Query         537021.9.peg.252_1
Match_columns 45
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 16:09:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_252.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG2753 consensus               39.9      10 0.00026   20.0   0.5   22    2-24    264-285 (378)
  2 cd01477 vWA_F09G8-8_type VWA F  15.5      83  0.0021   16.0   1.4   23   20-42      4-26  (193)
  3 TIGR02582 cas_TM1809 CRISPR-as  13.2      60  0.0015   16.6   0.2   15   16-30     58-72  (248)
  4 TIGR01429 AMP_deaminase AMP de   9.3      89  0.0023   15.9  -0.0   16    3-18    320-335 (616)
  5 TIGR02404 trehalos_R_Bsub treh   9.2 1.2E+02   0.003   15.4   0.6   26   20-45    208-235 (236)
  6 pfam01350 Flavi_NS4A Flaviviru   8.5      89  0.0023   15.9  -0.3   23    3-28    110-132 (145)
  7 TIGR01663 PNK-3'Pase polynucle   8.5 1.1E+02  0.0029   15.4   0.2   25   16-40     38-62  (526)
  8 pfam10584 Proteasome_A_N Prote   8.4      94  0.0024   15.8  -0.2   11    5-15      4-14  (26)
  9 TIGR02639 ClpA ATP-dependent C   7.9 1.1E+02  0.0027   15.5  -0.1   10    6-15    672-681 (774)
 10 pfam03852 Vsr DNA mismatch end   6.1 2.2E+02  0.0057   14.1   0.8   16    6-21      1-18  (75)

No 1  
>KOG2753 consensus
Probab=39.95  E-value=10  Score=20.03  Aligned_cols=22  Identities=45%  Similarity=0.536  Sum_probs=18.8

Q ss_pred             CCHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             40010114865620201111000
Q 537021.9.peg.2    2 EFIDSTVFSPEVRNMGKMRSLTD   24 (45)
Q Consensus         2 efidstvfspevrnmgkmrsltd   24 (45)
                      +|++|--+.-| .||.|||-||=
T Consensus       264 ~Fvqs~gl~~E-~~~~KMRLLTl  285 (378)
T KOG2753         264 GFVQSQGLVHE-QNMAKMRLLTL  285 (378)
T ss_pred             HHHHHHCCCHH-HHHHHHHHHHH
T ss_conf             89987064289-99999999999


No 2  
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=15.49  E-value=83  Score=16.03  Aligned_cols=23  Identities=30%  Similarity=0.648  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHEEHHHEEEEEEEE
Q ss_conf             11000024300010115556688
Q 537021.9.peg.2   20 RSLTDNRCSRTISRIQLDLRFLL   42 (45)
Q Consensus        20 rsltdnrcsrtisriqldlrfll   42 (45)
                      -+.||.+|...++.+.||.-|..
T Consensus         4 ~~~tdr~Cg~dl~nLWLDVv~VV   26 (193)
T cd01477           4 AAYTDRECGSDIKNLWLDIVFVV   26 (193)
T ss_pred             CCCCCCCCCCCHHHEEEEEEEEE
T ss_conf             54335766875122237899999


No 3  
>TIGR02582 cas_TM1809 CRISPR-associated RAMP protein, Csm3 family; InterPro: IPR013412    Members of this CRISPR-associated (cas) gene family are found in the mtube subtype CRISPR/cas locus, and and designated Csm3 for CRISPR/cas Subtype Mtube, protein 3..
Probab=13.23  E-value=60  Score=16.63  Aligned_cols=15  Identities=33%  Similarity=0.569  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHE
Q ss_conf             201111000024300
Q 537021.9.peg.2   16 MGKMRSLTDNRCSRT   30 (45)
Q Consensus        16 mgkmrsltdnrcsrt   30 (45)
                      -||||||-.+.-.+.
T Consensus        58 KGK~RsLLE~~~g~~   72 (248)
T TIGR02582        58 KGKLRSLLEKSLGKE   72 (248)
T ss_pred             HHHHHHHHHHHCCCE
T ss_conf             688888888771972


No 4  
>TIGR01429 AMP_deaminase AMP deaminase; InterPro: IPR006329   These sequences describe AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the conserved domain which defines this group of sequences.; GO: 0003876 AMP deaminase activity, 0009168 purine ribonucleoside monophosphate biosynthetic process.
Probab=9.30  E-value=89  Score=15.89  Aligned_cols=16  Identities=44%  Similarity=0.717  Sum_probs=11.6

Q ss_pred             CHHCCCCCHHHHHHHH
Q ss_conf             0010114865620201
Q 537021.9.peg.2    3 FIDSTVFSPEVRNMGK   18 (45)
Q Consensus         3 fidstvfspevrnmgk   18 (45)
                      +||..||||.||=+=.
T Consensus       320 ~i~~~lfSpn~RWLiQ  335 (616)
T TIGR01429       320 IIDNDLFSPNVRWLIQ  335 (616)
T ss_pred             HHHCCCCCCCCCEEEE
T ss_conf             9852655787334776


No 5  
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770    This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=9.24  E-value=1.2e+02  Score=15.38  Aligned_cols=26  Identities=42%  Similarity=0.437  Sum_probs=21.7

Q ss_pred             HHHHHHHH-HHEEHHHEEEE-EEEEEEC
Q ss_conf             11000024-30001011555-6688739
Q 537021.9.peg.2   20 RSLTDNRC-SRTISRIQLDL-RFLLIRR   45 (45)
Q Consensus        20 rsltdnrc-srtisriqldl-rfllirr   45 (45)
                      -.|.|++| --|-||-.||- +|.=++|
T Consensus       208 ~~L~Dt~~FqYTESRHRLDKF~f~D~AR  235 (236)
T TIGR02404       208 VYLEDTRLFQYTESRHRLDKFRFVDFAR  235 (236)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCEEEEEC
T ss_conf             4502586245512113235254320003


No 6  
>pfam01350 Flavi_NS4A Flavivirus non-structural protein NS4A. Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus.
Probab=8.54  E-value=89  Score=15.88  Aligned_cols=23  Identities=43%  Similarity=0.577  Sum_probs=16.5

Q ss_pred             CHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             00101148656202011110000243
Q 537021.9.peg.2    3 FIDSTVFSPEVRNMGKMRSLTDNRCS   28 (45)
Q Consensus         3 fidstvfspevrnmgkmrsltdnrcs   28 (45)
                      |+=-.|.-||   -||-||-.||+-.
T Consensus       110 filmvVLiPE---pg~QRS~~DN~LA  132 (145)
T pfam01350       110 FLLLVVLIPE---PGKQRSQQDNQLA  132 (145)
T ss_pred             HHHHHEECCC---CCCCCCCCCCHHH
T ss_conf             9999604468---8886675443589


No 7  
>TIGR01663 PNK-3'Pase polynucleotide kinase 3'-phosphatase; InterPro: IPR006550   These sequences represent the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3'-phosphates is essential for the further processing of the break by DNA polymerases , . The central phosphatase domain is a member of the IIIA subfamily (IPR006549 from INTERPRO) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by IPR006551 from INTERPRO. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. .
Probab=8.47  E-value=1.1e+02  Score=15.42  Aligned_cols=25  Identities=20%  Similarity=0.513  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHHHHEEHHHEEEEEE
Q ss_conf             2011110000243000101155566
Q 537021.9.peg.2   16 MGKMRSLTDNRCSRTISRIQLDLRF   40 (45)
Q Consensus        16 mgkmrsltdnrcsrtisriqldlrf   40 (45)
                      -|.....+|..|||+--.+|.|+.-
T Consensus        38 R~~~T~~~D~KCS~~Q~~L~~D~~~   62 (526)
T TIGR01663        38 RSRLTQVRDRKCSKRQVELVVDLKK   62 (526)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEECCC
T ss_conf             5755651004224320357770030


No 8  
>pfam10584 Proteasome_A_N Proteasome subunit A N-terminal signature. This domain is conserved in the A subunits of the proteasome complex proteins.
Probab=8.40  E-value=94  Score=15.78  Aligned_cols=11  Identities=45%  Similarity=0.570  Sum_probs=8.0

Q ss_pred             HCCCCCHHHHH
Q ss_conf             10114865620
Q 537021.9.peg.2    5 DSTVFSPEVRN   15 (45)
Q Consensus         5 dstvfspevrn   15 (45)
                      +.|+|||+-|-
T Consensus         4 ~~ttFSPdGrL   14 (26)
T pfam10584         4 SLTTFSPDGRL   14 (26)
T ss_pred             CCEEECCCCCE
T ss_conf             76058899805


No 9  
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=7.86  E-value=1.1e+02  Score=15.52  Aligned_cols=10  Identities=60%  Similarity=1.032  Sum_probs=7.3

Q ss_pred             CCCCCHHHHH
Q ss_conf             0114865620
Q 537021.9.peg.2    6 STVFSPEVRN   15 (45)
Q Consensus         6 stvfspevrn   15 (45)
                      ...||||-||
T Consensus       672 kk~F~PEFRN  681 (774)
T TIGR02639       672 KKLFSPEFRN  681 (774)
T ss_pred             HHHCCCCCCC
T ss_conf             7315874201


No 10 
>pfam03852 Vsr DNA mismatch endonuclease Vsr.
Probab=6.15  E-value=2.2e+02  Score=14.13  Aligned_cols=16  Identities=44%  Similarity=0.731  Sum_probs=0.0

Q ss_pred             CCCCCHHHH--HHHHHHH
Q ss_conf             011486562--0201111
Q 537021.9.peg.2    6 STVFSPEVR--NMGKMRS   21 (45)
Q Consensus         6 stvfspevr--nmgkmrs   21 (45)
                      |.+|+||.|  +|.+.+|
T Consensus         1 tD~~t~~~RS~~M~~irs   18 (75)
T pfam03852         1 TDVLTPAKRSKNMQAIRS   18 (75)
T ss_pred             CCCCCHHHHHHHHHHHCC
T ss_conf             983888999999972137


Done!