Query psy12192
Match_columns 82
No_of_seqs 26 out of 28
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 21:08:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12192.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12192hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2301|consensus 96.1 0.0027 5.9E-08 58.7 1.8 62 1-69 1498-1559(1592)
2 cd06171 Sigma70_r4 Sigma70, re 73.9 2.1 4.5E-05 21.8 1.2 18 15-32 38-55 (55)
3 PF04545 Sigma70_r4: Sigma-70, 73.8 2.8 6.1E-05 23.3 1.8 19 15-33 32-50 (50)
4 TIGR02937 sigma70-ECF RNA poly 66.5 5 0.00011 23.9 1.9 19 15-33 138-156 (158)
5 cd06170 LuxR_C_like C-terminal 66.1 4.3 9.4E-05 21.5 1.4 18 16-33 28-45 (57)
6 TIGR02985 Sig70_bacteroi1 RNA 61.1 7.3 0.00016 24.3 1.9 19 15-33 141-159 (161)
7 smart00421 HTH_LUXR helix_turn 58.5 7.5 0.00016 20.2 1.5 20 15-34 30-49 (58)
8 PRK09652 RNA polymerase sigma 56.7 9.7 0.00021 24.3 2.0 18 16-33 157-174 (182)
9 PRK06759 RNA polymerase factor 56.1 9.8 0.00021 24.2 1.9 18 16-33 135-152 (154)
10 PRK11924 RNA polymerase sigma 49.3 14 0.00031 23.4 1.9 17 17-33 155-171 (179)
11 PF13384 HTH_23: Homeodomain-l 48.9 7.6 0.00017 21.2 0.5 13 15-27 29-41 (50)
12 PRK09640 RNA polymerase sigma 46.0 18 0.00039 24.2 2.0 18 16-33 163-180 (188)
13 PF12240 Angiomotin_C: Angiomo 45.8 24 0.00052 27.2 2.9 38 17-54 26-63 (205)
14 PF10550 Toxin_36: Conantokin- 43.8 17 0.00036 18.1 1.2 8 12-19 2-9 (15)
15 TIGR02939 RpoE_Sigma70 RNA pol 42.6 23 0.00051 23.1 2.2 17 17-33 168-184 (190)
16 TIGR02983 SigE-fam_strep RNA p 42.4 23 0.0005 22.7 2.1 18 16-33 139-156 (162)
17 PF06405 RCC_reductase: Red ch 40.8 37 0.0008 26.9 3.3 23 6-28 176-201 (255)
18 PRK12519 RNA polymerase sigma 39.5 26 0.00056 23.3 2.0 18 16-33 170-187 (194)
19 PLN02581 red chlorophyll catab 39.4 35 0.00076 27.3 3.1 24 6-29 186-212 (267)
20 PF07037 DUF1323: Putative tra 39.3 18 0.00039 26.0 1.3 12 15-26 12-23 (122)
21 PRK12513 RNA polymerase sigma 38.4 26 0.00056 23.4 1.9 19 15-33 167-185 (194)
22 PRK09646 RNA polymerase sigma 38.4 25 0.00054 23.7 1.9 18 16-33 171-188 (194)
23 cd04761 HTH_MerR-SF Helix-Turn 35.5 21 0.00046 18.9 0.9 13 15-27 12-24 (49)
24 PRK05602 RNA polymerase sigma 33.4 40 0.00088 22.3 2.2 19 15-33 156-174 (186)
25 KOG2251|consensus 32.8 30 0.00065 27.2 1.7 28 11-38 66-99 (228)
26 PRK09644 RNA polymerase sigma 32.8 39 0.00085 21.9 2.0 18 16-33 137-154 (165)
27 cd04762 HTH_MerR-trunc Helix-T 32.1 25 0.00054 17.9 0.9 13 15-27 12-24 (49)
28 PRK12539 RNA polymerase sigma 31.7 41 0.0009 22.4 2.0 18 16-33 160-177 (184)
29 PF00196 GerE: Bacterial regul 31.6 47 0.001 18.8 2.0 20 15-34 30-49 (58)
30 PF13518 HTH_28: Helix-turn-he 31.6 27 0.00059 18.7 1.0 14 14-27 23-36 (52)
31 TIGR02952 Sig70_famx2 RNA poly 31.2 42 0.00092 21.4 2.0 18 16-33 151-168 (170)
32 COG3309 VapD Uncharacterized v 31.1 37 0.00081 23.7 1.8 19 13-33 61-79 (96)
33 cd00569 HTH_Hin_like Helix-tur 31.0 15 0.00032 16.3 -0.1 10 15-24 33-42 (42)
34 PF05581 MCP_N: Vibrio chemota 30.1 80 0.0017 21.7 3.3 25 3-27 30-60 (103)
35 PRK12524 RNA polymerase sigma 28.9 54 0.0012 22.1 2.3 19 15-33 164-182 (196)
36 PF01710 HTH_Tnp_IS630: Transp 28.5 40 0.00086 22.1 1.5 12 14-25 29-40 (119)
37 TIGR02479 FliA_WhiG RNA polyme 28.0 52 0.0011 22.9 2.1 18 16-33 204-221 (224)
38 PRK13919 putative RNA polymera 28.0 55 0.0012 21.5 2.1 18 16-33 164-181 (186)
39 PF13551 HTH_29: Winged helix- 27.9 35 0.00076 20.4 1.1 13 15-27 24-36 (112)
40 PRK09415 RNA polymerase factor 27.7 50 0.0011 22.0 1.9 17 17-33 157-173 (179)
41 PRK12547 RNA polymerase sigma 27.5 55 0.0012 21.4 2.0 18 16-33 141-158 (164)
42 TIGR02980 SigBFG RNA polymeras 26.7 61 0.0013 22.4 2.3 19 15-33 206-224 (227)
43 PF14766 RPA_interact_N: Repli 26.3 65 0.0014 18.7 2.0 19 25-46 21-39 (42)
44 PRK04439 S-adenosylmethionine 26.3 47 0.001 27.8 1.9 20 13-32 104-123 (399)
45 PRK08301 sporulation sigma fac 25.9 58 0.0013 22.7 2.0 19 15-33 210-228 (234)
46 TIGR02954 Sig70_famx3 RNA poly 25.7 56 0.0012 21.2 1.8 18 16-33 148-165 (169)
47 TIGR02948 SigW_bacill RNA poly 25.7 61 0.0013 21.1 2.0 18 16-33 165-182 (187)
48 PF04362 Iron_traffic: Bacteri 25.6 78 0.0017 21.4 2.6 32 6-48 25-56 (88)
49 KOG3908|consensus 25.6 62 0.0014 27.3 2.5 43 11-54 163-211 (396)
50 PRK09648 RNA polymerase sigma 25.4 61 0.0013 21.5 2.0 18 16-33 168-185 (189)
51 COG1804 CaiB Predicted acyl-Co 24.9 73 0.0016 26.0 2.7 27 3-29 284-310 (396)
52 PRK06811 RNA polymerase factor 24.8 61 0.0013 21.8 1.9 18 16-33 160-177 (189)
53 cd08786 CARD_RIP2_CARD3 Caspas 24.3 71 0.0015 22.0 2.2 30 1-30 31-60 (87)
54 PRK12537 RNA polymerase sigma 22.8 70 0.0015 21.3 1.9 19 15-33 161-179 (182)
55 KOG3250|consensus 22.5 1.2E+02 0.0027 24.3 3.5 17 17-33 170-189 (258)
56 TIGR02950 SigM_subfam RNA poly 22.4 80 0.0017 19.9 2.0 17 17-33 135-151 (154)
57 PF09337 zf-H2C2: His(2)-Cys(2 22.2 50 0.0011 18.8 1.0 12 17-28 25-36 (39)
58 PF01527 HTH_Tnp_1: Transposas 22.2 61 0.0013 18.6 1.4 15 14-28 34-48 (76)
59 PF00533 BRCT: BRCA1 C Terminu 22.0 58 0.0013 18.0 1.2 7 22-28 72-78 (78)
60 PRK11923 algU RNA polymerase s 22.0 82 0.0018 20.9 2.1 17 17-33 168-184 (193)
61 PRK09647 RNA polymerase sigma 21.8 75 0.0016 22.2 2.0 17 17-33 168-184 (203)
62 PF01941 AdoMet_Synthase: S-ad 21.5 68 0.0015 26.8 2.0 20 13-32 104-123 (396)
63 PRK05408 oxidative damage prot 21.4 1.7E+02 0.0037 19.9 3.6 32 6-48 25-56 (90)
64 PRK06986 fliA flagellar biosyn 21.3 80 0.0017 22.2 2.0 18 16-33 213-230 (236)
65 PRK12541 RNA polymerase sigma 21.2 83 0.0018 20.3 2.0 18 16-33 141-158 (161)
66 PF04218 CENP-B_N: CENP-B N-te 21.2 32 0.00069 20.1 0.0 14 13-26 32-45 (53)
67 smart00292 BRCT breast cancer 21.0 57 0.0012 17.2 1.0 8 22-29 71-78 (80)
68 PRK12514 RNA polymerase sigma 20.8 79 0.0017 20.7 1.8 17 17-33 159-175 (179)
69 PRK02998 prsA peptidylprolyl i 20.6 2.6E+02 0.0056 20.8 4.7 31 3-33 232-262 (283)
70 PRK12536 RNA polymerase sigma 20.5 89 0.0019 20.7 2.0 18 16-33 158-175 (181)
71 PF12876 Cellulase-like: Sugar 20.4 1.2E+02 0.0026 18.6 2.5 19 16-34 36-54 (88)
72 PF08281 Sigma70_r4_2: Sigma-7 20.1 1.1E+02 0.0023 16.7 2.1 16 16-31 39-54 (54)
73 PF04550 Phage_holin_2: Phage 20.1 60 0.0013 22.3 1.2 14 17-30 76-89 (89)
No 1
>KOG2301|consensus
Probab=96.14 E-value=0.0027 Score=58.74 Aligned_cols=62 Identities=11% Similarity=0.061 Sum_probs=46.1
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhhhhccccchhhhcccc
Q psy12192 1 MLAREEIEYIIEEEVAKQTIRNWLEACLKKIRATNKQQTSLIAGLRATNEMLHMQDHLEDKTKDKQAEK 69 (82)
Q Consensus 1 Ll~REelEy~IeEEVAkqTIr~WLe~CLkr~r~~~kqq~~li~~lr~~~~q~~~~~~~~~~~~~~~~~~ 69 (82)
++++|++++.|+++||++||++ +.+|++..+. ...|....+.....++..+..+ .+.+...+
T Consensus 1498 ~~q~e~~~~~~~~~i~~~~i~~-~l~~l~~~~~-----a~~i~~~y~~~~~~~~~~~~~~-~~~~~~~~ 1559 (1592)
T KOG2301|consen 1498 ELQEEEFLASIPSKISYEPITT-TLKRLQEPLS-----ATIIQRAYRGYLLRDSDKRSSK-DERDGDFR 1559 (1592)
T ss_pred HHHHHHHHhhcchhhccchHHH-HHHhhccchh-----hHHHHHHHHHHHHHHHHhhccc-cccccccc
Confidence 4689999999999999999999 9999998776 4556666665555555555555 55555544
No 2
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=73.95 E-value=2.1 Score=21.82 Aligned_cols=18 Identities=39% Similarity=0.717 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIR 32 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r 32 (82)
++..||..|+.+|..++|
T Consensus 38 ~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 38 ISRSTVRQRLHRALKKLR 55 (55)
T ss_pred cCHHHHHHHHHHHHHHcC
Confidence 345799999999877654
No 3
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.80 E-value=2.8 Score=23.27 Aligned_cols=19 Identities=37% Similarity=0.676 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
++.+||+.++.++|+++|.
T Consensus 32 ~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 32 ISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp SCHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhcC
Confidence 3468999999999999983
No 4
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=66.52 E-value=5 Score=23.90 Aligned_cols=19 Identities=26% Similarity=0.445 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
|...||+.++.+|++++|.
T Consensus 138 ~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 138 ISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHHHHHHHHHHh
Confidence 4567999999999999884
No 5
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=66.08 E-value=4.3 Score=21.49 Aligned_cols=18 Identities=17% Similarity=0.471 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||+.|+.++.+++..
T Consensus 28 s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 28 SEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CHHHHHHHHHHHHHHhCC
Confidence 456799999999888887
No 6
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=61.11 E-value=7.3 Score=24.26 Aligned_cols=19 Identities=21% Similarity=0.464 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
++..||+.++.+|++++|.
T Consensus 141 is~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 141 ISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHHHHHh
Confidence 3457999999999999885
No 7
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=58.52 E-value=7.5 Score=20.24 Aligned_cols=20 Identities=15% Similarity=0.469 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy12192 15 VAKQTIRNWLEACLKKIRAT 34 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~~ 34 (82)
|+..||+.|+.+.++++...
T Consensus 30 is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 30 ISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHHHHHHHHCCC
Confidence 56788999999998888763
No 8
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=56.66 E-value=9.7 Score=24.30 Aligned_cols=18 Identities=22% Similarity=0.263 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||++|+.+|++++|.
T Consensus 157 s~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 157 PIGTVRSRIFRAREALRA 174 (182)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 347999999999999986
No 9
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=56.06 E-value=9.8 Score=24.16 Aligned_cols=18 Identities=22% Similarity=0.283 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||++++.++++++|.
T Consensus 135 s~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 135 TYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CHHHHHHHHHHHHHHHhh
Confidence 457999999999999986
No 10
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=49.30 E-value=14 Score=23.42 Aligned_cols=17 Identities=18% Similarity=0.274 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||++|+.+|.+++|.
T Consensus 155 ~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 155 VGTVKSRLRRARQLLRE 171 (179)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46999999999999986
No 11
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=48.87 E-value=7.6 Score=21.17 Aligned_cols=13 Identities=23% Similarity=0.733 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEAC 27 (82)
Q Consensus 15 VAkqTIr~WLe~C 27 (82)
|+.+||..|+.+.
T Consensus 29 vs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 29 VSRSTVYRWIKRY 41 (50)
T ss_dssp S-HHHHHHHHT--
T ss_pred cCHHHHHHHHHHc
Confidence 5678999998764
No 12
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=46.01 E-value=18 Score=24.25 Aligned_cols=18 Identities=17% Similarity=0.257 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+-.||+++|.+|++++|.
T Consensus 163 s~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 163 GLSATKMRYKRALDKLRE 180 (188)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 457999999999999997
No 13
>PF12240 Angiomotin_C: Angiomotin C terminal; InterPro: IPR024646 This domain represents the C-terminal region of angiomotin. Angiomotin regulates the action of angiogenesis-inhibitor angiostatin []. The C-terminal region of angiomotin appears to be involved in directing the protein chemotactically [].
Probab=45.76 E-value=24 Score=27.19 Aligned_cols=38 Identities=24% Similarity=0.226 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhh
Q psy12192 17 KQTIRNWLEACLKKIRATNKQQTSLIAGLRATNEMLHM 54 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~~~kqq~~li~~lr~~~~q~~~ 54 (82)
-.-+|++||+=|+.+|.++++.++.-.+....+...++
T Consensus 26 E~rLR~~lE~EL~~lr~qq~~~~~~~~~~~~~~~~~L~ 63 (205)
T PF12240_consen 26 ERRLRTRLERELESLRAQQRQGNSSGSSSPSNNASNLK 63 (205)
T ss_pred HHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCcHHHHH
Confidence 34579999999999999888877777776665555555
No 14
>PF10550 Toxin_36: Conantokin-G mollusc-toxin; InterPro: IPR005918 The conantokins are a family of neuroactive peptides found in the venoms of fish-hunting cone snails. They possess a relatively high number of residues (4-5) of the non-standard amino acid gamma-carboxyglutamic acid (Gla), which is generated by the post-translational modification of glutamate (Glu) residues. Conantokins are the only naturally produced peptides known to be N-methyl-D-aspartate (NMDA) receptor antagonists and show therapeutic promise in treating conditions associated with NMDA receptor dysfunction. In animal models they have exhibited anticonvulsant and anti-Parkinsonian properties and have provided neuroprotection within therapeutically acceptable times following transient focal brain ischemia [, , , ]. Upon binding of Ca2+ to Gla, conantokin undergoes a conformational transition from a distorted curvilinear 3(10) helix to a linear alpha-helix. The binding of Ca2+ to conantokin leads to the exposure of a hydrophobic region on the opposite face of the helix []. Conantokins share relatively few sequence elements, which include include sequence identity at the first four residues, homologous positioning of the two most C-terminal Gla residues, and an Arg preceding the most C-terminal Gla []. The conantokin family is currently known to include: Conotoxin G from Conus geographus (Geography cone) (Nubecula geographus). Conantokin-L from Conus lynceus (Lynceus cone). Conantokin-R from Conus radiatus (Rayed cone). Conantokin-T from Conus tulipa (Fish-hunting cone snail) (Tulip cone). ; PDB: 1ONT_A.
Probab=43.79 E-value=17 Score=18.15 Aligned_cols=8 Identities=75% Similarity=0.808 Sum_probs=6.3
Q ss_pred HHHHHHHH
Q psy12192 12 EEEVAKQT 19 (82)
Q Consensus 12 eEEVAkqT 19 (82)
||||+||-
T Consensus 2 eee~~km~ 9 (15)
T PF10550_consen 2 EEEVAKMA 9 (15)
T ss_dssp HHHHHHHH
T ss_pred hHHHHHHH
Confidence 68888874
No 15
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=42.65 E-value=23 Score=23.12 Aligned_cols=17 Identities=18% Similarity=0.137 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||+++|-+|++++|.
T Consensus 168 ~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 168 VGTVRSRIFRAREAIAI 184 (190)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46999999999999987
No 16
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=42.35 E-value=23 Score=22.73 Aligned_cols=18 Identities=22% Similarity=0.444 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||++++.+|+++||.
T Consensus 139 s~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 139 SVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 457999999999999987
No 17
>PF06405 RCC_reductase: Red chlorophyll catabolite reductase (RCC reductase); InterPro: IPR009439 This family consists of several red chlorophyll catabolite reductase (RCC reductase) proteins. Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyse the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC) [].; PDB: 2ZXK_A 3AGA_B 3AGC_B 2ZXL_A 3AGB_A.
Probab=40.83 E-value=37 Score=26.90 Aligned_cols=23 Identities=35% Similarity=0.780 Sum_probs=17.3
Q ss_pred HHHHHHH---HHHHHHHHHHHHHHHH
Q psy12192 6 EIEYIIE---EEVAKQTIRNWLEACL 28 (82)
Q Consensus 6 elEy~Ie---EEVAkqTIr~WLe~CL 28 (82)
-+|.+|. .-+|+..+..||+.|.
T Consensus 176 ~leeIv~~~i~p~A~~vl~~WL~~c~ 201 (255)
T PF06405_consen 176 RLEEIVRDHIAPVAKEVLDIWLDSCA 201 (255)
T ss_dssp HHHHHHHHTHHHHHHHHHHHHHHHTT
T ss_pred hHHHHHHhhhhHHHHHHHHHHHHHhc
Confidence 3455554 3678999999999985
No 18
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=39.46 E-value=26 Score=23.35 Aligned_cols=18 Identities=22% Similarity=0.246 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+-.||++++.+|++++|.
T Consensus 170 s~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 170 PLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 457999999999999986
No 19
>PLN02581 red chlorophyll catabolite reductase
Probab=39.41 E-value=35 Score=27.26 Aligned_cols=24 Identities=33% Similarity=0.786 Sum_probs=19.1
Q ss_pred HHHHHHHHH---HHHHHHHHHHHHHHH
Q psy12192 6 EIEYIIEEE---VAKQTIRNWLEACLK 29 (82)
Q Consensus 6 elEy~IeEE---VAkqTIr~WLe~CLk 29 (82)
-+|.+|.+. +|+..+..||+.|..
T Consensus 186 ~leeiv~~~i~p~a~evl~~WL~~c~~ 212 (267)
T PLN02581 186 RLEEIVRDQVAPVAKEVLEIWLDSCAC 212 (267)
T ss_pred cHHHHHHhhhhHHHHHHHHHHHHHhcc
Confidence 466777764 689999999999954
No 20
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=39.27 E-value=18 Score=26.02 Aligned_cols=12 Identities=33% Similarity=0.792 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEA 26 (82)
Q Consensus 15 VAkqTIr~WLe~ 26 (82)
||+|||-.|+.+
T Consensus 12 ~srQTINrWvRk 23 (122)
T PF07037_consen 12 YSRQTINRWVRK 23 (122)
T ss_pred ccHHHHHHHHHh
Confidence 579999999854
No 21
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=38.39 E-value=26 Score=23.43 Aligned_cols=19 Identities=32% Similarity=0.581 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
++..||+++|.+|++++|.
T Consensus 167 is~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 167 VPEETVKSRLRYALQKLRE 185 (194)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 3467999999999999987
No 22
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=38.35 E-value=25 Score=23.73 Aligned_cols=18 Identities=17% Similarity=0.318 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||+++|.+|++++|.
T Consensus 171 s~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 171 PLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred ChHhHHHHHHHHHHHHHH
Confidence 457999999999999987
No 23
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=35.47 E-value=21 Score=18.87 Aligned_cols=13 Identities=23% Similarity=0.299 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEAC 27 (82)
Q Consensus 15 VAkqTIr~WLe~C 27 (82)
|+..|||.|.+.=
T Consensus 12 v~~~tlr~~~~~g 24 (49)
T cd04761 12 VSPSTLRYYERIG 24 (49)
T ss_pred cCHHHHHHHHHCC
Confidence 5678999996543
No 24
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.40 E-value=40 Score=22.33 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
+...||++.+-+|++++|.
T Consensus 156 is~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 156 ISVDALESLLARGRRALRA 174 (186)
T ss_pred cCHHHHHHHHHHHHHHHHH
Confidence 4568999999999999987
No 25
>KOG2251|consensus
Probab=32.85 E-value=30 Score=27.15 Aligned_cols=28 Identities=29% Similarity=0.501 Sum_probs=19.9
Q ss_pred HHHHHHHH------HHHHHHHHHHHHHHHhhhhh
Q psy12192 11 IEEEVAKQ------TIRNWLEACLKKIRATNKQQ 38 (82)
Q Consensus 11 IeEEVAkq------TIr~WLe~CLkr~r~~~kqq 38 (82)
.+||||.+ +|.-|++.==.|.|.+++|+
T Consensus 66 ~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 66 MREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred HHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 46899975 79999998655566554443
No 26
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=32.79 E-value=39 Score=21.95 Aligned_cols=18 Identities=22% Similarity=0.222 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+-.||+++|.+|.+++|.
T Consensus 137 s~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 137 KLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 346999999999999887
No 27
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=32.15 E-value=25 Score=17.86 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEAC 27 (82)
Q Consensus 15 VAkqTIr~WLe~C 27 (82)
|+..||+.|+..-
T Consensus 12 vs~~tl~~~~~~g 24 (49)
T cd04762 12 VSPSTLRRWVKEG 24 (49)
T ss_pred cCHHHHHHHHHcC
Confidence 5778999998753
No 28
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=31.72 E-value=41 Score=22.41 Aligned_cols=18 Identities=17% Similarity=0.268 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||+++|-+|++++|.
T Consensus 160 s~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 160 SESAVKVSVHRGLKALAA 177 (184)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 356999999999999986
No 29
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=31.62 E-value=47 Score=18.77 Aligned_cols=20 Identities=15% Similarity=0.385 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy12192 15 VAKQTIRNWLEACLKKIRAT 34 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~~ 34 (82)
|+..||+..+..+.+|+...
T Consensus 30 is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 30 ISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SHHHHHHHHHHHHHHHHT-S
T ss_pred cchhhHHHHHHHHHHHhCCC
Confidence 56789999999999998883
No 30
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.57 E-value=27 Score=18.68 Aligned_cols=14 Identities=14% Similarity=0.655 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHH
Q psy12192 14 EVAKQTIRNWLEAC 27 (82)
Q Consensus 14 EVAkqTIr~WLe~C 27 (82)
.|+..||..|+..=
T Consensus 23 gis~~tv~~w~~~y 36 (52)
T PF13518_consen 23 GISRSTVYRWIKRY 36 (52)
T ss_pred CCCHhHHHHHHHHH
Confidence 45678999998643
No 31
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=31.19 E-value=42 Score=21.42 Aligned_cols=18 Identities=11% Similarity=0.167 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||++.+.+|++++|.
T Consensus 151 s~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 151 TEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 457999999999999985
No 32
>COG3309 VapD Uncharacterized virulence-associated protein D [Function unknown]
Probab=31.13 E-value=37 Score=23.72 Aligned_cols=19 Identities=42% Similarity=0.987 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy12192 13 EEVAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 13 EEVAkqTIr~WLe~CLkr~r~ 33 (82)
.++|+| -.|+.+|++-+|+
T Consensus 61 q~~~~q--~~wf~~cV~dIr~ 79 (96)
T COG3309 61 QNLAKQ--FQWFDKCVRDIRA 79 (96)
T ss_pred HHHHHH--hHHHHHHHHHhHh
Confidence 356666 3799999999998
No 33
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=31.03 E-value=15 Score=16.26 Aligned_cols=10 Identities=30% Similarity=0.644 Sum_probs=6.4
Q ss_pred HHHHHHHHHH
Q psy12192 15 VAKQTIRNWL 24 (82)
Q Consensus 15 VAkqTIr~WL 24 (82)
+++.||..|+
T Consensus 33 is~~tv~~~~ 42 (42)
T cd00569 33 VSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHhC
Confidence 4566777774
No 34
>PF05581 MCP_N: Vibrio chemotaxis protein N terminus; InterPro: IPR008762 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the N-terminal domain found in chemotaxis methyl-accepting proteins primarily from from Vibrio species.; PDB: 3C8C_A.
Probab=30.13 E-value=80 Score=21.66 Aligned_cols=25 Identities=36% Similarity=0.621 Sum_probs=14.2
Q ss_pred hhhHHHHHHHHHH------HHHHHHHHHHHH
Q psy12192 3 AREEIEYIIEEEV------AKQTIRNWLEAC 27 (82)
Q Consensus 3 ~REelEy~IeEEV------AkqTIr~WLe~C 27 (82)
.|.+++..++.-| -..||.+||++=
T Consensus 30 vr~~i~~~ve~sv~Ei~~~v~~tI~~~l~~k 60 (103)
T PF05581_consen 30 VRNEIRSQVESSVNEIVDGVANTIQSWLNGK 60 (103)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4666666555443 467999999985
No 35
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.87 E-value=54 Score=22.14 Aligned_cols=19 Identities=5% Similarity=0.156 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
|...||+++|.++++++|.
T Consensus 164 is~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 164 IGVEAVESLTARGKRALAA 182 (196)
T ss_pred cCHHHHHHHHHHHHHHHHH
Confidence 3457999999999999987
No 36
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.55 E-value=40 Score=22.09 Aligned_cols=12 Identities=33% Similarity=0.850 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHH
Q psy12192 14 EVAKQTIRNWLE 25 (82)
Q Consensus 14 EVAkqTIr~WLe 25 (82)
.|+..||..|+.
T Consensus 29 ~VS~~Tv~~W~k 40 (119)
T PF01710_consen 29 GVSRNTVYRWLK 40 (119)
T ss_pred CcHHHHHHHHHH
Confidence 588999999998
No 37
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=28.01 E-value=52 Score=22.87 Aligned_cols=18 Identities=28% Similarity=0.418 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||+.++.+|++++|.
T Consensus 204 s~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 204 TESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 456999999999999985
No 38
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.99 E-value=55 Score=21.54 Aligned_cols=18 Identities=11% Similarity=0.289 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+--||+++|-+|++++|.
T Consensus 164 s~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 164 PLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 346999999999999986
No 39
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.87 E-value=35 Score=20.44 Aligned_cols=13 Identities=23% Similarity=0.790 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEAC 27 (82)
Q Consensus 15 VAkqTIr~WLe~C 27 (82)
++.+||..|+...
T Consensus 24 ~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 24 ISRRTVYRWLKRY 36 (112)
T ss_pred cCHHHHHHHHHHH
Confidence 4568999998774
No 40
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.70 E-value=50 Score=21.99 Aligned_cols=17 Identities=12% Similarity=0.325 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||+++|.+|++++|.
T Consensus 157 ~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 157 ENTVKTRLKKAKELLKK 173 (179)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46999999999999986
No 41
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.46 E-value=55 Score=21.40 Aligned_cols=18 Identities=17% Similarity=0.292 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+-.||+++|.+|.+++|.
T Consensus 141 s~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 141 AVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 357999999999999986
No 42
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=26.74 E-value=61 Score=22.41 Aligned_cols=19 Identities=26% Similarity=0.511 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
|...||+.|+.++++++|.
T Consensus 206 is~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 206 ISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCHHHHHHHHHHHHHHHHH
Confidence 4567999999999999985
No 43
>PF14766 RPA_interact_N: Replication protein A interacting N-terminal
Probab=26.31 E-value=65 Score=18.71 Aligned_cols=19 Identities=37% Similarity=0.726 Sum_probs=13.3
Q ss_pred HHHHHHHHHhhhhhhhhhhhhh
Q psy12192 25 EACLKKIRATNKQQTSLIAGLR 46 (82)
Q Consensus 25 e~CLkr~r~~~kqq~~li~~lr 46 (82)
+.|+.|+|. ....|+..+|
T Consensus 21 ~rC~~R~r~---~R~~lL~k~R 39 (42)
T PF14766_consen 21 ERCLERVRE---SRTQLLWKYR 39 (42)
T ss_pred HHHHHHHHH---HHHHHHHHhh
Confidence 689999997 4455555555
No 44
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=26.31 E-value=47 Score=27.78 Aligned_cols=20 Identities=20% Similarity=0.468 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy12192 13 EEVAKQTIRNWLEACLKKIR 32 (82)
Q Consensus 13 EEVAkqTIr~WLe~CLkr~r 32 (82)
+++|..+.|.||..+|+-+-
T Consensus 104 ~~Ia~~Aak~~L~~~l~~lD 123 (399)
T PRK04439 104 GEIAIEAAKEYLRENLRNLD 123 (399)
T ss_pred HHHHHHHHHHHHHHhCccCC
Confidence 68999999999999987443
No 45
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.95 E-value=58 Score=22.71 Aligned_cols=19 Identities=11% Similarity=0.316 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
|+..||++++.++++++|.
T Consensus 210 is~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 210 ISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHHHHHHHHHH
Confidence 3457999999999999987
No 46
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=25.73 E-value=56 Score=21.24 Aligned_cols=18 Identities=28% Similarity=0.615 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
.-.||++.+.+|++++|.
T Consensus 148 s~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 148 PEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 357999999999999885
No 47
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.68 E-value=61 Score=21.09 Aligned_cols=18 Identities=11% Similarity=0.208 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||+++|.+|.+++|.
T Consensus 165 s~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 165 PVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 356899999999999886
No 48
>PF04362 Iron_traffic: Bacterial Fe(2+) trafficking; InterPro: IPR007457 The protein represented by this entry, YggX, serves to protect Fe-S clusters from oxidative damage []. The effect is two-fold: proteins that rely on Fe-S clusters do not become inactivated, and the release of free iron and hydrogen peroxide--a DNA damaging agent--is prevented. These observations are consistent with the hypothesis that YggX chelates free iron, and recent experiments show that YggX can indeed bind Fe(II) in vitro and in vivo []. Furthermore, YggX has a positive effect on the action of at least one Fe(II)-responsive protein. The combined actions of YggX is reminiscent of iron trafficking proteins [], and YggX is therefore proposed to play a role in Fe(II) trafficking []. In Escherichia coli, YggX was shown to be under the transcriptional control of the redox-sensing SoxRS system []. ; GO: 0005506 iron ion binding; PDB: 1YHD_A 1T07_A 1XS8_A.
Probab=25.60 E-value=78 Score=21.45 Aligned_cols=32 Identities=34% Similarity=0.567 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhh
Q psy12192 6 EIEYIIEEEVAKQTIRNWLEACLKKIRATNKQQTSLIAGLRAT 48 (82)
Q Consensus 6 elEy~IeEEVAkqTIr~WLe~CLkr~r~~~kqq~~li~~lr~~ 48 (82)
+|--.|-+.|+|+.=..|+. +|+.||+-.|-+
T Consensus 25 ~lG~~I~~~iSk~AW~~W~~-----------~QTmLINE~rLn 56 (88)
T PF04362_consen 25 ELGQRIYDNISKEAWQEWLE-----------HQTMLINEYRLN 56 (88)
T ss_dssp HHHHHHHHHSBHHHHHHHHH-----------HHHHHHHHHT--
T ss_pred HHHHHHHHHHhHHHHHHHHH-----------HHHHHHHhccCC
Confidence 56678999999999888874 567777766654
No 49
>KOG3908|consensus
Probab=25.56 E-value=62 Score=27.26 Aligned_cols=43 Identities=33% Similarity=0.487 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHhhhh-----hhhhhhhhhhhhhhhhh
Q psy12192 11 IEEEVAKQTIRNWLEACLKK-IRATNKQ-----QTSLIAGLRATNEMLHM 54 (82)
Q Consensus 11 IeEEVAkqTIr~WLe~CLkr-~r~~~kq-----q~~li~~lr~~~~q~~~ 54 (82)
+-||--..+|| ||++|+-- -|-..+- |-.|-..||+.--.+.+
T Consensus 163 rveeAM~RsIR-WlDRCi~Ah~R~d~Q~lFpIiQGGLd~~LR~~c~~em~ 211 (396)
T KOG3908|consen 163 RVEEAMYRSIR-WLDRCIMAHNRDDEQNLFPIIQGGLDEGLRAECIAEML 211 (396)
T ss_pred HHHHHHHHHHH-HHHHHHHHhcCccchhhhhhhhcccchHHHHHHHHHHH
Confidence 34566678887 99999654 3331111 22333567776444433
No 50
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.44 E-value=61 Score=21.54 Aligned_cols=18 Identities=22% Similarity=0.307 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||++++.+|++++|.
T Consensus 168 s~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 168 TPGAVRVAQHRALARLRA 185 (189)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 346999999999999985
No 51
>COG1804 CaiB Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]
Probab=24.90 E-value=73 Score=25.96 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=24.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12192 3 AREEIEYIIEEEVAKQTIRNWLEACLK 29 (82)
Q Consensus 3 ~REelEy~IeEEVAkqTIr~WLe~CLk 29 (82)
.|++|...|++..+.+|...|+..+-+
T Consensus 284 ~r~~l~~~i~~~~~~~t~~e~~~~l~~ 310 (396)
T COG1804 284 NRDELDAILAAAFATNTAAEWAARLEA 310 (396)
T ss_pred hHHHHHHHHHHHHhhcCHHHHHHHHHh
Confidence 489999999999999999999998743
No 52
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=24.77 E-value=61 Score=21.76 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||++.+-+|++++|+
T Consensus 160 s~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 160 TRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 457999999999999997
No 53
>cd08786 CARD_RIP2_CARD3 Caspase activation and recruitment domain of Receptor Interacting Protein 2. Caspase activation and recruitment domain (CARD) of Receptor Interacting Protein 2 (RIP2/RIPK2/RICK/CARDIAK/CARD3). RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP2 harbors a C-terminal CARD domain and functions as an effector kinase downstream of the pattern recognition receptors from the Nod-like (NLR)-family, NOD1 and NOD2, which recognizes bacterial peptidoglycans released upon infection. This cascade is implicated in inflammatory immune responses and the clearance of intracellular pathogens. RIP2 associates with NOD1 and NOD2 via CARD-CARD interactions. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein
Probab=24.35 E-value=71 Score=22.04 Aligned_cols=30 Identities=27% Similarity=0.489 Sum_probs=19.1
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12192 1 MLAREEIEYIIEEEVAKQTIRNWLEACLKK 30 (82)
Q Consensus 1 Ll~REelEy~IeEEVAkqTIr~WLe~CLkr 30 (82)
+|.||+.|-.++.------+|.-|+.|++.
T Consensus 31 ~L~redyElV~~~~T~t~K~R~LLDt~~~~ 60 (87)
T cd08786 31 LLMREDYELISTKPTRTSKVRQLLDTCDCQ 60 (87)
T ss_pred HHhHHHHHHHHcccchHHHHHHHHHHHHhc
Confidence 467788777764332233368888888654
No 54
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.76 E-value=70 Score=21.25 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy12192 15 VAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 15 VAkqTIr~WLe~CLkr~r~ 33 (82)
++..||++++.+++++||.
T Consensus 161 is~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 161 APLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CChhhHHHHHHHHHHHHHH
Confidence 3457999999999999986
No 55
>KOG3250|consensus
Probab=22.54 E-value=1.2e+02 Score=24.30 Aligned_cols=17 Identities=47% Similarity=0.825 Sum_probs=12.9
Q ss_pred HHHHHHHHHHH---HHHHHH
Q psy12192 17 KQTIRNWLEAC---LKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~C---Lkr~r~ 33 (82)
+-|.-.|+++| |.-|-+
T Consensus 170 ~~TL~~w~~~cenvL~~ie~ 189 (258)
T KOG3250|consen 170 KYTLDEWCEGCENVLFGIEA 189 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHh
Confidence 56899999999 555544
No 56
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=22.43 E-value=80 Score=19.86 Aligned_cols=17 Identities=12% Similarity=0.163 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||++++-++.+++|.
T Consensus 135 ~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 135 LAKVKSNLFRARKELKK 151 (154)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46999999999999885
No 57
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 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 an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=22.24 E-value=50 Score=18.83 Aligned_cols=12 Identities=25% Similarity=0.659 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACL 28 (82)
Q Consensus 17 kqTIr~WLe~CL 28 (82)
+++|+.|+..|.
T Consensus 25 ~~~V~~~ir~C~ 36 (39)
T PF09337_consen 25 KKDVRRVIRSCP 36 (39)
T ss_pred HHHHHHHHhcCc
Confidence 688999999984
No 58
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=22.21 E-value=61 Score=18.60 Aligned_cols=15 Identities=20% Similarity=0.459 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHH
Q psy12192 14 EVAKQTIRNWLEACL 28 (82)
Q Consensus 14 EVAkqTIr~WLe~CL 28 (82)
.|...||.+|+..+.
T Consensus 34 gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 34 GISPSTLYNWRKQYR 48 (76)
T ss_dssp TS-HHHHHHHHHHHH
T ss_pred ccccccccHHHHHHh
Confidence 456789999998875
No 59
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=22.04 E-value=58 Score=18.02 Aligned_cols=7 Identities=43% Similarity=1.749 Sum_probs=5.0
Q ss_pred HHHHHHH
Q psy12192 22 NWLEACL 28 (82)
Q Consensus 22 ~WLe~CL 28 (82)
.||..||
T Consensus 72 ~Wi~~ci 78 (78)
T PF00533_consen 72 DWIEDCI 78 (78)
T ss_dssp HHHHHHH
T ss_pred HHHHHhC
Confidence 5777775
No 60
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=21.99 E-value=82 Score=20.92 Aligned_cols=17 Identities=18% Similarity=0.151 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||++.+-+|++++|.
T Consensus 168 ~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 168 VGTVRSRIFRAREAIDK 184 (193)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46899999999999886
No 61
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.76 E-value=75 Score=22.17 Aligned_cols=17 Identities=24% Similarity=0.350 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
-.||+++|.+|.+++|.
T Consensus 168 ~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 168 LGTVRSRIHRGRQQLRA 184 (203)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 36899999999999886
No 62
>PF01941 AdoMet_Synthase: S-adenosylmethionine synthetase (AdoMet synthetase); InterPro: IPR002795 A highly diverged class of S-adenosylmethionine synthetases have been identified in the archaea. S-adenosylmethionine is the primary alkylating agent in all known organisms. ATP:L-methionine S-adenosyltransferase (MAT) catalyses the only known biosynthetic route to this central metabolite. Although the amino acid sequence of MAT is strongly conserved among bacteria and eukarya (see IPR002133 from INTERPRO) no homologues had been recognised in the completed genome sequences of any archaea. The identification of a second major class of MAT emphasises the long evolutionary history of the archaeal lineage and the structural diversity found even in crucial metabolic enzymes []. Three bacterial genomes encode both the archaeal and eukaryotic/bacterial types of MAT [].; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon metabolic process
Probab=21.54 E-value=68 Score=26.83 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy12192 13 EEVAKQTIRNWLEACLKKIR 32 (82)
Q Consensus 13 EEVAkqTIr~WLe~CLkr~r 32 (82)
+++|..+.+.||..+|+-+-
T Consensus 104 ~~Ia~~aak~~l~~~l~~lD 123 (396)
T PF01941_consen 104 DEIAIEAAKEWLRENLRFLD 123 (396)
T ss_pred HHHHHHHHHHHHHHhcccCC
Confidence 68999999999999987554
No 63
>PRK05408 oxidative damage protection protein; Provisional
Probab=21.39 E-value=1.7e+02 Score=19.94 Aligned_cols=32 Identities=34% Similarity=0.526 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhh
Q psy12192 6 EIEYIIEEEVAKQTIRNWLEACLKKIRATNKQQTSLIAGLRAT 48 (82)
Q Consensus 6 elEy~IeEEVAkqTIr~WLe~CLkr~r~~~kqq~~li~~lr~~ 48 (82)
+|=-.|-++|+|+-=..|++ +|+.||+.-|-+
T Consensus 25 ~lGkrI~~~ISk~AW~~W~~-----------~QTmLINE~rLn 56 (90)
T PRK05408 25 ELGKRIYENISKEAWQEWLK-----------HQTMLINEKRLN 56 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----------hhHhhhhhccCC
Confidence 45568999999999888874 567777665544
No 64
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.28 E-value=80 Score=22.17 Aligned_cols=18 Identities=17% Similarity=0.396 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||+.++.++++++|.
T Consensus 213 s~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 213 SESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 356999999999999986
No 65
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.22 E-value=83 Score=20.26 Aligned_cols=18 Identities=11% Similarity=0.091 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
+..||+++|-+|.+++|.
T Consensus 141 s~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 141 SLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHHHHHHHHHh
Confidence 356899999999999986
No 66
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=21.17 E-value=32 Score=20.10 Aligned_cols=14 Identities=21% Similarity=0.280 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHH
Q psy12192 13 EEVAKQTIRNWLEA 26 (82)
Q Consensus 13 EEVAkqTIr~WLe~ 26 (82)
--|+..||.+|++.
T Consensus 32 fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 32 FGVSRSTVSTILKN 45 (53)
T ss_dssp HT--CCHHHHHHHC
T ss_pred hCCCHHHHHHHHHh
Confidence 34667899999864
No 67
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=21.01 E-value=57 Score=17.24 Aligned_cols=8 Identities=63% Similarity=1.497 Sum_probs=6.6
Q ss_pred HHHHHHHH
Q psy12192 22 NWLEACLK 29 (82)
Q Consensus 22 ~WLe~CLk 29 (82)
.||..|+.
T Consensus 71 ~Wi~~~~~ 78 (80)
T smart00292 71 DWLLDCLK 78 (80)
T ss_pred HHHHHHHH
Confidence 69999975
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=20.75 E-value=79 Score=20.72 Aligned_cols=17 Identities=41% Similarity=0.774 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKKIRA 33 (82)
Q Consensus 17 kqTIr~WLe~CLkr~r~ 33 (82)
..||+++|.++++++|.
T Consensus 159 ~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 159 LNTMRTWLRRSLLKLRE 175 (179)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 46999999999999986
No 69
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=20.57 E-value=2.6e+02 Score=20.81 Aligned_cols=31 Identities=13% Similarity=0.343 Sum_probs=24.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy12192 3 AREEIEYIIEEEVAKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 3 ~REelEy~IeEEVAkqTIr~WLe~CLkr~r~ 33 (82)
.|++++..|.++-+.+.++.|+..-+..++.
T Consensus 232 ~k~~I~~~L~~~k~~~~~~~~~~~~~~~l~~ 262 (283)
T PRK02998 232 VKDSIRKDLEQQRLQDTTGKWKQQVVNDLLK 262 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677888888888888888999888877665
No 70
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.45 E-value=89 Score=20.73 Aligned_cols=18 Identities=17% Similarity=0.274 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKIRA 33 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~ 33 (82)
...||++.|-+|++++|.
T Consensus 158 s~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 158 SESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 356999999999999986
No 71
>PF12876 Cellulase-like: Sugar-binding cellulase-like; InterPro: IPR024778 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This entry represents a family of putative cellulase enzymes.; PDB: 3GYC_B.
Probab=20.43 E-value=1.2e+02 Score=18.59 Aligned_cols=19 Identities=26% Similarity=0.585 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q psy12192 16 AKQTIRNWLEACLKKIRAT 34 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~r~~ 34 (82)
..+.++.||+.|.+.+|+-
T Consensus 36 ~~~~~~~~l~~~~~~iR~~ 54 (88)
T PF12876_consen 36 KAEAYAEWLKEAFRWIRAV 54 (88)
T ss_dssp TSHHHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHHHHHHHh
Confidence 3477899999999999984
No 72
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=20.14 E-value=1.1e+02 Score=16.72 Aligned_cols=16 Identities=25% Similarity=0.434 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHH
Q psy12192 16 AKQTIRNWLEACLKKI 31 (82)
Q Consensus 16 AkqTIr~WLe~CLkr~ 31 (82)
...||+.||.+-++++
T Consensus 39 s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 39 SESTVKRRLRRARKKL 54 (54)
T ss_dssp -HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhhC
Confidence 4578999998776654
No 73
>PF04550 Phage_holin_2: Phage holin family 2 ; InterPro: IPR007633 This entry represents the Bacteriophage P2, GpY, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=20.10 E-value=60 Score=22.25 Aligned_cols=14 Identities=36% Similarity=0.627 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q psy12192 17 KQTIRNWLEACLKK 30 (82)
Q Consensus 17 kqTIr~WLe~CLkr 30 (82)
.|.|+.||.+|+++
T Consensus 76 ~q~vE~~lrr~~~~ 89 (89)
T PF04550_consen 76 YQAVEAWLRRRLKG 89 (89)
T ss_pred HHHHHHHHHHHhcC
Confidence 57888888888763
Done!