Query T0548 OR3 , , 106 residues
Match_columns 106
No_of_seqs 116 out of 829
Neff 7.4
Searched_HMMs 11830
Date Fri May 21 18:06:13 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0548.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0548.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09337 zf-H2C2: His(2)-Cys(2 99.0 1.4E-10 1.2E-14 75.4 3.7 39 58-99 1-39 (39)
2 PF02022 Integrase_Zn: Integra 77.9 0.81 6.8E-05 22.2 3.3 38 55-101 2-39 (40)
3 PF11390 FdsD: NADH-dependant 21.9 21 0.0018 14.4 2.7 44 49-94 5-48 (61)
4 PF02381 MraZ: MraZ protein; 19.0 16 0.0013 15.1 1.1 20 36-55 9-28 (72)
5 PF09960 DUF2194: Uncharacteri 18.3 21 0.0018 14.4 1.6 19 73-91 281-299 (585)
6 PF09087 Cyc-maltodext_N: Cycl 14.7 5.1 0.00043 17.8 -2.3 10 77-86 4-13 (88)
7 PF09868 DUF2095: Uncharacteri 10.1 28 0.0024 13.7 0.3 18 80-97 59-76 (128)
8 PF01413 C4: C-terminal tandem 9.6 11 0.00089 16.1 -2.0 17 85-101 98-114 (114)
9 PF07656 KWG: KWG Leptospira; 7.5 47 0.0039 12.5 0.6 14 35-48 3-16 (17)
10 PF10107 Endonuc_Holl: Endonuc 6.6 47 0.004 12.5 0.2 21 2-23 79-99 (156)
No 1
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs that bind one or more zinc atoms, and which usually contain multiple finger-like protrusions that make tandem contacts with their target molecule. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis, however they are now recognised to bind DNA, RNA, protein and/or lipid substrates , , , , . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. (Note that in certain cases, some Znf domains have diverged such that they still maintain their core structure, but have lost their ability to bind zinc, using other means such as salt bridges or binding to other metals to stabilise the finger-like folds. These domains can show strong sequence identity to zinc-binding motifs, and may therefore be included in Znf entries). This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters . More information about these proteins can be found at Protein of the Month: Zinc Fingers .
Probab=98.96 E-value=1.4e-10 Score=75.37 Aligned_cols=39 Identities=21% Similarity=0.434 Sum_probs=32.9
Q ss_pred HCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHH
Q ss_conf 515667647899999998863278656899999973170653
Q T0548 58 HQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACA 99 (106)
Q Consensus 58 H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq 99 (106)
|...|.| +++|+.+|+++||||+|+++|.+||++|..||
T Consensus 1 H~~~H~G---inkT~~~i~~~Y~W~~ik~~V~~~ir~C~~Cq 39 (39)
T PF09337_consen 1 HNLAHPG---INKTTARIAQRYHWPGIKKTVSRVIRNCPQCQ 39 (39)
T ss_pred CCCCCCC---HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCC
T ss_conf 9756676---99999999887117676899999976283259
No 2
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains; the amino-terminal zinc binding domain, the central domain is the catalytic domain rve and the carboxyl terminal domain is a DNA binding domain. Often found as part of the POL polyprotein.; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0008907 integrase activity, 0015074 DNA integration; PDB: 3f9k_U 1e0e_B 1e27_C 1wjd_A 1wjb_A 1k6y_C 1wjf_B 1wje_B 1wja_A 1wjc_B ....
Probab=77.87 E-value=0.81 Score=22.15 Aligned_cols=38 Identities=16% Similarity=0.336 Sum_probs=26.9
Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHCC
Q ss_conf 99851566764789999999886327865689999997317065333
Q T0548 55 DFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITETCKACAQV 101 (106)
Q Consensus 55 ~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~C~~Cq~~ 101 (106)
++.|+..|.+...+ +..|--| ...++++|++|..||..
T Consensus 2 qe~H~k~H~n~~~L-------~~~f~ip--~~vAr~IV~~C~~Cq~~ 39 (40)
T PF02022_consen 2 QEEHEKYHSNWKAL-------RHKFGIP--RLVARQIVQQCPKCQQK 39 (40)
T ss_dssp HHHHHHHHH-HHHH-------HHHHT----HHHHHHHHHHSCCHHT-
T ss_pred CHHHHHHHCCHHHH-------HHHHCCC--HHHHHHHHHHHHHHHHC
T ss_conf 13789880489999-------9882989--99999999876898737
No 3
>PF11390 FdsD: NADH-dependant formate dehydrogenase delta subunit FdsD
Probab=21.93 E-value=21 Score=14.44 Aligned_cols=44 Identities=7% Similarity=0.117 Sum_probs=25.1
Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf 7899999985156676478999999988632786568999999731
Q T0548 49 FTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKNITET 94 (106)
Q Consensus 49 ~~~~il~~~H~~~h~G~~~~~~~l~~i~~~~~wp~m~~~v~~~v~~ 94 (106)
|.++|-.-+...+ ..-.........| .+||=|.|++.+..++..
T Consensus 5 MANQIa~fF~~~p-~~~~av~~va~Hi-~kFW~PrMR~~L~~~~~~ 48 (61)
T PF11390_consen 5 MANQIATFFESQP-DEEEAVAGVADHI-KKFWEPRMRRQLLAHLDA 48 (61)
T ss_pred HHHHHHHHHCCCC-CHHHHHHHHHHHH-HHHCCHHHHHHHHHHHHH
T ss_conf 9999999872079-8889999999999-982788999999999980
No 4
>PF02381 MraZ: MraZ protein; InterPro: IPR003444 This family is characterised by a 70 amino acid region and is found duplicated in a group of bacterial proteins. These proteins may be DNA-binding transcription factors, its members are probably enzymes containing a conserved DXXXR motif that probably forms part of the active site. ; PDB: 1n0f_D 1n0e_E 1n0g_B.
Probab=18.96 E-value=16 Score=15.10 Aligned_cols=20 Identities=15% Similarity=0.049 Sum_probs=14.0
Q ss_pred EEEECCEEEECHHHHHHHHH
Q ss_conf 54218844646587899999
Q T0548 36 YWVYQGKPVMPDQFTFELLD 55 (106)
Q Consensus 36 ~~~~~Gr~vvP~~~~~~il~ 55 (106)
.+...||+.||..++..+-.
T Consensus 9 ~lD~kGRi~iP~~~R~~~~~ 28 (72)
T PF02381_consen 9 SLDAKGRITIPAKLREYLGI 28 (72)
T ss_dssp -B-TTSEEE--CHHHHHTT-
T ss_pred CCCCCCCEECCHHHHHHHCC
T ss_conf 66888878269999997376
No 5
>PF09960 DUF2194: Uncharacterized protein conserved in bacteria (DUF2194)
Probab=18.34 E-value=21 Score=14.39 Aligned_cols=19 Identities=0% Similarity=-0.048 Sum_probs=12.8
Q ss_pred HHHHHHCCCCCHHHHHHHH
Q ss_conf 9988632786568999999
Q T0548 73 ERSHSPYYMLNRDRTLKNI 91 (106)
Q Consensus 73 ~~i~~~~~wp~m~~~v~~~ 91 (106)
...-+.-|||.|.+.++++
T Consensus 281 ~eFY~~IWWpDm~~la~~y 299 (585)
T PF09960_consen 281 TEFYRKIWWPDMKKLAEKY 299 (585)
T ss_pred HHHHHHHCCHHHHHHHHHC
T ss_conf 9998862236699999972
No 6
>PF09087 Cyc-maltodext_N: Cyclomaltodextrinase, N-terminal; InterPro: IPR015171 This domain is found at the N terminus of cyclomaltodextrinase. The domain assumes a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N-terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate . ; PDB: 3edj_B 3ede_A 3edf_B 1h3g_B 3edd_A 3edk_B.
Probab=14.74 E-value=5.1 Score=17.80 Aligned_cols=10 Identities=10% Similarity=0.484 Sum_probs=5.4
Q ss_pred HHCCCCCHHH
Q ss_conf 6327865689
Q T0548 77 SPYYMLNRDR 86 (106)
Q Consensus 77 ~~~~wp~m~~ 86 (106)
..|||-||..
T Consensus 4 P~~WW~GM~n 13 (88)
T PF09087_consen 4 PPFWWAGMKN 13 (88)
T ss_dssp SSEEE-----
T ss_pred CCHHHCCCCC
T ss_conf 9614527999
No 7
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095)
Probab=10.09 E-value=28 Score=13.72 Aligned_cols=18 Identities=17% Similarity=0.270 Sum_probs=9.9
Q ss_pred CCCCHHHHHHHHHHCCCH
Q ss_conf 786568999999731706
Q T0548 80 YMLNRDRTLKNITETCKA 97 (106)
Q Consensus 80 ~wp~m~~~v~~~v~~C~~ 97 (106)
=|.|..-.|.+|++.|.+
T Consensus 59 ~fsGYnPtviD~lrRC~T 76 (128)
T PF09868_consen 59 DFSGYNPTVIDYLRRCKT 76 (128)
T ss_pred CCCCCCCHHHHHHHHHCC
T ss_conf 877789709999998175
No 8
>PF01413 C4: C-terminal tandem repeated domain in type 4 procollagen; InterPro: IPR001442 This duplicated domain is present at the C-terminal of type 4 collagen, the major structural component of glomerular basement membranes (GMB) forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome.; GO: 0005201 extracellular matrix structural constituent, 0005581 collagen; PDB: 1m3d_B 1li1_D 1t61_F.
Probab=9.56 E-value=11 Score=16.06 Aligned_cols=17 Identities=12% Similarity=0.444 Sum_probs=13.0
Q ss_pred HHHHHHHHHCCCHHHCC
Q ss_conf 89999997317065333
Q T0548 85 DRTLKNITETCKACAQV 101 (106)
Q Consensus 85 ~~~v~~~v~~C~~Cq~~ 101 (106)
...++.+|.+|.+|.++
T Consensus 98 ~~~i~~~ISRC~VC~~~ 114 (114)
T PF01413_consen 98 GDNIRPYISRCVVCEAN 114 (114)
T ss_dssp GGCGGGGB--EEEEES-
T ss_pred CCCCCCCCCCCEEEECC
T ss_conf 63100336414041657
No 9
>PF07656 KWG: KWG Leptospira; InterPro: IPR011647 This motif occurs in multiple copies in Leptospira interrogans proteins.
Probab=7.48 E-value=47 Score=12.54 Aligned_cols=14 Identities=43% Similarity=0.544 Sum_probs=9.4
Q ss_pred CEEEECCEEEECHH
Q ss_conf 65421884464658
Q T0548 35 KYWVYQGKPVMPDQ 48 (106)
Q Consensus 35 ~~~~~~Gr~vvP~~ 48 (106)
|++...|++|||..
T Consensus 3 GyId~~G~~vI~p~ 16 (17)
T PF07656_consen 3 GYIDKSGKIVIPPQ 16 (17)
T ss_pred CCCCCCCCEEECCC
T ss_conf 51989998985774
No 10
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase
Probab=6.60 E-value=47 Score=12.52 Aligned_cols=21 Identities=33% Similarity=0.596 Sum_probs=14.4
Q ss_pred CCCCCCCCHHHHCCCHHHHHHH
Q ss_conf 6488898512213698899999
Q T0548 2 IENSSPYTSEHFHYTVTDIKDL 23 (106)
Q Consensus 2 ~~~~~P~~~~~~~y~~ed~~~~ 23 (106)
.|+=.|+.|+ |.|+|.|.+.+
T Consensus 79 ~EqlaP~~p~-F~ynPkD~RFl 99 (156)
T PF10107_consen 79 TEQLAPFFPE-FKYNPKDARFL 99 (156)
T ss_pred HHHHCCCCCC-CCCCCCCCCCC
T ss_conf 7664333678-89894011004
Done!