Query 041828
Match_columns 294
No_of_seqs 126 out of 391
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 11:03:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041828hhsearch_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 2.8E-67 6.2E-72 503.1 17.4 235 41-288 1-319 (362)
2 cd05833 Ribosomal_P2 Ribosomal 29.0 25 0.00055 28.5 0.8 21 88-108 5-25 (109)
3 PTZ00373 60S Acidic ribosomal 24.7 34 0.00073 28.0 0.8 21 88-108 7-27 (112)
4 PF12550 GCR1_C: Transcription 22.5 56 0.0012 24.6 1.6 18 2-19 4-21 (81)
5 PF00367 PTS_EIIB: phosphotran 21.8 77 0.0017 20.3 1.9 17 89-105 2-18 (35)
6 PRK10144 formate-dependent nit 18.8 76 0.0017 26.5 1.8 21 77-97 95-116 (126)
7 TIGR03147 cyt_nit_nrfF cytochr 17.6 85 0.0018 26.2 1.8 21 77-97 95-116 (126)
8 COG1264 PtsG Phosphotransferas 10.9 1E+02 0.0022 23.9 0.4 17 88-104 4-20 (88)
9 PRK15071 lipopolysaccharide AB 10.9 9.9E+02 0.022 22.4 7.4 14 83-96 334-347 (356)
10 PF13945 NST1: Salt tolerance 10.7 1.7E+02 0.0038 26.1 1.9 19 195-213 151-169 (190)
No 1
>PF13968 DUF4220: Domain of unknown function (DUF4220)
Probab=100.00 E-value=2.8e-67 Score=503.05 Aligned_cols=235 Identities=42% Similarity=0.732 Sum_probs=212.8
Q ss_pred HHHHHhhhhhHHHHHhhhhhcccCCCCcccccCCCCCCCcchhhhHHHHHHHHHhcCCCcceeeccccccccchhhhhhh
Q 041828 41 IWSAYLIADWAANFGVGLITERARDTPTAEYSSKQQPAENNELLAFWATFFMLHLGGPDTITAFALEDNELCLRHLFGFI 120 (294)
Q Consensus 41 lWlAY~~ad~~a~yaLG~l~~~~~~~~~~~~~~~~~~~~~~~L~~~WApfLLlhLGg~DtITAysleDn~lw~R~~l~l~ 120 (294)
+|+||+++|++|+|+||+||+++ +|.+++|++|||||||+||||||||||||+||||+|+||+++++
T Consensus 1 lWlay~~sd~~a~Y~LG~l~~~~-------------~~~~~~l~~~WAp~LLlhlgg~d~itaysleDn~lw~R~ll~ll 67 (362)
T PF13968_consen 1 LWLAYLLSDSLATYALGLLQSSS-------------SPFKSQLFPFWAPFLLLHLGGQDTITAYSLEDNELWLRHLLTLL 67 (362)
T ss_pred CchHHhhhHHHHHHHHHHHhcCC-------------CCCCcchhhhHHHHHHHHhCCCcceeeeecccchHHHHHHHHHH
Confidence 69999999999999999999875 25789999999999999999999999999999999999999999
Q ss_pred eeeeeeeEEEEeeCCCCcchhHHHHHHHHHHHhhhhHHHHHHHhchhhhhhcccc-------------C-----------
Q 041828 121 FQAVAAVYIFLTSLPGNKLFFPTALVFIAGTIKYFERIRALYLASMEKFRDSALR-------------G----------- 176 (294)
Q Consensus 121 ~Qv~~a~yv~~~s~~~~~l~~~~~lmfv~GiiKy~er~~aL~~as~~~~~~sm~~-------------g----------- 176 (294)
+|+++++||++++|+|+.+..|+++||++|++||+||+|||++||.+.+++||.+ |
T Consensus 68 ~qv~~a~Yv~~~~~~g~~l~~~~~lLfv~gi~K~~eR~~AL~~As~~~i~~s~~~~~~~~~~~~~~m~~~~~~~~~~~~~ 147 (362)
T PF13968_consen 68 VQVIWALYVFYKSWSGSRLLAPAILLFVVGIIKYGERIWALRRASSRSIRSSMMGEPDPGPNYAETMEGYKYLVEEEYPK 147 (362)
T ss_pred HHhhhhheeeeeecccchHHHHHHHHHHHHHHHHHHHHHHHHccchhhhHHhhhhhhcccccchhhccccchhccccccc
Confidence 9999999999999988889999999999999999999999999999998888764 1
Q ss_pred cc-----------------c------c-------cccccccc-----------------cc------------hHHHHHH
Q 041828 177 EV-----------------E------H-------LKRIRSLQ-----------------KK------------NEKALGI 197 (294)
Q Consensus 177 eI-----------------~------~-------~~l~lsf~-----------------~r------------~~~af~v 197 (294)
++ + + .++|+||+ +| +|+||||
T Consensus 148 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~k~l~ls~aLf~llrr~f~d~~~~~~~~~~~~~~~~~l~~~~~af~v 227 (362)
T PF13968_consen 148 EIRILKEEDLETLVTVDKVWESLLDSREESDPELKDLCLSFALFKLLRRRFVDFPLSESGRLKTRDFFRGLDDAERAFRV 227 (362)
T ss_pred eeeeccccccccCCccceecccccchhcccccHHHHHHHHHHHHHHHHhhhhCCCcchhhhHHHHHHHhccccHHHHHHH
Confidence 00 0 0 12666652 11 6999999
Q ss_pred HHHHHHHHHHhhhcCccccccchhHHHHHHHHHHHHHHHHHhhhhcc-CCCCCccchhHHHHHHHHHHHHHHHHHHHHHc
Q 041828 198 IEVELNLVYEVLHTKIQVTHSVLAIILRFICFCSVVAALSVFHFQVE-KHGFNEFDVCVTYTLFLGAIALDIIAFFKLVF 276 (294)
Q Consensus 198 ie~ELsf~yD~lYTK~~v~~t~~g~~lr~~s~~~~~~A~~lF~~~~~-k~~~~~~Dv~ITyvLL~gai~LE~~s~~~~l~ 276 (294)
+|+||+|+||++|||++++|++.|+++|+++++++++|+++|...++ +++|+++|++|||+|++|++++|+++++.+++
T Consensus 228 ie~ELsf~yD~~YTk~~v~~~~~~~~~~~~s~~~~~~a~~lf~~~~~~~~~~~~~Dv~ITy~Ll~~~~~lE~~~~~~~~~ 307 (362)
T PF13968_consen 228 IEMELSFLYDYLYTKAPVVHTWLGLFLRVISLLSTVAALVLFWLSHKKKHGYSRVDVIITYVLLVGAVLLEVWSLLVYLF 307 (362)
T ss_pred HHHHHHHHHHheeccceeeeeccchHHHHHHHHHHHHHHHHhhccccccccCCccCeehHHHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999999999999999999987532 47899999999999999999999999999999
Q ss_pred hHhHHHhhhcCC
Q 041828 277 SDWTFVALRNDD 288 (294)
Q Consensus 277 S~Wt~~~l~~~~ 288 (294)
||||+++|..+.
T Consensus 308 S~W~~v~l~~~~ 319 (362)
T PF13968_consen 308 SDWTKVSLLCRY 319 (362)
T ss_pred CccHHHHhhhcc
Confidence 999999887764
No 2
>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=29.02 E-value=25 Score=28.48 Aligned_cols=21 Identities=24% Similarity=0.468 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCCcceeecccc
Q 041828 88 ATFFMLHLGGPDTITAFALED 108 (294)
Q Consensus 88 ApfLLlhLGg~DtITAysleD 108 (294)
|..||++|||.+++|+-+|+-
T Consensus 5 aAylL~~l~g~~~pTa~dI~~ 25 (109)
T cd05833 5 AAYLLAVLGGNASPSAADVKK 25 (109)
T ss_pred HHHHHHHHcCCCCCCHHHHHH
Confidence 568999999999999977643
No 3
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=24.71 E-value=34 Score=27.97 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCCcceeecccc
Q 041828 88 ATFFMLHLGGPDTITAFALED 108 (294)
Q Consensus 88 ApfLLlhLGg~DtITAysleD 108 (294)
|..||.+|||.+++|+-+|+-
T Consensus 7 aAYlL~~lgG~~~pTaddI~k 27 (112)
T PTZ00373 7 AAYLMCVLGGNENPTKKEVKN 27 (112)
T ss_pred HHHHHHHHcCCCCCCHHHHHH
Confidence 678999999999999877653
No 4
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=22.47 E-value=56 Score=24.65 Aligned_cols=18 Identities=11% Similarity=0.612 Sum_probs=15.2
Q ss_pred CCCChhhHHHHHHHHHHH
Q 041828 2 LNPTPESIKKIWDNWNIR 19 (294)
Q Consensus 2 ~~~~~~~~~~~w~~w~lr 19 (294)
|.-.|.+|.++|+||..-
T Consensus 4 m~~~~~TV~dlw~Ew~~g 21 (81)
T PF12550_consen 4 MSRSIKTVYDLWREWFTG 21 (81)
T ss_pred cCCCCCcHHHHHHHHhcC
Confidence 566788999999999875
No 5
>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=21.83 E-value=77 Score=20.30 Aligned_cols=17 Identities=24% Similarity=0.460 Sum_probs=13.1
Q ss_pred HHHHHHhcCCCcceeec
Q 041828 89 TFFMLHLGGPDTITAFA 105 (294)
Q Consensus 89 pfLLlhLGg~DtITAys 105 (294)
.-++-++||.++|....
T Consensus 2 ~~il~~lGG~~NI~~v~ 18 (35)
T PF00367_consen 2 KQILEALGGKENIKSVT 18 (35)
T ss_dssp HHHHHHCTTCCCEEEEE
T ss_pred hHHHHHhCCHHHHHHHh
Confidence 34677899999998754
No 6
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=18.79 E-value=76 Score=26.47 Aligned_cols=21 Identities=24% Similarity=0.504 Sum_probs=13.9
Q ss_pred CCCcchhhhHH-HHHHHHHhcC
Q 041828 77 PAENNELLAFW-ATFFMLHLGG 97 (294)
Q Consensus 77 ~~~~~~L~~~W-ApfLLlhLGg 97 (294)
+|.+.....+| +|++++..||
T Consensus 95 Pp~~~~t~~LW~~P~~lll~g~ 116 (126)
T PRK10144 95 PPLTGQTLVLWALPVVLLLLMA 116 (126)
T ss_pred CCCCcchHHHHHHHHHHHHHHH
Confidence 34455566777 7888876665
No 7
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=17.57 E-value=85 Score=26.20 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=14.8
Q ss_pred CCCcchhhhHH-HHHHHHHhcC
Q 041828 77 PAENNELLAFW-ATFFMLHLGG 97 (294)
Q Consensus 77 ~~~~~~L~~~W-ApfLLlhLGg 97 (294)
+|.+.....+| +|++++.+|+
T Consensus 95 Pp~~~~t~~LW~~P~lll~~G~ 116 (126)
T TIGR03147 95 PPFKWQTLLLWLLPVLLLLLAF 116 (126)
T ss_pred CCCCcchHHHHHHHHHHHHHHH
Confidence 44455566777 8999888876
No 8
>COG1264 PtsG Phosphotransferase system IIB components [Carbohydrate transport and metabolism]
Probab=10.90 E-value=1e+02 Score=23.86 Aligned_cols=17 Identities=29% Similarity=0.456 Sum_probs=13.8
Q ss_pred HHHHHHHhcCCCcceee
Q 041828 88 ATFFMLHLGGPDTITAF 104 (294)
Q Consensus 88 ApfLLlhLGg~DtITAy 104 (294)
|.-+|-++||.|+|+..
T Consensus 4 a~~il~~lGG~eNI~~~ 20 (88)
T COG1264 4 AKDILEALGGKENIVSV 20 (88)
T ss_pred HHHHHHHcCCHHHHhhh
Confidence 45578889999999875
No 9
>PRK15071 lipopolysaccharide ABC transporter permease; Provisional
Probab=10.88 E-value=9.9e+02 Score=22.45 Aligned_cols=14 Identities=0% Similarity=-0.111 Sum_probs=10.9
Q ss_pred hhhHHHHHHHHHhc
Q 041828 83 LLAFWATFFMLHLG 96 (294)
Q Consensus 83 L~~~WApfLLlhLG 96 (294)
..+.|+|.++.-+.
T Consensus 334 ~laaw~P~iif~~~ 347 (356)
T PRK15071 334 IIGALLPSLLFLGI 347 (356)
T ss_pred HHHHHHHHHHHHHH
Confidence 67899998887543
No 10
>PF13945 NST1: Salt tolerance down-regulator
Probab=10.70 E-value=1.7e+02 Score=26.07 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHhhhcCc
Q 041828 195 LGIIEVELNLVYEVLHTKI 213 (294)
Q Consensus 195 f~vie~ELsf~yD~lYTK~ 213 (294)
--.||.||--+||.+|-..
T Consensus 151 ~~~ie~ele~ly~~~y~~l 169 (190)
T PF13945_consen 151 RTAIEEELERLYDAYYEEL 169 (190)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 3489999999999999643
Done!