Query 048164
Match_columns 72
No_of_seqs 15 out of 17
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 06:55:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048164hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2795 Catalytic subunit of t 98.1 2.1E-06 4.5E-11 68.2 3.4 41 27-67 143-184 (372)
2 PRK04342 DNA topoisomerase VI 97.1 0.00042 9.1E-09 53.5 3.3 41 26-66 140-180 (367)
3 PLN00060 meiotic recombination 96.9 0.00093 2E-08 52.7 3.3 40 27-66 159-199 (384)
4 COG1697 DNA topoisomerase VI, 95.5 0.011 2.3E-07 47.2 2.7 39 27-65 133-172 (356)
5 PF07943 PBP5_C: Penicillin-bi 47.1 25 0.00055 20.6 2.6 22 30-51 58-79 (91)
6 PF08272 Topo_Zn_Ribbon: Topoi 42.4 14 0.00031 21.4 1.0 20 30-49 18-37 (42)
7 PF06613 KorB_C: KorB C-termin 39.8 20 0.00044 22.6 1.5 14 38-51 33-46 (60)
8 KOG2852 Possible oxidoreductas 34.5 33 0.00072 28.2 2.3 37 5-41 23-62 (380)
9 KOG0021 Glutathione synthetase 31.2 19 0.00041 30.3 0.4 35 30-66 21-55 (468)
10 PF06030 DUF916: Bacterial pro 27.4 53 0.0011 21.7 2.0 13 33-45 108-120 (121)
11 PF15029 DUF4526: Protein of u 24.8 40 0.00087 26.1 1.2 8 37-44 48-55 (232)
12 PF10370 DUF2437: Domain of un 24.4 1.2E+02 0.0026 17.1 2.8 17 38-54 1-17 (50)
13 PTZ00116 signal peptidase; Pro 22.1 1.9E+02 0.0041 21.4 4.1 34 9-47 126-160 (185)
14 PRK09919 anti-adapter protein 21.1 67 0.0015 22.3 1.6 19 18-36 55-73 (114)
No 1
>KOG2795 consensus Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair]
Probab=98.13 E-value=2.1e-06 Score=68.23 Aligned_cols=41 Identities=27% Similarity=0.327 Sum_probs=36.1
Q ss_pred EeeeeeccceeEEEEEeee-cCeEEEeecCCCCcccceeeee
Q 048164 27 YHSISLCCRMVMGWLRFLE-SGAKFDCINSPNDVSGRMIYTF 67 (72)
Q Consensus 27 ~nVvsv~kGLVMGwLrF~E-ggr~iDCi~S~n~~~pIPV~ie 67 (72)
-||.|..||||+|||+|.| +|.++||.++...+.++|...+
T Consensus 143 LnI~a~~KGLV~G~l~~~~~ng~~id~~~~~~~~~~lp~d~~ 184 (372)
T KOG2795|consen 143 LNILAASKGLVAGRLRFLEENGDVIDCTESGGGPKALPPDID 184 (372)
T ss_pred CCeeeecCceEEeeEEEEEcCCcEEEeccCCCCCccCCCCHH
Confidence 3778999999999999955 9999999999999999997643
No 2
>PRK04342 DNA topoisomerase VI subunit A; Provisional
Probab=97.13 E-value=0.00042 Score=53.45 Aligned_cols=41 Identities=17% Similarity=0.043 Sum_probs=35.3
Q ss_pred EEeeeeeccceeEEEEEeeecCeEEEeecCCCCcccceeee
Q 048164 26 IYHSISLCCRMVMGWLRFLESGAKFDCINSPNDVSGRMIYT 66 (72)
Q Consensus 26 ~~nVvsv~kGLVMGwLrF~Eggr~iDCi~S~n~~~pIPV~i 66 (72)
-.||++..||+|.|.++|+++|.+|||.+....+..||...
T Consensus 140 ~L~I~a~~KGlv~G~i~i~~~~~~id~~~~g~~~~~ip~~~ 180 (367)
T PRK04342 140 ELHIRPEEDGSVVGPLRIRDGTDEIDCSKLGEGGYSIPPNV 180 (367)
T ss_pred HCCeeECCCeEEEeceEEEECCcEEEEeccCCCceeCCCch
Confidence 46899999999999999999999999998666777777543
No 3
>PLN00060 meiotic recombination protein SPO11-2; Provisional
Probab=96.89 E-value=0.00093 Score=52.66 Aligned_cols=40 Identities=13% Similarity=0.006 Sum_probs=33.5
Q ss_pred EeeeeeccceeEEEEEeee-cCeEEEeecCCCCcccceeee
Q 048164 27 YHSISLCCRMVMGWLRFLE-SGAKFDCINSPNDVSGRMIYT 66 (72)
Q Consensus 27 ~nVvsv~kGLVMGwLrF~E-ggr~iDCi~S~n~~~pIPV~i 66 (72)
.||+|..||+|.|.++|.+ ++..+||......|..||-.+
T Consensus 159 L~I~a~~KGlV~G~l~i~~~~~~~idcs~~g~~G~~Ip~~~ 199 (384)
T PLN00060 159 LGIMASSRGALIGRLVLQEPNEEPVDCSILGISGHAITGDL 199 (384)
T ss_pred CCeEecCCceEEeeeEEEecCCcEEEeeccCCCceeCCCcH
Confidence 5889999999999999976 668999987666788888543
No 4
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=95.52 E-value=0.011 Score=47.22 Aligned_cols=39 Identities=15% Similarity=-0.112 Sum_probs=34.3
Q ss_pred EeeeeeccceeEEEEEeee-cCeEEEeecCCCCcccceee
Q 048164 27 YHSISLCCRMVMGWLRFLE-SGAKFDCINSPNDVSGRMIY 65 (72)
Q Consensus 27 ~nVvsv~kGLVMGwLrF~E-ggr~iDCi~S~n~~~pIPV~ 65 (72)
.|+.+--+|+|+|-|++++ |+.+|||.+..-.|-.||..
T Consensus 133 l~i~p~ekG~V~G~l~I~~~g~~~i~~sk~G~~~y~Ip~~ 172 (356)
T COG1697 133 LGIRPEEKGLVYGPLRIREEGEDEIDASKLGGGGYLIPPD 172 (356)
T ss_pred cCCCcccCceEEcceEEEecCCcEEEeeecCCCCCcCCCC
Confidence 4678889999999999988 99999999988888888843
No 5
>PF07943 PBP5_C: Penicillin-binding protein 5, C-terminal domain; InterPro: IPR012907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (IPR001967 from INTERPRO) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides []. ; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3J_A 3MFD_B 1XP4_D 3MZD_A 1NZU_A 1NJ4_A 1Z6F_A 3MZF_A 1NZO_A 3MZE_A ....
Probab=47.08 E-value=25 Score=20.55 Aligned_cols=22 Identities=18% Similarity=0.149 Sum_probs=19.2
Q ss_pred eeeccceeEEEEEeeecCeEEE
Q 048164 30 ISLCCRMVMGWLRFLESGAKFD 51 (72)
Q Consensus 30 vsv~kGLVMGwLrF~Eggr~iD 51 (72)
.++-+|-++|.+++..+|+.+-
T Consensus 58 aPi~kG~~vG~~~v~~~~~~i~ 79 (91)
T PF07943_consen 58 APIKKGQVVGTLTVYLDGKLIG 79 (91)
T ss_dssp SGBGTTSEEEEEEEEETTEEEE
T ss_pred CcccCCCEEEEEEEEECCEEEE
Confidence 5779999999999999888764
No 6
>PF08272 Topo_Zn_Ribbon: Topoisomerase I zinc-ribbon-like ; InterPro: IPR013263 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the C-terminal zinc-ribbon-like domain found in bacterial topoisomerase I (type IA) enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1YUA_A.
Probab=42.43 E-value=14 Score=21.45 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=15.2
Q ss_pred eeeccceeEEEEEeeecCeE
Q 048164 30 ISLCCRMVMGWLRFLESGAK 49 (72)
Q Consensus 30 vsv~kGLVMGwLrF~Eggr~ 49 (72)
-+-..|+-+||-.|.++|+-
T Consensus 18 ~se~~Gk~tgw~af~~~gkw 37 (42)
T PF08272_consen 18 RSEADGKFTGWSAFYKDGKW 37 (42)
T ss_dssp EE-STTSEEEETCCCSSS-B
T ss_pred ecCCCCcEeeeeEeccCCeE
Confidence 34489999999999888764
No 7
>PF06613 KorB_C: KorB C-terminal beta-barrel domain; InterPro: IPR010575 This domain is found in several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This family is found in conjunction with IPR003115 from INTERPRO.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1IGQ_B 1IGU_A.
Probab=39.81 E-value=20 Score=22.58 Aligned_cols=14 Identities=21% Similarity=1.094 Sum_probs=9.9
Q ss_pred EEEEEeeecCeEEE
Q 048164 38 MGWLRFLESGAKFD 51 (72)
Q Consensus 38 MGwLrF~Eggr~iD 51 (72)
++|+.|.++|..|-
T Consensus 33 ~~WiKyED~G~e~E 46 (60)
T PF06613_consen 33 LAWIKYEDDGEEFE 46 (60)
T ss_dssp EEEEEETTT--EEE
T ss_pred eEEEEEccCCcEEE
Confidence 67999999888764
No 8
>KOG2852 consensus Possible oxidoreductase [General function prediction only]
Probab=34.54 E-value=33 Score=28.17 Aligned_cols=37 Identities=30% Similarity=0.612 Sum_probs=28.6
Q ss_pred eeeEEeeccCCCcccceeeeEEEeeeee---ccceeEEEE
Q 048164 5 CSIAYFLDSHSSYSGRKLDVNIYHSISL---CCRMVMGWL 41 (72)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~nVvsv---~kGLVMGwL 41 (72)
|.-||||-.|.||+-..+|+-|.-.-.+ ++|+--|-|
T Consensus 23 vctayyLt~~~sf~~~~~~ItifEs~~IA~gaSGkasgfL 62 (380)
T KOG2852|consen 23 VCTAYYLTEHPSFKKGELDITIFESKEIAGGASGKASGFL 62 (380)
T ss_pred eeeehhhhcCCccCCCceeEEEEeecccccccccccchhh
Confidence 5679999999999999999999876555 455544433
No 9
>KOG0021 consensus Glutathione synthetase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=31.15 E-value=19 Score=30.28 Aligned_cols=35 Identities=17% Similarity=0.092 Sum_probs=29.8
Q ss_pred eeeccceeEEEEEeeecCeEEEeecCCCCcccceeee
Q 048164 30 ISLCCRMVMGWLRFLESGAKFDCINSPNDVSGRMIYT 66 (72)
Q Consensus 30 vsv~kGLVMGwLrF~Eggr~iDCi~S~n~~~pIPV~i 66 (72)
-+...||||+..+|.+.++- |..+|-|-+|-|++.
T Consensus 21 wa~a~Glv~~~~~~~~s~~v--~~~~P~tl~Ps~~P~ 55 (468)
T KOG0021|consen 21 WAFAHGLVMRESSVSKSGEV--ASQAPITLFPSPIPH 55 (468)
T ss_pred HHHhcceeeccccccCCccc--ccccCceecCCcCcH
Confidence 35589999999999888887 888899999888764
No 10
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=27.43 E-value=53 Score=21.73 Aligned_cols=13 Identities=23% Similarity=0.398 Sum_probs=11.7
Q ss_pred ccceeEEEEEeee
Q 048164 33 CCRMVMGWLRFLE 45 (72)
Q Consensus 33 ~kGLVMGwLrF~E 45 (72)
-+|.++|-|+|.|
T Consensus 108 f~G~ilGGi~~~e 120 (121)
T PF06030_consen 108 FDGIILGGIYFSE 120 (121)
T ss_pred cCCEEEeeEEEEe
Confidence 5899999999976
No 11
>PF15029 DUF4526: Protein of unknown function (DUF4526)
Probab=24.79 E-value=40 Score=26.12 Aligned_cols=8 Identities=50% Similarity=1.560 Sum_probs=7.0
Q ss_pred eEEEEEee
Q 048164 37 VMGWLRFL 44 (72)
Q Consensus 37 VMGwLrF~ 44 (72)
||||+.|.
T Consensus 48 VmGWik~~ 55 (232)
T PF15029_consen 48 VMGWIKYQ 55 (232)
T ss_pred EEeeeecc
Confidence 89999885
No 12
>PF10370 DUF2437: Domain of unknown function (DUF2437); InterPro: IPR018833 This entry represents the N-terminal 50 amino acids of a group of bacterial proteins often annotated as fumarylacetoacetate hydrolase-containing enzymes. In most cases these proteins also contain IPR002529 from INTERPRO, which is found towards the C terminus. ; PDB: 3RR6_A 2DFU_D 3QDF_A.
Probab=24.37 E-value=1.2e+02 Score=17.14 Aligned_cols=17 Identities=24% Similarity=0.204 Sum_probs=12.1
Q ss_pred EEEEEeeecCeEEEeec
Q 048164 38 MGWLRFLESGAKFDCIN 54 (72)
Q Consensus 38 MGwLrF~Eggr~iDCi~ 54 (72)
|=|+||..+|+.....-
T Consensus 1 Mr~~Rf~~~g~~~~G~l 17 (50)
T PF10370_consen 1 MRIVRFSHGGEIRYGVL 17 (50)
T ss_dssp -EEEEEEETTEEEEEEE
T ss_pred CeEEEEeeCCCcEEEEE
Confidence 66889988888776653
No 13
>PTZ00116 signal peptidase; Provisional
Probab=22.05 E-value=1.9e+02 Score=21.41 Aligned_cols=34 Identities=15% Similarity=0.386 Sum_probs=24.8
Q ss_pred EeeccCCCcccceeeeEE-EeeeeeccceeEEEEEeeecC
Q 048164 9 YFLDSHSSYSGRKLDVNI-YHSISLCCRMVMGWLRFLESG 47 (72)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~-~nVvsv~kGLVMGwLrF~Egg 47 (72)
+|.|-.++..||.+.+.+ +||.+. .|++++.++.
T Consensus 126 ~l~D~~~~Lrg~~vtl~L~wnv~P~-----~G~l~~~~~~ 160 (185)
T PTZ00116 126 SLKDYNNGLRNNNINLQVCYKYMPI-----VGLSRSYEGA 160 (185)
T ss_pred eEEeCCCCccCCceEEEEEEEEEec-----ceeEeeeecc
Confidence 456999999998877765 688875 5777665543
No 14
>PRK09919 anti-adapter protein IraM; Provisional
Probab=21.11 E-value=67 Score=22.25 Aligned_cols=19 Identities=11% Similarity=0.293 Sum_probs=15.7
Q ss_pred ccceeeeEEEeeeeeccce
Q 048164 18 SGRKLDVNIYHSISLCCRM 36 (72)
Q Consensus 18 ~~~~~~~~~~nVvsv~kGL 36 (72)
.++...++||||.++.+-+
T Consensus 55 Ndk~~pItIYnvtpyn~~l 73 (114)
T PRK09919 55 NDKPYPITIYNITPFNKAL 73 (114)
T ss_pred CCcEeEEEEEEecccCHHH
Confidence 3677899999999997765
Done!