Query T0639 3NYM , Neisseria meningitidis MC58, 128 residues
Match_columns 128
No_of_seqs 2 out of 4
Neff 1.5
Searched_HMMs 11830
Date Thu Jul 22 14:54:11 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0639.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0639.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10663 EsxB: Virulence facto 46.8 6.5 0.00055 17.6 3.1 34 40-73 33-66 (101)
2 PF08823 PG_binding_2: Putativ 33.9 13 0.0011 15.7 3.1 34 7-65 18-51 (74)
3 PF05582 Peptidase_U57: YabG p 22.5 13 0.0011 15.7 1.2 35 62-96 183-221 (287)
4 PF06198 DUF999: Protein of un 14.1 17 0.0014 15.0 0.2 23 12-37 3-25 (143)
5 PF04285 DUF444: Protein of un 12.5 35 0.003 12.9 1.9 27 48-74 342-370 (421)
6 PF08671 SinI: Anti-repressor 12.5 35 0.003 12.9 2.1 12 58-69 19-30 (30)
7 PF10154 DUF2362: Uncharacteri 11.1 4.5 0.00038 18.6 -3.5 44 82-128 285-328 (510)
8 PF03666 NPR3: Nitrogen Permea 11.1 39 0.0033 12.7 1.9 35 94-128 198-233 (452)
9 PF06262 DUF1025: Domain of un 9.7 12 0.001 15.9 -1.7 27 16-44 28-54 (97)
10 PF12193 Sulf_coat_C: Sulfolob 8.9 29 0.0024 13.5 -0.0 24 16-39 14-37 (69)
No 1
>PF10663 EsxB: Virulence factor EsxB
Probab=46.81 E-value=6.5 Score=17.60 Aligned_cols=34 Identities=15% Similarity=0.437 Sum_probs=28.2
Q ss_pred CHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 0366542015776213689999999999999877
Q T0639 40 NMKWIKDYTSDGNWDNEFKEDLKNFLDYMEVCQL 73 (128)
Q Consensus 40 ~~~Wi~~YtSD~~W~~E~~ED~~~F~~~M~~~Q~ 73 (128)
..+=|+-|-....|+.+.+.-|..+++-|..|+-
T Consensus 33 ~~~~L~syI~sa~WsGktr~afl~~leli~qy~~ 66 (101)
T PF10663_consen 33 QAKELKSYIESADWSGKTRDAFLQYLELIIQYHK 66 (101)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999999974166687418899999999999998
No 2
>PF08823 PG_binding_2: Putative peptidoglycan binding domain; InterPro: IPR014927 This entry may be a peptidoglycan binding domain.
Probab=33.87 E-value=13 Score=15.75 Aligned_cols=34 Identities=24% Similarity=0.639 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 88999999972342264421224454421567303665420157762136899999999
Q T0639 7 LNDIKKILINVGLYQGFDLTDPKVSEEVNHETANMKWIKDYTSDGNWDNEFKEDLKNFL 65 (128)
Q Consensus 7 ~N~iK~~L~~~Gl~QGFDL~~~~~sE~~N~E~~~~~Wi~~YtSD~~W~~E~~ED~~~F~ 65 (128)
..-|...|..+|.|+| ..+|-|+.+.+..|..|.
T Consensus 18 ~~ev~~~L~rlGyy~~-------------------------~~~g~~dea~~~Al~~~~ 51 (74)
T PF08823_consen 18 ASEVQAALRRLGYYKG-------------------------PPSGVWDEATERALRAWA 51 (74)
T ss_pred HHHHHHHHHHCCCCCC-------------------------CCCCCCCHHHHHHHHHHH
T ss_conf 9999999998587558-------------------------866632389999999999
No 3
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. 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-, 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. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of Bacillus subtilis .
Probab=22.54 E-value=13 Score=15.73 Aligned_cols=35 Identities=26% Similarity=0.311 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHCCCH----HHHHHHHHHHHHHHHHH
Q ss_conf 999999999877615412----56788999999998610
Q T0639 62 KNFLDYMEVCQLALNDKN----FKIASNSLFMAMIYAGN 96 (128)
Q Consensus 62 ~~F~~~M~~~Q~Al~~~~----~K~A~~SL~~AMiY~GN 96 (128)
+.|.+-.++-.--..+.| |--||-|-|||+|-||-
T Consensus 183 kyFveaV~~aR~~~~~~D~LVIFAGACQS~fEail~AGA 221 (287)
T PF05582_consen 183 KYFVEAVKEARKYEPNLDDLVIFAGACQSHFEAILDAGA 221 (287)
T ss_pred HHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCC
T ss_conf 889999999982389954289982054788999997176
No 4
>PF06198 DUF999: Protein of unknown function (DUF999); InterPro: IPR009340 This is a family of conserved Schizosaccharomyces pombe proteins with unknown function.
Probab=14.12 E-value=17 Score=14.99 Aligned_cols=23 Identities=48% Similarity=0.705 Sum_probs=17.4
Q ss_pred HHHHHHHHHCCCCCCCHHHHHHHCCC
Q ss_conf 99997234226442122445442156
Q T0639 12 KILINVGLYQGFDLTDPKVSEEVNHE 37 (128)
Q Consensus 12 ~~L~~~Gl~QGFDL~~~~~sE~~N~E 37 (128)
+-.+||.+-||.||..| |+||..
T Consensus 3 ~d~~nvdle~gldlckp---ekvnkq 25 (143)
T PF06198_consen 3 EDVCNVDLEQGLDLCKP---EKVNKQ 25 (143)
T ss_pred CHHHCCCHHHHHHHCCH---HHHCHH
T ss_conf 21110567664421597---762457
No 5
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 These are Bacterial and Archaeal proteins of unknown function.
Probab=12.53 E-value=35 Score=12.95 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=12.2
Q ss_pred CCCC-CCCHHHHHHHHHHH-HHHHHHHHH
Q ss_conf 1577-62136899999999-999998776
Q T0639 48 TSDG-NWDNEFKEDLKNFL-DYMEVCQLA 74 (128)
Q Consensus 48 tSD~-~W~~E~~ED~~~F~-~~M~~~Q~A 74 (128)
-||| ||.+.-..-.+-.. +-+..|||-
T Consensus 342 aSDGDNw~~D~~~c~~lL~~~llp~~~~f 370 (421)
T PF04285_consen 342 ASDGDNWSDDNPRCVELLEEKLLPVCNYF 370 (421)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHCEE
T ss_conf 04777656777999999999888862527
No 6
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity . SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0045449 regulation of transcription; PDB: 1b0n_A.
Probab=12.45 E-value=35 Score=12.93 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999999
Q T0639 58 KEDLKNFLDYME 69 (128)
Q Consensus 58 ~ED~~~F~~~M~ 69 (128)
+|++..||+.+|
T Consensus 19 ~eevr~FL~~~K 30 (30)
T PF08671_consen 19 KEEVREFLESNK 30 (30)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHCCC
T ss_conf 999999987088
No 7
>PF10154 DUF2362: Uncharacterized conserved protein (DUF2362)
Probab=11.08 E-value=4.5 Score=18.63 Aligned_cols=44 Identities=23% Similarity=0.349 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 78899999999861089999999988999873000135557876689
Q T0639 82 IASNSLFMAMIYAGNLSLIFDSIKTDISTLLSAEYKKNSFSWPSLDE 128 (128)
Q Consensus 82 ~A~~SL~~AMiY~GNl~~~F~~iKtD~~~LL~~E~K~~~F~WP~~DE 128 (128)
.-|+|||--++-|-+--+++--+|.|+++.- -.-|+|..|++||
T Consensus 285 LYS~sL~GlVlLvd~~~n~~~~~k~~f~~~c---~~sTefHF~~~~~ 328 (510)
T PF10154_consen 285 LYSSSLCGLVLLVDSRINSYTGIKRDFAKNC---NESTEFHFPQIDE 328 (510)
T ss_pred HHHCCCEEEEEEECCCCCCCCCHHHHHHHHH---HHHHCCCCCCHHH
T ss_conf 8623650279983685232345446999998---8622248654789
No 8
>PF03666 NPR3: Nitrogen Permease regulator of amino acid transport activity 3; InterPro: IPR005365 This is a small family of proteins of unknown function.
Probab=11.07 E-value=39 Score=12.65 Aligned_cols=35 Identities=29% Similarity=0.203 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHCCCCCCCCCCCCC
Q ss_conf 6108999999998899-9873000135557876689
Q T0639 94 AGNLSLIFDSIKTDIS-TLLSAEYKKNSFSWPSLDE 128 (128)
Q Consensus 94 ~GNl~~~F~~iKtD~~-~LL~~E~K~~~F~WP~~DE 128 (128)
|--|+-+|+.|.+.-+ .|.-...+.-+||+|...|
T Consensus 198 Ar~l~~~y~~Is~~~ia~l~in~~~~~SlqiP~~~~ 233 (452)
T PF03666_consen 198 ARALKDCYESISTSGIANLTINNDKTVSLQIPIKTE 233 (452)
T ss_pred HHHHHHHHHHHHHCCEEEEEECCCCEEEEECCCCCC
T ss_conf 999999999997558059996487405884686344
No 9
>PF06262 DUF1025: Domain of unknown function (DUF1025); InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3e11_A.
Probab=9.74 E-value=12 Score=15.89 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=19.6
Q ss_pred HHHHHCCCCCCCHHHHHHHCCCCCCHHHH
Q ss_conf 72342264421224454421567303665
Q T0639 16 NVGLYQGFDLTDPKVSEEVNHETANMKWI 44 (128)
Q Consensus 16 ~~Gl~QGFDL~~~~~sE~~N~E~~~~~Wi 44 (128)
-+|+|+|-.|+++.+.. .+..|+.-||
T Consensus 28 llGLy~GvpL~~~~~~~--~~~~P~rI~l 54 (97)
T PF06262_consen 28 LLGLYEGVPLTERSVGD--SGGLPDRIVL 54 (97)
T ss_dssp ----EE---HHHCS----------EEEEE
T ss_pred CCCCCCCCCCCCCCCCC--CCCCCCEEEE
T ss_conf 56336787778577567--7898899999
No 10
>PF12193 Sulf_coat_C: Sulfolobus virus coat protein C terminal
Probab=8.86 E-value=29 Score=13.47 Aligned_cols=24 Identities=29% Similarity=0.526 Sum_probs=12.9
Q ss_pred HHHHHCCCCCCCHHHHHHHCCCCC
Q ss_conf 723422644212244544215673
Q T0639 16 NVGLYQGFDLTDPKVSEEVNHETA 39 (128)
Q Consensus 16 ~~Gl~QGFDL~~~~~sE~~N~E~~ 39 (128)
+-.|||||.|--...-..+.+-.+
T Consensus 14 ~raiyqg~~lkv~ralnrig~g~a 37 (69)
T PF12193_consen 14 NRAIYQGFGLKVARALNRIGSGPA 37 (69)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf 289997561999999985177678
Done!