Query 041147
Match_columns 222
No_of_seqs 111 out of 123
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 04:14:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041147hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05553 DUF761: Cotton fibre 99.3 1.4E-12 3.1E-17 86.7 2.3 36 185-222 2-37 (38)
2 PTZ00061 DNA-directed RNA poly 35.0 32 0.0007 30.7 2.5 31 12-42 5-38 (205)
3 KOG3446 NADH:ubiquinone oxidor 34.9 22 0.00047 28.2 1.3 36 165-207 12-47 (97)
4 KOG1328 Synaptic vesicle prote 23.3 69 0.0015 34.3 2.8 26 192-217 911-936 (1103)
5 PLN03111 DNA-directed RNA poly 23.0 77 0.0017 28.3 2.8 31 11-41 7-40 (206)
6 cd08057 MPN_euk_non_mb Mpr1p, 21.9 1E+02 0.0022 25.2 3.1 35 168-204 35-70 (157)
7 cd00795 NOS_oxygenase_euk Nitr 20.5 72 0.0016 31.3 2.2 19 186-204 53-71 (412)
8 COG4995 Uncharacterized protei 19.9 93 0.002 30.6 2.9 18 188-205 362-380 (420)
9 PF11563 Protoglobin: Protoglo 17.8 93 0.002 24.5 2.0 25 186-210 27-51 (158)
10 KOG4409 Predicted hydrolase/ac 17.1 1.4E+02 0.0031 28.9 3.4 32 159-205 124-155 (365)
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=99.28 E-value=1.4e-12 Score=86.65 Aligned_cols=36 Identities=39% Similarity=0.598 Sum_probs=33.5
Q ss_pred ChhhhHHHHHHHHHHHHHHhhHHhhhhcCCccccccCC
Q 041147 185 DGQVDKAAEDFIKKFYKDLMLQKSMAAFESPYHHSWDR 222 (222)
Q Consensus 185 ~~~VD~~AeeFI~rFy~qlr~Q~~~~~~~~~~~~~~~~ 222 (222)
+.+||++||+||++||+|||+|++.++. .|.+||+|
T Consensus 2 ~~evd~rAe~FI~~f~~qlrlqr~~S~~--ry~eml~R 37 (38)
T PF05553_consen 2 DDEVDRRAEEFIAKFREQLRLQRQESLQ--RYQEMLAR 37 (38)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhc
Confidence 4689999999999999999999999999 69999986
No 2
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=35.04 E-value=32 Score=30.68 Aligned_cols=31 Identities=16% Similarity=0.367 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHH-hc--cccchhhhhHHHH
Q 041147 12 AKKLWKIVRIVFFMIK-AG--ISKSKIMVDFHLM 42 (222)
Q Consensus 12 aKRlW~vvR~v~fMlR-KG--isKrKLmmDlhLm 42 (222)
..|||.+-|.++-|+| +| |+..-|-+.+.-.
T Consensus 5 ~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~F 38 (205)
T PTZ00061 5 ETRFFRCRRTCCEMLEDRGYIITSQEKLETFATF 38 (205)
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHcCCHHHH
Confidence 5699999999999999 77 6777676666533
No 3
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=34.85 E-value=22 Score=28.22 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=22.5
Q ss_pred CcccccceeecCCCCCCCCCChhhhHHHHHHHHHHHHHHhhHH
Q 041147 165 SPLVRQLRITDSPFPLKDEGDGQVDKAAEDFIKKFYKDLMLQK 207 (222)
Q Consensus 165 SP~~r~lrVtdSpfp~~d~~~~~VD~~AeeFI~rFy~qlr~Q~ 207 (222)
++.+|.+||---+=+ .+... ..+||++||..|+.-+
T Consensus 12 ~~~lkElRI~lcqks---paSag----vR~fvEk~Y~~lKkaN 47 (97)
T KOG3446|consen 12 TLKLKELRIHLCQKS---PASAG----VREFVEKFYVNLKKAN 47 (97)
T ss_pred chhhhhheeeecCCC---Ccchh----HHHHHHHhhhhhhhcC
Confidence 455788888532110 11222 4689999999998643
No 4
>KOG1328 consensus Synaptic vesicle protein BAIAP3, involved in vesicle priming/regulation [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=23.34 E-value=69 Score=34.28 Aligned_cols=26 Identities=38% Similarity=0.607 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhhHHhhhhcCCccc
Q 041147 192 AEDFIKKFYKDLMLQKSMAAFESPYH 217 (222)
Q Consensus 192 AeeFI~rFy~qlr~Q~~~~~~~~~~~ 217 (222)
-|+-|++||+|+-.|+.++--+.+|.
T Consensus 911 T~~lIe~fY~d~Lkqq~la~~~fg~l 936 (1103)
T KOG1328|consen 911 TEQLIEKFYKDLLKQQALADHQFGVL 936 (1103)
T ss_pred HHHHHHHHHHHHHHHHHHhhCcCCce
Confidence 57899999999999999888776664
No 5
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=23.02 E-value=77 Score=28.33 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHH-hc--cccchhhhhHHH
Q 041147 11 VAKKLWKIVRIVFFMIK-AG--ISKSKIMVDFHL 41 (222)
Q Consensus 11 vaKRlW~vvR~v~fMlR-KG--isKrKLmmDlhL 41 (222)
-..|||.+-|.++-|+| +| |+..-|-+.+.-
T Consensus 7 e~~rl~r~rrTv~eMl~DRGY~V~~~el~~s~~~ 40 (206)
T PLN03111 7 ESTRLYLVRRTVLEMLRDRGYLVSDSELNLTLSE 40 (206)
T ss_pred HHHHHHHHHHHHHHHHhccCCccCHHHHcCCHHH
Confidence 45799999999999999 77 676667666653
No 6
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=21.88 E-value=1e+02 Score=25.18 Aligned_cols=35 Identities=17% Similarity=0.345 Sum_probs=20.9
Q ss_pred cccceeecC-CCCCCCCCChhhhHHHHHHHHHHHHHHh
Q 041147 168 VRQLRITDS-PFPLKDEGDGQVDKAAEDFIKKFYKDLM 204 (222)
Q Consensus 168 ~r~lrVtdS-pfp~~d~~~~~VD~~AeeFI~rFy~qlr 204 (222)
-+.+.||+| |+|..++++. ..-.-+|+++.+++++
T Consensus 35 ~~~veV~nsF~lp~~~~~~~--~~~d~~y~~~m~~~~~ 70 (157)
T cd08057 35 GDKIEVTNSFELPFDEEEES--IFIDTEYLEKRYNLHK 70 (157)
T ss_pred CCEEEEEEeEEccccCCCcc--hhhhHHHHHHHHHHHH
Confidence 468999999 6666443222 1122457777677665
No 7
>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=20.47 E-value=72 Score=31.32 Aligned_cols=19 Identities=26% Similarity=0.604 Sum_probs=16.3
Q ss_pred hhhhHHHHHHHHHHHHHHh
Q 041147 186 GQVDKAAEDFIKKFYKDLM 204 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr 204 (222)
+.|=.+|++||..||+.++
T Consensus 53 e~l~~eA~~Fi~~~y~e~~ 71 (412)
T cd00795 53 EELLPQAKDFINQYYSSIK 71 (412)
T ss_pred HHHHHHHHHHHHHHHHhhc
Confidence 4578899999999998775
No 8
>COG4995 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=19.95 E-value=93 Score=30.56 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=14.4
Q ss_pred hhHH-HHHHHHHHHHHHhh
Q 041147 188 VDKA-AEDFIKKFYKDLML 205 (222)
Q Consensus 188 VD~~-AeeFI~rFy~qlr~ 205 (222)
||++ ....|-.||++|+.
T Consensus 362 VdD~sTa~LM~eFY~~L~~ 380 (420)
T COG4995 362 VDDESTAALMTEFYRKLQQ 380 (420)
T ss_pred eCcHHHHHHHHHHHHHHhh
Confidence 6444 46799999999998
No 9
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=17.75 E-value=93 Score=24.51 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=19.8
Q ss_pred hhhhHHHHHHHHHHHHHHhhHHhhh
Q 041147 186 GQVDKAAEDFIKKFYKDLMLQKSMA 210 (222)
Q Consensus 186 ~~VD~~AeeFI~rFy~qlr~Q~~~~ 210 (222)
..+...+++|++.||+.|......+
T Consensus 27 ~~~~~~~~~iv~~FY~~l~~~pe~~ 51 (158)
T PF11563_consen 27 PIIEPHAPEIVDDFYDHLLRFPETA 51 (158)
T ss_dssp HHHHCTHHHHHHHHHHHHHTSHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHH
Confidence 4577889999999999988765443
No 10
>KOG4409 consensus Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only]
Probab=17.06 E-value=1.4e+02 Score=28.87 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=19.0
Q ss_pred CCCCCCCcccccceeecCCCCCCCCCChhhhHHHHHHHHHHHHHHhh
Q 041147 159 LPGFGRSPLVRQLRITDSPFPLKDEGDGQVDKAAEDFIKKFYKDLML 205 (222)
Q Consensus 159 lpg~grSP~~r~lrVtdSpfp~~d~~~~~VD~~AeeFI~rFy~qlr~ 205 (222)
+||||+| -|| .|+.+.+..+. +||++ -||-|.
T Consensus 124 llG~G~S--SRP------~F~~d~~~~e~------~fves-iE~WR~ 155 (365)
T KOG4409|consen 124 LLGFGRS--SRP------KFSIDPTTAEK------EFVES-IEQWRK 155 (365)
T ss_pred ccCCCCC--CCC------CCCCCcccchH------HHHHH-HHHHHH
Confidence 6999997 232 56654322111 88888 466554
Done!