Query T0581 NP_252301.1, Pseudomonas aeruginosa PA01, 136 residues
Match_columns 136
No_of_seqs 11 out of 13
Neff 1.8
Searched_HMMs 11830
Date Sun Jun 13 15:17:14 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0581.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0581.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09936 DUF2168: Uncharacteri 45.3 1.9 0.00016 21.3 0.1 56 19-74 115-176 (184)
2 PF10697 DUF2502: Protein of u 40.2 2.7 0.00023 20.3 0.3 18 5-22 2-19 (99)
3 PF11479 Suppressor_P21: RNA s 20.6 13 0.0011 16.0 1.0 24 60-83 46-69 (177)
4 PF03548 LolA: Outer membrane 18.8 25 0.0021 14.2 2.1 27 100-126 137-163 (165)
5 PF09492 Pec_lyase: Pectic aci 15.6 18 0.0015 15.1 0.7 22 103-124 238-259 (289)
6 PF01799 Fer2_2: [2Fe-2S] bind 14.5 32 0.0027 13.5 2.2 49 50-102 23-71 (75)
7 PF03440 APT: Aerolysin/Pertus 14.5 2.5 0.00021 20.5 -3.9 30 70-100 13-42 (99)
8 PF05002 SGS: SGS domain ; In 12.5 32 0.0027 13.5 1.3 34 25-58 20-53 (78)
9 PF02788 RuBisCO_large_N: Ribu 12.3 31 0.0026 13.7 1.1 25 29-53 32-56 (126)
10 PF00879 Defensin_propep: Defe 11.4 40 0.0034 13.0 1.9 25 1-25 1-25 (52)
No 1
>PF09936 DUF2168: Uncharacterized protein conserved in bacteria (DUF2168); PDB: 3dcm_X.
Probab=45.28 E-value=1.9 Score=21.29 Aligned_cols=56 Identities=27% Similarity=0.348 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHHHHHH--CCCCCCHHHHHHHHHCCCC----CCHHHHHHHHHCCHHHHH
Q ss_conf 6546777899999998764--0578841201566531544----315788877522556788
Q T0581 19 AASLKDFELSKMLEKVAKE--SSVGTPRAINEDILDQGYT----VEGNQLINHLSVRASHAE 74 (136)
Q Consensus 19 AASl~e~el~~~LekVA~e--SsvgtPRaInEdiLdqgYT----VEG~~LinHLSVr~~hA~ 74 (136)
+.+..--++.+|+.+-.+. ---||---+-++++++..- +.|..=-||||||..-|-
T Consensus 115 ~~~is~~~lr~~l~~~~~P~LllFGTGwGL~~e~~~~~D~iLePI~g~~~yNHLSVRsAaAI 176 (184)
T PF09936_consen 115 PNTISYAELREMLKEDERPVLLLFGTGWGLAPEVMEQCDYILEPIRGPGDYNHLSVRSAAAI 176 (184)
T ss_dssp SS-B-S----HHHHH--S-EEEEE-------HHHHTT-SEEB--TTTTSS-----HHHHHHH
T ss_pred CCCCCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHCCEEECCCCCCCCCCCCHHHHHHHH
T ss_conf 99738999999985259808999647767889999734746634426999862049999999
No 2
>PF10697 DUF2502: Protein of unknown function (DUF2502)
Probab=40.18 E-value=2.7 Score=20.25 Aligned_cols=18 Identities=56% Similarity=0.718 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 999999998765656546
Q T0581 5 MALALCFVLPTAAHAASL 22 (136)
Q Consensus 5 ~alaL~lvlp~~AqAASl 22 (136)
.++++.++.|.+|||+|+
T Consensus 2 L~l~~l~~~Pl~a~a~sI 19 (99)
T PF10697_consen 2 LALSLLAVMPLAAQAASI 19 (99)
T ss_pred HHHHHHHHCHHHCCCCCE
T ss_conf 568887736223056744
No 3
>PF11479 Suppressor_P21: RNA silencing suppressor P21; PDB: 2cwo_C.
Probab=20.61 E-value=13 Score=15.99 Aligned_cols=24 Identities=33% Similarity=0.465 Sum_probs=20.5
Q ss_pred HHHHHHHHCCHHHHHHHHCCHHHH
Q ss_conf 788877522556788873288899
Q T0581 60 NQLINHLSVRASHAERMRSNPDSV 83 (136)
Q Consensus 60 ~~LinHLSVr~~hA~qMranP~~V 83 (136)
-+-.|||-|--.|-++|..+|++-
T Consensus 46 la~fnhllvtvehre~me~hp~qs 69 (177)
T PF11479_consen 46 LASFNHLLVTVEHREWMEQHPNQS 69 (177)
T ss_dssp HHHHHHHHHHHHHHHHT-------
T ss_pred HHHHHHHEEEEHHHHHHHHCCCCC
T ss_conf 876402034414688998585632
No 4
>PF03548 LolA: Outer membrane lipoprotein carrier protein LolA; InterPro: IPR004564 This protein, LolA, is known so far only in the gamma subdivision of the Proteobacteria. In Escherichia coli, lipoproteins are anchored to the periplasmic side of either the inner or outer membrane through N-terminal lipids, depending on the lipoprotein-sorting signal present at position 2 . Five Lol proteins are involved in the sorting and outer membrane localization of lipoproteins. LolCDE, an ATP binding cassette (ABC) transporter, in the inner membrane releases outer membrane-directed lipoproteins from the inner membrane in an ATP-dependent manner, leading to the formation of a water-soluble complex between the lipoprotein and the molecular chaperone, LolA. The LolA-lipoprotein complex crosses the periplasm and then interacts with outer membrane receptor LolB, which is essential for the anchoring of lipoproteins to the outer membrane. E. coli lipoproteins are anchored to the inner or outer membrane depending on the residue at position 2. Aspartate at this position makes lipoproteins specific to the inner membrane, whereas other residues cause the release of lipoproteins from the inner membrane.; GO: 0015031 protein transport, 0030288 outer membrane-bounded periplasmic space; PDB: 1ua8_A 2zpc_A 1iwl_A 2zpd_A.
Probab=18.76 E-value=25 Score=14.24 Aligned_cols=27 Identities=33% Similarity=0.441 Sum_probs=23.6
Q ss_pred HHHCCCEEEEEEEECCCCCCHHHHHHH
Q ss_conf 974375136542000245622343332
Q T0581 100 LLARGAILTYSFTEYKTNQPVATERFD 126 (136)
Q Consensus 100 LmakGAvlrY~fteyktN~pv~~~~f~ 126 (136)
.-..|-..+++|+..++|.|+.+..|.
T Consensus 137 ~d~~G~~t~i~f~~~~~n~~l~~~~F~ 163 (165)
T PF03548_consen 137 YDKNGNRTTIEFSNVKTNQPLDDSLFK 163 (165)
T ss_dssp EETTS-EEEEEEEEEE------GGGGS
T ss_pred EECCCCEEEEEEEEEECCCCCCCCCEE
T ss_conf 978979999999946748998811157
No 5
>PF09492 Pec_lyase: Pectic acid lyase; PDB: 1r76_A 1gxm_B 1gxo_A 1gxn_A.
Probab=15.57 E-value=18 Score=15.11 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=18.1
Q ss_pred CCCEEEEEEEECCCCCCHHHHH
Q ss_conf 3751365420002456223433
Q T0581 103 RGAILTYSFTEYKTNQPVATER 124 (136)
Q Consensus 103 kGAvlrY~fteyktN~pv~~~~ 124 (136)
.|..|-++|-|-.||||+-+-|
T Consensus 238 ~a~~lWaRFYel~TnrP~f~~R 259 (289)
T PF09492_consen 238 PAPPLWARFYELGTNRPIFSDR 259 (289)
T ss_dssp ----BEESEE-TTT--B-BE-T
T ss_pred CCCCHHHHHEECCCCCCEEECC
T ss_conf 8874124312547898535468
No 6
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands .; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0006118 electron transport; PDB: 3eub_A 3bdj_B 1n5x_B 1vdv_B 1v97_B 1fiq_A 3etr_L 1fo4_B 3b9j_A 2e3t_B ....
Probab=14.53 E-value=32 Score=13.54 Aligned_cols=49 Identities=22% Similarity=0.445 Sum_probs=29.9
Q ss_pred HHHCCCCCCHHHHHHHHHCCHHHHHHHHCCHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 65315443157888775225567888732888999997676524711688974
Q T0581 50 ILDQGYTVEGNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQLLA 102 (136)
Q Consensus 50 iLdqgYTVEG~~LinHLSVr~~hA~qMranP~~Vr~QLg~SVC~N~gyR~Lma 102 (136)
-+-=||--.|+-+.-.- -....-..+.+.++..|..-.||=.||++...
T Consensus 23 a~QCGyCtpG~vm~~~~----ll~~~~~p~~~eI~~al~GnlCRCTgY~~I~~ 71 (75)
T PF01799_consen 23 AVQCGYCTPGMVMSATA----LLRRNPNPSEDEIREALSGNLCRCTGYRPIVE 71 (75)
T ss_dssp -----------HHHHHH----HHHHSSS-CHHHHHHHTHH---S----HHHHH
T ss_pred CCCCCCCCCHHHHHHHH----HHHHCCCCCHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf 98568885469999999----99738998999999996378463889799999
No 7
>PF03440 APT: Aerolysin/Pertussis toxin (APT) domain; InterPro: IPR005138 This is the N-terminal domain of aerolysin and pertussis toxin which contains a type-C lectin like fold.; GO: 0005488 binding, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1pto_B 1prt_H 1bcp_B 3c0o_A 3c0m_A 1pre_B 1z52_B 3c0n_A.
Probab=14.51 E-value=2.5 Score=20.49 Aligned_cols=30 Identities=37% Similarity=0.497 Sum_probs=18.4
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHCCHHHHHH
Q ss_conf 5678887328889999976765247116889
Q T0581 70 ASHAERMRSNPDSVRSQLGDSVCSNTGYRQL 100 (136)
Q Consensus 70 ~~hA~qMranP~~Vr~QLg~SVC~N~gyR~L 100 (136)
..+|.-----|+.|..|||.-+|++ |||.|
T Consensus 13 ~~~a~~~IypdQ~~~~~lG~~~C~s-gYRpL 42 (99)
T PF03440_consen 13 QASAPAKIYPDQIVIDQLGYGVCRS-GYRPL 42 (99)
T ss_dssp ------S--GGGGGBEE-------T-TEEE-
T ss_pred HHCCCCCCCCCEEEEEECCCCCCCC-CCCCC
T ss_conf 6157876238505422037674577-87538
No 8
>PF05002 SGS: SGS domain ; InterPro: IPR007699 This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins. Sgt1p is a highly conserved eukaryotic protein that is required for both SCF (Skp1p/Cdc53p-Cullin-F-box)-mediated ubiquitination and kinetochore function in yeast and also plays a role in the cAMP pathway. Calcyclin (S100A6) is a member of the S100A family of calcium binding proteins and appears to play a role in cell proliferation .; PDB: 2jtt_D 1x5m_A.
Probab=12.45 E-value=32 Score=13.54 Aligned_cols=34 Identities=21% Similarity=0.237 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
Q ss_conf 7899999998764057884120156653154431
Q T0581 25 FELSKMLEKVAKESSVGTPRAINEDILDQGYTVE 58 (136)
Q Consensus 25 ~el~~~LekVA~eSsvgtPRaInEdiLdqgYTVE 58 (136)
..|+.|+++.-.+..-.|-|||+.--.+.+=||-
T Consensus 20 ~~l~~~fkkiY~~gDddtKRAM~KSf~ES~GtvL 53 (78)
T PF05002_consen 20 AGLMNFFKKIYANGDDDTKRAMMKSFVESNGTVL 53 (78)
T ss_dssp ---HHHHHHHHT----CHHHHHHHHHHCT-----
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 8999999999834999999999999998287510
No 9
>PF02788 RuBisCO_large_N: Ribulose bisphosphate carboxylase large chain, N-terminal domain; InterPro: IPR000685 Ribulose bisphosphate carboxylase (RuBisCO) , catalyzes the initial step in Calvin's reductive pentose phosphate cycle in plants as well as purple and green bacteria. It consists of a large catalytic unit and a small subunit of undetermined function. In plants, the large subunit is coded by the chloroplastic genome while the small subunit is encoded in the nuclear genome. Molecular activation of RuBisCO by CO_2 involves the formation of a carbamate with the epsilon-amino group of a conserved lysine residue. This carbamate is stabilized by a magnesium ion. One of the ligands of the magnesium ion is an aspartic acid residue close to the active site lysine .; GO: 0016984 ribulose-bisphosphate carboxylase activity, 0015977 carbon utilization by fixation of carbon dioxide, 0009573 chloroplast ribulose bisphosphate carboxylase complex; PDB: 1ir2_D 2vdi_G 1uzh_H 1uwa_O 1uw9_H 2v63_A 1uzd_B 2v68_C 2v6a_H 2v67_C ....
Probab=12.32 E-value=31 Score=13.68 Aligned_cols=25 Identities=36% Similarity=0.276 Sum_probs=18.0
Q ss_pred HHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 9999987640578841201566531
Q T0581 29 KMLEKVAKESSVGTPRAINEDILDQ 53 (136)
Q Consensus 29 ~~LekVA~eSsvgtPRaInEdiLdq 53 (136)
..-..||.|||.||=..+-.|-|.-
T Consensus 32 eaaa~vAaEsSTGTwt~v~tD~lt~ 56 (126)
T PF02788_consen 32 EAAAAVAAESSTGTWTTVWTDGLTS 56 (126)
T ss_dssp HHHHHHHHHTTS--SSSSTTGGGCC
T ss_pred EECCCCCCCCCHHHHCCEECCCHHH
T ss_conf 0013233312622201001033032
No 10
>PF00879 Defensin_propep: Defensin propeptide The pattern for this Prosite entry doesn't match the propeptide.; InterPro: IPR002366 Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses , containing three pairs of intramolecular disulphide bonds . On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract). Theta-defensins are cyclic and have so far only been identified in primate phagocytes. Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form 'channel-like' pores; others might bind to and cover the microbial membrane in a 'carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesized as propeptides which may be relevant to this process - in neutrophils only the mature peptides have been identified but in Paneth cells, the propeptide is stored in vesicles and appears to be cleaved by trypsin on activation. ; GO: 0006952 defense response
Probab=11.44 E-value=40 Score=12.97 Aligned_cols=25 Identities=28% Similarity=0.374 Sum_probs=18.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9238999999998765656546777
Q T0581 1 MSRFMALALCFVLPTAAHAASLKDF 25 (136)
Q Consensus 1 m~r~~alaL~lvlp~~AqAASl~e~ 25 (136)
|--++-|+-+|++..-|||-++++-
T Consensus 1 MrTl~LLaAlLllALqaQAe~~q~~ 25 (52)
T PF00879_consen 1 MRTLVLLAALLLLALQAQAEPLQER 25 (52)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 9059999999999999752676543
Done!