Query T0562 CmR116, , 123 residues
Match_columns 123
No_of_seqs 106 out of 630
Neff 7.6
Searched_HMMs 11830
Date Wed May 26 17:46:24 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0562.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0562.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04205 FMN_bind: FMN-binding 99.4 2E-14 1.7E-18 95.1 3.7 77 16-121 2-79 (79)
2 PF10437 Lip_prot_lig_C: Bacte 66.0 2.7 0.00023 19.1 3.7 22 16-37 14-35 (86)
3 PF02073 Peptidase_M29: Thermo 53.4 3.8 0.00032 18.2 2.7 36 3-38 253-288 (398)
4 PF05031 NEAT: Iron Transport- 50.9 3.9 0.00033 18.2 2.4 36 1-36 5-50 (124)
5 PF03404 Mo-co_dimer: Mo-co ox 29.5 15 0.0012 15.1 2.7 36 3-38 26-63 (131)
6 PF10055 DUF2292: Uncharacteri 29.4 15 0.0012 15.1 3.0 19 20-38 16-34 (38)
7 PF07311 DUF1458: Protein of u 19.0 12 0.001 15.5 0.5 14 108-121 14-27 (66)
8 PF00449 Urease_alpha: Urease 18.2 18 0.0015 14.6 1.2 20 17-36 79-98 (121)
9 PF02593 DUF166: Uncharacteriz 18.0 25 0.0021 13.9 2.9 26 18-43 131-156 (217)
10 PF03544 TonB: Gram-negative b 16.2 28 0.0024 13.6 4.1 26 16-41 14-40 (79)
No 1
>PF04205 FMN_bind: FMN-binding domain; InterPro: IPR007329 This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins.; GO: 0010181 FMN binding, 0016020 membrane; PDB: 3dcz_A.
Probab=99.44 E-value=2e-14 Score=95.08 Aligned_cols=77 Identities=32% Similarity=0.392 Sum_probs=61.2
Q ss_pred CCCEEEEEEEEEC-CEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHCCCCCC
Q ss_conf 8867899999758-988888888652788756422123431111224445434678888999988611560001014566
Q T0562 16 SGWKDTVTIEVKN-GKIVSVDWNAINKDGGDDKDTLSRNGGYKMVEYGGAQAEWHEQAEKVEAYLVEKQDPTDIKYKDND 94 (123)
Q Consensus 16 ~g~~~~v~vtvkd-gkI~~v~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~e~~~~l~~~li~~q~~~~~~~~~~~ 94 (123)
+++++.|.|+|++ |+|++|+++.+.+++...+.. +.+.+.++++++| .++
T Consensus 2 y~g~i~v~v~i~~dg~I~~v~~~~~~Et~g~~~~~---------------------~~~~~~~~~~~~~--------~~~ 52 (79)
T PF04205_consen 2 YGGPITVTVTIDNDGKITGVEILEHNETPGLGDKV---------------------ADEEFFDQFIGKQ--------DDS 52 (79)
T ss_dssp ----EEEEEEE-----EEEEEEES-----------------------------------TTGGGG--B------------
T ss_pred CCCCEEEEEEEECCCEEEEEEEEEECCCCCHHHCC---------------------CHHHHHHHHHHCC--------CCC
T ss_conf 77718999999079979999997706895553105---------------------5788999975103--------577
Q ss_pred CCCCCEEECEECHHHHHHHHHHHHHHH
Q ss_conf 542201202050899999999999984
Q T0562 95 GHTDAISGATIKVKKFFDLAQKALKDA 121 (123)
Q Consensus 95 ~~vD~vSGATiss~~~~~av~~AL~~A 121 (123)
.+||+|||||+||++|.+||++||++|
T Consensus 53 ~~vD~VSGAT~ss~~~~~av~~al~~A 79 (79)
T PF04205_consen 53 ADVDAVSGATISSNAIKKAVKNALEQA 79 (79)
T ss_dssp B-TT--------HHHHHHHHH------
T ss_pred CCCCEEECCCCCHHHHHHHHHHHCCCC
T ss_conf 898808786300999999998661379
No 2
>PF10437 Lip_prot_lig_C: Bacterial lipoate protein ligase C-terminus; PDB: 1vqz_A 1x2h_A 1x2g_C.
Probab=66.01 E-value=2.7 Score=19.09 Aligned_cols=22 Identities=18% Similarity=0.161 Sum_probs=19.3
Q ss_pred CCCEEEEEEEEECCEEEEEEEE
Q ss_conf 8867899999758988888888
Q T0562 16 SGWKDTVTIEVKNGKIVSVDWN 37 (123)
Q Consensus 16 ~g~~~~v~vtvkdgkI~~v~~~ 37 (123)
.||.+.+.+.|++|+|.+|.+-
T Consensus 14 ~~G~iei~l~V~~G~I~~i~i~ 35 (86)
T PF10437_consen 14 PWGTIEIQLNVKKGIIKDIKIY 35 (86)
T ss_dssp ----EEEEEEEETTEEEEEEEE
T ss_pred CCCEEEEEEEEECCEEEEEEEE
T ss_conf 8856999999979999899998
No 3
>PF02073 Peptidase_M29: Thermophilic metalloprotease (M29); InterPro: IPR000787 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . 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. This group of metallopeptidases belong to MEROPS peptidase family M29 (aminopeptidase T family, clan M-). The protein fold of the peptidase domain and the active site residues are not known for any members of the thermophilic metallo-aminopeptidases family. ; GO: 0004177 aminopeptidase activity, 0006508 proteolysis; PDB: 1zjc_A 2ayi_D.
Probab=53.39 E-value=3.8 Score=18.25 Aligned_cols=36 Identities=11% Similarity=0.242 Sum_probs=21.1
Q ss_pred CCEEEEEEECCCCCCCEEEEEEEEECCEEEEEEEEE
Q ss_conf 846889862636888678999997589888888886
Q T0562 3 DGTYYAEADDFDESGWKDTVTIEVKNGKIVSVDWNA 38 (123)
Q Consensus 3 DGtY~~~~~~~d~~g~~~~v~vtvkdgkI~~v~~~~ 38 (123)
+|+.....+-.....-...+.++|+||+|++++-..
T Consensus 253 ~G~v~~~~pl~~~G~~~~~i~l~fkdG~Vv~~~a~~ 288 (398)
T PF02073_consen 253 NGVVVFDKPLSYNGNLIENIRLTFKDGRVVDAEAEE 288 (398)
T ss_dssp B--EE-SS-EE----EEEEEEEEE----EEEEEEEE
T ss_pred EEEEEECCCCCCCCEEEECEEEEEECCEEEEEECCC
T ss_conf 589997733352888771529999899899998645
No 4
>PF05031 NEAT: Iron Transport-associated domain ; InterPro: IPR006635 This domain identifies a small family of protein with no known function which are found exclusively in bacteria.; PDB: 2z6f_A 2e7d_A 2h3k_A 2o1a_A 2itf_D 2ite_A 2k78_A 2o6p_B.
Probab=50.94 E-value=3.9 Score=18.21 Aligned_cols=36 Identities=28% Similarity=0.590 Sum_probs=20.9
Q ss_pred CCCCEEEEEEECCC--------CCCC-EEEEEEEEECCEEE-EEEE
Q ss_conf 98846889862636--------8886-78999997589888-8888
Q T0562 1 MKDGTYYAEADDFD--------ESGW-KDTVTIEVKNGKIV-SVDW 36 (123)
Q Consensus 1 lkDGtY~~~~~~~d--------~~g~-~~~v~vtvkdgkI~-~v~~ 36 (123)
|+||+|+....-.. .+++ .-.+.|+|+|||.. .+.+
T Consensus 5 l~dG~Y~v~~~v~k~~~~~~Sma~~y~~~~a~l~vknGk~~vtlt~ 50 (124)
T PF05031_consen 5 LEDGTYTVNFKVLKDGTDEPSMANGYINKPAKLTVKNGKYYVTLTF 50 (124)
T ss_dssp SSEEEEEEEEEEEESSSSSBTCGGGGB-SSEEEEEETTEEEEEEEE
T ss_pred CCCCEEEEEEEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE
T ss_conf 5796499999999889975173776337988999999989999998
No 5
>PF03404 Mo-co_dimer: Mo-co oxidoreductase dimerisation domain; InterPro: IPR005066 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , . In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) . This domain is found in molybdopterin cofactor oxidoreductases, such as in the C-terminal of Mo-containing sulphite oxidase, which catalyses the conversion of sulphite to sulphate, the terminal step in the oxidative degradation of cysteine and methionine . This domain is involved in dimer formation, and has an Ig-fold structure .; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding; PDB: 2ca3_A 2bpb_A 2c9x_A 2blf_A 2ca4_A 2a9d_A 2a9b_A 2a99_A 2a9a_B 2a9c_B ....
Probab=29.50 E-value=15 Score=15.13 Aligned_cols=36 Identities=17% Similarity=0.294 Sum_probs=27.5
Q ss_pred CCEEEEEEECCCCCC-CEEEEEEEEECCE-EEEEEEEE
Q ss_conf 846889862636888-6789999975898-88888886
Q T0562 3 DGTYYAEADDFDESG-WKDTVTIEVKNGK-IVSVDWNA 38 (123)
Q Consensus 3 DGtY~~~~~~~d~~g-~~~~v~vtvkdgk-I~~v~~~~ 38 (123)
||.|+...-.+++.| ....|+|.+.+|+ =..+++..
T Consensus 26 ~~~~~i~G~A~~Ggg~~I~rVEVS~DgG~tW~~A~l~~ 63 (131)
T PF03404_consen 26 DGPVTIRGYAWSGGGRGIERVEVSLDGGKTWQEAELEG 63 (131)
T ss_dssp S-EEEEE-EEE------EEEEEEES-----EEE-EEES
T ss_pred CEEEEEEEEEECCCCCCEEEEEEEECCCCCCEEEEECC
T ss_conf 82799999999299986889999818999556817516
No 6
>PF10055 DUF2292: Uncharacterized small protein (DUF2292)
Probab=29.41 E-value=15 Score=15.12 Aligned_cols=19 Identities=32% Similarity=0.688 Sum_probs=15.9
Q ss_pred EEEEEEEECCEEEEEEEEE
Q ss_conf 8999997589888888886
Q T0562 20 DTVTIEVKNGKIVSVDWNA 38 (123)
Q Consensus 20 ~~v~vtvkdgkI~~v~~~~ 38 (123)
..|+++|.||+|+-++..+
T Consensus 16 Gsvti~vqdg~VvQIe~~E 34 (38)
T PF10055_consen 16 GSVTITVQDGRVVQIERTE 34 (38)
T ss_pred CEEEEEEECCEEEEEEEHH
T ss_conf 3599999989999998134
No 7
>PF07311 DUF1458: Protein of unknown function (DUF1458); InterPro: IPR009923 This entry represents proteins with a Dodecin-like topology. Dodecin flavoprotein is a small dodecameric flavin-binding protein from Halobacterium salinarium (Halobacterium halobium) that contains two flavins stacked in a single binding pocket between two tryptophan residues to form an aromatic tetrade . Dodecin binds riboflavin, although it appears to have a broad specificity for flavins. Lumichrome, a molecule associated with flavin metabolism, appears to be a ligand of dodecin, which could act as a waste-trapping device. ; PDB: 2vxa_F 2ux9_A 2cz8_E 2v18_K 2v19_E 2v21_A 2deg_E 2dev_E 2deh_A 2vx9_A ....
Probab=19.04 E-value=12 Score=15.54 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99999999999984
Q T0562 108 KKFFDLAQKALKDA 121 (123)
Q Consensus 108 ~~~~~av~~AL~~A 121 (123)
.+|-.|+++|+..|
T Consensus 14 ~S~edAi~~Ai~~A 27 (66)
T PF07311_consen 14 KSWEDAIQNAIERA 27 (66)
T ss_dssp S-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH
T ss_conf 88999999999986
No 8
>PF00449 Urease_alpha: Urease alpha-subunit, N-terminal domain; InterPro: IPR011612 Urease (urea amidohydrolase, 3.5.1.5 from EC) catalyses the hydrolysis of urea to form ammonia and carbamate. The subunit composition of urease from different sources varies , but each holoenzyme consists of four structural domains : three structural domains and a nickel-binding catalytic domain common to amidohydrolases . Urease is unique among nickel metalloenzymes in that it catalyses a hydrolysis rather than a redox reaction. In Helicobacter pylori, the gamma and beta domains are fused and called the alpha subunit (IPR008223 from INTERPRO). The catalytic subunit (called beta or B) has the same organization as the Klebsiella alpha subunit. Jack bean (Canavalia ensiformis) urease has a fused gamma-beta-alpha organization (IPR008221 from INTERPRO). The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit . ; GO: 0009039 urease activity, 0016151 nickel ion binding, 0019627 urea metabolic process; PDB: 1s3t_C 3ubp_C 4ubp_C 1ubp_C 2ubp_C 1ie7_C 1nfg_B 1e9y_B 1e9z_B 1fwj_C ....
Probab=18.23 E-value=18 Score=14.63 Aligned_cols=20 Identities=25% Similarity=0.313 Sum_probs=15.3
Q ss_pred CCEEEEEEEEECCEEEEEEE
Q ss_conf 86789999975898888888
Q T0562 17 GWKDTVTIEVKNGKIVSVDW 36 (123)
Q Consensus 17 g~~~~v~vtvkdgkI~~v~~ 36 (123)
.+..+..|-|+||+|+.|--
T Consensus 79 ~Gi~kaDIGIkdGrI~~IGk 98 (121)
T PF00449_consen 79 TGIYKADIGIKDGRIVGIGK 98 (121)
T ss_dssp ---EEEEE---------B--
T ss_pred CCCEEEEEEECCCEEEEEEC
T ss_conf 77489577241889998504
No 9
>PF02593 DUF166: Uncharacterized ArCR, COG1810; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=18.00 E-value=25 Score=13.85 Aligned_cols=26 Identities=31% Similarity=0.287 Sum_probs=21.1
Q ss_pred CEEEEEEEEECCEEEEEEEEEECCCC
Q ss_conf 67899999758988888888652788
Q T0562 18 WKDTVTIEVKNGKIVSVDWNAINKDG 43 (123)
Q Consensus 18 ~~~~v~vtvkdgkI~~v~~~~~~~~~ 43 (123)
|...++|.|++|+|.+|.+..-..=|
T Consensus 131 G~P~lei~v~~~~i~~V~V~R~APCG 156 (217)
T PF02593_consen 131 GRPELEIEVEDGKIKDVKVLRGAPCG 156 (217)
T ss_pred CCCEEEEEECCCCEEEEEEEECCCCC
T ss_conf 99628998269937778886168885
No 10
>PF03544 TonB: Gram-negative bacterial tonB protein; InterPro: IPR003538 Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Such iron-protein complexes include haem in blood, lactoferrin in tears/saliva and transferrin in blood plasma. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins . The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis enzymes, and receptors that recognise iron-bound siderophores . An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin . To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors . B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0005381 iron ion transmembrane transporter activity, 0006826 iron ion transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2k9k_A 2gsk_B 1xx3_A 1ihr_A 1qxx_A 2grx_C 1u07_A 1lr0_A.
Probab=16.20 E-value=28 Score=13.61 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=21.3
Q ss_pred CCCEEEEEEEE-ECCEEEEEEEEEECC
Q ss_conf 88678999997-589888888886527
Q T0562 16 SGWKDTVTIEV-KNGKIVSVDWNAINK 41 (123)
Q Consensus 16 ~g~~~~v~vtv-kdgkI~~v~~~~~~~ 41 (123)
..+.+.|.++| .+|++.++++..-..
T Consensus 14 ~~G~v~v~~~I~~~G~v~~~~v~~s~~ 40 (79)
T PF03544_consen 14 IEGTVVVRFTIDPDGKVSNVKVVSSSG 40 (79)
T ss_dssp B---EEEEEEE-----EEEEEEEEESS
T ss_pred CCEEEEEEEEEECCCCEEEEEEEECCC
T ss_conf 917999999996999999999996586
Done!