Query psy16407
Match_columns 59
No_of_seqs 48 out of 50
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 20:31:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16407.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16407hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1419|consensus 99.3 3.8E-14 8.3E-19 113.3 -3.8 28 32-59 72-100 (654)
2 PF06590 PerB: PerB protein; 67.7 3.4 7.4E-05 28.1 1.4 16 39-54 15-30 (129)
3 PF02233 PNTB: NAD(P) transhyd 57.0 8.3 0.00018 30.6 2.0 26 2-27 392-424 (463)
4 PRK09444 pntB pyridine nucleot 46.8 14 0.0003 29.7 1.8 26 2-27 391-423 (462)
5 PF14709 DND1_DSRM: double str 39.0 24 0.00051 21.1 1.6 16 44-59 26-41 (80)
6 PF11533 DUF3225: Protein of u 33.9 37 0.0008 23.0 2.1 24 33-58 98-121 (125)
7 PF06045 Rhamnogal_lyase: Rham 29.3 36 0.00078 24.4 1.5 16 39-54 126-141 (203)
8 KOG0537|consensus 28.9 14 0.00031 24.1 -0.5 21 34-54 23-47 (124)
9 COG4598 HisP ABC-type histidin 25.0 15 0.00032 27.7 -1.1 13 38-50 49-61 (256)
10 TIGR03665 arCOG04150 arCOG0415 22.2 11 0.00024 25.2 -2.1 12 35-46 152-163 (172)
11 COG3335 Transposase and inacti 20.5 46 0.00099 18.7 0.6 17 4-20 73-89 (132)
No 1
>KOG1419|consensus
Probab=99.33 E-value=3.8e-14 Score=113.33 Aligned_cols=28 Identities=68% Similarity=1.246 Sum_probs=26.1
Q ss_pred cc-ceecceeeeeeecCCCceeeeeeeeC
Q psy16407 32 AG-ATFQGKVYNFLERPSGWKCFVYHFAV 59 (59)
Q Consensus 32 ~r-r~~Q~rvYNFLERP~Gwk~f~YH~~V 59 (59)
+| |++|++||||||||+|||||+|||+|
T Consensus 72 ~r~Rr~q~~vYN~LERPrGWkaf~YH~~V 100 (654)
T KOG1419|consen 72 ARYRRIQNKVYNFLERPRGWKAFLYHFFV 100 (654)
T ss_pred HHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence 44 99999999999999999999999986
No 2
>PF06590 PerB: PerB protein; InterPro: IPR009513 This family consists of several PerB or BfpV proteins found specifically in Escherichia coli. PerB is thought to play a role in regulating the expression of BfpA [].
Probab=67.71 E-value=3.4 Score=28.08 Aligned_cols=16 Identities=38% Similarity=0.677 Sum_probs=13.9
Q ss_pred eeeeeeecCCCceeee
Q psy16407 39 KVYNFLERPSGWKCFV 54 (59)
Q Consensus 39 rvYNFLERP~Gwk~f~ 54 (59)
-|-|.|..|.|||++.
T Consensus 15 gc~nvlslps~wkait 30 (129)
T PF06590_consen 15 GCMNVLSLPSEWKAIT 30 (129)
T ss_pred ceeeeeecCCcceecc
Confidence 4779999999999974
No 3
>PF02233 PNTB: NAD(P) transhydrogenase beta subunit; InterPro: IPR012136 NAD(P) transhydrogenase catalyses the transfer of reducing equivalents between NAD(H) and NADP(H), coupled to the translocation of protons across a membrane []. It is an integral membrane protein found in most organisms except for yeasts, plants and some bacterial species. In bacterial species it is located in the cytoplasmic membrane, while in mitochondria it is located in the inner membrane. Under most physiological conditions this enzyme synthesises NADPH, driven by consumption of the proton electrochemical gradient. The resulting NADPH is subsequently used for biosynthetic reactions or the reduction of glutathione. The global structure of this enzyme is similar in all organisms, consisting of three distinct domains, though the polypeptide composition can vary. Domain I binds NAD(+)/NADH, domain II is a hydrophobic membrane-spanning domain, and domain III binds NADP(+)/NADPH. Domain I is composed of two subdomains, both of which form a Rossman fold, while domain III consists of a single Rossman fold where the NADP(+) is flipped relative to the normal orientation of bound nucleotides within the Rossman fold [, , ]. Several residues within these domains are thought to make functionally important interdomain contacts for hydride transfer between these domains []. Proton translocation occurs through domain II and is thought to induce conformational changes which are transmitted across domain III to the site of hydride transfer between domains I and III. This entry represents the beta subunit found in bacterial two-subunit NADP(H) transhydrogenases. This subunit forms domain III and part of the transmembrane domain II. ; GO: 0008750 NAD(P)+ transhydrogenase (AB-specific) activity, 0050661 NADP binding, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1PT9_A 1DJL_A 1U31_B 2BRU_C 1PTJ_C 1HZZ_C 2FRD_C 2FSV_C 1XLT_C 1U2G_C ....
Probab=56.98 E-value=8.3 Score=30.65 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=19.0
Q ss_pred CCCC------CCCCcccC-cchhhhcccceeee
Q psy16407 2 NDTL------NPRSLLTN-PDCRLFDSHYLVKY 27 (59)
Q Consensus 2 ~~~l------~p~~~~~~-p~~~~~~~ry~~~~ 27 (59)
||+. ||.+||++ |.-+.|++|-+.++
T Consensus 392 NDvVNPaA~~d~~SpI~GMPil~v~~ak~Viv~ 424 (463)
T PF02233_consen 392 NDVVNPAAREDPNSPIYGMPILEVWKAKQVIVI 424 (463)
T ss_dssp SGGG-CHHCCSTTSTTTTSS---GGGSSEEEEE
T ss_pred ccccCchhccCCCCCCCCCeecchhhcCeEEEE
Confidence 7887 57888764 99999999999876
No 4
>PRK09444 pntB pyridine nucleotide transhydrogenase; Provisional
Probab=46.81 E-value=14 Score=29.66 Aligned_cols=26 Identities=23% Similarity=0.548 Sum_probs=21.1
Q ss_pred CCCC------CCCCccc-Ccchhhhcccceeee
Q psy16407 2 NDTL------NPRSLLT-NPDCRLFDSHYLVKY 27 (59)
Q Consensus 2 ~~~l------~p~~~~~-~p~~~~~~~ry~~~~ 27 (59)
||+. ||.+||+ -|.=+.|++|-..++
T Consensus 391 NDvVNPaA~~dp~SpIyGMPvL~v~kAk~Viv~ 423 (462)
T PRK09444 391 NDTVNPAAQEDPNSPIAGMPVLEVWKAQNVIVF 423 (462)
T ss_pred ccCCCcccccCCCCCcCCCceeehhhCCEEEEE
Confidence 7887 5677865 488889999999876
No 5
>PF14709 DND1_DSRM: double strand RNA binding domain from DEAD END PROTEIN 1
Probab=39.00 E-value=24 Score=21.12 Aligned_cols=16 Identities=25% Similarity=0.495 Sum_probs=13.5
Q ss_pred eecCCCceeeeeeeeC
Q psy16407 44 LERPSGWKCFVYHFAV 59 (59)
Q Consensus 44 LERP~Gwk~f~YH~~V 59 (59)
=+-|.||+-|.|.+.|
T Consensus 26 ~~Gp~~~~~F~ykV~i 41 (80)
T PF14709_consen 26 ESGPDHRKLFLYKVVI 41 (80)
T ss_pred ccCCCccEEEEEEEEE
Confidence 4689999999999865
No 6
>PF11533 DUF3225: Protein of unknown function (DUF3225); InterPro: IPR024507 This family of proteins has no known function.; PDB: 2OWP_A 2RCD_B.
Probab=33.85 E-value=37 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.486 Sum_probs=18.8
Q ss_pred cceecceeeeeeecCCCceeeeeeee
Q psy16407 33 GATFQGKVYNFLERPSGWKCFVYHFA 58 (59)
Q Consensus 33 rr~~Q~rvYNFLERP~Gwk~f~YH~~ 58 (59)
+.-.|.++|-=+ |.|||...=|++
T Consensus 98 ~~GRQsQtWvr~--~~gWrIvaAHVS 121 (125)
T PF11533_consen 98 RIGRQSQTWVRF--PDGWRIVAAHVS 121 (125)
T ss_dssp CEEEEEEEEEEE--TTEEEEEEEEEE
T ss_pred ceeEeEEEEEEC--CCCEEEEEEEEe
Confidence 456788877554 789999999986
No 7
>PF06045 Rhamnogal_lyase: Rhamnogalacturonate lyase family; InterPro: IPR010325 Rhamnogalacturonate lyase degrades the rhamnogalacturonan I (RG-I) backbone of pectin []. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.
Probab=29.29 E-value=36 Score=24.45 Aligned_cols=16 Identities=38% Similarity=0.939 Sum_probs=12.2
Q ss_pred eeeeeeecCCCceeee
Q psy16407 39 KVYNFLERPSGWKCFV 54 (59)
Q Consensus 39 rvYNFLERP~Gwk~f~ 54 (59)
.+|.-+|+|.||.+|-
T Consensus 126 Y~YAI~e~~~~~Pa~~ 141 (203)
T PF06045_consen 126 YSYAIFEHPAGWPAFD 141 (203)
T ss_pred EEEEEEecCCCCCCcc
Confidence 3555699999998763
No 8
>KOG0537|consensus
Probab=28.95 E-value=14 Score=24.10 Aligned_cols=21 Identities=38% Similarity=0.759 Sum_probs=16.8
Q ss_pred ceecceeeee---e-ecCCCceeee
Q psy16407 34 ATFQGKVYNF---L-ERPSGWKCFV 54 (59)
Q Consensus 34 r~~Q~rvYNF---L-ERP~Gwk~f~ 54 (59)
--+.++||+. | |+|-|++.+.
T Consensus 23 vii~gkVYDvT~Fl~eHPGG~~vLl 47 (124)
T KOG0537|consen 23 VIIHGKVYDVTSFLDEHPGGEDVLL 47 (124)
T ss_pred EEECCEEEeccchhhhCCChHHHHH
Confidence 5688999985 6 8999987654
No 9
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=24.96 E-value=15 Score=27.65 Aligned_cols=13 Identities=46% Similarity=0.641 Sum_probs=10.7
Q ss_pred ceeeeeeecCCCc
Q psy16407 38 GKVYNFLERPSGW 50 (59)
Q Consensus 38 ~rvYNFLERP~Gw 50 (59)
-||-||||.|.-=
T Consensus 49 LRCiN~LE~P~~G 61 (256)
T COG4598 49 LRCINFLEKPSAG 61 (256)
T ss_pred HHHHHhhcCCCCc
Confidence 4799999999753
No 10
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=22.21 E-value=11 Score=25.22 Aligned_cols=12 Identities=58% Similarity=0.999 Sum_probs=9.4
Q ss_pred eecceeeeeeec
Q psy16407 35 TFQGKVYNFLER 46 (59)
Q Consensus 35 ~~Q~rvYNFLER 46 (59)
+.++.||||||+
T Consensus 152 ~~~~~vy~~l~~ 163 (172)
T TIGR03665 152 APHGTVYKFLER 163 (172)
T ss_pred CCChhHHHHHHH
Confidence 467788888886
No 11
>COG3335 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.54 E-value=46 Score=18.66 Aligned_cols=17 Identities=29% Similarity=0.139 Sum_probs=15.1
Q ss_pred CCCCCCcccCcchhhhc
Q psy16407 4 TLNPRSLLTNPDCRLFD 20 (59)
Q Consensus 4 ~l~p~~~~~~p~~~~~~ 20 (59)
.|+|+.|...|+++.|.
T Consensus 73 flp~y~p~~n~ie~~~~ 89 (132)
T COG3335 73 FLPPYSPDLNPIEYAWK 89 (132)
T ss_pred EcCCCCCCccHHHHHHH
Confidence 46899999999999886
Done!