Query T0574 NP_250624.1, Pseudomonas aeruginosa PA01, 126 residues
Match_columns 126
No_of_seqs 12 out of 14
Neff 3.0
Searched_HMMs 11830
Date Fri Jun 4 14:25:24 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0574.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0574.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11611 TRF2: Telomeric repea 97.2 0.00013 1.1E-08 44.1 3.6 70 42-113 33-106 (123)
2 PF00932 IF_tail: Intermediate 79.1 0.6 5.1E-05 23.2 3.0 62 32-101 9-74 (118)
3 PF10633 NPCBM_assoc: NPCBM-as 49.0 7.2 0.00061 17.1 4.2 66 48-119 6-71 (78)
4 PF07610 DUF1573: Protein of u 42.3 8.2 0.00069 16.8 3.0 37 54-105 3-44 (45)
5 PF00677 Lum_binding: Lumazine 38.4 7.4 0.00063 17.0 2.3 41 61-101 38-81 (85)
6 PF06280 DUF1034: Fn3-like dom 30.1 15 0.0012 15.3 6.3 64 49-112 10-104 (112)
7 PF11906 DUF3426: Protein of u 30.1 15 0.0012 15.3 8.3 67 51-117 72-145 (149)
8 PF06474 MLTD_N: MLTD_N; Inte 25.5 14 0.0012 15.4 2.0 26 1-26 1-26 (95)
9 PF10807 DUF2541: Protein of u 23.5 19 0.0016 14.6 3.1 44 61-113 62-107 (134)
10 PF05079 DUF680: Protein of un 20.7 22 0.0019 14.3 2.4 25 1-26 1-25 (75)
No 1
>PF11611 TRF2: Telomeric repeat-binding factor 2; PDB: 3cfu_A.
Probab=97.15 E-value=0.00013 Score=44.10 Aligned_cols=70 Identities=26% Similarity=0.350 Sum_probs=56.4
Q ss_pred CCCEEEEEEEEEEEECCCCCCEECCCEEEEEECCCCCEEEEECCCCHH----HHHHHCCCCCCEEEEEEECCCCCH
Q ss_conf 873034566778885077674000330489886998278865043201----211202787311589983488301
Q T0574 42 GDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLDTVDEEL----TADTLKPGASVEGDAIFASEDDAV 113 (126)
Q Consensus 42 ~~k~~yTKtF~V~v~N~~~k~idL~~~Cl~A~~~~gkeFkldTVDe~L----~~g~Lk~g~~vkG~avFaS~d~sV 113 (126)
++..|+ ..+|.|.|.+++++.++...|++++++|+++..+...... ..+.|+||++++|..+|--+.++-
T Consensus 33 ~g~~fv--vV~v~v~N~~~e~~~~~~~~f~L~d~~g~~y~~~~~~~~~~~~~~~~~l~pG~~~~g~ivF~vp~~~~ 106 (123)
T PF11611_consen 33 EGGKFV--VVDVTVKNNGDEPISFSPSDFKLYDDDGKEYDPDFSASSDPDNFFSGELKPGESVEGKIVFEVPKDSQ 106 (123)
T ss_dssp --SEEE--EEEEEEEE-----B-B-----EEE-TT--B--EEE-CCC---------B----EE---EEEEE----G
T ss_pred CCCEEE--EEEEEEEECCCCCEEECCCCEEEEECCCCEECCCCCCCCCCCCCCCEEECCCCEEEEEEEEEECCCCC
T ss_conf 999899--99999999999957757571999949997981443310011554534999999899999999899994
No 2
>PF00932 IF_tail: Intermediate filament tail domain; InterPro: IPR001322 Intermediate filaments (IF) are primordial components of the cytoskeleton and the nuclear envelope . They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups, type I: acidic cytokeratins, type II: basic cytokeratins, type III: vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin, type IV: neurofilaments L, H and M, alpha-internexin and nestin, and type V: nuclear lamins A, B1, B2 and C. The lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane that may provide a framework for the nuclear envelope and may interact with chromatin. All IF proteins are structurally similar in that they consist of a central rod domain arranged in coiled-coil alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. The C-terminal domain has been charcterised for the lamins.; PDB: 3hn9_C 1ufg_A 1ifr_A 1ivt_A.
Probab=79.14 E-value=0.6 Score=23.20 Aligned_cols=62 Identities=23% Similarity=0.304 Sum_probs=44.1
Q ss_pred CCCCCCCEECCCCEEEEEEEEEEEECCCCCCEECCCEEEEEECCCCC----EEEEECCCCHHHHHHHCCCCCCE
Q ss_conf 05665405508730345667788850776740003304898869982----78865043201211202787311
Q T0574 32 RQGDKGSVSVGDKHFRTQAFKVRLVNAAKSEISLKNSCLVAQSAAGQ----SFRLDTVDEELTADTLKPGASVE 101 (126)
Q Consensus 32 t~~s~GsvS~~~k~~yTKtF~V~v~N~~~k~idL~~~Cl~A~~~~gk----eFkldTVDe~L~~g~Lk~g~~vk 101 (126)
+..++|.|+|.+-+---| =|.+.|.++++++|....|+--..++. .|++-- .=+|+||+.|+
T Consensus 9 ~~sakG~V~I~E~d~~Gk--fV~l~N~s~~~~~L~GW~L~r~v~~~~~~~~~y~Fp~------~~~L~pg~~vt 74 (118)
T PF00932_consen 9 QRSAKGPVSISECDPDGK--FVVLENTSSKDQDLGGWKLKRKVDGKEEKVVTYTFPP------GFVLKPGQTVT 74 (118)
T ss_dssp EEEE---EEEEEEE------EEEEEE-SSS-EE----EEEEE----E--EEEEE--T------T-EE----EEE
T ss_pred ECCCCCCEEEEEECCCCC--EEEEEECCCCCEECCCCEEEEEECCCCEEEEEEECCC------CEEECCCCEEE
T ss_conf 331479888999779998--9998838987472499799996089750258997489------85988999899
No 3
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; PDB: 1w8n_A 1eut_A 1euu_A 2bzd_A 1wcq_B 2ber_A 1w8o_A.
Probab=49.02 E-value=7.2 Score=17.09 Aligned_cols=66 Identities=23% Similarity=0.232 Sum_probs=41.5
Q ss_pred EEEEEEEEECCCCCCEECCCEEEEEECCCCCEEEEECCCCHHHHHHHCCCCCCEEEEEEECCCCCHHCEEEE
Q ss_conf 566778885077674000330489886998278865043201211202787311589983488301003578
Q T0574 48 TQAFKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLDTVDEELTADTLKPGASVEGDAIFASEDDAVYGASLV 119 (126)
Q Consensus 48 TKtF~V~v~N~~~k~idL~~~Cl~A~~~~gkeFkldTVDe~L~~g~Lk~g~~vkG~avFaS~d~sVy~A~~V 119 (126)
+.++.+.|.|.+..++. ++-+.+-.|.|-. ..++..-.. .|.||+++.--...--+.+..-+...|
T Consensus 6 ~~~~~vtv~N~g~~~~~--~v~~~l~~P~GW~---~~~~~~~~~-~l~~G~s~~~t~~V~vp~~a~~G~y~v 71 (78)
T PF10633_consen 6 TVTVTVTVTNTGSAPAT--NVTLSLELPEGWS---VSVSPASVP-SLAPGESATVTFTVTVPANAAPGTYPV 71 (78)
T ss_dssp EEEE--EEE------BS--S-EEE----TTSE------EE------B----EE---EEEE---------EEE
T ss_pred EEEEEEEEEECCCCCEE--EEEEEEECCCCCC---CCCCCCCCC-CCCCCCEEEEEEEEECCCCCCCCEEEE
T ss_conf 89999999979987122--1799997999931---035866442-089899899999998899989954899
No 4
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=42.28 E-value=8.2 Score=16.76 Aligned_cols=37 Identities=24% Similarity=0.453 Sum_probs=27.0
Q ss_pred EEECCCCCCEECCCE-----EEEEECCCCCEEEEECCCCHHHHHHHCCCCCCEEEEE
Q ss_conf 885077674000330-----4898869982788650432012112027873115899
Q T0574 54 RLVNAAKSEISLKNS-----CLVAQSAAGQSFRLDTVDEELTADTLKPGASVEGDAI 105 (126)
Q Consensus 54 ~v~N~~~k~idL~~~-----Cl~A~~~~gkeFkldTVDe~L~~g~Lk~g~~vkG~av 105 (126)
.+-|.|+.|+-+.++ |..+ .+.+..|+||++.+=-+.
T Consensus 3 ~~~N~g~~pl~I~~v~tsCgCt~~---------------~~~k~~i~PGes~~i~v~ 44 (45)
T PF07610_consen 3 KFTNTGDSPLVITDVTTSCGCTTA---------------EYSKKPIAPGESGEIKVT 44 (45)
T ss_pred EEEECCCCCEEEEEEEECCCCEEE---------------CCCCCEECCCCEEEEEEE
T ss_conf 999888997899986265266860---------------577640889998899998
No 5
>PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown , to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif. ; PDB: 1kzl_A 1i8d_B 3ddy_A 1pkv_A 1hze_B 1i18_B.
Probab=38.38 E-value=7.4 Score=17.01 Aligned_cols=41 Identities=27% Similarity=0.509 Sum_probs=33.3
Q ss_pred CCEECCCEEEEEECCCCCEEEEECCCCHHHH---HHHCCCCCCE
Q ss_conf 7400033048988699827886504320121---1202787311
Q T0574 61 SEISLKNSCLVAQSAAGQSFRLDTVDEELTA---DTLKPGASVE 101 (126)
Q Consensus 61 k~idL~~~Cl~A~~~~gkeFkldTVDe~L~~---g~Lk~g~~vk 101 (126)
.-|-++..||-...-++..|.++-+.|.|-. +.+++|..|+
T Consensus 38 ~SIavnGvcLTV~~i~~~~f~v~lipeTl~~T~l~~~~~G~~VN 81 (85)
T PF00677_consen 38 GSIAVNGVCLTVTEINEDTFTVDLIPETLRRTTLGSLKVGDRVN 81 (85)
T ss_dssp -EEEE---EEEEEEEESSEEEEEEEHHHHHHSSGGG--TT-EEE
T ss_pred CEEEECCEEEEEEEECCCEEEEEEEHHHHHHCCCCCCCCCCEEE
T ss_conf 88998878999999879999999819975225002388899899
No 6
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 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) , . 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 domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 1xf1_A 3eif_A.
Probab=30.13 E-value=15 Score=15.34 Aligned_cols=64 Identities=22% Similarity=0.196 Sum_probs=37.3
Q ss_pred EEEEEEEECCCCCCEECCCEEE---EEEC--CCCCEEEEEC-----------------------CCCHHHH-HHH--CCC
Q ss_conf 6677888507767400033048---9886--9982788650-----------------------4320121-120--278
Q T0574 49 QAFKVRLVNAAKSEISLKNSCL---VAQS--AAGQSFRLDT-----------------------VDEELTA-DTL--KPG 97 (126)
Q Consensus 49 KtF~V~v~N~~~k~idL~~~Cl---~A~~--~~gkeFkldT-----------------------VDe~L~~-g~L--k~g 97 (126)
++|.|.|.|.++++...+-... ..+. .+|+.+.... |.-.+.. ..+ ..+
T Consensus 10 ~~~tvtl~N~g~~~~tY~~~~~~~~T~~~~~~~g~~~~~~~~~~~~~~~~~~~~vTV~ag~s~~v~vt~~~p~~~~~~~~ 89 (112)
T PF06280_consen 10 FTFTVTLHNTGNKDKTYTLSHVGVLTDQTDKNDGYFTLPPIAPGAASVTFSPNTVTVPAGGSKTVTVTFTPPSGFDASNN 89 (112)
T ss_dssp EEEEEEEEE-SSS-EEEEEEEE-EEEEEE-----BEEEEEEE----EEE---EEEEE-TTEEEEEEEEEE--GGGHH---
T ss_pred EEEEEEEEECCCCCEEEEEEEEEEEEEEEECCCCCCCCCCCCCEEEEEEECCCEEEECCCCEEEEEEEEEECCCCCCCCC
T ss_conf 89999999589998899994068877897225771135655420256663798499999998999999976314664458
Q ss_pred CCCEEEEEEECCCCC
Q ss_conf 731158998348830
Q T0574 98 ASVEGDAIFASEDDA 112 (126)
Q Consensus 98 ~~vkG~avFaS~d~s 112 (126)
.-++|++.|-+.+..
T Consensus 90 ~~~eG~V~~~~~~~~ 104 (112)
T PF06280_consen 90 PFYEGFVRFTSSDGE 104 (112)
T ss_dssp ---E-EEEEESSTTS
T ss_pred CEEEEEEEEECCCCC
T ss_conf 899999999808998
No 7
>PF11906 DUF3426: Protein of unknown function (DUF3426)
Probab=30.09 E-value=15 Score=15.33 Aligned_cols=67 Identities=24% Similarity=0.193 Sum_probs=51.8
Q ss_pred EEEEEECCCCCCEECCCEEEEEECCCCCEEEEECC--CCHHHH-----HHHCCCCCCEEEEEEECCCCCHHCEE
Q ss_conf 77888507767400033048988699827886504--320121-----12027873115899834883010035
Q T0574 51 FKVRLVNAAKSEISLKNSCLVAQSAAGQSFRLDTV--DEELTA-----DTLKPGASVEGDAIFASEDDAVYGAS 117 (126)
Q Consensus 51 F~V~v~N~~~k~idL~~~Cl~A~~~~gkeFkldTV--De~L~~-----g~Lk~g~~vkG~avFaS~d~sVy~A~ 117 (126)
....+.|.++.+..+-.+=+..++.+|+..--.+. +|.|.. ..+.||+++.=...|......+-+-+
T Consensus 72 i~g~l~N~~~~~~~~P~l~l~L~D~~g~~v~~r~~~P~eyl~~~~~~~~~l~pg~~~~f~~~~~~~~~~a~~y~ 145 (149)
T PF11906_consen 72 ISGTLRNRADFPQAWPALELTLTDAQGQPVARRVFTPAEYLPPALANQAGLPPGQSVPFRVVFEDPPPNAAGYR 145 (149)
T ss_pred EEEEEEECCCCCCCCCEEEEEEECCCCCEEEEEEECHHHHCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEE
T ss_conf 99999938987534745999999899999999997757844643332344499986899999407998631589
No 8
>PF06474 MLTD_N: MLTD_N; InterPro: IPR010511 This entry comprises the N-terminal domain of membrane-bound lytic murein transglycosylase D .
Probab=25.46 E-value=14 Score=15.37 Aligned_cols=26 Identities=31% Similarity=0.287 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 94147878999887655431036564
Q T0574 1 MKNAMALTLAGLLAAPSLGFAAAPDA 26 (126)
Q Consensus 1 mk~a~~l~~~~l~a~~~~a~a~~~d~ 26 (126)
||-...++++.||++|.......++.
T Consensus 1 m~~~~~l~~~llLaGCqs~~~~~~~~ 26 (95)
T PF06474_consen 1 MRFLAVLALALLLAGCQSTPQPSPES 26 (95)
T ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 92999999999998467999999876
No 9
>PF10807 DUF2541: Protein of unknown function (DUF2541)
Probab=23.48 E-value=19 Score=14.63 Aligned_cols=44 Identities=25% Similarity=0.362 Sum_probs=34.8
Q ss_pred CCEECC--CEEEEEECCCCCEEEEECCCCHHHHHHHCCCCCCEEEEEEECCCCCH
Q ss_conf 740003--30489886998278865043201211202787311589983488301
Q T0574 61 SEISLK--NSCLVAQSAAGQSFRLDTVDEELTADTLKPGASVEGDAIFASEDDAV 113 (126)
Q Consensus 61 k~idL~--~~Cl~A~~~~gkeFkldTVDe~L~~g~Lk~g~~vkG~avFaS~d~sV 113 (126)
-+|+|+ ..-|++.....+.|+. +..||+|+. -|..-|.|||+.-
T Consensus 62 gdi~Lsgasv~fk~~~gas~~l~v--------~~~ikeg~t-T~Wi~insdndnk 107 (134)
T PF10807_consen 62 GDIQLSGASVYFKAARGASQSLNV--------PSRIKEGQT-TGWININSDNDNK 107 (134)
T ss_pred CCEEEECCEEEEEECCCCCEEECC--------CCCCCCCCC-CCCEEECCCCCCC
T ss_conf 761740328999732575316435--------301047882-5758961678873
No 10
>PF05079 DUF680: Protein of unknown function (DUF680); InterPro: IPR007771 This family contains uncharacterised proteins which seem to be found exclusively in Mesorhizobium loti.
Probab=20.67 E-value=22 Score=14.30 Aligned_cols=25 Identities=40% Similarity=0.456 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 94147878999887655431036564
Q T0574 1 MKNAMALTLAGLLAAPSLGFAAAPDA 26 (126)
Q Consensus 1 mk~a~~l~~~~l~a~~~~a~a~~~d~ 26 (126)
||+- .|+.+.+|.++..|||..++.
T Consensus 1 MkKi-~L~aaA~l~~sgsAFAgs~~~ 25 (75)
T PF05079_consen 1 MKKI-ALTAAALLLISGSAFAGSDHV 25 (75)
T ss_pred CHHH-HHHHHHHHHHHHHHHCCCCCC
T ss_conf 9169-999999999653765189888
Done!