Query 032699
Match_columns 135
No_of_seqs 113 out of 707
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 04:49:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032699.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032699hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10873 hypothetical protein; 100.0 1.9E-28 4.1E-33 184.3 10.2 98 26-127 1-107 (131)
2 KOG3472 Predicted small membra 99.9 2.2E-28 4.7E-33 178.8 7.0 97 28-128 3-102 (112)
3 COG2363 Uncharacterized small 99.9 8.5E-26 1.8E-30 169.0 7.2 94 29-126 3-104 (124)
4 PF04241 DUF423: Protein of un 99.9 5.3E-25 1.1E-29 155.4 6.0 78 44-125 1-87 (89)
5 PF11361 DUF3159: Protein of u 34.7 1E+02 0.0023 24.5 5.1 41 35-79 54-94 (187)
6 PF13706 PepSY_TM_3: PepSY-ass 30.5 59 0.0013 19.1 2.4 22 89-110 10-31 (37)
7 PF10518 TAT_signal: TAT (twin 24.5 1E+02 0.0022 16.9 2.5 19 26-44 2-20 (26)
8 PRK13823 conjugal transfer pro 23.0 97 0.0021 22.2 2.8 69 3-72 8-82 (94)
9 PF13055 DUF3917: Protein of u 22.5 41 0.00088 22.9 0.7 20 100-119 47-66 (71)
10 PF15061 DUF4538: Domain of un 20.7 2.7E+02 0.0058 18.5 4.5 23 29-51 6-28 (58)
No 1
>PRK10873 hypothetical protein; Provisional
Probab=99.95 E-value=1.9e-28 Score=184.27 Aligned_cols=98 Identities=26% Similarity=0.250 Sum_probs=84.8
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhhccCCCC-CChhHHHHHHHHHHHHHHHHHHHHHhhc--cCCc----hhhHHH--HHh
Q 032699 26 MDPVIWHKIAAVSGVAALGLGTYGAHGFKP-QNPSFKEVWQTASLYHLVHTAALVAAPI--TKNP----NIVSVV--AGI 96 (135)
Q Consensus 26 m~~r~~l~lgal~Ga~aValGAfGAHgL~~-~~~~~~~~~~TA~~Yq~~HalALl~l~~--~~~~----~~~~~l--~G~ 96 (135)
|.+|.++++++++|+++|++||||||++|+ .+|+++++||||+|||++|++||++++. .+.+ ++++++ +|+
T Consensus 1 m~~~~~l~la~l~g~~aValGA~gAH~l~~~l~~~~~~~~~ta~~Yq~~HalaLl~~~~~~~~~~~~~~~~a~~l~~~G~ 80 (131)
T PRK10873 1 MTSRFMLIFAAISGFIYVALGAFGAHVLSKTLGAVEMGWIQTGLEYQAFHTLAILGLAVAMQRRISIWFYWSSVFLALGT 80 (131)
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHccCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHH
Confidence 445789999999999999999999999999 6999999999999999999999999874 2222 234433 666
Q ss_pred hhhhhhhhhhHHHHHhhCcccchhhhHHHHH
Q 032699 97 SEVLLLFIDSTYISQNSVLCWLIHSDEIISF 127 (135)
Q Consensus 97 ~~givLFSGSLY~~altg~~~l~~~~~~~~~ 127 (135)
++||||+|++++++++++++.+|++-.
T Consensus 81 ----~lFsGSlY~~al~~~~~l~~itPiGG~ 107 (131)
T PRK10873 81 ----VLFSGSLYCLALSHLRLWAYITPVGGV 107 (131)
T ss_pred ----HHHhHHHHHHHHcCCcccccCccHHHH
Confidence 999999999999999999999999864
No 2
>KOG3472 consensus Predicted small membrane protein [Function unknown]
Probab=99.95 E-value=2.2e-28 Score=178.76 Aligned_cols=97 Identities=38% Similarity=0.600 Sum_probs=92.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhccCCCC-CChhHHHHHHHHHHHHHHHHHHHHHhhccCCchhhHHH--HHhhhhhhhhh
Q 032699 28 PVIWHKIAAVSGVAALGLGTYGAHGFKP-QNPSFKEVWQTASLYHLVHTAALVAAPITKNPNIVSVV--AGISEVLLLFI 104 (135)
Q Consensus 28 ~r~~l~lgal~Ga~aValGAfGAHgL~~-~~~~~~~~~~TA~~Yq~~HalALl~l~~~~~~~~~~~l--~G~~~givLFS 104 (135)
.+.|+.++|++|+.++.+||||+|++|+ .|+++++.||||++|||+|++|+++++..++|+|.+.+ +|+ ++||
T Consensus 3 ~~~~~rlaalsGa~AlglgaYgahvlk~~pd~~~~~~~dtA~~yh~~HSlAlma~P~~~~p~~tg~Ll~tG~----~lFs 78 (112)
T KOG3472|consen 3 PMTFIRLAALSGAAALGLGAYGAHVLKDVPDPKELKSWDTANRYHFLHSLALMAVPVARKPLWTGGLLITGI----TLFS 78 (112)
T ss_pred chHHHHHHHHhhHHHHhhhhhhhhhhhcCCCHHHHHHHHHHHHHHHHHHHHHHcCccccCcchhhhHHHHHH----HHhc
Confidence 3579999999999999999999999999 79999999999999999999999999999999998775 888 9999
Q ss_pred hhHHHHHhhCcccchhhhHHHHHH
Q 032699 105 DSTYISQNSVLCWLIHSDEIISFM 128 (135)
Q Consensus 105 GSLY~~altg~~~l~~~~~~~~~~ 128 (135)
|++|++++++++.++.++||+-|.
T Consensus 79 g~~Y~~aL~g~~~~~~lapiGG~~ 102 (112)
T KOG3472|consen 79 GTCYYLALSGDRILQPLAPIGGFV 102 (112)
T ss_pred chhheeeecCCcccccccccccHH
Confidence 999999999999999999999874
No 3
>COG2363 Uncharacterized small membrane protein [Function unknown]
Probab=99.92 E-value=8.5e-26 Score=169.01 Aligned_cols=94 Identities=29% Similarity=0.329 Sum_probs=83.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhccCCCC-CChhHHHHHHHHHHHHHHHHHHHHHhhcc--CCc---hhhHHH--HHhhhhh
Q 032699 29 VIWHKIAAVSGVAALGLGTYGAHGFKP-QNPSFKEVWQTASLYHLVHTAALVAAPIT--KNP---NIVSVV--AGISEVL 100 (135)
Q Consensus 29 r~~l~lgal~Ga~aValGAfGAHgL~~-~~~~~~~~~~TA~~Yq~~HalALl~l~~~--~~~---~~~~~l--~G~~~gi 100 (135)
|.++.+++++|+++|++||||+|++++ .++++.++|+|++||||+|++|++++++. +.. ++++++ +|+
T Consensus 3 ~~~~~l~al~g~l~v~lGAfgah~l~~~~~~~~l~~~~Tg~~yqm~Halall~l~l~~~~~~~~~~~ag~ll~~Gi---- 78 (124)
T COG2363 3 KTFLILAALSGFLAVALGAFGAHGLAKALHDGELAWLGTGAQYQMFHALALLALGLLALRLRSTVRWAGWLLLLGI---- 78 (124)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH----
Confidence 568999999999999999999999998 78899999999999999999999999863 222 445443 677
Q ss_pred hhhhhhHHHHHhhCcccchhhhHHHH
Q 032699 101 LLFIDSTYISQNSVLCWLIHSDEIIS 126 (135)
Q Consensus 101 vLFSGSLY~~altg~~~l~~~~~~~~ 126 (135)
++||||||.+++++.|++++.+||+-
T Consensus 79 ~LFSGsLy~l~lsg~rllg~iTPiGG 104 (124)
T COG2363 79 VLFSGSLYALALSGLRLLGAITPIGG 104 (124)
T ss_pred HHHcchHHHHHHcCcchhhccCCcch
Confidence 99999999999999999999999984
No 4
>PF04241 DUF423: Protein of unknown function (DUF423); InterPro: IPR006696 This is a potential integral membrane protein with no known function.
Probab=99.91 E-value=5.3e-25 Score=155.43 Aligned_cols=78 Identities=32% Similarity=0.398 Sum_probs=68.6
Q ss_pred HHHHhhccCCCC-CChhHHHHHHHHHHHHHHHHHHHHHhhc------cCCchhhHHH--HHhhhhhhhhhhhHHHHHhhC
Q 032699 44 GLGTYGAHGFKP-QNPSFKEVWQTASLYHLVHTAALVAAPI------TKNPNIVSVV--AGISEVLLLFIDSTYISQNSV 114 (135)
Q Consensus 44 alGAfGAHgL~~-~~~~~~~~~~TA~~Yq~~HalALl~l~~------~~~~~~~~~l--~G~~~givLFSGSLY~~altg 114 (135)
++||||||++|+ .+++++++|+||+|||++|++|++++++ .+.+++++++ +|+ ++||||||++++++
T Consensus 1 alGA~gaH~l~~~~~~~~~~~~~tA~~y~~~Halall~~~~~~~~~~~~~~~~a~~l~~~G~----~lFsGslY~~al~~ 76 (89)
T PF04241_consen 1 ALGAFGAHGLKDQLSPEQLEWFQTAVQYQFIHALALLALGLLAQRRSSRLLRLAGWLFLLGT----LLFSGSLYYLALTG 76 (89)
T ss_pred ChHHHHhccCcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchHHHHHHHHHHHHH----HHHhHHHHHHHHcC
Confidence 489999999999 7999999999999999999999999984 2334455443 777 99999999999999
Q ss_pred cccchhhhHHH
Q 032699 115 LCWLIHSDEII 125 (135)
Q Consensus 115 ~~~l~~~~~~~ 125 (135)
++++++.+||+
T Consensus 77 ~~~~~~itPiG 87 (89)
T PF04241_consen 77 PKSLGPITPIG 87 (89)
T ss_pred CcccccCCCCC
Confidence 99999999987
No 5
>PF11361 DUF3159: Protein of unknown function (DUF3159); InterPro: IPR016566 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Probab=34.68 E-value=1e+02 Score=24.52 Aligned_cols=41 Identities=15% Similarity=0.149 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHhhccCCCCCChhHHHHHHHHHHHHHHHHHHHH
Q 032699 35 AAVSGVAALGLGTYGAHGFKPQNPSFKEVWQTASLYHLVHTAALV 79 (135)
Q Consensus 35 gal~Ga~aValGAfGAHgL~~~~~~~~~~~~TA~~Yq~~HalALl 79 (135)
.+++|+++|+++|+-|.--.+ ..+.|-.+.-+...-+++.+
T Consensus 54 ~a~~gl~gV~i~a~~A~~tG~----A~~~Fl~gi~~n~~~~~~~l 94 (187)
T PF11361_consen 54 PALSGLFGVAISAAIAWRTGS----AKDFFLPGIWTNAVYAVVFL 94 (187)
T ss_pred HHHHHHHHHHHHHHHHHHHCC----hhhhhHHHHHHHHHHHHHHH
Confidence 478999999999988864333 23445444444444444443
No 6
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=30.47 E-value=59 Score=19.09 Aligned_cols=22 Identities=5% Similarity=0.274 Sum_probs=14.2
Q ss_pred hhHHHHHhhhhhhhhhhhHHHH
Q 032699 89 IVSVVAGISEVLLLFIDSTYIS 110 (135)
Q Consensus 89 ~~~~l~G~~~givLFSGSLY~~ 110 (135)
|.++.+|..+-++.|+|++...
T Consensus 10 W~Gl~~g~~l~~~~~tG~~~~f 31 (37)
T PF13706_consen 10 WLGLILGLLLFVIFLTGAVMVF 31 (37)
T ss_pred HHHHHHHHHHHHHHHHhHHHHH
Confidence 3444466666678888887654
No 7
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=24.53 E-value=1e+02 Score=16.91 Aligned_cols=19 Identities=21% Similarity=0.052 Sum_probs=12.4
Q ss_pred cchHHHHHHHHHHHHHHHH
Q 032699 26 MDPVIWHKIAAVSGVAALG 44 (135)
Q Consensus 26 m~~r~~l~lgal~Ga~aVa 44 (135)
++.|.|+..++..++.+..
T Consensus 2 ~sRR~fLk~~~a~~a~~~~ 20 (26)
T PF10518_consen 2 LSRRQFLKGGAAAAAAAAL 20 (26)
T ss_pred CcHHHHHHHHHHHHHHHHh
Confidence 4567888877666665444
No 8
>PRK13823 conjugal transfer protein TrbD; Provisional
Probab=22.97 E-value=97 Score=22.19 Aligned_cols=69 Identities=10% Similarity=0.020 Sum_probs=34.9
Q ss_pred CccccchhhhhhcCCchhhhhcccchHHHHHHHHHHH---HHHHHHHHhhccCCCC---CChhHHHHHHHHHHHHH
Q 032699 3 RHSTMSEERLIRREPKERRRIIMMDPVIWHKIAAVSG---VAALGLGTYGAHGFKP---QNPSFKEVWQTASLYHL 72 (135)
Q Consensus 3 ~~~~~s~~~~~~~~p~~~~~~~~m~~r~~l~lgal~G---a~aValGAfGAHgL~~---~~~~~~~~~~TA~~Yq~ 72 (135)
-|.+++|+-+....|-+.-..+-... ..+++|.-.- ..++++...+-..+.- -||+..+.|..-.+|+-
T Consensus 8 IhrsL~rp~Ll~Ga~R~l~i~~g~la-~~l~~g~~~~~a~~~gl~lw~v~h~~l~~mAK~DP~~~~V~~Rh~ry~~ 82 (94)
T PRK13823 8 IRRAGNRPNLFMGGDRELVMFSGLLA-GILIFVAQTWRAALFGIALWFGALFALRLMAKADPKMRHVYLRHRRYKP 82 (94)
T ss_pred HHHhccccHhhCCcchHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHhhccc
Confidence 38899999999998877621111100 0112222111 2344444333222222 37777777777666653
No 9
>PF13055 DUF3917: Protein of unknown function (DUF3917)
Probab=22.49 E-value=41 Score=22.87 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=15.7
Q ss_pred hhhhhhhHHHHHhhCcccch
Q 032699 100 LLLFIDSTYISQNSVLCWLI 119 (135)
Q Consensus 100 ivLFSGSLY~~altg~~~l~ 119 (135)
|.+|+||+..+-..|.-++.
T Consensus 47 itlfags~mvlmvagii~fi 66 (71)
T PF13055_consen 47 ITLFAGSIMVLMVAGIILFI 66 (71)
T ss_pred hHHHhchHHHHHHhhheEEE
Confidence 38999999988877765554
No 10
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=20.75 E-value=2.7e+02 Score=18.52 Aligned_cols=23 Identities=9% Similarity=-0.102 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcc
Q 032699 29 VIWHKIAAVSGVAALGLGTYGAH 51 (135)
Q Consensus 29 r~~l~lgal~Ga~aValGAfGAH 51 (135)
|..+++||+.|+++.++-..--|
T Consensus 6 r~~~~~ggfVg~iG~a~Ypi~~~ 28 (58)
T PF15061_consen 6 RYALFVGGFVGLIGAALYPIYFR 28 (58)
T ss_pred cchhhHHHHHHHHHHHHhhhhcc
Confidence 55678889988888887776655
Done!