Query 032454
Match_columns 140
No_of_seqs 109 out of 1078
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 14:18:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00059 L17 ribosomal protei 100.0 4.8E-47 1E-51 281.9 11.5 94 1-94 19-112 (112)
2 COG0203 RplQ Ribosomal protein 100.0 9.1E-47 2E-51 281.3 10.2 93 1-93 24-116 (116)
3 PRK05591 rplQ 50S ribosomal pr 100.0 1.9E-46 4.1E-51 279.0 11.4 93 1-93 21-113 (113)
4 PF01196 Ribosomal_L17: Riboso 100.0 1.8E-46 3.8E-51 272.3 8.7 93 1-93 5-97 (97)
5 PTZ00076 60S ribosomal protein 100.0 3.1E-44 6.6E-49 295.8 12.0 110 1-110 36-146 (253)
6 KOG3280 Mitochondrial/chloropl 100.0 4.9E-44 1.1E-48 280.4 8.3 134 1-138 31-167 (171)
7 PF02082 Rrf2: Transcriptional 50.5 32 0.00069 23.2 3.9 47 26-72 12-66 (83)
8 PRK13848 conjugal transfer pro 44.0 43 0.00093 24.8 3.9 24 49-72 45-68 (98)
9 PF04079 DUF387: Putative tran 39.9 53 0.0011 25.6 4.2 46 25-72 3-48 (159)
10 PF05848 CtsR: Firmicute trans 32.7 4.2 9.2E-05 32.0 -3.0 29 68-96 64-92 (152)
11 COG1775 HgdB Benzoyl-CoA reduc 31.3 1.8E+02 0.0038 26.3 6.5 86 10-95 164-260 (379)
12 COG4463 CtsR Transcriptional r 30.6 29 0.00064 27.5 1.4 13 68-80 64-76 (153)
13 PRK00135 scpB segregation and 30.1 1.6E+02 0.0034 23.6 5.5 49 21-71 5-55 (188)
14 COG1959 Predicted transcriptio 28.3 1.2E+02 0.0026 23.0 4.4 48 25-72 11-66 (150)
15 PF07820 TraC: TraC-like prote 26.6 1.5E+02 0.0033 21.6 4.4 21 49-69 44-64 (92)
16 PF07227 DUF1423: Protein of u 23.3 1.4E+02 0.0029 27.6 4.4 48 16-63 371-424 (446)
No 1
>TIGR00059 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model.
Probab=100.00 E-value=4.8e-47 Score=281.87 Aligned_cols=94 Identities=49% Similarity=0.829 Sum_probs=93.0
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcccCC
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIR 80 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl~~R 80 (140)
|+||||+||||+||++||||+|+|||+|||+||+|++|++|++.+||.|+++++|||++|+|||++|+||||||+|+++|
T Consensus 19 l~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lapry~~R~GGYTRI~kl~~R 98 (112)
T TIGR00059 19 LASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAPRYAQRPGGYTRILKLGPR 98 (112)
T ss_pred HHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHHHhCCCCCCeEEEEECCCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEEeec
Q 032454 81 VGDAAPMAYIEFVD 94 (140)
Q Consensus 81 ~GD~A~maiIELVd 94 (140)
.||+||||||||||
T Consensus 99 ~gD~A~maiiElVd 112 (112)
T TIGR00059 99 RGDAAEMAIIELVD 112 (112)
T ss_pred CCCCCCeEEEEecC
Confidence 99999999999996
No 2
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.1e-47 Score=281.28 Aligned_cols=93 Identities=51% Similarity=0.828 Sum_probs=92.1
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcccCC
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIR 80 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl~~R 80 (140)
|++|||+||+|+||++||||+|+++|+|||+||+|++|++|+|.++|.|+++++|||++|+|||.+|+||||||+|+|+|
T Consensus 24 la~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF~~iapry~~R~GGYtRIlK~g~R 103 (116)
T COG0203 24 LATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEIAPRYAERNGGYTRILKLGFR 103 (116)
T ss_pred HHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHHHHhChhhcCCCCCeeEEEecCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEEee
Q 032454 81 VGDAAPMAYIEFV 93 (140)
Q Consensus 81 ~GD~A~maiIELV 93 (140)
.||+|||||||||
T Consensus 104 ~GD~A~maiiElV 116 (116)
T COG0203 104 RGDNAPMAIIELV 116 (116)
T ss_pred CCCCCceEEEEeC
Confidence 9999999999997
No 3
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=1.9e-46 Score=279.01 Aligned_cols=93 Identities=53% Similarity=0.864 Sum_probs=92.1
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcccCC
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIR 80 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl~~R 80 (140)
||||||+||||+||++||||+|+|||+|||+||+|++|++|+|.+||.|+++++|||++|+|||++|+||||||+|+++|
T Consensus 21 l~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~lapry~~R~GGYTRI~k~~~R 100 (113)
T PRK05591 21 LATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEIAPRYADRNGGYTRILKLGFR 100 (113)
T ss_pred HHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHHHHHhCcCCCCeEEEEECCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEEee
Q 032454 81 VGDAAPMAYIEFV 93 (140)
Q Consensus 81 ~GD~A~maiIELV 93 (140)
.||+|||||||||
T Consensus 101 ~gD~A~ma~iElV 113 (113)
T PRK05591 101 RGDNAPMAIIELV 113 (113)
T ss_pred CCCCCCeEEEEeC
Confidence 9999999999997
No 4
>PF01196 Ribosomal_L17: Ribosomal protein L17; InterPro: IPR000456 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3F1F_R 1VSP_L 3PYV_N 3PYR_N 3PYO_N 1VSA_L 3MS1_N 3F1H_R 3D5B_R 3MRZ_N ....
Probab=100.00 E-value=1.8e-46 Score=272.30 Aligned_cols=93 Identities=54% Similarity=0.876 Sum_probs=91.1
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcccCC
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRSRIR 80 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl~~R 80 (140)
|||+||+||||+||++||||+|+|||+|||+||+|++|+++++.+||.|+++++|||++|+|||++|+||||||+|+++|
T Consensus 5 lvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~kl~~R 84 (97)
T PF01196_consen 5 LVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIKLGPR 84 (97)
T ss_dssp HHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEEEEEC
T ss_pred HHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEeCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCeeEEEee
Q 032454 81 VGDAAPMAYIEFV 93 (140)
Q Consensus 81 ~GD~A~maiIELV 93 (140)
.||+|||||||||
T Consensus 85 ~gD~A~maiiElV 97 (97)
T PF01196_consen 85 RGDAAPMAIIELV 97 (97)
T ss_dssp SSSTCEEEEEEET
T ss_pred CCCCCCEEEEEeC
Confidence 9999999999997
No 5
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=3.1e-44 Score=295.78 Aligned_cols=110 Identities=34% Similarity=0.544 Sum_probs=105.5
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcc-cC
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRS-RI 79 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl-~~ 79 (140)
|+||||+||||+||++||||+|+|||+|||+||+|++|++|+|.++|.|+++++|||++|+|||++|+||||||+|+ ++
T Consensus 36 LvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAPRY~dR~GGYTRIlK~~g~ 115 (253)
T PTZ00076 36 QLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVPLYRDRPFFFTRVVNQWRL 115 (253)
T ss_pred HHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhhHhcCCCCCeeEEEeCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999997 69
Q ss_pred CCCCCCCeeEEEeecCchhhhcCCCCCCCCC
Q 032454 80 RVGDAAPMAYIEFVDRENELRQSKPAVPQPP 110 (140)
Q Consensus 80 R~GD~A~maiIELVd~~~~~~~~~~~~~~~~ 110 (140)
|.||+||||||||||+|.++++++|++....
T Consensus 116 R~GD~ApMAiIELVd~p~e~r~A~pvg~d~~ 146 (253)
T PTZ00076 116 RLRDAAPMAYIEFVDRPGEIRPAKPVGFDKI 146 (253)
T ss_pred CCCCCCCEEEEEeccCcCccccccccchhHH
Confidence 9999999999999999999999888875543
No 6
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-44 Score=280.41 Aligned_cols=134 Identities=53% Similarity=0.776 Sum_probs=125.2
Q ss_pred ChhhhhhcCceEeCHHHHHHHHHhHHHHHHhh-cCCCHHHH--HHHHHhcCChhHHHHHHHHHHHHhCCCCCCeEEEEcc
Q 032454 1 MVSQLVKHERIETTVAKAKEVRRLADNMVQLG-KEGSLCAA--RRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLRS 77 (140)
Q Consensus 1 LvtsLi~herI~TT~~KAKelr~~aErLIt~A-K~g~~~~~--r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYTRI~kl 77 (140)
|||+||+||||+|||+||||+|+|||+|||+| |.|++|.+ +++.+||..+++++|||++|+|||.+|+|||||++|+
T Consensus 31 lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~KlF~vl~pRY~dr~ggYTRllrl 110 (171)
T KOG3280|consen 31 LVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLHKLFTVLAPRYKDRNGGYTRLLRL 110 (171)
T ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHHHHHHHhchhhccCCCCceehhcc
Confidence 68999999999999999999999999999999 78999987 9999999999999999999999999999999999999
Q ss_pred cCCCCCCCCeeEEEeecCchhhhcCCCCCCCCCCCCCCCHHHHHHhhhhcCCCcCCcCCCc
Q 032454 78 RIRVGDAAPMAYIEFVDRENELRQSKPAVPQPPPRAALDPWTRSRLTKNFAPPKQEKSSDA 138 (140)
Q Consensus 78 ~~R~GD~A~maiIELVd~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 138 (140)
.+|.||+|||||||+++|+. ....+.-+.++.+|.+|++..|.++|.+|++|+-.+.
T Consensus 111 ppr~~d~apmavlE~~Gn~~----p~~~a~~p~~r~~lh~vll~~l~r~~~~~~~e~l~~~ 167 (171)
T KOG3280|consen 111 PPRRGDRAPMAVLELVGNPL----PQQAADRPDTRVNLHKVLLFRLLREFRPPKEEKLDDS 167 (171)
T ss_pred CcccccccCceeeeecCCcc----ccccCCCchhhhhhHHHHHHHHHHHhccchhhcccCc
Confidence 99999999999999998764 4566777788889999999999999999999986553
No 7
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=50.46 E-value=32 Score=23.21 Aligned_cols=47 Identities=17% Similarity=0.317 Sum_probs=31.8
Q ss_pred HHHHHhhcCCC---HHHHHHHHHhcCChhHHHHHHHHHHHH-----hCCCCCCeE
Q 032454 26 DNMVQLGKEGS---LCAARRAAAFVRGDDVIHKLFTELAYR-----YKDRAGGYT 72 (140)
Q Consensus 26 ErLIt~AK~g~---~~~~r~a~~~L~~~~~v~KLf~~lapR-----y~~R~GGYT 72 (140)
.=|+.+|..++ ......+...=.++..+.+++..|... ...++|||.
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~ 66 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYR 66 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCcee
Confidence 34566676554 445666666666788999999999875 356778885
No 8
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=44.01 E-value=43 Score=24.78 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=20.3
Q ss_pred ChhHHHHHHHHHHHHhCCCCCCeE
Q 032454 49 GDDVIHKLFTELAYRYKDRAGGYT 72 (140)
Q Consensus 49 ~~~~v~KLf~~lapRy~~R~GGYT 72 (140)
++..+.+.|++|+.||++..|+-|
T Consensus 45 ~d~eL~~aFeeiAaRFR~g~~~~~ 68 (98)
T PRK13848 45 EEAELQAAFEELAKRFRGGKGAAT 68 (98)
T ss_pred CHHHHHHHHHHHHHHHhcCCCccc
Confidence 466789999999999999888654
No 9
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=39.93 E-value=53 Score=25.60 Aligned_cols=46 Identities=15% Similarity=0.299 Sum_probs=29.5
Q ss_pred HHHHHHhhcCCCHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCeE
Q 032454 25 ADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYT 72 (140)
Q Consensus 25 aErLIt~AK~g~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGYT 72 (140)
+|-++-.+-++ -+.......+.+.+.+.++.++|..+|.++++|+.
T Consensus 3 iEAlLF~s~~p--vs~~~La~~l~~~~~v~~~l~~L~~~y~~~~~gl~ 48 (159)
T PF04079_consen 3 IEALLFASGEP--VSIEELAEILGSEDEVEEALEELQEEYNEEDRGLE 48 (159)
T ss_dssp HHHHHHH-SS---B-HHHHHHHCT-HHHHHHHHHHHHHHHHHCT-SEE
T ss_pred hHhhHHHcCCC--CCHHHHHHHhCCHHHHHHHHHHHHHHhccCCCCEE
Confidence 45666665444 23344455555888999999999999977777764
No 10
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=32.69 E-value=4.2 Score=32.02 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=18.0
Q ss_pred CCCeEEEEcccCCCCCCCCeeEEEeecCc
Q 032454 68 AGGYTRLLRSRIRVGDAAPMAYIEFVDRE 96 (140)
Q Consensus 68 ~GGYTRI~kl~~R~GD~A~maiIELVd~~ 96 (140)
.|||-||.|+.....+.--..+++.+++.
T Consensus 64 GGGyIRI~rv~~~~~~~~~~~l~~~ig~~ 92 (152)
T PF05848_consen 64 GGGYIRIVRVPLDDEEDLLDHLIESIGDS 92 (152)
T ss_dssp TT-EEEEEEEEESTCHHHHHHHHCCS-S-
T ss_pred CCceEEEEEEccCCcHHHHHHHHHHhcCc
Confidence 68999999988765544445556666543
No 11
>COG1775 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]
Probab=31.28 E-value=1.8e+02 Score=26.32 Aligned_cols=86 Identities=24% Similarity=0.344 Sum_probs=55.1
Q ss_pred ceEeCHHHHHHHHHhHHHHHHhhcCC------CHHHHHHHHH-hcCChhHHHHHHHHHHHHhCCC--CCCeEEEEcccCC
Q 032454 10 RIETTVAKAKEVRRLADNMVQLGKEG------SLCAARRAAA-FVRGDDVIHKLFTELAYRYKDR--AGGYTRLLRSRIR 80 (140)
Q Consensus 10 rI~TT~~KAKelr~~aErLIt~AK~g------~~~~~r~a~~-~L~~~~~v~KLf~~lapRy~~R--~GGYTRI~kl~~R 80 (140)
..+=+.+|.-++|..--+++.+++.. .-+...++.+ +++|.+...-.++++..+++.| .|+=+||+-.|.|
T Consensus 164 ~L~da~~r~N~~rea~~k~~kL~~~~P~plsg~D~~~~~~~~~~~~d~d~~~~~l~~l~eelekr~~eg~~~Ri~~~g~p 243 (379)
T COG1775 164 KLRDAIARYNRLREALAKLYKLAKHKPSPLSGSDAFNVMAFAVFLRDKDAFIEELEELIEELEKRVEEGEGPRILITGIP 243 (379)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhHHHHHhhHHHHhcchHHHHHHHHHHHHHHHHHHhccCCceEEeecCc
Confidence 33445677777787778888888753 2344556666 7888877666666666665443 2333999999998
Q ss_pred C-CCCCCe-eEEEeecC
Q 032454 81 V-GDAAPM-AYIEFVDR 95 (140)
Q Consensus 81 ~-GD~A~m-aiIELVd~ 95 (140)
. +|+-+. -++|.+.+
T Consensus 244 ~~~~~~~v~~~~e~~~~ 260 (379)
T COG1775 244 ILGDNPKVWEILEEVGE 260 (379)
T ss_pred ccCCCcchhHHHHhhcc
Confidence 4 466553 24555554
No 12
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=30.64 E-value=29 Score=27.46 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=11.2
Q ss_pred CCCeEEEEcccCC
Q 032454 68 AGGYTRLLRSRIR 80 (140)
Q Consensus 68 ~GGYTRI~kl~~R 80 (140)
.|||-||.|..++
T Consensus 64 GGGYIRI~Kv~~~ 76 (153)
T COG4463 64 GGGYIRIIKVEYS 76 (153)
T ss_pred CCceEEEEEeccc
Confidence 6899999998765
No 13
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=30.12 E-value=1.6e+02 Score=23.63 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=33.1
Q ss_pred HHHhHHHHHHhhcCC--CHHHHHHHHHhcCChhHHHHHHHHHHHHhCCCCCCe
Q 032454 21 VRRLADNMVQLGKEG--SLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGY 71 (140)
Q Consensus 21 lr~~aErLIt~AK~g--~~~~~r~a~~~L~~~~~v~KLf~~lapRy~~R~GGY 71 (140)
++..+|-++-.+... ++..-..+.. .+...|.++.++|...|.++++|+
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~--~~~~~v~~~l~~L~~~y~~~~~gi 55 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILE--LEPTEVQQLLEELQEKYEGDDRGL 55 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHhhCCCCE
Confidence 456788888887664 3333222221 345679999999999999776554
No 14
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=28.26 E-value=1.2e+02 Score=23.04 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=33.3
Q ss_pred HHHHHHhhcCCC--HH-HHHHHHHhcCChhHHHHHHHHHHHH-----hCCCCCCeE
Q 032454 25 ADNMVQLGKEGS--LC-AARRAAAFVRGDDVIHKLFTELAYR-----YKDRAGGYT 72 (140)
Q Consensus 25 aErLIt~AK~g~--~~-~~r~a~~~L~~~~~v~KLf~~lapR-----y~~R~GGYT 72 (140)
.--|+.+|+.+. .. ....|...=-++.-+.|+|..|..- .+.++|||.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~ 66 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYR 66 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCcc
Confidence 345777887654 33 5566666666788899999988763 566777773
No 15
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=26.58 E-value=1.5e+02 Score=21.65 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=17.7
Q ss_pred ChhHHHHHHHHHHHHhCCCCC
Q 032454 49 GDDVIHKLFTELAYRYKDRAG 69 (140)
Q Consensus 49 ~~~~v~KLf~~lapRy~~R~G 69 (140)
+++.+.+.|++|+.||....+
T Consensus 44 ~d~eL~~~FeeIa~RFrk~~~ 64 (92)
T PF07820_consen 44 SDAELQAAFEEIAARFRKGKK 64 (92)
T ss_pred CHHHHHHHHHHHHHHHhcccc
Confidence 467899999999999987644
No 16
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=23.25 E-value=1.4e+02 Score=27.58 Aligned_cols=48 Identities=29% Similarity=0.316 Sum_probs=34.6
Q ss_pred HHHHHHHHhHHHHHH--hhcCCCH---HHHHHHHHhcCCh-hHHHHHHHHHHHH
Q 032454 16 AKAKEVRRLADNMVQ--LGKEGSL---CAARRAAAFVRGD-DVIHKLFTELAYR 63 (140)
Q Consensus 16 ~KAKelr~~aErLIt--~AK~g~~---~~~r~a~~~L~~~-~~v~KLf~~lapR 63 (140)
.||.|+|+-||+|=. +||.... ++.+.+.-.|.+- +-.+++|++|---
T Consensus 371 ~kAdEARrEAE~LqrI~~aK~~k~EEEYas~~~kl~l~eaee~r~~~~eelk~~ 424 (446)
T PF07227_consen 371 LKADEARREAEGLQRIALAKSEKIEEEYASRYLKLRLNEAEEERKKKFEELKVL 424 (446)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 699999999999854 5566543 4566666666664 4678899988543
Done!