Query 031308
Match_columns 161
No_of_seqs 119 out of 1023
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 12:16:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05591 rplQ 50S ribosomal pr 100.0 1.7E-54 3.7E-59 329.1 14.2 113 1-114 1-113 (113)
2 COG0203 RplQ Ribosomal protein 100.0 1.7E-54 3.8E-59 329.3 12.9 112 2-114 5-116 (116)
3 TIGR00059 L17 ribosomal protei 100.0 2.9E-54 6.3E-59 327.4 14.0 112 3-115 1-112 (112)
4 PTZ00076 60S ribosomal protein 100.0 9.3E-51 2E-55 341.5 14.5 127 3-130 18-145 (253)
5 KOG3280 Mitochondrial/chloropl 100.0 2.9E-49 6.2E-54 316.3 11.2 150 5-159 15-167 (171)
6 PF01196 Ribosomal_L17: Riboso 100.0 1.6E-47 3.4E-52 283.8 10.4 97 17-114 1-97 (97)
7 PF02082 Rrf2: Transcriptional 48.5 41 0.00088 23.2 4.3 47 46-92 12-66 (83)
8 PRK13266 Thf1-like protein; Re 45.7 38 0.00081 29.0 4.4 78 9-98 68-147 (225)
9 PRK13848 conjugal transfer pro 42.5 52 0.0011 24.9 4.3 45 42-92 24-68 (98)
10 COG1775 HgdB Benzoyl-CoA reduc 36.1 76 0.0016 29.2 5.1 90 26-116 160-260 (379)
11 PF05598 DUF772: Transposase d 34.1 1.4E+02 0.0031 19.8 6.0 73 8-81 1-77 (77)
12 PF04079 DUF387: Putative tran 33.4 83 0.0018 25.1 4.4 46 45-92 3-48 (159)
13 PLN00047 photosystem II biogen 29.8 1.2E+02 0.0025 27.0 5.1 78 9-98 119-197 (283)
14 PF05848 CtsR: Firmicute trans 28.8 11 0.00024 30.4 -1.3 37 79-116 45-91 (152)
15 PRK00135 scpB segregation and 27.1 1.9E+02 0.0041 23.7 5.6 51 41-91 5-55 (188)
16 COG4463 CtsR Transcriptional r 26.8 39 0.00085 27.3 1.5 13 88-100 64-76 (153)
17 COG1959 Predicted transcriptio 25.7 1.5E+02 0.0032 23.1 4.6 47 46-92 12-66 (150)
18 PF07820 TraC: TraC-like prote 23.9 2E+02 0.0044 21.5 4.7 41 43-89 24-64 (92)
19 cd00491 4Oxalocrotonate_Tautom 20.5 1.2E+02 0.0027 18.8 2.7 21 8-28 10-30 (58)
20 COG2257 Uncharacterized homolo 20.3 1.1E+02 0.0024 23.0 2.7 43 42-84 31-79 (92)
No 1
>PRK05591 rplQ 50S ribosomal protein L17; Validated
Probab=100.00 E-value=1.7e-54 Score=329.11 Aligned_cols=113 Identities=51% Similarity=0.824 Sum_probs=111.6
Q ss_pred CCcccCCCCCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHH
Q 031308 1 MTKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 80 (161)
Q Consensus 1 m~~~rkLgR~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~el 80 (161)
|++++||||+++||++|||||+||||+||+|+||++||||+|+|||+|||+||+|++|++|+|.+||.|+++++|||++|
T Consensus 1 ~~~~rkl~r~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~aK~~~~~~rR~~~~~L~~~~~v~KLf~~l 80 (113)
T PRK05591 1 RKKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLHARRQAFARLRDKEAVHKLFDEI 80 (113)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHcCeEEecHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHhCCHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCCCCeEEEEeccCCCCCCCcceeeeccc
Q 031308 81 AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFV 114 (161)
Q Consensus 81 aPRy~~R~GGYTRI~kl~~R~GD~A~maiIE~lV 114 (161)
+|||++|+||||||+|+++|.||+||||||| ||
T Consensus 81 apry~~R~GGYTRI~k~~~R~gD~A~ma~iE-lV 113 (113)
T PRK05591 81 APRYADRNGGYTRILKLGFRRGDNAPMAIIE-LV 113 (113)
T ss_pred HHHhCcCCCCeEEEEECCCCCCCCCCeEEEE-eC
Confidence 9999999999999999999999999999999 87
No 2
>COG0203 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-54 Score=329.32 Aligned_cols=112 Identities=50% Similarity=0.807 Sum_probs=110.5
Q ss_pred CcccCCCCCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHH
Q 031308 2 TKFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELA 81 (161)
Q Consensus 2 ~~~rkLgR~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~ela 81 (161)
++++||||+++||++|||||++|||+||+|+||++||||+|++||+|||+||+|+++++|+|.++|.|+++|+|||++|+
T Consensus 5 ~~~rkl~rtsshR~amlrnla~sLi~he~I~TT~~KAKelr~~vEkLITlaK~~~l~~RR~a~~~l~d~~~v~kLF~~ia 84 (116)
T COG0203 5 KKGRKLGRTSSHRKAMLRNLATSLIEHERIETTLPKAKELRRVVEKLITLAKKGDLANRRLAFARLRDKDAVKKLFDEIA 84 (116)
T ss_pred ccCCCCCCCHHHHHHHHHHHHHHHHHcCceeecHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHcccHHHHHHHHHHhC
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccCCCCeEEEEeccCCCCCCCcceeeeccc
Q 031308 82 YRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFV 114 (161)
Q Consensus 82 PRy~~R~GGYTRI~kl~~R~GD~A~maiIE~lV 114 (161)
|||++|+||||||+|+|+|.||+||||||| ||
T Consensus 85 pry~~R~GGYtRIlK~g~R~GD~A~maiiE-lV 116 (116)
T COG0203 85 PRYAERNGGYTRILKLGFRRGDNAPMAIIE-LV 116 (116)
T ss_pred hhhcCCCCCeeEEEecCCCCCCCCceEEEE-eC
Confidence 999999999999999999999999999999 87
No 3
>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=2.9e-54 Score=327.44 Aligned_cols=112 Identities=47% Similarity=0.832 Sum_probs=110.3
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHH
Q 031308 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (161)
Q Consensus 3 ~~rkLgR~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaP 82 (161)
.++||||+++||++|||||+||||+||+|+||++||||+|+|||+|||+||+|++|++|++.+||.|+++|+|||++|+|
T Consensus 1 ~~~klgr~~~hR~allrnl~tsLi~herI~TT~~KAKelr~~aEklIt~AK~~~~~~rR~~~~~l~~~~~v~KLf~~lap 80 (112)
T TIGR00059 1 SYRKLGRTSAHRKALLRNLASALIRHEKIKTTLAKAKELRRVVEKLITLAKVDNFNNRREAKAYIRNKEIVHKLFSEIAP 80 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCeEEECHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCeEEEEeccCCCCCCCcceeeecccC
Q 031308 83 RYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVD 115 (161)
Q Consensus 83 Ry~~R~GGYTRI~kl~~R~GD~A~maiIE~lVd 115 (161)
||++|+||||||+|+++|.||+||||||| |||
T Consensus 81 ry~~R~GGYTRI~kl~~R~gD~A~maiiE-lVd 112 (112)
T TIGR00059 81 RYAQRPGGYTRILKLGPRRGDAAEMAIIE-LVD 112 (112)
T ss_pred HhCCCCCCeEEEEECCCCCCCCCCeEEEE-ecC
Confidence 99999999999999999999999999999 996
No 4
>PTZ00076 60S ribosomal protein L17; Provisional
Probab=100.00 E-value=9.3e-51 Score=341.49 Aligned_cols=127 Identities=31% Similarity=0.541 Sum_probs=122.7
Q ss_pred cccCCCCCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHH
Q 031308 3 KFRKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAY 82 (161)
Q Consensus 3 ~~rkLgR~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaP 82 (161)
+++||||+++||++|||||+||||+||||+||++||||+|+|||+|||+||+|++|++|+|.++|.|+++|+|||++|+|
T Consensus 18 ~~rKLgR~ssHR~AlLRNLvtsLI~hERIeTTlaKAKELR~~AEKLITlAKk~tl~sRR~a~s~L~d~~av~KLF~eLAP 97 (253)
T PTZ00076 18 LFRRAHGQPHHRWDSIKNQLDELLRYGRLELTLPRAKELQQYAEELIYLAKKDTPESNLKVESMLRTPQGRRKLYEKYVP 97 (253)
T ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHcCcEEecHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCHHHHHHHHHHhhh
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCCeEEEEec-cCCCCCCCcceeeecccCCchhhccCCCCCCCC
Q 031308 83 RYKDRAGGYTRLLRS-RIRVGDAAPMAYIDRFVDRENELRQSKPAVPQP 130 (161)
Q Consensus 83 Ry~~R~GGYTRI~kl-~~R~GD~A~maiIE~lVd~~~e~~~~~~~~~~~ 130 (161)
||++|+||||||+|+ ++|.||+||||||| |||++.++++++|++...
T Consensus 98 RY~dR~GGYTRIlK~~g~R~GD~ApMAiIE-LVd~p~e~r~A~pvg~d~ 145 (253)
T PTZ00076 98 LYRDRPFFFTRVVNQWRLRLRDAAPMAYIE-FVDRPGEIRPAKPVGFDK 145 (253)
T ss_pred HhcCCCCCeeEEEeCCCCCCCCCCCEEEEE-eccCcCccccccccchhH
Confidence 999999999999997 69999999999999 999999999998886544
No 5
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-49 Score=316.32 Aligned_cols=150 Identities=52% Similarity=0.794 Sum_probs=140.6
Q ss_pred cCCCCCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHh-hcCChHHH--HHHHHhhcChhHHHHHHHHHH
Q 031308 5 RKLNRPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLG-KEGSLCAA--RRAAAFVRGDDVIHKLFTELA 81 (161)
Q Consensus 5 rkLgR~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~A-K~g~~~~r--r~a~~~L~d~~~v~KLF~ela 81 (161)
.|+||++.||.+|||||||+||+||||+|||+||||+|+|||+|||+| |.|+++++ +++.+||..+++++|||+||+
T Consensus 15 ~Klgr~~~~R~~lLR~lvt~LvkHErIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~KlF~vl~ 94 (171)
T KOG3280|consen 15 LKLGRPPAHRLALLRNLVTQLVKHERIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLHKLFTVLA 94 (171)
T ss_pred hhcCCCcHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHHHHHHHhc
Confidence 499999999999999999999999999999999999999999999999 78999988 999999999999999999999
Q ss_pred HhhccCCCCeEEEEeccCCCCCCCcceeeecccCCchhhccCCCCCCCCCCCCCCCHHHHHhhhhhcCCCCCCCCCcc
Q 031308 82 YRYKDRAGGYTRLLRSRIRVGDAAPMAYIDRFVDRENELRQSKPAVPQPPPRAALDPWTRSRLTKNFAPPKQEKSSDA 159 (161)
Q Consensus 82 PRy~~R~GGYTRI~kl~~R~GD~A~maiIE~lVd~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (161)
|||++|+|||||++|+++|.||+||||||| |++++ .....++-+.++.+|.+|....+.++|+||++|+-.+.
T Consensus 95 pRY~dr~ggYTRllrlppr~~d~apmavlE-~~Gn~----~p~~~a~~p~~r~~lh~vll~~l~r~~~~~~~e~l~~~ 167 (171)
T KOG3280|consen 95 PRYKDRNGGYTRLLRLPPRRGDRAPMAVLE-LVGNP----LPQQAADRPDTRVNLHKVLLFRLLREFRPPKEEKLDDS 167 (171)
T ss_pred hhhccCCCCceehhccCcccccccCceeee-ecCCc----cccccCCCchhhhhhHHHHHHHHHHHhccchhhcccCc
Confidence 999999999999999999999999999999 99865 34566677788999999999999999999999986553
No 6
>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=1.6e-47 Score=283.83 Aligned_cols=97 Identities=53% Similarity=0.878 Sum_probs=95.2
Q ss_pred HHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhhccCCCCeEEEEe
Q 031308 17 MLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYTRLLR 96 (161)
Q Consensus 17 llRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy~~R~GGYTRI~k 96 (161)
|||||+|+||+||||+||++||||+|+|||+|||+||+|++|+++++.+||.|+++++|||++|+|||++|+||||||+|
T Consensus 1 llrnlvt~Li~herI~TT~~KAke~r~~aErlIt~ak~~~~~~~r~~~~~l~~~~~v~KLf~~l~pRy~~r~GgYTRi~k 80 (97)
T PF01196_consen 1 LLRNLVTSLIRHERIETTLAKAKELRPYAERLITLAKKGDLHARRQALSWLRDKELVKKLFKELAPRYADRNGGYTRIIK 80 (97)
T ss_dssp HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHTSSTHHHHHHHHHCSSSHHHHHHHHTTHHHHTTTSSS-SEEEEE
T ss_pred ChHHHHHHHHhCCeEEecHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHhcchHHHHHHHHHHHHHHccCCCCeEEEEe
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCCcceeeeccc
Q 031308 97 SRIRVGDAAPMAYIDRFV 114 (161)
Q Consensus 97 l~~R~GD~A~maiIE~lV 114 (161)
+++|.||+||||||| ||
T Consensus 81 l~~R~gD~A~maiiE-lV 97 (97)
T PF01196_consen 81 LGPRRGDAAPMAIIE-LV 97 (97)
T ss_dssp EEECSSSTCEEEEEE-ET
T ss_pred CCCCCCCCCCEEEEE-eC
Confidence 999999999999999 97
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=48.54 E-value=41 Score=23.22 Aligned_cols=47 Identities=17% Similarity=0.317 Sum_probs=32.2
Q ss_pred HHHHHHhhcCC---hHHHHHHHHhhcChhHHHHHHHHHHHh-----hccCCCCeE
Q 031308 46 DNMVQLGKEGS---LCAARRAAAFVRGDDVIHKLFTELAYR-----YKDRAGGYT 92 (161)
Q Consensus 46 EkLIt~AK~g~---~~~rr~a~~~L~d~~~v~KLF~elaPR-----y~~R~GGYT 92 (161)
.=|+.+|..++ ......+...=..+..+.++++.|... ...++|||.
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 556667776667888999999999865 356677775
No 8
>PRK13266 Thf1-like protein; Reviewed
Probab=45.72 E-value=38 Score=28.97 Aligned_cols=78 Identities=19% Similarity=0.279 Sum_probs=59.8
Q ss_pred CCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcCh--hHHHHHHHHHHHhhcc
Q 031308 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGD--DVIHKLFTELAYRYKD 86 (161)
Q Consensus 9 R~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~--~~v~KLF~elaPRy~~ 86 (161)
++.+|+..++..||.++= --+.++|..|++|..+|+..+.. .+.+||... .....|...+...=.+
T Consensus 68 ~Pee~~~~IF~Alc~a~~---------~dp~~~r~dA~~l~~~a~~~s~~---~i~~~l~~~~~~~~~~l~~~l~~ia~~ 135 (225)
T PRK13266 68 RPEEHKDSIFNALCQAVG---------FDPEQLRQDAERLLELAKGKSLK---EILSWLTQKALGEPGGLLATLLAIANN 135 (225)
T ss_pred CChHHHHHHHHHHHHHcC---------CCHHHHHHHHHHHHHHHhcCCHH---HHHHHHhccccccchhHHHHHHHHhcC
Confidence 477899999999999863 45899999999999999977665 455677643 2233366666666677
Q ss_pred CCCCeEEEEecc
Q 031308 87 RAGGYTRLLRSR 98 (161)
Q Consensus 87 R~GGYTRI~kl~ 98 (161)
.+--|.|++=+|
T Consensus 136 ~~f~YSRl~AIG 147 (225)
T PRK13266 136 SKFKYSRLFAIG 147 (225)
T ss_pred CCCchHHHHHHH
Confidence 888899998877
No 9
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=42.50 E-value=52 Score=24.87 Aligned_cols=45 Identities=22% Similarity=0.337 Sum_probs=30.0
Q ss_pred HHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhhccCCCCeE
Q 031308 42 RRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYT 92 (161)
Q Consensus 42 r~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy~~R~GGYT 92 (161)
.+-+||+-.+|-+.-+.. +=-++..+.+.|++|+-||.+..|+-|
T Consensus 24 ~keAERigRiAlKAGLge------ieI~d~eL~~aFeeiAaRFR~g~~~~~ 68 (98)
T PRK13848 24 TREAERIGRIALKAGLGE------IEIEEAELQAAFEELAKRFRGGKGAAT 68 (98)
T ss_pred HHHHHHHHHHHHHcCccc------cccCHHHHHHHHHHHHHHHhcCCCccc
Confidence 345666666664433321 112566789999999999999888654
No 10
>COG1775 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]
Probab=36.10 E-value=76 Score=29.25 Aligned_cols=90 Identities=22% Similarity=0.327 Sum_probs=61.4
Q ss_pred HhcCceeecHHhHHHHHHhHHHHHHHhhcCC------hHHHHHHHH-hhcChhHHHHHHHHHHHhhccC--CCCeEEEEe
Q 031308 26 VKHERIETTVAKAKEVRRLADNMVQLGKEGS------LCAARRAAA-FVRGDDVIHKLFTELAYRYKDR--AGGYTRLLR 96 (161)
Q Consensus 26 i~herI~TT~~KAKelr~~aEkLIt~AK~g~------~~~rr~a~~-~L~d~~~v~KLF~elaPRy~~R--~GGYTRI~k 96 (161)
|..+..+-+.++.-++|..--+++.+++... -+....+.+ ++.|.+...-.++++..+++.| .|+=+||+-
T Consensus 160 iT~e~L~da~~r~N~~rea~~k~~kL~~~~P~plsg~D~~~~~~~~~~~~d~d~~~~~l~~l~eelekr~~eg~~~Ri~~ 239 (379)
T COG1775 160 ITEEKLRDAIARYNRLREALAKLYKLAKHKPSPLSGSDAFNVMAFAVFLRDKDAFIEELEELIEELEKRVEEGEGPRILI 239 (379)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCchhHHHHHhhHHHHhcchHHHHHHHHHHHHHHHHHHhccCCceEEe
Confidence 3455666778888888888888999998542 344455555 7888887777777777766555 233399999
Q ss_pred ccCC-CCCCCcce-eeecccCC
Q 031308 97 SRIR-VGDAAPMA-YIDRFVDR 116 (161)
Q Consensus 97 l~~R-~GD~A~ma-iIE~lVd~ 116 (161)
.|.| .+|+-+.- ++| .+.+
T Consensus 240 ~g~p~~~~~~~v~~~~e-~~~~ 260 (379)
T COG1775 240 TGIPILGDNPKVWEILE-EVGE 260 (379)
T ss_pred ecCcccCCCcchhHHHH-hhcc
Confidence 9988 56776643 344 4443
No 11
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=34.10 E-value=1.4e+02 Score=19.80 Aligned_cols=73 Identities=14% Similarity=0.115 Sum_probs=37.0
Q ss_pred CCCchHHHHHHHHHHHHHHhcC-ceeecHHhHHHHHHhHHHHHHH---hhcCChHHHHHHHHhhcChhHHHHHHHHHH
Q 031308 8 NRPTGHRMSMLRTMVSQLVKHE-RIETTVAKAKEVRRLADNMVQL---GKEGSLCAARRAAAFVRGDDVIHKLFTELA 81 (161)
Q Consensus 8 gR~~~hR~allRnLvtsLi~he-rI~TT~~KAKelr~~aEkLIt~---AK~g~~~~rr~a~~~L~d~~~v~KLF~ela 81 (161)
||++-+-..|++-++-+-...- ...-....++. ....-.+.-+ ...-+..+-......+.++++.++||++++
T Consensus 1 GRp~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~-~~~~r~~~g~~~~~~~pd~stl~rfr~rl~~~~~~~~lf~~~v 77 (77)
T PF05598_consen 1 GRPAYPPRMMLKALLLKYLFGLRSDRELEERLRD-NLSFRYFCGLSLEEPVPDHSTLSRFRKRLIQHGLIEKLFDQVV 77 (77)
T ss_pred CcCCCCHHHHHHHHHHHHHHhcchHHHHHhhHhh-hhHHHHHHhcccCCCCCChHHHHHHHHHHhhccHHHHHHHHhC
Confidence 7787888888888887776643 22111111111 0111111111 111122233333356777889999998864
No 12
>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=33.37 E-value=83 Score=25.10 Aligned_cols=46 Identities=15% Similarity=0.299 Sum_probs=29.7
Q ss_pred HHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhhccCCCCeE
Q 031308 45 ADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGYT 92 (161)
Q Consensus 45 aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy~~R~GGYT 92 (161)
+|-++-.+-++ -+......++.+.+.+.++.++|...|.+.++|+.
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 55666655443 33444555555888999999999999987777764
No 13
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=29.78 E-value=1.2e+02 Score=27.00 Aligned_cols=78 Identities=13% Similarity=0.231 Sum_probs=61.2
Q ss_pred CCchHHHHHHHHHHHHHHhcCceeecHHhHHHHHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhh-ccC
Q 031308 9 RPTGHRMSMLRTMVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRY-KDR 87 (161)
Q Consensus 9 R~~~hR~allRnLvtsLi~herI~TT~~KAKelr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy-~~R 87 (161)
++.+|+..++..||.++=. -+.++|..|++|..+|+..+.. .+..|+.....+...+..|+.+= .+.
T Consensus 119 ~Pee~~~~IF~Alc~a~g~---------Dp~qyr~dA~~l~~~A~~~s~~---~l~~~l~~~~~l~~~l~~IA~~a~~~~ 186 (283)
T PLN00047 119 PSDEDRDAIFKAYIKALGE---------DPEQYRKDAAKLEEWARSQTGS---SLVDFSSKEGEIEGILKDIAERAGSKG 186 (283)
T ss_pred CChHHHHHHHHHHHHHcCC---------CHHHHHHHHHHHHHHHhcCCHH---HHHHHHhcchHHHHHHHHHHHhhccCC
Confidence 4678999999999998743 4789999999999999976655 45577777788888888888554 334
Q ss_pred CCCeEEEEecc
Q 031308 88 AGGYTRLLRSR 98 (161)
Q Consensus 88 ~GGYTRI~kl~ 98 (161)
+--|.|++-+|
T Consensus 187 ~f~YSRlfAIG 197 (283)
T PLN00047 187 KFSYSRFFAIG 197 (283)
T ss_pred CcchHHHHHHH
Confidence 55799998776
No 14
>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=28.83 E-value=11 Score=30.35 Aligned_cols=37 Identities=22% Similarity=0.403 Sum_probs=20.8
Q ss_pred HHHHhhccC----------CCCeEEEEeccCCCCCCCcceeeecccCC
Q 031308 79 ELAYRYKDR----------AGGYTRLLRSRIRVGDAAPMAYIDRFVDR 116 (161)
Q Consensus 79 elaPRy~~R----------~GGYTRI~kl~~R~GD~A~maiIE~lVd~ 116 (161)
+|.-||..- .|||-||.|+.....+.--..+++ .++.
T Consensus 45 Vl~TRFT~e~GY~VESrRGGGGyIRI~rv~~~~~~~~~~~l~~-~ig~ 91 (152)
T PF05848_consen 45 VLSTRFTPERGYIVESRRGGGGYIRIVRVPLDDEEDLLDHLIE-SIGD 91 (152)
T ss_dssp HHHHHSSCCCTEEEEEE-STT-EEEEEEEEESTCHHHHHHHHC-CS-S
T ss_pred eeeccccCCCCeEEEeccCCCceEEEEEEccCCcHHHHHHHHH-HhcC
Confidence 456677543 579999999876543333333444 4443
No 15
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=27.14 E-value=1.9e+02 Score=23.74 Aligned_cols=51 Identities=16% Similarity=0.287 Sum_probs=33.8
Q ss_pred HHHhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhhccCCCCe
Q 031308 41 VRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAGGY 91 (161)
Q Consensus 41 lr~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy~~R~GGY 91 (161)
+...+|-++-.+-...+...+.+.-+=.+...|.++.++|...|.++++|+
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi 55 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGL 55 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCE
Confidence 456688888887664233333333222345679999999999999776554
No 16
>COG4463 CtsR Transcriptional repressor of class III stress genes [Transcription]
Probab=26.76 E-value=39 Score=27.35 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=11.2
Q ss_pred CCCeEEEEeccCC
Q 031308 88 AGGYTRLLRSRIR 100 (161)
Q Consensus 88 ~GGYTRI~kl~~R 100 (161)
.|||.||.|..++
T Consensus 64 GGGYIRI~Kv~~~ 76 (153)
T COG4463 64 GGGYIRIIKVEYS 76 (153)
T ss_pred CCceEEEEEeccc
Confidence 6899999998765
No 17
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=25.65 E-value=1.5e+02 Score=23.13 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=32.7
Q ss_pred HHHHHHhhcCC--h-HHHHHHHHhhcChhHHHHHHHHHHHh-----hccCCCCeE
Q 031308 46 DNMVQLGKEGS--L-CAARRAAAFVRGDDVIHKLFTELAYR-----YKDRAGGYT 92 (161)
Q Consensus 46 EkLIt~AK~g~--~-~~rr~a~~~L~d~~~v~KLF~elaPR-----y~~R~GGYT 92 (161)
--|+.+|++++ . .....|...=-++.-+.|+|..|..- ...++|||.
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~ 66 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYR 66 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCcc
Confidence 44778887654 3 35666666666888899999988653 566677773
No 18
>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=23.91 E-value=2e+02 Score=21.49 Aligned_cols=41 Identities=17% Similarity=0.305 Sum_probs=25.9
Q ss_pred HhHHHHHHHhhcCChHHHHHHHHhhcChhHHHHHHHHHHHhhccCCC
Q 031308 43 RLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTELAYRYKDRAG 89 (161)
Q Consensus 43 ~~aEkLIt~AK~g~~~~rr~a~~~L~d~~~v~KLF~elaPRy~~R~G 89 (161)
+.+||+-.+|-+.-+. .+--+.+.+.+.|++|+-||....+
T Consensus 24 keaERigr~AlKaGL~------eieI~d~eL~~~FeeIa~RFrk~~~ 64 (92)
T PF07820_consen 24 KEAERIGRIALKAGLG------EIEISDAELQAAFEEIAARFRKGKK 64 (92)
T ss_pred HHHHHHHHHHHHcccc------cccCCHHHHHHHHHHHHHHHhcccc
Confidence 4455555555332222 2223567899999999999987644
No 19
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=20.54 E-value=1.2e+02 Score=18.83 Aligned_cols=21 Identities=5% Similarity=0.224 Sum_probs=17.8
Q ss_pred CCCchHHHHHHHHHHHHHHhc
Q 031308 8 NRPTGHRMSMLRTMVSQLVKH 28 (161)
Q Consensus 8 gR~~~hR~allRnLvtsLi~h 28 (161)
||+.+++.+|.+.+...|.++
T Consensus 10 grt~eqk~~l~~~i~~~l~~~ 30 (58)
T cd00491 10 GRTDEQKRELIERVTEAVSEI 30 (58)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 788889999999888888765
No 20
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=20.27 E-value=1.1e+02 Score=22.95 Aligned_cols=43 Identities=16% Similarity=0.363 Sum_probs=24.0
Q ss_pred HHhHHHHHHHhhcCChH---HHHHHHHhhc---ChhHHHHHHHHHHHhh
Q 031308 42 RRLADNMVQLGKEGSLC---AARRAAAFVR---GDDVIHKLFTELAYRY 84 (161)
Q Consensus 42 r~~aEkLIt~AK~g~~~---~rr~a~~~L~---d~~~v~KLF~elaPRy 84 (161)
=..||++|..||+.+.+ +..++...+. +...=..||+++|.-|
T Consensus 31 G~iAe~II~~Ake~~Vpi~edp~Lv~~L~~lelg~~IPeelY~vVAEif 79 (92)
T COG2257 31 GEIAEKIIEKAKEHGVPIQEDPLLVELLLKLELGDEIPEELYEVVAEIF 79 (92)
T ss_pred hHHHHHHHHHHHHcCCCcccCHHHHHHHHhccccccCCHHHHHHHHHHH
Confidence 35799999999987653 2222222222 3344445555555443
Done!