Query psy11277
Match_columns 66
No_of_seqs 126 out of 614
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 22:45:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11277.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11277hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03098 An_peroxidase: Animal 99.9 3E-23 6.5E-28 157.1 5.4 54 11-66 202-255 (530)
2 KOG2408|consensus 99.9 1.6E-22 3.5E-27 159.7 5.1 57 8-66 366-422 (719)
3 PLN02283 alpha-dioxygenase 99.9 3.4E-22 7.4E-27 156.2 6.3 55 9-66 250-304 (633)
4 PF10929 DUF2811: Protein of u 79.9 2 4.4E-05 25.0 2.3 15 48-62 19-33 (57)
5 PF02093 Gag_p30: Gag P30 core 61.8 6 0.00013 28.3 1.8 24 43-66 32-69 (211)
6 PF01630 Glyco_hydro_56: Hyalu 44.8 23 0.0005 26.8 2.7 20 45-64 132-151 (337)
7 PF12424 ATP_Ca_trans_C: Plasm 42.5 5.7 0.00012 23.4 -0.7 21 32-52 2-22 (66)
8 PF02845 CUE: CUE domain; Int 40.1 37 0.0008 17.4 2.3 20 41-60 3-22 (42)
9 PRK07373 DNA polymerase III su 39.3 66 0.0014 24.9 4.5 40 26-65 46-89 (449)
10 PRK09651 RNA polymerase sigma 39.2 84 0.0018 20.0 4.4 35 28-62 9-44 (172)
11 PF13456 RVT_3: Reverse transc 35.6 23 0.0005 19.4 1.2 14 36-49 70-83 (87)
12 TIGR01677 pln_FAD_oxido plant- 35.4 12 0.00027 29.6 -0.0 30 26-55 447-486 (557)
13 PLN00107 FAD-dependent oxidore 34.8 10 0.00022 27.8 -0.6 30 26-55 141-180 (257)
14 PF07872 DUF1659: Protein of u 33.5 39 0.00085 18.2 1.8 18 46-63 29-46 (47)
15 PF02477 Nairo_nucleo: Nucleoc 31.5 37 0.00081 26.6 2.0 19 37-55 196-220 (442)
16 PF04542 Sigma70_r2: Sigma-70 30.7 89 0.0019 16.4 3.1 26 37-62 4-30 (71)
17 PLN02465 L-galactono-1,4-lacto 29.3 19 0.00041 28.9 0.1 26 35-64 520-553 (573)
18 PRK15366 type III secretion sy 29.1 36 0.00078 21.1 1.3 13 30-42 61-73 (80)
19 PF07907 YibE_F: YibE/F-like p 27.8 66 0.0014 22.9 2.6 22 44-65 152-173 (244)
20 PF09957 DUF2191: Uncharacteri 26.5 39 0.00084 18.4 1.0 11 55-65 8-18 (47)
21 PF15056 NRN1: Neuritin protei 23.7 36 0.00078 21.4 0.6 38 27-65 31-71 (89)
22 COG4323 Predicted membrane pro 23.7 60 0.0013 20.8 1.6 24 26-49 10-34 (105)
23 PRK12532 RNA polymerase sigma 23.5 1.6E+02 0.0035 19.0 3.7 30 33-62 9-40 (195)
24 PF14730 DUF4468: Domain of un 22.7 54 0.0012 19.5 1.2 16 50-65 7-22 (91)
25 PF08701 GN3L_Grn1: GNL3L/Grn1 22.3 87 0.0019 19.0 2.1 20 36-55 10-29 (79)
26 KOG2948|consensus 22.2 69 0.0015 24.4 2.0 22 44-65 152-179 (327)
27 PRK09640 RNA polymerase sigma 22.1 2.1E+02 0.0045 18.4 4.0 33 30-62 27-60 (188)
28 PRK09415 RNA polymerase factor 21.8 1.9E+02 0.0042 18.4 3.8 37 26-62 13-50 (179)
29 PRK09637 RNA polymerase sigma 21.1 2.3E+02 0.0049 18.3 4.1 32 31-62 3-35 (181)
30 PF15189 DUF4582: Domain of un 21.1 2.1E+02 0.0046 19.8 4.0 38 4-49 45-82 (172)
31 PF15523 Toxin_44: Putative to 20.9 35 0.00076 20.9 0.1 14 9-22 55-68 (84)
32 PRK13919 putative RNA polymera 20.9 2.2E+02 0.0047 18.1 3.9 34 29-62 23-57 (186)
33 PRK06759 RNA polymerase factor 20.5 2.2E+02 0.0047 17.3 4.2 32 31-63 6-38 (154)
34 PF14436 EndoU_bacteria: Bacte 20.3 70 0.0015 19.9 1.5 14 51-64 72-85 (128)
35 PF11691 DUF3288: Protein of u 20.2 74 0.0016 20.0 1.5 36 28-65 28-72 (90)
36 PF03690 UPF0160: Uncharacteri 20.1 82 0.0018 23.5 2.0 16 41-56 144-159 (318)
No 1
>PF03098 An_peroxidase: Animal haem peroxidase; InterPro: IPR002007 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin [, , ]. MPO plays a major role in the oxygen-dependent microbicidal system of neutrophils. EPO from eosinophilic granulocytes participates in immunological reactions, and potentiates tumor necrosis factor (TNF) production and hydrogen peroxide release by human monocyte-derived macrophages [, ]. In the main, MPO (and possibly EPO) utilises Cl-ions and H2O2 to form hypochlorous acid (HOCl), which can effectively kill bacteria or parasites. In secreted fluids, LPO catalyses the oxidation of thiocyanate ions (SCN-) by H2O2, producing the weak oxidising agent hypothiocyanite (OSCN-), which has bacteriostatic activity []. TPO uses I- ions and H2O2 to generate iodine, and plays a central role in the biosynthesis of thyroid hormones T(3) and T(4). To date, the 3D structures of MPO and PGHS have been reported. MPO is a homodimer: each monomer consists of a light (A or B) and a heavy (C or D) chain resulting from post-translational excision of 6 residues from the common precursor. Monomers are linked by a single inter-chain disulphide. Each monomer includes a bound calcium ion []. PGHS exists as a symmetric dimer, each monomer of which consists of 3 domains: an N-terminal epidermal growth factor (EGF) like module; a membrane-binding domain; and a large C-terminal catalytic domain containing the cyclooxygenase and the peroxidase active sites. The catalytic domain shows striking structural similarity to MPO. The cyclooxygenase active site, which catalyses the formation of prostaglandin G2 (PGG2) from arachidonic acid, resides at the apex of a long hydrophobic channel, extending from the membrane-binding domain to the centre of the molecule. The peroxidase active site, which catalyses the reduction of PGG2 to PGH2, is located on the other side of the molecule, at the haem binding site []. Both MPO and the catalytic domain of PGHS are mainly alpha-helical, 19 helices being identified as topologically and spatially equivalent; PGHS contains 5 additional N-terminal helices that have no equivalent in MPO. In both proteins, three Asn residues in each monomer are glycosylated.; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1FE2_A 1PGG_B 1PGF_A 3N8W_B 1IGZ_A 3KK6_B 3N8Z_A 1Q4G_A 1PTH_A 1EQH_A ....
Probab=99.88 E-value=3e-23 Score=157.15 Aligned_cols=54 Identities=48% Similarity=0.849 Sum_probs=50.6
Q ss_pred CCcCCCcccchhhhhHHHHHHHHHHHHhhHHHHHHHHhhCCCCChHHHHHHHhhcC
Q psy11277 11 QSSPGGNRTHNLMLFSMFAAMHTILMREHNRLAEQLVQINPHWNDEQLFQHARRIM 66 (66)
Q Consensus 11 ~~~~~gd~~~~~n~~p~L~~~htlf~ReHNriA~~L~~~nP~W~De~lfqeARkIv 66 (66)
+||.+||.|+||| |+|+++||+|+|||||||++|++.||+|+||+||||||+||
T Consensus 202 ~~f~~GD~R~ne~--~~l~~lhtlflReHNria~~L~~~np~w~de~lFqeAR~iv 255 (530)
T PF03098_consen 202 RCFLAGDPRVNEN--PGLTALHTLFLREHNRIADELKKINPHWDDERLFQEARRIV 255 (530)
T ss_dssp GSB-TSSTTTTSB--HHHHHHHHHHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHH
T ss_pred cccccccccccch--HHHHHHHHHHHHHHHHHHHHHHHhCCCCChhHHHHHHHHHH
Confidence 7899999999997 99999999999999999999999999999999999999986
No 2
>KOG2408|consensus
Probab=99.86 E-value=1.6e-22 Score=159.73 Aligned_cols=57 Identities=44% Similarity=0.761 Sum_probs=54.3
Q ss_pred ccCCCcCCCcccchhhhhHHHHHHHHHHHHhhHHHHHHHHhhCCCCChHHHHHHHhhcC
Q psy11277 8 LALQSSPGGNRTHNLMLFSMFAAMHTILMREHNRLAEQLVQINPHWNDEQLFQHARRIM 66 (66)
Q Consensus 8 ~~~~~~~~gd~~~~~n~~p~L~~~htlf~ReHNriA~~L~~~nP~W~De~lfqeARkIv 66 (66)
....||.+||.|+++ +|+|+++||+|+|||||||++|++.||+|+||+|||||||||
T Consensus 366 ~~~~cf~aGD~R~~~--~pgL~~~hti~lREHNRiA~~Lk~~np~W~dE~lfQeaRkI~ 422 (719)
T KOG2408|consen 366 APKPCFTAGDERANE--QPGLAALHTLFLREHNRIATELKALNPHWSDERLFQEARKIV 422 (719)
T ss_pred CCCcccccCcccccc--CcchHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH
Confidence 347899999999999 599999999999999999999999999999999999999996
No 3
>PLN02283 alpha-dioxygenase
Probab=99.86 E-value=3.4e-22 Score=156.22 Aligned_cols=55 Identities=22% Similarity=0.442 Sum_probs=51.0
Q ss_pred cCCCcCCCcccchhhhhHHHHHHHHHHHHhhHHHHHHHHhhCCCCChHHHHHHHhhcC
Q psy11277 9 ALQSSPGGNRTHNLMLFSMFAAMHTILMREHNRLAEQLVQINPHWNDEQLFQHARRIM 66 (66)
Q Consensus 9 ~~~~~~~gd~~~~~n~~p~L~~~htlf~ReHNriA~~L~~~nP~W~De~lfqeARkIv 66 (66)
...|+.+||.|| ++ |+|+++||||+||||+||++|++.||+|+||+||||||+||
T Consensus 250 ~~~~~~~Gd~rn-~~--pGL~~lhtLF~REHNrIad~L~~~nP~w~DE~LFQeAR~Iv 304 (633)
T PLN02283 250 EDGIPISGDVRN-SW--AGVSLLQALFVKEHNAVCDALKEEYPDFDDEELYRHARLVT 304 (633)
T ss_pred ccCCcccCcccc-cc--HHHHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence 356999999995 53 99999999999999999999999999999999999999985
No 4
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=79.87 E-value=2 Score=24.99 Aligned_cols=15 Identities=40% Similarity=0.944 Sum_probs=13.4
Q ss_pred hhCCCCChHHHHHHH
Q psy11277 48 QINPHWNDEQLFQHA 62 (66)
Q Consensus 48 ~~nP~W~De~lfqeA 62 (66)
..||+||-.+|||.|
T Consensus 19 e~hP~WDQ~Rl~~aA 33 (57)
T PF10929_consen 19 ETHPNWDQYRLFQAA 33 (57)
T ss_pred HcCCCchHHHHHHHH
Confidence 459999999999987
No 5
>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []. Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.
Probab=61.81 E-value=6 Score=28.28 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=14.2
Q ss_pred HHHHHhhCCCCCh--------------HHHHHHHhhcC
Q psy11277 43 AEQLVQINPHWND--------------EQLFQHARRIM 66 (66)
Q Consensus 43 A~~L~~~nP~W~D--------------e~lfqeARkIv 66 (66)
-..+..-+|.|+| ++|.++|||.|
T Consensus 32 e~i~~Th~pTWdDcqqLL~~LfT~EEr~rI~~~Ark~v 69 (211)
T PF02093_consen 32 ESIFQTHQPTWDDCQQLLQTLFTTEERERILQEARKYV 69 (211)
T ss_dssp HHHHHHT---HHHHHHHHHHHS-HHHHHHHHHHHHHT-
T ss_pred HHHHHhcCCCHHHHHHHHHHHcCHHHHHHHHHHHHHHh
Confidence 3344555799999 67888898864
No 6
>PF01630 Glyco_hydro_56: Hyaluronidase; InterPro: IPR018155 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 56 GH56 from CAZY comprises enzymes with only one known activity; hyaluronidase 3.2.1.35 from EC. The venom of Apis mellifera (Honeybee) contains several biologically-active peptides and two enzymes, one of which is a hyaluronidase []. The amino acid sequence of bee venom hyaluronidase contains 349 amino acids, and includes four cysteines and a number of potential glycosylation sites []. The sequence shows a high degree of similarity to PH-20, a membrane protein of mammalian sperm involved in sperm-egg adhesion, supporting the view that hyaluronidases play a role in fertilisation []. PH-20 is required for sperm adhesion to the egg zona pellucida; it is located on both the sperm plasma membrane and acrosomal membrane []. The amino acid sequence of the mature protein contains 468 amino acids, and includes six potential N-linked glycosylation sites and twelve cysteines, eight of which are tightly clustered near the C terminus [].; GO: 0004415 hyalurononglucosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 1FCQ_A 1FCV_A 1FCU_A 2J88_A 2PE4_A 2ATM_A.
Probab=44.82 E-value=23 Score=26.76 Aligned_cols=20 Identities=20% Similarity=0.609 Sum_probs=15.1
Q ss_pred HHHhhCCCCChHHHHHHHhh
Q psy11277 45 QLVQINPHWNDEQLFQHARR 64 (66)
Q Consensus 45 ~L~~~nP~W~De~lfqeARk 64 (66)
..++.||.|+.+++-.+|++
T Consensus 132 lv~~~hp~ws~~~v~~~A~~ 151 (337)
T PF01630_consen 132 LVRQQHPDWSEKEVEKEAKK 151 (337)
T ss_dssp HHHHHSTTS-HHHHHHHHHH
T ss_pred HHHHhCCCCCHHHHHHHHHH
Confidence 34567999999999888875
No 7
>PF12424 ATP_Ca_trans_C: Plasma membrane calcium transporter ATPase C terminal; InterPro: IPR022141 This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with PF00689 from PFAM, PF00122 from PFAM, PF00702 from PFAM, PF00690 from PFAM. There is a conserved QTQ sequence motif. This family is the C-terminal of a calcium transporting ATPase located in the plasma membrane. ; GO: 0005388 calcium-transporting ATPase activity; PDB: 2KNE_B 1CFF_B.
Probab=42.50 E-value=5.7 Score=23.38 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=13.2
Q ss_pred HHHHHHhhHHHHHHHHhhCCC
Q psy11277 32 HTILMREHNRLAEQLVQINPH 52 (66)
Q Consensus 32 htlf~ReHNriA~~L~~~nP~ 52 (66)
++||+|..|||-.+++..|-.
T Consensus 2 q~lw~rgl~r~QtQIrVV~AF 22 (66)
T PF12424_consen 2 QILWFRGLNRIQTQIRVVNAF 22 (66)
T ss_dssp CCCHHHHHHHHHHCH------
T ss_pred CEEEEeCCCccHhHHHHHHHH
Confidence 368999999999988776543
No 8
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=40.13 E-value=37 Score=17.43 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=14.9
Q ss_pred HHHHHHHhhCCCCChHHHHH
Q psy11277 41 RLAEQLVQINPHWNDEQLFQ 60 (66)
Q Consensus 41 riA~~L~~~nP~W~De~lfq 60 (66)
-....|+..-|+|+.+.|-.
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~ 22 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEA 22 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHH
Confidence 34578899999999988754
No 9
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=39.35 E-value=66 Score=24.95 Aligned_cols=40 Identities=5% Similarity=0.188 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHhhCCCCC--h--HHHHHHHhhc
Q psy11277 26 SMFAAMHTILMREHNRLAEQLVQINPHWN--D--EQLFQHARRI 65 (66)
Q Consensus 26 p~L~~~htlf~ReHNriA~~L~~~nP~W~--D--e~lfqeARkI 65 (66)
=++.+.+|.|++-|....-.-+-.+-..+ | ..+.+|||+.
T Consensus 46 YA~iaYqtAYLKahYP~EFmaAlLs~~~~~~~Ki~~yi~Ear~~ 89 (449)
T PRK07373 46 YAYVTYQTAYLKANYPVEYMAALLTANSGNQDKVQKYRENCQKM 89 (449)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHhhcCCCCchHHHHHHHHHHHc
Confidence 47889999999999876555444433333 3 3466899873
No 10
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=39.20 E-value=84 Score=20.01 Aligned_cols=35 Identities=14% Similarity=0.110 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhHHHHHHHHhhCCCCCh-HHHHHHH
Q psy11277 28 FAAMHTILMREHNRLAEQLVQINPHWND-EQLFQHA 62 (66)
Q Consensus 28 L~~~htlf~ReHNriA~~L~~~nP~W~D-e~lfqeA 62 (66)
-.++..+|.+.+..+-..+.+.-++.++ |.+.|++
T Consensus 9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~ 44 (172)
T PRK09651 9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDT 44 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHH
Confidence 3567778888888888888777777666 7788875
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=35.64 E-value=23 Score=19.43 Aligned_cols=14 Identities=36% Similarity=0.641 Sum_probs=11.4
Q ss_pred HHhhHHHHHHHHhh
Q psy11277 36 MREHNRLAEQLVQI 49 (66)
Q Consensus 36 ~ReHNriA~~L~~~ 49 (66)
-|+.|..|+.|++.
T Consensus 70 ~r~~N~~A~~LA~~ 83 (87)
T PF13456_consen 70 PREQNKVADALAKF 83 (87)
T ss_dssp -GGGSHHHHHHHHH
T ss_pred ChHHhHHHHHHHHH
Confidence 58999999999874
No 12
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown.
Probab=35.42 E-value=12 Score=29.62 Aligned_cols=30 Identities=7% Similarity=0.214 Sum_probs=25.2
Q ss_pred HHHHHHHHH----------HHHhhHHHHHHHHhhCCCCCh
Q psy11277 26 SMFAAMHTI----------LMREHNRLAEQLVQINPHWND 55 (66)
Q Consensus 26 p~L~~~htl----------f~ReHNriA~~L~~~nP~W~D 55 (66)
+-+..+-.| |-+.|+.-++.|++..|.|+|
T Consensus 447 ~~f~~~E~i~l~~yggRPHWGK~h~~~~~~l~~~YP~~~d 486 (557)
T TIGR01677 447 DVIEEIEQMAFFKYGALPHWGKNRNLAFDGVIRKYPNADK 486 (557)
T ss_pred HHHHHHHHHHHhhcCCCCCccccccchHHHHHHhCCCHHH
Confidence 556666666 678899999999999999988
No 13
>PLN00107 FAD-dependent oxidoreductase; Provisional
Probab=34.76 E-value=10 Score=27.82 Aligned_cols=30 Identities=3% Similarity=0.068 Sum_probs=24.5
Q ss_pred HHHHHHHHH----------HHHhhHHHHHHHHhhCCCCCh
Q psy11277 26 SMFAAMHTI----------LMREHNRLAEQLVQINPHWND 55 (66)
Q Consensus 26 p~L~~~htl----------f~ReHNriA~~L~~~nP~W~D 55 (66)
+-+..+-.+ |-+.||.-++.|++..|.|+|
T Consensus 141 ~~f~eiEqial~kygGRPHWGK~h~l~~~~l~~lYPr~~d 180 (257)
T PLN00107 141 DAMEEIEQMAILKYGALPHWGKNRNAAFDGAIAKYKKAGE 180 (257)
T ss_pred HHHHHHHHHHHHhcCCcCCchhccCCCHHHHHHHCcCHHH
Confidence 455556645 788999999999999999987
No 14
>PF07872 DUF1659: Protein of unknown function (DUF1659); InterPro: IPR012454 This family consists of hypothetical bacterial proteins of unknown function
Probab=33.52 E-value=39 Score=18.24 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=14.3
Q ss_pred HHhhCCCCChHHHHHHHh
Q psy11277 46 LVQINPHWNDEQLFQHAR 63 (66)
Q Consensus 46 L~~~nP~W~De~lfqeAR 63 (66)
++...|+=+||.||+.|.
T Consensus 29 ~~nvk~~Atdedl~~Va~ 46 (47)
T PF07872_consen 29 FSNVKPDATDEDLYDVAQ 46 (47)
T ss_pred hhhcCCCCCHHHHHHHhh
Confidence 455678999999998873
No 15
>PF02477 Nairo_nucleo: Nucleocapsid N protein; InterPro: IPR003486 The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle.; GO: 0019013 viral nucleocapsid; PDB: 3U3I_A.
Probab=31.47 E-value=37 Score=26.61 Aligned_cols=19 Identities=42% Similarity=0.845 Sum_probs=13.3
Q ss_pred HhhHHHHHHHHh------hCCCCCh
Q psy11277 37 REHNRLAEQLVQ------INPHWND 55 (66)
Q Consensus 37 ReHNriA~~L~~------~nP~W~D 55 (66)
|||=-+|++|+. .||-|+|
T Consensus 196 rehv~w~re~a~gkf~~~fnppwgd 220 (442)
T PF02477_consen 196 REHVDWGRELAAGKFQVVFNPPWGD 220 (442)
T ss_dssp --HHHHHHHHHHT--GGGGS-SSSS
T ss_pred HHHHHHHHHHhcCeeEEEeCCCccc
Confidence 888888888875 5999998
No 16
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=30.66 E-value=89 Score=16.38 Aligned_cols=26 Identities=23% Similarity=0.068 Sum_probs=14.4
Q ss_pred HhhHHHHHHHHhhCCCC-ChHHHHHHH
Q psy11277 37 REHNRLAEQLVQINPHW-NDEQLFQHA 62 (66)
Q Consensus 37 ReHNriA~~L~~~nP~W-~De~lfqeA 62 (66)
+.+..+...+.+..++. +-|.++|+|
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~eD~~qe~ 30 (71)
T PF04542_consen 4 RYYPLLYRYARRYTGDPEDAEDLVQEA 30 (71)
T ss_dssp HTHHHHHHHHHTCTTCSSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCHhhHHHHhhHH
Confidence 34444445455444443 557788876
No 17
>PLN02465 L-galactono-1,4-lactone dehydrogenase
Probab=29.27 E-value=19 Score=28.89 Aligned_cols=26 Identities=27% Similarity=0.356 Sum_probs=19.6
Q ss_pred HHHhhH--------HHHHHHHhhCCCCChHHHHHHHhh
Q psy11277 35 LMREHN--------RLAEQLVQINPHWNDEQLFQHARR 64 (66)
Q Consensus 35 f~ReHN--------riA~~L~~~nP~W~De~lfqeARk 64 (66)
|-+.|. .-+++|++..| |+| |+.+|+
T Consensus 520 WgK~h~~~~~~~~~~~~~~L~~~YP-~d~---F~~~R~ 553 (573)
T PLN02465 520 WAKIEVPKDKEELEALRERLRKRFP-VDA---FNKARK 553 (573)
T ss_pred cceeccccccchhhcCHHHHHhhCC-HHH---HHHHHH
Confidence 356677 88899999999 887 555554
No 18
>PRK15366 type III secretion system chaperone SsaE; Provisional
Probab=29.06 E-value=36 Score=21.07 Aligned_cols=13 Identities=31% Similarity=0.424 Sum_probs=10.8
Q ss_pred HHHHHHHHhhHHH
Q psy11277 30 AMHTILMREHNRL 42 (66)
Q Consensus 30 ~~htlf~ReHNri 42 (66)
.+-+||.|.||.-
T Consensus 61 IIn~i~~ryhn~~ 73 (80)
T PRK15366 61 IINIIYYRYHNSA 73 (80)
T ss_pred HHHHHHHHHhccc
Confidence 4789999999963
No 19
>PF07907 YibE_F: YibE/F-like protein; InterPro: IPR012507 The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE (Q9CHC5 from SWISSPROT) and YibF (Q9CHC4 from SWISSPROT). Most of the members of this family are annotated as being putative membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues.
Probab=27.81 E-value=66 Score=22.94 Aligned_cols=22 Identities=27% Similarity=0.430 Sum_probs=18.7
Q ss_pred HHHHhhCCCCChHHHHHHHhhc
Q psy11277 44 EQLVQINPHWNDEQLFQHARRI 65 (66)
Q Consensus 44 ~~L~~~nP~W~De~lfqeARkI 65 (66)
.++++.||+.+-.+||+..++|
T Consensus 152 ~El~~~~p~is~~eL~~SG~~I 173 (244)
T PF07907_consen 152 FELKRHNPDISRKELFKSGMNI 173 (244)
T ss_pred HHHHHhCCCCCHHHHHHHHHHH
Confidence 4677889999999999988765
No 20
>PF09957 DUF2191: Uncharacterized protein conserved in bacteria (DUF2191); InterPro: IPR019239 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=26.51 E-value=39 Score=18.37 Aligned_cols=11 Identities=36% Similarity=0.712 Sum_probs=8.7
Q ss_pred hHHHHHHHhhc
Q psy11277 55 DEQLFQHARRI 65 (66)
Q Consensus 55 De~lfqeARkI 65 (66)
|++|+++|+++
T Consensus 8 Dd~Ll~eA~~l 18 (47)
T PF09957_consen 8 DDELLAEAMRL 18 (47)
T ss_pred CHHHHHHHHHH
Confidence 67888888875
No 21
>PF15056 NRN1: Neuritin protein family
Probab=23.73 E-value=36 Score=21.44 Aligned_cols=38 Identities=18% Similarity=0.189 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhhHHHHHHHHhhCCC-CCh--HHHHHHHhhc
Q psy11277 27 MFAAMHTILMREHNRLAEQLVQINPH-WND--EQLFQHARRI 65 (66)
Q Consensus 27 ~L~~~htlf~ReHNriA~~L~~~nP~-W~D--e~lfqeARkI 65 (66)
.|-.+-.-|=-+|..-...|+. .|. =.+ |.|-||+||+
T Consensus 31 ~l~tiC~~Wd~FH~Ca~~aLa~-C~eeAa~iWEsLrqESrk~ 71 (89)
T PF15056_consen 31 NLETICRSWDDFHTCASTALAD-CPEEAAAIWESLRQESRKM 71 (89)
T ss_pred chhhhhhhHHHHHHHHHHHHhC-CcHHHHHHHHHHHHHHHcC
Confidence 3445555667777666666654 232 111 7899999986
No 22
>COG4323 Predicted membrane protein [Function unknown]
Probab=23.71 E-value=60 Score=20.78 Aligned_cols=24 Identities=25% Similarity=0.415 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHhh-HHHHHHHHhh
Q psy11277 26 SMFAAMHTILMREH-NRLAEQLVQI 49 (66)
Q Consensus 26 p~L~~~htlf~ReH-NriA~~L~~~ 49 (66)
-+.+.+.--++-|| |++|++|.-.
T Consensus 10 ~SFAeFYPyYl~EH~N~vcRRLH~v 34 (105)
T COG4323 10 KSFAEFYPYYLTEHANPVCRRLHVV 34 (105)
T ss_pred hhHHHhchHHHHhccchhHhhhhhh
Confidence 45577778889999 9999998754
No 23
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.50 E-value=1.6e+02 Score=18.97 Aligned_cols=30 Identities=23% Similarity=0.206 Sum_probs=19.4
Q ss_pred HHHHHhhHHHHHHHHhhCCCCCh--HHHHHHH
Q psy11277 33 TILMREHNRLAEQLVQINPHWND--EQLFQHA 62 (66)
Q Consensus 33 tlf~ReHNriA~~L~~~nP~W~D--e~lfqeA 62 (66)
..|.+.+..+...+.+..++.+| |.|.|++
T Consensus 9 ~~~~~~~~~l~~~a~~~~~~~~~~AEDivQev 40 (195)
T PRK12532 9 AELIESRKLLLHFARLQLPDHPDLAEDLVQET 40 (195)
T ss_pred hhHHHHHHHHHHHHHHHcCChhhhHHHHHHHH
Confidence 44556666666666666666554 7777775
No 24
>PF14730 DUF4468: Domain of unknown function (DUF4468) with TBP-like fold
Probab=22.75 E-value=54 Score=19.48 Aligned_cols=16 Identities=25% Similarity=0.551 Sum_probs=13.7
Q ss_pred CCCCChHHHHHHHhhc
Q psy11277 50 NPHWNDEQLFQHARRI 65 (66)
Q Consensus 50 nP~W~De~lfqeARkI 65 (66)
-|..+.++||+.++++
T Consensus 7 vpg~sk~~ly~~~~~W 22 (91)
T PF14730_consen 7 VPGMSKDQLYDRAKKW 22 (91)
T ss_pred cCCCCHHHHHHHHHHH
Confidence 4888999999999875
No 25
>PF08701 GN3L_Grn1: GNL3L/Grn1 putative GTPase; InterPro: IPR014813 Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA []. This family contains a potential nuclear localisation signal.
Probab=22.27 E-value=87 Score=18.96 Aligned_cols=20 Identities=35% Similarity=0.738 Sum_probs=17.7
Q ss_pred HHhhHHHHHHHHhhCCCCCh
Q psy11277 36 MREHNRLAEQLVQINPHWND 55 (66)
Q Consensus 36 ~ReHNriA~~L~~~nP~W~D 55 (66)
+++||+=....+.-+|.|..
T Consensus 10 v~eh~RK~rK~aKK~~~~k~ 29 (79)
T PF08701_consen 10 VKEHNRKLRKEAKKNPTWKS 29 (79)
T ss_pred HHHHhHHHHHHHhcCccccC
Confidence 68999999999999999854
No 26
>KOG2948|consensus
Probab=22.18 E-value=69 Score=24.40 Aligned_cols=22 Identities=32% Similarity=0.774 Sum_probs=16.5
Q ss_pred HHHHhhCCCCCh------HHHHHHHhhc
Q psy11277 44 EQLVQINPHWND------EQLFQHARRI 65 (66)
Q Consensus 44 ~~L~~~nP~W~D------e~lfqeARkI 65 (66)
.+..+.||+|++ ++-||+|=.+
T Consensus 152 ~rv~~~N~~w~e~~~~~~~e~F~~Am~~ 179 (327)
T KOG2948|consen 152 HRVGRFNPDWNEDSDDDEDERFQRAMDL 179 (327)
T ss_pred HHHhhcCCCcccCcchhHHHHHHHHHHH
Confidence 677788999993 5678887544
No 27
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=22.07 E-value=2.1e+02 Score=18.38 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=22.5
Q ss_pred HHHHHHHHhhHHHHHHHHhhCCCCCh-HHHHHHH
Q psy11277 30 AMHTILMREHNRLAEQLVQINPHWND-EQLFQHA 62 (66)
Q Consensus 30 ~~htlf~ReHNriA~~L~~~nP~W~D-e~lfqeA 62 (66)
++..+|-+..+.+-..+.+.-.+++| |.++|++
T Consensus 27 a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~ 60 (188)
T PRK09640 27 AYEELMRRYQRTLFNVCARYLGNDRDADDVCQEV 60 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHH
Confidence 45566666667777777666556555 7888876
No 28
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.78 E-value=1.9e+02 Score=18.42 Aligned_cols=37 Identities=11% Similarity=0.011 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHhhCCCCCh-HHHHHHH
Q psy11277 26 SMFAAMHTILMREHNRLAEQLVQINPHWND-EQLFQHA 62 (66)
Q Consensus 26 p~L~~~htlf~ReHNriA~~L~~~nP~W~D-e~lfqeA 62 (66)
+.-.++.-++.+.+..+.....+.-.+.+| |.+.|++
T Consensus 13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~ 50 (179)
T PRK09415 13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEI 50 (179)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Confidence 445677778888888777777666544444 7788876
No 29
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.12 E-value=2.3e+02 Score=18.32 Aligned_cols=32 Identities=16% Similarity=0.167 Sum_probs=18.8
Q ss_pred HHHHHHHhhHHHHHHHHhh-CCCCChHHHHHHH
Q psy11277 31 MHTILMREHNRLAEQLVQI-NPHWNDEQLFQHA 62 (66)
Q Consensus 31 ~htlf~ReHNriA~~L~~~-nP~W~De~lfqeA 62 (66)
+.-+|-+.+..+-..+... ....+-|.++|++
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEv 35 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEV 35 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHH
Confidence 4556666666665554433 3444567777776
No 30
>PF15189 DUF4582: Domain of unknown function (DUF4582)
Probab=21.08 E-value=2.1e+02 Score=19.79 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=27.7
Q ss_pred ccccccCCCcCCCcccchhhhhHHHHHHHHHHHHhhHHHHHHHHhh
Q psy11277 4 LQNSLALQSSPGGNRTHNLMLFSMFAAMHTILMREHNRLAEQLVQI 49 (66)
Q Consensus 4 ~~~~~~~~~~~~gd~~~~~n~~p~L~~~htlf~ReHNriA~~L~~~ 49 (66)
+|+..+.+=..+++.+.+- +-.-++|||-++...|.+.
T Consensus 45 S~n~~~iprl~~~psrvdr--------livdq~re~arv~tll~KM 82 (172)
T PF15189_consen 45 SQNNIPIPRLPPNPSRVDR--------LIVDQFREHARVVTLLRKM 82 (172)
T ss_pred ccCCCCCCCCCCCCchhhh--------hHHHHHhhhHHHHHHHHHH
Confidence 5677777777777777743 4456789998888888775
No 31
>PF15523 Toxin_44: Putative toxin 44
Probab=20.93 E-value=35 Score=20.88 Aligned_cols=14 Identities=21% Similarity=0.237 Sum_probs=11.8
Q ss_pred cCCCcCCCcccchh
Q psy11277 9 ALQSSPGGNRTHNL 22 (66)
Q Consensus 9 ~~~~~~~gd~~~~~ 22 (66)
..+||.|||....+
T Consensus 55 ~~kCf~GgD~gH~~ 68 (84)
T PF15523_consen 55 NNKCFGGGDAGHRD 68 (84)
T ss_pred HhHccCCCCHHHHH
Confidence 46899999998876
No 32
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.90 E-value=2.2e+02 Score=18.07 Aligned_cols=34 Identities=12% Similarity=0.139 Sum_probs=22.8
Q ss_pred HHHHHHHHHhhHHHHHHHHhhCCCC-ChHHHHHHH
Q psy11277 29 AAMHTILMREHNRLAEQLVQINPHW-NDEQLFQHA 62 (66)
Q Consensus 29 ~~~htlf~ReHNriA~~L~~~nP~W-~De~lfqeA 62 (66)
.++..+|-+.+..+...+.+...+. +-|.++|++
T Consensus 23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~ 57 (186)
T PRK13919 23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEV 57 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 4566677777777777776665443 457788876
No 33
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.47 E-value=2.2e+02 Score=17.34 Aligned_cols=32 Identities=13% Similarity=0.285 Sum_probs=19.1
Q ss_pred HHHHHHHhhHHHHHHHHhhCCCCCh-HHHHHHHh
Q psy11277 31 MHTILMREHNRLAEQLVQINPHWND-EQLFQHAR 63 (66)
Q Consensus 31 ~htlf~ReHNriA~~L~~~nP~W~D-e~lfqeAR 63 (66)
+..++-+.+..+...+.... ..+| |.++|++-
T Consensus 6 f~~l~~~y~~~l~~~~~~~~-~~~~aeDi~Qe~~ 38 (154)
T PRK06759 6 FTEAVVLYEGLIVNQIKKLG-IYQDYEEYYQCGL 38 (154)
T ss_pred HHHHHHHHHHHHHHHHHHhC-CcccHHHHHHHHH
Confidence 44555566666666555543 3344 78888874
No 34
>PF14436 EndoU_bacteria: Bacterial EndoU nuclease
Probab=20.29 E-value=70 Score=19.88 Aligned_cols=14 Identities=21% Similarity=0.778 Sum_probs=11.3
Q ss_pred CCCChHHHHHHHhh
Q psy11277 51 PHWNDEQLFQHARR 64 (66)
Q Consensus 51 P~W~De~lfqeARk 64 (66)
.+|+|++|.++...
T Consensus 72 ~~ws~~~I~~~i~~ 85 (128)
T PF14436_consen 72 KNWSDEKILDEIQE 85 (128)
T ss_pred ccCCHHHHHHHHHH
Confidence 47999999987764
No 35
>PF11691 DUF3288: Protein of unknown function (DUF3288); InterPro: IPR021705 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=20.20 E-value=74 Score=19.99 Aligned_cols=36 Identities=25% Similarity=0.438 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhhH---------HHHHHHHhhCCCCChHHHHHHHhhc
Q psy11277 28 FAAMHTILMREHN---------RLAEQLVQINPHWNDEQLFQHARRI 65 (66)
Q Consensus 28 L~~~htlf~ReHN---------riA~~L~~~nP~W~De~lfqeARkI 65 (66)
|+-+--|++|..+ -+...|+.. ..+-|+||..||.|
T Consensus 28 L~eLARL~iRY~gFPGA~diq~DL~kiL~~W--~lteeeLf~kTR~I 72 (90)
T PF11691_consen 28 LAELARLRIRYQGFPGARDIQKDLDKILQKW--GLTEEELFEKTREI 72 (90)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHHc--CCCHHHHHHHHHHH
Confidence 4555555666654 233333332 23789999999987
No 36
>PF03690 UPF0160: Uncharacterised protein family (UPF0160); InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=20.09 E-value=82 Score=23.52 Aligned_cols=16 Identities=31% Similarity=0.897 Sum_probs=12.7
Q ss_pred HHHHHHHhhCCCCChH
Q psy11277 41 RLAEQLVQINPHWNDE 56 (66)
Q Consensus 41 riA~~L~~~nP~W~De 56 (66)
-+...++..||.|+++
T Consensus 144 ~ls~~V~~~Np~w~~~ 159 (318)
T PF03690_consen 144 SLSSRVSRLNPSWNEP 159 (318)
T ss_pred CHHHHHHHhCCCCCCC
Confidence 4567788899999975
Done!