Query 046669
Match_columns 187
No_of_seqs 131 out of 165
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:17:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046669.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046669hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05553 DUF761: Cotton fibre 99.5 4.9E-14 1.1E-18 91.2 4.2 35 152-186 2-36 (38)
2 PF12651 RHH_3: Ribbon-helix-h 38.5 29 0.00063 22.6 2.1 21 23-43 22-42 (44)
3 KOG3446 NADH:ubiquinone oxidor 28.3 33 0.00071 26.5 1.2 15 159-173 32-46 (97)
4 PF13473 Cupredoxin_1: Cupredo 26.6 30 0.00064 25.4 0.8 14 60-73 83-96 (104)
5 cd00795 NOS_oxygenase_euk Nitr 20.6 70 0.0015 30.5 2.1 21 152-172 52-72 (412)
6 PRK01005 V-type ATP synthase s 17.2 74 0.0016 27.2 1.4 32 149-187 175-206 (207)
7 PHA01623 hypothetical protein 15.4 2.3E+02 0.0049 19.4 3.2 25 18-42 28-52 (56)
8 KOG2298 Glycyl-tRNA synthetase 15.1 1.5E+02 0.0033 29.3 3.1 29 15-43 299-328 (599)
9 KOG4245 Predicted metal-depend 14.3 1E+02 0.0023 27.4 1.6 45 140-185 247-291 (297)
10 PF01402 RHH_1: Ribbon-helix-h 14.0 1.6E+02 0.0035 17.6 2.0 19 23-41 19-37 (39)
No 1
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=99.47 E-value=4.9e-14 Score=91.20 Aligned_cols=35 Identities=46% Similarity=0.600 Sum_probs=33.3
Q ss_pred cchhhHHHHHHHHHHHHHHhhhHHHHhhhhHhhhc
Q 046669 152 DCHVDKEAEEFIKKFYQQLRLQKWNAAREAAATLY 186 (187)
Q Consensus 152 ~~~vD~~Ae~FI~~Fy~qlr~Q~~~s~~~~~e~~~ 186 (187)
+++||.+||+||++||+|||||++.|+.+|+|||.
T Consensus 2 ~~evd~rAe~FI~~f~~qlrlqr~~S~~ry~eml~ 36 (38)
T PF05553_consen 2 DDEVDRRAEEFIAKFREQLRLQRQESLQRYQEMLA 36 (38)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56899999999999999999999999999999985
No 2
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=38.47 E-value=29 Score=22.55 Aligned_cols=21 Identities=38% Similarity=0.479 Sum_probs=18.2
Q ss_pred HHcCcchhhhHHHHHHHHHhh
Q 046669 23 IQKGITKSKFIGKALNDAVLY 43 (187)
Q Consensus 23 lRKGisKrKL~~Kal~nlm~h 43 (187)
-..||++++|+.+||..++..
T Consensus 22 ~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 22 EETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHCCCHHHHHHHHHHHHHHh
Confidence 467999999999999998854
No 3
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=28.27 E-value=33 Score=26.45 Aligned_cols=15 Identities=40% Similarity=0.822 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHhhh
Q 046669 159 AEEFIKKFYQQLRLQ 173 (187)
Q Consensus 159 Ae~FI~~Fy~qlr~Q 173 (187)
..+||++||..|+.-
T Consensus 32 vR~fvEk~Y~~lKka 46 (97)
T KOG3446|consen 32 VREFVEKFYVNLKKA 46 (97)
T ss_pred HHHHHHHhhhhhhhc
Confidence 468999999999853
No 4
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=26.64 E-value=30 Score=25.39 Aligned_cols=14 Identities=50% Similarity=1.044 Sum_probs=8.5
Q ss_pred CCCceeeecCCCCC
Q 046669 60 VCPREYEFSCSNSP 73 (187)
Q Consensus 60 ~~~~EYEFSCSnTP 73 (187)
..++||||.|+=.|
T Consensus 83 ~~~G~y~~~C~~~~ 96 (104)
T PF13473_consen 83 LKPGEYEFYCTMHP 96 (104)
T ss_dssp -S-EEEEEB-SSS-
T ss_pred CCCEEEEEEcCCCC
Confidence 47999999999444
No 5
>cd00795 NOS_oxygenase_euk Nitric oxide synthase (NOS) eukaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain, which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOS's also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN.
Probab=20.64 E-value=70 Score=30.52 Aligned_cols=21 Identities=19% Similarity=0.524 Sum_probs=17.2
Q ss_pred cchhhHHHHHHHHHHHHHHhh
Q 046669 152 DCHVDKEAEEFIKKFYQQLRL 172 (187)
Q Consensus 152 ~~~vD~~Ae~FI~~Fy~qlr~ 172 (187)
.++|=.+|++||..||+.++.
T Consensus 52 ~e~l~~eA~~Fi~~~y~e~~~ 72 (412)
T cd00795 52 KEELLPQAKDFINQYYSSIKR 72 (412)
T ss_pred HHHHHHHHHHHHHHHHHhhcC
Confidence 355788999999999987753
No 6
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=17.25 E-value=74 Score=27.22 Aligned_cols=32 Identities=9% Similarity=0.340 Sum_probs=25.9
Q ss_pred CCCcchhhHHHHHHHHHHHHHHhhhHHHHhhhhHhhhcC
Q 046669 149 DDKDCHVDKEAEEFIKKFYQQLRLQKWNAAREAAATLYG 187 (187)
Q Consensus 149 ~~~~~~vD~~Ae~FI~~Fy~qlr~Q~~~s~~~~~e~~~~ 187 (187)
.|++-.||--.|+|++.|.+.|| .+..++|||
T Consensus 175 ~dg~~~vd~t~d~i~~~~~~~l~-------~~~~~~LF~ 206 (207)
T PRK01005 175 EEKNWVLDLSSQTLLDLLTRYLQ-------KDFREMIFQ 206 (207)
T ss_pred cCCeeEEeCcHHHHHHHHHHHhh-------HHHHHHhcC
Confidence 35677899999999999999998 556677765
No 7
>PHA01623 hypothetical protein
Probab=15.38 E-value=2.3e+02 Score=19.37 Aligned_cols=25 Identities=8% Similarity=0.270 Sum_probs=20.7
Q ss_pred HHHHHHHcCcchhhhHHHHHHHHHh
Q 046669 18 VILFMIQKGITKSKFIGKALNDAVL 42 (187)
Q Consensus 18 ~~~fmlRKGisKrKL~~Kal~nlm~ 42 (187)
+=.+...+|++++.++..||+.++.
T Consensus 28 Ld~y~~~~g~~rSe~IreAI~~yL~ 52 (56)
T PHA01623 28 LKVYCAKNNLQLTQAIEEAIKEYLQ 52 (56)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3456789999999999999998874
No 8
>KOG2298 consensus Glycyl-tRNA synthetase and related class II tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=15.12 E-value=1.5e+02 Score=29.33 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=25.9
Q ss_pred HHHHHHHHHHcCcchhhh-HHHHHHHHHhh
Q 046669 15 MVRVILFMIQKGITKSKF-IGKALNDAVLY 43 (187)
Q Consensus 15 ~vR~~~fmlRKGisKrKL-~~Kal~nlm~h 43 (187)
+-|+.+|.++-||.|.+| .+..+.|-|.|
T Consensus 299 i~Ri~~fL~~lGid~~rlRFRqH~~nEMAH 328 (599)
T KOG2298|consen 299 IGRIYLFLNKLGIDKERLRFRQHMANEMAH 328 (599)
T ss_pred HHHHHHHHHHhCcchhhcchHHHhhhhhhh
Confidence 679999999999999999 67889999976
No 9
>KOG4245 consensus Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]
Probab=14.27 E-value=1e+02 Score=27.44 Aligned_cols=45 Identities=29% Similarity=0.311 Sum_probs=36.3
Q ss_pred ecCCCCCCCCCCcchhhHHHHHHHHHHHHHHhhhHHHHhhhhHhhh
Q 046669 140 TDSPFPLRDDDKDCHVDKEAEEFIKKFYQQLRLQKWNAAREAAATL 185 (187)
Q Consensus 140 tdSpf~~~~~~~~~~vD~~Ae~FI~~Fy~qlr~Q~~~s~~~~~e~~ 185 (187)
||-|||+.+-| -..+-.+-|+|-++=.+.|+--...+++...|.|
T Consensus 247 tdypfplgele-~gkliee~~~f~a~~ke~l~~~nal~~l~id~nl 291 (297)
T KOG4245|consen 247 TDYPFPLGELE-PGKLIEEMEEFDAEDKEDLKAGNALAFLDIDENL 291 (297)
T ss_pred cCCCCcCcccc-cchHHHhhcccchhhHHHhhhccchhhcccchhh
Confidence 99999998543 3456677888988889999988888888888865
No 10
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=13.97 E-value=1.6e+02 Score=17.59 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=15.3
Q ss_pred HHcCcchhhhHHHHHHHHH
Q 046669 23 IQKGITKSKFIGKALNDAV 41 (187)
Q Consensus 23 lRKGisKrKL~~Kal~nlm 41 (187)
-+.|+|++.++..+|.+.+
T Consensus 19 ~~~g~s~s~~ir~ai~~~l 37 (39)
T PF01402_consen 19 KELGRSRSELIREAIREYL 37 (39)
T ss_dssp HHHTSSHHHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHHHHHH
Confidence 4778999999888887654
Done!