Query psy17501
Match_columns 101
No_of_seqs 106 out of 222
Neff 5.6
Searched_HMMs 46136
Date Sat Aug 17 00:11:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01213 CAP_N: Adenylate cycl 99.9 1E-25 2.2E-30 177.3 9.2 86 15-100 34-119 (312)
2 KOG2675|consensus 99.9 1.1E-21 2.4E-26 159.6 10.2 81 20-100 43-123 (480)
3 PRK09400 secE preprotein trans 76.0 7.8 0.00017 23.9 4.3 23 67-89 15-37 (61)
4 PRK09639 RNA polymerase sigma 71.1 9.9 0.00021 25.9 4.4 40 26-65 1-40 (166)
5 PRK09641 RNA polymerase sigma 59.8 23 0.00051 24.4 4.6 40 26-65 16-55 (187)
6 PTZ00478 Sec superfamily; Prov 59.7 20 0.00043 23.5 3.9 19 71-89 32-50 (81)
7 PRK12516 RNA polymerase sigma 58.5 28 0.00061 24.8 4.9 44 22-65 4-47 (187)
8 TIGR02939 RpoE_Sigma70 RNA pol 58.3 24 0.00053 24.4 4.5 38 28-65 20-57 (190)
9 TIGR00327 secE_euk_arch protei 58.0 17 0.00037 22.5 3.2 22 68-89 12-33 (61)
10 PRK09638 RNA polymerase sigma 57.4 26 0.00056 24.1 4.5 39 27-65 17-55 (176)
11 COG2443 Sss1 Preprotein transl 56.7 38 0.00083 21.3 4.7 29 58-89 10-38 (65)
12 PF05739 SNARE: SNARE domain; 56.6 32 0.00069 20.0 4.2 30 33-62 8-37 (63)
13 PRK11922 RNA polymerase sigma 56.1 48 0.0011 24.3 6.0 38 28-65 30-67 (231)
14 PRK12520 RNA polymerase sigma 55.8 18 0.0004 25.4 3.6 38 28-65 2-39 (191)
15 PRK05602 RNA polymerase sigma 55.7 30 0.00065 24.1 4.6 40 26-65 18-57 (186)
16 TIGR02954 Sig70_famx3 RNA poly 53.9 34 0.00075 23.4 4.6 39 26-64 14-52 (169)
17 TIGR02985 Sig70_bacteroi1 RNA 53.6 32 0.0007 22.7 4.3 36 29-64 2-37 (161)
18 PRK12524 RNA polymerase sigma 53.3 33 0.00072 24.3 4.6 38 27-64 25-62 (196)
19 PF08822 DUF1804: Protein of u 53.3 68 0.0015 23.6 6.2 59 34-97 104-163 (165)
20 KOG3498|consensus 52.8 30 0.00065 21.9 3.7 24 66-89 15-38 (67)
21 TIGR02948 SigW_bacill RNA poly 52.2 36 0.00077 23.5 4.5 40 26-65 16-55 (187)
22 PRK09640 RNA polymerase sigma 51.1 37 0.0008 23.8 4.5 40 26-65 24-63 (188)
23 PRK12537 RNA polymerase sigma 50.8 38 0.00083 23.6 4.5 39 27-65 22-60 (182)
24 PRK09651 RNA polymerase sigma 49.3 52 0.0011 22.8 5.0 43 22-64 4-46 (172)
25 PRK12541 RNA polymerase sigma 49.1 45 0.00098 22.6 4.6 38 28-65 5-42 (161)
26 PRK09652 RNA polymerase sigma 48.8 44 0.00095 22.6 4.5 39 27-65 9-47 (182)
27 PRK13919 putative RNA polymera 48.6 46 0.00099 23.1 4.6 39 27-65 22-60 (186)
28 PRK09647 RNA polymerase sigma 48.0 71 0.0015 23.1 5.7 41 25-65 25-65 (203)
29 PRK12515 RNA polymerase sigma 46.8 50 0.0011 23.1 4.6 39 27-65 21-59 (189)
30 PRK12519 RNA polymerase sigma 46.3 50 0.0011 23.1 4.5 39 27-65 28-66 (194)
31 TIGR02947 SigH_actino RNA poly 46.2 50 0.0011 23.2 4.6 40 26-65 9-48 (193)
32 PRK12534 RNA polymerase sigma 45.8 52 0.0011 22.9 4.5 37 28-64 25-61 (187)
33 PRK09415 RNA polymerase factor 44.7 56 0.0012 22.7 4.6 40 25-64 13-52 (179)
34 PF10415 FumaraseC_C: Fumarase 43.8 70 0.0015 19.0 4.4 39 54-92 13-51 (55)
35 PRK12533 RNA polymerase sigma 42.6 57 0.0012 24.0 4.5 40 26-65 16-55 (216)
36 PRK12522 RNA polymerase sigma 41.6 64 0.0014 22.1 4.5 37 28-64 3-39 (173)
37 PRK12514 RNA polymerase sigma 41.6 70 0.0015 22.0 4.6 38 27-64 18-55 (179)
38 TIGR02952 Sig70_famx2 RNA poly 41.3 61 0.0013 21.9 4.2 39 26-64 9-47 (170)
39 TIGR02989 Sig-70_gvs1 RNA poly 40.5 61 0.0013 21.6 4.1 36 29-64 2-37 (159)
40 COG1595 RpoE DNA-directed RNA 40.3 68 0.0015 22.4 4.5 40 25-64 12-51 (182)
41 PRK12547 RNA polymerase sigma 40.2 67 0.0015 22.0 4.4 37 28-64 6-42 (164)
42 PRK11923 algU RNA polymerase s 39.6 71 0.0015 22.3 4.5 38 28-65 20-57 (193)
43 PRK12538 RNA polymerase sigma 38.7 73 0.0016 23.7 4.6 38 27-64 62-99 (233)
44 PRK09645 RNA polymerase sigma 38.7 1E+02 0.0022 21.0 5.1 41 24-64 5-45 (173)
45 TIGR02983 SigE-fam_strep RNA p 38.5 83 0.0018 21.2 4.6 39 27-65 5-43 (162)
46 TIGR02859 spore_sigH RNA polym 38.3 44 0.00096 23.3 3.2 39 26-64 17-55 (198)
47 PRK12543 RNA polymerase sigma 36.9 89 0.0019 21.7 4.6 39 27-65 6-44 (179)
48 PRK12529 RNA polymerase sigma 36.4 1.2E+02 0.0027 21.0 5.3 48 15-65 3-52 (178)
49 KOG4514|consensus 36.3 1.9E+02 0.0042 22.0 8.0 41 34-77 137-177 (222)
50 PRK12542 RNA polymerase sigma 36.2 93 0.002 21.6 4.6 38 27-64 8-45 (185)
51 PF04591 DUF596: Protein of un 35.6 27 0.00059 22.3 1.6 18 48-65 15-32 (70)
52 PRK12523 RNA polymerase sigma 35.6 92 0.002 21.4 4.5 39 26-64 8-46 (172)
53 TIGR02941 Sigma_B RNA polymera 35.5 43 0.00094 24.9 3.0 50 26-79 27-76 (255)
54 PRK09646 RNA polymerase sigma 35.3 95 0.0021 21.9 4.6 39 27-65 29-67 (194)
55 PRK09643 RNA polymerase sigma 35.1 89 0.0019 22.1 4.4 39 27-65 26-64 (192)
56 PRK11924 RNA polymerase sigma 34.3 1E+02 0.0022 20.7 4.5 40 26-65 11-50 (179)
57 PRK12517 RNA polymerase sigma 33.9 1.2E+02 0.0025 21.5 4.9 44 21-64 16-59 (188)
58 KOG0532|consensus 33.7 37 0.0008 30.2 2.5 47 34-80 637-690 (722)
59 TIGR02885 spore_sigF RNA polym 33.0 1.5E+02 0.0032 21.5 5.4 47 27-76 10-56 (231)
60 PRK12513 RNA polymerase sigma 32.7 1.1E+02 0.0024 21.4 4.6 39 27-65 25-63 (194)
61 cd00193 t_SNARE Soluble NSF (N 32.6 93 0.002 17.3 3.8 27 34-60 11-37 (60)
62 cd00633 Secretoglobin Secretog 32.0 1.2E+02 0.0026 18.3 4.2 42 25-66 3-46 (67)
63 PRK12528 RNA polymerase sigma 31.9 77 0.0017 21.4 3.6 37 28-64 4-40 (161)
64 PF00957 Synaptobrevin: Synapt 31.7 1.3E+02 0.0029 18.8 6.3 43 26-68 11-53 (89)
65 TIGR03001 Sig-70_gmx1 RNA poly 31.7 1.7E+02 0.0036 22.0 5.6 37 28-64 39-75 (244)
66 PRK12531 RNA polymerase sigma 31.2 1.2E+02 0.0027 21.2 4.6 38 27-64 26-63 (194)
67 PRK08583 RNA polymerase sigma 30.8 57 0.0012 24.3 2.9 38 27-64 28-65 (257)
68 PHA02662 ORF131 putative membr 30.8 64 0.0014 25.0 3.2 36 10-45 3-39 (226)
69 PF09361 Phasin_2: Phasin prot 29.0 1.4E+02 0.0031 18.2 8.8 65 30-94 4-74 (102)
70 PF10303 DUF2408: Protein of u 28.8 1.7E+02 0.0037 20.4 4.9 47 55-101 9-56 (134)
71 TIGR02999 Sig-70_X6 RNA polyme 28.7 1.1E+02 0.0024 20.9 4.0 38 27-64 16-58 (183)
72 smart00040 CSF2 Granulocyte-ma 28.6 42 0.00091 23.4 1.7 39 24-67 13-51 (121)
73 PF06148 COG2: COG (conserved 28.5 75 0.0016 21.5 3.0 28 31-58 47-74 (133)
74 PRK09644 RNA polymerase sigma 28.1 1.3E+02 0.0029 20.3 4.3 36 29-64 2-37 (165)
75 PF12395 DUF3658: Protein of u 27.9 36 0.00077 22.8 1.3 43 26-68 45-88 (111)
76 PRK08295 RNA polymerase factor 27.8 74 0.0016 22.4 3.0 38 27-64 23-60 (208)
77 TIGR02960 SigX5 RNA polymerase 27.4 1.2E+02 0.0026 23.0 4.3 38 27-64 4-41 (324)
78 cd07072 NR_LBD_DHR38_like Liga 26.8 1.7E+02 0.0037 22.1 4.9 63 15-79 32-98 (239)
79 PF09989 DUF2229: CoA enzyme a 26.5 1.2E+02 0.0026 22.6 4.1 41 36-76 130-170 (221)
80 TIGR02850 spore_sigG RNA polym 26.2 2.2E+02 0.0047 21.2 5.4 38 27-64 33-70 (254)
81 TIGR02980 SigBFG RNA polymeras 26.2 76 0.0017 23.0 2.9 37 28-64 3-39 (227)
82 PF06260 DUF1024: Protein of u 25.8 2E+02 0.0043 18.9 4.8 22 25-46 34-55 (82)
83 PRK12526 RNA polymerase sigma 25.7 1.6E+02 0.0036 21.0 4.5 39 27-65 37-75 (206)
84 PF09025 YopR_core: YopR Core; 25.5 1.3E+02 0.0027 21.8 3.7 41 56-96 12-58 (142)
85 PF01099 Uteroglobin: Uteroglo 25.2 1.2E+02 0.0025 18.4 3.2 39 27-65 5-45 (67)
86 PRK08241 RNA polymerase factor 24.8 1.5E+02 0.0032 22.9 4.3 39 27-65 18-56 (339)
87 PRK05572 sporulation sigma fac 24.7 2.3E+02 0.005 21.0 5.3 48 27-77 31-78 (252)
88 PRK08301 sporulation sigma fac 24.3 87 0.0019 22.8 2.9 39 26-64 50-88 (234)
89 PF08225 Antimicrobial19: Pseu 23.7 1.1E+02 0.0024 15.3 2.5 18 84-101 5-22 (23)
90 TIGR02509 type_III_yopR type I 23.6 1.6E+02 0.0035 21.0 3.9 33 64-96 11-46 (131)
91 TIGR02997 Sig70-cyanoRpoD RNA 23.2 89 0.0019 24.0 2.9 38 27-64 73-110 (298)
92 PRK10061 DNA damage-inducible 23.0 2.5E+02 0.0054 19.0 5.0 51 26-78 24-76 (96)
93 PRK08215 sporulation sigma fac 22.8 2.6E+02 0.0057 20.7 5.3 47 27-76 36-82 (258)
94 TIGR02937 sigma70-ECF RNA poly 22.7 1.8E+02 0.0039 18.3 3.9 20 30-49 28-47 (158)
95 TIGR02846 spore_sigmaK RNA pol 22.7 90 0.002 22.8 2.7 38 27-64 47-84 (227)
96 PRK07405 RNA polymerase sigma 22.4 3.7E+02 0.0079 21.1 6.2 59 28-90 81-140 (317)
97 cd00040 CSF2 Granulocyte Macro 22.0 60 0.0013 22.7 1.5 50 16-67 2-51 (121)
98 PRK12525 RNA polymerase sigma 21.8 1.6E+02 0.0034 20.1 3.7 41 24-64 5-45 (168)
99 COG5490 Uncharacterized conser 20.8 1.9E+02 0.0042 21.1 3.9 46 51-99 106-151 (158)
100 KOG3901|consensus 20.7 1.8E+02 0.0039 20.1 3.6 30 20-49 26-55 (109)
101 COG5506 Uncharacterized conser 20.5 86 0.0019 22.7 2.1 18 62-79 71-88 (144)
102 PF06744 DUF1215: Protein of u 20.1 58 0.0013 22.0 1.1 17 30-46 80-96 (125)
103 PF13949 ALIX_LYPXL_bnd: ALIX 20.1 3.8E+02 0.0083 20.0 7.2 43 29-71 190-232 (296)
No 1
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=99.93 E-value=1e-25 Score=177.33 Aligned_cols=86 Identities=47% Similarity=0.735 Sum_probs=71.8
Q ss_pred CCCCCCcccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHhhHHHHH
Q psy17501 15 TPVTSPIHLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKDPGQSDKMRLLQPTSDK 94 (101)
Q Consensus 15 ~p~~~~~~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~~~~~~lLkPls~~ 94 (101)
+++...++.|++|++||++|+++|++|+++|++|||+|++|+++|++||++||+||++|++||||++.+|+++|+||+++
T Consensus 34 ~~~~~~~~~p~sV~afD~~i~~~l~~f~~~S~~igg~V~~~a~~v~~aF~~qr~~L~~as~~kKP~~~~~~~lL~Pl~~~ 113 (312)
T PF01213_consen 34 APSAAVASVPPSVEAFDELINGPLKPFVELSKKIGGDVAEQAQLVKKAFQAQRKFLLVASKCKKPDQSELQELLKPLSEA 113 (312)
T ss_dssp ---------HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHBE---HHHHHHHCHHHHHH
T ss_pred CCcccccCCCchHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHccCCCChhhHHHHHHHHHHH
Confidence 34444568999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh
Q psy17501 95 IAAIHI 100 (101)
Q Consensus 95 I~~i~~ 100 (101)
|++|++
T Consensus 114 i~~i~~ 119 (312)
T PF01213_consen 114 IQKIQE 119 (312)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 999975
No 2
>KOG2675|consensus
Probab=99.86 E-value=1.1e-21 Score=159.61 Aligned_cols=81 Identities=41% Similarity=0.665 Sum_probs=78.6
Q ss_pred CcccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHhhHHHHHHHHHh
Q psy17501 20 PIHLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKDPGQSDKMRLLQPTSDKIAAIH 99 (101)
Q Consensus 20 ~~~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~~~~~~lLkPls~~I~~i~ 99 (101)
-+++|++|.+||++|.++|.+|+++|++|||+|.+++++|+.+|..||.||++|++++||+..+|+++|+||++.|.+|+
T Consensus 43 v~~~p~~i~Ayd~~i~~~l~~~~~lS~kIggdv~~~~~~v~~~F~s~R~~L~~A~q~qKPds~elad~LkPI~e~i~eI~ 122 (480)
T KOG2675|consen 43 VAAVPPSIRAYDDLISEPLAEYLKLSKKIGGDVADVAEMVKSAFASQRAFLWVASQKQKPDSNELADLLKPINEEIGEIN 122 (480)
T ss_pred cccCchHHHHHHHHHHhHHHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHHHHhccCCChHHHHHHhhhHHHhhhHHh
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred h
Q psy17501 100 I 100 (101)
Q Consensus 100 ~ 100 (101)
+
T Consensus 123 ~ 123 (480)
T KOG2675|consen 123 N 123 (480)
T ss_pred h
Confidence 5
No 3
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=75.99 E-value=7.8 Score=23.93 Aligned_cols=23 Identities=9% Similarity=0.303 Sum_probs=17.3
Q ss_pred HHHHHHHhhcCCCCchHHHHHhh
Q psy17501 67 QQFLTVASQSKDPGQSDKMRLLQ 89 (101)
Q Consensus 67 R~fL~~As~~kKP~~~~~~~lLk 89 (101)
++..++-..|+|||..+|....+
T Consensus 15 ~d~~rvl~~~~KPd~~Ef~~ia~ 37 (61)
T PRK09400 15 EDYKRVLKVARKPTREEFLLVAK 37 (61)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHH
Confidence 45566677899999988877654
No 4
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=71.10 E-value=9.9 Score=25.88 Aligned_cols=40 Identities=20% Similarity=0.169 Sum_probs=34.7
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
|..+|+.++..+-..+......++++-.+.-++++++|-.
T Consensus 1 ~~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~ 40 (166)
T PRK09639 1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLR 40 (166)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 4678999999999999999999999888888888888764
No 5
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=59.78 E-value=23 Score=24.42 Aligned_cols=40 Identities=20% Similarity=0.211 Sum_probs=34.7
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|+++++.+...+...+..++++..+.-++++++|-.
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~ 55 (187)
T PRK09641 16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIR 55 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 4578999999999999999999999888888888888763
No 6
>PTZ00478 Sec superfamily; Provisional
Probab=59.70 E-value=20 Score=23.55 Aligned_cols=19 Identities=5% Similarity=0.188 Sum_probs=13.9
Q ss_pred HHHhhcCCCCchHHHHHhh
Q psy17501 71 TVASQSKDPGQSDKMRLLQ 89 (101)
Q Consensus 71 ~~As~~kKP~~~~~~~lLk 89 (101)
....+|+|||-.+|.+..+
T Consensus 32 r~vkrctKPdrkEf~kiak 50 (81)
T PTZ00478 32 RLIRKCTKPDAKEYTNIAY 50 (81)
T ss_pred HHHHHhcCCCHHHHHHHHH
Confidence 3347899999988876543
No 7
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=58.51 E-value=28 Score=24.75 Aligned_cols=44 Identities=16% Similarity=0.152 Sum_probs=37.5
Q ss_pred ccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 22 HLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 22 ~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
+.+..-.+|.+++..+-..+......+-++-...-++++++|-.
T Consensus 4 ~~~~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~ 47 (187)
T PRK12516 4 PSVEGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMK 47 (187)
T ss_pred CccccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHH
Confidence 34456788999999999999999999999988888999998864
No 8
>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=58.30 E-value=24 Score=24.41 Aligned_cols=38 Identities=24% Similarity=0.236 Sum_probs=33.9
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.+|+++++.+-..+......++++....-++|+++|-.
T Consensus 20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~ 57 (190)
T TIGR02939 20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVK 57 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 57999999999999999999999988999999998763
No 9
>TIGR00327 secE_euk_arch protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic. This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam pfam00584 (SecE) has been created.
Probab=57.97 E-value=17 Score=22.52 Aligned_cols=22 Identities=14% Similarity=0.231 Sum_probs=15.6
Q ss_pred HHHHHHhhcCCCCchHHHHHhh
Q psy17501 68 QFLTVASQSKDPGQSDKMRLLQ 89 (101)
Q Consensus 68 ~fL~~As~~kKP~~~~~~~lLk 89 (101)
+-..+-..|+|||-.+|....+
T Consensus 12 ~~~r~lk~~~KPd~~Ef~~iak 33 (61)
T TIGR00327 12 EGTRVLAVCKKPDLEEYLKVAK 33 (61)
T ss_pred HHHHHHHHhcCCCHHHHHHHHH
Confidence 3444556799999988876654
No 10
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=57.40 E-value=26 Score=24.07 Aligned_cols=39 Identities=18% Similarity=0.096 Sum_probs=34.4
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|+.++..+...+...+..++++-...-++|+++|-.
T Consensus 17 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~ 55 (176)
T PRK09638 17 DAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLK 55 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHH
Confidence 467999999999999999999999988889999998764
No 11
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=56.69 E-value=38 Score=21.31 Aligned_cols=29 Identities=14% Similarity=0.312 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCchHHHHHhh
Q psy17501 58 LVSEAFQAQQQFLTVASQSKDPGQSDKMRLLQ 89 (101)
Q Consensus 58 lv~~aF~~qR~fL~~As~~kKP~~~~~~~lLk 89 (101)
.+++=+.+-|.||.+ |+|||-.++....|
T Consensus 10 ~~~~~lke~~rvl~~---arKP~~eEy~~~aK 38 (65)
T COG2443 10 ELREFLKEYRRVLKV---ARKPDWEEYSKIAK 38 (65)
T ss_pred HHHHHHHHHHHHHHH---HhCCCHHHHHHHHH
Confidence 333334455666654 78999888766554
No 12
>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes [, ]. Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure []. The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related []. This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; GO: 0005515 protein binding; PDB: 1URQ_B 3RL0_R 1HVV_B 1SFC_B 1N7S_B 3IPD_B 3C98_B 3HD7_F 3RK2_B 1KIL_B ....
Probab=56.60 E-value=32 Score=20.00 Aligned_cols=30 Identities=10% Similarity=0.255 Sum_probs=25.6
Q ss_pred HhhchhHHHHHHHhhHhhHHHHHHHHHHHH
Q psy17501 33 IVAGPLASYIALSNKIGGDVATHAKLVSEA 62 (101)
Q Consensus 33 li~~~l~~fv~lS~~IGg~V~e~a~lv~~a 62 (101)
-|.+.|..+-.++..||..|.+|..++...
T Consensus 8 ~l~~~i~~l~~~~~~i~~ev~~Q~~~ld~i 37 (63)
T PF05739_consen 8 ELEQSIQELKQMFQDIGEEVEEQNEMLDRI 37 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCHhhHHHH
Confidence 367889999999999999999998887653
No 13
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=56.08 E-value=48 Score=24.28 Aligned_cols=38 Identities=21% Similarity=0.197 Sum_probs=32.9
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.+|+.++..+-..+...+..+++.-...-++++++|-.
T Consensus 30 ~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~ 67 (231)
T PRK11922 30 AAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLR 67 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHH
Confidence 78999999999999999999988877778888888763
No 14
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=55.75 E-value=18 Score=25.40 Aligned_cols=38 Identities=16% Similarity=0.045 Sum_probs=32.8
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.+|++++..+-..+...+..+.++....-++++++|-.
T Consensus 2 ~~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~ 39 (191)
T PRK12520 2 TIAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLA 39 (191)
T ss_pred cchHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 47999999999999999999999888888888888764
No 15
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=55.74 E-value=30 Score=24.15 Aligned_cols=40 Identities=33% Similarity=0.440 Sum_probs=36.1
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
...+|++++..+...+...+.++.++-...-+++.++|-.
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~ 57 (186)
T PRK05602 18 DPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLR 57 (186)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Confidence 4679999999999999999999999988889999999874
No 16
>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=53.87 E-value=34 Score=23.38 Aligned_cols=39 Identities=8% Similarity=0.045 Sum_probs=34.1
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.-.+|++++..+-..+...+..+.++....-++++++|-
T Consensus 14 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l 52 (169)
T TIGR02954 14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVY 52 (169)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 356899999999999999999999998888888888865
No 17
>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=53.60 E-value=32 Score=22.72 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=27.9
Q ss_pred HHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 29 AFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 29 afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
+|+++++.+.......+..+.++-.+.-++++++|-
T Consensus 2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~ 37 (161)
T TIGR02985 2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFV 37 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 678888888888888888877777777777777776
No 18
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=53.32 E-value=33 Score=24.30 Aligned_cols=38 Identities=21% Similarity=0.217 Sum_probs=34.4
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|++++..+-..+......+.++..+.-++++++|-
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l 62 (196)
T PRK12524 25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAML 62 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 57899999999999999999999998898899888876
No 19
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=53.29 E-value=68 Score=23.59 Aligned_cols=59 Identities=15% Similarity=0.294 Sum_probs=41.6
Q ss_pred hhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCc-hHHHHHhhHHHHHHHH
Q psy17501 34 VAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKDPGQ-SDKMRLLQPTSDKIAA 97 (101)
Q Consensus 34 i~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~-~~~~~lLkPls~~I~~ 97 (101)
+.....+.++.|+++-+++.+.+-..+-. + .|..=.+.+.|.- ..|.++|.|.++.|.+
T Consensus 104 LaDsf~K~vaaskr~lPets~LavA~~vl----~-~l~~fv~e~~P~h~~af~eiLepFg~~l~k 163 (165)
T PF08822_consen 104 LADSFSKMVAASKRVLPETSELAVAMEVL----E-LLAAFVQERYPQHLAAFLEILEPFGEELEK 163 (165)
T ss_pred HHHHHHHHHHHHhhcCchHHHHHHHHHHH----H-HHHHHHHhcCHHHHHHHHHHHHHHHHHHHh
Confidence 45678888999999999888776443321 1 2333345677854 5699999999998865
No 20
>KOG3498|consensus
Probab=52.82 E-value=30 Score=21.94 Aligned_cols=24 Identities=4% Similarity=0.257 Sum_probs=18.2
Q ss_pred HHHHHHHHhhcCCCCchHHHHHhh
Q psy17501 66 QQQFLTVASQSKDPGQSDKMRLLQ 89 (101)
Q Consensus 66 qR~fL~~As~~kKP~~~~~~~lLk 89 (101)
-|+-+....+|.|||-.+|++..+
T Consensus 15 ~k~s~rf~krC~KPdrKEf~ki~~ 38 (67)
T KOG3498|consen 15 AKDSIRFVKRCTKPDRKEFTKIAK 38 (67)
T ss_pred HHHHHHHHHHhcCCcHHHHHHHHH
Confidence 355567788999999988877654
No 21
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=52.23 E-value=36 Score=23.48 Aligned_cols=40 Identities=25% Similarity=0.294 Sum_probs=34.0
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|.++++.+...+......+.++-.+.-++|+++|-.
T Consensus 16 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~ 55 (187)
T TIGR02948 16 DENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIR 55 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 3568999999999999999999998888888888888763
No 22
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=51.12 E-value=37 Score=23.82 Aligned_cols=40 Identities=8% Similarity=0.150 Sum_probs=35.4
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|.+++..+-..+...+..+.++-.+.-++|+++|-.
T Consensus 24 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~ 63 (188)
T PRK09640 24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLK 63 (188)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 4568999999999999999999999988889999998874
No 23
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=50.76 E-value=38 Score=23.63 Aligned_cols=39 Identities=21% Similarity=0.258 Sum_probs=34.8
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+......+.|+-...-++++++|-.
T Consensus 22 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~ 60 (182)
T PRK12537 22 RRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIK 60 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHH
Confidence 468999999999999999999999999999999998764
No 24
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=49.25 E-value=52 Score=22.78 Aligned_cols=43 Identities=5% Similarity=0.023 Sum_probs=36.6
Q ss_pred ccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 22 HLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 22 ~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
..+-+-.+|.+++..+-..+...+..+.++..+.-++++++|-
T Consensus 4 ~~~~~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~fl 46 (172)
T PRK09651 4 ATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFL 46 (172)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHH
Confidence 3455778899999999999999999999988888888888876
No 25
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=49.11 E-value=45 Score=22.58 Aligned_cols=38 Identities=16% Similarity=0.263 Sum_probs=33.1
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.+|++++..+-..+...+....|+....-++++++|-.
T Consensus 5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~ 42 (161)
T PRK12541 5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYR 42 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 57999999999999999999999888888888888764
No 26
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=48.76 E-value=44 Score=22.60 Aligned_cols=39 Identities=28% Similarity=0.265 Sum_probs=32.7
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+...+..++++-.+.-++++++|-.
T Consensus 9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~ 47 (182)
T PRK09652 9 RAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIK 47 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 468999999998888899999988777888888888864
No 27
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=48.64 E-value=46 Score=23.08 Aligned_cols=39 Identities=23% Similarity=0.355 Sum_probs=32.6
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|+++++.+..........++++-.+.-++++++|-.
T Consensus 22 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~ 60 (186)
T PRK13919 22 EEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIR 60 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 468999999998988899999988777788888888764
No 28
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=47.97 E-value=71 Score=23.08 Aligned_cols=41 Identities=15% Similarity=0.314 Sum_probs=36.7
Q ss_pred hhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 25 MSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 25 ~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-..+|.+++..+-.........++++-...-++++++|-.
T Consensus 25 ~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflk 65 (203)
T PRK09647 25 ATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIR 65 (203)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHH
Confidence 36779999999999999999999999888888999998864
No 29
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=46.84 E-value=50 Score=23.10 Aligned_cols=39 Identities=21% Similarity=0.193 Sum_probs=33.9
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+...+..+.++..+.-++++++|-.
T Consensus 21 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~ 59 (189)
T PRK12515 21 RTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLD 59 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 457999999999999999999998888888999988763
No 30
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=46.33 E-value=50 Score=23.12 Aligned_cols=39 Identities=23% Similarity=0.208 Sum_probs=32.9
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|+++++.+-.........+.++....-++++++|-.
T Consensus 28 ~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~ 66 (194)
T PRK12519 28 SAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLS 66 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 357899999999999999999988888888888888763
No 31
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=46.20 E-value=50 Score=23.18 Aligned_cols=40 Identities=18% Similarity=0.181 Sum_probs=35.7
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|+.++..+...+...+..+.++-...-++++++|-.
T Consensus 9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~ 48 (193)
T TIGR02947 9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAK 48 (193)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 4678999999999999999999999988889999988863
No 32
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=45.76 E-value=52 Score=22.89 Aligned_cols=37 Identities=11% Similarity=0.197 Sum_probs=32.6
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.+|++++..+...+......+.++....-++++++|-
T Consensus 25 ~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl 61 (187)
T PRK12534 25 HAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFT 61 (187)
T ss_pred HHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 5799999999999999999999988888888888874
No 33
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=44.72 E-value=56 Score=22.74 Aligned_cols=40 Identities=13% Similarity=0.050 Sum_probs=34.7
Q ss_pred hhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 25 MSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 25 ~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
+.-.+|++++..+-..+...+..+.++-...-++++++|-
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl 52 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFV 52 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 4567899999999999999999999988888888888876
No 34
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=43.76 E-value=70 Score=19.02 Aligned_cols=39 Identities=18% Similarity=0.199 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHhhHHH
Q psy17501 54 THAKLVSEAFQAQQQFLTVASQSKDPGQSDKMRLLQPTS 92 (101)
Q Consensus 54 e~a~lv~~aF~~qR~fL~~As~~kKP~~~~~~~lLkPls 92 (101)
+.+++.++|+..-|.+-.++-...-=+.+.+.++|.|-+
T Consensus 13 ~aa~iAk~A~~~g~svre~v~~~g~lt~ee~d~ll~p~~ 51 (55)
T PF10415_consen 13 KAAEIAKEALAEGRSVREVVLEEGLLTEEELDELLDPER 51 (55)
T ss_dssp HHHHHHHHHHHHT--HHHHHHHTTSS-HHHHHHHTSHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHcCHHH
Confidence 568899999999999999988777656677888888854
No 35
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=42.58 E-value=57 Score=24.03 Aligned_cols=40 Identities=20% Similarity=0.240 Sum_probs=35.6
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|.+++..+-..+...+..+.++-...-++|+++|-.
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflk 55 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMR 55 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 5679999999999999999999999988888888888864
No 36
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=41.62 E-value=64 Score=22.14 Aligned_cols=37 Identities=8% Similarity=0.122 Sum_probs=27.0
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
..|++++..+-..+...+..++++..+.-++++++|-
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i 39 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWI 39 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 4577777777777777777777777777777776664
No 37
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=41.59 E-value=70 Score=22.05 Aligned_cols=38 Identities=13% Similarity=0.223 Sum_probs=32.2
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|+++++.+...+........++-...-+++.++|-
T Consensus 18 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl 55 (179)
T PRK12514 18 RDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYV 55 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHH
Confidence 45799999999999998888888888888888888876
No 38
>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=41.29 E-value=61 Score=21.87 Aligned_cols=39 Identities=23% Similarity=0.098 Sum_probs=28.9
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.-.+|++++..+-..+......+.|+-...-++|+++|-
T Consensus 9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l 47 (170)
T TIGR02952 9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFE 47 (170)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHH
Confidence 345788888888888888666776666667777777765
No 39
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=40.46 E-value=61 Score=21.65 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=27.0
Q ss_pred HHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 29 AFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 29 afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
+|.++++.+-..+...+..++++-...-++|+++|-
T Consensus 2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l 37 (159)
T TIGR02989 2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFV 37 (159)
T ss_pred HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHH
Confidence 577777777777777788887777777777777764
No 40
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=40.30 E-value=68 Score=22.37 Aligned_cols=40 Identities=28% Similarity=0.343 Sum_probs=35.7
Q ss_pred hhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 25 MSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 25 ~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
..-.+|.+++......+......+.|.....-++|+++|-
T Consensus 12 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~l 51 (182)
T COG1595 12 GDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFL 51 (182)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 3456799999999999999999999999899999999987
No 41
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=40.18 E-value=67 Score=21.95 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=31.9
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
..|.+++..+-..+...+..+.++-.+.-++++++|-
T Consensus 6 ~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl 42 (164)
T PRK12547 6 KNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLM 42 (164)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHH
Confidence 5788899999999999999999888888888888875
No 42
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=39.58 E-value=71 Score=22.28 Aligned_cols=38 Identities=24% Similarity=0.218 Sum_probs=30.9
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.+|+++++.+-..+...+..+.++-.+.-++|+++|-.
T Consensus 20 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~ 57 (193)
T PRK11923 20 RAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIK 57 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 46889998888888888888888888888888887753
No 43
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=38.75 E-value=73 Score=23.70 Aligned_cols=38 Identities=24% Similarity=0.295 Sum_probs=32.7
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|.+++..+...+......+.|+-.+.-++++++|-
T Consensus 62 ~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl 99 (233)
T PRK12538 62 EAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTML 99 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 34799999999999999999999888888888888876
No 44
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.72 E-value=1e+02 Score=20.99 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=33.9
Q ss_pred chhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 24 SMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 24 p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
+..-.+|.+++..+-..+......+.|+-.+.-+++.++|-
T Consensus 5 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl 45 (173)
T PRK09645 5 TAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLL 45 (173)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 34567899999999999999999999887777788887765
No 45
>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=38.51 E-value=83 Score=21.18 Aligned_cols=39 Identities=23% Similarity=0.299 Sum_probs=32.7
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+...+..+.++-.+.-+++.++|-.
T Consensus 5 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~ 43 (162)
T TIGR02983 5 EEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVR 43 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 468899999998888888888888888888888888764
No 46
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=38.34 E-value=44 Score=23.29 Aligned_cols=39 Identities=10% Similarity=-0.062 Sum_probs=29.5
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
...+|++++..+-..+......+.+.-.+.-++|+++|-
T Consensus 17 d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl 55 (198)
T TIGR02859 17 NTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMI 55 (198)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHH
Confidence 467889999888888888888887665666667776664
No 47
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=36.88 E-value=89 Score=21.66 Aligned_cols=39 Identities=18% Similarity=0.173 Sum_probs=32.8
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|.+++..+-.........+.++-.+.-++++++|-.
T Consensus 6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~ 44 (179)
T PRK12543 6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQ 44 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 368999999999999998888888888888888888763
No 48
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=36.41 E-value=1.2e+02 Score=20.99 Aligned_cols=48 Identities=8% Similarity=0.036 Sum_probs=33.0
Q ss_pred CCCCCCcccchhHHHHHHHhhchhHHHHHH-HhhHhh-HHHHHHHHHHHHHHH
Q psy17501 15 TPVTSPIHLSMSVAAFSDIVAGPLASYIAL-SNKIGG-DVATHAKLVSEAFQA 65 (101)
Q Consensus 15 ~p~~~~~~~p~sV~afDeli~~~l~~fv~l-S~~IGg-~V~e~a~lv~~aF~~ 65 (101)
+|+.++.++ -.+|..+++.+-..+... ...++. +-...-++|++.|-.
T Consensus 3 ~~~~~~~~d---~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~ 52 (178)
T PRK12529 3 APSSCLSAD---RDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLR 52 (178)
T ss_pred CCccCCCCC---HHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHH
Confidence 455555554 368999999998888884 556662 556677778777653
No 49
>KOG4514|consensus
Probab=36.34 E-value=1.9e+02 Score=22.03 Aligned_cols=41 Identities=15% Similarity=0.276 Sum_probs=30.4
Q ss_pred hhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q psy17501 34 VAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSK 77 (101)
Q Consensus 34 i~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~k 77 (101)
+.++|+. +-+.+||.+...+.+.....+..|+-+..++..-
T Consensus 137 l~~~vD~---llr~lgg~lh~is~lt~~~vq~yr~aV~kl~d~~ 177 (222)
T KOG4514|consen 137 LASSVDN---LLRNLGGLLHSISSLTADNVQVYRNAVNKLTDTL 177 (222)
T ss_pred HHHHHHH---HHHHhhhHHHHHHHhhhhHHHHHHHHHHHHHHHh
Confidence 3444444 4467999999999999999999888777665443
No 50
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=36.24 E-value=93 Score=21.63 Aligned_cols=38 Identities=11% Similarity=0.076 Sum_probs=31.3
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|+++++.+-..+......+.++-...-++++++|-
T Consensus 8 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl 45 (185)
T PRK12542 8 YEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFI 45 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 46899999999999999888888887777777777765
No 51
>PF04591 DUF596: Protein of unknown function, DUF596; InterPro: IPR007670 This family contains several uncharacterised proteins.; PDB: 2O5H_B.
Probab=35.57 E-value=27 Score=22.30 Aligned_cols=18 Identities=17% Similarity=0.468 Sum_probs=11.8
Q ss_pred HhhHHHHHHHHHHHHHHH
Q psy17501 48 IGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 48 IGg~V~e~a~lv~~aF~~ 65 (101)
|.|.+.+|.++++++|-.
T Consensus 15 l~Gt~eEqve~fr~~fP~ 32 (70)
T PF04591_consen 15 LEGTTEEQVEMFRKSFPA 32 (70)
T ss_dssp E---HHHHHHHHHHH--S
T ss_pred ecCCHHHHHHHHHHHCCC
Confidence 678899999999999974
No 52
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.57 E-value=92 Score=21.38 Aligned_cols=39 Identities=8% Similarity=-0.008 Sum_probs=34.3
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.-.+|.+++..+-..+......+.++-...-++++++|-
T Consensus 8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevfl 46 (172)
T PRK12523 8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFV 46 (172)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHH
Confidence 458999999999999999999999988888888888876
No 53
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=35.53 E-value=43 Score=24.88 Aligned_cols=50 Identities=18% Similarity=0.028 Sum_probs=37.8
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKDP 79 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP 79 (101)
...+|++++..+.......+.++.++-...-++++++|- -|+.+...-+|
T Consensus 27 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i----~l~~a~~~~~~ 76 (255)
T TIGR02941 27 NGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGML----GLLGAIRRYDY 76 (255)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH----HHHHHHHHcCC
Confidence 356899999999999999999998876677788888875 23444444444
No 54
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.28 E-value=95 Score=21.86 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=33.6
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|.+++..+-..+.....++.++-.+.-++++++|-.
T Consensus 29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~ 67 (194)
T PRK09646 29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLE 67 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 458999999999999999999999888888888888763
No 55
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.05 E-value=89 Score=22.08 Aligned_cols=39 Identities=15% Similarity=0.222 Sum_probs=33.4
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+......+.++-.+.-+++++.|-.
T Consensus 26 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~ 64 (192)
T PRK09643 26 RYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLS 64 (192)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHH
Confidence 457999999999999998889988888888899888864
No 56
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.31 E-value=1e+02 Score=20.67 Aligned_cols=40 Identities=25% Similarity=0.298 Sum_probs=33.8
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
.-.+|.++++.+...+......++++-...-+++.++|-.
T Consensus 11 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~ 50 (179)
T PRK11924 11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLR 50 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 4568999999999999999999888888888888888873
No 57
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=33.85 E-value=1.2e+02 Score=21.49 Aligned_cols=44 Identities=16% Similarity=0.136 Sum_probs=38.2
Q ss_pred cccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 21 IHLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 21 ~~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.+...+-.+|++++..+-..+...+..+.++-...-+++.+.|-
T Consensus 16 ~~~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvfl 59 (188)
T PRK12517 16 SDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFL 59 (188)
T ss_pred HhhhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 44555788999999999999999999999998888888888875
No 58
>KOG0532|consensus
Probab=33.68 E-value=37 Score=30.18 Aligned_cols=47 Identities=11% Similarity=0.286 Sum_probs=35.7
Q ss_pred hhchhHHHHHHHhhHh---hHHHHHHHHHHHHHHHHHHHHH----HHhhcCCCC
Q psy17501 34 VAGPLASYIALSNKIG---GDVATHAKLVSEAFQAQQQFLT----VASQSKDPG 80 (101)
Q Consensus 34 i~~~l~~fv~lS~~IG---g~V~e~a~lv~~aF~~qR~fL~----~As~~kKP~ 80 (101)
...+|..|+++++||| .++-.+.+++.+-|--+|+... +..+..-|+
T Consensus 637 crrNVdnFLeaCRkiGVpEa~lCS~~Dilq~~~r~~rk~~~t~~~~~~~a~~~~ 690 (722)
T KOG0532|consen 637 CRRNVDNFLEACRKIGVPEADLCSPMDILQKIERNPRKVARTVLTVGKKAQPQS 690 (722)
T ss_pred HHHhHHHHHHHHHHcCCChHhhcCHHHhhhhhcccchhHHHHHHhhccccCCCC
Confidence 4678999999999999 4677889999998877766554 444444443
No 59
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=33.00 E-value=1.5e+02 Score=21.52 Aligned_cols=47 Identities=6% Similarity=-0.014 Sum_probs=35.9
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQS 76 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~ 76 (101)
-.+|++++..+.......+..+.+.-...-++++++|- .++....+.
T Consensus 10 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i---~l~~a~~~f 56 (231)
T TIGR02885 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCI---GLVKAIDKF 56 (231)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH---HHHHHHHhc
Confidence 46899999999999999999987766677788888876 344444444
No 60
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.65 E-value=1.1e+02 Score=21.35 Aligned_cols=39 Identities=18% Similarity=0.219 Sum_probs=32.6
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+.....++.+.-...-++++++|-.
T Consensus 25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~ 63 (194)
T PRK12513 25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLR 63 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 478889999998999999988888877888888888763
No 61
>cd00193 t_SNARE Soluble NSF (N-ethylmaleimide-sensitive fusion protein)-Attachment protein (SNAP) REceptor domain; these alpha-helical motifs form twisted and parallel heterotetrameric helix bundles; the core complex contains one helix from a protein that is anchored in the vesicle membrane (synaptobrevin), one helix from a protein of the target membrane (syntaxin), and two helices from another protein anchored in the target membrane (SNAP-25); their interaction forms a core which is composed of a polar zero layer, a flanking leucine-zipper layer acts as a water tight shield to isolate ionic interactions in the zero layer from the surrounding solvent
Probab=32.63 E-value=93 Score=17.25 Aligned_cols=27 Identities=11% Similarity=0.309 Sum_probs=21.5
Q ss_pred hhchhHHHHHHHhhHhhHHHHHHHHHH
Q psy17501 34 VAGPLASYIALSNKIGGDVATHAKLVS 60 (101)
Q Consensus 34 i~~~l~~fv~lS~~IGg~V~e~a~lv~ 60 (101)
|...+..+-.+...||..|.+|..++.
T Consensus 11 l~~~i~~l~~l~~~i~~~v~~Q~~~ld 37 (60)
T cd00193 11 LEASIGELKQIFLDLGTEVEEQGELLD 37 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888888889988888876653
No 62
>cd00633 Secretoglobin Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer structure is composed of four alpha helices that do not form a canonical four helix-bundle motif but rather a boomerang-shaped structure in which helices H1, H3, and H4 are able to bind a homodimeric partner. The hydrophobic pocket binds steroids, particularly progesterone, with high specificity. However, the true biological function of uteroglobin is poorly understood. In mammals, uteroglobin has immunosuppressive and anti-inflammatory properties through the inhibition of phospholipase A2. The other four main subfamilies of secretoglobins are found in heterodimeri
Probab=31.97 E-value=1.2e+02 Score=18.27 Aligned_cols=42 Identities=12% Similarity=0.173 Sum_probs=33.7
Q ss_pred hhHHHHHHHhhchhHHHHHHHhhHhh--HHHHHHHHHHHHHHHH
Q psy17501 25 MSVAAFSDIVAGPLASYIALSNKIGG--DVATHAKLVSEAFQAQ 66 (101)
Q Consensus 25 ~sV~afDeli~~~l~~fv~lS~~IGg--~V~e~a~lv~~aF~~q 66 (101)
.....+..++.|+...|...=++... +..+...-++++|+.+
T Consensus 3 ~~~~~~~~~l~gs~~~y~~~L~~f~~~~~~~~A~~~lK~C~d~~ 46 (67)
T cd00633 3 ALESVIEGFLLGSEEEYKAELEKFNATPEAVEAKEKLKQCVDEQ 46 (67)
T ss_pred hHHHHHHHHhcCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHhcC
Confidence 45667888888888888887777764 6788888999999875
No 63
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.93 E-value=77 Score=21.41 Aligned_cols=37 Identities=14% Similarity=0.101 Sum_probs=26.8
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.+|++++..+-..+......+.|+-.+.-++++++|-
T Consensus 4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl 40 (161)
T PRK12528 4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFV 40 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHH
Confidence 4678888877777777777777766666667666654
No 64
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=31.71 E-value=1.3e+02 Score=18.76 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=35.4
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQ 68 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~ 68 (101)
-|++-.+.+.+++...++...+|+..+....++...+...++.
T Consensus 11 ~v~~v~~im~~Ni~~ll~Rge~L~~L~~kt~~L~~~a~~F~k~ 53 (89)
T PF00957_consen 11 QVEEVKNIMRENIDKLLERGEKLEELEDKTEELSDNAKQFKKN 53 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCchHHHHHHHHHHHHHHhHHHHHH
Confidence 3555667888999999999999999998888888888776654
No 65
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=31.67 E-value=1.7e+02 Score=22.01 Aligned_cols=37 Identities=16% Similarity=0.038 Sum_probs=31.2
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.+|++++..+-..+......++++-...-+++++.|-
T Consensus 39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFl 75 (244)
T TIGR03001 39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQ 75 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 5799999999999999999998877777788888765
No 66
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=31.16 E-value=1.2e+02 Score=21.25 Aligned_cols=38 Identities=16% Similarity=0.143 Sum_probs=32.1
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|++++..+-..+...+..+.++-...-++++++|-
T Consensus 26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l 63 (194)
T PRK12531 26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMS 63 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 46799999999999999999998887777788888875
No 67
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=30.82 E-value=57 Score=24.28 Aligned_cols=38 Identities=18% Similarity=0.093 Sum_probs=31.4
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|++++..+...+...+..+.+.-...-++++++|-
T Consensus 28 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l 65 (257)
T PRK08583 28 EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMV 65 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 45899999999999999999988766667778888775
No 68
>PHA02662 ORF131 putative membrane protein; Provisional
Probab=30.81 E-value=64 Score=24.96 Aligned_cols=36 Identities=22% Similarity=0.236 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCcccchhH-HHHHHHhhchhHHHHHHH
Q psy17501 10 PLTASTPVTSPIHLSMSV-AAFSDIVAGPLASYIALS 45 (101)
Q Consensus 10 ~~~a~~p~~~~~~~p~sV-~afDeli~~~l~~fv~lS 45 (101)
+.|-++|+.+|+..|..+ .-||.|+..+|.++-..|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~tLY~lf~~ryL~kLs~~s 39 (226)
T PHA02662 3 PRTPPTPPRPPEPTPAAPGSLYDVFLARFLRRLAARA 39 (226)
T ss_pred CCCCCCCCCCCCCCccchhhHHHHHHHHHHHHHHhcc
Confidence 446677777777777665 358888888887776554
No 69
>PF09361 Phasin_2: Phasin protein; InterPro: IPR018968 Phasins (or granule-associate proteins) are surface proteins found covering Polyhydroxyalkanoate (PHA) storage granules in bacteria. Polyhydroxyalkanoates are linear polyesters produced by bacterial fermentation of sugar or lipids for the purpose of storing carbon and energy, and are accumulated as intracellular granules by many bacteria under unfavorable conditions, enhancing their fitness and stress resistance []. The layer of phasins stabilises the granules and prevents coalescence of separated granules in the cytoplasm and nonspecific binding of other proteins to the hydrophobic surfaces of the granules. For example, in Ralstonia eutropha (strain ATCC 17699/H16/DSM 428/Stanier 337) (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)), the major surface protein of polyhydroxybutyrate (PHB) granules is phasin PhaP1(Reu), which occurs along with three homologues (PhaP2, PhaP3, and PhaP4) that have the capacity to bind to PHB granules but are present at minor levels [, ]. These four phasins lack a highly conserved domain but share homologous hydrophobic regions. This entry describes a group of phasins that associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB).
Probab=29.00 E-value=1.4e+02 Score=18.22 Aligned_cols=65 Identities=15% Similarity=0.181 Sum_probs=41.7
Q ss_pred HHHHhhchhHHHHHHHh----hHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCch-H-HHHHhhHHHHH
Q psy17501 30 FSDIVAGPLASYIALSN----KIGGDVATHAKLVSEAFQAQQQFLTVASQSKDPGQS-D-KMRLLQPTSDK 94 (101)
Q Consensus 30 fDeli~~~l~~fv~lS~----~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~~-~-~~~lLkPls~~ 94 (101)
|.+.-...+..+.+++. .+......+.+.++..++..-.++.....|+.|..- . -.+++++..+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~a~~~~e~~~~Q~~~~~~~~e~ 74 (102)
T PF09361_consen 4 FSEAQQKNLEAFQALAEAALEGAEALAALNLEAARQNVEEAFAQAQQLASAKDPQELVALQSEFAQEQFER 74 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 34444455555555544 334456677888899999999999999999998431 1 23444444443
No 70
>PF10303 DUF2408: Protein of unknown function (DUF2408); InterPro: IPR018810 This entry represents a family of proteins conserved in fungi whose function is unknown.
Probab=28.84 E-value=1.7e+02 Score=20.40 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCc-hHHHHHhhHHHHHHHHHhhC
Q psy17501 55 HAKLVSEAFQAQQQFLTVASQSKDPGQ-SDKMRLLQPTSDKIAAIHIH 101 (101)
Q Consensus 55 ~a~lv~~aF~~qR~fL~~As~~kKP~~-~~~~~lLkPls~~I~~i~~~ 101 (101)
..-...+.|.--|.++.+++.++..+. .....=|.|++..+.+|.++
T Consensus 9 L~pi~ekLisIrR~L~~~~t~~k~~~~~~~~~~el~~lq~qL~eIe~~ 56 (134)
T PF10303_consen 9 LQPIYEKLISIRRSLLSLNTRSKFSDSSEESSSELKPLQEQLKEIESM 56 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCCccccccHHHHHHHHHHHHHHHHh
Confidence 345667888888999999999888733 23456678888888888764
No 71
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=28.71 E-value=1.1e+02 Score=20.94 Aligned_cols=38 Identities=16% Similarity=0.120 Sum_probs=28.2
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHH-----HHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVA-----THAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~-----e~a~lv~~aF~ 64 (101)
-.+|++++..+-..+......+.++-. ..-++|.++|-
T Consensus 16 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl 58 (183)
T TIGR02999 16 AAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYL 58 (183)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHH
Confidence 358888888888888888888777655 56666766654
No 72
>smart00040 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic activity of white blood cells.
Probab=28.60 E-value=42 Score=23.43 Aligned_cols=39 Identities=26% Similarity=0.288 Sum_probs=26.4
Q ss_pred chhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHH
Q psy17501 24 SMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQ 67 (101)
Q Consensus 24 p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR 67 (101)
-..|.|-.| .+ .++..|...+....+-.+.|.+-|+-|+
T Consensus 13 ~kHVdAIkE----Al-sLLn~s~dt~a~mnEtVeVVSe~Fd~qe 51 (121)
T smart00040 13 WKHVDAIKE----AL-SLLNDSRDTAAVMNETVEVVSEMFDLQE 51 (121)
T ss_pred HHHHHHHHH----HH-HHHhcCCchHhHhcchHHHHHhccCCCC
Confidence 345555443 33 3667788888888888888888888554
No 73
>PF06148 COG2: COG (conserved oligomeric Golgi) complex component, COG2; InterPro: IPR024602 This entry represents the uncharacterised N-terminal domain of subunit 2 of the COG complex. The COG complex comprises eight proteins COG1-8 and plays critical roles in Golgi structure and function [].; PDB: 2JQQ_A.
Probab=28.53 E-value=75 Score=21.54 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=0.4
Q ss_pred HHHhhchhHHHHHHHhhHhhHHHHHHHH
Q psy17501 31 SDIVAGPLASYIALSNKIGGDVATHAKL 58 (101)
Q Consensus 31 Deli~~~l~~fv~lS~~IGg~V~e~a~l 58 (101)
=++||.....|+.+|..+.|.-.....+
T Consensus 47 i~lIN~dY~dFv~Ls~~L~g~~~~i~~l 74 (133)
T PF06148_consen 47 IELINDDYADFVSLSTNLVGMDEKIEEL 74 (133)
T ss_dssp ---------------------------H
T ss_pred HHHHHhhHHHHHHHHHHHccHHHHHHHH
Confidence 3678999999999999988854433333
No 74
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.11 E-value=1.3e+02 Score=20.33 Aligned_cols=36 Identities=11% Similarity=0.089 Sum_probs=26.9
Q ss_pred HHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 29 AFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 29 afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.|++++..+-......+..++++-.+.-++|+++|-
T Consensus 2 ~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl 37 (165)
T PRK09644 2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFY 37 (165)
T ss_pred cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 367777777777777788877777777777777765
No 75
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=27.91 E-value=36 Score=22.80 Aligned_cols=43 Identities=9% Similarity=0.145 Sum_probs=34.0
Q ss_pred hHHHHHHHhhch-hHHHHHHHhhHhhHHHHHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGP-LASYIALSNKIGGDVATHAKLVSEAFQAQQQ 68 (101)
Q Consensus 26 sV~afDeli~~~-l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~ 68 (101)
....||.+|-.. =..|...++-||..++.....+...|-.-|-
T Consensus 45 ~ed~yD~~Il~~~~~~~~~~arvIg~vl~~~~~~i~D~f~~~Ri 88 (111)
T PF12395_consen 45 PEDYYDDFILEQAPDEFQKAARVIGEVLGHSDQGIGDWFLEYRI 88 (111)
T ss_pred ChHHhhHHHHhcCCccccHHHHHHHHHHHhcCcCCChHHHHHHH
Confidence 568899887544 4788999999999888877778888877664
No 76
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.81 E-value=74 Score=22.38 Aligned_cols=38 Identities=13% Similarity=-0.074 Sum_probs=30.5
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|++++..+-......+..++++-...-++++++|-
T Consensus 23 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l 60 (208)
T PRK08295 23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMI 60 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 36899999999999999888888876677777777665
No 77
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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.
Probab=27.36 E-value=1.2e+02 Score=23.02 Aligned_cols=38 Identities=21% Similarity=0.265 Sum_probs=31.9
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|++++..+-..+...+..+.|+....-++++++|-
T Consensus 4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl 41 (324)
T TIGR02960 4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLL 41 (324)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHH
Confidence 46899999999999999998888887777788887765
No 78
>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=26.82 E-value=1.7e+02 Score=22.14 Aligned_cols=63 Identities=17% Similarity=0.285 Sum_probs=49.2
Q ss_pred CCCCCCcccchhHHHHHHHhhchhHHHHHHHhhHhh----HHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q psy17501 15 TPVTSPIHLSMSVAAFSDIVAGPLASYIALSNKIGG----DVATHAKLVSEAFQAQQQFLTVASQSKDP 79 (101)
Q Consensus 15 ~p~~~~~~~p~sV~afDeli~~~l~~fv~lS~~IGg----~V~e~a~lv~~aF~~qR~fL~~As~~kKP 79 (101)
.|..++......++.|-++....+...++-+++|=| ...+|..+++.+|-+. |+.-.+.+..|
T Consensus 32 ~~~~~~~~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El--l~L~~a~r~~~ 98 (239)
T cd07072 32 SPLEPPMSEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLEL--FVLRLAYRTAP 98 (239)
T ss_pred CcccCCcchHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHH--HHHHHHHHccC
Confidence 344566777888999999999999999999999987 6889999999999865 33333443344
No 79
>PF09989 DUF2229: CoA enzyme activase uncharacterised domain (DUF2229); InterPro: IPR018709 Proteins containing this domain include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined.
Probab=26.50 E-value=1.2e+02 Score=22.65 Aligned_cols=41 Identities=15% Similarity=0.194 Sum_probs=33.3
Q ss_pred chhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy17501 36 GPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQS 76 (101)
Q Consensus 36 ~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~ 76 (101)
...+.++++.+.+|-.-.+..+-+.+|+.+|++|-....+-
T Consensus 130 ~~~~~l~~~~~~lg~~~~~~~~A~~~A~~~~~~~~~~l~~~ 170 (221)
T PF09989_consen 130 SLAKALYELGKRLGISRKEIRRAFEKALEAQKAFRRELRKG 170 (221)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566777889999889999999999999999997765443
No 80
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=26.25 E-value=2.2e+02 Score=21.21 Aligned_cols=38 Identities=11% Similarity=0.125 Sum_probs=31.6
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|+.++..+.......+..+-+.-...-++++.+|-
T Consensus 33 ~~a~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i 70 (254)
T TIGR02850 33 TTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 70 (254)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 46899999999999999999887665667788888876
No 81
>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=26.24 E-value=76 Score=22.95 Aligned_cols=37 Identities=16% Similarity=0.119 Sum_probs=27.1
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.+|++++..+..-....+..+.+.-.+.-++++.+|-
T Consensus 3 ~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i 39 (227)
T TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTI 39 (227)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 5788888888888888888876554455666666655
No 82
>PF06260 DUF1024: Protein of unknown function (DUF1024); InterPro: IPR009368 This entry is represented by Bacteriophage 92, Orf64. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical proteins from Staphylococcus aureus, which are related to Orf64 from Staphylococcus phage 92 (Bacteriophage 92). The function of this family is unknown.
Probab=25.82 E-value=2e+02 Score=18.89 Aligned_cols=22 Identities=14% Similarity=0.144 Sum_probs=17.3
Q ss_pred hhHHHHHHHhhchhHHHHHHHh
Q psy17501 25 MSVAAFSDIVAGPLASYIALSN 46 (101)
Q Consensus 25 ~sV~afDeli~~~l~~fv~lS~ 46 (101)
+-=++||+++.+....+....+
T Consensus 34 KKAqaFDeI~e~~~~~~~~~~~ 55 (82)
T PF06260_consen 34 KKAQAFDEILEDINNQIQEYRK 55 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3457899999988888887766
No 83
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.66 E-value=1.6e+02 Score=20.98 Aligned_cols=39 Identities=21% Similarity=0.157 Sum_probs=30.7
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+........++-...-++++++|-.
T Consensus 37 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~ 75 (206)
T PRK12526 37 KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSN 75 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHH
Confidence 457888888888888888888888777777888887753
No 84
>PF09025 YopR_core: YopR Core; InterPro: IPR013349 Proteins in this entry are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.; GO: 0009405 pathogenesis, 0030254 protein secretion by the type III secretion system, 0030257 type III protein secretion system complex; PDB: 1Z21_A.
Probab=25.53 E-value=1.3e+02 Score=21.79 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=22.1
Q ss_pred HHHHHHHHH-----HHHHHHHHHhhcCCCCc-hHHHHHhhHHHHHHH
Q psy17501 56 AKLVSEAFQ-----AQQQFLTVASQSKDPGQ-SDKMRLLQPTSDKIA 96 (101)
Q Consensus 56 a~lv~~aF~-----~qR~fL~~As~~kKP~~-~~~~~lLkPls~~I~ 96 (101)
+.-++++|. +||+.||-+-+...+.. ..-.+|+.|+.+.+-
T Consensus 12 ~~~Le~~l~~~~pa~qre~lWq~y~kg~~~~~~v~~~L~~pv~~~L~ 58 (142)
T PF09025_consen 12 GSSLENALGGESPAAQREALWQAYQKGTDQAAQVGSELFTPVKQELL 58 (142)
T ss_dssp ------------HHHHHHHHHHHHHH-SS--HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHhcCCChHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHH
Confidence 444556665 79999999988433322 235789999888754
No 85
>PF01099 Uteroglobin: Uteroglobin family; InterPro: IPR006038 Uteroglobin (or blastokinin) is a mammalian steroid-inducible secreted protein originally isolated from the uterus of rabbits during early pregnancy. The mucosal epithelia of several organs that communicate with the external environment express uteroglobin. Its tissue-specific expression is regulated by steroid hormones, and is augmented in the uterus by non-steroidal prolactin. Uteroglobin may be a multi-functional protein with anti-inflammatory/immunomodulatory properties, acting to inhibit phospholipase A2 activity, and binding to (and possibly sequestering) several hydrophobic ligands such as progesterone, retinols, polychlorinated biphenyls, phospholipids and prostaglandins. In addition, uteroglobin has anti-chemotactic, anti-allergic, anti-tumourigenic and embryo growth-stimulatory properties. Uteroglobin may have a homeostatic role against oxidative damage, inflammation, autoimmunity and cancer [, , , ]. Uteroglobin consists of a disulphide-linked dimer of two identical polypeptides, each polypeptide being composed of four helices. It is a member of the secretoglobin superfamily. This entry represents uteroglobin proteins from several mammalian species, as well as other members of the secretoglobin superfamily, such as lipophilin B [], prostatic steroid-binding protein [], mammaglobin [], and the related allergen Fel d 1 (Felis domesticus allergen 1) [].; GO: 0005488 binding, 0005576 extracellular region; PDB: 1UTR_B 1CCD_A 1UTG_A 2UTG_A 1ZKR_B 1PUO_B 2EJN_B.
Probab=25.16 E-value=1.2e+02 Score=18.44 Aligned_cols=39 Identities=8% Similarity=0.090 Sum_probs=28.7
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhh--HHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGG--DVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg--~V~e~a~lv~~aF~~ 65 (101)
....+.++.+....|...=++.+. ++.+...-++++|+.
T Consensus 5 ~~~v~~~l~~s~~~Y~~~l~~y~~~~~~~~A~~~lK~C~d~ 45 (67)
T PF01099_consen 5 EDVVTKFLFGSPEEYKESLQKYNPPPEAVEAKLELKQCVDK 45 (67)
T ss_dssp HHHHHHHHHS-HHHHHHHHHCC---HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHhcCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh
Confidence 445567788888888888888776 488889999999874
No 86
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=24.78 E-value=1.5e+02 Score=22.87 Aligned_cols=39 Identities=21% Similarity=0.236 Sum_probs=32.8
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQA 65 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~ 65 (101)
-.+|++++..+-..+...+..+.++-.+.-++++++|-.
T Consensus 18 ~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~ 56 (339)
T PRK08241 18 RDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLR 56 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHH
Confidence 467999999999999999999888877888888887764
No 87
>PRK05572 sporulation sigma factor SigF; Validated
Probab=24.70 E-value=2.3e+02 Score=21.00 Aligned_cols=48 Identities=10% Similarity=0.007 Sum_probs=36.6
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSK 77 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~k 77 (101)
-.+|+.++..+.......+..+.++-...-++++++|- .++....+..
T Consensus 31 ~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l---~l~~~~~~f~ 78 (252)
T PRK05572 31 QEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCI---GLLKAVDKFD 78 (252)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHH---HHHHHHHHcC
Confidence 36899999999999999999988776677788888876 3444444444
No 88
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.35 E-value=87 Score=22.83 Aligned_cols=39 Identities=15% Similarity=0.061 Sum_probs=30.2
Q ss_pred hHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 26 SVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 26 sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
.-.+|++++..+-..+...+..+.++-.+.-++++++|-
T Consensus 50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl 88 (234)
T PRK08301 50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTI 88 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence 346899999999999989898888765556667776665
No 89
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=23.73 E-value=1.1e+02 Score=15.28 Aligned_cols=18 Identities=22% Similarity=0.268 Sum_probs=12.4
Q ss_pred HHHHhhHHHHHHHHHhhC
Q psy17501 84 KMRLLQPTSDKIAAIHIH 101 (101)
Q Consensus 84 ~~~lLkPls~~I~~i~~~ 101 (101)
+.+.++.+.+.|.=|++|
T Consensus 5 lkkv~qglhe~ikli~nh 22 (23)
T PF08225_consen 5 LKKVFQGLHEVIKLINNH 22 (23)
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 556667777777777766
No 90
>TIGR02509 type_III_yopR type III secretion effector, YopR family. Members of this family are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yops protein is unusual in that it is released to extracellularly rather than injected directly into the target cell as are most Yops.
Probab=23.61 E-value=1.6e+02 Score=20.97 Aligned_cols=33 Identities=21% Similarity=0.316 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhcCCCCc---hHHHHHhhHHHHHHH
Q psy17501 64 QAQQQFLTVASQSKDPGQ---SDKMRLLQPTSDKIA 96 (101)
Q Consensus 64 ~~qR~fL~~As~~kKP~~---~~~~~lLkPls~~I~ 96 (101)
..||+.||-+-+..+|.- ..-.+++.|+.+.+-
T Consensus 11 ~~~re~lWq~~~q~~~~~~~~~~~~~L~~pv~e~Ll 46 (131)
T TIGR02509 11 ATQRELLWQQYQQGKPAAGTADLVPELLSPVKERLL 46 (131)
T ss_pred HHHHHHHHHHHHccCCCcchhHHHHHHHHHHHHHHH
Confidence 468999999888777732 336789999998764
No 91
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=23.25 E-value=89 Score=24.03 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=32.8
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|+.+|..++.-.+..+..+-+.-...-++++++|-
T Consensus 73 ~~A~~~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~i 110 (298)
T TIGR02997 73 QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSL 110 (298)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 47999999999999999999987766677788888876
No 92
>PRK10061 DNA damage-inducible protein YebG; Provisional
Probab=23.03 E-value=2.5e+02 Score=18.98 Aligned_cols=51 Identities=14% Similarity=0.173 Sum_probs=35.5
Q ss_pred hHHHHHHHh--hchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q psy17501 26 SVAAFSDIV--AGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKD 78 (101)
Q Consensus 26 sV~afDeli--~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kK 78 (101)
-=.+||..+ ...|.+|+..|.- +.=.++.+-+-=-+..+|+.|..+.+.++
T Consensus 24 EADAyDKMLD~Ad~L~~~L~~s~~--~ldE~q~E~L~l~LA~nKd~l~~~lk~~~ 76 (96)
T PRK10061 24 EADAYDKMLDTADLLDTWLTNSPV--QMEDEQREALSLWLAEQKDVLSTILKTGK 76 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCC--CCCHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 346899986 4999999998874 22234444455556678888888887773
No 93
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=22.82 E-value=2.6e+02 Score=20.75 Aligned_cols=47 Identities=9% Similarity=0.113 Sum_probs=35.5
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQS 76 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~ 76 (101)
-.+|++++..+..-....+..+.+.-...-++++.+|- .++..+.+.
T Consensus 36 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i---~l~~a~~~f 82 (258)
T PRK08215 36 KEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCI---GLMKAIDNF 82 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH---HHHHHHHhc
Confidence 46899999999999999999987766667788888876 344444444
No 94
>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=22.67 E-value=1.8e+02 Score=18.32 Aligned_cols=20 Identities=10% Similarity=0.243 Sum_probs=8.2
Q ss_pred HHHHhhchhHHHHHHHhhHh
Q psy17501 30 FSDIVAGPLASYIALSNKIG 49 (101)
Q Consensus 30 fDeli~~~l~~fv~lS~~IG 49 (101)
+|++++.-+-.+.......+
T Consensus 28 ~~D~~qe~~~~l~~~~~~~~ 47 (158)
T TIGR02937 28 AEDLVQEAFLKLLEALDRFD 47 (158)
T ss_pred HHHHHHHHHHHHHHhHHhcC
Confidence 34444444444444333333
No 95
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=22.66 E-value=90 Score=22.82 Aligned_cols=38 Identities=13% Similarity=0.032 Sum_probs=29.5
Q ss_pred HHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 27 VAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 27 V~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
-.+|+.++..+...+...+..+.++-...-++++++|-
T Consensus 47 ~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi 84 (227)
T TIGR02846 47 EEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTI 84 (227)
T ss_pred HHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 46899999999999988888887765556667776655
No 96
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=22.43 E-value=3.7e+02 Score=21.05 Aligned_cols=59 Identities=15% Similarity=0.036 Sum_probs=42.4
Q ss_pred HHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCc-hHHHHHhhH
Q psy17501 28 AAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLTVASQSKDPGQ-SDKMRLLQP 90 (101)
Q Consensus 28 ~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~-~~~~~lLkP 90 (101)
.+|+.++..++..++..+.++-+.-...-+++.++|- =|+.+...=.|+. ..|...+..
T Consensus 81 ~A~~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i----~L~~a~~~fd~~~g~rf~tYa~~ 140 (317)
T PRK07405 81 AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTI----GMQRGVEKFDPTKGYRFSTYAYW 140 (317)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH----HHHHHHHHhCcCCCCChHHHHHH
Confidence 7999999999999999999998776677889999886 2344444444532 235544443
No 97
>cd00040 CSF2 Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) is a member of the large family of polypeptide growth factors called cytokines. It stimulates a wide variety of hematopoietic and nonhematopoietic cell types via binding to members of the cytokine receptor family, mainly the GM-CSF receptor.
Probab=21.96 E-value=60 Score=22.72 Aligned_cols=50 Identities=24% Similarity=0.331 Sum_probs=28.8
Q ss_pred CCCCCcccchhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHH
Q psy17501 16 PVTSPIHLSMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQ 67 (101)
Q Consensus 16 p~~~~~~~p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR 67 (101)
|+.+|..+..-.+--| .|.+.+ .++..|+.......+-.+.|.+.|+.|+
T Consensus 2 Pt~~P~~VT~p~~hVd-AikEAl-~lLn~s~d~~avmne~vevvse~Fd~qe 51 (121)
T cd00040 2 PTRSPSPVTRPWQHVD-AIKEAL-SLLNNSNDTAAVMNETVEVVSEMFDPQE 51 (121)
T ss_pred CCCCCCCCCchhHHHH-HHHHHH-HHhhcCCchhhhcchhHHHHHhccCCCC
Confidence 4444444444333322 244443 3556677777677777888888888543
No 98
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=21.85 E-value=1.6e+02 Score=20.14 Aligned_cols=41 Identities=12% Similarity=0.081 Sum_probs=29.7
Q ss_pred chhHHHHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHH
Q psy17501 24 SMSVAAFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQ 64 (101)
Q Consensus 24 p~sV~afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~ 64 (101)
+-+-+.|++++..+-..+......+-++..+.-+++.++|-
T Consensus 5 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~ 45 (168)
T PRK12525 5 SIKNTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFL 45 (168)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHH
Confidence 44567788888888888888777777766666777777654
No 99
>COG5490 Uncharacterized conserved protein [Function unknown]
Probab=20.80 E-value=1.9e+02 Score=21.14 Aligned_cols=46 Identities=13% Similarity=0.226 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHhhHHHHHHHHHh
Q psy17501 51 DVATHAKLVSEAFQAQQQFLTVASQSKDPGQSDKMRLLQPTSDKIAAIH 99 (101)
Q Consensus 51 ~V~e~a~lv~~aF~~qR~fL~~As~~kKP~~~~~~~lLkPls~~I~~i~ 99 (101)
.|.-|..+.++.|.. .|..+...+.-....-.+.++||++.|.+..
T Consensus 106 lvelQTafark~~Ea---aveqa~~~qe~arks~~es~kplk~r~e~Am 151 (158)
T COG5490 106 LVELQTAFARKSFEA---AVEQAKEVQELARKSAEESIKPLKARIEKAM 151 (158)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 455556666666553 1222222111111224567889888877654
No 100
>KOG3901|consensus
Probab=20.71 E-value=1.8e+02 Score=20.11 Aligned_cols=30 Identities=20% Similarity=0.191 Sum_probs=26.7
Q ss_pred CcccchhHHHHHHHhhchhHHHHHHHhhHh
Q psy17501 20 PIHLSMSVAAFSDIVAGPLASYIALSNKIG 49 (101)
Q Consensus 20 ~~~~p~sV~afDeli~~~l~~fv~lS~~IG 49 (101)
..+-+.+|...++++-+++.....+...||
T Consensus 26 ~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g 55 (109)
T KOG3901|consen 26 VNPYPETVDLLEDIVLEYITELTHAAMEIG 55 (109)
T ss_pred CCccHhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445677999999999999999999999998
No 101
>COG5506 Uncharacterized conserved protein [Function unknown]
Probab=20.51 E-value=86 Score=22.66 Aligned_cols=18 Identities=28% Similarity=0.676 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHhhcCCC
Q psy17501 62 AFQAQQQFLTVASQSKDP 79 (101)
Q Consensus 62 aF~~qR~fL~~As~~kKP 79 (101)
.|+.||.+|++|.+|.-|
T Consensus 71 ~~q~~~~YiklA~e~~~~ 88 (144)
T COG5506 71 EFQSQRFYIKLAKETDSP 88 (144)
T ss_pred cHHHHhHHHHHHHHcCCC
Confidence 699999999999999988
No 102
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=20.09 E-value=58 Score=21.96 Aligned_cols=17 Identities=12% Similarity=0.262 Sum_probs=12.2
Q ss_pred HHHHhhchhHHHHHHHh
Q psy17501 30 FSDIVAGPLASYIALSN 46 (101)
Q Consensus 30 fDeli~~~l~~fv~lS~ 46 (101)
+|.|++++|++|+..+.
T Consensus 80 ld~F~~~~L~~fvd~~~ 96 (125)
T PF06744_consen 80 LDQFFNQYLKPFVDTSG 96 (125)
T ss_pred HHHHHHHHHHHHHhCCC
Confidence 46677777888887664
No 103
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=20.06 E-value=3.8e+02 Score=20.04 Aligned_cols=43 Identities=21% Similarity=0.420 Sum_probs=38.3
Q ss_pred HHHHHhhchhHHHHHHHhhHhhHHHHHHHHHHHHHHHHHHHHH
Q psy17501 29 AFSDIVAGPLASYIALSNKIGGDVATHAKLVSEAFQAQQQFLT 71 (101)
Q Consensus 29 afDeli~~~l~~fv~lS~~IGg~V~e~a~lv~~aF~~qR~fL~ 71 (101)
.|+.++...|++|-.....|...+..|..++...-.....|..
T Consensus 190 ~~~~lf~~eL~k~~~~~~~i~~~~~~Q~~ll~~i~~~~~~~~~ 232 (296)
T PF13949_consen 190 DFEALFEEELKKFDPLQNRIQQNLSKQEELLQEIQEANEEFAQ 232 (296)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999999999999999999888888843
Done!