Query 040228
Match_columns 831
No_of_seqs 151 out of 571
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 06:21:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040228.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040228hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13968 DUF4220: Domain of un 100.0 7.1E-80 1.5E-84 688.7 25.5 349 52-445 1-361 (362)
2 PF04578 DUF594: Protein of un 99.9 7.7E-25 1.7E-29 178.3 6.2 49 764-812 11-59 (59)
3 TIGR02587 putative integral me 29.7 1E+02 0.0022 33.4 5.6 50 15-73 35-84 (271)
4 cd05833 Ribosomal_P2 Ribosomal 22.8 38 0.00082 31.7 0.9 20 94-113 5-24 (109)
5 PTZ00373 60S Acidic ribosomal 19.4 50 0.0011 31.1 0.9 20 94-113 7-26 (112)
6 PF09323 DUF1980: Domain of un 18.0 4.4E+02 0.0096 26.7 7.5 55 19-74 2-57 (182)
7 PF00367 PTS_EIIB: phosphotran 15.5 98 0.0021 22.9 1.5 16 95-110 2-17 (35)
8 COG3336 Predicted membrane pro 12.9 2E+02 0.0042 31.6 3.5 82 16-106 12-100 (299)
9 KOG4788 Members of chemokine-l 11.8 5.9E+02 0.013 25.7 6.4 31 269-299 37-67 (172)
10 COG1264 PtsG Phosphotransferas 9.6 1.1E+02 0.0024 27.4 0.3 17 94-110 4-20 (88)
No 1
>PF13968 DUF4220: Domain of unknown function (DUF4220)
Probab=100.00 E-value=7.1e-80 Score=688.71 Aligned_cols=349 Identities=40% Similarity=0.670 Sum_probs=296.0
Q ss_pred HHHHHhhhhhHHHHHhhHhhccCCCCCCCCCCCCcccccchhhHHHHHhhcCCCcccccccchhhhhhHHHHhhhhheee
Q 040228 52 IWSAYLLADWAANYAVGLISDSQGDNPGPSDPKHNNQLLAFWPTFLLLHLGGPDTITALALEDNELWLRHSLGLITQAAS 131 (831)
Q Consensus 52 lWlAYl~ad~vA~YaLG~Ls~~~~~~~~~~~~~~~~~L~~fWAPfLLlHLGG~DtITAySlEDN~LW~Rhll~L~~Qv~~ 131 (831)
+|+||++||++|+||||+|++++. +.+++|++|||||||+||||||||||||+|||+||+||++++++|+++
T Consensus 1 lWlay~~sd~~a~Y~LG~l~~~~~--------~~~~~l~~~WAp~LLlhlgg~d~itaysleDn~lw~R~ll~ll~qv~~ 72 (362)
T PF13968_consen 1 LWLAYLLSDSLATYALGLLQSSSS--------PFKSQLFPFWAPFLLLHLGGQDTITAYSLEDNELWLRHLLTLLVQVIW 72 (362)
T ss_pred CchHHhhhHHHHHHHHHHHhcCCC--------CCCcchhhhHHHHHHHHhCCCcceeeeecccchHHHHHHHHHHHHhhh
Confidence 699999999999999999999862 577999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEccCCCchHHHHHHHHHHHHHhhhhhHHHHhhCChhhhhhcccCCCCCCCchHHhHHHHHHHhhhcCCcccccc
Q 040228 132 AVYVFLLSLPNNKVLVPSILMFIAGVIKYFERSRALYLGSVDRFRESMLSDADPGPNYAKLMEEYESKIKAQLPARIITI 211 (831)
Q Consensus 132 a~YV~~ks~~~~~l~~~~ilmFv~GviKygER~wAL~~as~~~~~~S~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~ 211 (831)
++||++++|+|.++.+|+++||++|++||+||+|||++||.+.+++||..+++++++|+..|++|++....+.+.+....
T Consensus 73 a~Yv~~~~~~g~~l~~~~~lLfv~gi~K~~eR~~AL~~As~~~i~~s~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~ 152 (362)
T PF13968_consen 73 ALYVFYKSWSGSRLLAPAILLFVVGIIKYGERIWALRRASSRSIRSSMMGEPDPGPNYAETMEGYKYLVEEEYPKEIRIL 152 (362)
T ss_pred hheeeeeecccchHHHHHHHHHHHHHHHHHHHHHHHHccchhhhHHhhhhhhcccccchhhccccchhccccccceeeec
Confidence 99999999998889999999999999999999999999999999999999999999999999999876655544443221
Q ss_pred chhhh-----HHHH-----HHhhhccCchHHHHHHhHHHHHhhhhhhccccccccchhhHHHHhhc-ChhhHHHHHHHHH
Q 040228 212 PEAEK-----KLKV-----ELKKRALTNLDVVHYAHHYFSIFKGLLVDIIYSFRERDDSRNFFRTL-HAEDSLKIIEVEL 280 (831)
Q Consensus 212 ~e~~~-----~~~~-----~~~~~~~~~~~~l~~A~~lf~~~k~lfvD~~~s~~~~~~s~~~~~~~-~~~~afkvvE~EL 280 (831)
.+.+. ..+. ....++.++++++|.||++|+++|++|+|++++++++.+++++|.++ ++++||||+|+||
T Consensus 153 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~k~l~ls~aLf~llrr~f~d~~~~~~~~~~~~~~~~~l~~~~~af~vie~EL 232 (362)
T PF13968_consen 153 KEEDLETLVTVDKVWESLLDSREESDPELKDLCLSFALFKLLRRRFVDFPLSESGRLKTRDFFRGLDDAERAFRVIEMEL 232 (362)
T ss_pred cccccccCCccceecccccchhcccccHHHHHHHHHHHHHHHHhhhhCCCcchhhhHHHHHHHhccccHHHHHHHHHHHH
Confidence 11110 0000 01123456788999999999999999999999999999999999886 4899999999999
Q ss_pred HHHHHhhhcccccccchhhHHHHHHHHHHHHHHHHHHhhccc-CCcccccchhhHHHHHHHHHHHHHHHHHHHHhchhhH
Q 040228 281 NFIYEVFYTKVNVTHSWWGVIFRLTASGSVAAALCYFYFRVK-KDEYEGFDVGITYTLFWGAIALDVVAFFMFIFSDWTL 359 (831)
Q Consensus 281 sfmYD~LYTKa~v~~t~~G~~~R~is~~~t~aAl~lF~~~~~-k~~y~~~DV~ITYvLl~gai~LE~~si~~~~~S~Wt~ 359 (831)
|||||+||||++|+||+.|+++|+++++++++|+++|...++ +++|+++||+|||+||+|++++|+++++++++|+||+
T Consensus 233 sf~yD~~YTk~~v~~~~~~~~~~~~s~~~~~~a~~lf~~~~~~~~~~~~~Dv~ITy~Ll~~~~~lE~~~~~~~~~S~W~~ 312 (362)
T PF13968_consen 233 SFLYDYLYTKAPVVHTWLGLFLRVISLLSTVAALVLFWLSHKKKHGYSRVDVIITYVLLVGAVLLEVWSLLVYLFSDWTK 312 (362)
T ss_pred HHHHHheeccceeeeeccchHHHHHHHHHHHHHHHHhhccccccccCCccCeehHHHHHHHHHHHHHHHHHHHHcCccHH
Confidence 999999999999999999999999999999999999998732 3789999999999999999999999999999999999
Q ss_pred HHhhccCCCCcchhhHhhhhhhHHHHHHHHhhhcCCCcccccccccccccchhhhhhhhhcCCCCCcccccccchhhhhH
Q 040228 360 AALTRDRDSNSGFRIIKMVKSFFAKILQLFLYFKSPWWQDYHWEENVTDKSNVKLKHQLLATPTLFRRWSGYVSGHNLIR 439 (831)
Q Consensus 360 ~~L~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~w~~~~~~~~~~~~~~~~~~~~~l~~~~~~rrWs~sigQyNLl~ 439 (831)
+++.|+..... +. ..|+.. ..+.+.+. ..+|||++|||||||+
T Consensus 313 v~l~~~~~~~~----------~~---~~~~~~-----------------------~~~~~~~~-~~~rWs~~~gQynll~ 355 (362)
T PF13968_consen 313 VSLLCRYRPWW----------RH---SRWVRR-----------------------LIRCLRRW-SRRRWSNKMGQYNLLD 355 (362)
T ss_pred HHhhhccCccc----------cc---cHHHHH-----------------------HHHHhccc-ccCCcCCccccHHHHH
Confidence 99987531110 00 111111 11112222 4567999999999999
Q ss_pred HhhhcC
Q 040228 440 FCLRRR 445 (831)
Q Consensus 440 ~c~~~~ 445 (831)
+|++++
T Consensus 356 ~c~~~~ 361 (362)
T PF13968_consen 356 SCLRER 361 (362)
T ss_pred HHHhCC
Confidence 999875
No 2
>PF04578 DUF594: Protein of unknown function, DUF594; InterPro: IPR007658 This is a family of uncharacterised proteins.
Probab=99.91 E-value=7.7e-25 Score=178.28 Aligned_cols=49 Identities=53% Similarity=1.148 Sum_probs=48.5
Q ss_pred hHHHHHHHHHHHHHhHhccCCCHHHHHHHhcCCcchHHHHHHHHHhcCC
Q 040228 764 DRWELMSKVWLELLSYAATHCDPRAHAQLVSSGGELITFVWLLMAHFGL 812 (831)
Q Consensus 764 ~~WevIa~VWvEmL~YaA~~c~~~~HAkqLs~GGEliT~VWlL~~H~Gl 812 (831)
++|++|++||+|||||+||+|++++|||||++|||||||||+|++|+||
T Consensus 11 ~~w~~l~~vWvemL~y~A~~c~~~~Ha~~L~~GGE~iT~vW~L~~H~Gi 59 (59)
T PF04578_consen 11 DRWKVLADVWVEMLCYAAPSCSAESHAKQLSSGGEFITHVWLLLTHAGI 59 (59)
T ss_pred HHHHHHHHHHHHHHHHHhccCCHHHHHHHHccCchHHHHHHHHHHhcCC
Confidence 8999999999999999999999999999999999999999999999997
No 3
>TIGR02587 putative integral membrane protein TIGR02587. Members of this family are found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighborhood. This family, as defined, includes some members of COG4711 but is narrower and strictly bacterial. Members appear to span the membrane seven times.
Probab=29.68 E-value=1e+02 Score=33.40 Aligned_cols=50 Identities=16% Similarity=0.134 Sum_probs=40.8
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHcCccCCCCchhHHHHHHHHHhhhhhHHHHHhhHhhcc
Q 040228 15 DDWNIRGIILLSLSLQTFLILFAPSRKGSGNKLLVMLIWSAYLLADWAANYAVGLISDS 73 (831)
Q Consensus 15 ~eW~ir~LVl~Sl~lQ~~L~~~~~~Rrr~~~~~lr~~lWlAYl~ad~vA~YaLG~Ls~~ 73 (831)
+-|.+=.++.+|+.+-+.+.+.+++||+... ..- ..|.+..|++|.+-+.
T Consensus 35 ~p~~lllll~~sl~i~~~lv~~~GFr~~~~~--~~~-------i~eti~ay~Iglv~S~ 84 (271)
T TIGR02587 35 KPRRLVLLIALMFPVLFLLNYTEGFRKRKRV--REA-------VIDTVEAMAIGFVCSA 84 (271)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhccccccch--HHH-------HHHHHHHHHHHHHHHH
Confidence 6788889999999999999999999998433 322 4599999999987753
No 4
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=22.78 E-value=38 Score=31.70 Aligned_cols=20 Identities=30% Similarity=0.519 Sum_probs=17.2
Q ss_pred hHHHHHhhcCCCcccccccc
Q 040228 94 PTFLLLHLGGPDTITALALE 113 (831)
Q Consensus 94 APfLLlHLGG~DtITAySlE 113 (831)
|..||++|||.++||+-.|+
T Consensus 5 aAylL~~l~g~~~pTa~dI~ 24 (109)
T cd05833 5 AAYLLAVLGGNASPSAADVK 24 (109)
T ss_pred HHHHHHHHcCCCCCCHHHHH
Confidence 67899999999999997654
No 5
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=19.38 E-value=50 Score=31.11 Aligned_cols=20 Identities=25% Similarity=0.488 Sum_probs=17.0
Q ss_pred hHHHHHhhcCCCcccccccc
Q 040228 94 PTFLLLHLGGPDTITALALE 113 (831)
Q Consensus 94 APfLLlHLGG~DtITAySlE 113 (831)
|..||++|||.++||+-.|+
T Consensus 7 aAYlL~~lgG~~~pTaddI~ 26 (112)
T PTZ00373 7 AAYLMCVLGGNENPTKKEVK 26 (112)
T ss_pred HHHHHHHHcCCCCCCHHHHH
Confidence 67899999999999986554
No 6
>PF09323 DUF1980: Domain of unknown function (DUF1980); InterPro: IPR015402 Members of this occur in gene pairs with members of PF03773 from PFAM. The N-terminal region contains several predicted transmembrane helix regions while the few invariant residues (G, CxxD, and W) occur in the C-terminal region. Members of this family are found in a set of prokaryotic hypothetical proteins. Their exact function has not, as yet, been defined.
Probab=17.99 E-value=4.4e+02 Score=26.65 Aligned_cols=55 Identities=16% Similarity=0.130 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHcC-ccCCCCchhHHHHHHHHHhhhhhHHHHHhhHhhccC
Q 040228 19 IRGIILLSLSLQTFLILFAP-SRKGSGNKLLVMLIWSAYLLADWAANYAVGLISDSQ 74 (831)
Q Consensus 19 ir~LVl~Sl~lQ~~L~~~~~-~Rrr~~~~~lr~~lWlAYl~ad~vA~YaLG~Ls~~~ 74 (831)
||+|+|+.|+..++-+...+ .-++-.++..-+ ++.|=.+.=.+|.+.+-.+.+..
T Consensus 2 ir~liL~~~~~l~~~l~~sG~i~~YI~P~~~~~-~~~a~i~l~ilai~q~~~~~~~~ 57 (182)
T PF09323_consen 2 IRFLILLGFGILLFYLILSGKILLYIHPRYIPL-LYFAAILLLILAIVQLWRWFRPK 57 (182)
T ss_pred HHHHHHHHHHHHHHHHHHhCcHHHHhCccHHHH-HHHHHHHHHHHHHHHHHHHHhcc
Confidence 78999999988877555554 455555554444 44444444445556665555543
No 7
>PF00367 PTS_EIIB: phosphotransferase system, EIIB; InterPro: IPR018113 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar. This entry covers the phosphorylation site of EIIB domains. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity; PDB: 3IPJ_B 3BP3_A 1O2F_B 3BP8_C 1IBA_A.
Probab=15.46 E-value=98 Score=22.86 Aligned_cols=16 Identities=31% Similarity=0.574 Sum_probs=12.7
Q ss_pred HHHHHhhcCCCccccc
Q 040228 95 TFLLLHLGGPDTITAL 110 (831)
Q Consensus 95 PfLLlHLGG~DtITAy 110 (831)
.-++-++||.+||+..
T Consensus 2 ~~il~~lGG~~NI~~v 17 (35)
T PF00367_consen 2 KQILEALGGKENIKSV 17 (35)
T ss_dssp HHHHHHCTTCCCEEEE
T ss_pred hHHHHHhCCHHHHHHH
Confidence 3467889999999874
No 8
>COG3336 Predicted membrane protein [Function unknown]
Probab=12.94 E-value=2e+02 Score=31.64 Aligned_cols=82 Identities=23% Similarity=0.251 Sum_probs=49.7
Q ss_pred HhhHHHHHHHHHHHHHHHHHHcCcc-CCCCch--hHHHHHHHHHhhhhhHHH----HHhhHhhccCCCCCCCCCCCCccc
Q 040228 16 DWNIRGIILLSLSLQTFLILFAPSR-KGSGNK--LLVMLIWSAYLLADWAAN----YAVGLISDSQGDNPGPSDPKHNNQ 88 (831)
Q Consensus 16 eW~ir~LVl~Sl~lQ~~L~~~~~~R-rr~~~~--~lr~~lWlAYl~ad~vA~----YaLG~Ls~~~~~~~~~~~~~~~~~ 88 (831)
-|+-+.+..+-...-..+.+.+..| ||+.+. .-|.+.|+.=+.+-+.|+ ++.|+...+-- =-++.
T Consensus 12 ~w~~~l~l~l~~i~~~~~y~~~~~r~rr~g~~wp~~r~~~~~lG~val~~a~~Spv~~~g~~mfs~H--------Ma~hm 83 (299)
T COG3336 12 MWRFDLLLGLLGIVLLYFYIAGRVRSRREGISWPLGRVILWLLGCVALYGAVGSPVRAYGHAMFSLH--------MAEHM 83 (299)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHHhCCchhhhccccHHHH--------HHHHH
Confidence 4677777666666666666666655 444455 588998876655554443 44444333210 02466
Q ss_pred ccchhhHHHHHhhcCCCc
Q 040228 89 LLAFWPTFLLLHLGGPDT 106 (831)
Q Consensus 89 L~~fWAPfLLlHLGG~Dt 106 (831)
+...=||-||+ ||+|=|
T Consensus 84 ~L~mvappLlV-Lg~P~~ 100 (299)
T COG3336 84 LLMMVAPPLLV-LGAPVT 100 (299)
T ss_pred HHHHHHHHHHH-HcchHH
Confidence 77788887766 999865
No 9
>KOG4788 consensus Members of chemokine-like factor super family and related proteins [Defense mechanisms]
Probab=11.79 E-value=5.9e+02 Score=25.68 Aligned_cols=31 Identities=23% Similarity=0.165 Sum_probs=26.1
Q ss_pred hhhHHHHHHHHHHHHHHhhhcccccccchhh
Q 040228 269 AEDSLKIIEVELNFIYEVFYTKVNVTHSWWG 299 (831)
Q Consensus 269 ~~~afkvvE~ELsfmYD~LYTKa~v~~t~~G 299 (831)
.....|++|++|+++-=++.+.....|...|
T Consensus 37 ~~G~Lki~e~~l~li~fi~i~~~~~~~~~~~ 67 (172)
T KOG4788|consen 37 LLGLLKILEIVLGLIIFICIASSLAYHLALA 67 (172)
T ss_pred hHhHHHHHHHHHHHHHheeeecCcccCCcce
Confidence 4678999999999999999999998774443
No 10
>COG1264 PtsG Phosphotransferase system IIB components [Carbohydrate transport and metabolism]
Probab=9.55 E-value=1.1e+02 Score=27.37 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=12.0
Q ss_pred hHHHHHhhcCCCccccc
Q 040228 94 PTFLLLHLGGPDTITAL 110 (831)
Q Consensus 94 APfLLlHLGG~DtITAy 110 (831)
|.-+|-+|||.|||+..
T Consensus 4 a~~il~~lGG~eNI~~~ 20 (88)
T COG1264 4 AKDILEALGGKENIVSV 20 (88)
T ss_pred HHHHHHHcCCHHHHhhh
Confidence 34567778888888764
Done!