Query 028127
Match_columns 213
No_of_seqs 164 out of 476
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 06:40:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028127hhsearch_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 6.5E-55 1.4E-59 372.4 16.7 154 58-213 56-209 (209)
2 PRK06369 nac nascent polypepti 100.0 1.1E-37 2.3E-42 247.8 11.6 106 67-213 5-114 (115)
3 COG1308 EGD2 Transcription fac 100.0 6.5E-33 1.4E-37 222.0 8.5 113 67-213 6-122 (122)
4 TIGR00264 alpha-NAC-related pr 100.0 1.1E-31 2.4E-36 213.6 10.8 107 64-213 6-116 (116)
5 PF01849 NAC: NAC domain; Int 99.8 6.6E-21 1.4E-25 134.2 6.7 58 69-126 1-58 (58)
6 KOG2240 RNA polymerase II gene 98.5 7.3E-08 1.6E-12 81.2 2.8 64 66-129 38-101 (162)
7 PF00627 UBA: UBA/TS-N domain; 97.7 5.2E-05 1.1E-09 48.6 3.3 37 174-211 1-37 (37)
8 KOG3450 Huntingtin interacting 97.5 7.3E-05 1.6E-09 59.8 2.4 43 171-213 76-118 (119)
9 PF14555 UBA_4: UBA-like domai 95.6 0.018 3.8E-07 38.0 3.5 33 177-209 2-34 (43)
10 cd00194 UBA Ubiquitin Associat 95.0 0.041 8.8E-07 34.7 3.7 32 179-211 5-36 (38)
11 smart00165 UBA Ubiquitin assoc 94.7 0.054 1.2E-06 34.0 3.7 32 179-211 5-36 (37)
12 COG4008 Predicted metal-bindin 85.2 1.3 2.7E-05 37.0 3.9 36 172-209 111-146 (153)
13 COG2103 Predicted sugar phosph 84.5 1.2 2.7E-05 41.1 3.9 38 174-211 232-269 (298)
14 PRK05441 murQ N-acetylmuramic 82.4 1.7 3.7E-05 39.5 4.0 38 174-211 234-271 (299)
15 PF02845 CUE: CUE domain; Int 76.9 3.9 8.4E-05 26.5 3.3 33 179-211 5-38 (42)
16 cd05007 SIS_Etherase N-acetylm 76.8 1.5 3.3E-05 38.8 1.8 36 174-209 221-256 (257)
17 TIGR00274 N-acetylmuramic acid 76.6 3.3 7.2E-05 37.6 4.0 36 175-210 230-265 (291)
18 PF10411 DsbC_N: Disulfide bon 74.4 7 0.00015 27.1 4.3 40 73-122 2-50 (57)
19 PF10446 DUF2457: Protein of u 73.4 1.8 3.9E-05 42.2 1.5 12 115-126 193-204 (458)
20 PRK12570 N-acetylmuramic acid- 71.4 5.1 0.00011 36.4 3.9 35 176-210 232-266 (296)
21 smart00546 CUE Domain that may 70.1 7.3 0.00016 25.2 3.4 34 178-211 5-39 (43)
22 PF03474 DMA: DMRTA motif; In 68.7 5.9 0.00013 26.4 2.7 21 189-209 16-36 (39)
23 PF14474 RTC4: RTC4-like domai 66.6 6.1 0.00013 31.8 3.0 32 174-206 88-119 (124)
24 PF10446 DUF2457: Protein of u 64.4 4 8.7E-05 39.9 1.7 8 89-96 121-128 (458)
25 PF05861 PhnI: Bacterial phosp 62.4 8.7 0.00019 36.5 3.5 33 179-211 45-78 (358)
26 COG3626 PhnI Uncharacterized e 60.4 8.7 0.00019 36.0 3.1 33 179-211 45-78 (367)
27 PF11626 Rap1_C: TRF2-interact 56.5 16 0.00035 27.3 3.5 30 179-209 1-30 (87)
28 PF06970 RepA_N: Replication i 56.4 12 0.00026 27.8 2.7 22 178-199 54-75 (76)
29 PRK10877 protein disulfide iso 56.3 29 0.00064 30.3 5.6 43 69-122 23-72 (232)
30 PRK05441 murQ N-acetylmuramic 54.3 17 0.00036 33.1 3.9 33 179-211 266-298 (299)
31 PF12244 DUF3606: Protein of u 54.2 25 0.00053 24.7 3.9 31 175-205 19-49 (57)
32 TIGR00274 N-acetylmuramic acid 53.2 17 0.00036 33.1 3.7 30 179-208 261-290 (291)
33 TIGR00632 vsr DNA mismatch end 51.6 21 0.00046 28.8 3.7 34 63-96 18-57 (117)
34 PLN02150 terpene synthase/cycl 49.2 16 0.00035 28.1 2.6 26 175-200 6-31 (96)
35 PF13730 HTH_36: Helix-turn-he 49.0 22 0.00048 23.5 2.9 22 178-199 27-48 (55)
36 PF02796 HTH_7: Helix-turn-hel 48.9 14 0.0003 24.2 1.8 23 178-200 23-45 (45)
37 PRK12570 N-acetylmuramic acid- 47.2 24 0.00052 32.2 3.7 30 179-208 262-291 (296)
38 PF04931 DNA_pol_phi: DNA poly 44.6 27 0.00059 35.7 4.1 13 69-81 701-714 (784)
39 COG4004 Uncharacterized protei 44.3 41 0.00089 26.5 4.1 33 69-101 14-56 (96)
40 KOG1071 Mitochondrial translat 44.2 26 0.00055 33.2 3.5 36 174-209 45-80 (340)
41 COG1654 BirA Biotin operon rep 44.0 24 0.00051 26.6 2.7 25 180-204 23-50 (79)
42 KOG3130 Uncharacterized conser 42.7 16 0.00034 35.8 1.9 21 178-198 489-512 (514)
43 PF03861 ANTAR: ANTAR domain; 42.2 30 0.00065 23.6 2.8 22 179-200 19-40 (56)
44 PF04931 DNA_pol_phi: DNA poly 40.8 19 0.0004 36.9 2.2 12 70-81 706-717 (784)
45 PF06972 DUF1296: Protein of u 40.7 60 0.0013 23.6 4.2 33 179-211 9-42 (60)
46 COG0100 RpsK Ribosomal protein 37.4 26 0.00057 28.9 2.2 93 86-212 19-114 (129)
47 KOG1832 HIV-1 Vpr-binding prot 37.0 24 0.00052 38.1 2.3 15 175-189 1489-1503(1516)
48 PF00392 GntR: Bacterial regul 36.8 33 0.00072 23.6 2.3 21 179-199 27-47 (64)
49 KOG0944 Ubiquitin-specific pro 33.5 37 0.0008 35.2 2.9 24 185-208 644-667 (763)
50 smart00400 ZnF_CHCC zinc finge 33.0 47 0.001 22.5 2.6 20 178-197 35-54 (55)
51 PF08680 DUF1779: Protein of u 32.6 33 0.00072 29.2 2.1 54 68-122 130-197 (203)
52 COG2188 PhnF Transcriptional r 32.0 39 0.00084 29.3 2.5 18 182-199 37-54 (236)
53 PF11699 CENP-C_C: Mif2/CENP-C 31.7 71 0.0015 24.2 3.6 35 83-120 39-73 (85)
54 smart00804 TAP_C C-terminal do 31.6 98 0.0021 22.2 4.2 35 177-211 14-48 (63)
55 KOG3198 Signal recognition par 30.4 83 0.0018 26.8 4.1 42 64-105 41-95 (152)
56 cd07377 WHTH_GntR Winged helix 27.8 79 0.0017 20.7 3.0 22 178-199 27-48 (66)
57 PF10975 DUF2802: Protein of u 27.7 49 0.0011 24.2 2.1 21 177-197 45-65 (70)
58 smart00345 HTH_GNTR helix_turn 27.6 81 0.0018 20.2 3.0 22 178-199 22-43 (60)
59 PF14242 DUF4342: Domain of un 26.8 1.3E+02 0.0028 22.8 4.3 27 70-102 20-46 (84)
60 PHA01748 hypothetical protein 26.7 81 0.0018 22.2 3.0 21 177-197 15-35 (60)
61 PF03943 TAP_C: TAP C-terminal 26.2 34 0.00074 23.4 0.9 31 179-209 4-34 (51)
62 PF13276 HTH_21: HTH-like doma 25.3 59 0.0013 22.0 2.0 19 66-84 37-55 (60)
63 PRK14897 unknown domain/DNA-di 25.0 1.1E+02 0.0023 30.7 4.4 28 69-96 329-356 (509)
64 PF12614 RRF_GI: Ribosome recy 24.2 56 0.0012 27.0 2.0 23 178-200 104-126 (128)
65 smart00411 BHL bacterial (prok 23.4 87 0.0019 22.6 2.7 29 179-207 7-35 (90)
66 TIGR02325 C_P_lyase_phnF phosp 23.2 72 0.0016 26.9 2.6 19 181-199 37-55 (238)
67 PF01807 zf-CHC2: CHC2 zinc fi 23.1 88 0.0019 23.7 2.8 22 178-199 66-87 (97)
68 KOG0943 Predicted ubiquitin-pr 23.0 48 0.001 37.3 1.7 6 100-105 1849-1854(3015)
69 PHA01623 hypothetical protein 22.9 1.1E+02 0.0023 21.5 2.9 19 177-195 26-44 (56)
70 PRK10079 phosphonate metabolis 22.4 75 0.0016 27.2 2.6 20 180-199 39-58 (241)
71 cd00591 HU_IHF Integration hos 22.3 91 0.002 22.3 2.6 29 179-207 6-34 (87)
72 COG3636 Predicted transcriptio 21.5 95 0.0021 24.7 2.7 31 180-210 53-83 (100)
73 PF00403 HMA: Heavy-metal-asso 21.1 2.4E+02 0.0053 18.6 4.4 32 69-105 13-44 (62)
74 KOG3705 Glycoprotein 6-alpha-L 20.8 1.1E+02 0.0023 30.4 3.5 32 64-97 343-374 (580)
75 KOG3130 Uncharacterized conser 20.6 63 0.0014 31.8 1.8 21 23-43 267-287 (514)
76 PRK00523 hypothetical protein; 20.4 77 0.0017 23.8 1.9 17 67-83 40-56 (72)
77 TIGR02404 trehalos_R_Bsub treh 20.3 89 0.0019 26.5 2.6 19 181-199 29-47 (233)
78 PF13056 DUF3918: Protein of u 20.1 64 0.0014 22.0 1.3 16 64-79 27-42 (43)
No 1
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=100.00 E-value=6.5e-55 Score=372.42 Aligned_cols=154 Identities=65% Similarity=0.921 Sum_probs=138.2
Q ss_pred CCCCCcccCccHHHHHHHHHHcCCeecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEecceeecchhhHHHHHHHH
Q 028127 58 AQGWSSKQSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLSTQLQTQAAQ 137 (213)
Q Consensus 58 ~~~~~~k~sR~eKK~rKamkKLGlk~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfGeak~ed~s~q~q~~aae 137 (213)
+.++ +||||++||.||+|.||||++|+||+|||||+++|++|+|++|+|||+|+++||+|||+++++++++|+|.+|++
T Consensus 56 ~~~~-akqsrsekKark~m~KLGlk~v~gV~RVti~ksKNilfvI~kPdVyKsp~sdtYiiFGeakiedls~q~q~~aae 134 (209)
T KOG2239|consen 56 PVAK-AKQSRSEKKARKAMLKLGLKQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIIFGEAKIEDLSQQAQMQAAE 134 (209)
T ss_pred chhh-hhcchHHHHHHHHHHhcCCccccceeEEEEEecccEEEEecCCceeccCCCceEEEecccccchhHHHHHHHHHH
Confidence 4445 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCCCCCCCCcchhhccCCCCccchhhccCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028127 138 QFRMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~eeevde~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt~ 213 (213)
+|+.+..+.........+ ..+.++++++++||++||+.+||+|||+|+||||++||+|||+|+||||||||+||+
T Consensus 135 ~fk~~~~~~~~~~~~~~~-~~~~~ee~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 135 RFKVPQEAPGLIQEDTSA-TPPAQEESDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred hccCCccccccccccccC-CCccccccchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 999887766655544333 122234556677999999999999999999999999999999999999999999996
No 2
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=100.00 E-value=1.1e-37 Score=247.83 Aligned_cols=106 Identities=30% Similarity=0.496 Sum_probs=97.1
Q ss_pred ccHHHHHHHHHHcCCe--ecCCeeEEEEEecCceEEEecCCeEE--eeCCCceEEEecceeecchhhHHHHHHHHHhcCC
Q 028127 67 RSEKKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDVF--KSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 142 (213)
Q Consensus 67 R~eKK~rKamkKLGlk--~v~gV~rVtIrk~d~~~fVI~~PeV~--k~~gs~TYvIfGeak~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~~~~~------------ 70 (115)
T PRK06369 5 MNPRKMKQMMKQMGIDVEEL-DVEEVIIRLKD-KEIVFENPQVTVMDAQGQKTYQIVGEPEEVEKEAE------------ 70 (115)
T ss_pred CCHHHHHHHHHHcCCcchhc-CeEEEEEEeCC-EEEEEcCCeEEEEecCCCcEEEEEeccEEeecccc------------
Confidence 3689999999999999 99 99999999998 79999999999 7999999999999999875421
Q ss_pred CCCCCCCCCCcchhhccCCCCccchhhccCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028127 143 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~e~eeevde~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt~ 213 (213)
.+++|+++||+|||+||||||++|++||++||||||+|||.|+.
T Consensus 71 ---------------------------~~~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 71 ---------------------------KEVEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred ---------------------------ccCCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHhc
Confidence 03589999999999999999999999999999999999999973
No 3
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.98 E-value=6.5e-33 Score=221.96 Aligned_cols=113 Identities=40% Similarity=0.613 Sum_probs=95.4
Q ss_pred ccHHHHHHHHHHcCC--eecCCeeEEEEEecCceEEEecCCeEEe--eCCCceEEEecceeecchhhHHHHHHHHHhcCC
Q 028127 67 RSEKKSRKAMLKLGM--KPVTGVSRVTIKRTKNILFFISKPDVFK--SPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMP 142 (213)
Q Consensus 67 R~eKK~rKamkKLGl--k~v~gV~rVtIrk~d~~~fVI~~PeV~k--~~gs~TYvIfGeak~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~~~~~~---------------- 68 (122)
T COG1308 6 MNPRKLKKLMKQMGIDVEELDGVERVIIKLKDTE-YVIENPQVTVMKAMGQKTYQISGDPSAKE---------------- 68 (122)
T ss_pred CCHHHHHHHHHHhCCCceeccCceEEEEEcCCce-EEeeCCcEEeehhcchhHHHHhcchhhhc----------------
Confidence 468999999999994 59999999999999985 9999999985 56899999999864000
Q ss_pred CCCCCCCCCCcchhhccCCCCccchhhccCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028127 143 DMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~e~eeevde~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt~ 213 (213)
..+.+++..+++..|+++||+|||+||||||++|||||+++|||||+|||+||.
T Consensus 69 -----------------~~~~~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~~ 122 (122)
T COG1308 69 -----------------AVKKPEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLTE 122 (122)
T ss_pred -----------------ccccchhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhcC
Confidence 001223444677789999999999999999999999999999999999999984
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=213.57 Aligned_cols=107 Identities=32% Similarity=0.488 Sum_probs=91.0
Q ss_pred ccCccHHHHHHHHHHcCCe--ecCCeeEEEEEecCceEEEecCCeE--EeeCCCceEEEecceeecchhhHHHHHHHHHh
Q 028127 64 KQSRSEKKSRKAMLKLGMK--PVTGVSRVTIKRTKNILFFISKPDV--FKSPNSETYVIFGEAKIEDLSTQLQTQAAQQF 139 (213)
Q Consensus 64 k~sR~eKK~rKamkKLGlk--~v~gV~rVtIrk~d~~~fVI~~PeV--~k~~gs~TYvIfGeak~ed~s~q~q~~aae~~ 139 (213)
.++|.-|+||+||+||||+ ++. |.+|+|++.++ .++|++|+| |+++|+.||||||+++++++.
T Consensus 6 ~nPr~~~~mkkmMk~MGi~~~eid-V~~ViIk~~~k-~ivf~~p~V~~m~~~G~~tYqI~G~~~~~~~~----------- 72 (116)
T TIGR00264 6 MNPKMLKQMQKMMKQMGMEMEDLD-VEEVIIVFDDE-EWIFENPKVQVMDILGVKTYQITGKPKKEKVE----------- 72 (116)
T ss_pred CCcccHHHHHHHHHHcCCCccccc-cEEEEEEeCCc-eEEEecCeeEEEecCCcEEEEEecccEEeecc-----------
Confidence 3445556999999999998 355 99999999876 678999988 678899999999999865321
Q ss_pred cCCCCCCCCCCCCcchhhccCCCCccchhhccCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028127 140 RMPDMGSVMAKPDASSAAAGAQQDEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~e~eeevde~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt~ 213 (213)
+ +.+|+++||+|||+||||||++|++||++||||||+|||.|+.
T Consensus 73 -----------------------~-------~~~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~~ 116 (116)
T TIGR00264 73 -----------------------E-------EEEITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLEE 116 (116)
T ss_pred -----------------------c-------ccCCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhhC
Confidence 0 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=134.16 Aligned_cols=58 Identities=48% Similarity=0.824 Sum_probs=48.3
Q ss_pred HHHHHHHHHHcCCeecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEecceeecc
Q 028127 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIED 126 (213)
Q Consensus 69 eKK~rKamkKLGlk~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfGeak~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 6899999999999999999999999999999999999999999999999999998764
No 6
>KOG2240 consensus RNA polymerase II general transcription factor BTF3 and related proteins [Transcription]
Probab=98.48 E-value=7.3e-08 Score=81.19 Aligned_cols=64 Identities=23% Similarity=0.468 Sum_probs=60.0
Q ss_pred CccHHHHHHHHHHcCCeecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEecceeecchhh
Q 028127 66 SRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEAKIEDLST 129 (213)
Q Consensus 66 sR~eKK~rKamkKLGlk~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfGeak~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 5678999999999999999999999999999999999999999999999999999999886543
No 7
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=97.65 E-value=5.2e-05 Score=48.56 Aligned_cols=37 Identities=30% Similarity=0.494 Sum_probs=32.0
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~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 356789999999 9999999999999999999998754
No 8
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=97.46 E-value=7.3e-05 Score=59.75 Aligned_cols=43 Identities=30% Similarity=0.612 Sum_probs=39.9
Q ss_pred cCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhcC
Q 028127 171 ETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELTT 213 (213)
Q Consensus 171 e~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt~ 213 (213)
...|..+||+|+|...-+++.-|.+-|++++||+|.|+-.|+.
T Consensus 76 kV~IkkeDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 76 KVTIKKEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 4568999999999999999999999999999999999988863
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=95.57 E-value=0.018 Score=38.03 Aligned_cols=33 Identities=24% Similarity=0.361 Sum_probs=27.5
Q ss_pred ccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 177 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 177 eDIeLVM~QagvSRekAikALke~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=95.00 E-value=0.041 Score=34.66 Aligned_cols=32 Identities=31% Similarity=0.483 Sum_probs=26.2
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~nGDIV~AIM~L 211 (213)
|..+++ .|.+++.|+.||+.++||+-.|+--|
T Consensus 5 v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 5 LEQLLE-MGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred HHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 444444 69999999999999999999887544
No 11
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=94.73 E-value=0.054 Score=33.98 Aligned_cols=32 Identities=41% Similarity=0.591 Sum_probs=25.5
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~nGDIV~AIM~L 211 (213)
|..+++ .|.+++.|+.||+.++||+-.|+--|
T Consensus 5 v~~L~~-mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 5 IDQLLE-MGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 444444 49999999999999999998887443
No 12
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=85.20 E-value=1.3 Score=36.98 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=28.4
Q ss_pred CCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 172 TGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 172 ~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM 209 (213)
..+..+-++.+..- +||.++|++||.++| |+..|+-
T Consensus 111 s~~~~e~v~v~a~a-~v~~eeAr~aleeag-Dl~~A~k 146 (153)
T COG4008 111 SEPPVEEVEVLADA-FVTPEEAREALEEAG-DLRTAMK 146 (153)
T ss_pred CCCcHHHHHHHHHh-cCCHHHHHHHHHHcC-CHHHHHH
Confidence 34566677776665 599999999999995 9999863
No 13
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=84.48 E-value=1.2 Score=41.06 Aligned_cols=38 Identities=29% Similarity=0.447 Sum_probs=33.5
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~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 45677899999999999999999999999998887654
No 14
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=82.40 E-value=1.7 Score=39.50 Aligned_cols=38 Identities=34% Similarity=0.531 Sum_probs=30.4
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~L 211 (213)
+-..=+.+||+-+|||+++|.++|.+++|.+=-||+-+
T Consensus 234 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 234 LVDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 34556778888999999999999999999887777643
No 15
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=76.87 E-value=3.9 Score=26.50 Aligned_cols=33 Identities=24% Similarity=0.350 Sum_probs=21.9
Q ss_pred HHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~Qa-gvSRekAikALke~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 33344443 6788888888888889886666544
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=76.82 E-value=1.5 Score=38.84 Aligned_cols=36 Identities=42% Similarity=0.648 Sum_probs=31.0
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM 209 (213)
+-..=+.+||+-+|||+++|.++|..++|++=-||+
T Consensus 221 l~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~~ 256 (257)
T cd05007 221 LRERAIRIVMEATGVSRDEAEAALEQAGGDVKTAIL 256 (257)
T ss_pred HHHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeeee
Confidence 445667889999999999999999999999876664
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=76.62 E-value=3.3 Score=37.63 Aligned_cols=36 Identities=17% Similarity=0.265 Sum_probs=29.7
Q ss_pred CcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028127 175 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIME 210 (213)
Q Consensus 175 ~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~ 210 (213)
-..=+.+||+=+|||+++|.++|..++|.+=-||+-
T Consensus 230 ~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~ 265 (291)
T TIGR00274 230 KARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVM 265 (291)
T ss_pred HHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHH
Confidence 345667788889999999999999999998888764
No 18
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=74.37 E-value=7 Score=27.13 Aligned_cols=40 Identities=25% Similarity=0.603 Sum_probs=24.4
Q ss_pred HHHHHHc--CCe-------ecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEecce
Q 028127 73 RKAMLKL--GMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 122 (213)
Q Consensus 73 rKamkKL--Glk-------~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfGea 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-------LYVDE-DGRYLIQGQL 50 (57)
T ss_dssp HHHHHCT--T-TCEEEEE-SSTTEEEEEE--TTE-E-------EEEET-TSSEEEES-E
T ss_pred hhHHHhhcCCCceeEEEcCCCCCeEEEEE-CCCe-E-------EEEcC-CCCEEEEeEE
Confidence 4566666 665 6789989888 3443 2 24444 4479999975
No 19
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=73.37 E-value=1.8 Score=42.16 Aligned_cols=12 Identities=17% Similarity=0.213 Sum_probs=7.3
Q ss_pred eEEEecceeecc
Q 028127 115 TYVIFGEAKIED 126 (213)
Q Consensus 115 TYvIfGeak~ed 126 (213)
|-.|-|..-+..
T Consensus 193 TDFVCGTLDEDR 204 (458)
T PF10446_consen 193 TDFVCGTLDEDR 204 (458)
T ss_pred ccccCCCcCCcc
Confidence 455667766554
No 20
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=71.44 E-value=5.1 Score=36.45 Aligned_cols=35 Identities=31% Similarity=0.484 Sum_probs=27.3
Q ss_pred cccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028127 176 PRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIME 210 (213)
Q Consensus 176 eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~ 210 (213)
..=+.+||+=+|||++.|.++|..++|.|=-||+-
T Consensus 232 ~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~ 266 (296)
T PRK12570 232 ARAVRIVMQATGCSEDEAKELLKESDNDVKLAILM 266 (296)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHH
Confidence 45566788888888888888888888888777764
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=70.10 E-value=7.3 Score=25.21 Aligned_cols=34 Identities=15% Similarity=0.237 Sum_probs=25.5
Q ss_pred cHHHHHhhh-CCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 178 DIDLVMTQA-GVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 178 DIeLVM~Qa-gvSRekAikALke~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 7899999999999999998887444
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=68.73 E-value=5.9 Score=26.42 Aligned_cols=21 Identities=43% Similarity=0.469 Sum_probs=16.5
Q ss_pred CHHHHHHHHHhcCCcHHHHHh
Q 028127 189 SRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 189 SRekAikALke~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 455555678999999999984
No 23
>PF14474 RTC4: RTC4-like domain
Probab=66.64 E-value=6.1 Score=31.77 Aligned_cols=32 Identities=22% Similarity=0.325 Sum_probs=25.8
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHH
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVS 206 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~nGDIV~ 206 (213)
+++==|.|||+-.||++++|++.|+++ .++-.
T Consensus 88 vPEl~~~LI~EDm~v~~~~A~~il~eS-~~~G~ 119 (124)
T PF14474_consen 88 VPELAVRLIMEDMGVDDEEARQILEES-SEYGE 119 (124)
T ss_pred hHHHHHHHHHHHhCCCHHHHHHHHHHH-HHHHH
Confidence 344468999999999999999999998 34433
No 24
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=64.43 E-value=4 Score=39.87 Aligned_cols=8 Identities=0% Similarity=-0.213 Sum_probs=3.6
Q ss_pred EEEEEecC
Q 028127 89 RVTIKRTK 96 (213)
Q Consensus 89 rVtIrk~d 96 (213)
...|++..
T Consensus 121 d~~~WtP~ 128 (458)
T PF10446_consen 121 DYEFWTPG 128 (458)
T ss_pred cceeeccc
Confidence 44444443
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=62.45 E-value=8.7 Score=36.55 Aligned_cols=33 Identities=33% Similarity=0.524 Sum_probs=28.1
Q ss_pred HHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~Qagv-SRekAikALke~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 4557887765 78889999999999999999876
No 26
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=60.40 E-value=8.7 Score=35.96 Aligned_cols=33 Identities=45% Similarity=0.612 Sum_probs=27.2
Q ss_pred HHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~Qagv-SRekAikALke~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 4566666654 68889999999999999999877
No 27
>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=56.47 E-value=16 Score=27.30 Aligned_cols=30 Identities=30% Similarity=0.238 Sum_probs=24.8
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 899999999999999999999987754
No 28
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=56.45 E-value=12 Score=27.80 Aligned_cols=22 Identities=32% Similarity=0.380 Sum_probs=19.8
Q ss_pred cHHHHHhhhCCCHHHHHHHHHh
Q 028127 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke 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 4777899999999999999986
No 29
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=56.26 E-value=29 Score=30.27 Aligned_cols=43 Identities=21% Similarity=0.463 Sum_probs=28.2
Q ss_pred HHHHHHHHHHcCCe-------ecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEecce
Q 028127 69 EKKSRKAMLKLGMK-------PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFGEA 122 (213)
Q Consensus 69 eKK~rKamkKLGlk-------~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfGea 122 (213)
...+++.|.++|++ +++|+-+|++ .++ + +|.++ ...|+|+|..
T Consensus 23 ~~~~~~~l~~~~~~v~~v~~sp~~Gl~ev~~--~~~-i-------~Y~~~-dg~y~i~G~l 72 (232)
T PRK10877 23 DAAIQQTLAKLGIQSADIQPSPVAGMKTVLT--ESG-V-------LYITD-DGKHIIQGPM 72 (232)
T ss_pred HHHHHHHHHHcCCceeEEccCCCCCeEEEEE--CCe-E-------EEEcC-CCCEEEeeee
Confidence 36788888988876 5678877765 222 2 24443 4469999863
No 30
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=54.26 E-value=17 Score=33.09 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=29.0
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 457899999999999999999999999988443
No 31
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=54.25 E-value=25 Score=24.70 Aligned_cols=31 Identities=16% Similarity=0.292 Sum_probs=27.2
Q ss_pred CcccHHHHHhhhCCCHHHHHHHHHhcCCcHH
Q 028127 175 EPRDIDLVMTQAGVSRSKAVKALKTHNGDIV 205 (213)
Q Consensus 175 ~eeDIeLVM~QagvSRekAikALke~nGDIV 205 (213)
.+-.|...+...|||.++...|.+..++++.
T Consensus 19 e~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~ 49 (57)
T PF12244_consen 19 EPYEVRYWAKRFGVTEEQLREAVRAVGNSRA 49 (57)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHHCcCHH
Confidence 3578999999999999999999999977753
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=53.24 E-value=17 Score=33.11 Aligned_cols=30 Identities=30% Similarity=0.383 Sum_probs=26.9
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 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=51.64 E-value=21 Score=28.79 Aligned_cols=34 Identities=18% Similarity=0.415 Sum_probs=26.4
Q ss_pred cccCccHHHHHHHHHHcCCe------ecCCeeEEEEEecC
Q 028127 63 SKQSRSEKKSRKAMLKLGMK------PVTGVSRVTIKRTK 96 (213)
Q Consensus 63 ~k~sR~eKK~rKamkKLGlk------~v~gV~rVtIrk~d 96 (213)
+++.+.|..++++|..+|++ .++|+--+++.+.+
T Consensus 18 ~~~T~pE~~lr~~L~~~G~rfR~q~~~lpg~pD~~~~~~k 57 (117)
T TIGR00632 18 TKGTKPEKALASLLTGLGLRFRLQDASLPGTPDIVFDEYR 57 (117)
T ss_pred cCCCHHHHHHHHHHHhCCCEEEEecCCCCCcccEEecCCC
Confidence 67788999999999999997 35676666666553
No 34
>PLN02150 terpene synthase/cyclase family protein
Probab=49.24 E-value=16 Score=28.05 Aligned_cols=26 Identities=31% Similarity=0.454 Sum_probs=21.9
Q ss_pred CcccHHHHHhhhCCCHHHHHHHHHhc
Q 028127 175 EPRDIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 175 ~eeDIeLVM~QagvSRekAikALke~ 200 (213)
.+.=|+--|.|-|||.++|++.|++-
T Consensus 6 vaSsIeCYMke~g~seeeA~~~i~~l 31 (96)
T PLN02150 6 VANGVNCYMKQHGVTKEEAVSELKKM 31 (96)
T ss_pred chHHHHHHhccCCCCHHHHHHHHHHH
Confidence 34568999999999999999988763
No 35
>PF13730 HTH_36: Helix-turn-helix domain
Probab=49.04 E-value=22 Score=23.46 Aligned_cols=22 Identities=27% Similarity=0.415 Sum_probs=19.2
Q ss_pred cHHHHHhhhCCCHHHHHHHHHh
Q 028127 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke 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 6899999999999988888765
No 36
>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=48.93 E-value=14 Score=24.23 Aligned_cols=23 Identities=35% Similarity=0.423 Sum_probs=17.8
Q ss_pred cHHHHHhhhCCCHHHHHHHHHhc
Q 028127 178 DIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke~ 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 37778999999999999988764
No 37
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=47.20 E-value=24 Score=32.15 Aligned_cols=30 Identities=27% Similarity=0.392 Sum_probs=27.4
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHH
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 38
>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=44.58 E-value=27 Score=35.72 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=7.4
Q ss_pred HHHHHHHHHH-cCC
Q 028127 69 EKKSRKAMLK-LGM 81 (213)
Q Consensus 69 eKK~rKamkK-LGl 81 (213)
.++++..|.+ ||.
T Consensus 701 d~~~~~~l~~aL~~ 714 (784)
T PF04931_consen 701 DEEFRSALAKALGD 714 (784)
T ss_pred HHHHHHHHHHHhcc
Confidence 3456666554 665
No 39
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.28 E-value=41 Score=26.51 Aligned_cols=33 Identities=24% Similarity=0.455 Sum_probs=25.3
Q ss_pred HHHHHHHHHHcCCe----------ecCCeeEEEEEecCceEEE
Q 028127 69 EKKSRKAMLKLGMK----------PVTGVSRVTIKRTKNILFF 101 (213)
Q Consensus 69 eKK~rKamkKLGlk----------~v~gV~rVtIrk~d~~~fV 101 (213)
+-.+.++|..||.. ..||+++|.|+..++.++|
T Consensus 14 ~dri~~~l~e~g~~v~~eGD~ivas~pgis~ieik~E~kkL~v 56 (96)
T COG4004 14 PDRIMRGLSELGWTVSEEGDRIVASSPGISRIEIKPENKKLLV 56 (96)
T ss_pred HHHHHHHHHHhCeeEeecccEEEEecCCceEEEEecccceEEE
Confidence 55678889999965 4678899999988775544
No 40
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=44.23 E-value=26 Score=33.22 Aligned_cols=36 Identities=25% Similarity=0.243 Sum_probs=32.7
Q ss_pred CCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 174 VEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 174 i~eeDIeLVM~QagvSRekAikALke~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
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=43.97 E-value=24 Score=26.60 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=20.3
Q ss_pred HHHHhhhCCCH---HHHHHHHHhcCCcH
Q 028127 180 DLVMTQAGVSR---SKAVKALKTHNGDI 204 (213)
Q Consensus 180 eLVM~QagvSR---ekAikALke~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 45678899999 58899999987665
No 42
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.65 E-value=16 Score=35.85 Aligned_cols=21 Identities=24% Similarity=0.287 Sum_probs=11.6
Q ss_pred cHHHHHhhh---CCCHHHHHHHHH
Q 028127 178 DIDLVMTQA---GVSRSKAVKALK 198 (213)
Q Consensus 178 DIeLVM~Qa---gvSRekAikALk 198 (213)
-+.|+.+.+ -|||=||-+||-
T Consensus 489 ~~~~~~s~~~~krvs~fk~~r~~~ 512 (514)
T KOG3130|consen 489 EVLLEASEETGKRVSKFKAARLQQ 512 (514)
T ss_pred cceeecccccchhHHHHHHHHHhc
Confidence 444444443 466666666663
No 43
>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=42.21 E-value=30 Score=23.63 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=17.3
Q ss_pred HHHHHhhhCCCHHHHHHHHHhc
Q 028127 179 IDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~ 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 4589999999999999999863
No 44
>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=40.85 E-value=19 Score=36.92 Aligned_cols=12 Identities=17% Similarity=-0.006 Sum_probs=6.6
Q ss_pred HHHHHHHHHcCC
Q 028127 70 KKSRKAMLKLGM 81 (213)
Q Consensus 70 KK~rKamkKLGl 81 (213)
.+++++|..-+.
T Consensus 706 ~~l~~aL~~~~~ 717 (784)
T PF04931_consen 706 SALAKALGDADA 717 (784)
T ss_pred HHHHHHhccccc
Confidence 456666665444
No 45
>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=40.67 E-value=60 Score=23.64 Aligned_cols=33 Identities=24% Similarity=0.248 Sum_probs=25.2
Q ss_pred HHHHHhhhCC-CHHHHHHHHHhcCCcHHHHHhhh
Q 028127 179 IDLVMTQAGV-SRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 179 IeLVM~Qagv-SRekAikALke~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 3444456788 99999999999999987776544
No 46
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=37.43 E-value=26 Score=28.89 Aligned_cols=93 Identities=24% Similarity=0.343 Sum_probs=56.3
Q ss_pred CeeEEEEEec-CceEEEecCCe--EEeeCCCceEEEecceeecchhhHHHHHHHHHhcCCCCCCCCCCCCcchhhccCCC
Q 028127 86 GVSRVTIKRT-KNILFFISKPD--VFKSPNSETYVIFGEAKIEDLSTQLQTQAAQQFRMPDMGSVMAKPDASSAAAGAQQ 162 (213)
Q Consensus 86 gV~rVtIrk~-d~~~fVI~~Pe--V~k~~gs~TYvIfGeak~ed~s~q~q~~aae~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (213)
|| +.|+.+ +|+++.|.++. +.....+.+-.+.|..+.-..+.|+.+..+++-
T Consensus 19 Gv--ahI~asfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~----------------------- 73 (129)
T COG0100 19 GV--AHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKK----------------------- 73 (129)
T ss_pred ce--EEEEcccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHH-----------------------
Confidence 66 455555 67888898885 333334455667777755555555444332221
Q ss_pred CccchhhccCCCCcccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhhc
Q 028127 163 DEEEEEVDETGVEPRDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMELT 212 (213)
Q Consensus 163 ~e~eeevde~gi~eeDIeLVM~QagvSRekAikALke~nGDIV~AIM~Lt 212 (213)
.-+-||. .|++++.=.|--|+-|++||-.. |.-|..|+..|
T Consensus 74 ------a~e~Gi~--~v~v~vkgpG~GreaAiraL~~a-g~~i~~I~DvT 114 (129)
T COG0100 74 ------AKEHGIK--SVEVKVKGPGPGREAAIRALAAA-GLKITRIEDVT 114 (129)
T ss_pred ------HHHhCcc--EEEEEEECCCCcHHHHHHHHHHc-cceEEEEEEcC
Confidence 1123444 67777777899999999999855 55555554443
No 47
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=37.03 E-value=24 Score=38.08 Aligned_cols=15 Identities=27% Similarity=0.029 Sum_probs=10.7
Q ss_pred CcccHHHHHhhhCCC
Q 028127 175 EPRDIDLVMTQAGVS 189 (213)
Q Consensus 175 ~eeDIeLVM~QagvS 189 (213)
..++.+++|+-.+-|
T Consensus 1489 ~Dee~~~~~~d~~ss 1503 (1516)
T KOG1832|consen 1489 EDEEDDGEMQDFMSS 1503 (1516)
T ss_pred cchhhhhhhhcccCC
Confidence 346778888887766
No 48
>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=36.77 E-value=33 Score=23.56 Aligned_cols=21 Identities=29% Similarity=0.338 Sum_probs=17.0
Q ss_pred HHHHHhhhCCCHHHHHHHHHh
Q 028127 179 IDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke 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 456899999999999999874
No 49
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=33.51 E-value=37 Score=35.18 Aligned_cols=24 Identities=42% Similarity=0.653 Sum_probs=21.1
Q ss_pred hhCCCHHHHHHHHHhcCCcHHHHH
Q 028127 185 QAGVSRSKAVKALKTHNGDIVSAI 208 (213)
Q Consensus 185 QagvSRekAikALke~nGDIV~AI 208 (213)
-.|.+|..||+||+.+||+|-.|.
T Consensus 644 smGf~~~qa~~aL~~~n~nverav 667 (763)
T KOG0944|consen 644 SMGFSRNQAIKALKATNNNVERAV 667 (763)
T ss_pred eecCcHHHHHHHHHhcCccHHHHH
Confidence 359999999999999999997763
No 50
>smart00400 ZnF_CHCC zinc finger.
Probab=33.01 E-value=47 Score=22.45 Aligned_cols=20 Identities=35% Similarity=0.340 Sum_probs=18.0
Q ss_pred cHHHHHhhhCCCHHHHHHHH
Q 028127 178 DIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 178 DIeLVM~QagvSRekAikAL 197 (213)
=|+|||..-|+|-.+|++-|
T Consensus 35 ~i~fv~~~~~~sf~eA~~~L 54 (55)
T smart00400 35 VISFLMKYDKLSFVEAVKKL 54 (55)
T ss_pred HHHHHHHHHCcCHHHHHHHh
Confidence 38999999999999999876
No 51
>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=32.59 E-value=33 Score=29.18 Aligned_cols=54 Identities=24% Similarity=0.409 Sum_probs=19.2
Q ss_pred cHHHHHHHHHHcCCeecCCeeE-----EEEEec--CceEEEecCC----eE---EeeCCCceEEEecce
Q 028127 68 SEKKSRKAMLKLGMKPVTGVSR-----VTIKRT--KNILFFISKP----DV---FKSPNSETYVIFGEA 122 (213)
Q Consensus 68 ~eKK~rKamkKLGlk~v~gV~r-----VtIrk~--d~~~fVI~~P----eV---~k~~gs~TYvIfGea 122 (213)
-.+++.++|++||.++|+.+.. |+=..+ +. .+-+..= +| |..-++.||+++|.|
T Consensus 130 l~~~~~~~l~~l~A~~vE~~~~~~~vSvsaYt~~~~~-~i~~~~~k~NlqiAlr~~~~~~~T~I~iGTP 197 (203)
T PF08680_consen 130 LEKIAERLLKKLGAKPVESLKDENFVSVSAYTPKWDD-SIQTGGKKMNLQIALRYNSYGGKTYITIGTP 197 (203)
T ss_dssp HHHHHHHHHHHH---------BTTEEEEEE--TTSS---EEETTEEE-EEEEEE--------EEEEESS
T ss_pred HHHHHHHHHHHcCCcEeeEEecccEEEEEEEccchhh-hhhcCCeEEEEEEEEEecCCCCCEEEEEEec
Confidence 3677889999999998876532 222222 11 1111111 22 223478899999987
No 52
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=32.00 E-value=39 Score=29.28 Aligned_cols=18 Identities=44% Similarity=0.466 Sum_probs=16.1
Q ss_pred HHhhhCCCHHHHHHHHHh
Q 028127 182 VMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 182 VM~QagvSRekAikALke 199 (213)
.++|.||||-.++|||..
T Consensus 37 La~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 37 LAEQFGVSRMTVRKALDE 54 (236)
T ss_pred HHHHHCCcHHHHHHHHHH
Confidence 689999999999999965
No 53
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=31.66 E-value=71 Score=24.20 Aligned_cols=35 Identities=29% Similarity=0.472 Sum_probs=27.0
Q ss_pred ecCCeeEEEEEecCceEEEecCCeEEeeCCCceEEEec
Q 028127 83 PVTGVSRVTIKRTKNILFFISKPDVFKSPNSETYVIFG 120 (213)
Q Consensus 83 ~v~gV~rVtIrk~d~~~fVI~~PeV~k~~gs~TYvIfG 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 56799999986 347999999999999999999873
No 54
>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=31.64 E-value=98 Score=22.25 Aligned_cols=35 Identities=17% Similarity=0.220 Sum_probs=29.8
Q ss_pred ccHHHHHhhhCCCHHHHHHHHHhcCCcHHHHHhhh
Q 028127 177 RDIDLVMTQAGVSRSKAVKALKTHNGDIVSAIMEL 211 (213)
Q Consensus 177 eDIeLVM~QagvSRekAikALke~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 34677889999999999999999999998887543
No 55
>KOG3198 consensus Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.42 E-value=83 Score=26.76 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=32.3
Q ss_pred ccCccHHHHHHHHHHcCCee-------------cCCeeEEEEEecCceEEEecCC
Q 028127 64 KQSRSEKKSRKAMLKLGMKP-------------VTGVSRVTIKRTKNILFFISKP 105 (213)
Q Consensus 64 k~sR~eKK~rKamkKLGlk~-------------v~gV~rVtIrk~d~~~fVI~~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 34555678999999999972 1256788898889999998775
No 56
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=27.77 E-value=79 Score=20.68 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=18.2
Q ss_pred cHHHHHhhhCCCHHHHHHHHHh
Q 028127 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke 199 (213)
-+.-++.+.|+||..+.++|+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 27 SERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999998888765
No 57
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=27.71 E-value=49 Score=24.19 Aligned_cols=21 Identities=29% Similarity=0.476 Sum_probs=17.6
Q ss_pred ccHHHHHhhhCCCHHHHHHHH
Q 028127 177 RDIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 177 eDIeLVM~QagvSRekAikAL 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 58
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=27.60 E-value=81 Score=20.18 Aligned_cols=22 Identities=32% Similarity=0.335 Sum_probs=18.4
Q ss_pred cHHHHHhhhCCCHHHHHHHHHh
Q 028127 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke 199 (213)
.+.-+++..||||.-+.++|+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5666899999999998888865
No 59
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=26.83 E-value=1.3e+02 Score=22.82 Aligned_cols=27 Identities=30% Similarity=0.442 Sum_probs=19.3
Q ss_pred HHHHHHHHHcCCeecCCeeEEEEEecCceEEEe
Q 028127 70 KKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFI 102 (213)
Q Consensus 70 KK~rKamkKLGlk~v~gV~rVtIrk~d~~~fVI 102 (213)
.++|.+++| -+++|+.|++.+..++-|
T Consensus 20 ~~iK~li~k------GNv~Ri~Ikk~~~tll~i 46 (84)
T PF14242_consen 20 DKIKELIKK------GNVTRIIIKKDDKTLLDI 46 (84)
T ss_pred HHHHHHHHh------cCeEEEEEEcCCeEEEEe
Confidence 355555555 368999999999766555
No 60
>PHA01748 hypothetical protein
Probab=26.73 E-value=81 Score=22.23 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.1
Q ss_pred ccHHHHHhhhCCCHHHHHHHH
Q 028127 177 RDIDLVMTQAGVSRSKAVKAL 197 (213)
Q Consensus 177 eDIeLVM~QagvSRekAikAL 197 (213)
+-++..+.+.|+||.++|+..
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~A 35 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKA 35 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHH
Confidence 357778999999999998844
No 61
>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=26.21 E-value=34 Score=23.44 Aligned_cols=31 Identities=23% Similarity=0.254 Sum_probs=24.9
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHHHh
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSAIM 209 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 5567899999999999999999999876664
No 62
>PF13276 HTH_21: HTH-like domain
Probab=25.25 E-value=59 Score=22.04 Aligned_cols=19 Identities=26% Similarity=0.499 Sum_probs=15.5
Q ss_pred CccHHHHHHHHHHcCCeec
Q 028127 66 SRSEKKSRKAMLKLGMKPV 84 (213)
Q Consensus 66 sR~eKK~rKamkKLGlk~v 84 (213)
.=|.|+.+++|++|||...
T Consensus 37 ~v~~krV~RlM~~~gL~~~ 55 (60)
T PF13276_consen 37 RVSRKRVRRLMREMGLRSK 55 (60)
T ss_pred cccHHHHHHHHHHcCCccc
Confidence 3467999999999999743
No 63
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=25.00 E-value=1.1e+02 Score=30.65 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=20.9
Q ss_pred HHHHHHHHHHcCCeecCCeeEEEEEecC
Q 028127 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTK 96 (213)
Q Consensus 69 eKK~rKamkKLGlk~v~gV~rVtIrk~d 96 (213)
-+++++.|.++-++-++||.||+|++.+
T Consensus 329 L~~l~~~l~~i~I~GipgI~r~~i~~~~ 356 (509)
T PRK14897 329 LYLLAEKVKSLTIKGIKGIKRAIARKEN 356 (509)
T ss_pred HHHHHHHhhccEEeCCCCccEEEEecCC
Confidence 3445556666778899999999998654
No 64
>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=24.21 E-value=56 Score=26.99 Aligned_cols=23 Identities=13% Similarity=0.091 Sum_probs=19.4
Q ss_pred cHHHHHhhhCCCHHHHHHHHHhc
Q 028127 178 DIDLVMTQAGVSRSKAVKALKTH 200 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke~ 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 65
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=23.36 E-value=87 Score=22.64 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=21.6
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 207 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~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 67889999999999998887653333433
No 66
>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=23.25 E-value=72 Score=26.87 Aligned_cols=19 Identities=21% Similarity=0.357 Sum_probs=16.7
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028127 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVM~QagvSRekAikALke 199 (213)
-.+++.||||..+++||..
T Consensus 37 eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 37 QLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999965
No 67
>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=23.11 E-value=88 Score=23.69 Aligned_cols=22 Identities=45% Similarity=0.451 Sum_probs=18.1
Q ss_pred cHHHHHhhhCCCHHHHHHHHHh
Q 028127 178 DIDLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 178 DIeLVM~QagvSRekAikALke 199 (213)
=|.|||.--|||..+|++-|.+
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 68
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=23.04 E-value=48 Score=37.28 Aligned_cols=6 Identities=50% Similarity=1.209 Sum_probs=2.5
Q ss_pred EEecCC
Q 028127 100 FFISKP 105 (213)
Q Consensus 100 fVI~~P 105 (213)
|+|..|
T Consensus 1849 Fmiad~ 1854 (3015)
T KOG0943|consen 1849 FMIADP 1854 (3015)
T ss_pred eeecCC
Confidence 444444
No 69
>PHA01623 hypothetical protein
Probab=22.89 E-value=1.1e+02 Score=21.46 Aligned_cols=19 Identities=5% Similarity=0.252 Sum_probs=16.8
Q ss_pred ccHHHHHhhhCCCHHHHHH
Q 028127 177 RDIDLVMTQAGVSRSKAVK 195 (213)
Q Consensus 177 eDIeLVM~QagvSRekAik 195 (213)
.-++..+.+-|++|.+||+
T Consensus 26 ~~Ld~y~~~~g~~rSe~Ir 44 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIE 44 (56)
T ss_pred HHHHHHHHHcCCCHHHHHH
Confidence 4678899999999999987
No 70
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=22.44 E-value=75 Score=27.18 Aligned_cols=20 Identities=15% Similarity=0.229 Sum_probs=17.2
Q ss_pred HHHHhhhCCCHHHHHHHHHh
Q 028127 180 DLVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 180 eLVM~QagvSRekAikALke 199 (213)
.-.+++-||||..+++||..
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 34789999999999999975
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=22.31 E-value=91 Score=22.31 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=21.8
Q ss_pred HHHHHhhhCCCHHHHHHHHHhcCCcHHHH
Q 028127 179 IDLVMTQAGVSRSKAVKALKTHNGDIVSA 207 (213)
Q Consensus 179 IeLVM~QagvSRekAikALke~nGDIV~A 207 (213)
|+.|+..+|+|+..|...|..--.=|.++
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=21.54 E-value=95 Score=24.72 Aligned_cols=31 Identities=29% Similarity=0.359 Sum_probs=24.3
Q ss_pred HHHHhhhCCCHHHHHHHHHhcCCcHHHHHhh
Q 028127 180 DLVMTQAGVSRSKAVKALKTHNGDIVSAIME 210 (213)
Q Consensus 180 eLVM~QagvSRekAikALke~nGDIV~AIM~ 210 (213)
--|..++|+||+--.|||...+|=-...||+
T Consensus 53 sqvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 53 SQVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 3577899999999999999887755555543
No 73
>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=21.09 E-value=2.4e+02 Score=18.61 Aligned_cols=32 Identities=31% Similarity=0.415 Sum_probs=21.6
Q ss_pred HHHHHHHHHHcCCeecCCeeEEEEEecCceEEEecCC
Q 028127 69 EKKSRKAMLKLGMKPVTGVSRVTIKRTKNILFFISKP 105 (213)
Q Consensus 69 eKK~rKamkKLGlk~v~gV~rVtIrk~d~~~fVI~~P 105 (213)
.++++++|+++ +||..|.+-...+.+-+.-+|
T Consensus 13 ~~~v~~~l~~~-----~GV~~v~vd~~~~~v~v~~~~ 44 (62)
T PF00403_consen 13 AKKVEKALSKL-----PGVKSVKVDLETKTVTVTYDP 44 (62)
T ss_dssp HHHHHHHHHTS-----TTEEEEEEETTTTEEEEEEST
T ss_pred HHHHHHHHhcC-----CCCcEEEEECCCCEEEEEEec
Confidence 46777777764 788888888776655444333
No 74
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.84 E-value=1.1e+02 Score=30.45 Aligned_cols=32 Identities=28% Similarity=0.474 Sum_probs=24.9
Q ss_pred ccCccHHHHHHHHHHcCCeecCCeeEEEEEecCc
Q 028127 64 KQSRSEKKSRKAMLKLGMKPVTGVSRVTIKRTKN 97 (213)
Q Consensus 64 k~sR~eKK~rKamkKLGlk~v~gV~rVtIrk~d~ 97 (213)
-|+.-++++-++|++||++. | |.-|.+|+.|+
T Consensus 343 pqp~t~~~l~~a~k~lg~~~-P-ivGvhvRRTDK 374 (580)
T KOG3705|consen 343 PQPATQEKLDKALKSLGLDK-P-IVGVHVRRTDK 374 (580)
T ss_pred CChhhHHHHHHHHHhCCCCC-c-eeeEEEEeccc
Confidence 46778899999999999985 3 45667777653
No 75
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.56 E-value=63 Score=31.84 Aligned_cols=21 Identities=38% Similarity=0.661 Sum_probs=10.5
Q ss_pred CCCCceecCCCCCCcCCCCCC
Q 028127 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 344555665555544444443
No 76
>PRK00523 hypothetical protein; Provisional
Probab=20.41 E-value=77 Score=23.82 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=14.3
Q ss_pred ccHHHHHHHHHHcCCee
Q 028127 67 RSEKKSRKAMLKLGMKP 83 (213)
Q Consensus 67 R~eKK~rKamkKLGlk~ 83 (213)
=+|+-+|.||.+||-|+
T Consensus 40 ine~mir~M~~QMGqKP 56 (72)
T PRK00523 40 ITENMIRAMYMQMGRKP 56 (72)
T ss_pred CCHHHHHHHHHHhCCCc
Confidence 46888999999999885
No 77
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=20.26 E-value=89 Score=26.45 Aligned_cols=19 Identities=42% Similarity=0.438 Sum_probs=16.6
Q ss_pred HHHhhhCCCHHHHHHHHHh
Q 028127 181 LVMTQAGVSRSKAVKALKT 199 (213)
Q Consensus 181 LVM~QagvSRekAikALke 199 (213)
-.|++.||||...++||..
T Consensus 29 eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNL 47 (233)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999865
No 78
>PF13056 DUF3918: Protein of unknown function (DUF3918)
Probab=20.12 E-value=64 Score=22.00 Aligned_cols=16 Identities=38% Similarity=0.439 Sum_probs=12.9
Q ss_pred ccCccHHHHHHHHHHc
Q 028127 64 KQSRSEKKSRKAMLKL 79 (213)
Q Consensus 64 k~sR~eKK~rKamkKL 79 (213)
..+|+.||+|+.+.|+
T Consensus 27 ~n~R~MKKmrkrv~k~ 42 (43)
T PF13056_consen 27 MNKRQMKKMRKRVMKA 42 (43)
T ss_pred cchHHHHHHHHHHHhc
Confidence 3568999999998874
Done!