Query 046032
Match_columns 464
No_of_seqs 159 out of 562
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 08:05:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046032hhsearch_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 1.4E-37 3E-42 320.4 11.0 123 51-178 1-123 (362)
2 PF04578 DUF594: Protein of un 99.9 2.4E-26 5.2E-31 176.5 5.2 58 399-457 2-59 (59)
3 TIGR02587 putative integral me 52.6 29 0.00064 34.9 5.6 49 14-71 35-83 (271)
4 PF12273 RCR: Chitin synthesis 27.9 33 0.00072 30.4 1.4 39 16-54 2-41 (130)
5 cd05833 Ribosomal_P2 Ribosomal 22.9 37 0.0008 29.5 0.8 20 90-109 5-24 (109)
6 PRK15071 lipopolysaccharide AB 22.3 4.4E+02 0.0095 26.9 8.7 81 12-99 267-348 (356)
7 PRK15120 lipopolysaccharide AB 21.4 3.6E+02 0.0079 27.8 7.9 81 12-99 262-342 (366)
8 PTZ00373 60S Acidic ribosomal 19.8 47 0.001 29.1 0.8 20 90-109 7-26 (112)
9 PF00367 PTS_EIIB: phosphotran 19.8 85 0.0018 21.6 1.9 16 91-106 2-17 (35)
10 PF09925 DUF2157: Predicted me 17.8 3.8E+02 0.0082 23.9 6.3 30 59-94 102-131 (145)
No 1
>PF13968 DUF4220: Domain of unknown function (DUF4220)
Probab=100.00 E-value=1.4e-37 Score=320.40 Aligned_cols=123 Identities=50% Similarity=0.841 Sum_probs=115.8
Q ss_pred HHHhhhhhhhHHHHHHHHhhhcccCCCCCCCCcchhhhHHHHHHHHhcCCCceeecccchhHHHHHHHHHHHHhhhheee
Q 046032 51 IWSAYFLADSAATFAIGLIAERAINSQTPTKSNELLVLWAPFLLLHLGGPDTITAVALEDNELWLRQLFGLIFQAGFTFY 130 (464)
Q Consensus 51 ~W~aY~~ad~~a~yalG~ls~~~~~~~~~~~~~~l~~~WApfLLlhLGg~DtITAysleDn~lW~RhlL~l~~Qv~~~~y 130 (464)
+|+||++||++|+||||+||+++. +.+++|++|||||||+||||||||||||+||||+|+||++++++|+++++|
T Consensus 1 lWlay~~sd~~a~Y~LG~l~~~~~-----~~~~~l~~~WAp~LLlhlgg~d~itaysleDn~lw~R~ll~ll~qv~~a~Y 75 (362)
T PF13968_consen 1 LWLAYLLSDSLATYALGLLQSSSS-----PFKSQLFPFWAPFLLLHLGGQDTITAYSLEDNELWLRHLLTLLVQVIWALY 75 (362)
T ss_pred CchHHhhhHHHHHHHHHHHhcCCC-----CCCcchhhhHHHHHHHHhCCCcceeeeecccchHHHHHHHHHHHHhhhhhe
Confidence 699999999999999999999862 268999999999999999999999999999999999999999999999999
Q ss_pred EEEeccCCCcchHHHHHHHHHHHHhhhhhHHHHHhhChhhhhhhhHHH
Q 046032 131 VFLLSLPGNKLFVPTILVFIAGIIKCFERTRAMYLASWEKFRESTIIE 178 (464)
Q Consensus 131 v~~~s~~~~~l~~~~~~~f~~gi~Ky~er~~al~~as~~~~~~s~~~~ 178 (464)
|++++|+|+.+.+|+++||++|++||+||+||+++||.+.+++++..+
T Consensus 76 v~~~~~~g~~l~~~~~lLfv~gi~K~~eR~~AL~~As~~~i~~s~~~~ 123 (362)
T PF13968_consen 76 VFYKSWSGSRLLAPAILLFVVGIIKYGERIWALRRASSRSIRSSMMGE 123 (362)
T ss_pred eeeeecccchHHHHHHHHHHHHHHHHHHHHHHHHccchhhhHHhhhhh
Confidence 999999887899999999999999999999999999998888776543
No 2
>PF04578 DUF594: Protein of unknown function, DUF594; InterPro: IPR007658 This is a family of uncharacterised proteins.
Probab=99.93 E-value=2.4e-26 Score=176.54 Aligned_cols=58 Identities=38% Similarity=0.834 Sum_probs=52.9
Q ss_pred HhccccCchhHHHHHHHHHHHHhhHhccCCccchhHHHHhccCcchHHHHHHHHHhcCC
Q 046032 399 LQSLDYLKDKKWEIVSKVWVELMSYAACHSRATRTHVEQVSNGGELFTFVWVLMAHFGL 457 (464)
Q Consensus 399 L~~~~~~~~~~W~~i~~vWvEmL~YaA~~c~~~~~HAkqL~~GGEllT~VWlL~~H~Gi 457 (464)
|++...+++++|++|++||+|||||+||+|+++ +|||||++|||||||||+|++|+||
T Consensus 2 L~~~~~~~~~~w~~l~~vWvemL~y~A~~c~~~-~Ha~~L~~GGE~iT~vW~L~~H~Gi 59 (59)
T PF04578_consen 2 LLEEEEDEEDRWKVLADVWVEMLCYAAPSCSAE-SHAKQLSSGGEFITHVWLLLTHAGI 59 (59)
T ss_pred hhhHccChhHHHHHHHHHHHHHHHHHhccCCHH-HHHHHHccCchHHHHHHHHHHhcCC
Confidence 443333678999999999999999999999999 9999999999999999999999997
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=52.63 E-value=29 Score=34.87 Aligned_cols=49 Identities=16% Similarity=0.192 Sum_probs=40.1
Q ss_pred hHhhHHHHHHHHHHHHHHHHHhcCccccCchhHHHHHHHHhhhhhhhHHHHHHHHhhh
Q 046032 14 DNWNIRGVILFSLLLQTVLILLAPLRKGMGYKLIILLIWSAYFLADSAATFAIGLIAE 71 (464)
Q Consensus 14 ~eW~i~~lVl~S~~lq~~L~~~~~~Rr~~~~~~l~~~~W~aY~~ad~~a~yalG~ls~ 71 (464)
+-|.+=+++.+|+.+-+.+.+.+++||+.. +..- ..|.+.+|++|.+.+
T Consensus 35 ~p~~lllll~~sl~i~~~lv~~~GFr~~~~--~~~~-------i~eti~ay~Iglv~S 83 (271)
T TIGR02587 35 KPRRLVLLIALMFPVLFLLNYTEGFRKRKR--VREA-------VIDTVEAMAIGFVCS 83 (271)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhccccccc--hHHH-------HHHHHHHHHHHHHHH
Confidence 578999999999999999999999999843 2332 458899999998753
No 4
>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=27.86 E-value=33 Score=30.36 Aligned_cols=39 Identities=23% Similarity=0.370 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhcCccccCc-hhHHHHHHHHh
Q 046032 16 WNIRGVILFSLLLQTVLILLAPLRKGMG-YKLIILLIWSA 54 (464)
Q Consensus 16 W~i~~lVl~S~~lq~~L~~~~~~Rr~~~-~~~l~~~~W~a 54 (464)
|-|=+++++.+++-+|++++-++||++. ..-+..--|++
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR~r~G~~P~~gt~w~~ 41 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRRRRRGLQPIYGTRWMA 41 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCCceecC
Confidence 6566666666666666666555555443 23345555655
No 5
>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=22.92 E-value=37 Score=29.55 Aligned_cols=20 Identities=35% Similarity=0.571 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCceeecccc
Q 046032 90 APFLLLHLGGPDTITAVALE 109 (464)
Q Consensus 90 ApfLLlhLGg~DtITAysle 109 (464)
|..||++|||.++||+-.|+
T Consensus 5 aAylL~~l~g~~~pTa~dI~ 24 (109)
T cd05833 5 AAYLLAVLGGNASPSAADVK 24 (109)
T ss_pred HHHHHHHHcCCCCCCHHHHH
Confidence 67899999999999986654
No 6
>PRK15071 lipopolysaccharide ABC transporter permease; Provisional
Probab=22.33 E-value=4.4e+02 Score=26.93 Aligned_cols=81 Identities=7% Similarity=-0.167 Sum_probs=37.9
Q ss_pred HHhHhhHHHHHHHHHHHHHHHHHhcCccc-cCchhHHHHHHHHhhhhhhhHHHHHHHHhhhcccCCCCCCCCcchhhhHH
Q 046032 12 TWDNWNIRGVILFSLLLQTVLILLAPLRK-GMGYKLIILLIWSAYFLADSAATFAIGLIAERAINSQTPTKSNELLVLWA 90 (464)
Q Consensus 12 ~W~eW~i~~lVl~S~~lq~~L~~~~~~Rr-~~~~~~l~~~~W~aY~~ad~~a~yalG~ls~~~~~~~~~~~~~~l~~~WA 90 (464)
..-|+.-|...-++++..+++.+.-..+. |+.+...++.+=+.-..++++..-..+.+.... .=+...+.|+
T Consensus 267 ~~~~l~~r~a~Pl~~~~~~lla~~~~~~~~R~~~~~~~i~~~i~~~~~y~~~~~~~~~lg~~g-------~l~P~laaw~ 339 (356)
T PRK15071 267 YELAMWRKIFQPLSVAVMMLMALSFIFGPLRSVTMGARVVTGISFGFVFYVSNEIFGPLSLVY-------GIPPIIGALL 339 (356)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccchHHHHHHHHHHHHHHHHHHHHHHHHHhc-------CccHHHHHHH
Confidence 34455556665555555554444222222 222222333222222333433333444444332 2356789999
Q ss_pred HHHHHHhcC
Q 046032 91 PFLLLHLGG 99 (464)
Q Consensus 91 pfLLlhLGg 99 (464)
|.++.-+.|
T Consensus 340 P~iif~~~~ 348 (356)
T PRK15071 340 PSLLFLGIS 348 (356)
T ss_pred HHHHHHHHH
Confidence 988775543
No 7
>PRK15120 lipopolysaccharide ABC transporter permease LptF; Provisional
Probab=21.37 E-value=3.6e+02 Score=27.78 Aligned_cols=81 Identities=11% Similarity=0.159 Sum_probs=42.8
Q ss_pred HHhHhhHHHHHHHHHHHHHHHHHhcCccccCchhHHHHHHHHhhhhhhhHHHHHHHHhhhcccCCCCCCCCcchhhhHHH
Q 046032 12 TWDNWNIRGVILFSLLLQTVLILLAPLRKGMGYKLIILLIWSAYFLADSAATFAIGLIAERAINSQTPTKSNELLVLWAP 91 (464)
Q Consensus 12 ~W~eW~i~~lVl~S~~lq~~L~~~~~~Rr~~~~~~l~~~~W~aY~~ad~~a~yalG~ls~~~~~~~~~~~~~~l~~~WAp 91 (464)
..-|+.-|...-+++.+..++.+--+.+.++++...++++=..-..+++...-..+.+.... .=+...+.|.|
T Consensus 262 ~~~El~~Rla~Pl~~l~l~llavpl~~~~~R~g~~~~i~~~i~~~~~y~~l~~~~~~l~~~g-------~lpp~la~Wlp 334 (366)
T PRK15120 262 ARAELHWRLTLVFSVFIMALMVVPLSVVNPRQGRVLSMLPAMLLYLIFFLLQTSLRSNGGKG-------KLDPMIWMWAV 334 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcccCCccccchhHHHHHHHHHHHHHHHHHHHHHHHCC-------CCChHHHHHHH
Confidence 34566667777777777777766555544444444454433333333322222233333221 23567889999
Q ss_pred HHHHHhcC
Q 046032 92 FLLLHLGG 99 (464)
Q Consensus 92 fLLlhLGg 99 (464)
-++.-+.|
T Consensus 335 ~i~~~~~~ 342 (366)
T PRK15120 335 NLIYLALA 342 (366)
T ss_pred HHHHHHHH
Confidence 87765543
No 8
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=19.84 E-value=47 Score=29.12 Aligned_cols=20 Identities=30% Similarity=0.524 Sum_probs=16.8
Q ss_pred HHHHHHHhcCCCceeecccc
Q 046032 90 APFLLLHLGGPDTITAVALE 109 (464)
Q Consensus 90 ApfLLlhLGg~DtITAysle 109 (464)
|..||++|||.++||+-.|+
T Consensus 7 aAYlL~~lgG~~~pTaddI~ 26 (112)
T PTZ00373 7 AAYLMCVLGGNENPTKKEVK 26 (112)
T ss_pred HHHHHHHHcCCCCCCHHHHH
Confidence 67899999999999986553
No 9
>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=19.78 E-value=85 Score=21.63 Aligned_cols=16 Identities=38% Similarity=0.592 Sum_probs=12.9
Q ss_pred HHHHHHhcCCCceeec
Q 046032 91 PFLLLHLGGPDTITAV 106 (464)
Q Consensus 91 pfLLlhLGg~DtITAy 106 (464)
.-++-++||.+||+..
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 3467889999999875
No 10
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=17.77 E-value=3.8e+02 Score=23.90 Aligned_cols=30 Identities=30% Similarity=0.389 Sum_probs=18.4
Q ss_pred hhHHHHHHHHhhhcccCCCCCCCCcchhhhHHHHHH
Q 046032 59 DSAATFAIGLIAERAINSQTPTKSNELLVLWAPFLL 94 (464)
Q Consensus 59 d~~a~yalG~ls~~~~~~~~~~~~~~l~~~WApfLL 94 (464)
-.....-+|.+.+... ...+++..|+...+
T Consensus 102 ~ga~ialigQ~y~~~~------~~~~~~~~W~~~~l 131 (145)
T PF09925_consen 102 FGALIALIGQIYQTGA------DPWQLFLLWALLAL 131 (145)
T ss_pred HHHHHHHHHhHhcCCC------chHHHHHHHHHHHH
Confidence 4445555666655432 35689999987654
Done!