Query 028211
Match_columns 212
No_of_seqs 157 out of 479
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:00:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028211.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028211hhsearch_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 6.2E-55 1.4E-59 372.1 16.6 156 56-212 54-209 (209)
2 PRK06369 nac nascent polypepti 100.0 1.1E-37 2.3E-42 247.6 11.3 106 66-212 5-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 5.3E-33 1.2E-37 222.2 7.7 113 66-212 6-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 2.6E-31 5.7E-36 211.1 11.0 101 69-212 12-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 6.6E-21 1.4E-25 134.0 6.6 58 68-125 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.6 3.4E-08 7.4E-13 83.0 3.5 64 65-128 38-101 (162)
7 PF00627 UBA: UBA/TS-N domain; 97.7 4.3E-05 9.4E-10 48.9 3.1 36 174-210 2-37 (37)
8 KOG3450 Huntingtin interacting 97.6 3.4E-05 7.4E-10 61.5 2.3 42 171-212 77-118 (119)
9 PF14555 UBA_4: UBA-like domai 95.5 0.026 5.6E-07 37.2 4.0 33 176-208 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.3 0.03 6.6E-07 35.2 3.8 32 178-210 5-36 (38)
11 smart00165 UBA Ubiquitin assoc 95.0 0.041 8.9E-07 34.5 3.7 28 183-210 9-36 (37)
12 COG2103 Predicted sugar phosph 86.1 0.92 2E-05 41.8 3.9 38 173-210 232-269 (298)
13 COG4008 Predicted metal-bindin 85.5 1.1 2.5E-05 37.2 3.8 35 172-208 112-146 (153)
14 PRK05441 murQ N-acetylmuramic 84.0 1.3 2.9E-05 40.2 4.0 37 174-210 235-271 (299)
15 cd05007 SIS_Etherase N-acetylm 78.7 1.3 2.8E-05 39.3 1.8 36 173-208 221-256 (257)
16 TIGR00274 N-acetylmuramic acid 78.6 2.7 5.8E-05 38.2 3.9 36 175-210 231-266 (291)
17 PF02845 CUE: CUE domain; Int 78.5 3.3 7.1E-05 26.8 3.3 33 178-210 5-38 (42)
18 PRK12570 N-acetylmuramic acid- 73.9 4.1 8.9E-05 37.0 3.8 36 175-210 232-267 (296)
19 PF10446 DUF2457: Protein of u 73.2 1.8 3.9E-05 42.1 1.4 10 114-123 193-202 (458)
20 smart00546 CUE Domain that may 71.6 6.4 0.00014 25.4 3.4 34 177-210 5-39 (43)
21 PF14474 RTC4: RTC4-like domai 71.4 4.2 9E-05 32.7 2.9 30 175-205 90-119 (124)
22 PF03474 DMA: DMRTA motif; In 68.0 6.3 0.00014 26.3 2.7 21 188-208 16-36 (39)
23 PF10411 DsbC_N: Disulfide bon 63.6 13 0.00029 25.7 3.9 40 72-121 2-50 (57)
24 PF11626 Rap1_C: TRF2-interact 61.8 11 0.00024 28.1 3.5 30 178-208 1-30 (87)
25 PF06970 RepA_N: Replication i 61.0 8.8 0.00019 28.4 2.7 22 177-198 54-75 (76)
26 PF02796 HTH_7: Helix-turn-hel 58.7 7.5 0.00016 25.5 1.8 23 177-199 23-45 (45)
27 PF05861 PhnI: Bacterial phosp 57.8 12 0.00025 35.7 3.5 33 178-210 45-78 (358)
28 PF13730 HTH_36: Helix-turn-he 56.5 14 0.0003 24.4 2.9 22 177-198 27-48 (55)
29 COG3626 PhnI Uncharacterized e 55.7 12 0.00025 35.1 3.1 33 178-210 45-78 (367)
30 PF12244 DUF3606: Protein of u 55.7 21 0.00046 25.0 3.8 30 175-204 20-49 (57)
31 PRK05441 murQ N-acetylmuramic 54.7 16 0.00035 33.2 3.9 33 178-210 266-298 (299)
32 TIGR00274 N-acetylmuramic acid 53.9 16 0.00035 33.2 3.7 30 178-207 261-290 (291)
33 TIGR00632 vsr DNA mismatch end 50.3 21 0.00046 28.8 3.5 35 60-94 16-56 (117)
34 COG1654 BirA Biotin operon rep 49.6 17 0.00037 27.3 2.6 25 179-203 23-50 (79)
35 PF06972 DUF1296: Protein of u 48.2 38 0.00083 24.6 4.1 33 178-210 9-42 (60)
36 PRK10877 protein disulfide iso 48.0 50 0.0011 28.8 5.7 43 68-121 23-72 (232)
37 PLN02150 terpene synthase/cycl 47.8 17 0.00038 27.8 2.5 25 175-199 7-31 (96)
38 PRK12570 N-acetylmuramic acid- 47.4 23 0.0005 32.2 3.7 30 178-207 262-291 (296)
39 KOG1071 Mitochondrial translat 45.0 23 0.0005 33.5 3.3 36 173-208 45-80 (340)
40 PF04931 DNA_pol_phi: DNA poly 43.8 19 0.00042 36.8 2.8 13 68-80 701-714 (784)
41 PF03861 ANTAR: ANTAR domain; 41.6 31 0.00067 23.6 2.8 22 178-199 19-40 (56)
42 PF00392 GntR: Bacterial regul 41.5 25 0.00055 24.1 2.3 21 178-198 27-47 (64)
43 KOG3130 Uncharacterized conser 39.4 22 0.00048 34.8 2.3 21 177-197 489-512 (514)
44 COG4004 Uncharacterized protei 37.7 61 0.0013 25.5 4.1 34 67-100 13-56 (96)
45 COG2188 PhnF Transcriptional r 36.6 29 0.00064 30.0 2.5 18 181-198 37-54 (236)
46 KOG0944 Ubiquitin-specific pro 36.0 32 0.00069 35.6 2.9 25 182-206 642-666 (763)
47 PF04931 DNA_pol_phi: DNA poly 36.0 24 0.00052 36.1 2.1 12 69-80 706-717 (784)
48 PF10975 DUF2802: Protein of u 34.5 32 0.00069 25.1 2.0 21 176-196 45-65 (70)
49 smart00804 TAP_C C-terminal do 34.3 82 0.0018 22.6 4.1 35 176-210 14-48 (63)
50 KOG1832 HIV-1 Vpr-binding prot 33.1 22 0.00047 38.3 1.3 27 29-55 1407-1433(1516)
51 PHA01748 hypothetical protein 32.9 54 0.0012 23.1 2.9 21 176-196 15-35 (60)
52 smart00345 HTH_GNTR helix_turn 32.7 58 0.0013 20.9 2.9 22 177-198 22-43 (60)
53 KOG0943 Predicted ubiquitin-pr 32.7 24 0.00052 39.3 1.6 11 189-199 1893-1903(3015)
54 smart00400 ZnF_CHCC zinc finge 32.4 49 0.0011 22.4 2.6 20 177-196 35-54 (55)
55 PF11699 CENP-C_C: Mif2/CENP-C 31.1 73 0.0016 24.1 3.6 35 82-119 39-73 (85)
56 PHA01623 hypothetical protein 31.1 61 0.0013 22.7 2.9 19 176-194 26-44 (56)
57 KOG3130 Uncharacterized conser 30.8 31 0.00067 33.8 1.8 19 24-42 268-286 (514)
58 PF08680 DUF1779: Protein of u 30.4 40 0.00088 28.6 2.3 54 68-121 131-197 (203)
59 cd07377 WHTH_GntR Winged helix 29.3 70 0.0015 20.9 2.9 22 177-198 27-48 (66)
60 PF04239 DUF421: Protein of un 28.7 78 0.0017 24.2 3.4 40 65-105 26-65 (99)
61 KOG3198 Signal recognition par 28.3 1E+02 0.0022 26.1 4.3 43 62-104 40-95 (152)
62 TIGR02325 C_P_lyase_phnF phosp 27.6 53 0.0012 27.6 2.6 19 180-198 37-55 (238)
63 PRK10079 phosphonate metabolis 27.5 53 0.0011 28.1 2.6 19 180-198 40-58 (241)
64 PF03943 TAP_C: TAP C-terminal 26.5 33 0.00071 23.5 0.9 31 178-208 4-34 (51)
65 PF12614 RRF_GI: Ribosome recy 25.4 49 0.0011 27.3 1.8 23 177-199 104-126 (128)
66 KOG0943 Predicted ubiquitin-pr 25.4 37 0.0008 38.0 1.4 7 98-104 1848-1854(3015)
67 smart00411 BHL bacterial (prok 25.3 74 0.0016 23.0 2.7 29 178-206 7-35 (90)
68 TIGR02404 trehalos_R_Bsub treh 25.0 63 0.0014 27.4 2.6 19 180-198 29-47 (233)
69 PF13276 HTH_21: HTH-like doma 24.7 62 0.0013 21.9 2.0 19 65-83 37-55 (60)
70 COG0100 RpsK Ribosomal protein 23.6 74 0.0016 26.2 2.6 93 84-210 18-113 (129)
71 cd00591 HU_IHF Integration hos 23.6 81 0.0018 22.6 2.6 29 178-206 6-34 (87)
72 COG3636 Predicted transcriptio 23.0 85 0.0018 24.9 2.7 31 179-209 53-83 (100)
73 PF01978 TrmB: Sugar-specific 22.9 1.1E+02 0.0023 21.1 3.0 23 176-198 23-45 (68)
74 PF01807 zf-CHC2: CHC2 zinc fi 22.8 89 0.0019 23.6 2.8 22 177-198 66-87 (97)
75 PRK04984 fatty acid metabolism 22.4 76 0.0016 26.9 2.6 19 180-198 36-54 (239)
76 PRK11402 DNA-binding transcrip 22.0 77 0.0017 27.0 2.6 19 180-198 38-56 (241)
77 PRK14897 unknown domain/DNA-di 21.9 1.3E+02 0.0028 30.1 4.3 27 69-95 330-356 (509)
78 PRK07993 DNA polymerase III su 21.8 5.1E+02 0.011 23.9 8.0 104 64-207 86-202 (334)
79 PRK14999 histidine utilization 21.2 82 0.0018 26.9 2.6 20 179-198 40-59 (241)
80 PF00403 HMA: Heavy-metal-asso 20.8 2.4E+02 0.0052 18.6 4.4 32 68-104 13-44 (62)
81 PF00216 Bac_DNA_binding: Bact 20.3 96 0.0021 22.2 2.4 29 178-206 7-35 (90)
82 PRK00523 hypothetical protein; 20.3 78 0.0017 23.7 1.9 17 66-82 40-56 (72)
83 PF00356 LacI: Bacterial regul 20.2 1.1E+02 0.0024 20.4 2.5 22 178-199 2-23 (46)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=6.2e-55 Score=372.07 Aligned_cols=156 Identities=64% Similarity=0.921 Sum_probs=139.0
Q ss_pred CCCCCCcccCcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecchhhHHHHHHH
Q 028211 56 DGAQGSSKQSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLSTQLQTQAA 135 (212)
Q Consensus 56 ~~~~~~~k~sr~eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfGeak~edls~q~q~~aa 135 (212)
..+.+++||||++||.||+|.||||++|+||+|||||+++|++|+|++|+|||+|+++||+|||+++++++++|+|.+|+
T Consensus 54 ~~~~~~akqsrsekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q~~aa 133 (209)
T KOG2239|consen 54 EEPVAKAKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQMQAA 133 (209)
T ss_pred ccchhhhhcchHHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhHHHHHHHHH
Confidence 45677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCCcchhhccCCCccchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028211 136 QQFRMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 212 (212)
Q Consensus 136 ~~~~~~~~~~~~~~~~~~~~a~~~~~~e~eeevd~~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~Lt~ 212 (212)
++|+.+..++........+. .+.++++++++||++||+.+||+|||+|+||||++||+|||+|+||||||||+||+
T Consensus 134 e~fk~~~~~~~~~~~~~~~~-~~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 134 ERFKVPQEAPGLIQEDTSAT-PPAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred HhccCCccccccccccccCC-CccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 99998776655444333331 11223456677999999999999999999999999999999999999999999985
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=1.1e-37 Score=247.56 Aligned_cols=106 Identities=30% Similarity=0.487 Sum_probs=97.0
Q ss_pred cCHHHHHHHHHHcCCe--ecCCceEEEEEecCceEEEecCCeEE--eeCCCceEEEeccceecchhhHHHHHHHHhhcCC
Q 028211 66 RSEKKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDVF--KSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 141 (212)
Q Consensus 66 r~eKK~rK~mkKLGlk--~I~gV~rVtIrk~d~~~fvI~~P~V~--ks~gs~TYvVfGeak~edls~q~q~~aa~~~~~~ 141 (212)
=||||+||||+||||+ +| ||+||+|++.+ ..|+|++|+|| +++|++||+|||+++.++++++.
T Consensus 5 ~nprk~rkmmkkmGik~e~i-~v~~V~Ir~~~-~~~Vi~~P~V~~m~~~g~~tY~I~Ge~~~e~~~~~~----------- 71 (115)
T PRK06369 5 MNPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKEAEK----------- 71 (115)
T ss_pred CCHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEeccEEeeccccc-----------
Confidence 4689999999999999 99 99999999987 89999999999 78999999999999997764310
Q ss_pred CCCCCCCCCCcchhhccCCCccchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028211 142 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 212 (212)
Q Consensus 142 ~~~~~~~~~~~~~~a~~~~~~e~eeevd~~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~Lt~ 212 (212)
+++|+++||+|||+||||||++|++||++||||||+|||.|+.
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 2479999999999999999999999999999999999999973
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.98 E-value=5.3e-33 Score=222.18 Aligned_cols=113 Identities=40% Similarity=0.611 Sum_probs=95.5
Q ss_pred cCHHHHHHHHHHcCC--eecCCceEEEEEecCceEEEecCCeEEe--eCCCceEEEeccceecchhhHHHHHHHHhhcCC
Q 028211 66 RSEKKSRKAMLKLGM--KPVTGVSRVTIKRTKNILFFISKPDVFK--SPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 141 (212)
Q Consensus 66 r~eKK~rK~mkKLGl--k~I~gV~rVtIrk~d~~~fvI~~P~V~k--s~gs~TYvVfGeak~edls~q~q~~aa~~~~~~ 141 (212)
=|+|+|+|+|++||| ++|+||.||+|++.++. |+|++|.||. ++|+.||+|.|.+.. .++
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 468999999999995 59999999999998876 9999999986 589999999997630 000
Q ss_pred CCCCCCCCCCcchhhccCCCccchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028211 142 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 212 (212)
Q Consensus 142 ~~~~~~~~~~~~~~a~~~~~~e~eeevd~~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~Lt~ 212 (212)
. +..++..+++.+|+++||+|||+||||||++|||||+++|||||+|||+||.
T Consensus 70 ---------------~---~~~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 70 ---------------V---KKPEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred ---------------c---ccchhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 0 1123445677789999999999999999999999999999999999999984
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=2.6e-31 Score=211.13 Aligned_cols=101 Identities=34% Similarity=0.513 Sum_probs=86.9
Q ss_pred HHHHHHHHHcCCe--ecCCceEEEEEecCceEEEecCCeE--EeeCCCceEEEeccceecchhhHHHHHHHHhhcCCCCC
Q 028211 69 KKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDV--FKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPDMG 144 (212)
Q Consensus 69 KK~rK~mkKLGlk--~I~gV~rVtIrk~d~~~fvI~~P~V--~ks~gs~TYvVfGeak~edls~q~q~~aa~~~~~~~~~ 144 (212)
|+||+||+||||+ ++. |.+|+|++.++ .++|++|+| |+++|+.||||||+++.+++..
T Consensus 12 ~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~~---------------- 73 (116)
T TIGR00264 12 KQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVEE---------------- 73 (116)
T ss_pred HHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeeccc----------------
Confidence 3999999999998 466 99999999765 567999987 6789999999999998642210
Q ss_pred CCCCCCCcchhhccCCCccchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028211 145 SVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 212 (212)
Q Consensus 145 ~~~~~~~~~~~a~~~~~~e~eeevd~~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~Lt~ 212 (212)
..+|+++||+|||+||||||++|++||++||||||+|||.|+.
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=99.83 E-value=6.6e-21 Score=134.04 Aligned_cols=58 Identities=48% Similarity=0.824 Sum_probs=48.3
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecc
Q 028211 68 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIED 125 (212)
Q Consensus 68 eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfGeak~ed 125 (212)
|||||++|+||||++|+||.||+|++.+|.+|+|++|+||+++|++||+|||++++++
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=98.59 E-value=3.4e-08 Score=83.04 Aligned_cols=64 Identities=23% Similarity=0.468 Sum_probs=60.6
Q ss_pred CcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccceecchhh
Q 028211 65 SRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLST 128 (212)
Q Consensus 65 sr~eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfGeak~edls~ 128 (212)
....||++.-|+||++..|+||.+|.|++.++.+++|++|.|.++...+||.|+|.++.+.++.
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 6778999999999999999999999999999999999999999999999999999999887654
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=97.67 E-value=4.3e-05 Score=48.85 Aligned_cols=36 Identities=31% Similarity=0.479 Sum_probs=31.4
Q ss_pred CccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 174 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 174 ~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
+++.|..+++. |+|++.|++||+.++||+-.||.-|
T Consensus 2 ~~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 2 DEEKVQQLMEM-GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CHHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 45788999999 9999999999999999999998754
No 8
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.60 E-value=3.4e-05 Score=61.53 Aligned_cols=42 Identities=31% Similarity=0.617 Sum_probs=39.2
Q ss_pred CCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028211 171 TGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 212 (212)
Q Consensus 171 ~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~Lt~ 212 (212)
..|..+||+|||...-+++.-|.+-|++++||+|.|+-.|++
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 458899999999999999999999999999999999998864
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=95.45 E-value=0.026 Score=37.16 Aligned_cols=33 Identities=24% Similarity=0.361 Sum_probs=27.5
Q ss_pred cchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 176 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 176 eDIeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
+-|.-.|+=|||++..|+..|+.+|+||-.||=
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=35.21 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=26.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
|..++ ..|.+++.|+.||+.++||+-.|+--|
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=95.00 E-value=0.041 Score=34.48 Aligned_cols=28 Identities=39% Similarity=0.542 Sum_probs=23.8
Q ss_pred hhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 183 TQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 183 ~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
...|.+++.|+.||+.++||+-.|+--|
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
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=86.12 E-value=0.92 Score=41.81 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=33.2
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 173 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 173 i~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
+-..-+.+||+-|||+|++|..+|++++|++=-||+-+
T Consensus 232 L~dRa~RIv~~aT~~~~~~A~~~L~~~~~~vK~AIvm~ 269 (298)
T COG2103 232 LRDRAVRIVMEATGCSAEEAEALLEEAGGNVKLAIVML 269 (298)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCccHhHHHHH
Confidence 44567899999999999999999999999998887654
No 13
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=85.54 E-value=1.1 Score=37.18 Aligned_cols=35 Identities=17% Similarity=0.250 Sum_probs=27.4
Q ss_pred CCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 172 GVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 172 gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
.+..+-++.+..- +||.++|++||.++| |+..|+-
T Consensus 112 ~~~~e~v~v~a~a-~v~~eeAr~aleeag-Dl~~A~k 146 (153)
T COG4008 112 EPPVEEVEVLADA-FVTPEEAREALEEAG-DLRTAMK 146 (153)
T ss_pred CCcHHHHHHHHHh-cCCHHHHHHHHHHcC-CHHHHHH
Confidence 4555667766654 599999999999995 9999853
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=83.99 E-value=1.3 Score=40.15 Aligned_cols=37 Identities=35% Similarity=0.529 Sum_probs=30.6
Q ss_pred CccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 174 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 174 ~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
-..=+.+||+-+|||+++|.++|..++|.+=-||+-+
T Consensus 235 ~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 235 VDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 3456778999999999999999999999998887644
No 15
>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=78.66 E-value=1.3 Score=39.33 Aligned_cols=36 Identities=42% Similarity=0.648 Sum_probs=30.8
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 173 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 173 i~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
+-..=+.+||+-+|||+++|.++|..++|++=-||+
T Consensus 221 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~~ 256 (257)
T cd05007 221 LRERAIRIVMEATGVSRDEAEAALEQAGGDVKTAIL 256 (257)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeeee
Confidence 334667889999999999999999999999877764
No 16
>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=78.56 E-value=2.7 Score=38.20 Aligned_cols=36 Identities=17% Similarity=0.279 Sum_probs=30.1
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 175 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 175 eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
..=+.+||+=+|||+++|.++|..++|.+=-||+-+
T Consensus 231 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~ 266 (291)
T TIGR00274 231 ARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMI 266 (291)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 455778899999999999999999999998887643
No 17
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=78.53 E-value=3.3 Score=26.82 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=22.4
Q ss_pred hHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~Qa-gvSRekAikALke~nGDIV~AIM~L 210 (212)
|..+.+-. +++++....+|+.++||+-.||-.|
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 6788888889999999986666554
No 18
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=73.90 E-value=4.1 Score=37.04 Aligned_cols=36 Identities=31% Similarity=0.496 Sum_probs=28.7
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 175 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 175 eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
..=+.+||+=+|||+++|.++|..++|.|=-||+-+
T Consensus 232 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~ 267 (296)
T PRK12570 232 ARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMI 267 (296)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHH
Confidence 355677888889999999999998888887777643
No 19
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=73.17 E-value=1.8 Score=42.12 Aligned_cols=10 Identities=20% Similarity=0.175 Sum_probs=5.9
Q ss_pred eEEEecccee
Q 028211 114 TYVIFGEAKI 123 (212)
Q Consensus 114 TYvVfGeak~ 123 (212)
|=.|-|..-+
T Consensus 193 TDFVCGTLDE 202 (458)
T PF10446_consen 193 TDFVCGTLDE 202 (458)
T ss_pred ccccCCCcCC
Confidence 4456676655
No 20
>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=71.60 E-value=6.4 Score=25.42 Aligned_cols=34 Identities=15% Similarity=0.237 Sum_probs=25.9
Q ss_pred chHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 177 DIDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 177 DIeLVm~Qa-gvSRekAikALke~nGDIV~AIM~L 210 (212)
.|+.+.+=. .+++..++..|+.++|++-.||=.|
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 7899999999999999998887554
No 21
>PF14474 RTC4: RTC4-like domain
Probab=71.43 E-value=4.2 Score=32.70 Aligned_cols=30 Identities=20% Similarity=0.315 Sum_probs=24.7
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHHH
Q 028211 175 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVS 205 (212)
Q Consensus 175 eeDIeLVm~QagvSRekAikALke~nGDIV~ 205 (212)
|==|.|||+-.||++++|++-|+++ .++-.
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 22
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=67.95 E-value=6.3 Score=26.26 Aligned_cols=21 Identities=43% Similarity=0.469 Sum_probs=16.5
Q ss_pred CHHHHHHHHHhcCCcHHHHHh
Q 028211 188 SRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 188 SRekAikALke~nGDIV~AIM 208 (212)
.|+.---.|.-+|||+|.||=
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 23
>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=63.63 E-value=13 Score=25.67 Aligned_cols=40 Identities=25% Similarity=0.627 Sum_probs=23.9
Q ss_pred HHHHHHc--CCe-------ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccc
Q 028211 72 RKAMLKL--GMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 121 (212)
Q Consensus 72 rK~mkKL--Glk-------~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfGea 121 (212)
++.|+++ |++ +++|+-+|++ +..+ + +|.+..+ .|+|+|..
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 4566666 555 6899999988 3333 3 2444433 68898964
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=61.80 E-value=11 Score=28.09 Aligned_cols=30 Identities=30% Similarity=0.238 Sum_probs=24.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
|+- |.++|.++.....||..+.||+..|..
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
>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=60.97 E-value=8.8 Score=28.45 Aligned_cols=22 Identities=32% Similarity=0.380 Sum_probs=19.8
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028211 177 DIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke 198 (212)
-|+-+|+-.|||+.++++++++
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 26
>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=58.68 E-value=7.5 Score=25.45 Aligned_cols=23 Identities=35% Similarity=0.423 Sum_probs=18.0
Q ss_pred chHHHHhhhCCCHHHHHHHHHhc
Q 028211 177 DIDLVMTQAGVSRSKAVKALKTH 199 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke~ 199 (212)
-|.-|+.++||||....+.|.+|
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 37788999999999999988764
No 27
>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=57.76 E-value=12 Score=35.67 Aligned_cols=33 Identities=33% Similarity=0.524 Sum_probs=27.7
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~Qagv-SRekAikALke~nGDIV~AIM~L 210 (212)
|+-||+..+. .++=|--|||.+.||+++||.-|
T Consensus 45 vdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLL 78 (358)
T PF05861_consen 45 VDRVMSEGSLYDPELAALAIKQARGDLIEAIFLL 78 (358)
T ss_pred HHHHhccccccCHHHHHHHHHHhcCCHHHHHHHH
Confidence 4457777764 78889999999999999999876
No 28
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.47 E-value=14 Score=24.41 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=19.4
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028211 177 DIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke 198 (212)
-++-++..+|+||....++|++
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 29
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=55.69 E-value=12 Score=35.10 Aligned_cols=33 Identities=45% Similarity=0.612 Sum_probs=26.8
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~Qagv-SRekAikALke~nGDIV~AIM~L 210 (212)
|+-||...++ .|+=|-=|||.+.||+++||+-|
T Consensus 45 VdRVM~EgslyDreLAALAikQa~GD~~EAIFLl 78 (367)
T COG3626 45 VDRVMTEGSLYDRELAALALKQASGDLVEAIFLL 78 (367)
T ss_pred HHHHhhccchhHHHHHHHHHHHhcchHHHHHHHH
Confidence 4556666654 68889999999999999999876
No 30
>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=55.68 E-value=21 Score=24.97 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=26.6
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhcCCcHH
Q 028211 175 PRDIDLVMTQAGVSRSKAVKALKTHNGDIV 204 (212)
Q Consensus 175 eeDIeLVm~QagvSRekAikALke~nGDIV 204 (212)
+-.|...+...|||.++...|.+..++++.
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~ 49 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLREAVRAVGNSRA 49 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHHCcCHH
Confidence 468999999999999999999999977753
No 31
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=54.73 E-value=16 Score=33.17 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=29.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
.-+||--+||+..+|.+.|..++|.|-.||=.+
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence 457899999999999999999999999988443
No 32
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=53.89 E-value=16 Score=33.21 Aligned_cols=30 Identities=30% Similarity=0.383 Sum_probs=26.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 207 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AI 207 (212)
.-++|-.+||+..+|++.|..++|.|-.||
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l 290 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQAL 290 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhh
Confidence 457889999999999999999999998775
No 33
>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=50.30 E-value=21 Score=28.75 Aligned_cols=35 Identities=17% Similarity=0.333 Sum_probs=27.7
Q ss_pred CCcccCcCHHHHHHHHHHcCCe------ecCCceEEEEEec
Q 028211 60 GSSKQSRSEKKSRKAMLKLGMK------PVTGVSRVTIKRT 94 (212)
Q Consensus 60 ~~~k~sr~eKK~rK~mkKLGlk------~I~gV~rVtIrk~ 94 (212)
-+++.++.|..++++|..+|++ .++|+--+++.+-
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 4577889999999999999997 2677766666654
No 34
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=49.63 E-value=17 Score=27.33 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=20.5
Q ss_pred HHHHhhhCCCH---HHHHHHHHhcCCcH
Q 028211 179 DLVMTQAGVSR---SKAVKALKTHNGDI 203 (212)
Q Consensus 179 eLVm~QagvSR---ekAikALke~nGDI 203 (212)
+-+.+..|||| .|.|++|++.+-+|
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 35678999999 57899999987765
No 35
>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=48.21 E-value=38 Score=24.57 Aligned_cols=33 Identities=24% Similarity=0.248 Sum_probs=26.3
Q ss_pred hHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028211 178 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 178 IeLVm~Qagv-SRekAikALke~nGDIV~AIM~L 210 (212)
|.-+=+=+|| |.++....|+++|.|.=+|.=+|
T Consensus 9 VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrL 42 (60)
T PF06972_consen 9 VQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRL 42 (60)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 4444556788 99999999999999997776555
No 36
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=47.97 E-value=50 Score=28.79 Aligned_cols=43 Identities=21% Similarity=0.486 Sum_probs=27.8
Q ss_pred HHHHHHHHHHcCCe-------ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEeccc
Q 028211 68 EKKSRKAMLKLGMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 121 (212)
Q Consensus 68 eKK~rK~mkKLGlk-------~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfGea 121 (212)
...+++.|.++|++ +|+|+-+|++. .+ + +|-++. ..|+|+|..
T Consensus 23 ~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~~--~~-i-------~Y~~~d-g~y~i~G~l 72 (232)
T PRK10877 23 DAAIQQTLAKLGIQSADIQPSPVAGMKTVLTE--SG-V-------LYITDD-GKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHHcCCceeEEccCCCCCeEEEEEC--Ce-E-------EEEcCC-CCEEEeeee
Confidence 36778888888876 57888888652 22 2 233333 358888863
No 37
>PLN02150 terpene synthase/cyclase family protein
Probab=47.79 E-value=17 Score=27.84 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=21.5
Q ss_pred ccchHHHHhhhCCCHHHHHHHHHhc
Q 028211 175 PRDIDLVMTQAGVSRSKAVKALKTH 199 (212)
Q Consensus 175 eeDIeLVm~QagvSRekAikALke~ 199 (212)
+.-|+--|.|-|||.++|++.|++-
T Consensus 7 aSsIeCYMke~g~seeeA~~~i~~l 31 (96)
T PLN02150 7 ANGVNCYMKQHGVTKEEAVSELKKM 31 (96)
T ss_pred hHHHHHHhccCCCCHHHHHHHHHHH
Confidence 3568999999999999999988753
No 38
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=47.44 E-value=23 Score=32.19 Aligned_cols=30 Identities=27% Similarity=0.392 Sum_probs=27.3
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 207 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AI 207 (212)
+-++|-.+|||.++|.+.|..++|.|-.||
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l 291 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAI 291 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHH
Confidence 567899999999999999999999998886
No 39
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=45.04 E-value=23 Score=33.45 Aligned_cols=36 Identities=25% Similarity=0.243 Sum_probs=32.4
Q ss_pred CCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 173 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 173 i~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
++...|+-.=+.||.|---.++||.++|||++.|--
T Consensus 45 ~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~ 80 (340)
T KOG1071|consen 45 SSKALLKKLREKTGASMVNCKKALEECGGDLVLAEE 80 (340)
T ss_pred ccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHH
Confidence 567789999999999999999999999999998853
No 40
>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=43.82 E-value=19 Score=36.78 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=7.6
Q ss_pred HHHHHHHHHH-cCC
Q 028211 68 EKKSRKAMLK-LGM 80 (212)
Q Consensus 68 eKK~rK~mkK-LGl 80 (212)
.++++..|.+ ||.
T Consensus 701 d~~~~~~l~~aL~~ 714 (784)
T PF04931_consen 701 DEEFRSALAKALGD 714 (784)
T ss_pred HHHHHHHHHHHhcc
Confidence 4566666554 665
No 41
>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=41.62 E-value=31 Score=23.55 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=17.3
Q ss_pred hHHHHhhhCCCHHHHHHHHHhc
Q 028211 178 IDLVMTQAGVSRSKAVKALKTH 199 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~ 199 (212)
+-++|.+.|||..+|.+.|+..
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 4689999999999999999863
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=41.46 E-value=25 Score=24.14 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=16.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHh
Q 028211 178 IDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke 198 (212)
..-++++.||||.-+++||..
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 355899999999999999864
No 43
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.38 E-value=22 Score=34.79 Aligned_cols=21 Identities=24% Similarity=0.287 Sum_probs=11.5
Q ss_pred chHHHHhhh---CCCHHHHHHHHH
Q 028211 177 DIDLVMTQA---GVSRSKAVKALK 197 (212)
Q Consensus 177 DIeLVm~Qa---gvSRekAikALk 197 (212)
-+.|+.+.+ -|||=||-+||-
T Consensus 489 ~~~~~~s~~~~krvs~fk~~r~~~ 512 (514)
T KOG3130|consen 489 EVLLEASEETGKRVSKFKAARLQQ 512 (514)
T ss_pred cceeecccccchhHHHHHHHHHhc
Confidence 344444443 366767666663
No 44
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.72 E-value=61 Score=25.52 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHcCCe----------ecCCceEEEEEecCceEEE
Q 028211 67 SEKKSRKAMLKLGMK----------PVTGVSRVTIKRTKNILFF 100 (212)
Q Consensus 67 ~eKK~rK~mkKLGlk----------~I~gV~rVtIrk~d~~~fv 100 (212)
.+-.+.++|..||.. -+||+++|.|+..++.+++
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 345677889999965 3688888888887765544
No 45
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=36.65 E-value=29 Score=30.00 Aligned_cols=18 Identities=44% Similarity=0.466 Sum_probs=16.2
Q ss_pred HHhhhCCCHHHHHHHHHh
Q 028211 181 VMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 181 Vm~QagvSRekAikALke 198 (212)
.++|.||||-.++|||..
T Consensus 37 La~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 37 LAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHCCcHHHHHHHHHH
Confidence 689999999999999965
No 46
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=36.02 E-value=32 Score=35.59 Aligned_cols=25 Identities=40% Similarity=0.619 Sum_probs=21.8
Q ss_pred HhhhCCCHHHHHHHHHhcCCcHHHH
Q 028211 182 MTQAGVSRSKAVKALKTHNGDIVSA 206 (212)
Q Consensus 182 m~QagvSRekAikALke~nGDIV~A 206 (212)
|--.|.+|..||+||+.+||+|-.|
T Consensus 642 i~smGf~~~qa~~aL~~~n~nvera 666 (763)
T KOG0944|consen 642 IVSMGFSRNQAIKALKATNNNVERA 666 (763)
T ss_pred eeeecCcHHHHHHHHHhcCccHHHH
Confidence 3346999999999999999999776
No 47
>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=35.97 E-value=24 Score=36.11 Aligned_cols=12 Identities=17% Similarity=-0.006 Sum_probs=6.4
Q ss_pred HHHHHHHHHcCC
Q 028211 69 KKSRKAMLKLGM 80 (212)
Q Consensus 69 KK~rK~mkKLGl 80 (212)
.+++++|..-+.
T Consensus 706 ~~l~~aL~~~~~ 717 (784)
T PF04931_consen 706 SALAKALGDADA 717 (784)
T ss_pred HHHHHHhccccc
Confidence 455666655443
No 48
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=34.50 E-value=32 Score=25.14 Aligned_cols=21 Identities=29% Similarity=0.476 Sum_probs=17.6
Q ss_pred cchHHHHhhhCCCHHHHHHHH
Q 028211 176 RDIDLVMTQAGVSRSKAVKAL 196 (212)
Q Consensus 176 eDIeLVm~QagvSRekAikAL 196 (212)
-||+-||..+|.||++|.=.+
T Consensus 45 a~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999996443
No 49
>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=34.31 E-value=82 Score=22.62 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=30.1
Q ss_pred cchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 176 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 176 eDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
.=|..++.|||...+=+.+.|..+|-|.=.|+-.+
T Consensus 14 ~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F 48 (63)
T smart00804 14 EMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNF 48 (63)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 45778899999999999999999999998887543
No 50
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=33.07 E-value=22 Score=38.33 Aligned_cols=27 Identities=30% Similarity=0.724 Sum_probs=0.0
Q ss_pred ecCCCCCCcCCCCCCCCCCCCcCCCcC
Q 028211 29 EDVKDDEEEDDDHDNDDDDEDDDDNKD 55 (212)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 (212)
+|.++|++.+|.|+|||+++++++++.
T Consensus 1407 ~DeeeD~e~Ed~dEddd~edd~D~dd~ 1433 (1516)
T KOG1832|consen 1407 SDEEEDDETEDEDEDDDEEDDLDRDDG 1433 (1516)
T ss_pred cCccccchhhccccccccccccccccc
No 51
>PHA01748 hypothetical protein
Probab=32.92 E-value=54 Score=23.10 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.3
Q ss_pred cchHHHHhhhCCCHHHHHHHH
Q 028211 176 RDIDLVMTQAGVSRSKAVKAL 196 (212)
Q Consensus 176 eDIeLVm~QagvSRekAikAL 196 (212)
+-++..+.+.|+||+++|+..
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 357788999999999999844
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.67 E-value=58 Score=20.88 Aligned_cols=22 Identities=32% Similarity=0.335 Sum_probs=18.5
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028211 177 DIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke 198 (212)
.+.-+++..||||.-+.++|+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999999888865
No 53
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=32.66 E-value=24 Score=39.33 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=5.1
Q ss_pred HHHHHHHHHhc
Q 028211 189 RSKAVKALKTH 199 (212)
Q Consensus 189 RekAikALke~ 199 (212)
|+.|..||.+.
T Consensus 1893 Raralealaar 1903 (3015)
T KOG0943|consen 1893 RARALEALAAR 1903 (3015)
T ss_pred HHHHHHHHHhh
Confidence 44444444443
No 54
>smart00400 ZnF_CHCC zinc finger.
Probab=32.37 E-value=49 Score=22.37 Aligned_cols=20 Identities=35% Similarity=0.340 Sum_probs=18.1
Q ss_pred chHHHHhhhCCCHHHHHHHH
Q 028211 177 DIDLVMTQAGVSRSKAVKAL 196 (212)
Q Consensus 177 DIeLVm~QagvSRekAikAL 196 (212)
=|.|||.--|+|-.+|++-|
T Consensus 35 ~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 35 VISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred HHHHHHHHHCcCHHHHHHHh
Confidence 48999999999999999876
No 55
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=31.10 E-value=73 Score=24.11 Aligned_cols=35 Identities=29% Similarity=0.472 Sum_probs=27.0
Q ss_pred ecCCceEEEEEecCceEEEecCCeEEeeCCCceEEEec
Q 028211 82 PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFG 119 (212)
Q Consensus 82 ~I~gV~rVtIrk~d~~~fvI~~P~V~ks~gs~TYvVfG 119 (212)
-+.|..+|+|- ++.|++..-..+..|..|+|-|--
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 47888899985 457999999999999999999864
No 56
>PHA01623 hypothetical protein
Probab=31.06 E-value=61 Score=22.65 Aligned_cols=19 Identities=5% Similarity=0.252 Sum_probs=16.9
Q ss_pred cchHHHHhhhCCCHHHHHH
Q 028211 176 RDIDLVMTQAGVSRSKAVK 194 (212)
Q Consensus 176 eDIeLVm~QagvSRekAik 194 (212)
.-++..+.+-|++|.++|+
T Consensus 26 ~~Ld~y~~~~g~~rSe~Ir 44 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIE 44 (56)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 4678899999999999988
No 57
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.79 E-value=31 Score=33.84 Aligned_cols=19 Identities=37% Similarity=0.678 Sum_probs=9.1
Q ss_pred CCCceecCCCCCCcCCCCC
Q 028211 24 DEPVVEDVKDDEEEDDDHD 42 (212)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~ 42 (212)
..|+-||++|||++|||++
T Consensus 268 ~ss~~edD~Dddd~dDdee 286 (514)
T KOG3130|consen 268 SSSYHEDDDDDDDDDDDEE 286 (514)
T ss_pred CCCccccccccccccchhh
Confidence 4455555555444444443
No 58
>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=30.40 E-value=40 Score=28.62 Aligned_cols=54 Identities=24% Similarity=0.388 Sum_probs=18.6
Q ss_pred HHHHHHHHHHcCCeecCCceEEEE-----EecC-ceEEEecCC----eE---EeeCCCceEEEeccc
Q 028211 68 EKKSRKAMLKLGMKPVTGVSRVTI-----KRTK-NILFFISKP----DV---FKSPNSETYVIFGEA 121 (212)
Q Consensus 68 eKK~rK~mkKLGlk~I~gV~rVtI-----rk~d-~~~fvI~~P----~V---~ks~gs~TYvVfGea 121 (212)
.++++++|++||.++|..+..-++ ..+. +..+-...= +| |...++.||+++|.|
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 567888999999998766543221 1111 001111111 22 224678899999987
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=29.34 E-value=70 Score=20.92 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=18.1
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028211 177 DIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke 198 (212)
-+.-++.++|+||..+.++|+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3566899999999998888765
No 60
>PF04239 DUF421: Protein of unknown function (DUF421); InterPro: IPR007353 This family of uncharacterised proteins is known as YDFR family; PDB: 3C6F_D.
Probab=28.65 E-value=78 Score=24.20 Aligned_cols=40 Identities=20% Similarity=0.292 Sum_probs=26.6
Q ss_pred CcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCe
Q 028211 65 SRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPD 105 (212)
Q Consensus 65 sr~eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P~ 105 (212)
.-....+..+|++-|+..+.+|..+++.. +|.+.+|.+.+
T Consensus 26 ~it~~dl~~~LR~~gi~~l~dV~~a~lE~-~G~lsv~~k~~ 65 (99)
T PF04239_consen 26 RITEEDLLSALREQGIESLSDVKAAVLEP-NGQLSVIKKED 65 (99)
T ss_dssp T--HHHHHHHHHHTT--SGGGEEEEEE-T-TS-EEEEE-GG
T ss_pred CCCHHHHHHHHHhhCCCCHHHcCEEEECC-CCCEEEEEcCC
Confidence 33456788889999999999999999996 47777777663
No 61
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.30 E-value=1e+02 Score=26.15 Aligned_cols=43 Identities=21% Similarity=0.291 Sum_probs=33.7
Q ss_pred cccCcCHHHHHHHHHHcCCee-------------cCCceEEEEEecCceEEEecCC
Q 028211 62 SKQSRSEKKSRKAMLKLGMKP-------------VTGVSRVTIKRTKNILFFISKP 104 (212)
Q Consensus 62 ~k~sr~eKK~rK~mkKLGlk~-------------I~gV~rVtIrk~d~~~fvI~~P 104 (212)
+.+|=.-+.++.+++.|||+- =+|=.||.|+..+|++|++.-|
T Consensus 40 aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~n~GRVRvqlk~edG~l~~~~~~ 95 (152)
T KOG3198|consen 40 AVENPLAKEIADVLRALGLNCLLEPNKKHPRDFVNPGRVRVQLKNEDGTLYVIAFI 95 (152)
T ss_pred hhcCcchhHHHHHHHHhCCcccccccccCchhcCCCceEEEEeeccCCcEEeecch
Confidence 345666788999999999982 2456788999889999998775
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=27.61 E-value=53 Score=27.65 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=16.8
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028211 180 LVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 180 LVm~QagvSRekAikALke 198 (212)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999965
No 63
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=27.55 E-value=53 Score=28.11 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=16.9
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028211 180 LVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 180 LVm~QagvSRekAikALke 198 (212)
-.+++.||||..+++||..
T Consensus 40 eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 40 QLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999975
No 64
>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=26.51 E-value=33 Score=23.49 Aligned_cols=31 Identities=23% Similarity=0.254 Sum_probs=24.9
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 208 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~AIM 208 (212)
|.-++.|||...+=+.+-|.+|+-|+=.|+-
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 5567899999999999999999999876654
No 65
>PF12614 RRF_GI: Ribosome recycling factor ; InterPro: IPR022253 This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression.
Probab=25.40 E-value=49 Score=27.30 Aligned_cols=23 Identities=13% Similarity=0.091 Sum_probs=19.2
Q ss_pred chHHHHhhhCCCHHHHHHHHHhc
Q 028211 177 DIDLVMTQAGVSRSKAVKALKTH 199 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke~ 199 (212)
.+--.|.+||||-.+|+.|.-+.
T Consensus 104 TlaELm~~T~Ctl~eAR~ARf~~ 126 (128)
T PF12614_consen 104 TLAELMAATHCTLAEARRARFEA 126 (128)
T ss_pred cHHHHHHHhCCcHHHHHHHhhhc
Confidence 56668999999999999997553
No 66
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=25.35 E-value=37 Score=38.03 Aligned_cols=7 Identities=43% Similarity=0.980 Sum_probs=3.3
Q ss_pred EEEecCC
Q 028211 98 LFFISKP 104 (212)
Q Consensus 98 ~fvI~~P 104 (212)
.|+|..|
T Consensus 1848 aFmiad~ 1854 (3015)
T KOG0943|consen 1848 AFMIADP 1854 (3015)
T ss_pred ceeecCC
Confidence 3445444
No 67
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.29 E-value=74 Score=22.99 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=21.7
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 206 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~A 206 (212)
|+.|.+++|+|+..+...|..--.=|.++
T Consensus 7 i~~ia~~~~~~~~~v~~vl~~l~~~i~~~ 35 (90)
T smart00411 7 IDAIAEKAGLSKKDAKAAVDAFLEIITEA 35 (90)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999998887653333333
No 68
>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=25.01 E-value=63 Score=27.36 Aligned_cols=19 Identities=42% Similarity=0.438 Sum_probs=16.7
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028211 180 LVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 180 LVm~QagvSRekAikALke 198 (212)
-.|++.||||...++||..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999875
No 69
>PF13276 HTH_21: HTH-like domain
Probab=24.74 E-value=62 Score=21.91 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=16.0
Q ss_pred CcCHHHHHHHHHHcCCeec
Q 028211 65 SRSEKKSRKAMLKLGMKPV 83 (212)
Q Consensus 65 sr~eKK~rK~mkKLGlk~I 83 (212)
.-|.|+++++|+++||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 4568999999999999743
No 70
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=23.60 E-value=74 Score=26.25 Aligned_cols=93 Identities=23% Similarity=0.339 Sum_probs=53.9
Q ss_pred CCceEEEEEec-CceEEEecCCe--EEeeCCCceEEEeccceecchhhHHHHHHHHhhcCCCCCCCCCCCCcchhhccCC
Q 028211 84 TGVSRVTIKRT-KNILFFISKPD--VFKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPDMGSVMAKPDASSAAAGAQ 160 (212)
Q Consensus 84 ~gV~rVtIrk~-d~~~fvI~~P~--V~ks~gs~TYvVfGeak~edls~q~q~~aa~~~~~~~~~~~~~~~~~~~~a~~~~ 160 (212)
.|| +.|..+ +|++++|.++. +.....+-+..++|..+.-..+.|+.++.+.+-
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 444444 46788888874 333233344566777655555554443322221
Q ss_pred CccchhhhccCCCCccchHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028211 161 QDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 210 (212)
Q Consensus 161 ~~e~eeevd~~gi~eeDIeLVm~QagvSRekAikALke~nGDIV~AIM~L 210 (212)
..+-|| +.|+.++.=.|--|+-|++||-.. |.-|..|+..
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 111344 477777777899999999999855 5555445443
No 71
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=23.58 E-value=81 Score=22.56 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=21.8
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 206 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~A 206 (212)
|+.|++.+|+|+..|...|..-..=|.++
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~~i~~~ 34 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLDVITEA 34 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999887654333333
No 72
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=22.99 E-value=85 Score=24.93 Aligned_cols=31 Identities=29% Similarity=0.359 Sum_probs=24.5
Q ss_pred HHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028211 179 DLVMTQAGVSRSKAVKALKTHNGDIVSAIME 209 (212)
Q Consensus 179 eLVm~QagvSRekAikALke~nGDIV~AIM~ 209 (212)
--|..++|+||+--.|||...+|=-...||+
T Consensus 53 sqvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 53 SQVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 3577899999999999999887755555544
No 73
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=22.91 E-value=1.1e+02 Score=21.11 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=19.6
Q ss_pred cchHHHHhhhCCCHHHHHHHHHh
Q 028211 176 RDIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 176 eDIeLVm~QagvSRekAikALke 198 (212)
-.+.-++..+|+||..+.++|+.
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 35667899999999999999875
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=22.84 E-value=89 Score=23.64 Aligned_cols=22 Identities=45% Similarity=0.451 Sum_probs=18.2
Q ss_pred chHHHHhhhCCCHHHHHHHHHh
Q 028211 177 DIDLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 177 DIeLVm~QagvSRekAikALke 198 (212)
=|.|||.--|||-.+|++-|.+
T Consensus 66 ~i~~v~~~~~~~f~eAv~~l~~ 87 (97)
T PF01807_consen 66 VIDFVMKYEGCSFKEAVKWLAE 87 (97)
T ss_dssp HHHHHHHHHT--HHHHHHHHHH
T ss_pred HHhHHHHHhCCCHHHHHHHHHH
Confidence 4899999999999999999876
No 75
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=22.44 E-value=76 Score=26.85 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=16.8
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028211 180 LVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 180 LVm~QagvSRekAikALke 198 (212)
-++++.||||.-.++||+.
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4799999999999999874
No 76
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=22.02 E-value=77 Score=27.01 Aligned_cols=19 Identities=37% Similarity=0.279 Sum_probs=16.6
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028211 180 LVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 180 LVm~QagvSRekAikALke 198 (212)
-.|++.||||..+++||..
T Consensus 38 eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 38 ELCTQYNVSRITIRKAISD 56 (241)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 3689999999999999964
No 77
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=21.85 E-value=1.3e+02 Score=30.09 Aligned_cols=27 Identities=15% Similarity=0.286 Sum_probs=20.4
Q ss_pred HHHHHHHHHcCCeecCCceEEEEEecC
Q 028211 69 KKSRKAMLKLGMKPVTGVSRVTIKRTK 95 (212)
Q Consensus 69 KK~rK~mkKLGlk~I~gV~rVtIrk~d 95 (212)
+++++.|.++-++-++||.||+|+..+
T Consensus 330 ~~l~~~l~~i~I~GipgI~r~~i~~~~ 356 (509)
T PRK14897 330 YLLAEKVKSLTIKGIKGIKRAIARKEN 356 (509)
T ss_pred HHHHHHhhccEEeCCCCccEEEEecCC
Confidence 445556666778899999999998654
No 78
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=21.83 E-value=5.1e+02 Score=23.85 Aligned_cols=104 Identities=15% Similarity=0.176 Sum_probs=62.4
Q ss_pred cCcCHHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCCeEE---------ee---CCCceEEEeccceecchhhHHH
Q 028211 64 QSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVF---------KS---PNSETYVIFGEAKIEDLSTQLQ 131 (212)
Q Consensus 64 ~sr~eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P~V~---------ks---~gs~TYvVfGeak~edls~q~q 131 (212)
.+..-..+|.+.+++.+++..|-.||+| |..++-+ |. |..+||.|+-......+-..+.
T Consensus 86 ~~I~idqiR~l~~~~~~~~~~g~~kV~i---------I~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIr 156 (334)
T PRK07993 86 SSLGVDAVREVTEKLYEHARLGGAKVVW---------LPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLR 156 (334)
T ss_pred ccCCHHHHHHHHHHHhhccccCCceEEE---------EcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHH
Confidence 4566788999999999998876555544 4444443 22 6777888777655443322222
Q ss_pred HHHHHhhcCCCCCCCCCCCCcchhhccCCCccchhhhccCCCCccchHH-HHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028211 132 TQAAQQFRMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDL-VMTQAGVSRSKAVKALKTHNGDIVSAI 207 (212)
Q Consensus 132 ~~aa~~~~~~~~~~~~~~~~~~~~a~~~~~~e~eeevd~~gi~eeDIeL-Vm~QagvSRekAikALke~nGDIV~AI 207 (212)
+.- +.+.. ..++.+.+.- ..++.|++.++|..+++-++|.+..|+
T Consensus 157 SRC-q~~~~------------------------------~~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al 202 (334)
T PRK07993 157 SRC-RLHYL------------------------------APPPEQYALTWLSREVTMSQDALLAALRLSAGAPGAAL 202 (334)
T ss_pred hcc-ccccC------------------------------CCCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHH
Confidence 110 01110 0123345543 445568888888888888888887775
No 79
>PRK14999 histidine utilization repressor; Provisional
Probab=21.23 E-value=82 Score=26.92 Aligned_cols=20 Identities=30% Similarity=0.375 Sum_probs=17.1
Q ss_pred HHHHhhhCCCHHHHHHHHHh
Q 028211 179 DLVMTQAGVSRSKAVKALKT 198 (212)
Q Consensus 179 eLVm~QagvSRekAikALke 198 (212)
.-.+++.||||..+++||..
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRE 59 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999964
No 80
>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=20.76 E-value=2.4e+02 Score=18.60 Aligned_cols=32 Identities=28% Similarity=0.392 Sum_probs=20.9
Q ss_pred HHHHHHHHHHcCCeecCCceEEEEEecCceEEEecCC
Q 028211 68 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKP 104 (212)
Q Consensus 68 eKK~rK~mkKLGlk~I~gV~rVtIrk~d~~~fvI~~P 104 (212)
.++++++|++ ++||..|.+-...+.+-+.-+|
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 4788888887776655444333
No 81
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=20.35 E-value=96 Score=22.24 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=22.0
Q ss_pred hHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028211 178 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 206 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~nGDIV~A 206 (212)
|+.|..++|+|+..+..+|..--.-|.++
T Consensus 7 i~~ia~~~~~s~~~v~~vl~~~~~~i~~~ 35 (90)
T PF00216_consen 7 IKRIAEKTGLSKKDVEAVLDALFDVIKEA 35 (90)
T ss_dssp HHHHHHHHTSSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 67888999999999999887654333333
No 82
>PRK00523 hypothetical protein; Provisional
Probab=20.33 E-value=78 Score=23.73 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.5
Q ss_pred cCHHHHHHHHHHcCCee
Q 028211 66 RSEKKSRKAMLKLGMKP 82 (212)
Q Consensus 66 r~eKK~rK~mkKLGlk~ 82 (212)
-+|+-+|.||.+||-|+
T Consensus 40 ine~mir~M~~QMGqKP 56 (72)
T PRK00523 40 ITENMIRAMYMQMGRKP 56 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46899999999999885
No 83
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=20.22 E-value=1.1e+02 Score=20.40 Aligned_cols=22 Identities=32% Similarity=0.433 Sum_probs=18.6
Q ss_pred hHHHHhhhCCCHHHHHHHHHhc
Q 028211 178 IDLVMTQAGVSRSKAVKALKTH 199 (212)
Q Consensus 178 IeLVm~QagvSRekAikALke~ 199 (212)
|+-|...+|||+...-++|-..
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 5668899999999999999554
Done!