Query 048240
Match_columns 664
No_of_seqs 157 out of 579
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 07:41:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048240hhsearch_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 2.1E-76 4.5E-81 639.6 25.6 337 51-396 1-344 (362)
2 PF04578 DUF594: Protein of un 99.9 2.6E-26 5.6E-31 178.8 6.1 51 595-645 9-59 (59)
3 TIGR02587 putative integral me 33.2 1.4E+02 0.003 31.0 7.0 49 14-71 35-83 (271)
4 cd05833 Ribosomal_P2 Ribosomal 23.4 35 0.00075 30.5 0.7 19 91-109 5-23 (109)
5 PF09323 DUF1980: Domain of un 21.4 3.1E+02 0.0067 26.6 7.0 53 18-71 2-55 (182)
6 PTZ00373 60S Acidic ribosomal 20.3 44 0.00095 30.0 0.7 19 91-109 7-25 (112)
7 PF00367 PTS_EIIB: phosphotran 18.5 80 0.0017 22.1 1.5 17 91-107 1-17 (35)
8 COG3336 Predicted membrane pro 17.9 1.4E+02 0.003 31.4 3.7 83 15-104 12-101 (299)
9 PF02999 Borrelia_orfD: Borrel 14.2 1.2E+02 0.0025 26.3 1.8 13 502-514 22-34 (97)
10 PF12273 RCR: Chitin synthesis 12.1 1.2E+02 0.0025 27.8 1.4 26 16-41 2-27 (130)
No 1
>PF13968 DUF4220: Domain of unknown function (DUF4220)
Probab=100.00 E-value=2.1e-76 Score=639.62 Aligned_cols=337 Identities=39% Similarity=0.645 Sum_probs=286.6
Q ss_pred HHHHHhhhhhHHHHHhhhhccccccccCCCCCCccchhhhHHHHHHhhcCCCccccccccchHHHHHHHHHHHHHHhhhh
Q 048240 51 IWSAYLLADWAANFAVGLIGDTHRDNQASKPEKSDLLAFWAPFLLLHLGGPDTITAFALEDNELWIRHFFGFVFQAIAAV 130 (664)
Q Consensus 51 lWlAYl~ad~va~yaLG~l~~~~~~~~~~~~~~~~L~~fWApfLLlHLGG~DtITAysleDn~LW~Rhll~l~~Qv~~a~ 130 (664)
+|+||++||++|+||||+||+ ++ ++.+++|++|||||||+||||||||||||+|||++|+||++++++|+++++
T Consensus 1 lWlay~~sd~~a~Y~LG~l~~----~~--~~~~~~l~~~WAp~LLlhlgg~d~itaysleDn~lw~R~ll~ll~qv~~a~ 74 (362)
T PF13968_consen 1 LWLAYLLSDSLATYALGLLQS----SS--SPFKSQLFPFWAPFLLLHLGGQDTITAYSLEDNELWLRHLLTLLVQVIWAL 74 (362)
T ss_pred CchHHhhhHHHHHHHHHHHhc----CC--CCCCcchhhhHHHHHHHHhCCCcceeeeecccchHHHHHHHHHHHHhhhhh
Confidence 699999999999999999999 22 478999999999999999999999999999999999999999999999999
Q ss_pred eeeeeccCCCcchHHHHHHHHHhHhhhhHHHHHHHhcCchhHhhccccCCCCCChhHHHHHHhhhhhhccCCccccccCC
Q 048240 131 YIFLLSLPGNKLFIPTILTFAAGLIKYFERTCALYFASLDRFRDSMLQEPDPGLNYVKIMEEYASWIEAKIPTKIFMLPE 210 (664)
Q Consensus 131 Yv~~~s~~~~~l~~~~~lmfv~GiiKy~ER~wAL~~as~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e 210 (664)
||++++|+|+.+.+|+++||++|++||+||+|||++||.+.+++||..++++++++...|++|++..+.+.+.+....++
T Consensus 75 Yv~~~~~~g~~l~~~~~lLfv~gi~K~~eR~~AL~~As~~~i~~s~~~~~~~~~~~~~~m~~~~~~~~~~~~~~~~~~~~ 154 (362)
T PF13968_consen 75 YVFYKSWSGSRLLAPAILLFVVGIIKYGERIWALRRASSRSIRSSMMGEPDPGPNYAETMEGYKYLVEEEYPKEIRILKE 154 (362)
T ss_pred eeeeeecccchHHHHHHHHHHHHHHHHHHHHHHHHccchhhhHHhhhhhhcccccchhhccccchhccccccceeeeccc
Confidence 99999998888999999999999999999999999999999999999999999999899999988665554443322111
Q ss_pred CCCC-CCCCCCCCc----ccccccCcHHHHHHHhhhhHHHhhhhhccccccccchhhhhhhccC-ChhhHHHHHHHHHHH
Q 048240 211 PTRK-PIFNDTDNQ----TKVVEFDDLDVVHRACYFSKIFKGLLVDIIFSFRERDESRHFFYGR-KPEEAYRIIEVELNL 284 (664)
Q Consensus 211 ~~~~-~~~~~~~~~----~~~~~~~~~~~l~~A~~lf~~~k~~f~D~~~~~~~~~~~~~~~~~~-~~~~afkvvE~ELsf 284 (664)
.+.. .+..+++.+ ...++.++++++|.||++|+++|++|+|++++++++.+++++|.+. +++++|||+|+||||
T Consensus 155 ~~~~~~~~~~~v~~~~~~~~~~~~~~~k~l~ls~aLf~llrr~f~d~~~~~~~~~~~~~~~~~l~~~~~af~vie~ELsf 234 (362)
T PF13968_consen 155 EDLETLVTVDKVWESLLDSREESDPELKDLCLSFALFKLLRRRFVDFPLSESGRLKTRDFFRGLDDAERAFRVIEMELSF 234 (362)
T ss_pred cccccCCccceecccccchhcccccHHHHHHHHHHHHHHHHhhhhCCCcchhhhHHHHHHHhccccHHHHHHHHHHHHHH
Confidence 1111 001111110 1123556788999999999999999999999999999999999876 489999999999999
Q ss_pred HHHhhcccchhhccchhHHHHHHHHHHHHHHHhhheecc-ccCCCCccchhHHHHHHHHHHHHHHHHHHHHHhhhhhHHH
Q 048240 285 FYETFYTKVEVIRSAAGYIMRFLSFGSVVVALSFFHLNV-EKHGFDNFDVRVTYILIFGAICLDTIALFMLVFSDRTFAA 363 (664)
Q Consensus 285 myD~lYTK~~vi~t~~g~~~r~is~~~~~~A~~LF~~~~-~k~~~~~~Dv~ITyvLl~gai~lE~~s~~~~l~S~Wt~~~ 363 (664)
|||+||||++|+||+.|+++|+++++++++|+++|...+ ++++|+++||+|||+|++|++++|+++++++++|+||+++
T Consensus 235 ~yD~~YTk~~v~~~~~~~~~~~~s~~~~~~a~~lf~~~~~~~~~~~~~Dv~ITy~Ll~~~~~lE~~~~~~~~~S~W~~v~ 314 (362)
T PF13968_consen 235 LYDYLYTKAPVVHTWLGLFLRVISLLSTVAALVLFWLSHKKKHGYSRVDVIITYVLLVGAVLLEVWSLLVYLFSDWTKVS 314 (362)
T ss_pred HHHheeccceeeeeccchHHHHHHHHHHHHHHHHhhccccccccCCccCeehHHHHHHHHHHHHHHHHHHHHcCccHHHH
Confidence 999999999999999999999999999999999999864 2478999999999999999999999999999999999999
Q ss_pred hhccccccccCCCCchhhhhHHHhhhccCCCcc
Q 048240 364 LKKTEHESKSSGRKKPGMATALGWFFALKRPRW 396 (664)
Q Consensus 364 l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~rW 396 (664)
+.|++..... .++....+++++.+.+++||
T Consensus 315 l~~~~~~~~~---~~~~~~~~~~~~~~~~~~rW 344 (362)
T PF13968_consen 315 LLCRYRPWWR---HSRWVRRLIRCLRRWSRRRW 344 (362)
T ss_pred hhhccCcccc---ccHHHHHHHHHhcccccCCc
Confidence 9998733211 12223445555555566679
No 2
>PF04578 DUF594: Protein of unknown function, DUF594; InterPro: IPR007658 This is a family of uncharacterised proteins.
Probab=99.93 E-value=2.6e-26 Score=178.78 Aligned_cols=51 Identities=53% Similarity=1.111 Sum_probs=49.3
Q ss_pred hhhHHHHHHHHHHHHHhhhcCCCChHHHHHHhcCCCchHHHHHHHHHhcCC
Q 048240 595 QKSKWKLISKMWVELSSYAASHCDARSHAQQLSKGGELITFVWLLMSHFGL 645 (664)
Q Consensus 595 ~~~~W~~ia~vWvEmL~YaA~~c~~~~Hak~L~~GGEfiT~VWlLl~H~Gi 645 (664)
++++|++|++||+|||||+||+|++++|||||++|||||||||+|++|+||
T Consensus 9 ~~~~w~~l~~vWvemL~y~A~~c~~~~Ha~~L~~GGE~iT~vW~L~~H~Gi 59 (59)
T PF04578_consen 9 EEDRWKVLADVWVEMLCYAAPSCSAESHAKQLSSGGEFITHVWLLLTHAGI 59 (59)
T ss_pred hhHHHHHHHHHHHHHHHHHhccCCHHHHHHHHccCchHHHHHHHHHHhcCC
Confidence 347999999999999999999999999999999999999999999999997
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=33.24 E-value=1.4e+02 Score=31.04 Aligned_cols=49 Identities=16% Similarity=0.162 Sum_probs=41.1
Q ss_pred hhhhHHHHHHHHHHHHHHHHHhcCcccCchhhHHHHHHHHHHhhhhhHHHHHhhhhcc
Q 048240 14 DNWNIRGIILFSLFLQTILILFAPFRKSTANRLMIMLIWSAYLLADWAANFAVGLIGD 71 (664)
Q Consensus 14 ~~w~i~~LVl~S~~lq~~L~~~~~~Rrr~~~~~lr~~lWlAYl~ad~va~yaLG~l~~ 71 (664)
+-|.+=.++.+|+.+-+.+.+.+++||+... ... ..|.+..|++|.+.+
T Consensus 35 ~p~~lllll~~sl~i~~~lv~~~GFr~~~~~--~~~-------i~eti~ay~Iglv~S 83 (271)
T TIGR02587 35 KPRRLVLLIALMFPVLFLLNYTEGFRKRKRV--REA-------VIDTVEAMAIGFVCS 83 (271)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhccccccch--HHH-------HHHHHHHHHHHHHHH
Confidence 6788999999999999999999999998432 222 459999999998887
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=23.43 E-value=35 Score=30.51 Aligned_cols=19 Identities=37% Similarity=0.538 Sum_probs=16.6
Q ss_pred HHHHHHhhcCCCccccccc
Q 048240 91 APFLLLHLGGPDTITAFAL 109 (664)
Q Consensus 91 ApfLLlHLGG~DtITAysl 109 (664)
|..||++|||.++||+-.|
T Consensus 5 aAylL~~l~g~~~pTa~dI 23 (109)
T cd05833 5 AAYLLAVLGGNASPSAADV 23 (109)
T ss_pred HHHHHHHHcCCCCCCHHHH
Confidence 6689999999999998664
No 5
>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=21.41 E-value=3.1e+02 Score=26.57 Aligned_cols=53 Identities=19% Similarity=0.095 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHhcC-cccCchhhHHHHHHHHHHhhhhhHHHHHhhhhcc
Q 048240 18 IRGIILFSLFLQTILILFAP-FRKSTANRLMIMLIWSAYLLADWAANFAVGLIGD 71 (664)
Q Consensus 18 i~~LVl~S~~lq~~L~~~~~-~Rrr~~~~~lr~~lWlAYl~ad~va~yaLG~l~~ 71 (664)
||+|+|+.|+..++-+...+ .-+..+++ ..-+++.|=.+.=.+|++.+-.+..
T Consensus 2 ir~liL~~~~~l~~~l~~sG~i~~YI~P~-~~~~~~~a~i~l~ilai~q~~~~~~ 55 (182)
T PF09323_consen 2 IRFLILLGFGILLFYLILSGKILLYIHPR-YIPLLYFAAILLLILAIVQLWRWFR 55 (182)
T ss_pred HHHHHHHHHHHHHHHHHHhCcHHHHhCcc-HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 78999999988777555544 44454444 4444444444444455555555554
No 6
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=20.33 E-value=44 Score=30.01 Aligned_cols=19 Identities=32% Similarity=0.503 Sum_probs=16.3
Q ss_pred HHHHHHhhcCCCccccccc
Q 048240 91 APFLLLHLGGPDTITAFAL 109 (664)
Q Consensus 91 ApfLLlHLGG~DtITAysl 109 (664)
|..||++|||.++||+-.|
T Consensus 7 aAYlL~~lgG~~~pTaddI 25 (112)
T PTZ00373 7 AAYLMCVLGGNENPTKKEV 25 (112)
T ss_pred HHHHHHHHcCCCCCCHHHH
Confidence 6789999999999998654
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=18.46 E-value=80 Score=22.09 Aligned_cols=17 Identities=35% Similarity=0.540 Sum_probs=13.1
Q ss_pred HHHHHHhhcCCCccccc
Q 048240 91 APFLLLHLGGPDTITAF 107 (664)
Q Consensus 91 ApfLLlHLGG~DtITAy 107 (664)
|.-++-++||.++|+..
T Consensus 1 A~~il~~lGG~~NI~~v 17 (35)
T PF00367_consen 1 AKQILEALGGKENIKSV 17 (35)
T ss_dssp HHHHHHHCTTCCCEEEE
T ss_pred ChHHHHHhCCHHHHHHH
Confidence 34467889999999874
No 8
>COG3336 Predicted membrane protein [Function unknown]
Probab=17.94 E-value=1.4e+02 Score=31.38 Aligned_cols=83 Identities=22% Similarity=0.229 Sum_probs=47.7
Q ss_pred hhhHHHHHHHHHHHHHHHHHhcCccc-Cchhh--HHHHHHHHHHhhhhhHHH----HHhhhhccccccccCCCCCCccch
Q 048240 15 NWNIRGIILFSLFLQTILILFAPFRK-STANR--LMIMLIWSAYLLADWAAN----FAVGLIGDTHRDNQASKPEKSDLL 87 (664)
Q Consensus 15 ~w~i~~LVl~S~~lq~~L~~~~~~Rr-r~~~~--~lr~~lWlAYl~ad~va~----yaLG~l~~~~~~~~~~~~~~~~L~ 87 (664)
-|+-+.+..+-...-..+.+.+..|. |+.+. .-|.+.|+.=..+-+.|+ ++.|+... +. .=.+|.+.
T Consensus 12 ~w~~~l~l~l~~i~~~~~y~~~~~r~rr~g~~wp~~r~~~~~lG~val~~a~~Spv~~~g~~mf----s~--HMa~hm~L 85 (299)
T COG3336 12 MWRFDLLLGLLGIVLLYFYIAGRVRSRREGISWPLGRVILWLLGCVALYGAVGSPVRAYGHAMF----SL--HMAEHMLL 85 (299)
T ss_pred hcchHHHHHHHHHHHHHHHHHHHHHhcccCCcccHHHHHHHHHHHHHHHHHhCCchhhhccccH----HH--HHHHHHHH
Confidence 46666666655555555555555553 44444 678999976555554432 34433322 00 01246677
Q ss_pred hhhHHHHHHhhcCCCcc
Q 048240 88 AFWAPFLLLHLGGPDTI 104 (664)
Q Consensus 88 ~fWApfLLlHLGG~DtI 104 (664)
-.=||.||+ ||+|=|.
T Consensus 86 ~mvappLlV-Lg~P~~l 101 (299)
T COG3336 86 MMVAPPLLV-LGAPVTL 101 (299)
T ss_pred HHHHHHHHH-HcchHHH
Confidence 777888777 8888653
No 9
>PF02999 Borrelia_orfD: Borrelia orf-D family; InterPro: IPR004248 Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames called Orf-A, Orf-B, Orf-C and Orf-D. This entry represents the putative Orf-D protein, which has no known function [].
Probab=14.18 E-value=1.2e+02 Score=26.32 Aligned_cols=13 Identities=46% Similarity=0.690 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHhh
Q 048240 502 RLLSDYMLYLLIT 514 (664)
Q Consensus 502 ~~LSnYmmYLl~~ 514 (664)
.+||+|.|||.+.
T Consensus 22 A~L~~YvmyL~~f 34 (97)
T PF02999_consen 22 AQLSDYVMYLNTF 34 (97)
T ss_pred HHHHHHHHHHHHH
Confidence 3699999999865
No 10
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=12.13 E-value=1.2e+02 Score=27.80 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=12.8
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCcccC
Q 048240 16 WNIRGIILFSLFLQTILILFAPFRKS 41 (664)
Q Consensus 16 w~i~~LVl~S~~lq~~L~~~~~~Rrr 41 (664)
|-|=+++++.+++-+|++++-+.||+
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR~ 27 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRRR 27 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444555555555555544444443
Done!