Query 033806
Match_columns 111
No_of_seqs 142 out of 203
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 06:30:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033806.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033806hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3450 Huntingtin interacting 100.0 5E-32 1.1E-36 195.5 8.7 111 1-111 1-118 (119)
2 COG1308 EGD2 Transcription fac 99.4 7.2E-13 1.6E-17 97.1 5.0 49 62-110 73-121 (122)
3 KOG2239 Transcription factor c 99.3 4.1E-12 9E-17 99.9 4.1 50 62-111 160-209 (209)
4 PRK06369 nac nascent polypepti 99.2 3.7E-11 8E-16 87.3 5.4 42 69-110 72-113 (115)
5 TIGR00264 alpha-NAC-related pr 99.1 1.6E-10 3.4E-15 84.2 5.2 41 70-110 75-115 (116)
6 PF00627 UBA: UBA/TS-N domain; 97.7 0.00011 2.3E-09 42.6 4.7 37 72-109 1-37 (37)
7 cd00194 UBA Ubiquitin Associat 96.8 0.0044 9.6E-08 35.3 5.2 35 75-110 3-37 (38)
8 PF14555 UBA_4: UBA-like domai 96.0 0.022 4.8E-07 33.9 5.0 35 75-109 2-36 (43)
9 smart00165 UBA Ubiquitin assoc 96.0 0.014 3.1E-07 33.0 4.0 33 76-109 4-36 (37)
10 smart00546 CUE Domain that may 94.7 0.14 3E-06 30.2 5.2 37 74-110 3-40 (43)
11 PF02845 CUE: CUE domain; Int 91.8 0.71 1.5E-05 27.1 5.1 36 75-110 3-39 (42)
12 PF03474 DMA: DMRTA motif; In 90.5 0.38 8.2E-06 29.2 3.0 25 85-109 14-38 (39)
13 PF12244 DUF3606: Protein of u 88.7 1.5 3.3E-05 27.8 5.0 41 69-110 14-55 (57)
14 PRK12332 tsf elongation factor 88.3 1.3 2.7E-05 34.7 5.3 39 71-109 2-40 (198)
15 COG4008 Predicted metal-bindin 87.5 2.5 5.4E-05 32.2 6.2 42 66-109 107-148 (153)
16 PRK09377 tsf elongation factor 86.6 1.6 3.6E-05 36.0 5.2 39 71-109 3-41 (290)
17 TIGR00116 tsf translation elon 86.0 1.8 3.8E-05 35.8 5.2 38 72-109 3-40 (290)
18 PRK05441 murQ N-acetylmuramic 81.5 2.6 5.6E-05 34.3 4.3 32 77-108 266-297 (299)
19 COG2103 Predicted sugar phosph 81.1 2.7 5.9E-05 35.3 4.3 30 77-106 237-266 (298)
20 KOG2561 Adaptor protein NUB1, 80.1 4.7 0.0001 36.2 5.7 45 65-110 295-339 (568)
21 TIGR00274 N-acetylmuramic acid 76.7 4 8.6E-05 33.2 4.0 30 77-106 261-290 (291)
22 PRK05441 murQ N-acetylmuramic 76.4 4.9 0.00011 32.6 4.5 35 75-109 237-271 (299)
23 CHL00098 tsf elongation factor 75.1 7.5 0.00016 30.5 5.0 36 74-109 2-37 (200)
24 PRK12570 N-acetylmuramic acid- 74.5 5 0.00011 32.7 4.1 31 77-107 262-292 (296)
25 PF10975 DUF2802: Protein of u 71.4 5.5 0.00012 26.3 3.0 25 75-99 45-69 (70)
26 COG0264 Tsf Translation elonga 71.3 9.6 0.00021 32.0 5.1 39 71-109 3-41 (296)
27 PF14474 RTC4: RTC4-like domai 70.3 5.8 0.00013 28.6 3.2 31 69-99 85-115 (124)
28 smart00804 TAP_C C-terminal do 63.0 25 0.00053 22.9 4.8 36 75-110 14-49 (63)
29 TIGR00274 N-acetylmuramic acid 62.8 15 0.00032 29.9 4.5 32 77-108 234-265 (291)
30 KOG1071 Mitochondrial translat 59.1 17 0.00038 31.1 4.4 43 67-109 40-82 (340)
31 COG2103 Predicted sugar phosph 58.5 15 0.00034 30.8 4.0 33 77-109 264-296 (298)
32 cd05007 SIS_Etherase N-acetylm 58.2 7.7 0.00017 30.7 2.1 31 76-106 225-255 (257)
33 PF11626 Rap1_C: TRF2-interact 56.5 29 0.00063 23.2 4.4 29 81-109 4-32 (87)
34 PRK12570 N-acetylmuramic acid- 54.2 23 0.00051 28.8 4.3 33 77-109 235-267 (296)
35 PF03943 TAP_C: TAP C-terminal 49.7 13 0.00027 23.1 1.6 34 77-110 4-37 (51)
36 PF03861 ANTAR: ANTAR domain; 49.2 26 0.00056 21.5 3.0 22 77-98 19-40 (56)
37 PF05861 PhnI: Bacterial phosp 46.2 30 0.00065 29.8 3.9 32 77-108 45-77 (358)
38 COG3626 PhnI Uncharacterized e 44.7 81 0.0017 27.1 6.1 58 39-109 9-78 (367)
39 PF02954 HTH_8: Bacterial regu 44.4 29 0.00063 20.1 2.6 22 88-109 7-28 (42)
40 PF00392 GntR: Bacterial regul 44.2 28 0.0006 21.4 2.6 22 76-97 26-47 (64)
41 PF14490 HHH_4: Helix-hairpin- 43.8 68 0.0015 21.5 4.7 34 75-108 9-42 (94)
42 PF11972 HTH_13: HTH DNA bindi 42.8 39 0.00085 21.7 3.2 24 76-99 15-38 (54)
43 TIGR00678 holB DNA polymerase 41.9 37 0.00081 24.6 3.4 35 71-105 154-188 (188)
44 PF06970 RepA_N: Replication i 41.2 34 0.00075 22.8 2.9 21 77-97 55-75 (76)
45 PF02796 HTH_7: Helix-turn-hel 40.5 26 0.00056 20.5 2.0 21 77-97 24-44 (45)
46 TIGR00601 rad23 UV excision re 40.4 43 0.00094 28.6 4.0 36 75-111 158-193 (378)
47 PF06972 DUF1296: Protein of u 39.4 1E+02 0.0022 20.4 4.7 27 84-110 16-43 (60)
48 KOG0010 Ubiquitin-like protein 37.0 41 0.00088 30.2 3.4 25 86-110 467-491 (493)
49 PF04760 IF2_N: Translation in 36.9 34 0.00073 20.6 2.1 47 27-86 5-53 (54)
50 PF03333 PapB: Adhesin biosynt 34.4 62 0.0013 22.7 3.4 37 62-98 13-49 (91)
51 smart00345 HTH_GNTR helix_turn 32.8 75 0.0016 18.1 3.1 22 76-97 22-43 (60)
52 PRK10079 phosphonate metabolis 32.2 45 0.00099 25.4 2.6 25 71-97 34-58 (241)
53 KOG2561 Adaptor protein NUB1, 32.1 2.2E+02 0.0048 26.0 7.1 37 72-109 374-410 (568)
54 KOG0944 Ubiquitin-specific pro 31.9 41 0.0009 31.6 2.7 36 71-107 633-668 (763)
55 COG2188 PhnF Transcriptional r 31.2 47 0.001 25.6 2.6 25 71-97 30-54 (236)
56 cd07377 WHTH_GntR Winged helix 30.9 82 0.0018 18.3 3.1 23 76-98 27-49 (66)
57 PF02022 Integrase_Zn: Integra 30.5 79 0.0017 18.8 2.9 23 76-98 11-33 (40)
58 PF13730 HTH_36: Helix-turn-he 29.8 86 0.0019 18.3 3.1 22 76-97 27-48 (55)
59 COG3413 Predicted DNA binding 29.5 63 0.0014 24.5 3.0 32 75-106 179-210 (215)
60 PRK04984 fatty acid metabolism 29.0 56 0.0012 24.6 2.6 19 79-97 36-54 (239)
61 cd00052 EH Eps15 homology doma 28.8 1.3E+02 0.0027 17.5 3.8 29 71-99 15-43 (67)
62 TIGR02325 C_P_lyase_phnF phosp 28.3 59 0.0013 24.3 2.6 25 71-97 31-55 (238)
63 COG1654 BirA Biotin operon rep 28.3 71 0.0015 21.6 2.8 25 78-102 23-50 (79)
64 TIGR02404 trehalos_R_Bsub treh 27.7 61 0.0013 24.4 2.6 25 71-97 23-47 (233)
65 PF04967 HTH_10: HTH DNA bindi 26.9 96 0.0021 19.4 3.0 24 75-98 24-47 (53)
66 PRK07993 DNA polymerase III su 26.6 1.6E+02 0.0034 24.4 5.0 39 71-109 166-205 (334)
67 PRK07217 replication factor A; 26.1 95 0.0021 26.3 3.7 28 75-102 29-61 (311)
68 cd08313 Death_TNFR1 Death doma 26.1 1.8E+02 0.004 19.5 4.5 28 69-96 20-47 (80)
69 PF01978 TrmB: Sugar-specific 25.8 1.1E+02 0.0024 18.7 3.2 24 74-97 22-45 (68)
70 smart00418 HTH_ARSR helix_turn 25.5 1.2E+02 0.0026 17.0 3.1 22 76-97 12-33 (66)
71 PRK14999 histidine utilization 24.8 73 0.0016 24.2 2.6 20 78-97 40-59 (241)
72 PF12959 DUF3848: Protein of u 24.8 84 0.0018 22.6 2.7 24 74-97 39-62 (101)
73 PRK10753 transcriptional regul 24.2 1.1E+02 0.0024 20.5 3.1 30 77-106 7-36 (90)
74 PRK03837 transcriptional regul 23.6 77 0.0017 23.7 2.5 20 78-97 41-60 (241)
75 PF14502 HTH_41: Helix-turn-he 23.3 93 0.002 19.6 2.4 28 25-52 6-33 (48)
76 PRK11402 DNA-binding transcrip 23.3 82 0.0018 23.9 2.6 25 71-97 32-56 (241)
77 TIGR02812 fadR_gamma fatty aci 23.1 79 0.0017 23.8 2.5 19 79-97 35-53 (235)
78 PRK11414 colanic acid/biofilm 22.7 68 0.0015 23.9 2.1 27 69-98 32-58 (221)
79 PRK12522 RNA polymerase sigma 22.4 1.4E+02 0.0031 21.0 3.6 40 72-111 133-172 (173)
80 PF12668 DUF3791: Protein of u 22.3 1.4E+02 0.003 18.6 3.2 24 77-100 8-31 (62)
81 PRK11923 algU RNA polymerase s 22.2 1.3E+02 0.0028 21.6 3.4 40 71-110 151-190 (193)
82 PF08220 HTH_DeoR: DeoR-like h 21.8 1.4E+02 0.0031 18.2 3.1 22 76-97 16-37 (57)
83 cd04447 DEP_BRCC3 DEP (Disheve 21.7 1.5E+02 0.0032 21.0 3.4 29 69-97 28-64 (92)
84 PRK09764 DNA-binding transcrip 21.6 93 0.002 23.7 2.6 25 71-97 28-52 (240)
85 PRK10225 DNA-binding transcrip 21.4 89 0.0019 23.9 2.5 20 78-97 37-56 (257)
86 PF08279 HTH_11: HTH domain; 21.2 1.5E+02 0.0033 17.2 3.1 22 77-98 18-39 (55)
87 PF00216 Bac_DNA_binding: Bact 21.2 1.4E+02 0.003 19.1 3.1 30 77-106 7-36 (90)
88 PRK09464 pdhR transcriptional 20.9 92 0.002 23.7 2.5 20 79-98 39-58 (254)
89 PRK09990 DNA-binding transcrip 20.9 93 0.002 23.6 2.5 19 79-97 36-54 (251)
90 PF01325 Fe_dep_repress: Iron 20.8 1.2E+02 0.0026 19.0 2.6 20 78-97 26-45 (60)
91 TIGR03337 phnR transcriptional 20.7 88 0.0019 23.2 2.3 23 78-100 29-51 (231)
92 cd08315 Death_TRAILR_DR4_DR5 D 20.4 2.9E+02 0.0064 18.9 5.0 26 70-95 29-54 (96)
93 COG2186 FadR Transcriptional r 20.2 85 0.0018 24.4 2.2 19 79-97 39-57 (241)
94 TIGR02018 his_ut_repres histid 20.2 1E+02 0.0023 23.1 2.6 20 78-97 29-48 (230)
95 PRK12402 replication factor C 20.0 3.1E+02 0.0068 21.2 5.3 40 70-109 182-227 (337)
No 1
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=99.97 E-value=5e-32 Score=195.54 Aligned_cols=111 Identities=40% Similarity=0.589 Sum_probs=106.8
Q ss_pred CCCCCccccccccCchhHHHH-------HHhhhhhhhhHHhhhcCHHHHHHHHHHHHHhhhcchHHHHHhHHHHhhcCCC
Q 033806 1 MDGADGGEVDRIVDSKDLQQQ-------SKALDKLTDRVEDRQLDSTRVQEAMASIAASKAGDLNAMRMREKELAAVKIN 73 (111)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~-------aaaLekvTD~~Eekeid~eai~~Am~~l~~~~~~~~~a~~~~e~el~~v~V~ 73 (111)
|+|..+++.+...|++|++|+ +++|+|||||+|||+|+++.|+.+|.+|++.++++..+++.|+++|++|+|+
T Consensus 1 ~eg~~e~~~E~e~de~d~kqq~~khd~gaadlekvTD~~Eekei~ss~l~sam~~ign~rnae~~ak~~rEKELakV~Ik 80 (119)
T KOG3450|consen 1 TEGDVELELETETDEPDRKQQKPKHDSGAADLEKVTDYAEEKEIQSSNLESAMSVIGNRRNAEQKAKQEREKELAKVTIK 80 (119)
T ss_pred CcchhhccchhccCCchhhhccccccchHHHHHHHhhHHHHhhcchhHHHHHHHHHHHHhhhhhHHHHHHHhhccccccC
Confidence 578889999999999999997 6689999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHhC
Q 033806 74 AADVDIIANELELDKKVAERTLREHKGDAVAAIRHLLR 111 (111)
Q Consensus 74 ~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~~ 111 (111)
++||+|||++|+|++..|++.||+|+||+|.|+++||.
T Consensus 81 keDlelImnELei~k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 81 KEDLELIMNELEISKAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHhc
Confidence 99999999999999999999999999999999999974
No 2
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=99.36 E-value=7.2e-13 Score=97.12 Aligned_cols=49 Identities=24% Similarity=0.384 Sum_probs=45.0
Q ss_pred HhHHHHhhcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 62 MREKELAAVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 62 ~~e~el~~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
+.++..+...|+.+||+|||+|++|||..|+++|.++|||+++|||+|+
T Consensus 73 ~ee~~~d~~~i~eeDIkLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 73 PEEKTVDESDISEEDIKLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred chhcccccCCCCHHHHHHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 3455567888999999999999999999999999999999999999996
No 3
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=99.26 E-value=4.1e-12 Score=99.88 Aligned_cols=50 Identities=22% Similarity=0.436 Sum_probs=46.9
Q ss_pred HhHHHHhhcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHhC
Q 033806 62 MREKELAAVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLLR 111 (111)
Q Consensus 62 ~~e~el~~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~~ 111 (111)
..|.+++..+|...||+|||.|.+|||.+|+++|++|+||+|+|||+|+.
T Consensus 160 ~dEeeVD~tgve~kDIeLVmsQanvSR~kAVkALk~~~~DiVnAIM~LT~ 209 (209)
T KOG2239|consen 160 SDEEEVDETGVEAKDIELVMSQANVSRAKAVKALKNNNNDIVNAIMELTK 209 (209)
T ss_pred cchhccCcccCchhhHHHHHHHhhhhHHHHHHHHHhccchHHHHHHHhhC
Confidence 45677999999999999999999999999999999999999999999974
No 4
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=99.18 E-value=3.7e-11 Score=87.26 Aligned_cols=42 Identities=29% Similarity=0.483 Sum_probs=40.4
Q ss_pred hcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 69 AVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 69 ~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
.+.|+.+||+|||+|++||+.+|+++|++|+||+++||+.|.
T Consensus 72 ~~~i~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~ 113 (115)
T PRK06369 72 EVEIPEEDIELVAEQTGVSEEEARKALEEANGDLAEAILKLS 113 (115)
T ss_pred cCCCCHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHh
Confidence 478999999999999999999999999999999999999986
No 5
>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=99.09 E-value=1.6e-10 Score=84.18 Aligned_cols=41 Identities=29% Similarity=0.459 Sum_probs=39.3
Q ss_pred cCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 70 VKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 70 v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
..|+.+||+||++|++||+.+|+++|+++|||+++||+.|.
T Consensus 75 ~~i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 75 EEITEDDIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred cCCCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 36999999999999999999999999999999999999986
No 6
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=97.69 E-value=0.00011 Score=42.60 Aligned_cols=37 Identities=22% Similarity=0.371 Sum_probs=31.8
Q ss_pred CChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 72 INAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 72 V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
|+++.|+.|++. |.++..++++|+.++||+..|+.-|
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 467788888876 9999999999999999999998754
No 7
>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=96.85 E-value=0.0044 Score=35.28 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=29.3
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
+.|+.++ +||.++..+.++|+.++||+..|+.-|.
T Consensus 3 ~~v~~L~-~mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLL-EMGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHH-HcCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4455555 4899999999999999999999987664
No 8
>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=96.04 E-value=0.022 Score=33.89 Aligned_cols=35 Identities=20% Similarity=0.165 Sum_probs=29.5
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+-|.-.|.=+++++..|+..|..|++|+-.||-.+
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y 36 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAY 36 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHH
Confidence 45777888899999999999999999999999775
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.04 E-value=0.014 Score=33.04 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=27.3
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.|+.+ .+||.++..|.++|+.++||+..|+.-|
T Consensus 4 ~v~~L-~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQL-LEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHH-HHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 34444 4679999999999999999999998655
No 10
>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=94.69 E-value=0.14 Score=30.18 Aligned_cols=37 Identities=24% Similarity=0.429 Sum_probs=31.5
Q ss_pred hhhHHHHHHhh-CCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 74 AADVDIIANEL-ELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 74 ~eDV~LI~~el-evsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
.+.|+.|.+-+ .+++...+..|+.++||+..||..|+
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL 40 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLL 40 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45666666666 89999999999999999999998876
No 11
>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=91.82 E-value=0.71 Score=27.06 Aligned_cols=36 Identities=36% Similarity=0.524 Sum_probs=28.2
Q ss_pred hhHHHHHHhh-CCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 75 ADVDIIANEL-ELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 75 eDV~LI~~el-evsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
+.|+-|.+=+ ++++..-...|+.|+||+..|+..|+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL 39 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALL 39 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3455555555 78999999999999999999998875
No 12
>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=90.47 E-value=0.38 Score=29.23 Aligned_cols=25 Identities=32% Similarity=0.469 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 85 ELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 85 evsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+-.|..=+-.|+-++||+++||-.+
T Consensus 14 ~~kr~~Le~iL~~C~GDvv~AIE~~ 38 (39)
T PF03474_consen 14 HQKRSVLELILQRCNGDVVQAIEQF 38 (39)
T ss_pred CCChHHHHHHHHHcCCcHHHHHHHh
Confidence 3456677888999999999999765
No 13
>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=88.69 E-value=1.5 Score=27.84 Aligned_cols=41 Identities=17% Similarity=0.277 Sum_probs=32.3
Q ss_pred hcCCC-hhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 69 AVKIN-AADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 69 ~v~V~-~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
.|.++ +-+|...+++|+||..+.+++.+.+|.+ +.+++..+
T Consensus 14 ~I~~~e~~ev~ywa~~~gvt~~~L~~AV~~vG~~-~~~V~~~L 55 (57)
T PF12244_consen 14 RIDLSEPYEVRYWAKRFGVTEEQLREAVRAVGNS-RAAVRAYL 55 (57)
T ss_pred hcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHCcC-HHHHHHHH
Confidence 44433 4789999999999999999999999888 45555543
No 14
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=88.29 E-value=1.3 Score=34.66 Aligned_cols=39 Identities=26% Similarity=0.258 Sum_probs=36.1
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.|+.++|.-+=+.++.+-....++|.+++||+..||.-|
T Consensus 2 ~i~a~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~l 40 (198)
T PRK12332 2 AITAKLVKELREKTGAGMMDCKKALEEANGDMEKAIEWL 40 (198)
T ss_pred CCCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999999999999999999999998765
No 15
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=87.47 E-value=2.5 Score=32.19 Aligned_cols=42 Identities=21% Similarity=0.327 Sum_probs=35.5
Q ss_pred HHhhcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 66 ELAAVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 66 el~~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
=+....+..+.|+.++.-+ ||+..|+++|-+.| |++.|+.-|
T Consensus 107 il~~s~~~~e~v~v~a~a~-v~~eeAr~aleeag-Dl~~A~k~l 148 (153)
T COG4008 107 ILGHSEPPVEEVEVLADAF-VTPEEAREALEEAG-DLRTAMKIL 148 (153)
T ss_pred HhccCCCcHHHHHHHHHhc-CCHHHHHHHHHHcC-CHHHHHHHH
Confidence 3456678889999998887 99999999999988 999998654
No 16
>PRK09377 tsf elongation factor Ts; Provisional
Probab=86.55 E-value=1.6 Score=35.95 Aligned_cols=39 Identities=28% Similarity=0.267 Sum_probs=36.5
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.|+.++|.-+=+.+|.+-....++|.+++||+..|+.-|
T Consensus 3 ~is~~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~L 41 (290)
T PRK09377 3 AITAALVKELRERTGAGMMDCKKALTEADGDIEKAIEWL 41 (290)
T ss_pred ccCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 588999999999999999999999999999999998765
No 17
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=86.04 E-value=1.8 Score=35.77 Aligned_cols=38 Identities=26% Similarity=0.281 Sum_probs=35.7
Q ss_pred CChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 72 INAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 72 V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
|++++|.-+=+.+|.+--...++|.+++||+-.||.-|
T Consensus 3 isa~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~L 40 (290)
T TIGR00116 3 ITAQLVKELRERTGAGMMDCKKALTEANGDFEKAIKNL 40 (290)
T ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 78899999999999999999999999999999998765
No 18
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=81.55 E-value=2.6 Score=34.28 Aligned_cols=32 Identities=25% Similarity=0.211 Sum_probs=23.7
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIRH 108 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~~ 108 (111)
+.++|-..+++...|++.|..++|.+..||..
T Consensus 266 ~a~~~~~~~~~~~~a~~~l~~~~g~~~~~~~~ 297 (299)
T PRK05441 266 LAIVMILTGLDAAEAKALLARHGGFLRKALAE 297 (299)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCHHHHHhh
Confidence 45666677778888888888888888777754
No 19
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=81.13 E-value=2.7 Score=35.26 Aligned_cols=30 Identities=30% Similarity=0.321 Sum_probs=15.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
+.+|++-++|++..|+++|++.+|++.-||
T Consensus 237 ~RIv~~aT~~~~~~A~~~L~~~~~~vK~AI 266 (298)
T COG2103 237 VRIVMEATGCSAEEAEALLEEAGGNVKLAI 266 (298)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCccHhHH
Confidence 344455555555555555555555554444
No 20
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=80.09 E-value=4.7 Score=36.25 Aligned_cols=45 Identities=22% Similarity=0.446 Sum_probs=39.5
Q ss_pred HHHhhcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 65 KELAAVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 65 ~el~~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
..+..++|+.+-..++| .||.-+..|+.+||.++|||..|+.-++
T Consensus 295 ~~l~elki~d~~lsllv-~mGfeesdaRlaLRsc~g~Vd~AvqfI~ 339 (568)
T KOG2561|consen 295 AKLLELKINDETLSLLV-GMGFEESDARLALRSCNGDVDSAVQFII 339 (568)
T ss_pred HHHHHeeccchHHHHHH-HcCCCchHHHHHHHhccccHHHHHHHHH
Confidence 45778999999999888 5899999999999999999999987654
No 21
>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=76.70 E-value=4 Score=33.22 Aligned_cols=30 Identities=23% Similarity=0.175 Sum_probs=21.1
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
+.++|--.+++...|++.|..++|++..||
T Consensus 261 ~Ai~~~~~~~~~~~a~~~l~~~~g~~~~~l 290 (291)
T TIGR00274 261 LAIVMILSTLSASEAKVLLDRHGGFLRQAL 290 (291)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCCcHHHhh
Confidence 345566667777777777777777777765
No 22
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=76.41 E-value=4.9 Score=32.63 Aligned_cols=35 Identities=23% Similarity=0.306 Sum_probs=30.3
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
==+.+|++-++||+..|+++|.+.+|++.-||.-+
T Consensus 237 ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~ 271 (299)
T PRK05441 237 RAVRIVMEATGVSREEAEAALEAADGSVKLAIVMI 271 (299)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHH
Confidence 34567899999999999999999999998887644
No 23
>CHL00098 tsf elongation factor Ts
Probab=75.11 E-value=7.5 Score=30.50 Aligned_cols=36 Identities=22% Similarity=0.247 Sum_probs=31.9
Q ss_pred hhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 74 AADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 74 ~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.++|.-+=+.++.+-....++|-+++||+..|+.-|
T Consensus 2 a~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~L 37 (200)
T CHL00098 2 AELVKELRDKTGAGMMDCKKALQEANGDFEKALESL 37 (200)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 467888889999999999999999999999998654
No 24
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=74.53 E-value=5 Score=32.68 Aligned_cols=31 Identities=23% Similarity=0.189 Sum_probs=25.9
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIR 107 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~ 107 (111)
+.++|-..+++...|++.|..++|.+..||.
T Consensus 262 ~ai~~~~~~~~~~~a~~~l~~~~~~~~~~l~ 292 (296)
T PRK12570 262 LAILMILTGMDVEQARAALSHADGFLRKAIE 292 (296)
T ss_pred HHHHHHHhCCCHHHHHHHHHHcCChHHHHHH
Confidence 4567777889999999999999999888885
No 25
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=71.36 E-value=5.5 Score=26.33 Aligned_cols=25 Identities=32% Similarity=0.371 Sum_probs=22.1
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhc
Q 033806 75 ADVDIIANELELDKKVAERTLREHK 99 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~ 99 (111)
.||+-||+++|+|+..|+=.++-|+
T Consensus 45 a~~~el~~~CgL~~aEAeLl~~Lh~ 69 (70)
T PF10975_consen 45 ASVEELMEECGLSRAEAELLLSLHR 69 (70)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHhc
Confidence 5788999999999999998888764
No 26
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=71.27 E-value=9.6 Score=31.96 Aligned_cols=39 Identities=28% Similarity=0.295 Sum_probs=35.7
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.|+.++|.-+=+.+|.+--...++|-+++||+-.||--|
T Consensus 3 ~ita~~VKeLRe~TgAGMmdCKkAL~E~~Gd~EkAie~L 41 (296)
T COG0264 3 EITAALVKELREKTGAGMMDCKKALEEANGDIEKAIEWL 41 (296)
T ss_pred cccHHHHHHHHHHhCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence 477899999999999999999999999999999998655
No 27
>PF14474 RTC4: RTC4-like domain
Probab=70.31 E-value=5.8 Score=28.64 Aligned_cols=31 Identities=23% Similarity=0.351 Sum_probs=25.8
Q ss_pred hcCCChhhHHHHHHhhCCCHHHHHHHHHHhc
Q 033806 69 AVKINAADVDIIANELELDKKVAERTLREHK 99 (111)
Q Consensus 69 ~v~V~~eDV~LI~~elevsk~kA~~aLre~~ 99 (111)
.|=|+.==|.|||+.|+|+...|++.|++..
T Consensus 85 ~VLvPEl~~~LI~EDm~v~~~~A~~il~eS~ 115 (124)
T PF14474_consen 85 YVLVPELAVRLIMEDMGVDDEEARQILEESS 115 (124)
T ss_pred HHhhHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4445555689999999999999999999864
No 28
>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=62.97 E-value=25 Score=22.89 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=31.6
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
+=|..+..++++...=+++.|..++-|+-.||..+.
T Consensus 14 ~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~ 49 (63)
T smart00804 14 EMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFT 49 (63)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 446778899999999999999999999999998764
No 29
>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=62.79 E-value=15 Score=29.93 Aligned_cols=32 Identities=28% Similarity=0.331 Sum_probs=28.4
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIRH 108 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~~ 108 (111)
+.+|++-++||+..|+++|...+|++.-||.-
T Consensus 234 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~ 265 (291)
T TIGR00274 234 VRIVRQATDCNKELAEQTLLAADQNVKLAIVM 265 (291)
T ss_pred HHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHH
Confidence 45788889999999999999999999888764
No 30
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=59.11 E-value=17 Score=31.07 Aligned_cols=43 Identities=19% Similarity=0.169 Sum_probs=37.1
Q ss_pred HhhcCCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 67 LAAVKINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 67 l~~v~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+..+++++++|.-+=++++-|-.--.++|-+||||++.|-.-|
T Consensus 40 ~~~s~~~~allk~LR~kTgas~~ncKkALee~~gDl~~A~~~L 82 (340)
T KOG1071|consen 40 VSPSASSKALLKKLREKTGASMVNCKKALEECGGDLVLAEEWL 82 (340)
T ss_pred CCcccccHHHHHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHH
Confidence 3444578999999999999999999999999999999886543
No 31
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=58.54 E-value=15 Score=30.85 Aligned_cols=33 Identities=21% Similarity=0.150 Sum_probs=29.9
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+.+||--+++|...|++.|..|+|.+.+||...
T Consensus 264 ~AIvm~~~~~~a~~A~~~L~~~~g~lr~Al~~~ 296 (298)
T COG2103 264 LAIVMLLTGLSAEEAKRLLERAGGFLRQALSEE 296 (298)
T ss_pred hHHHHHHhCCCHHHHHHHHHHccChHHHHHhhc
Confidence 568899999999999999999999999999753
No 32
>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=58.25 E-value=7.7 Score=30.75 Aligned_cols=31 Identities=26% Similarity=0.412 Sum_probs=27.6
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
=+..|++-++||+..|+++|...+|++.-||
T Consensus 225 a~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 225 AIRIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 3567899999999999999999999997776
No 33
>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=56.51 E-value=29 Score=23.20 Aligned_cols=29 Identities=24% Similarity=0.324 Sum_probs=25.1
Q ss_pred HHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 81 ANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 81 ~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+.++|+++....++|..+.||+..|...+
T Consensus 4 ~~~~g~~~~~v~~aL~~tSgd~~~a~~~v 32 (87)
T PF11626_consen 4 YEELGYSREFVTHALYATSGDPELARRFV 32 (87)
T ss_dssp HHHHTB-HHHHHHHHHHTTTBHHHHHHHH
T ss_pred HHHhCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 78999999999999999999998887744
No 34
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=54.24 E-value=23 Score=28.79 Aligned_cols=33 Identities=24% Similarity=0.286 Sum_probs=28.5
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
+.+|++-++||+..|+++|...+|.+.-||.-+
T Consensus 235 ~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~ 267 (296)
T PRK12570 235 VRIVMQATGCSEDEAKELLKESDNDVKLAILMI 267 (296)
T ss_pred HHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHH
Confidence 456788899999999999999999998887643
No 35
>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=49.66 E-value=13 Score=23.08 Aligned_cols=34 Identities=15% Similarity=0.241 Sum_probs=28.2
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
|.-+..++++...=+.+-|-+++-|+..|+..+.
T Consensus 4 v~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~ 37 (51)
T PF03943_consen 4 VQQFSQQTGMNLEWSQKCLEENNWDYERALQNFE 37 (51)
T ss_dssp HHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5667889999999999999999999999987764
No 36
>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=49.18 E-value=26 Score=21.49 Aligned_cols=22 Identities=27% Similarity=0.327 Sum_probs=17.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHh
Q 033806 77 VDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~ 98 (111)
+-+||...+||...|-+.||..
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 5688999999999999999874
No 37
>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=46.20 E-value=30 Score=29.85 Aligned_cols=32 Identities=31% Similarity=0.458 Sum_probs=26.6
Q ss_pred HHHHHHhhCC-CHHHHHHHHHHhcCcHHHHHHH
Q 033806 77 VDIIANELEL-DKKVAERTLREHKGDAVAAIRH 108 (111)
Q Consensus 77 V~LI~~elev-sk~kA~~aLre~~GDvv~Ai~~ 108 (111)
|+-||.|-++ ++.-|--+|+...||+++||--
T Consensus 45 vdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFL 77 (358)
T PF05861_consen 45 VDRVMSEGSLYDPELAALAIKQARGDLIEAIFL 77 (358)
T ss_pred HHHHhccccccCHHHHHHHHHHhcCCHHHHHHH
Confidence 4456777766 8999999999999999999854
No 38
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=44.75 E-value=81 Score=27.07 Aligned_cols=58 Identities=29% Similarity=0.428 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHhhhcchHHHHHhHHHHhhcCCChhhHHHHHHhhC-----------C-CHHHHHHHHHHhcCcHHHHH
Q 033806 39 STRVQEAMASIAASKAGDLNAMRMREKELAAVKINAADVDIIANELE-----------L-DKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 39 ~eai~~Am~~l~~~~~~~~~a~~~~e~el~~v~V~~eDV~LI~~ele-----------v-sk~kA~~aLre~~GDvv~Ai 106 (111)
..+|.++-..|+..+--+ ..|+.=.++-|.+||+ + +|+-|-=+|+...||+++||
T Consensus 9 E~AI~nah~Ll~~~RRGD-------------~~lp~lt~~QI~qQl~LaVdRVM~EgslyDreLAALAikQa~GD~~EAI 75 (367)
T COG3626 9 EKAIANAHRLLASRRRGD-------------TALPELTVAQIEQQLGLAVDRVMTEGSLYDRELAALALKQASGDLVEAI 75 (367)
T ss_pred HHHHHHHHHHHHhhhcCC-------------cccccccHHHHHHHhhhHHHHHhhccchhHHHHHHHHHHHhcchHHHHH
Confidence 356777777777653322 1222334444555544 3 67888889999999999998
Q ss_pred HHH
Q 033806 107 RHL 109 (111)
Q Consensus 107 ~~L 109 (111)
--|
T Consensus 76 FLl 78 (367)
T COG3626 76 FLL 78 (367)
T ss_pred HHH
Confidence 643
No 39
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=44.44 E-value=29 Score=20.10 Aligned_cols=22 Identities=27% Similarity=0.403 Sum_probs=16.1
Q ss_pred HHHHHHHHHHhcCcHHHHHHHH
Q 033806 88 KKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 88 k~kA~~aLre~~GDvv~Ai~~L 109 (111)
+.-=..+|+.|+|++..|=..|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 4555789999999998876654
No 40
>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=44.21 E-value=28 Score=21.44 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=17.3
Q ss_pred hHHHHHHhhCCCHHHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre 97 (111)
...-|++.++||+..+.++|+.
T Consensus 26 s~~~la~~~~vsr~tvr~al~~ 47 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRR 47 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHH
Confidence 3556899999999999999875
No 41
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=43.78 E-value=68 Score=21.48 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=25.5
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHH
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRH 108 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~ 108 (111)
.++-....++|+|...|.+..+.++.+.++.|..
T Consensus 9 ~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~ 42 (94)
T PF14490_consen 9 RELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKE 42 (94)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHH
Confidence 3555667889999999999999999998887763
No 42
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=42.79 E-value=39 Score=21.72 Aligned_cols=24 Identities=25% Similarity=0.398 Sum_probs=19.9
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHhc
Q 033806 76 DVDIIANELELDKKVAERTLREHK 99 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre~~ 99 (111)
.+.+|.++++||+..|.+.+.+-+
T Consensus 15 sa~mva~~L~vT~~~A~~li~eLg 38 (54)
T PF11972_consen 15 SAPMVAKELGVTPQAAQRLIAELG 38 (54)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHhh
Confidence 367889999999999999887654
No 43
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=41.90 E-value=37 Score=24.58 Aligned_cols=35 Identities=17% Similarity=0.067 Sum_probs=29.5
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAA 105 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~A 105 (111)
+++.+++.-++.+.++++..+...+...+||+..|
T Consensus 154 ~~~~~~~~~~l~~~gi~~~~~~~i~~~~~g~~r~~ 188 (188)
T TIGR00678 154 PLSEEALLQWLIRQGISEEAAELLLALAGGSPGAA 188 (188)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHcCCCcccC
Confidence 46778887777777999999999999999998654
No 44
>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=41.21 E-value=34 Score=22.76 Aligned_cols=21 Identities=14% Similarity=0.246 Sum_probs=19.2
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre 97 (111)
++-+|+-|+||+.++.++++|
T Consensus 55 ~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 55 IEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 778899999999999999886
No 45
>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=40.50 E-value=26 Score=20.55 Aligned_cols=21 Identities=19% Similarity=0.335 Sum_probs=16.5
Q ss_pred HHHHHHhhCCCHHHHHHHHHH
Q 033806 77 VDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre 97 (111)
|.-|+.+++||+..--+.|++
T Consensus 24 i~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 24 IAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHCcCHHHHHHHHhc
Confidence 667799999999988887765
No 46
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.39 E-value=43 Score=28.57 Aligned_cols=36 Identities=25% Similarity=0.388 Sum_probs=30.3
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHhC
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAIRHLLR 111 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~~ 111 (111)
+-|+-|| +||.+|...+++||..=++.-.|+-.|++
T Consensus 158 ~~I~~i~-eMGf~R~qV~~ALRAafNNPdRAVEYL~t 193 (378)
T TIGR00601 158 TTIEEIM-EMGYEREEVERALRAAFNNPDRAVEYLLT 193 (378)
T ss_pred HHHHHHH-HhCCCHHHHHHHHHHHhCCHHHHHHHHHh
Confidence 3455555 68999999999999999999999988863
No 47
>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=39.40 E-value=1e+02 Score=20.40 Aligned_cols=27 Identities=22% Similarity=0.255 Sum_probs=15.4
Q ss_pred hCC-CHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 84 LEL-DKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 84 lev-sk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
.++ |.+.--..|++++.|.-.|...|+
T Consensus 16 v~~hse~eIya~L~ecnMDpnea~qrLL 43 (60)
T PF06972_consen 16 VGCHSEEEIYAMLKECNMDPNEAVQRLL 43 (60)
T ss_pred hcCCCHHHHHHHHHHhCCCHHHHHHHHH
Confidence 344 555555566666666666655554
No 48
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=36.96 E-value=41 Score=30.21 Aligned_cols=25 Identities=40% Similarity=0.590 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 86 LDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 86 vsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
++|+...++|+..+|||-.|+-.|+
T Consensus 467 ~nre~nlqAL~atgGdi~aAverll 491 (493)
T KOG0010|consen 467 LDREANLQALRATGGDINAAVERLL 491 (493)
T ss_pred ccHHHHHHHHHHhcCcHHHHHHHHh
Confidence 5899999999999999999998875
No 49
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=36.92 E-value=34 Score=20.61 Aligned_cols=47 Identities=11% Similarity=0.330 Sum_probs=31.5
Q ss_pred hhhhhHHhhhcCHHHHHHHH-HHHHHh-hhcchHHHHHhHHHHhhcCCChhhHHHHHHhhCC
Q 033806 27 KLTDRVEDRQLDSTRVQEAM-ASIAAS-KAGDLNAMRMREKELAAVKINAADVDIIANELEL 86 (111)
Q Consensus 27 kvTD~~Eekeid~eai~~Am-~~l~~~-~~~~~~a~~~~e~el~~v~V~~eDV~LI~~elev 86 (111)
+|.+.+.+=.+++..|-+.+ +.++-. .+ ..-.|+.+.+.+|..++++
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~~~~-------------~~~~ld~e~~~~i~~~~~~ 53 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIMVKS-------------INSSLDEEEAELIAEEFGV 53 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS---S-------------SSS-EETTGGGHHHHHH--
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcCcCC-------------CCCcCCHHHHHHHHHHhCc
Confidence 57788888889988887777 547654 22 2446888899999888874
No 50
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=34.37 E-value=62 Score=22.66 Aligned_cols=37 Identities=11% Similarity=0.088 Sum_probs=25.1
Q ss_pred HhHHHHhhcCCChhhHHHHHHhhCCCHHHHHHHHHHh
Q 033806 62 MREKELAAVKINAADVDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 62 ~~e~el~~v~V~~eDV~LI~~elevsk~kA~~aLre~ 98 (111)
.+...|....|+++...|+++=..+.-.+-+.+|+.|
T Consensus 13 ~~~~~L~pG~vs~e~F~lLl~ls~IrS~kiI~AL~dy 49 (91)
T PF03333_consen 13 KKNGYLIPGKVSEEHFWLLLELSSIRSEKIIAALRDY 49 (91)
T ss_dssp HHHC---TT-S-HHHHHHHHHHS----HHHHHHHHHH
T ss_pred HhcCccCCCCcCHHHHHHHHHHCCCCcHHHHHHHHHH
Confidence 3566788899999999999999999999999999987
No 51
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.76 E-value=75 Score=18.10 Aligned_cols=22 Identities=14% Similarity=0.247 Sum_probs=18.5
Q ss_pred hHHHHHHhhCCCHHHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre 97 (111)
.+.-|++.++||+....++|+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4666899999999999988865
No 52
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=32.18 E-value=45 Score=25.37 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=19.8
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.| .-|+++++|||...+++|..
T Consensus 34 ~LPsE--~eLa~~~~VSR~TVR~Al~~ 58 (241)
T PRK10079 34 YLPAE--QQLAARYEVNRHTLRRAIDQ 58 (241)
T ss_pred cCCCH--HHHHHHHCCCHHHHHHHHHH
Confidence 45544 45799999999999999875
No 53
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=32.06 E-value=2.2e+02 Score=26.01 Aligned_cols=37 Identities=19% Similarity=0.425 Sum_probs=31.9
Q ss_pred CChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 72 INAADVDIIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 72 V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
|++--|..++ .||.++.-|.++|+.+++|+-.|+--|
T Consensus 374 vn~rs~~rL~-~mGyer~la~eaL~r~~Ndi~~aldll 410 (568)
T KOG2561|consen 374 VNPRSLERLV-SMGYERELAAEALRRNENDIQKALDLL 410 (568)
T ss_pred cCHHHHHHHH-hcchHhHHHHHHHHhccCcHHHHHHhc
Confidence 5777777776 589999999999999999999998654
No 54
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=31.90 E-value=41 Score=31.59 Aligned_cols=36 Identities=14% Similarity=0.323 Sum_probs=29.6
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAAIR 107 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~ 107 (111)
.++++-|..|+ .||.++.+|+++|+..+|+|..|.-
T Consensus 633 ~~~e~~v~si~-smGf~~~qa~~aL~~~n~nveravD 668 (763)
T KOG0944|consen 633 EVDEESVASIV-SMGFSRNQAIKALKATNNNVERAVD 668 (763)
T ss_pred CCChhHheeee-eecCcHHHHHHHHHhcCccHHHHHH
Confidence 35666666665 6899999999999999999988753
No 55
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=31.20 E-value=47 Score=25.63 Aligned_cols=25 Identities=16% Similarity=0.360 Sum_probs=19.5
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.|. -++++++|||...+++|.+
T Consensus 30 ~LPsE~--eLa~~f~VSR~TvRkAL~~ 54 (236)
T COG2188 30 KLPSER--ELAEQFGVSRMTVRKALDE 54 (236)
T ss_pred CCCCHH--HHHHHHCCcHHHHHHHHHH
Confidence 355442 4689999999999999975
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=30.90 E-value=82 Score=18.30 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=18.9
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHh
Q 033806 76 DVDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre~ 98 (111)
.+.-|++.+++|+..+.++|..-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L 49 (66)
T cd07377 27 SERELAEELGVSRTTVREALREL 49 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 46678999999999999888653
No 57
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=30.47 E-value=79 Score=18.84 Aligned_cols=23 Identities=9% Similarity=0.304 Sum_probs=16.4
Q ss_pred hHHHHHHhhCCCHHHHHHHHHHh
Q 033806 76 DVDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre~ 98 (111)
++.-+..++++|+..|++..+.+
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~C 33 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQC 33 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHS
T ss_pred CHHHHHHHHccCHHHHHHHHHHC
Confidence 45667889999999999988764
No 58
>PF13730 HTH_36: Helix-turn-helix domain
Probab=29.80 E-value=86 Score=18.32 Aligned_cols=22 Identities=18% Similarity=0.560 Sum_probs=18.5
Q ss_pred hHHHHHHhhCCCHHHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre 97 (111)
-++-|+..+++|+....++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4788999999999988887765
No 59
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=29.50 E-value=63 Score=24.52 Aligned_cols=32 Identities=22% Similarity=0.316 Sum_probs=26.5
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 75 ADVDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
-.+.-|.++||||+....+.||..-.-++.++
T Consensus 179 ~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~ 210 (215)
T COG3413 179 VSLKDLAKELGISKSTLSEHLRRAERKLIEAY 210 (215)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 45666899999999999999998877776654
No 60
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=28.97 E-value=56 Score=24.57 Aligned_cols=19 Identities=5% Similarity=0.202 Sum_probs=17.1
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 033806 79 IIANELELDKKVAERTLRE 97 (111)
Q Consensus 79 LI~~elevsk~kA~~aLre 97 (111)
-|+++++|||...+++|+.
T Consensus 36 eLae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 36 ELSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 5799999999999999975
No 61
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=28.78 E-value=1.3e+02 Score=17.53 Aligned_cols=29 Identities=10% Similarity=0.077 Sum_probs=20.5
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhc
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHK 99 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~ 99 (111)
.|+.+++.-++..++++...+.+.++..+
T Consensus 15 ~i~~~el~~~l~~~g~~~~~~~~i~~~~d 43 (67)
T cd00052 15 LISGDEARPFLGKSGLPRSVLAQIWDLAD 43 (67)
T ss_pred cCcHHHHHHHHHHcCCCHHHHHHHHHHhc
Confidence 46667777777777777777777776654
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=28.34 E-value=59 Score=24.31 Aligned_cols=25 Identities=12% Similarity=0.272 Sum_probs=19.5
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.| .-++++++|||...+++|..
T Consensus 31 ~LPsE--~eLa~~~~VSR~TvR~Al~~ 55 (238)
T TIGR02325 31 YLPAE--MQLAERFGVNRHTVRRAIAA 55 (238)
T ss_pred cCcCH--HHHHHHHCCCHHHHHHHHHH
Confidence 45433 35799999999999999875
No 63
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=28.29 E-value=71 Score=21.63 Aligned_cols=25 Identities=28% Similarity=0.376 Sum_probs=19.3
Q ss_pred HHHHHhhCCCHH---HHHHHHHHhcCcH
Q 033806 78 DIIANELELDKK---VAERTLREHKGDA 102 (111)
Q Consensus 78 ~LI~~elevsk~---kA~~aLre~~GDv 102 (111)
+-|.++|||||. +..+.||+.|=+|
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~~I 50 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGVDI 50 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCCce
Confidence 346789999996 6788899887654
No 64
>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=27.75 E-value=61 Score=24.42 Aligned_cols=25 Identities=4% Similarity=0.166 Sum_probs=19.8
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.| .-++++++|||...+++|.+
T Consensus 23 ~LPsE--~eLa~~~gVSR~TVR~Al~~ 47 (233)
T TIGR02404 23 YLPSE--HELMDQYGASRETVRKALNL 47 (233)
T ss_pred CCcCH--HHHHHHHCCCHHHHHHHHHH
Confidence 45544 35799999999999999875
No 65
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=26.92 E-value=96 Score=19.44 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=20.1
Q ss_pred hhHHHHHHhhCCCHHHHHHHHHHh
Q 033806 75 ADVDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLre~ 98 (111)
-.+.-|.++||||+...-+.||..
T Consensus 24 ~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 356678899999999999999864
No 66
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=26.58 E-value=1.6e+02 Score=24.37 Aligned_cols=39 Identities=18% Similarity=0.137 Sum_probs=30.3
Q ss_pred CCChhhHH-HHHHhhCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 71 KINAADVD-IIANELELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 71 ~V~~eDV~-LI~~elevsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.++.+.+. .+.++.+++...|..+++-.+|++..|+.-+
T Consensus 166 ~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~ 205 (334)
T PRK07993 166 PPPEQYALTWLSREVTMSQDALLAALRLSAGAPGAALALL 205 (334)
T ss_pred CCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 34566666 4556679999999999999999999887543
No 67
>PRK07217 replication factor A; Reviewed
Probab=26.08 E-value=95 Score=26.25 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=24.1
Q ss_pred hhHHHHHHhhCCCHHHHHHHHH-----HhcCcH
Q 033806 75 ADVDIIANELELDKKVAERTLR-----EHKGDA 102 (111)
Q Consensus 75 eDV~LI~~elevsk~kA~~aLr-----e~~GDv 102 (111)
++.++++.++.|+...|++.++ +++++.
T Consensus 29 ~~L~~Lv~ey~VP~~EA~rSv~~~~~~k~g~~~ 61 (311)
T PRK07217 29 ERLDTLVTEFKVPEDEARRSVTNYYLKEAGIDR 61 (311)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCc
Confidence 5668999999999999999877 888865
No 68
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=26.05 E-value=1.8e+02 Score=19.54 Aligned_cols=28 Identities=4% Similarity=0.159 Sum_probs=15.2
Q ss_pred hcCCChhhHHHHHHhhCCCHHHHHHHHH
Q 033806 69 AVKINAADVDIIANELELDKKVAERTLR 96 (111)
Q Consensus 69 ~v~V~~eDV~LI~~elevsk~kA~~aLr 96 (111)
..+++..+|+-|-..--..+++..+.|+
T Consensus 20 ~LGlse~~Id~ie~~~~~~~Eq~yqmL~ 47 (80)
T cd08313 20 RLGLSDNEIERVELDHRRCRDAQYQMLK 47 (80)
T ss_pred HcCCCHHHHHHHHHhCCChHHHHHHHHH
Confidence 3455566666665554444555555554
No 69
>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=25.85 E-value=1.1e+02 Score=18.73 Aligned_cols=24 Identities=29% Similarity=0.454 Sum_probs=20.0
Q ss_pred hhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 74 AADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 74 ~eDV~LI~~elevsk~kA~~aLre 97 (111)
+-.+.-|.+.+++|+..+.+.|+.
T Consensus 22 ~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 22 PATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp HEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 445677899999999999998875
No 70
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=25.48 E-value=1.2e+02 Score=16.96 Aligned_cols=22 Identities=23% Similarity=0.237 Sum_probs=17.2
Q ss_pred hHHHHHHhhCCCHHHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre 97 (111)
.+.-|++++++|+..+.+.|+.
T Consensus 12 ~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 12 CVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cHHHHHHHHCCCHHHHHHHHHH
Confidence 3445788899999998888764
No 71
>PRK14999 histidine utilization repressor; Provisional
Probab=24.83 E-value=73 Score=24.22 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=17.4
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 033806 78 DIIANELELDKKVAERTLRE 97 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre 97 (111)
.-++++++|||...+++|..
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~ 59 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRE 59 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 45799999999999999875
No 72
>PF12959 DUF3848: Protein of unknown function (DUF3848); InterPro: IPR024380 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences[].
Probab=24.82 E-value=84 Score=22.65 Aligned_cols=24 Identities=29% Similarity=0.403 Sum_probs=21.6
Q ss_pred hhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 74 AADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 74 ~eDV~LI~~elevsk~kA~~aLre 97 (111)
++||-+.|+++++|..+|..+|+.
T Consensus 39 keDi~m~~ee~~l~~~qa~ALl~s 62 (101)
T PF12959_consen 39 KEDILMAMEELELPDQQAKALLKS 62 (101)
T ss_pred HHHHHHHHHHccCCHHHHHHHHcC
Confidence 689999999999999999888864
No 73
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=24.23 E-value=1.1e+02 Score=20.50 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=19.5
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
|+.|.+++++|+..+...+..--.-+.++|
T Consensus 7 i~~ia~~~~~s~~~~~~~v~~~~~~i~~~L 36 (90)
T PRK10753 7 IDVIADKAELSKTQAKAALESTLAAITESL 36 (90)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 566777788888888777755444444443
No 74
>PRK03837 transcriptional regulator NanR; Provisional
Probab=23.60 E-value=77 Score=23.73 Aligned_cols=20 Identities=5% Similarity=0.122 Sum_probs=17.6
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 033806 78 DIIANELELDKKVAERTLRE 97 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre 97 (111)
.-|+++++|||...+++|+.
T Consensus 41 ~~Lae~~gVSRt~VREAL~~ 60 (241)
T PRK03837 41 RELMAFFGVGRPAVREALQA 60 (241)
T ss_pred HHHHHHhCCCHHHHHHHHHH
Confidence 45799999999999999975
No 75
>PF14502 HTH_41: Helix-turn-helix domain
Probab=23.32 E-value=93 Score=19.58 Aligned_cols=28 Identities=11% Similarity=0.234 Sum_probs=24.9
Q ss_pred hhhhhhhHHhhhcCHHHHHHHHHHHHHh
Q 033806 25 LDKLTDRVEDRQLDSTRVQEAMASIAAS 52 (111)
Q Consensus 25 LekvTD~~Eekeid~eai~~Am~~l~~~ 52 (111)
|..|++|.++=.++.=-||+|++.|...
T Consensus 6 i~tI~e~~~~~~vs~GtiQ~Alk~Le~~ 33 (48)
T PF14502_consen 6 IPTISEYSEKFGVSRGTIQNALKFLEEN 33 (48)
T ss_pred cCCHHHHHHHhCcchhHHHHHHHHHHHC
Confidence 6689999999999999999999998754
No 76
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=23.28 E-value=82 Score=23.89 Aligned_cols=25 Identities=4% Similarity=0.298 Sum_probs=19.7
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.| .-++++++|||...+++|..
T Consensus 32 kLPsE--~eLa~~~~VSR~TvR~Al~~ 56 (241)
T PRK11402 32 QIPTE--NELCTQYNVSRITIRKAISD 56 (241)
T ss_pred cCcCH--HHHHHHHCCCHHHHHHHHHH
Confidence 45554 34699999999999999865
No 77
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=23.08 E-value=79 Score=23.77 Aligned_cols=19 Identities=5% Similarity=0.202 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 033806 79 IIANELELDKKVAERTLRE 97 (111)
Q Consensus 79 LI~~elevsk~kA~~aLre 97 (111)
-|++++||||.-.+++|+.
T Consensus 35 ~La~~lgVSRtpVREAL~~ 53 (235)
T TIGR02812 35 ELSELIGVTRTTLREVLQR 53 (235)
T ss_pred HHHHHHCcCHHHHHHHHHH
Confidence 5799999999999999975
No 78
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=22.69 E-value=68 Score=23.95 Aligned_cols=27 Identities=11% Similarity=0.162 Sum_probs=20.9
Q ss_pred hcCCChhhHHHHHHhhCCCHHHHHHHHHHh
Q 033806 69 AVKINAADVDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 69 ~v~V~~eDV~LI~~elevsk~kA~~aLre~ 98 (111)
.-+++.. -|++++||||.-.+++|+.-
T Consensus 32 G~~L~e~---~La~~lgVSRtpVREAL~~L 58 (221)
T PRK11414 32 GARLITK---NLAEQLGMSITPVREALLRL 58 (221)
T ss_pred CCccCHH---HHHHHHCCCchhHHHHHHHH
Confidence 3456542 48999999999999999753
No 79
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=1.4e+02 Score=21.03 Aligned_cols=40 Identities=8% Similarity=0.056 Sum_probs=31.6
Q ss_pred CChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHhC
Q 033806 72 INAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLLR 111 (111)
Q Consensus 72 V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~~ 111 (111)
+..-..+-|.+.||+|.......|....-.+.+.|..++|
T Consensus 133 ~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~~ 172 (173)
T PRK12522 133 YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFVH 172 (173)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5566777889999999999888888777777777776664
No 80
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=22.29 E-value=1.4e+02 Score=18.64 Aligned_cols=24 Identities=13% Similarity=0.189 Sum_probs=19.6
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcC
Q 033806 77 VDIIANELELDKKVAERTLREHKG 100 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~G 100 (111)
|+...+.+++|...|-+.|.+.++
T Consensus 8 Ie~~A~~~~~s~~ea~~~~~~~~~ 31 (62)
T PF12668_consen 8 IEEFAKKLNISGEEAYNYFKRSGV 31 (62)
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCc
Confidence 566778889999999999887775
No 81
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.20 E-value=1.3e+02 Score=21.59 Aligned_cols=40 Identities=13% Similarity=0.146 Sum_probs=33.9
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHHhcCcHHHHHHHHh
Q 033806 71 KINAADVDIIANELELDKKVAERTLREHKGDAVAAIRHLL 110 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre~~GDvv~Ai~~L~ 110 (111)
-+..-.++-|.+.||+|.......|.....-+...|..|+
T Consensus 151 ~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~ 190 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLL 190 (193)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4667788999999999999999999888888888887654
No 82
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=21.77 E-value=1.4e+02 Score=18.19 Aligned_cols=22 Identities=23% Similarity=0.372 Sum_probs=18.1
Q ss_pred hHHHHHHhhCCCHHHHHHHHHH
Q 033806 76 DVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 76 DV~LI~~elevsk~kA~~aLre 97 (111)
-|.-+++.|+||+..+++=|..
T Consensus 16 s~~ela~~~~VS~~TiRRDl~~ 37 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRRDLNK 37 (57)
T ss_pred EHHHHHHHHCcCHHHHHHHHHH
Confidence 3667889999999999987753
No 83
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=21.73 E-value=1.5e+02 Score=20.96 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=23.8
Q ss_pred hcCCChhhHHHHHHhh--------CCCHHHHHHHHHH
Q 033806 69 AVKINAADVDIIANEL--------ELDKKVAERTLRE 97 (111)
Q Consensus 69 ~v~V~~eDV~LI~~el--------evsk~kA~~aLre 97 (111)
.-=+-.|=|+.|++.+ ++||.+|.++++.
T Consensus 28 ~CF~gsEAVDwL~~~l~~n~~fg~~vtR~~av~l~qk 64 (92)
T cd04447 28 NCFTASEAVDWLHELLRSNSNFGPEVTRQQTVQLLKK 64 (92)
T ss_pred cccchHHHHHHHHHHHHhccccCCCCCHHHHHHHHHH
Confidence 3345678899999999 9999999998764
No 84
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=21.65 E-value=93 Score=23.71 Aligned_cols=25 Identities=12% Similarity=0.348 Sum_probs=19.8
Q ss_pred CCChhhHHHHHHhhCCCHHHHHHHHHH
Q 033806 71 KINAADVDIIANELELDKKVAERTLRE 97 (111)
Q Consensus 71 ~V~~eDV~LI~~elevsk~kA~~aLre 97 (111)
+++.| .-++++++|||...+++|..
T Consensus 28 ~LPsE--~eL~~~~~VSR~TvR~Al~~ 52 (240)
T PRK09764 28 ALPTE--SALQTEFGVSRVTVRQALRQ 52 (240)
T ss_pred cCCCH--HHHHHHHCCCHHHHHHHHHH
Confidence 45544 35799999999999999875
No 85
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=21.36 E-value=89 Score=23.88 Aligned_cols=20 Identities=25% Similarity=0.303 Sum_probs=17.5
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 033806 78 DIIANELELDKKVAERTLRE 97 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre 97 (111)
.-|++++||||.-.+++|+.
T Consensus 37 ~eLa~~~gVSRtpVREAL~~ 56 (257)
T PRK10225 37 REIAEMLDVTRTVVREALIM 56 (257)
T ss_pred HHHHHHhCCCHHHHHHHHHH
Confidence 35799999999999999975
No 86
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.20 E-value=1.5e+02 Score=17.21 Aligned_cols=22 Identities=23% Similarity=0.456 Sum_probs=16.3
Q ss_pred HHHHHHhhCCCHHHHHHHHHHh
Q 033806 77 VDIIANELELDKKVAERTLREH 98 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~ 98 (111)
+.-|+++|+||+....+-|..-
T Consensus 18 ~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 18 AKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHHHH
Confidence 4567899999999888877653
No 87
>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=21.20 E-value=1.4e+02 Score=19.05 Aligned_cols=30 Identities=27% Similarity=0.192 Sum_probs=19.8
Q ss_pred HHHHHHhhCCCHHHHHHHHHHhcCcHHHHH
Q 033806 77 VDIIANELELDKKVAERTLREHKGDAVAAI 106 (111)
Q Consensus 77 V~LI~~elevsk~kA~~aLre~~GDvv~Ai 106 (111)
|..|.+++++|+..+...|...-.-+.++|
T Consensus 7 i~~ia~~~~~s~~~v~~vl~~~~~~i~~~L 36 (90)
T PF00216_consen 7 IKRIAEKTGLSKKDVEAVLDALFDVIKEAL 36 (90)
T ss_dssp HHHHHHHHTSSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHH
Confidence 566777778888887777766554444444
No 88
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=20.94 E-value=92 Score=23.68 Aligned_cols=20 Identities=5% Similarity=0.270 Sum_probs=17.5
Q ss_pred HHHHhhCCCHHHHHHHHHHh
Q 033806 79 IIANELELDKKVAERTLREH 98 (111)
Q Consensus 79 LI~~elevsk~kA~~aLre~ 98 (111)
-|++++||||.-.+++|+.-
T Consensus 39 eLa~~lgVSRtpVREAL~~L 58 (254)
T PRK09464 39 ELAKQFDVSRPSLREAIQRL 58 (254)
T ss_pred HHHHHhCCCHHHHHHHHHHH
Confidence 57999999999999999753
No 89
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=20.89 E-value=93 Score=23.63 Aligned_cols=19 Identities=11% Similarity=0.212 Sum_probs=17.0
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 033806 79 IIANELELDKKVAERTLRE 97 (111)
Q Consensus 79 LI~~elevsk~kA~~aLre 97 (111)
-|++++||||.-.+++|+.
T Consensus 36 eLa~~~gVSRtpVREAL~~ 54 (251)
T PRK09990 36 RLCEKLGFSRSALREGLTV 54 (251)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 5789999999999999975
No 90
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=20.80 E-value=1.2e+02 Score=18.98 Aligned_cols=20 Identities=20% Similarity=0.262 Sum_probs=15.7
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 033806 78 DIIANELELDKKVAERTLRE 97 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre 97 (111)
.-|.+.|+||+..+.+.|+.
T Consensus 26 ~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 26 KDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp HHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHCCChHHHHHHHHH
Confidence 34688999999999998875
No 91
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=20.73 E-value=88 Score=23.24 Aligned_cols=23 Identities=4% Similarity=0.157 Sum_probs=19.3
Q ss_pred HHHHHhhCCCHHHHHHHHHHhcC
Q 033806 78 DIIANELELDKKVAERTLREHKG 100 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre~~G 100 (111)
.-++++++|||...+++|+.-.+
T Consensus 29 ~eLa~~~~Vsr~Tvr~Al~~L~~ 51 (231)
T TIGR03337 29 RDLGERFNTTRVTIREALQQLEA 51 (231)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 45799999999999999987554
No 92
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.43 E-value=2.9e+02 Score=18.86 Aligned_cols=26 Identities=8% Similarity=0.257 Sum_probs=11.6
Q ss_pred cCCChhhHHHHHHhhCCCHHHHHHHH
Q 033806 70 VKINAADVDIIANELELDKKVAERTL 95 (111)
Q Consensus 70 v~V~~eDV~LI~~elevsk~kA~~aL 95 (111)
.+++..+|+-|...---++.+..+.|
T Consensus 29 LGLse~~I~~i~~~~~~~~eq~~qmL 54 (96)
T cd08315 29 LGLSENEIDVAKANERVTREQLYQML 54 (96)
T ss_pred cCCCHHHHHHHHHHCCCCHHHHHHHH
Confidence 44444455444444333344444444
No 93
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=20.21 E-value=85 Score=24.45 Aligned_cols=19 Identities=16% Similarity=0.389 Sum_probs=16.6
Q ss_pred HHHHhhCCCHHHHHHHHHH
Q 033806 79 IIANELELDKKVAERTLRE 97 (111)
Q Consensus 79 LI~~elevsk~kA~~aLre 97 (111)
-++++|||||..-+++|+.
T Consensus 39 eLae~fgVSR~~vREAl~~ 57 (241)
T COG2186 39 ELAERFGVSRTVVREALKR 57 (241)
T ss_pred HHHHHHCCCcHHHHHHHHH
Confidence 4689999999999999874
No 94
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=20.15 E-value=1e+02 Score=23.14 Aligned_cols=20 Identities=20% Similarity=0.336 Sum_probs=17.4
Q ss_pred HHHHHhhCCCHHHHHHHHHH
Q 033806 78 DIIANELELDKKVAERTLRE 97 (111)
Q Consensus 78 ~LI~~elevsk~kA~~aLre 97 (111)
.-++++++|||...+++|..
T Consensus 29 ~eLa~~~~VSR~TVR~Al~~ 48 (230)
T TIGR02018 29 HELVAQYGCSRMTVNRALRE 48 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 45789999999999999865
No 95
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=20.03 E-value=3.1e+02 Score=21.20 Aligned_cols=40 Identities=18% Similarity=0.087 Sum_probs=30.2
Q ss_pred cCCChhhHHHHHHh------hCCCHHHHHHHHHHhcCcHHHHHHHH
Q 033806 70 VKINAADVDIIANE------LELDKKVAERTLREHKGDAVAAIRHL 109 (111)
Q Consensus 70 v~V~~eDV~LI~~e------levsk~kA~~aLre~~GDvv~Ai~~L 109 (111)
.+++.+++.-++.+ +.++...+...++..+||+..++..|
T Consensus 182 ~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l 227 (337)
T PRK12402 182 RAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTL 227 (337)
T ss_pred cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 34566776655544 35789999999999999999888765
Done!