Query psy6426
Match_columns 74
No_of_seqs 101 out of 175
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 17:41:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6426.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6426hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3313|consensus 99.7 1.1E-17 2.3E-22 119.2 3.8 54 9-63 8-61 (187)
2 PF11728 DUF939_C: DUF939 C-te 45.9 13 0.00027 25.6 1.4 43 13-57 97-139 (167)
3 COG1110 Reverse gyrase [DNA re 43.9 15 0.00033 33.0 1.8 26 17-44 204-229 (1187)
4 PF00145 DNA_methylase: C-5 cy 38.0 7.8 0.00017 27.2 -0.7 30 17-46 103-132 (335)
5 PRK03947 prefoldin subunit alp 38.0 58 0.0013 21.2 3.5 25 37-61 4-28 (140)
6 PF07160 DUF1395: Protein of u 37.8 11 0.00024 27.7 0.0 47 9-57 119-174 (243)
7 PF09006 Surfac_D-trimer: Lung 36.4 63 0.0014 18.6 3.0 21 36-56 10-30 (46)
8 PF12983 DUF3867: Protein of u 36.2 42 0.0009 24.4 2.8 53 16-69 37-93 (186)
9 KOG1602|consensus 31.2 60 0.0013 24.9 3.0 59 13-73 78-137 (271)
10 smart00315 RGS Regulator of G 31.1 62 0.0013 19.2 2.6 33 17-52 26-58 (118)
11 PF00615 RGS: Regulator of G p 30.8 69 0.0015 18.7 2.8 32 17-51 26-57 (118)
12 TIGR00444 mazG MazG family pro 28.9 89 0.0019 23.1 3.6 31 35-65 201-232 (248)
13 PF13837 Myb_DNA-bind_4: Myb/S 27.6 39 0.00084 19.8 1.3 40 15-54 30-70 (90)
14 PHA02540 61 DNA primase; Provi 25.5 93 0.002 24.2 3.3 34 23-59 297-330 (337)
15 PF02093 Gag_p30: Gag P30 core 25.0 19 0.00042 26.5 -0.5 38 16-54 120-157 (211)
16 smart00685 DM14 Repeats in fly 24.0 84 0.0018 18.7 2.2 21 42-62 2-22 (59)
17 COG4974 XerD Site-specific rec 24.0 78 0.0017 24.5 2.6 26 8-33 103-128 (300)
18 PRK15325 type III secretion sy 23.9 2E+02 0.0044 18.2 4.5 39 24-63 29-71 (80)
19 COG4678 Muramidase (phage lamb 23.6 54 0.0012 23.7 1.6 18 40-57 160-177 (180)
20 PF12221 HflK_N: Bacterial mem 22.9 89 0.0019 17.4 2.1 16 35-50 21-36 (42)
21 TIGR00675 dcm DNA-methyltransf 22.6 66 0.0014 23.9 1.9 30 17-46 101-130 (315)
22 PRK00036 primosomal replicatio 22.2 41 0.00089 22.2 0.7 14 9-22 16-29 (107)
23 COG2178 Predicted RNA-binding 22.0 33 0.00072 25.2 0.3 45 14-58 106-151 (204)
24 KOG0738|consensus 21.5 65 0.0014 26.5 1.8 53 16-68 304-357 (491)
25 PF14084 DUF4264: Protein of u 21.5 38 0.00083 19.9 0.4 17 52-68 21-37 (52)
26 PRK10458 DNA cytosine methylas 21.3 69 0.0015 25.8 1.9 32 16-47 219-250 (467)
27 COG3909 Cytochrome c556 [Energ 20.2 90 0.0019 22.0 2.1 35 18-53 104-145 (147)
28 PF08360 TetR_C_5: QacR-like p 20.1 1.7E+02 0.0038 19.2 3.4 41 22-64 39-79 (131)
No 1
>KOG3313|consensus
Probab=99.70 E-value=1.1e-17 Score=119.19 Aligned_cols=54 Identities=50% Similarity=0.708 Sum_probs=47.7
Q ss_pred cCCCCCCCCcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHHHHHhhhhhh
Q psy6426 9 KVKSYGGIPEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKYKFMEYSLSLLGV 63 (74)
Q Consensus 9 ~~~n~rgIP~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KYKfME~~l~~~~~ 63 (74)
..+++||||+|+|||||++|+++|++...++ ++.+||+|+||||||.++..+-.
T Consensus 8 ~~k~~rGIPeA~fiedV~s~~~qp~~~~~~~-l~~~~E~~~kYkfme~~l~a~~~ 61 (187)
T KOG3313|consen 8 LSKNARGIPEAKFIEDVESYISQPELESLEA-LKKLQERYGKYKFMEASLLAQKR 61 (187)
T ss_pred hhhccCCCChhHHHHHHHHHHcCcccccchH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 3689999999999999999999998655554 99999999999999999987643
No 2
>PF11728 DUF939_C: DUF939 C-terminal domain; InterPro: IPR021062 This entry represents a C-terminal domain found in a set of bacterial proteins. The proteins are about 160 amino acids in length and are predicted to be multi-pass membrane proteins. ; PDB: 3KMI_B.
Probab=45.92 E-value=13 Score=25.65 Aligned_cols=43 Identities=16% Similarity=0.251 Sum_probs=30.7
Q ss_pred CCCCCcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHHHHH
Q psy6426 13 YGGIPEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKYKFMEYS 57 (74)
Q Consensus 13 ~rgIP~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KYKfME~~ 57 (74)
+-+.+-|.|++++..-+... .++...+..+.++...||-|+.=
T Consensus 97 ~q~~~ia~~~~~~a~~~~e~--n~~~~ll~~L~~l~~~fr~~~LP 139 (167)
T PF11728_consen 97 KQAEIIADFLEELAESLHEN--NTAEELLEELEELKEEFREMPLP 139 (167)
T ss_dssp HHHHHHHHHHHHHHH----T--THHHHHHHHHHHHHHHHHTS---
T ss_pred HHHHHHHHHHHHHHHHhCCC--CcHHHHHHHHHHHHHHHhcCCCC
Confidence 34566789999999999753 58999999999999999988753
No 3
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=43.87 E-value=15 Score=32.98 Aligned_cols=26 Identities=31% Similarity=0.560 Sum_probs=19.8
Q ss_pred CcccccccHHHhhcCCCCCcHHHHHHHH
Q psy6426 17 PEAVFVDDVDKYMSLPENDRIEVVLKKL 44 (74)
Q Consensus 17 P~A~FIedVe~fm~~~~~~~~e~vl~~l 44 (74)
+.-.||||||++++.. .+++.+|+.+
T Consensus 204 FdfifVDDVDA~Lkas--kNvDriL~Ll 229 (1187)
T COG1110 204 FDFIFVDDVDAILKAS--KNVDRLLRLL 229 (1187)
T ss_pred CCEEEEccHHHHHhcc--ccHHHHHHHc
Confidence 4567999999999864 5788877543
No 4
>PF00145 DNA_methylase: C-5 cytosine-specific DNA methylase; InterPro: IPR001525 C-5 cytosine-specific DNA methylases (2.1.1.37 from EC) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon of cytosines in DNA to produce C5-methylcytosine [, , ]. In mammalian cells, cytosine-specific methyltransferases methylate certain CpG sequences, which are believed to modulate gene expression and cell differentiation. In bacteria, these enzymes are a component of restriction-modification systems and serve as valuable tools for the manipulation of DNA [, ]. The structure of HhaI methyltransferase (M.HhaI) has been resolved to 2.5 A []: the molecule folds into 2 domains - a larger catalytic domain containing catalytic and cofactor binding sites, and a smaller DNA recognition domain.; GO: 0003677 DNA binding, 0006306 DNA methylation; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 1DCT_A 3LX6_A 3ME5_A 2QRV_A ....
Probab=37.97 E-value=7.8 Score=27.17 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=18.5
Q ss_pred CcccccccHHHhhcCCCCCcHHHHHHHHHH
Q psy6426 17 PEAVFVDDVDKYMSLPENDRIEVVLKKLDE 46 (74)
Q Consensus 17 P~A~FIedVe~fm~~~~~~~~e~vl~~lqE 46 (74)
|++.++|||..++........+.+++.|.+
T Consensus 103 Pk~~~~ENV~~l~~~~~~~~~~~i~~~l~~ 132 (335)
T PF00145_consen 103 PKYFLLENVPGLLSSKNGEVFKEILEELEE 132 (335)
T ss_dssp -SEEEEEEEGGGGTGGGHHHHHHHHHHHHH
T ss_pred ceEEEecccceeeccccccccccccccccc
Confidence 999999999999974311234444444433
No 5
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=37.96 E-value=58 Score=21.18 Aligned_cols=25 Identities=16% Similarity=0.049 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhhHHHHHHHhhhh
Q psy6426 37 IEVVLKKLDEEHNKYKFMEYSLSLL 61 (74)
Q Consensus 37 ~e~vl~~lqE~~~KYKfME~~l~~~ 61 (74)
.+.-++.++++|++|+....++...
T Consensus 4 ~~~~l~~l~~~~~~l~~~~~~l~~~ 28 (140)
T PRK03947 4 SEQELEELAAQLQALQAQIEALQQQ 28 (140)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566899999999999887777654
No 6
>PF07160 DUF1395: Protein of unknown function (DUF1395); InterPro: IPR009829 This family consists of several hypothetical eukaryotic proteins of around 250 residues in length. The function of this family is unknown.; PDB: 4AJ5_G.
Probab=37.75 E-value=11 Score=27.71 Aligned_cols=47 Identities=32% Similarity=0.436 Sum_probs=0.0
Q ss_pred cCCCCCCCCccccc-----ccHHHhhcCCCCCcHHHHHHHHHHH----HhhHHHHHHH
Q psy6426 9 KVKSYGGIPEAVFV-----DDVDKYMSLPENDRIEVVLKKLDEE----HNKYKFMEYS 57 (74)
Q Consensus 9 ~~~n~rgIP~A~FI-----edVe~fm~~~~~~~~e~vl~~lqE~----~~KYKfME~~ 57 (74)
..+..|+||.-.|| +.|-.||... -+.|.+-..++|+ ..||+++-..
T Consensus 119 ~~kk~~~i~~~~~IT~eEF~sIPkYMrGR--LTleqlN~~i~ein~~~~~Ky~iL~~p 174 (243)
T PF07160_consen 119 PPKKGRGIPPMWFITVEEFDSIPKYMRGR--LTLEQLNAAIDEINKAVEAKYKILAKP 174 (243)
T ss_dssp ----------------------------------------------------------
T ss_pred CCccCCCCCccccccHHHHhcchHHHHhh--ccHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34566789999998 6788999743 2444444444443 4788877554
No 7
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=36.44 E-value=63 Score=18.58 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=17.2
Q ss_pred cHHHHHHHHHHHHhhHHHHHH
Q psy6426 36 RIEVVLKKLDEEHNKYKFMEY 56 (74)
Q Consensus 36 ~~e~vl~~lqE~~~KYKfME~ 56 (74)
.-+.-++.||..+++||-.|.
T Consensus 10 aL~~qv~~Lq~~fs~yKKa~l 30 (46)
T PF09006_consen 10 ALQGQVQRLQAAFSQYKKAEL 30 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 356678999999999998775
No 8
>PF12983 DUF3867: Protein of unknown function (DUF3867); InterPro: IPR024218 This entry represents a family of functionally uncharacterised proteins that are found in bacteria. Proteins in this family are approximately 190 amino acids in length.
Probab=36.18 E-value=42 Score=24.43 Aligned_cols=53 Identities=21% Similarity=0.246 Sum_probs=43.6
Q ss_pred CCcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhHH----HHHHHhhhhhhhhheec
Q psy6426 16 IPEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKYK----FMEYSLSLLGVLFSLVG 69 (74)
Q Consensus 16 IP~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KYK----fME~~l~~~~~~~~~~~ 69 (74)
.--+.|..+|-+||... |-+-|..++-...++-+|- -+|.++.+.|+-.+-+|
T Consensus 37 lsm~dFsk~I~~YmeeN-NISqeKf~niQkk~mERYGfd~~~iE~q~K~~Gid~~~~~ 93 (186)
T PF12983_consen 37 LSMADFSKKIMEYMEEN-NISQEKFLNIQKKFMERYGFDPSEIEKQMKSMGIDMSSLN 93 (186)
T ss_pred ccHHHHHHHHHHHHHHc-CCcHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCccccc
Confidence 44578999999999754 5788999888888888997 69999999998776665
No 9
>KOG1602|consensus
Probab=31.16 E-value=60 Score=24.87 Aligned_cols=59 Identities=17% Similarity=0.230 Sum_probs=45.0
Q ss_pred CCCCCccccc-ccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHHHHHhhhhhhhhheeccccC
Q psy6426 13 YGGIPEAVFV-DDVDKYMSLPENDRIEVVLKKLDEEHNKYKFMEYSLSLLGVLFSLVGSASA 73 (74)
Q Consensus 13 ~rgIP~A~FI-edVe~fm~~~~~~~~e~vl~~lqE~~~KYKfME~~l~~~~~~~~~~~~~~~ 73 (74)
.-||+++.+. =.+|.|--++ .+|+.++..+++.+.+-..-...+.+.||-++.+|--|-
T Consensus 78 ~lGI~~vT~fAFSieNFkRs~--eEVd~LM~L~~~k~~~~~~~~~~~~~~gvririiGdlsl 137 (271)
T KOG1602|consen 78 ELGIKEVTVFAFSIENFKRSP--EEVDGLMDLALEKIERLLEQGEKLDKYGVRIRVIGDLSL 137 (271)
T ss_pred HcCCcEEEEEEEehhhhCCCH--HHHHHHHHHHHHHHHHHHHHhhhhhhcCeEEEEEcchhh
Confidence 3577775433 3567776654 579999999999888877777789999999999997654
No 10
>smart00315 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Probab=31.13 E-value=62 Score=19.19 Aligned_cols=33 Identities=18% Similarity=0.139 Sum_probs=23.2
Q ss_pred CcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhHH
Q psy6426 17 PEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKYK 52 (74)
Q Consensus 17 P~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KYK 52 (74)
---.|.++|++|-... +.....+..+..|+||=
T Consensus 26 e~l~F~~~v~~~~~~~---~~~~~~~~a~~I~~~yi 58 (118)
T smart00315 26 ENLEFWLAVEEFKKAE---DDEERIAKAREIYDKFL 58 (118)
T ss_pred HhHHHHHHHHHHHhcC---CHHHHHHHHHHHHHHHh
Confidence 3457889999998653 23456777888888773
No 11
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=30.85 E-value=69 Score=18.66 Aligned_cols=32 Identities=22% Similarity=0.204 Sum_probs=23.8
Q ss_pred CcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhH
Q psy6426 17 PEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKY 51 (74)
Q Consensus 17 P~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KY 51 (74)
....|..+|++|-.. .+.+...+..+..|.+|
T Consensus 26 ~~l~F~~~v~~~~~~---~~~~~~~~~a~~I~~~f 57 (118)
T PF00615_consen 26 ENLQFWLEVEEFKSS---ESEEQRKKLAQQIYNKF 57 (118)
T ss_dssp HHHHHHHHHHHHHTS---CSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhh---cchhhHHHHHHHHHHHH
Confidence 455788899999874 24666777788888777
No 12
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=28.94 E-value=89 Score=23.14 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=24.8
Q ss_pred CcHHHHHHHHHHHH-hhHHHHHHHhhhhhhhh
Q psy6426 35 DRIEVVLKKLDEEH-NKYKFMEYSLSLLGVLF 65 (74)
Q Consensus 35 ~~~e~vl~~lqE~~-~KYKfME~~l~~~~~~~ 65 (74)
-|+|.+|++-...+ ..+.+||..+.++|.-+
T Consensus 201 iDpE~ALr~a~~KF~~Rf~~~E~~~~~~g~~~ 232 (248)
T TIGR00444 201 TDAEIALQKANEKFERRFREVERIVAARGLEL 232 (248)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCh
Confidence 57888988777666 45999999999998643
No 13
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=27.59 E-value=39 Score=19.77 Aligned_cols=40 Identities=15% Similarity=0.112 Sum_probs=27.2
Q ss_pred CCCcccccccHHHhhcCCC-CCcHHHHHHHHHHHHhhHHHH
Q psy6426 15 GIPEAVFVDDVDKYMSLPE-NDRIEVVLKKLDEEHNKYKFM 54 (74)
Q Consensus 15 gIP~A~FIedVe~fm~~~~-~~~~e~vl~~lqE~~~KYKfM 54 (74)
..+.....+.|.+.|...| +.+++.+-.++..+-.+|+-.
T Consensus 30 ~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~ 70 (90)
T PF13837_consen 30 KKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKI 70 (90)
T ss_dssp SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCS
T ss_pred cccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4555567888888887655 357888888999988888843
No 14
>PHA02540 61 DNA primase; Provisional
Probab=25.46 E-value=93 Score=24.16 Aligned_cols=34 Identities=15% Similarity=0.237 Sum_probs=24.4
Q ss_pred ccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHHHHHhh
Q psy6426 23 DDVDKYMSLPENDRIEVVLKKLDEEHNKYKFMEYSLS 59 (74)
Q Consensus 23 edVe~fm~~~~~~~~e~vl~~lqE~~~KYKfME~~l~ 59 (74)
.|+++|+.+.| .+.+.+++-+.+ .+|+-+|..++
T Consensus 297 kDpde~i~~~G-~~~~~~~~~i~~--n~~~gl~ak~~ 330 (337)
T PHA02540 297 KDINDMIMKGG-ATPEDIMEYIKS--NTYQGLMAKLR 330 (337)
T ss_pred cCHHHHHHhcC-CCHHHHHHHHHH--ccccHHHHHHH
Confidence 79999998765 577888877776 45565555543
No 15
>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=25.04 E-value=19 Score=26.53 Aligned_cols=38 Identities=21% Similarity=0.281 Sum_probs=23.9
Q ss_pred CCcccccccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHH
Q psy6426 16 IPEAVFVDDVDKYMSLPENDRIEVVLKKLDEEHNKYKFM 54 (74)
Q Consensus 16 IP~A~FIedVe~fm~~~~~~~~e~vl~~lqE~~~KYKfM 54 (74)
.|+..=+..|.+....+ ++++-.-|++|.|.|.||-=+
T Consensus 120 a~Kp~NlsKv~~v~Qg~-~EsPs~FLeRL~ea~r~yTp~ 157 (211)
T PF02093_consen 120 ARKPTNLSKVREVTQGP-NESPSAFLERLREAYRKYTPF 157 (211)
T ss_dssp HHH-----S--TTTTTG-GGHHHHHHHHHHHHHHHTS--
T ss_pred CCCCccHHHHHHHHhCC-CCCHHHHHHHHHHHHHhcCCC
Confidence 55666677777778766 377888999999999999743
No 16
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=24.05 E-value=84 Score=18.66 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=16.3
Q ss_pred HHHHHHHhhHHHHHHHhhhhh
Q psy6426 42 KKLDEEHNKYKFMEYSLSLLG 62 (74)
Q Consensus 42 ~~lqE~~~KYKfME~~l~~~~ 62 (74)
..|++...+||-...+=.+.|
T Consensus 2 ~~L~~R~~~yk~Aa~~AK~~g 22 (59)
T smart00685 2 ALLQQRQEQYKQAALQAKRAG 22 (59)
T ss_pred hHHHHHHHHHHHHHHHHHHcC
Confidence 468889999998877766655
No 17
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=24.03 E-value=78 Score=24.49 Aligned_cols=26 Identities=15% Similarity=0.313 Sum_probs=23.0
Q ss_pred ccCCCCCCCCcccccccHHHhhcCCC
Q psy6426 8 KKVKSYGGIPEAVFVDDVDKYMSLPE 33 (74)
Q Consensus 8 ~~~~n~rgIP~A~FIedVe~fm~~~~ 33 (74)
...+.++.+|+.-.++.|++++..++
T Consensus 103 ~~PK~~~~LPk~Ls~~eve~Ll~~~~ 128 (300)
T COG4974 103 DSPKLPKRLPKFLSEEEVEALLEAPD 128 (300)
T ss_pred cCCCCCCcCCcccCHHHHHHHHhCCC
Confidence 46688899999999999999998775
No 18
>PRK15325 type III secretion system needle complex protein PrgJ; Provisional
Probab=23.90 E-value=2e+02 Score=18.24 Aligned_cols=39 Identities=18% Similarity=0.185 Sum_probs=26.7
Q ss_pred cHHHhhcCCC-CCcHHHHHHHHHHHHhhHH---HHHHHhhhhhh
Q psy6426 24 DVDKYMSLPE-NDRIEVVLKKLDEEHNKYK---FMEYSLSLLGV 63 (74)
Q Consensus 24 dVe~fm~~~~-~~~~e~vl~~lqE~~~KYK---fME~~l~~~~~ 63 (74)
++..-+..++ ..+++.+ -++|+.+.+|. -|=..|.|+||
T Consensus 29 ~i~~~~~~~~~~snP~~L-l~lQ~~~~~Ysl~vslvSTLtrK~v 71 (80)
T PRK15325 29 TITNRIEDPNLVTDPKEL-AISQEMISDYNLYVSMVSTLTRKGV 71 (80)
T ss_pred HHHHHhcCCcccCCHHHH-HHHHHHHHhHhHHHHHHHHHHHHHH
Confidence 4455555554 2467654 56888888887 57788889987
No 19
>COG4678 Muramidase (phage lambda lysozyme) [Carbohydrate transport and metabolism]
Probab=23.65 E-value=54 Score=23.72 Aligned_cols=18 Identities=28% Similarity=0.281 Sum_probs=14.6
Q ss_pred HHHHHHHHHhhHHHHHHH
Q psy6426 40 VLKKLDEEHNKYKFMEYS 57 (74)
Q Consensus 40 vl~~lqE~~~KYKfME~~ 57 (74)
.-++|.|+++||+-+|..
T Consensus 160 ~~~sl~~L~~k~l~~~~~ 177 (180)
T COG4678 160 IERSLPELYQKYLQEELT 177 (180)
T ss_pred chhhHHHHHHHHHHhcce
Confidence 447899999999988854
No 20
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=22.92 E-value=89 Score=17.35 Aligned_cols=16 Identities=13% Similarity=0.387 Sum_probs=13.4
Q ss_pred CcHHHHHHHHHHHHhh
Q psy6426 35 DRIEVVLKKLDEEHNK 50 (74)
Q Consensus 35 ~~~e~vl~~lqE~~~K 50 (74)
-|.|+++++|+..+.+
T Consensus 21 PDLdel~r~l~~kl~~ 36 (42)
T PF12221_consen 21 PDLDELFRKLQDKLGG 36 (42)
T ss_pred CCHHHHHHHHHHHHhc
Confidence 5899999999987754
No 21
>TIGR00675 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.56 E-value=66 Score=23.87 Aligned_cols=30 Identities=20% Similarity=0.484 Sum_probs=19.9
Q ss_pred CcccccccHHHhhcCCCCCcHHHHHHHHHH
Q psy6426 17 PEAVFVDDVDKYMSLPENDRIEVVLKKLDE 46 (74)
Q Consensus 17 P~A~FIedVe~fm~~~~~~~~e~vl~~lqE 46 (74)
|++.++|||..+++.........+++.|++
T Consensus 101 P~~~v~ENV~~l~~~~~~~~~~~i~~~l~~ 130 (315)
T TIGR00675 101 PKFFLLENVKGLVSHDKGRTFKVIIETLEE 130 (315)
T ss_pred CCEEEeeccHHHHhcccchHHHHHHHHHHh
Confidence 899999999999975422334444444443
No 22
>PRK00036 primosomal replication protein N; Reviewed
Probab=22.20 E-value=41 Score=22.20 Aligned_cols=14 Identities=14% Similarity=0.330 Sum_probs=11.8
Q ss_pred cCCCCCCCCccccc
Q psy6426 9 KVKSYGGIPEAVFV 22 (74)
Q Consensus 9 ~~~n~rgIP~A~FI 22 (74)
-..+|.|||.+.|+
T Consensus 16 lryTPAGIp~~~~~ 29 (107)
T PRK00036 16 MRHTPAGLPALELL 29 (107)
T ss_pred cccCCCCCceEEEE
Confidence 35789999999997
No 23
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=22.01 E-value=33 Score=25.21 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=29.2
Q ss_pred CCCCcccccccHHHhhcCCCCCcHHHHH-HHHHHHHhhHHHHHHHh
Q psy6426 14 GGIPEAVFVDDVDKYMSLPENDRIEVVL-KKLDEEHNKYKFMEYSL 58 (74)
Q Consensus 14 rgIP~A~FIedVe~fm~~~~~~~~e~vl-~~lqE~~~KYKfME~~l 58 (74)
-|||.+.||--|.++++.-.---.+.+. ..+++.-+-|+|||.=.
T Consensus 106 L~V~~~~YilGl~D~vGELrR~~le~l~~~~~~~Ae~~~~~ME~lY 151 (204)
T COG2178 106 LGVPPIAYILGLADAVGELRRHVLELLRKGSFEEAERFLKFMEKLY 151 (204)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHH
Confidence 4788888998888888522101223222 36777788899999643
No 24
>KOG0738|consensus
Probab=21.51 E-value=65 Score=26.54 Aligned_cols=53 Identities=19% Similarity=0.223 Sum_probs=37.0
Q ss_pred CCcccccccHHHhhcCCCC-CcHHHHHHHHHHHHhhHHHHHHHhhhhhhhhhee
Q psy6426 16 IPEAVFVDDVDKYMSLPEN-DRIEVVLKKLDEEHNKYKFMEYSLSLLGVLFSLV 68 (74)
Q Consensus 16 IP~A~FIedVe~fm~~~~~-~~~e~vl~~lqE~~~KYKfME~~l~~~~~~~~~~ 68 (74)
-|...|||.||+...+.|+ .+-|.--+.=.|++.+--=++..+.+.-+.|-|.
T Consensus 304 APStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLA 357 (491)
T KOG0738|consen 304 APSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLA 357 (491)
T ss_pred CCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEe
Confidence 4889999999999998875 3455444555677777666666666655555543
No 25
>PF14084 DUF4264: Protein of unknown function (DUF4264)
Probab=21.49 E-value=38 Score=19.91 Aligned_cols=17 Identities=24% Similarity=0.471 Sum_probs=14.3
Q ss_pred HHHHHHhhhhhhhhhee
Q psy6426 52 KFMEYSLSLLGVLFSLV 68 (74)
Q Consensus 52 KfME~~l~~~~~~~~~~ 68 (74)
-|+-.+|..++++|+|.
T Consensus 21 DfLNktLK~~~lmFGLs 37 (52)
T PF14084_consen 21 DFLNKTLKDKNLMFGLS 37 (52)
T ss_pred HHHhhhhhhccEEEEEe
Confidence 37888999999999874
No 26
>PRK10458 DNA cytosine methylase; Provisional
Probab=21.25 E-value=69 Score=25.76 Aligned_cols=32 Identities=19% Similarity=0.393 Sum_probs=22.8
Q ss_pred CCcccccccHHHhhcCCCCCcHHHHHHHHHHH
Q psy6426 16 IPEAVFVDDVDKYMSLPENDRIEVVLKKLDEE 47 (74)
Q Consensus 16 IP~A~FIedVe~fm~~~~~~~~e~vl~~lqE~ 47 (74)
=|++.++|||..++........+.+++.|.++
T Consensus 219 kPk~fvlENV~gl~s~~~g~~f~~i~~~L~~l 250 (467)
T PRK10458 219 RPAIFVLENVKNLKSHDKGKTFRIIMQTLDEL 250 (467)
T ss_pred CCCEEEEeCcHhhhcccccHHHHHHHHHHHHc
Confidence 48999999999999643223566666666653
No 27
>COG3909 Cytochrome c556 [Energy production and conversion]
Probab=20.22 E-value=90 Score=21.95 Aligned_cols=35 Identities=23% Similarity=0.288 Sum_probs=23.0
Q ss_pred cccccccHHHhhcCCCCCcHHHHHHHHHHH-------HhhHHH
Q psy6426 18 EAVFVDDVDKYMSLPENDRIEVVLKKLDEE-------HNKYKF 53 (74)
Q Consensus 18 ~A~FIedVe~fm~~~~~~~~e~vl~~lqE~-------~~KYKf 53 (74)
.++|+.||+.....- ..+.+.|-..+.++ |++|+.
T Consensus 104 ~~kf~~d~~~l~a~~-p~d~dgv~~a~~~lg~dC~sCH~tyR~ 145 (147)
T COG3909 104 AAKFGADVEKLLAAA-PTDQDGVKAAYGTLGADCGSCHQTYRA 145 (147)
T ss_pred HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhhhHHHHHHHhhc
Confidence 367888888888533 24667666666554 777763
No 28
>PF08360 TetR_C_5: QacR-like protein, C-terminal region; InterPro: IPR013571 This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (P23217 from SWISSPROT) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (P23215 from SWISSPROT), a multidrug efflux pump []. The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites []. The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G0E_E 1JUM_A 1RPW_D 1QVT_B 2HQ5_D 1JT0_B 2DTZ_E 1JUP_D 1JT6_D 1JUS_E ....
Probab=20.11 E-value=1.7e+02 Score=19.22 Aligned_cols=41 Identities=22% Similarity=0.180 Sum_probs=29.6
Q ss_pred cccHHHhhcCCCCCcHHHHHHHHHHHHhhHHHHHHHhhhhhhh
Q psy6426 22 VDDVDKYMSLPENDRIEVVLKKLDEEHNKYKFMEYSLSLLGVL 64 (74)
Q Consensus 22 IedVe~fm~~~~~~~~e~vl~~lqE~~~KYKfME~~l~~~~~~ 64 (74)
.--.++|..... .+. .+++++.++..+|--+=..+.++|+-
T Consensus 39 ~~a~~EF~~~~~-~~~-ev~~~l~~i~~~~~~~~~~ileeGI~ 79 (131)
T PF08360_consen 39 SKAGEEFYSNQS-KNP-EVLEKLNEIRRKYLEFFQKILEEGID 79 (131)
T ss_dssp HHHHHHHHHHCS-SSH-HHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHccc-CCH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334667776432 344 48899999999998777888888863
Done!