Query 018668
Match_columns 352
No_of_seqs 64 out of 66
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 03:01:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018668.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018668hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03663 conserved hypothetic 61.5 17 0.00036 36.7 5.5 65 237-301 285-352 (439)
2 PF12273 RCR: Chitin synthesis 46.7 18 0.00039 30.4 2.6 28 272-299 2-29 (130)
3 cd03423 SirA SirA (also known 39.0 24 0.00053 26.5 2.1 20 189-208 5-24 (69)
4 cd03420 SirA_RHOD_Pry_redox Si 33.2 34 0.00075 25.8 2.1 18 190-207 6-23 (69)
5 cd03421 SirA_like_N SirA_like_ 32.4 35 0.00076 25.2 2.0 18 189-207 5-22 (67)
6 PF01206 TusA: Sulfurtransfera 29.8 45 0.00098 24.5 2.2 19 189-207 6-24 (70)
7 cd00291 SirA_YedF_YeeD SirA, Y 29.4 48 0.001 24.0 2.2 20 189-208 5-24 (69)
8 PRK10782 DL-methionine transpo 29.3 2.2E+02 0.0048 24.9 6.7 39 226-264 24-72 (217)
9 COG2011 AbcD ABC-type metal io 28.8 89 0.0019 30.2 4.4 57 227-283 30-107 (222)
10 PF06610 DUF1144: Protein of u 26.7 2E+02 0.0043 26.4 6.0 83 215-298 40-134 (143)
11 COG0425 SirA Predicted redox p 22.7 53 0.0011 26.1 1.5 18 190-207 12-29 (78)
12 cd03422 YedF YedF is a bacteri 22.6 68 0.0015 24.3 2.0 19 190-208 6-24 (69)
13 COG1183 PssA Phosphatidylserin 20.8 1.8E+02 0.004 27.7 4.9 60 230-291 168-227 (234)
14 PF04895 DUF651: Archaeal prot 20.4 23 0.00051 30.4 -0.9 43 198-245 17-61 (110)
No 1
>TIGR03663 conserved hypothetical protein TIGR03663. Members of this protein family, uncommon and rather sporadically distributed, are found almost always in the same genomes as members of family TIGR03662, and frequently as a nearby gene. Members show some N-terminal sequence similarity with Pfam family pfam02366, dolichyl-phosphate-mannose-protein mannosyltransferase. The few invariant residues in this family, found toward the N-terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three members may be found in a genome. The function is unknown.
Probab=61.45 E-value=17 Score=36.70 Aligned_cols=65 Identities=12% Similarity=0.055 Sum_probs=50.2
Q ss_pred hhhhccc---cccchhHHHHhhhhhhHHHHHHHhcCCChhHHHHHHHHHHHHHHhhhHHHHHHHHHhh
Q 018668 237 GIWREHT---EKFSVSWIVAVHAAVPFIAMMRKSVLMPKSAMAFTIAASVLGQVIGSRAERYRMKAVT 301 (352)
Q Consensus 237 GyWRe~t---kKFS~~WFlAVHapVPfIa~LRi~~glpw~~Ip~tIaAailGQ~IGgRl~R~r~k~~a 301 (352)
++|++.+ ++.+..-|+.+=.-+-++++.=...-+||..+|+.+.-+++.-.--+++.|++.++..
T Consensus 285 ~~~~~r~~~~~~~~~~~f~~~W~~~~~v~ys~~~~K~Pwy~l~~~~PlAll~g~~l~~~~~~~~~~~~ 352 (439)
T TIGR03663 285 GFLANRYATDKRRSFFLFACYWTLASLLFYSYIQEKVPWLVVHILVPLAILAAVGLSAVVLTGKKAIA 352 (439)
T ss_pred HHHHHHhcccCcchHHHHHHHHHHHHHHHHhhcccCCcchhHHHHHhHHHHHHHHHHHHHHhhhhhhc
Confidence 5677654 6677777777777777888887888999999999999888888777777776666433
No 2
>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=46.72 E-value=18 Score=30.39 Aligned_cols=28 Identities=21% Similarity=0.051 Sum_probs=22.6
Q ss_pred hhHHHHHHHHHHHHHHhhhHHHHHHHHH
Q 018668 272 KSAMAFTIAASVLGQVIGSRAERYRMKA 299 (352)
Q Consensus 272 w~~Ip~tIaAailGQ~IGgRl~R~r~k~ 299 (352)
|.++.++|++.+|-=+++.+..|||.+.
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~rRR~r~ 29 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHNRRRRRR 29 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 6778888888888888888888888775
No 3
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=38.98 E-value=24 Score=26.51 Aligned_cols=20 Identities=15% Similarity=0.398 Sum_probs=16.8
Q ss_pred CcccCcHHHHHHHHHHHhhh
Q 018668 189 MKYKCPPVVVAARAAIARTA 208 (352)
Q Consensus 189 ~k~~CP~aiVaaRAAlart~ 208 (352)
.-++||-+++.++.||..-.
T Consensus 5 ~G~~CP~P~i~~k~~l~~l~ 24 (69)
T cd03423 5 RGLRCPEPVMMLHKKVRKMK 24 (69)
T ss_pred cCCcCCHHHHHHHHHHHcCC
Confidence 35799999999999997653
No 4
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=33.24 E-value=34 Score=25.79 Aligned_cols=18 Identities=17% Similarity=0.497 Sum_probs=15.6
Q ss_pred cccCcHHHHHHHHHHHhh
Q 018668 190 KYKCPPVVVAARAAIART 207 (352)
Q Consensus 190 k~~CP~aiVaaRAAlart 207 (352)
-++||-+|+.++.||..-
T Consensus 6 G~~CP~Pvl~~kkal~~l 23 (69)
T cd03420 6 GLQCPGPILKLKKEIDKL 23 (69)
T ss_pred CCcCCHHHHHHHHHHHcC
Confidence 479999999999999754
No 5
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=32.43 E-value=35 Score=25.15 Aligned_cols=18 Identities=22% Similarity=0.504 Sum_probs=15.2
Q ss_pred CcccCcHHHHHHHHHHHhh
Q 018668 189 MKYKCPPVVVAARAAIART 207 (352)
Q Consensus 189 ~k~~CP~aiVaaRAAlart 207 (352)
.-+.||.+++.++.|| ..
T Consensus 5 rG~~CP~P~l~~k~al-~~ 22 (67)
T cd03421 5 RGLACPQPVIKTKKAL-EL 22 (67)
T ss_pred CCCCCCHHHHHHHHHH-hc
Confidence 3578999999999999 44
No 6
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=29.82 E-value=45 Score=24.53 Aligned_cols=19 Identities=21% Similarity=0.422 Sum_probs=15.5
Q ss_pred CcccCcHHHHHHHHHHHhh
Q 018668 189 MKYKCPPVVVAARAAIART 207 (352)
Q Consensus 189 ~k~~CP~aiVaaRAAlart 207 (352)
..+.||-+++.++.||...
T Consensus 6 rg~~CP~Pll~~~~~l~~l 24 (70)
T PF01206_consen 6 RGLSCPMPLLKAKKALKEL 24 (70)
T ss_dssp SS-STTHHHHHHHHHHHTS
T ss_pred CCCCCCHHHHHHHHHHHhc
Confidence 3578999999999999874
No 7
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=29.38 E-value=48 Score=24.00 Aligned_cols=20 Identities=20% Similarity=0.426 Sum_probs=16.8
Q ss_pred CcccCcHHHHHHHHHHHhhh
Q 018668 189 MKYKCPPVVVAARAAIARTA 208 (352)
Q Consensus 189 ~k~~CP~aiVaaRAAlart~ 208 (352)
..+.||.+++.++.||.+..
T Consensus 5 rg~~CP~Pl~~~~~~l~~l~ 24 (69)
T cd00291 5 RGLPCPLPVLKTKKALEKLK 24 (69)
T ss_pred cCCcCCHHHHHHHHHHhcCC
Confidence 35799999999999998743
No 8
>PRK10782 DL-methionine transporter permease subunit; Provisional
Probab=29.28 E-value=2.2e+02 Score=24.87 Aligned_cols=39 Identities=26% Similarity=0.571 Sum_probs=28.4
Q ss_pred HHHHHHhhccchhhhcccc----------ccchhHHHHhhhhhhHHHHH
Q 018668 226 GMLGMAANVPLGIWREHTE----------KFSVSWIVAVHAAVPFIAMM 264 (352)
Q Consensus 226 ~~la~llNIPfGyWRe~tk----------KFS~~WFlAVHapVPfIa~L 264 (352)
.++++++-+|+||+....+ +.-+..++.+-.+||.++.+
T Consensus 24 ~~l~~~ig~~lg~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~iP~~vll 72 (217)
T PRK10782 24 GFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTLSALVNIFRSIPFIILL 72 (217)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHhhHHHHHH
Confidence 3688889999999986443 23455566778899998764
No 9
>COG2011 AbcD ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]
Probab=28.84 E-value=89 Score=30.21 Aligned_cols=57 Identities=26% Similarity=0.356 Sum_probs=39.8
Q ss_pred HHHHHhhccchhhhcccccc----------chhHHHHhhhhhhHHHHH-------HHhcCCChhH----HHHHHHHHH
Q 018668 227 MLGMAANVPLGIWREHTEKF----------SVSWIVAVHAAVPFIAMM-------RKSVLMPKSA----MAFTIAASV 283 (352)
Q Consensus 227 ~la~llNIPfGyWRe~tkKF----------S~~WFlAVHapVPfIa~L-------Ri~~glpw~~----Ip~tIaAai 283 (352)
++++++-+|+|.+=--|+|= -+.+.+-+--++|||+.+ |.-+|-+-+. .|++|++.-
T Consensus 30 ~~~~~iGlplGvlL~~T~~g~i~~n~~~~~il~~ivNi~Rs~PFiILlv~liP~Tr~ivGTsiG~~AAivPL~i~a~P 107 (222)
T COG2011 30 LFAFLIGLPLGVLLFLTGPGGLLENKLLYRILSAIVNILRSIPFIILLVALIPLTRLIVGTSIGTTAAIVPLTIGAAP 107 (222)
T ss_pred HHHHHHHHhhhheEEEcCCCcccchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhcccccchhHhhhHHHHHH
Confidence 78899999999986555553 345666778899999986 4444443222 788887764
No 10
>PF06610 DUF1144: Protein of unknown function (DUF1144); InterPro: IPR010574 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.69 E-value=2e+02 Score=26.35 Aligned_cols=83 Identities=18% Similarity=0.302 Sum_probs=54.9
Q ss_pred CCCchhHHHHHHHHHHHhhccchhhhccccccc-----hhH-------HHHhhhhhhHHHHHHHhcCCChhHHHHHHHHH
Q 018668 215 PQPLPAKVLVIGMLGMAANVPLGIWREHTEKFS-----VSW-------IVAVHAAVPFIAMMRKSVLMPKSAMAFTIAAS 282 (352)
Q Consensus 215 PQpLP~K~l~I~~la~llNIPfGyWRe~tkKFS-----~~W-------FlAVHapVPfIa~LRi~~glpw~~Ip~tIaAa 282 (352)
.|-|-++++.|- +-+++.-|.|+||.-+-+.+ -+| +.+|-.-+|+-+..=..+|-+|.-|---+.+.
T Consensus 40 eQsL~sRll~iP-vnI~iA~PYG~~RD~~lr~~~~~~~~~~~~~l~D~lAyvsFQsPVYaaIL~~vGA~~~qivtav~sn 118 (143)
T PF06610_consen 40 EQSLSSRLLSIP-VNILIAWPYGIYRDWVLRQAARLSPSRWSKNLADLLAYVSFQSPVYAAILWFVGADGDQIVTAVSSN 118 (143)
T ss_pred HHHHHHHHHhhh-hhhhhccchhHHHHHHHHHhcccCchHHHHHHHHHHHHHHhchHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 467788888777 55677789999998654442 234 56777778888887778888877765555544
Q ss_pred HHHHHhhhHHHHHHHH
Q 018668 283 VLGQVIGSRAERYRMK 298 (352)
Q Consensus 283 ilGQ~IGgRl~R~r~k 298 (352)
.+=-.+=|+.+-+.+.
T Consensus 119 avvs~~mG~~YG~FLd 134 (143)
T PF06610_consen 119 AVVSMVMGRPYGYFLD 134 (143)
T ss_pred HHHHHHhhhHHHHHHH
Confidence 4444444455444443
No 11
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=22.72 E-value=53 Score=26.09 Aligned_cols=18 Identities=33% Similarity=0.667 Sum_probs=15.6
Q ss_pred cccCcHHHHHHHHHHHhh
Q 018668 190 KYKCPPVVVAARAAIART 207 (352)
Q Consensus 190 k~~CP~aiVaaRAAlart 207 (352)
-++||-++|.+|-||+.-
T Consensus 12 G~~CP~Pv~~~kk~l~~m 29 (78)
T COG0425 12 GLRCPGPVVETKKALAKL 29 (78)
T ss_pred CCcCCccHHHHHHHHHcC
Confidence 478999999999999764
No 12
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=22.58 E-value=68 Score=24.27 Aligned_cols=19 Identities=21% Similarity=0.307 Sum_probs=16.0
Q ss_pred cccCcHHHHHHHHHHHhhh
Q 018668 190 KYKCPPVVVAARAAIARTA 208 (352)
Q Consensus 190 k~~CP~aiVaaRAAlart~ 208 (352)
-+.||-+++.++.||.+-.
T Consensus 6 G~~CP~Pvi~~kkal~~l~ 24 (69)
T cd03422 6 GEPCPYPAIATLEALPSLK 24 (69)
T ss_pred CCcCCHHHHHHHHHHHcCC
Confidence 4789999999999997643
No 13
>COG1183 PssA Phosphatidylserine synthase [Lipid metabolism]
Probab=20.81 E-value=1.8e+02 Score=27.68 Aligned_cols=60 Identities=17% Similarity=0.185 Sum_probs=47.2
Q ss_pred HHhhccchhhhccccccchhHHHHhhhhhhHHHHHHHhcCCChhHHHHHHHHHHHHHHhhhH
Q 018668 230 MAANVPLGIWREHTEKFSVSWIVAVHAAVPFIAMMRKSVLMPKSAMAFTIAASVLGQVIGSR 291 (352)
Q Consensus 230 ~llNIPfGyWRe~tkKFS~~WFlAVHapVPfIa~LRi~~glpw~~Ip~tIaAailGQ~IGgR 291 (352)
|+-|||+.=+|....-=...|.+..|..+. .+.....-.+|..+.++...|.+.-.+..+
T Consensus 168 mvs~i~~~~~k~~~~~v~~~~~~~~~~~l~--~~~~~~~~~~~~~l~~~~~~y~~~~~~~~~ 227 (234)
T COG1183 168 MVSNIPFPSLKKLNALVRVVLLLAGILLLA--LLALVLILYPWLLLLVIASGYLLSIPIRVR 227 (234)
T ss_pred heeccccCCccccchhccHHHHHHHHHHHH--HHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 345999988888877778889999888876 344455557888899999999888777776
No 14
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=20.44 E-value=23 Score=30.42 Aligned_cols=43 Identities=37% Similarity=0.599 Sum_probs=24.1
Q ss_pred HHHHHHHHhhhhhhhcCCCCchhHHHHHHHHHHHhhccchhh--hccccc
Q 018668 198 VAARAAIARTAFAKSLRPQPLPAKVLVIGMLGMAANVPLGIW--REHTEK 245 (352)
Q Consensus 198 VaaRAAlart~~vk~LRPQpLP~K~l~I~~la~llNIPfGyW--Re~tkK 245 (352)
-|||-|+ ....+..|=| |+++++==++=--++|+|.| ||++|+
T Consensus 17 YAaRLaV--lE~L~~~~RQ---A~viv~REI~p~Y~~PlGvW~VRE~vR~ 61 (110)
T PF04895_consen 17 YAARLAV--LEYLRRRRRQ---AGVIVLREITPEYYAPLGVWQVRENVRK 61 (110)
T ss_pred HHHHHHH--HHHHHHcCcc---ceEEEEEEecCCceeeeeeehHHHHHHH
Confidence 4555433 2344444444 34444333333458999999 788876
Done!