-++..+.+.|+||+++|+..
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 357788999999999998844
No 52
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=33.48 E-value=2.6e+02 Score=25.86 Aligned_cols=104 Identities=13% Similarity=0.180 Sum_probs=64.7
Q ss_pred cCcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEe---------e---CCCceEEEeccceecchhhHHH
Q 028148 65 QSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFK---------S---PNSETYVIFGEAKIEDLSTQLQ 132 (213)
Q Consensus 65 ~sr~eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~PdVyK---------s---pgsdTYvVFGEak~eD~s~q~q 132 (213)
.+..=.++|.+.+++.+++..|-.| +|+|..++-+. . |..+||.|+-....+.+-..+.
T Consensus 86 ~~I~idqiR~l~~~~~~~~~~g~~k---------V~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIr 156 (334)
T PRK07993 86 SSLGVDAVREVTEKLYEHARLGGAK---------VVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLR 156 (334)
T ss_pred ccCCHHHHHHHHHHHhhccccCCce---------EEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHH
Confidence 4566789999999999998765544 45555555542 2 7788888887766554432222
Q ss_pred HHHHHhhcCCCCCCCCCCCCcchhhccCCCCcchhhhccCCCCccchH-HHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028148 133 TQAAQQFRMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDID-LVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 133 ~~aae~~~~~~~~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIe-LVmeQagvSRekAvkALke~nGDIV~AI 208 (213)
+.- +.+..+ -++.+.+. ...++.|++.++|..+++-++|.+..|+
T Consensus 157 SRC-q~~~~~------------------------------~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al 202 (334)
T PRK07993 157 SRC-RLHYLA------------------------------PPPEQYALTWLSREVTMSQDALLAALRLSAGAPGAAL 202 (334)
T ss_pred hcc-ccccCC------------------------------CCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHH
Confidence 110 011100 12334554 3445668888888888888888887775
No 53
>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=33.35 E-value=86 Score=22.54 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=29.9
Q ss_pred cchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 177 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
.=|..++.|||...+=+.+.|..+|-|.=.|+-.+
T Consensus 14 ~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 14 EMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 35778889999999999999999999998887543
No 54
>smart00400 ZnF_CHCC zinc finger.
Probab=33.03 E-value=46 Score=22.50 Aligned_cols=20 Identities=35% Similarity=0.340 Sum_probs=18.2
Q ss_pred chHHHHhhhCCCHHHHHHHH
Q 028148 178 DIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkAL 197 (213)
=|.|||.--|+|-.+|++-|
T Consensus 35 ~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 35 VISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred HHHHHHHHHCcCHHHHHHHh
Confidence 49999999999999999876
No 55
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.50 E-value=26 Score=34.32 Aligned_cols=21 Identities=38% Similarity=0.661 Sum_probs=10.4
Q ss_pred CCCCceecCCCCCCcCCCCCC
Q 028148 23 EDEPVVEDVKDDEEEDDDHDN 43 (213)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~ 43 (213)
...|+-||++|||++|||++.
T Consensus 267 ~~ss~~edD~Dddd~dDdeeN 287 (514)
T KOG3130|consen 267 GSSSYHEDDDDDDDDDDDEEN 287 (514)
T ss_pred CCCCccccccccccccchhhc
Confidence 344555555555444444443
No 56
>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=32.26 E-value=30 Score=35.46 Aligned_cols=12 Identities=17% Similarity=-0.006 Sum_probs=5.9
Q ss_pred HHHHHHHHHcCC
Q 028148 70 KKSRKAMLKLGM 81 (213)
Q Consensus 70 KK~rK~mkKLGl 81 (213)
.+++++|..-+.
T Consensus 706 ~~l~~aL~~~~~ 717 (784)
T PF04931_consen 706 SALAKALGDADA 717 (784)
T ss_pred HHHHHHhccccc
Confidence 345555554443
No 57
>PHA01623 hypothetical protein
Probab=32.22 E-value=56 Score=22.87 Aligned_cols=20 Identities=5% Similarity=0.240 Sum_probs=17.3
Q ss_pred cchHHHHhhhCCCHHHHHHH
Q 028148 177 RDIDLVMTQAGVSRSKAVKA 196 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkA 196 (213)
.-++..+.+-|++|+++|+-
T Consensus 26 ~~Ld~y~~~~g~~rSe~Ire 45 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIEE 45 (56)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 46788999999999999883
No 58
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=31.40 E-value=42 Score=34.79 Aligned_cols=24 Identities=42% Similarity=0.610 Sum_probs=21.4
Q ss_pred hhhCCCHHHHHHHHHhcCCcHHHH
Q 028148 184 TQAGVSRSKAVKALKTHNGDIVSA 207 (213)
Q Consensus 184 eQagvSRekAvkALke~nGDIV~A 207 (213)
--.|.+|..||+||+.+||+|-.|
T Consensus 643 ~smGf~~~qa~~aL~~~n~nvera 666 (763)
T KOG0944|consen 643 VSMGFSRNQAIKALKATNNNVERA 666 (763)
T ss_pred eeecCcHHHHHHHHHhcCccHHHH
Confidence 346999999999999999999776
No 59
>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=30.67 E-value=64 Score=21.13 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=18.2
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028148 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke 199 (213)
-+.-++.++|+||..+.++|+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3566899999999998888865
No 60
>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=30.25 E-value=40 Score=28.65 Aligned_cols=54 Identities=24% Similarity=0.388 Sum_probs=18.5
Q ss_pred HHHHHHHHHHcCCeecCCceEEEE-----EecC-ceEEEecCC----eE---EeeCCCceEEEeccc
Q 028148 69 EKKSRKAMLKLGMKPVTGVSRVTI-----KRTK-NILFFISKP----DV---FKSPNSETYVIFGEA 122 (213)
Q Consensus 69 eKK~rK~mkKLGlk~V~gV~rVtI-----rk~d-n~lfvI~~P----dV---yKspgsdTYvVFGEa 122 (213)
.++++++|++||.++|..+..-++ ..+. ...+-+..= +| |..-++.|||++|.|
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 567889999999998765543211 1111 001111111 11 223578899999987
No 61
>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=29.28 E-value=47 Score=27.97 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=16.9
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028148 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVmeQagvSRekAvkALke 199 (213)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 62
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.89 E-value=48 Score=28.38 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=17.0
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028148 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVmeQagvSRekAvkALke 199 (213)
-.|++-||||..+++||..
T Consensus 40 eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 40 QLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 63
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=28.09 E-value=89 Score=23.91 Aligned_cols=39 Identities=18% Similarity=0.257 Sum_probs=25.8
Q ss_pred CcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCC
Q 028148 66 SRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKP 105 (213)
Q Consensus 66 sr~eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~P 105 (213)
.-....+..+|++-|+..+.+|..+++... |.+.||.+.
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 334567788899999999999999999965 657676665
No 64
>PF13276 HTH_21: HTH-like domain
Probab=27.69 E-value=51 Score=22.38 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=16.0
Q ss_pred CcCHHHHHHHHHHcCCeec
Q 028148 66 SRSEKKSRKAMLKLGMKPV 84 (213)
Q Consensus 66 sr~eKK~rK~mkKLGlk~V 84 (213)
.-|.|+++++|++|||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 4678999999999999743
No 65
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=27.66 E-value=44 Score=27.59 Aligned_cols=23 Identities=13% Similarity=0.091 Sum_probs=19.5
Q ss_pred chHHHHhhhCCCHHHHHHHHHhc
Q 028148 178 DIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 178 DIeLVmeQagvSRekAvkALke~ 200 (213)
.+--.|.+||||-.+|+.|.-+.
T Consensus 104 TlaELm~~T~Ctl~eAR~ARf~~ 126 (128)
T PF12614_consen 104 TLAELMAATHCTLAEARRARFEA 126 (128)
T ss_pred cHHHHHHHhCCcHHHHHHHhhhc
Confidence 56678999999999999997553
No 66
>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=26.40 E-value=57 Score=27.65 Aligned_cols=19 Identities=42% Similarity=0.438 Sum_probs=16.8
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028148 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVmeQagvSRekAvkALke 199 (213)
-.|++.||||...++||..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999875
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=26.35 E-value=33 Score=23.51 Aligned_cols=31 Identities=23% Similarity=0.254 Sum_probs=24.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM 209 (213)
|.-++.|||...+=+.+-|.+|+-|+=.|+-
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 5567899999999999999999999877653
No 68
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=25.89 E-value=55 Score=35.49 Aligned_cols=14 Identities=21% Similarity=-0.054 Sum_probs=10.2
Q ss_pred ccchHHHHhhhCCC
Q 028148 176 PRDIDLVMTQAGVS 189 (213)
Q Consensus 176 eeDIeLVmeQagvS 189 (213)
.++.++||+-.+-|
T Consensus 1490 Dee~~~~~~d~~ss 1503 (1516)
T KOG1832|consen 1490 DEEDDGEMQDFMSS 1503 (1516)
T ss_pred chhhhhhhhcccCC
Confidence 35677888887766
No 69
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=24.56 E-value=69 Score=26.47 Aligned_cols=93 Identities=23% Similarity=0.339 Sum_probs=56.8
Q ss_pred CCceEEEEEec-CceEEEecCCe--EEeeCCCceEEEeccceecchhhHHHHHHHHhhcCCCCCCCCCCCCcchhhccCC
Q 028148 85 TGVSRVTIKRT-KNILFFISKPD--VFKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPDMGSVMAKPDASSAAAGAQ 161 (213)
Q Consensus 85 ~gV~rVtIrk~-dn~lfvI~~Pd--VyKspgsdTYvVFGEak~eD~s~q~q~~aae~~~~~~~~~~~~~~~~~~~~~~~~ 161 (213)
.|| +.|+.+ +|+++.|.++. +.-...+.+..++|..+.-..+.|+.+..+++-
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 455 455544 47888898885 444344566778887765555555443322221
Q ss_pred CCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028148 162 QDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 162 ~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke~nGDIV~AIM~L 211 (213)
..+-|| +.|++++.=.|--|+-|++||-.. |.-|..|+..
T Consensus 74 -------a~e~Gi--~~v~v~vkgpG~GreaAiraL~~a-g~~i~~I~Dv 113 (129)
T COG0100 74 -------AKEHGI--KSVEVKVKGPGPGREAAIRALAAA-GLKITRIEDV 113 (129)
T ss_pred -------HHHhCc--cEEEEEEECCCCcHHHHHHHHHHc-cceEEEEEEc
Confidence 112344 477777777899999999999855 5444444443
No 70
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=23.90 E-value=68 Score=27.17 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=16.9
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028148 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVmeQagvSRekAvkALke 199 (213)
-++++.||||.-.++||+.
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4799999999999999874
No 71
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=23.87 E-value=97 Score=21.31 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=19.7
Q ss_pred cchHHHHhhhCCCHHHHHHHHHh
Q 028148 177 RDIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 177 eDIeLVmeQagvSRekAvkALke 199 (213)
-.+.-++..+|+||..+.++|+.
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 35677899999999999999975
No 72
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.60 E-value=84 Score=22.71 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=21.7
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 207 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~A 207 (213)
|+.|.+++|+|+..+..+|..--.=|.++
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
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.18 E-value=71 Score=27.28 Aligned_cols=19 Identities=37% Similarity=0.279 Sum_probs=16.7
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028148 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVmeQagvSRekAvkALke 199 (213)
-.|++.||||..+++||..
T Consensus 38 eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 38 ELCTQYNVSRITIRKAISD 56 (241)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 3689999999999999964
No 74
>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=23.17 E-value=86 Score=23.75 Aligned_cols=76 Identities=25% Similarity=0.309 Sum_probs=45.0
Q ss_pred HHHHHHHHcCCeecCCceEEEEEecCceEEEe-------cCCeEEeeCCCceEEEeccceecchhhHHHHHHHHhhcCCC
Q 028148 71 KSRKAMLKLGMKPVTGVSRVTIKRTKNILFFI-------SKPDVFKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPD 143 (213)
Q Consensus 71 K~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI-------~~PdVyKspgsdTYvVFGEak~eD~s~q~q~~aae~~~~~~ 143 (213)
.+..+..++-|..|-.-- +.+++.++. +.. .+|..+-.+..++|-.||--.-
T Consensus 5 ~~~~i~~~~~i~~v~~~~-~~l~~~G~~-~~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~~------------------- 63 (97)
T PF01807_consen 5 FIEEIKSRIDIVDVIERY-IKLKRRGRE-YRCLCPFHDDKTPSFSINPDKNRFKCFGCGKG------------------- 63 (97)
T ss_dssp HHHHHHHCS-HHHHHCCC-S--EEETTE-EEE--SSS--SS--EEEETTTTEEEETTT--E-------------------
T ss_pred HHHHHHHhCCHHHHHHHh-ccccccCCe-EEEECcCCCCCCCceEEECCCCeEEECCCCCC-------------------
Confidence 344555566665442222 566666543 555 4576677788889999984110
Q ss_pred CCCCCCCCCcchhhccCCCCcchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHh
Q 028148 144 MGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~~~e~eeevde~gv~eeDIeLVmeQagvSRekAvkALke 199 (213)
| .=|.|||.--|||--+|++-|.+
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 34999999999999999999976
No 75
>PRK00523 hypothetical protein; Provisional
Probab=22.55 E-value=66 Score=24.16 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.7
Q ss_pred cCHHHHHHHHHHcCCee
Q 028148 67 RSEKKSRKAMLKLGMKP 83 (213)
Q Consensus 67 r~eKK~rK~mkKLGlk~ 83 (213)
-+|+.+|.||.+||-|+
T Consensus 40 ine~mir~M~~QMGqKP 56 (72)
T PRK00523 40 ITENMIRAMYMQMGRKP 56 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
No 76
>PRK14999 histidine utilization repressor; Provisional
Probab=22.47 E-value=74 Score=27.21 Aligned_cols=20 Identities=30% Similarity=0.375 Sum_probs=17.2
Q ss_pred HHHHhhhCCCHHHHHHHHHh
Q 028148 180 DLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 180 eLVmeQagvSRekAvkALke 199 (213)
.-.|++.||||...++||..
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRE 59 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999964
No 77
>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=22.24 E-value=1.9e+02 Score=22.08 Aligned_cols=33 Identities=27% Similarity=0.325 Sum_probs=21.7
Q ss_pred eEEEEEec-CceEEEecCCeEEeeCCCceEEEecccee
Q 028148 88 SRVTIKRT-KNILFFISKPDVFKSPNSETYVIFGEAKI 124 (213)
Q Consensus 88 ~rVtIrk~-dn~lfvI~~PdVyKspgsdTYvVFGEak~ 124 (213)
.+|.++-. .+. .+..-.+|-. .+++||||+...
T Consensus 19 VKvYv~G~l~~~--~~~~~~~fg~--~~~~vvfGd~~~ 52 (83)
T PF08503_consen 19 VKVYVKGDLAGI--DFEDVKVFGS--GNFGVVFGDWDE 52 (83)
T ss_dssp EEEEEEESCTC-----TTSEEEEE--SSEEEEEEEHHH
T ss_pred EEEEEeeeecCC--ChhheEEEeC--CCcEEEEecHHH
Confidence 37777755 343 3477788875 578999998643
No 78
>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=22.01 E-value=2.2e+02 Score=18.83 Aligned_cols=32 Identities=28% Similarity=0.392 Sum_probs=21.0
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCC
Q 028148 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKP 105 (213)
Q Consensus 69 eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfvI~~P 105 (213)
.++++++|++ ++||..|.+-...+.+-+.-+|
T Consensus 13 ~~~v~~~l~~-----~~GV~~v~vd~~~~~v~v~~~~ 44 (62)
T PF00403_consen 13 AKKVEKALSK-----LPGVKSVKVDLETKTVTVTYDP 44 (62)
T ss_dssp HHHHHHHHHT-----STTEEEEEEETTTTEEEEEEST
T ss_pred HHHHHHHHhc-----CCCCcEEEEECCCCEEEEEEec
Confidence 3566777765 4788888888776655444333
No 79
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=21.99 E-value=91 Score=24.81 Aligned_cols=32 Identities=28% Similarity=0.374 Sum_probs=25.1
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIME 210 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM~ 210 (213)
.--|..++|+||+--.|||...+|=-...||+
T Consensus 52 MsqvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 52 MSQVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 34578899999999999999987765555544
No 80
>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=21.94 E-value=92 Score=22.28 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=21.8
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 207 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~A 207 (213)
|+.|++.+|+|+..|...|..--.=|.++
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~~i~~~ 34 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLDVITEA 34 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999887653333333
No 81
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=21.78 E-value=97 Score=30.74 Aligned_cols=60 Identities=25% Similarity=0.490 Sum_probs=41.0
Q ss_pred ccCcCHHHHHHHHHHcCCeecCCceEEEEEecCc----------------------------------eEEEecCCeEEe
Q 028148 64 KQSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKN----------------------------------ILFFISKPDVFK 109 (213)
Q Consensus 64 k~sr~eKK~rK~mkKLGlk~V~gV~rVtIrk~dn----------------------------------~lfvI~~PdVyK 109 (213)
-|+.-++++-++|++||++. | |.-|.+||+|. +.+.-..|.|.+
T Consensus 343 pqp~t~~~l~~a~k~lg~~~-P-ivGvhvRRTDKVGTEAAfH~~eEYM~~vE~~f~~le~rg~~~~rRiflAsDDp~vv~ 420 (580)
T KOG3705|consen 343 PQPATQEKLDKALKSLGLDK-P-IVGVHVRRTDKVGTEAAFHALEEYMEWVEIWFKVLEKRGKPLERRIFLASDDPTVVP 420 (580)
T ss_pred CChhhHHHHHHHHHhCCCCC-c-eeeEEEEecccccchhhhhhHHHHHHHHHHHHHHHHHhCCchhheEEEecCCchhch
Confidence 36777899999999999985 2 45677777763 233456677765
Q ss_pred eCCC--ceEEEeccceec
Q 028148 110 SPNS--ETYVIFGEAKIE 125 (213)
Q Consensus 110 spgs--dTYvVFGEak~e 125 (213)
-... -.|.|+|..++-
T Consensus 421 EAk~kYPnYe~igd~eia 438 (580)
T KOG3705|consen 421 EAKNKYPNYEVIGDTEIA 438 (580)
T ss_pred HhhccCCCcEEeccHHHH
Confidence 2111 268899987653
No 82
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.27 E-value=1e+02 Score=20.63 Aligned_cols=22 Identities=32% Similarity=0.433 Sum_probs=18.6
Q ss_pred hHHHHhhhCCCHHHHHHHHHhc
Q 028148 179 IDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~ 200 (213)
|+-|...+|||+...-++|...
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHHCcCHHHHHHHHhCC
Confidence 5668899999999999999654
No 83
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=21.14 E-value=52 Score=36.99 Aligned_cols=26 Identities=46% Similarity=0.975 Sum_probs=0.0
Q ss_pred ecCCCCCCcCCCCCCCCCCCCccCCc
Q 028148 29 EDVKDDEEEDDDHDNDDDDEDDDDNK 54 (213)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 54 (213)
++-+++++||++.++++||+++++++
T Consensus 1739 ddnddddddd~EaEdddDddDdDdeD 1764 (3015)
T KOG0943|consen 1739 DDNDDDDDDDAEAEDDDDDDDDDDED 1764 (3015)
T ss_pred cccccccccchhhccccccccccccc
No 84
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=20.84 E-value=1.8e+02 Score=28.82 Aligned_cols=54 Identities=19% Similarity=0.289 Sum_probs=39.4
Q ss_pred CCccCcCHHHHHHHHHHcCCee-cCCceEEEEEecCceEEEecCCeE-EeeCCCceEEE
Q 028148 62 SSKQSRSEKKSRKAMLKLGMKP-VTGVSRVTIKRTKNILFFISKPDV-FKSPNSETYVI 118 (213)
Q Consensus 62 ~~k~sr~eKK~rK~mkKLGlk~-V~gV~rVtIrk~dn~lfvI~~PdV-yKspgsdTYvV 118 (213)
+.+-+++|-.+++.|...||.. ..=.+.++++..+|.. -+||| .+.||+...||
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 3445899999999999999974 3335677777665542 37997 56798876555
No 85
>PF07717 OB_NTP_bind: Oligonucleotide/oligosaccharide-binding (OB)-fold; InterPro: IPR011709 This domain is found towards the C terminus of the DEAD-box helicases (IPR011545 from INTERPRO). In these helicases it appears to be always found in association with IPR007502 from INTERPRO. ; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=20.78 E-value=2.4e+02 Score=21.04 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=16.3
Q ss_pred cCceEEEe-cCCeEEeeCCCc------eEEEecccee
Q 028148 95 TKNILFFI-SKPDVFKSPNSE------TYVIFGEAKI 124 (213)
Q Consensus 95 ~dn~lfvI-~~PdVyKspgsd------TYvVFGEak~ 124 (213)
.++....+ .+..|+-.|+|- -|+||++.-.
T Consensus 54 ~~~~y~~~~~~~~v~iHPsS~l~~~~p~~vvy~e~~~ 90 (114)
T PF07717_consen 54 NKGSYKTLSNGQPVFIHPSSVLFKKPPKWVVYHELVR 90 (114)
T ss_dssp TTSSEEETTTG-EEEE-TTSTTTTTT-SEEEEEEEEE
T ss_pred CCCCEEEecCCCEEEEecCccccccccccchhhhhee
Confidence 44445555 334565555443 5999998543
No 86
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=20.37 E-value=1.2e+02 Score=28.30 Aligned_cols=32 Identities=28% Similarity=0.412 Sum_probs=28.4
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028148 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIME 210 (213)
Q Consensus 179 IeLVmeQagvSRekAvkALke~nGDIV~AIM~ 210 (213)
.-+||--+|+|.++|.+.|..|+|=|=+||=.
T Consensus 264 ~AIvm~~~~~~a~~A~~~L~~~~g~lr~Al~~ 295 (298)
T COG2103 264 LAIVMLLTGLSAEEAKRLLERAGGFLRQALSE 295 (298)
T ss_pred hHHHHHHhCCCHHHHHHHHHHccChHHHHHhh
Confidence 45799999999999999999999999888743
No 87
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=20.23 E-value=86 Score=25.35 Aligned_cols=28 Identities=29% Similarity=0.400 Sum_probs=21.2
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEE
Q 028148 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFF 101 (213)
Q Consensus 69 eKK~rK~mkKLGlk~V~gV~rVtIrk~dn~lfv 101 (213)
.+.+|.+|.++|+..|. |...++|.+|.
T Consensus 21 MaeLr~~l~~~Gf~~V~-----Tyi~SGNvvf~ 48 (137)
T PF08002_consen 21 MAELREALEDLGFTNVR-----TYIQSGNVVFE 48 (137)
T ss_dssp HHHHHHHHHHCT-EEEE-----EETTTTEEEEE
T ss_pred HHHHHHHHHHcCCCCce-----EEEeeCCEEEe
Confidence 89999999999998762 66667776655
No 88
>PRK01844 hypothetical protein; Provisional
Probab=20.12 E-value=79 Score=23.75 Aligned_cols=17 Identities=29% Similarity=0.559 Sum_probs=14.6
Q ss_pred cCHHHHHHHHHHcCCee
Q 028148 67 RSEKKSRKAMLKLGMKP 83 (213)
Q Consensus 67 r~eKK~rK~mkKLGlk~ 83 (213)
-+|+-+|.||.+||-|+
T Consensus 39 ine~mir~Mm~QMGqkP 55 (72)
T PRK01844 39 INEQMLKMMMMQMGQKP 55 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
Done!