Query T0572 SuR18C, , 93 residues
Match_columns 93
No_of_seqs 101 out of 301
Neff 7.1
Searched_HMMs 11830
Date Fri Jun 4 14:27:35 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0572.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0572.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07949 YbbR: YbbR-like prote 99.4 7.4E-13 6.2E-17 77.9 8.8 77 12-88 1-82 (82)
2 PF03698 UPF0180: Uncharacteri 19.3 22 0.0019 13.8 2.3 42 23-64 19-68 (80)
3 PF06442 DHFR_2: R67 dihydrofo 6.5 63 0.0053 11.6 1.1 20 22-42 51-70 (78)
4 PF07809 RTP801_C: RTP801 C-te 3.6 1E+02 0.0088 10.6 2.2 28 13-40 43-70 (116)
5 PF00698 Acyl_transf_1: Acyl t 2.9 1.2E+02 0.01 10.2 1.1 27 25-52 147-173 (318)
6 PF01025 GrpE: GrpE; InterPro 2.8 1.3E+02 0.011 10.2 0.8 20 22-41 145-164 (165)
7 PF05137 PilN: Fimbrial assemb 2.4 1.5E+02 0.013 9.8 3.4 33 19-51 103-135 (162)
8 PF07987 DUF1775: Domain of un 2.0 1.8E+02 0.016 9.4 2.6 45 37-81 18-63 (77)
9 PF03275 GLF: UDP-galactopyran 1.8 91 0.0077 10.9 -1.8 45 7-51 21-75 (204)
10 PF12392 DUF3656: Collagenase 1.8 2.2E+02 0.018 9.1 5.2 38 7-44 19-56 (122)
No 1
>PF07949 YbbR: YbbR-like protein; InterPro: IPR012505 The members of this family are all hypothetical bacterial proteins of unknown function, and are similar to the YbbR protein expressed by Bacillus subtilis (O34659 from SWISSPROT, O87088 from SWISSPROT). One member (Q97EN2 from SWISSPROT) is annotated as an uncharacterised secreted protein, whereas another member (P43521 from SWISSPROT) is described as a hypothetical protein in the 5,region of the def gene of Thermus thermophilus, which encodes a deformylase , but no further information was found in either case. This region is found repeated up to four times in many members of this family.
Probab=99.38 E-value=7.4e-13 Score=77.89 Aligned_cols=77 Identities=31% Similarity=0.469 Sum_probs=68.4
Q ss_pred EEE-EEEEEEECCCCCEEEEEEECCCEEEEEECHHHHCCCEEEEEE--EEEECCCCCEEEEEEEC--CCCEEECCCEEEE
Q ss_conf 878-767764447783787758518879999466771572278888--85205866769988817--8865837972799
Q T0572 12 VPV-KLELTGDKASNVSSISYSFDRGHVTIVGSQEAMDKIDSITVP--VDISQVTEDTSKTLELK--AEGVTVQPSTVKV 86 (93)
Q Consensus 12 VpV-~~~~~G~~~~gy~~~~~~~~p~~V~i~G~~~~l~~I~~i~~~--vdis~~t~~~~~~v~lp--~~~~~i~p~~V~V 86 (93)
||| .+...|.+++||.+.+...+|.+|+|+|+++.|++|+++.+. +|++|+++++..+++++ .....+.|+.++|
T Consensus 1 VPV~~~~~~~~~~~g~~v~~~~~~~~~V~v~Gp~~~l~~i~~~~~~~~iDls~~~~~~~~~v~~~~~~~~~~~~p~~V~V 80 (82)
T PF07949_consen 1 VPVEKVNVIGNLADGYVVSSITPEPVTVTVSGPESVLNKIDSVDTKVYIDLSGLKETVTVQVTLPPPDGVVSVSPSKVTV 80 (82)
T ss_pred CCEEEEEEECCCCCCCEEEECCCCEEEEEEEECHHHHHCCCEEEEEEEECCCCCCCEEEEEEEEECCCCCEEECCCEEEE
T ss_conf 91858400103899989970402326999997999951131343799882203964289999877588857884668999
Q ss_pred EE
Q ss_conf 98
Q T0572 87 NL 88 (93)
Q Consensus 87 ~v 88 (93)
+|
T Consensus 81 ~v 82 (82)
T PF07949_consen 81 TV 82 (82)
T ss_pred EC
T ss_conf 79
No 2
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=19.30 E-value=22 Score=13.79 Aligned_cols=42 Identities=19% Similarity=0.340 Sum_probs=31.0
Q ss_pred CCCCEEEEEEECC-----CEEEEEECHHHHCCCEEE-E-EE-EEEECCCC
Q ss_conf 7783787758518-----879999466771572278-8-88-85205866
Q T0572 23 ASNVSSISYSFDR-----GHVTIVGSQEAMDKIDSI-T-VP-VDISQVTE 64 (93)
Q Consensus 23 ~~gy~~~~~~~~p-----~~V~i~G~~~~l~~I~~i-~-~~-vdis~~t~ 64 (93)
..||.+-.+.-.. +-+.++|-..-+.+|... + +| ||-+|+|-
T Consensus 19 ~~GYeVv~l~~~~~~~~~Da~VitG~d~N~mgi~d~~t~~pVI~A~G~Ta 68 (80)
T PF03698_consen 19 EKGYEVVDLDNEQDAQPVDAIVITGQDTNMMGIQDTNTKAPVINASGLTA 68 (80)
T ss_pred HCCCEEEECCCCCCCCCCCEEEEECCCCCHHCCCCCCCCCCEEECCCCCH
T ss_conf 78988972665355677278999689853011313345773697589999
No 3
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) , and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood . Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar . The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself . This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule . Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug; PDB: 2rk1_A 1vif_A 1vie_A 2p4t_A 2rh2_A 2gqv_A 2rk2_A.
Probab=6.53 E-value=63 Score=11.65 Aligned_cols=20 Identities=20% Similarity=0.079 Sum_probs=13.8
Q ss_pred CCCCCEEEEEEECCCEEEEEE
Q ss_conf 477837877585188799994
Q T0572 22 KASNVSSISYSFDRGHVTIVG 42 (93)
Q Consensus 22 ~~~gy~~~~~~~~p~~V~i~G 42 (93)
.++||.+.+- ..|.+|+||-
T Consensus 51 tpegyavese-shpgsvqiyp 70 (78)
T PF06442_consen 51 TPEGYAVESE-SHPGSVQIYP 70 (78)
T ss_dssp -----EEE-S-S----EEE--
T ss_pred CCCCEEEECC-CCCCCEEEEE
T ss_conf 6661166615-6898178876
No 4
>PF07809 RTP801_C: RTP801 C-terminal region; InterPro: IPR012918 The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene . Two members of this family expressed by Drosophila melanogaster, Scylla (Q9NHN4 from SWISSPROT) and Charybde (Q9NHN5 from SWISSPROT), are designated as Hox targets . RTP801 is thought to be involved in various cellular processes . Over expression of the gene caused the apoptosis-resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells . Moreover, the protein product of the mouse homolog of RTP801 (dig2 (Q9D3F7 from SWISSPROT)) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment . ; GO: 0009968 negative regulation of signal transduction, 0005737 cytoplasm
Probab=3.61 E-value=1e+02 Score=10.60 Aligned_cols=28 Identities=11% Similarity=0.158 Sum_probs=19.0
Q ss_pred EEEEEEEEECCCCCEEEEEEECCCEEEE
Q ss_conf 7876776444778378775851887999
Q T0572 13 PVKLELTGDKASNVSSISYSFDRGHVTI 40 (93)
Q Consensus 13 pV~~~~~G~~~~gy~~~~~~~~p~~V~i 40 (93)
-+.+.+..++.+--.++.++++|..|..
T Consensus 43 ~i~i~~E~e~~~~~~ia~ik~Dp~~VsT 70 (116)
T PF07809_consen 43 TIYIEFEDEPKNCRRIAQIKVDPDTVST 70 (116)
T ss_pred EEEEEECCCCCCEEEEEEEECCCCCCCE
T ss_conf 8999974587501352467628886753
No 5
>PF00698 Acyl_transf_1: Acyl transferase domain; InterPro: IPR014043 Enzymes like bacterial malonyl CoA-acly carrier protein transacylase (2.3.1.39 from EC) and eukaryotic fatty acid synthase (2.3.1.85 from EC) that are involved in fatty acid biosynthesis belong to this group. Also included are the polyketide synthases 6-methylsalicylic acid synthase (2.3.1 from EC), a multifunctional enzyme that involved in the biosynthesis of patulin and conidial green pigment synthase (2.3.1 from EC).; PDB: 2hg4_C 2qo3_A 2jfd_D 2jfk_A 2vz9_B 2vz8_A 2h1y_B 2c2n_B 2vkz_H 2uv8_I ....
Probab=2.91 E-value=1.2e+02 Score=10.23 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=19.9
Q ss_pred CCEEEEEEECCCEEEEEECHHHHCCCEE
Q ss_conf 8378775851887999946677157227
Q T0572 25 NVSSISYSFDRGHVTIVGSQEAMDKIDS 52 (93)
Q Consensus 25 gy~~~~~~~~p~~V~i~G~~~~l~~I~~ 52 (93)
+..+ ...-+|+++.|.|+++.++.+.+
T Consensus 147 ~v~i-A~~Nsp~q~visG~~~~l~~~~~ 173 (318)
T PF00698_consen 147 DVEI-ANINSPRQVVISGDKEALDALVE 173 (318)
T ss_dssp TTEE-EEEEETTEEEEE--HHHHHHHHH
T ss_pred CEEE-EEECCCCCEEEECCHHHHHHHHH
T ss_conf 6188-78735750898778999999999
No 6
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaK_ATPase monomer . GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 1dkg_A.
Probab=2.80 E-value=1.3e+02 Score=10.16 Aligned_cols=20 Identities=5% Similarity=-0.067 Sum_probs=10.8
Q ss_pred CCCCCEEEEEEECCCEEEEE
Q ss_conf 47783787758518879999
Q T0572 22 KASNVSSISYSFDRGHVTIV 41 (93)
Q Consensus 22 ~~~gy~~~~~~~~p~~V~i~ 41 (93)
...||.+.+-.+-|..|.|+
T Consensus 145 ~~~GY~~~~rvlRpA~V~V~ 164 (165)
T PF01025_consen 145 VQPGYKLGDRVLRPAKVIVS 164 (165)
T ss_dssp -B---B----BSS-EEEEEE
T ss_pred EECCEEECCEEEEEEEEEEC
T ss_conf 76698889999652078867
No 7
>PF05137 PilN: Fimbrial assembly protein (PilN); InterPro: IPR007813 PilN is a plasmid-encoded, lipoprotein which locates to the outer membrane of bacteria and are part of a thin pilus required only for liquid mating .
Probab=2.40 E-value=1.5e+02 Score=9.85 Aligned_cols=33 Identities=15% Similarity=0.162 Sum_probs=26.6
Q ss_pred EEECCCCCEEEEEEECCCEEEEEECHHHHCCCE
Q ss_conf 644477837877585188799994667715722
Q T0572 19 TGDKASNVSSISYSFDRGHVTIVGSQEAMDKID 51 (93)
Q Consensus 19 ~G~~~~gy~~~~~~~~p~~V~i~G~~~~l~~I~ 51 (93)
...+|+|-.+.++..+.+++.+.|....-+.+.
T Consensus 103 ~~~lP~~v~L~~i~~~~~~l~l~G~a~~~~~v~ 135 (162)
T PF05137_consen 103 SNILPDGVWLTSISINGNTLELQGSAKSEQAVA 135 (162)
T ss_pred HHHCCCCEEEEEEEECCCEEEEEEEECCHHHHH
T ss_conf 971999869989987298899998889778999
No 8
>PF07987 DUF1775: Domain of unkown function (DUF1775); InterPro: IPR012533 GLE1 is an essential nuclear export factor involved in RNA export.; PDB: 3esm_A.
Probab=2.00 E-value=1.8e+02 Score=9.40 Aligned_cols=45 Identities=22% Similarity=0.243 Sum_probs=23.0
Q ss_pred EEEEEECHHHHCCCEEEEEEEEE-ECCCCCEEEEEEECCCCEEECC
Q ss_conf 79999466771572278888852-0586676998881788658379
Q T0572 37 HVTIVGSQEAMDKIDSITVPVDI-SQVTEDTSKTLELKAEGVTVQP 81 (93)
Q Consensus 37 ~V~i~G~~~~l~~I~~i~~~vdi-s~~t~~~~~~v~lp~~~~~i~p 81 (93)
.|++.-.+..-++-..++..|-- .+...++...+.||.|.....|
T Consensus 18 HVtv~p~~a~~gs~~~~~~rVPhe~d~~~Ttkv~V~lP~gv~~~~p 63 (77)
T PF07987_consen 18 HVTVEPKEAAAGSYYKATFRVPHECDGSATTKVRVKLPEGVISVKP 63 (77)
T ss_dssp S-EEE----B----EEEEEEEE---SS--EEEEEEEEEE-ES--EE
T ss_pred EEEECCCCCCCCCEEEEEEECCCCCCCCCCEEEEEECCCHHCCCCC
T ss_conf 8998888869995399999777887998836999988850200675
No 9
>PF03275 GLF: UDP-galactopyranose mutase; InterPro: IPR015899 UDP-galactopyranose mutase (5.4.99.9 from EC) is involved in the conversion of UDP-GALP into UDP-GALF through a 2-keto intermediate, and contains FAD as a cofactor. The gene is known as glf, ceoA, and rfbD. It is known experimentally in Escherichia coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae.; PDB: 1i8t_B 1wam_A 2bi7_A 3gf4_A 2bi8_A 1v0j_C.
Probab=1.82 E-value=91 Score=10.87 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=26.0
Q ss_pred ECCCEEEEEEEE---------EEECCCCCEE-EEEEECCCEEEEEECHHHHCCCE
Q ss_conf 343188787677---------6444778378-77585188799994667715722
Q T0572 7 KLSKSVPVKLEL---------TGDKASNVSS-ISYSFDRGHVTIVGSQEAMDKID 51 (93)
Q Consensus 7 ~~~K~VpV~~~~---------~G~~~~gy~~-~~~~~~p~~V~i~G~~~~l~~I~ 51 (93)
.+.|+|||+... +|-|.+||+. ..-.++-..|.|.=.-+.++-.+
T Consensus 21 sv~~RvPvr~~~Dd~YF~d~yQg~P~~GYT~~fe~mL~h~~I~V~L~td~~~~~~ 75 (204)
T PF03275_consen 21 SVIKRVPVRFNYDDRYFNDRYQGMPKDGYTKMFENMLDHPNIEVRLNTDFFDIRE 75 (204)
T ss_dssp GGCSSS-BBSSS---S--SSB---B----HHHHHHHC-STTEEEECS--HHGCHH
T ss_pred HHHCCCCEEECCCCCCCCCHHHHCCHHCHHHHHHHHHCCCCEEEEECCCHHHHHC
T ss_conf 7834621574788764237233061238999999974779759993898156433
No 10
>PF12392 DUF3656: Collagenase
Probab=1.75 E-value=2.2e+02 Score=9.08 Aligned_cols=38 Identities=13% Similarity=0.249 Sum_probs=27.1
Q ss_pred ECCCEEEEEEEEEEECCCCCEEEEEEECCCEEEEEECH
Q ss_conf 34318878767764447783787758518879999466
Q T0572 7 KLSKSVPVKLELTGDKASNVSSISYSFDRGHVTIVGSQ 44 (93)
Q Consensus 7 ~~~K~VpV~~~~~G~~~~gy~~~~~~~~p~~V~i~G~~ 44 (93)
...+++||...+.+...+...+.-....-.++++.|..
T Consensus 19 ~~~~k~~v~~~~~~~~g~p~~l~~~~~~~~~~~v~~~~ 56 (122)
T PF12392_consen 19 SPERKIPVDLKFSAKVGEPLTLTVTDEDGNSVEVESEE 56 (122)
T ss_pred CCCCEEEEEEEEEEECCCCEEEEEEECCCCEEEEECCC
T ss_conf 43344668999999159978999998899689998376
Done!