Query 024650
Match_columns 265
No_of_seqs 69 out of 71
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:20:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024650.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024650hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04755 PAP_fibrillin: PAP_fi 99.2 7.9E-10 1.7E-14 93.7 13.5 148 99-252 21-196 (198)
2 PF04405 ScdA_N: Domain of Unk 67.7 5.4 0.00012 29.2 2.6 24 90-113 32-55 (56)
3 PF08770 SoxZ: Sulphur oxidati 54.6 25 0.00055 28.3 4.5 39 190-235 36-74 (100)
4 COG3818 Predicted acetyltransf 52.9 6.8 0.00015 34.6 1.1 19 233-251 84-102 (167)
5 cd06341 PBP1_ABC_ligand_bindin 39.6 33 0.00072 30.6 3.4 55 84-140 279-339 (341)
6 TIGR02116 toxin_Txe_YoeB toxin 25.7 2.6E+02 0.0056 20.8 5.7 38 103-143 20-66 (80)
7 TIGR00244 transcriptional regu 22.1 1.9E+02 0.0042 25.4 5.0 98 55-161 32-134 (147)
8 PF05015 Plasmid_killer: Plasm 20.8 69 0.0015 25.0 1.8 22 124-145 54-81 (93)
9 PF03861 ANTAR: ANTAR domain; 19.8 2E+02 0.0043 20.3 3.9 27 84-110 29-55 (56)
10 PF03724 META: META domain; I 18.1 4.2E+02 0.009 19.6 5.6 56 134-195 4-59 (101)
No 1
>PF04755 PAP_fibrillin: PAP_fibrillin; InterPro: IPR006843 This family identifies a conserved domain found in a number of plastid lipid-associated proteins (PAPs) that are thought to form together with other plastoglobulins a coat on the surface of the lipoprotein particle. The coat may contain receptors for attachment to the thylakoid membrane as well as regulatory proteins that may function in the transfer of lipids to and from the thylakoid membranes.). This entry also represents a number of putative fibrillin proteins.; GO: 0005198 structural molecule activity, 0009507 chloroplast
Probab=99.16 E-value=7.9e-10 Score=93.67 Aligned_cols=148 Identities=22% Similarity=0.276 Sum_probs=95.9
Q ss_pred CCCChHHHHHHHHHHHHhhcccCcc--ccccCCCCCCCCceEEEEEeeeecc------cccceec-eeEEeeecccceEE
Q 024650 99 RKVAAAEILSALSVIEKAKIDYSGF--LETLGGSESPGRTWMLIFTAEKKLK------SGRYFPV-TAVQRFDAAAKRIE 169 (265)
Q Consensus 99 rkv~~~~V~~ALl~LEKa~~~~s~f--~e~L~G~~~pg~~WrLvFtt~k~l~------~G~Y~P~-~avq~fda~~~~Ie 169 (265)
....-++|.+++.+||...-.+... .+.|.| .|+|+|++..... ...++++ .+.|.+|...++++
T Consensus 21 ~~~~~~~i~~~v~~LE~~np~~~p~~s~~~L~G------~W~Lvytt~~~~~~~l~~~~~~~~~~~~v~Q~id~~~~~~~ 94 (198)
T PF04755_consen 21 SPEDREEIEELVEELEALNPTPDPADSLPLLDG------RWELVYTTSPEIRSLLQRGRLPGVRVGRVFQTIDADNGRVE 94 (198)
T ss_pred CHHHHHHHHHHHHHHHHhCCCCCCcCCchhcCc------EEEEEeecCCCccccccccccccccccceEEEEECCCceEE
Confidence 3445578999999999987444332 255788 9999999844222 2223445 67777899889999
Q ss_pred eeeEeccce----eeEEEeeeec-CceeeeEEeceEEEeecCC--------cce--eecCCCC----CCCCCCCCCCCCc
Q 024650 170 NGVYLGPIG----CLTFEGRFSW-KKRMLAFIFERVHIKIGPL--------KPL--EIGFGQK----DNREPSTVSKDPF 230 (265)
Q Consensus 170 N~V~LGpl~----~L~F~G~f~~-kk~lLaF~F~~i~lklG~~--------~l~--~i~lg~~----~~f~p~~~kk~PF 230 (265)
|.|.+.++| .+...+.+.. ...-+.+.|++..++.... .-. .++.... ..+.........+
T Consensus 95 N~v~~~~~~~~~~~~~v~a~~~~~~~~rv~v~f~~~~l~~~~~l~~~l~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~g~ 174 (198)
T PF04755_consen 95 NVVELSGFPLLEGSVSVRASLEVRSPRRVEVTFERASLKPPSLLKGVLGPLKDALNNVPRGISDELPVPLPLPGGSPKGW 174 (198)
T ss_pred EEEEEeccCceEEEEEEEEEEEEccccEEEEEEEeeEEcccceeeccchhhhhhhhhcccccccccccccccCCCCCceE
Confidence 999987764 2333445555 3577899999987755221 000 0100000 0111111346679
Q ss_pred eEEEEecCceEEeecCCCeeEe
Q 024650 231 FVWFYIDEEIAVARGRAGGTAF 252 (265)
Q Consensus 231 Fa~f~vde~iiaARGRGGGLAL 252 (265)
|...|+||++-+.||..|++-+
T Consensus 175 l~~tYLDedlRI~Rg~~G~~fV 196 (198)
T PF04755_consen 175 LDTTYLDEDLRISRGNKGSLFV 196 (198)
T ss_pred EEEEEECCCeEEEEcCCCCEEE
Confidence 9999999999999999999754
No 2
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=67.71 E-value=5.4 Score=29.24 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=20.9
Q ss_pred HHHHHHHhcCCCChHHHHHHHHHH
Q 024650 90 KILKKAAKTRKVAAAEILSALSVI 113 (265)
Q Consensus 90 ~vLk~AA~trkv~~~~V~~ALl~L 113 (265)
..|..|++.+.+++++|+++|..+
T Consensus 32 ~~L~eA~~~~~ld~~~vl~~L~~l 55 (56)
T PF04405_consen 32 RSLEEACEEKGLDPEEVLEELNAL 55 (56)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHc
Confidence 468899999999999999998754
No 3
>PF08770 SoxZ: Sulphur oxidation protein SoxZ; InterPro: IPR014880 SoxZ forms an anti parallel beta structure and forms a complex with SoxY. Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit []. ; PDB: 1V8H_B 2OX5_E 2OXG_E 2OXH_C.
Probab=54.57 E-value=25 Score=28.25 Aligned_cols=39 Identities=18% Similarity=0.437 Sum_probs=27.8
Q ss_pred ceeeeEEeceEEEeecCCcceeecCCCCCCCCCCCCCCCCceEEEE
Q 024650 190 KRMLAFIFERVHIKIGPLKPLEIGFGQKDNREPSTVSKDPFFVWFY 235 (265)
Q Consensus 190 k~lLaF~F~~i~lklG~~~l~~i~lg~~~~f~p~~~kk~PFFa~f~ 235 (265)
+.+=+|.-+.++++.+|..++...++. .+.++|||.|-+
T Consensus 36 ~~iPa~~I~~v~v~~ng~~v~~~~~~~-------siS~NP~l~F~~ 74 (100)
T PF08770_consen 36 KYIPAHFIEEVEVTYNGKPVFRADWGP-------SISENPYLRFSF 74 (100)
T ss_dssp -BB--B-EEEEEEEETTEEEEEEEE-T-------TB-SS-EEEEEE
T ss_pred CCCChHheEEEEEEECCEEEEEEEeCC-------cccCCCcEEEEE
Confidence 356789999999999999999888776 277999999877
No 4
>COG3818 Predicted acetyltransferase, GNAT superfamily [General function prediction only]
Probab=52.91 E-value=6.8 Score=34.62 Aligned_cols=19 Identities=37% Similarity=0.833 Sum_probs=16.8
Q ss_pred EEEecCceEEeecCCCeeE
Q 024650 233 WFYIDEEIAVARGRAGGTA 251 (265)
Q Consensus 233 ~f~vde~iiaARGRGGGLA 251 (265)
|||||-=+.++|-||||+|
T Consensus 84 F~YvDRvVVA~~aRGrG~a 102 (167)
T COG3818 84 FFYVDRVVVASRARGRGVA 102 (167)
T ss_pred eEEEEEEEEEecccccchH
Confidence 5799999999999999986
No 5
>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=39.63 E-value=33 Score=30.59 Aligned_cols=55 Identities=13% Similarity=0.178 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHhcC--CCChHH-HHHHHHHHHHhhcccCccccccC---CCCCCCCceEEE
Q 024650 84 EVEESVKILKKAAKTR--KVAAAE-ILSALSVIEKAKIDYSGFLETLG---GSESPGRTWMLI 140 (265)
Q Consensus 84 ~~~e~v~vLk~AA~tr--kv~~~~-V~~ALl~LEKa~~~~s~f~e~L~---G~~~pg~~WrLv 140 (265)
..=+++.+|.+|.+.- ..+.+. |.++|..++.-. ..+....+. |-..|.+||+|+
T Consensus 279 ~~yda~~~~~~a~~~ag~~~~~~~~v~~al~~~~~~~--~~g~~~~~~~~~~~~~~~~~~~~~ 339 (341)
T cd06341 279 IGYIAADLFLRGLSGAGGCPTRASQFLRALRAVTDYD--AGGLTPPCDGKAGPGRPSTCYSFV 339 (341)
T ss_pred HHHHHHHHHHHHHHhcCCCCChHHHHHHHhhcCCCCC--CCCcccCccCccCCCCCchhhhhe
Confidence 4457788888888862 345666 888887775432 222222333 334578999987
No 6
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=25.68 E-value=2.6e+02 Score=20.85 Aligned_cols=38 Identities=21% Similarity=0.230 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHhhcccC---ccccccCCCCCC------CCceEEEEEe
Q 024650 103 AAEILSALSVIEKAKIDYS---GFLETLGGSESP------GRTWMLIFTA 143 (265)
Q Consensus 103 ~~~V~~ALl~LEKa~~~~s---~f~e~L~G~~~p------g~~WrLvFtt 143 (265)
.+.+.++|.+|+. +|. .-.+.|-|.-.. |..||+||..
T Consensus 20 ~~~i~~~i~~l~~---~P~~~~~~~~~L~G~~~g~~r~rig~dyRIIY~i 66 (80)
T TIGR02116 20 KKKINELIKDVRR---DPFKGKGKPEPLKGDLSGYWSRRITDEHRLVYRV 66 (80)
T ss_pred HHHHHHHHHHHHc---CCCCCCCCcccCCCCCCCcEEEEcCCCeEEEEEE
Confidence 3566777766543 342 223567774221 2378899984
No 7
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.08 E-value=1.9e+02 Score=25.42 Aligned_cols=98 Identities=18% Similarity=0.217 Sum_probs=55.3
Q ss_pred ccccccccccccCCCCCCchhhhcccchH--hHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcccCc--cccccCCC
Q 024650 55 VKTRATLGEKDDIAPPTPLLVQEKEQSNR--EVEESVKILKKAAKTRKVAAAEILSALSVIEKAKIDYSG--FLETLGGS 130 (265)
Q Consensus 55 ~~~ra~~~~~~~~~~~~~~~~~~~~~~~~--~~~e~v~vLk~AA~trkv~~~~V~~ALl~LEKa~~~~s~--f~e~L~G~ 130 (265)
..|..-++-.|..-. .|+.|...+..-+ +-+--+.=|.+|.+.|.|+++++-+....+|+.-++... ...+.+|
T Consensus 32 ~~C~~RFTTyErve~-~~l~ViKkdG~re~Fdr~Kl~~gl~~Ac~KRpVs~e~ie~~v~~Ie~~l~~~~~~EI~S~~IG- 109 (147)
T TIGR00244 32 LECHERFTTFERAEL-LPPTVIKQDGVREPFNREKLLRGMVRACEKRPVSFDDLEHAINHIEAQLRAQGEREVPSELIG- 109 (147)
T ss_pred CccCCccceeeeccc-cccEEEcCCCCCCCCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHcCCCcccHHHHH-
Confidence 566665555554333 4444445442211 223344557899999999999999999999997532211 2233344
Q ss_pred CCCCCceEEEEEeeeecccccceeceeEEe-e
Q 024650 131 ESPGRTWMLIFTAEKKLKSGRYFPVTAVQR-F 161 (265)
Q Consensus 131 ~~pg~~WrLvFtt~k~l~~G~Y~P~~avq~-f 161 (265)
.+ |----+.++.=.|+....++. |
T Consensus 110 -----e~--Vm~~L~~lD~VAYVRFASVYr~F 134 (147)
T TIGR00244 110 -----QM--VMQYLKKLDEVAYIRFASVYRSF 134 (147)
T ss_pred -----HH--HHHHHhhcCcchhhhhhhhcCCC
Confidence 11 000123555666777655555 5
No 8
>PF05015 Plasmid_killer: Plasmid maintenance system killer protein; InterPro: IPR007711 Several plasmids with proteic killer gene systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of those systems result in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin.
Probab=20.78 E-value=69 Score=24.98 Aligned_cols=22 Identities=36% Similarity=0.643 Sum_probs=14.5
Q ss_pred ccccCCCCCC------CCceEEEEEeee
Q 024650 124 LETLGGSESP------GRTWMLIFTAEK 145 (265)
Q Consensus 124 ~e~L~G~~~p------g~~WrLvFtt~k 145 (265)
++.|.|.... ...|||||.+..
T Consensus 54 ~h~L~G~~~g~~Si~i~~~~RliF~~~~ 81 (93)
T PF05015_consen 54 LHKLKGDRKGQWSIRINGNWRLIFRFED 81 (93)
T ss_pred cccccCCCCCcEEEEeCCCEEEEEEEeC
Confidence 4777773322 258999999744
No 9
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=19.79 E-value=2e+02 Score=20.31 Aligned_cols=27 Identities=19% Similarity=0.438 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHhcCCCChHHHHHHH
Q 024650 84 EVEESVKILKKAAKTRKVAAAEILSAL 110 (265)
Q Consensus 84 ~~~e~v~vLk~AA~trkv~~~~V~~AL 110 (265)
+-++|...|++.|-...++..+|-+.|
T Consensus 29 ~e~~A~~~Lr~~Am~~~~~l~~vA~~i 55 (56)
T PF03861_consen 29 SEDEAYRLLRRQAMRRRRSLADVAEEI 55 (56)
T ss_dssp -HHHHHHHHHHHHHHCTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 468899999999999999999998765
No 10
>PF03724 META: META domain; InterPro: IPR005184 A domain found in proteins of unknown function [], some of which are described as heat shock protein (HslJ). In Helicobacter pylori (Campylobacter pylori) the protein is secreted e.g. (O25998 from SWISSPROT) and implicated in motility. In Leishmania spp. it is described as an essential protein, over-expression of which, in Leishmania amazonensis increases virulence (O43987 from SWISSPROT; []). A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond. ; PDB: 2KTS_A 2LA7_A.
Probab=18.07 E-value=4.2e+02 Score=19.61 Aligned_cols=56 Identities=29% Similarity=0.525 Sum_probs=29.2
Q ss_pred CCceEEEEEeeeecccccceeceeEEeeecccceEEeeeEeccceeeEEEeeeecCceeeeE
Q 024650 134 GRTWMLIFTAEKKLKSGRYFPVTAVQRFDAAAKRIENGVYLGPIGCLTFEGRFSWKKRMLAF 195 (265)
Q Consensus 134 g~~WrLvFtt~k~l~~G~Y~P~~avq~fda~~~~IeN~V~LGpl~~L~F~G~f~~kk~lLaF 195 (265)
++.|+|..+..... .....+......|+..++++ -|-.|+=.|+|++.++.+-|.|
T Consensus 4 ~~~W~l~~~~~~~~-~~~~~~~~~~l~~~~~~~~~-----~g~~gCN~~~g~~~~~~~~l~~ 59 (101)
T PF03724_consen 4 GGTWQLTSIDGDGK-TGVPPPAKPTLTFDFEDGRV-----SGSAGCNRFSGTYTIEGNTLSF 59 (101)
T ss_dssp TEEEEEEEE-SSS--B---TTSSSEEEEECCCCEE-----EEE-SSSEEEEEEEECTTEEEE
T ss_pred CCEEEEEEEecCCc-cccCCCCCcEEEEEeCCCEE-----EEEECCeeeEEEEEECCCEEEE
Confidence 35999985532210 11111345555576554433 2333455889999997764433
Done!