Query 024459
Match_columns 267
No_of_seqs 127 out of 1015
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:45:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024459hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944 Peroxisomal membrane p 100.0 9.1E-40 2E-44 292.1 15.8 181 84-264 31-216 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 6.7E-23 1.4E-27 151.3 4.5 68 194-261 1-68 (68)
3 PF11998 DUF3493: Protein of u 33.4 2.2E+02 0.0047 21.7 6.6 49 132-181 14-62 (75)
4 PF03818 MadM: Malonate/sodium 32.0 2E+02 0.0044 21.0 6.5 34 94-127 4-37 (60)
5 TIGR02163 napH_ ferredoxin-typ 31.4 1.6E+02 0.0036 26.7 6.7 67 134-200 4-79 (255)
6 PRK09609 hypothetical protein; 22.0 4.5E+02 0.0099 25.2 7.8 55 108-166 57-111 (312)
7 PF10929 DUF2811: Protein of u 18.9 1.7E+02 0.0038 21.1 3.4 30 117-148 11-40 (57)
8 PF00140 Sigma70_r1_2: Sigma-7 16.4 80 0.0017 20.3 1.1 18 89-106 2-19 (37)
9 PF01554 MatE: MatE; InterPro 15.5 5.7E+02 0.012 20.0 8.1 93 108-201 44-139 (162)
10 cd02577 PSTD1 PSTD1: Pseudouri 14.8 1.6E+02 0.0035 28.0 3.1 29 232-260 228-257 (319)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=9.1e-40 Score=292.14 Aligned_cols=181 Identities=36% Similarity=0.716 Sum_probs=167.9
Q ss_pred CcchhHHHHHHHHH-hhhCChhHHHHHHHHHH-HHHHHHHHhhcCCC---CCCCcHHHHHHHHHHHHhhhhhhHhHHHHH
Q 024459 84 SSSKFGFVGWYLGK-LESHPLTTKGISSSLIY-VAADLTSQMITLPP---SGSIDSIRTLRMAVYGMLILGPSQHYWFNF 158 (267)
Q Consensus 84 ~~~~~~l~~~Y~~~-L~~~Pl~Tk~iTsgvl~-~~gDllAQ~i~~~~---~~~~D~~Rt~r~a~~G~~~~GP~~h~Wy~~ 158 (267)
+....++..|+... ...+|+.+++++.+.+. ..||+++|.++... ...+|+.|++||+++|+++.||.+|+||..
T Consensus 31 ~~~~~~l~~~~~~~~~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~ 110 (222)
T KOG1944|consen 31 SLAQNGLVLWLLLKRFSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKKLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRL 110 (222)
T ss_pred hhhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHhchhhhhhhhhhcccccccccHHHHHHHHhhhhheeccchhHHHHH
Confidence 34444466666555 57799999999999888 99999999998765 578999999999999999999999999999
Q ss_pred HhhhcCCCchhHHHHHHHHhhhhhhhhHHHHHHHHHHhhcCCChHHHHHHHhhchHHHHhhccccchHHHhhhhceecCC
Q 024459 159 LSRILPKRDALTTLKKIFMGQAIYGPLTTTIFFSYNAALQGETTGEIVARLKRDLLPTMGRNLVYWPICDFITFKFIPVH 238 (267)
Q Consensus 159 Ldrlfp~~~~~~vl~KVllDQ~v~aP~~~~~F~~~~~~leG~s~~~i~~~lk~~~~~~l~~sw~~Wpp~q~INF~~VP~~ 238 (267)
||+++|+++..++++|+++||++++|+.+.+|+.+++++||++.++++++++++++|+++++|++||++|++||.+||++
T Consensus 111 L~~~~p~~~~~~~~~kvl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP~~ 190 (222)
T KOG1944|consen 111 LSKLFPKKTLITVVKKVLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVPLQ 190 (222)
T ss_pred HHHHccCccHHHHHHHHHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHHHHHHhccccc
Q 024459 239 LQPLVNSSFAYVWTIYLTYKASLSKV 264 (267)
Q Consensus 239 ~Rvlf~n~vs~~Wn~yLS~~a~~~~~ 264 (267)
+|++++|+++++|++|||+++++.++
T Consensus 191 ~rvl~~~~vsl~W~~~Ls~~~~~~~~ 216 (222)
T KOG1944|consen 191 YRVLFVNIVSLVWNTYLSYKNASLVE 216 (222)
T ss_pred ceehhhhhHHHHHHHHHHHHhhcccc
Confidence 99999999999999999999999844
No 2
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=99.87 E-value=6.7e-23 Score=151.29 Aligned_cols=68 Identities=31% Similarity=0.707 Sum_probs=66.2
Q ss_pred HHhhcCCChHHHHHHHhhchHHHHhhccccchHHHhhhhceecCCcchhhhhHHHHHHHHHHHHHhcc
Q 024459 194 NAALQGETTGEIVARLKRDLLPTMGRNLVYWPICDFITFKFIPVHLQPLVNSSFAYVWTIYLTYKASL 261 (267)
Q Consensus 194 ~~~leG~s~~~i~~~lk~~~~~~l~~sw~~Wpp~q~INF~~VP~~~Rvlf~n~vs~~Wn~yLS~~a~~ 261 (267)
|+++||++++++++++++|++++++++|++|||+|++||.|||+++|++|+|+++++||+|||+++|+
T Consensus 1 Mg~l~g~s~~~~~~~l~~~~~~~~~~~~~~Wp~~~~vnF~~vP~~~Rv~~~~~v~~~W~~~LS~~~~r 68 (68)
T PF04117_consen 1 MGLLEGKSWEEIKEKLKRDYWPTLKASWKFWPPAQIVNFRYVPPHYRVLFVNVVSFFWNTYLSYIANR 68 (68)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHhcccChhhhhhhhhhHHHHHHHHHHHHhcC
Confidence 57899999999999999999999999999999999999999999999999999999999999999985
No 3
>PF11998 DUF3493: Protein of unknown function (DUF3493); InterPro: IPR021883 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length.
Probab=33.39 E-value=2.2e+02 Score=21.66 Aligned_cols=49 Identities=22% Similarity=0.255 Sum_probs=36.9
Q ss_pred CcHHHHHHHHHHHHhhhhhhHhHHHHHHhhhcCCCchhHHHHHHHHhhhh
Q 024459 132 IDSIRTLRMAVYGMLILGPSQHYWFNFLSRILPKRDALTTLKKIFMGQAI 181 (267)
Q Consensus 132 ~D~~Rt~r~a~~G~~~~GP~~h~Wy~~Ldrlfp~~~~~~vl~KVllDQ~v 181 (267)
..+-|.+|+++||++.. --.-.-+-.+-++..++++.+++.-.++|-.+
T Consensus 14 ~aPfR~lR~f~y~a~~a-Sa~iG~~i~~~rl~a~~~l~~~l~nlaI~iga 62 (75)
T PF11998_consen 14 QAPFRGLRRFFYGAFGA-SAGIGLFIFLFRLIAGPDLNEALPNLAIQIGA 62 (75)
T ss_pred HCchHHHHHHHHHHHHH-HHHHHHHHHHHHHHcCccHHHHhhhHhHHHHH
Confidence 45679999999999744 43445677778888888888888888888544
No 4
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=31.98 E-value=2e+02 Score=20.96 Aligned_cols=34 Identities=18% Similarity=-0.003 Sum_probs=31.0
Q ss_pred HHHHhhhCChhHHHHHHHHHHHHHHHHHHhhcCC
Q 024459 94 YLGKLESHPLTTKGISSSLIYVAADLTSQMITLP 127 (267)
Q Consensus 94 Y~~~L~~~Pl~Tk~iTsgvl~~~gDllAQ~i~~~ 127 (267)
-.+.++++.++|..+.-|+++.++..++-+++..
T Consensus 4 i~~vl~~ngLitaFa~vG~~m~~S~~lS~~LT~G 37 (60)
T PF03818_consen 4 IEKVLTKNGLITAFAVVGIIMWVSYWLSKKLTRG 37 (60)
T ss_pred HHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4577899999999999999999999999999875
No 5
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=31.39 E-value=1.6e+02 Score=26.68 Aligned_cols=67 Identities=25% Similarity=0.513 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHhhhhhhHhHHH--HHHh--hh---cCCCchhHHHHHHHHhhhhhhhhHHHHHH--HHHHhhcCC
Q 024459 134 SIRTLRMAVYGMLILGPSQHYWF--NFLS--RI---LPKRDALTTLKKIFMGQAIYGPLTTTIFF--SYNAALQGE 200 (267)
Q Consensus 134 ~~Rt~r~a~~G~~~~GP~~h~Wy--~~Ld--rl---fp~~~~~~vl~KVllDQ~v~aP~~~~~F~--~~~~~leG~ 200 (267)
+||+...++...++.||....|. +.|. ++ +|..+...++.-++....+..+++..... ...+++-|+
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~l~~GR 79 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGTIPLSDPLITLQILLAGHSPPTNALIGALIIVAFYALFGGR 79 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCCccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhcc
Confidence 68999999999988999877765 3332 22 45567777888788777776666655433 333555555
No 6
>PRK09609 hypothetical protein; Provisional
Probab=21.96 E-value=4.5e+02 Score=25.19 Aligned_cols=55 Identities=25% Similarity=0.393 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCcHHHHHHHHHHHHhhhhhhHhHHHHHHhhhcCCC
Q 024459 108 ISSSLIYVAADLTSQMITLPPSGSIDSIRTLRMAVYGMLILGPSQHYWFNFLSRILPKR 166 (267)
Q Consensus 108 iTsgvl~~~gDllAQ~i~~~~~~~~D~~Rt~r~a~~G~~~~GP~~h~Wy~~Ldrlfp~~ 166 (267)
+.+++..+++|++.-.+.. ..+.+.=++..++.|++ .|-+..+.|+.+.++|.++
T Consensus 57 v~G~ivG~lsDLLs~li~p---G~ffPgFTLsa~l~GlI-~Glf~~~~fk~~~~~f~~~ 111 (312)
T PRK09609 57 IVGFFTGLLSDLISFLFVP---GVYHPYYTLAAMVYGFI-PGIVGWFFFKFGKKFFGKE 111 (312)
T ss_pred HHHHHHHHHHHHHHHHhcC---CccCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhHH
Confidence 3477888899999977642 47888888888888874 8888888999999998765
No 7
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=18.93 E-value=1.7e+02 Score=21.09 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=22.8
Q ss_pred HHHHHHhhcCCCCCCCcHHHHHHHHHHHHhhh
Q 024459 117 ADLTSQMITLPPSGSIDSIRTLRMAVYGMLIL 148 (267)
Q Consensus 117 gDllAQ~i~~~~~~~~D~~Rt~r~a~~G~~~~ 148 (267)
-|.+.+.|+.. ..||-.|.+..|+-||++.
T Consensus 11 ~~~m~~fie~h--P~WDQ~Rl~~aALa~FL~Q 40 (57)
T PF10929_consen 11 HQAMKDFIETH--PNWDQYRLFQAALAGFLLQ 40 (57)
T ss_pred HHHHHHHHHcC--CCchHHHHHHHHHHHHHHH
Confidence 35566667654 3799999999999999764
No 8
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 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 [, ]. ; 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: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=16.40 E-value=80 Score=20.27 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=14.2
Q ss_pred HHHHHHHHHhhhCChhHH
Q 024459 89 GFVGWYLGKLESHPLTTK 106 (267)
Q Consensus 89 ~l~~~Y~~~L~~~Pl~Tk 106 (267)
..++.|.+.+.++|++|.
T Consensus 2 D~l~~Yl~ei~~~~LLt~ 19 (37)
T PF00140_consen 2 DSLRLYLKEIGRYPLLTA 19 (37)
T ss_dssp HHHHHHHHHHHHS-EETT
T ss_pred cHHHHHHHHHcCCCCCCH
Confidence 346789999999999985
No 9
>PF01554 MatE: MatE; InterPro: IPR002528 Characterised members of the Multi Antimicrobial Extrusion (MATE) family function as drug/sodium antiporters. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones, aminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions, some of the animal proteins may have an additional C-terminal helix. ; GO: 0015238 drug transmembrane transporter activity, 0015297 antiporter activity, 0006855 drug transmembrane transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 3MKU_B 3MKT_B.
Probab=15.53 E-value=5.7e+02 Score=20.04 Aligned_cols=93 Identities=17% Similarity=0.159 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCc--HHHHHHHHHHHHhhhhhhHhHHHHHHhhhcCCC-chhHHHHHHHHhhhhhhh
Q 024459 108 ISSSLIYVAADLTSQMITLPPSGSID--SIRTLRMAVYGMLILGPSQHYWFNFLSRILPKR-DALTTLKKIFMGQAIYGP 184 (267)
Q Consensus 108 iTsgvl~~~gDllAQ~i~~~~~~~~D--~~Rt~r~a~~G~~~~GP~~h~Wy~~Ldrlfp~~-~~~~vl~KVllDQ~v~aP 184 (267)
+..|+..+..=+++|.+-+++.++.+ .++...+.+.=.+....+....-+.+-.++..+ +....+.+.+.=.....|
T Consensus 44 ~~~g~~~a~~~~~s~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~f~~~~~~~~~~~~~~~~~~~~~~ 123 (162)
T PF01554_consen 44 LIFGLATALQILISQNIGAGDYKRAKKVVRQGLLLSLIIGLLLSLVLLLFSEFILSLFGNDPEVIEIARQYLRIMAFSIP 123 (162)
T ss_dssp HHHHHHHHHHHHHCCCCCSSSTTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHCTSSSTTCCHHHHHHHHCCHHHHHH
T ss_pred hcccccccccceeecccccccccccccccccccccchhcccchhhhhhhHHHHHHHHhhhhHHHHHHhhccchhhhhHHH
Confidence 44444445555556655333222221 223333332222223333333334444555543 344444444432222222
Q ss_pred hHHHHHHHHHHhhcCCC
Q 024459 185 LTTTIFFSYNAALQGET 201 (267)
Q Consensus 185 ~~~~~F~~~~~~leG~s 201 (267)
....+....++++|..
T Consensus 124 -~~~~~~~~~~~l~~~g 139 (162)
T PF01554_consen 124 -FFALFFVFSGILQGIG 139 (162)
T ss_dssp -HHHHHHHHCCCCGCCS
T ss_pred -HHHHHHHHHHHHHHCC
Confidence 2334445556677664
No 10
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=14.77 E-value=1.6e+02 Score=27.98 Aligned_cols=29 Identities=17% Similarity=0.462 Sum_probs=23.5
Q ss_pred hceecCCcchhhhhHH-HHHHHHHHHHHhc
Q 024459 232 FKFIPVHLQPLVNSSF-AYVWTIYLTYKAS 260 (267)
Q Consensus 232 F~~VP~~~Rvlf~n~v-s~~Wn~yLS~~a~ 260 (267)
|.-+|...|.+|++.. +++||-.+|..-.
T Consensus 228 l~~iP~~lr~myvhAYQSylfN~~lS~Ri~ 257 (319)
T cd02577 228 FLALPKNLRRMFVHAYQSYLFNEILSERIE 257 (319)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3459999998887765 9999999997654
Done!