Query 027603
Match_columns 221
No_of_seqs 26 out of 28
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 12:24:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1277 Endosomal membrane pro 76.4 26 0.00056 35.6 10.1 83 106-207 159-263 (593)
2 PRK10030 hypothetical protein; 50.4 11 0.00025 32.4 2.0 27 9-35 4-30 (197)
3 PF09574 DUF2374: Protein of 43.9 9.4 0.0002 26.7 0.5 26 173-198 17-42 (42)
4 PF10966 DUF2768: Protein of u 40.9 28 0.00061 25.7 2.6 30 176-208 6-36 (58)
5 PF10447 EXOSC1: Exosome compo 38.1 15 0.00033 28.1 0.8 12 22-33 65-76 (82)
6 COG5616 Predicted integral mem 34.4 62 0.0013 27.9 4.0 39 92-131 58-114 (152)
7 PF04327 DUF464: Protein of un 33.0 56 0.0012 25.1 3.3 19 108-126 1-19 (103)
8 TIGR02808 short_TIGR02808 cons 31.2 21 0.00046 24.9 0.6 26 173-198 17-42 (42)
9 PF14012 DUF4229: Protein of u 31.2 44 0.00095 24.7 2.3 38 171-208 30-67 (69)
10 PF00309 Sigma54_AID: Sigma-54 29.0 90 0.002 21.4 3.4 29 184-212 16-44 (49)
11 PF06305 DUF1049: Protein of u 24.7 1.3E+02 0.0028 20.8 3.7 36 154-192 6-43 (68)
12 COG2868 Predicted ribosomal pr 24.4 88 0.0019 25.5 3.1 57 108-199 1-57 (109)
13 PF07172 GRP: Glycine rich pro 23.5 52 0.0011 25.8 1.6 27 1-28 1-27 (95)
14 PRK14553 hypothetical protein; 23.4 1.1E+02 0.0024 23.9 3.4 19 108-126 1-19 (108)
15 PLN03207 stomagen; Provisional 22.2 1.1E+02 0.0024 25.2 3.3 20 22-41 28-47 (113)
16 PF12381 Peptidase_C3G: Tungro 22.0 47 0.001 30.4 1.2 31 123-154 87-117 (231)
17 PF12955 DUF3844: Domain of un 20.7 51 0.0011 26.6 1.1 30 165-194 60-91 (103)
No 1
>KOG1277 consensus Endosomal membrane proteins, EMP70 [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.35 E-value=26 Score=35.57 Aligned_cols=83 Identities=18% Similarity=0.488 Sum_probs=49.3
Q ss_pred cCeEEEEEEEeCCeEeeeeeeeecCChhhhhhCCCCcccccCCCCCCceEEEEEEEEEee-------eeeccceee----
Q 027603 106 VPMIDVHLRYSGNDLLGVTAKIVDMPQRYVEIHPDLPKYFWQPESWPKHVLIRYTWEEQS-------EIDVASGFY---- 174 (221)
Q Consensus 106 vpmIDv~l~ysg~dllgVtakvvdmp~~yv~~H~~~~~ef~d~~~WPKhvlV~Y~W~e~~-------eiDv~~Gly---- 174 (221)
-.+.++++-|.||.|+.|...+ |.-+..-|+..-+ +--.=+|+|.+ |+=...+||
T Consensus 159 ~thk~f~i~yn~drii~vnlt~----~~~v~L~~~~~~~----------~tYsV~W~~t~v~f~~rfdkyld~~ff~h~I 224 (593)
T KOG1277|consen 159 YTHKKFEIGYNGDRIIDVNLTT----HGLVDLRPDKKLT----------FTYSVKWKETEVEFEKRFDKYLDPSFFPHRI 224 (593)
T ss_pred EEeeeEEEeecCceEEEEEeee----cccccCCCCCCCc----------eEEEEEeeeccCcHHHHhHhhccccccccee
Confidence 3589999999999999999886 3334333443222 33344687642 222334443
Q ss_pred -----------eeehhhHHHHHHHhHhhhhccHHHHHHHHHHHh
Q 027603 175 -----------VLFASGLMLSFILSIYILESSREKFTRFLQETV 207 (221)
Q Consensus 175 -----------VLF~~gl~ls~il~iyil~~~~~kl~rf~~e~v 207 (221)
|+|..|| ++.-..+.-|.-.+|+-+|--
T Consensus 225 HWfSIfNSfmmVifLvGl-----vamILMRtLrnDyarY~~dee 263 (593)
T KOG1277|consen 225 HWFSIFNSFMMVIFLVGL-----VAMILMRTLRNDYARYAKDEE 263 (593)
T ss_pred ehhhHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHhccchh
Confidence 3444443 333345677777888777654
No 2
>PRK10030 hypothetical protein; Provisional
Probab=50.37 E-value=11 Score=32.39 Aligned_cols=27 Identities=30% Similarity=0.416 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhhhhhccCCCCCccccc
Q 027603 9 MTSLLLLLLSLPSISLAYRPGDIVPMS 35 (221)
Q Consensus 9 ~~llllll~~~i~~~~ayr~GDiVp~s 35 (221)
..+++++|.+++..+..+++||+|=.+
T Consensus 4 ~~~~~~~~~~~~~~~~~l~~GDlif~~ 30 (197)
T PRK10030 4 RLLILSLLVSVPAFAWQPQTGDIIFQI 30 (197)
T ss_pred hhHHHHHHHhchhhhcCCCCCCEEEEe
Confidence 345556677888888899999999654
No 3
>PF09574 DUF2374: Protein of unknown function (Duf2374); InterPro: IPR014175 This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.
Probab=43.94 E-value=9.4 Score=26.69 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=22.2
Q ss_pred eeeeehhhHHHHHHHhHhhhhccHHH
Q 027603 173 FYVLFASGLMLSFILSIYILESSREK 198 (221)
Q Consensus 173 lyVLF~~gl~ls~il~iyil~~~~~k 198 (221)
.=|+|.+|++...+.|+.+|.-+.+|
T Consensus 17 mPvI~L~GF~~Vav~~~~lL~~~~dk 42 (42)
T PF09574_consen 17 MPVIILSGFAAVAVASIWLLSLTKDK 42 (42)
T ss_pred chHHHHhhHHHHHHHHHHHHHhhcCC
Confidence 34789999999999999999877765
No 4
>PF10966 DUF2768: Protein of unknown function (DUF2768); InterPro: IPR020076 This entry contains proteins with no known function.
Probab=40.94 E-value=28 Score=25.67 Aligned_cols=30 Identities=40% Similarity=0.526 Sum_probs=22.8
Q ss_pred eehhhHHHHHHHhHhhhhccHHHHHH-HHHHHhh
Q 027603 176 LFASGLMLSFILSIYILESSREKFTR-FLQETVA 208 (221)
Q Consensus 176 LF~~gl~ls~il~iyil~~~~~kl~r-f~~e~v~ 208 (221)
+.+.|+++-.+..||. ||.|++. |+|-.++
T Consensus 6 ~~~iglMfisv~~i~~---sR~Klk~~~lk~i~~ 36 (58)
T PF10966_consen 6 FGAIGLMFISVILIYF---SRYKLKGKFLKFIVS 36 (58)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHhChHHHHHHH
Confidence 4677888888888886 7889987 8776543
No 5
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=38.15 E-value=15 Score=28.12 Aligned_cols=12 Identities=50% Similarity=0.897 Sum_probs=8.4
Q ss_pred hhccCCCCCccc
Q 027603 22 ISLAYRPGDIVP 33 (221)
Q Consensus 22 ~~~ayr~GDiVp 33 (221)
+...|||||||+
T Consensus 65 ~~~~FrpGDIVr 76 (82)
T PF10447_consen 65 MYDCFRPGDIVR 76 (82)
T ss_dssp GGGT--SSSEEE
T ss_pred HHhccCCCCEEE
Confidence 577899999996
No 6
>COG5616 Predicted integral membrane protein [Function unknown]
Probab=34.38 E-value=62 Score=27.90 Aligned_cols=39 Identities=38% Similarity=0.515 Sum_probs=30.7
Q ss_pred eeceEEEecCCCCCc--------C----------eEEEEEEEeCCeEeeeeeeeecCC
Q 027603 92 RVPWLFVINRKSSQV--------P----------MIDVHLRYSGNDLLGVTAKIVDMP 131 (221)
Q Consensus 92 ~tpWl~vi~~~~~~v--------p----------mIDv~l~ysg~dllgVtakvvdmp 131 (221)
..+||.||.||+++- + .++=..|++||.+. |+|++||+-
T Consensus 58 r~~~l~VIArnssft~kgka~dv~~v~~~Lgv~YvleGsvRr~g~RvR-vtaqLvda~ 114 (152)
T COG5616 58 RFRELFVIARNSSFTYKGKAVDVREVGEELGVRYVLEGSVRRAGGRVR-VTAQLVDAS 114 (152)
T ss_pred hccCceEEEccceeeccCCCCCHHHHHHHhCCcEEEeeeEeecCCEEE-EEEEEEecc
Confidence 348999999988732 1 35668899999987 999999973
No 7
>PF04327 DUF464: Protein of unknown function (DUF464); InterPro: IPR007422 This entry is represented by Bacteriophage Cp-1, Orf13. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2IDL_A 2G0J_D 2G0I_B 2P92_B 1S12_C.
Probab=33.02 E-value=56 Score=25.13 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=18.3
Q ss_pred eEEEEEEEeCCeEeeeeee
Q 027603 108 MIDVHLRYSGNDLLGVTAK 126 (221)
Q Consensus 108 mIDv~l~ysg~dllgVtak 126 (221)
||.+.+++.+|.+.+++++
T Consensus 1 MI~v~i~~~~~~i~~~~v~ 19 (103)
T PF04327_consen 1 MIKVTIYKKNGQIIGFEVS 19 (103)
T ss_dssp SEEEEEEECTSEEEEEEEE
T ss_pred CEEEEEEECCCeEEEEEEE
Confidence 8999999999999999998
No 8
>TIGR02808 short_TIGR02808 conserved hypothetical protein TIGR02808. This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC7966.
Probab=31.23 E-value=21 Score=24.94 Aligned_cols=26 Identities=23% Similarity=0.360 Sum_probs=21.9
Q ss_pred eeeeehhhHHHHHHHhHhhhhccHHH
Q 027603 173 FYVLFASGLMLSFILSIYILESSREK 198 (221)
Q Consensus 173 lyVLF~~gl~ls~il~iyil~~~~~k 198 (221)
.=|+|.+|++...+.||.+|.-..||
T Consensus 17 mPvIil~GF~~Va~~si~lLs~~~dk 42 (42)
T TIGR02808 17 MPFIILSGFVAVAVTSILLLNAFGDK 42 (42)
T ss_pred cchHHhhhhHHHHHHHHHHHHhhcCC
Confidence 44789999999999999999877665
No 9
>PF14012 DUF4229: Protein of unknown function (DUF4229)
Probab=31.17 E-value=44 Score=24.67 Aligned_cols=38 Identities=18% Similarity=0.169 Sum_probs=32.2
Q ss_pred ceeeeeehhhHHHHHHHhHhhhhccHHHHHHHHHHHhh
Q 027603 171 SGFYVLFASGLMLSFILSIYILESSREKFTRFLQETVA 208 (221)
Q Consensus 171 ~GlyVLF~~gl~ls~il~iyil~~~~~kl~rf~~e~v~ 208 (221)
..+.+....++++|+.+|.-.+.+-+++.++-+.|..+
T Consensus 30 ~p~~~~~l~A~vis~~lS~~ll~~~R~~~~~~ia~~~~ 67 (69)
T PF14012_consen 30 VPLLVAALLALVISMPLSYVLLRRLRDRASADIAARDE 67 (69)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45667778899999999999999999999988877643
No 10
>PF00309 Sigma54_AID: Sigma-54 factor, Activator interacting domain (AID) ; InterPro: IPR000394 Sigma factors [] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor [, ] required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognised by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent
Probab=28.97 E-value=90 Score=21.40 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=26.1
Q ss_pred HHHHhHhhhhccHHHHHHHHHHHhhcCCC
Q 027603 184 SFILSIYILESSREKFTRFLQETVAESSM 212 (221)
Q Consensus 184 s~il~iyil~~~~~kl~rf~~e~v~e~s~ 212 (221)
..+.++-|||.+..-|..|+++.+.|-++
T Consensus 16 ~l~qsl~iLqm~~~eL~~~i~~~~~eNP~ 44 (49)
T PF00309_consen 16 QLQQSLKILQMSSQELEEYIEEEAEENPF 44 (49)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhCcC
Confidence 47889999999999999999999988774
No 11
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.66 E-value=1.3e+02 Score=20.76 Aligned_cols=36 Identities=19% Similarity=0.423 Sum_probs=20.1
Q ss_pred eEEEEEEEEEeeeeeccceeee--eehhhHHHHHHHhHhhh
Q 027603 154 HVLIRYTWEEQSEIDVASGFYV--LFASGLMLSFILSIYIL 192 (221)
Q Consensus 154 hvlV~Y~W~e~~eiDv~~GlyV--LF~~gl~ls~il~iyil 192 (221)
-|-|+|-+-+.. .+-|+.+ -|++|++++.+++....
T Consensus 6 ~V~v~~~~~~~~---~pl~l~il~~f~~G~llg~l~~~~~~ 43 (68)
T PF06305_consen 6 PVTVNFLFGQFP---LPLGLLILIAFLLGALLGWLLSLPSR 43 (68)
T ss_pred eEEEEEEeeecc---chHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467787666543 4444433 35566666665555444
No 12
>COG2868 Predicted ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=24.37 E-value=88 Score=25.52 Aligned_cols=57 Identities=21% Similarity=0.257 Sum_probs=39.1
Q ss_pred eEEEEEEEeCCeEeeeeeeeecCChhhhhhCCCCcccccCCCCCCceEEEEEEEEEeeeeeccceeeeeehhhHHHHHHH
Q 027603 108 MIDVHLRYSGNDLLGVTAKIVDMPQRYVEIHPDLPKYFWQPESWPKHVLIRYTWEEQSEIDVASGFYVLFASGLMLSFIL 187 (221)
Q Consensus 108 mIDv~l~ysg~dllgVtakvvdmp~~yv~~H~~~~~ef~d~~~WPKhvlV~Y~W~e~~eiDv~~GlyVLF~~gl~ls~il 187 (221)
||++.+++-+|.|++++|+ =|.+.-+.=.| + |=+| .|+++++++.
T Consensus 1 MI~v~i~rk~~~i~s~~~s----------GHA~~ge~G~D-------------------i-VCAa-----vS~i~~~~vn 45 (109)
T COG2868 1 MIKVVIKRKNGQIVSLTAS----------GHADFGEHGSD-------------------I-VCAA-----VSAILFGAVN 45 (109)
T ss_pred CeEEEEEecCCeEEEEEEe----------ccccccccCCc-------------------E-EEee-----hHHHHHHHHH
Confidence 8999999999999999999 45554443222 1 1122 4677888888
Q ss_pred hHhhhhccHHHH
Q 027603 188 SIYILESSREKF 199 (221)
Q Consensus 188 ~iyil~~~~~kl 199 (221)
+|..+-..++..
T Consensus 46 ~ie~~~~~~~~~ 57 (109)
T COG2868 46 GIEELADQEPVT 57 (109)
T ss_pred HHHHhccceeee
Confidence 888766665544
No 13
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=23.50 E-value=52 Score=25.81 Aligned_cols=27 Identities=33% Similarity=0.359 Sum_probs=0.0
Q ss_pred CCCccchhHHHHHHHHHhhhhhhccCCC
Q 027603 1 MTPRRRTIMTSLLLLLLSLPSISLAYRP 28 (221)
Q Consensus 1 ~~~~~~~~~~llllll~~~i~~~~ayr~ 28 (221)
|+ ++.-++..|+|..++||++..+-|+
T Consensus 1 Ma-SK~~llL~l~LA~lLlisSevaa~~ 27 (95)
T PF07172_consen 1 MA-SKAFLLLGLLLAALLLISSEVAARE 27 (95)
T ss_pred Cc-hhHHHHHHHHHHHHHHHHhhhhhHH
No 14
>PRK14553 hypothetical protein; Provisional
Probab=23.44 E-value=1.1e+02 Score=23.94 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=17.5
Q ss_pred eEEEEEEEeCCeEeeeeee
Q 027603 108 MIDVHLRYSGNDLLGVTAK 126 (221)
Q Consensus 108 mIDv~l~ysg~dllgVtak 126 (221)
||.+++++.+|.+.+.+++
T Consensus 1 MI~v~i~~~~~~i~~~~i~ 19 (108)
T PRK14553 1 MIKVTIKRKNGQIISFTMS 19 (108)
T ss_pred CEEEEEEEeCCEEEEEEEE
Confidence 8999998899999999988
No 15
>PLN03207 stomagen; Provisional
Probab=22.17 E-value=1.1e+02 Score=25.24 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=14.2
Q ss_pred hhccCCCCCcccccccceec
Q 027603 22 ISLAYRPGDIVPMSKMSQYH 41 (221)
Q Consensus 22 ~~~ayr~GDiVp~sr~~Q~H 41 (221)
.+.+-|+|+++|..-+.-++
T Consensus 28 v~qgsr~~~~~~~~~~~s~~ 47 (113)
T PLN03207 28 VIQGSRNQSILPYDQSISYP 47 (113)
T ss_pred HHhccccccccCcccccccC
Confidence 67788999999875553333
No 16
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase; InterPro: IPR024387 This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Probab=22.04 E-value=47 Score=30.44 Aligned_cols=31 Identities=32% Similarity=0.405 Sum_probs=27.7
Q ss_pred eeeeeecCChhhhhhCCCCcccccCCCCCCce
Q 027603 123 VTAKIVDMPQRYVEIHPDLPKYFWQPESWPKH 154 (221)
Q Consensus 123 Vtakvvdmp~~yv~~H~~~~~ef~d~~~WPKh 154 (221)
..+-|.||| ..+-.|.|+.+.|-+.+.|+|.
T Consensus 87 ~d~vl~~lg-n~V~~~~Di~k~f~t~ed~~~~ 117 (231)
T PF12381_consen 87 QDAVLWDLG-NSVCPHIDITKHFPTAEDWSKF 117 (231)
T ss_pred eeEEEEecC-CccCCccCHHHhCCChhHhhhc
Confidence 556679999 8899999999999999999974
No 17
>PF12955 DUF3844: Domain of unknown function (DUF3844); InterPro: IPR024382 This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins thought to be located in the endoplasmic reticulum.
Probab=20.69 E-value=51 Score=26.62 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=19.3
Q ss_pred eeeeccceeeeeehhhHHHH--HHHhHhhhhc
Q 027603 165 SEIDVASGFYVLFASGLMLS--FILSIYILES 194 (221)
Q Consensus 165 ~eiDv~~GlyVLF~~gl~ls--~il~iyil~~ 194 (221)
.-+|++.-|++++++++++. ++.+|..|-+
T Consensus 60 qKkDvS~~F~L~~~~ti~lv~~~~~~I~lL~s 91 (103)
T PF12955_consen 60 QKKDVSVPFWLFAGFTIALVVLVAGAIGLLFS 91 (103)
T ss_pred ccccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788888887777665554 4555655543
Done!