Query 537021.9.peg.186_1
Match_columns 45
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Tue May 24 15:31:45 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_186.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00455 apsK adenylylsulfate 24.2 34 0.00086 17.7 1.0 13 32-44 14-26 (187)
2 KOG4079 consensus 16.7 59 0.0015 16.5 0.9 19 24-42 34-52 (169)
3 pfam03043 Herpes_UL87 Herpesvi 16.2 52 0.0013 16.8 0.5 11 35-45 342-352 (533)
4 TIGR02957 SigX4 RNA polymerase 15.6 49 0.0012 16.9 0.3 31 14-44 222-254 (287)
5 TIGR03060 PS_II_psb29 photosys 9.5 1.5E+02 0.0037 14.5 1.1 18 13-30 5-22 (214)
6 pfam05763 DUF835 Protein of un 9.1 1.3E+02 0.0034 14.7 0.8 18 28-45 32-49 (136)
7 PRK13266 Thf1-like protein; Re 9.1 1.5E+02 0.0039 14.4 1.1 18 13-30 5-22 (224)
8 pfam11264 ThylakoidFormat Thyl 9.0 1.5E+02 0.0039 14.4 1.1 16 15-30 2-17 (216)
9 COG1582 FlgEa Uncharacterized 8.5 85 0.0022 15.7 -0.4 15 24-38 11-25 (67)
10 TIGR02717 AcCoA-syn-alpha acet 7.9 1.3E+02 0.0032 14.8 0.3 10 26-35 347-357 (457)
No 1
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=24.20 E-value=34 Score=17.71 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=11.1
Q ss_pred CCCCEEEEEEEEC
Q ss_conf 0112012301224
Q 537021.9.peg.1 32 INGMRSFVFWITN 44 (45)
Q Consensus 32 ingmrsfvfwitn 44 (45)
.|+-+|+|.|+|-
T Consensus 14 ~~~h~g~vlWlTG 26 (187)
T TIGR00455 14 LNKHRGVVLWLTG 26 (187)
T ss_pred HCCCCEEEEEEEC
T ss_conf 6279738985116
No 2
>KOG4079 consensus
Probab=16.69 E-value=59 Score=16.50 Aligned_cols=19 Identities=37% Similarity=0.765 Sum_probs=14.8
Q ss_pred HHHCCCCCCCCCEEEEEEE
Q ss_conf 6333800201120123012
Q 537021.9.peg.1 24 EFFLNPVDINGMRSFVFWI 42 (45)
Q Consensus 24 efflnpvdingmrsfvfwi 42 (45)
.|--|+-.-.|.|.||||-
T Consensus 34 nynt~g~~~~GARdFVfwN 52 (169)
T KOG4079 34 NYNTNGPEQSGARDFVFWN 52 (169)
T ss_pred ECCCCCCCCCCCCCEEEEC
T ss_conf 5567884436742068855
No 3
>pfam03043 Herpes_UL87 Herpesvirus UL87 family. Members of this family are functionally uncharacterized. This family groups together EBV BcRF1, HSV-6 U58, HVS-1 24 and HCMV UL87. The proteins range from 575 to 950 amino acids in length.
Probab=16.21 E-value=52 Score=16.75 Aligned_cols=11 Identities=55% Similarity=0.824 Sum_probs=8.6
Q ss_pred CEEEEEEEECC
Q ss_conf 20123012249
Q 537021.9.peg.1 35 MRSFVFWITNV 45 (45)
Q Consensus 35 mrsfvfwitnv 45 (45)
-|+=|||.||-
T Consensus 342 ~R~~VfWTTNF 352 (533)
T pfam03043 342 GRKDVFWTTNF 352 (533)
T ss_pred CCCCEEEECCC
T ss_conf 67751884587
No 4
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=15.64 E-value=49 Score=16.91 Aligned_cols=31 Identities=19% Similarity=0.352 Sum_probs=24.7
Q ss_pred HHHHHHHHHH-HHHCCCCCCCCCEEEEEE-EEC
Q ss_conf 8603365578-633380020112012301-224
Q 537021.9.peg.1 14 VFSQSKRLFL-EFFLNPVDINGMRSFVFW-ITN 44 (45)
Q Consensus 14 vfsqskrlfl-efflnpvdingmrsfvfw-itn 44 (45)
.+.--+|+.- ++-+.|++|||+...++. +-|
T Consensus 222 ~~g~~~r~~~i~~~~~p~~vNG~pa~~~~d~~g 254 (287)
T TIGR02957 222 FLGLVRRLGPIGMRVDPKDVNGQPAVLVRDVDG 254 (287)
T ss_pred HHHHHCCCCCCEEEEEEEEECCCCCEEEEECCC
T ss_conf 987644663002699888875885079970178
No 5
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=9.47 E-value=1.5e+02 Score=14.55 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHCCCC
Q ss_conf 986033655786333800
Q 537021.9.peg.1 13 KVFSQSKRLFLEFFLNPV 30 (45)
Q Consensus 13 kvfsqskrlflefflnpv 30 (45)
...|.|||.|.+.|--|+
T Consensus 5 ~TVsDsKr~F~~~~p~pI 22 (214)
T TIGR03060 5 RTVSDSKRAFHAAFPRVI 22 (214)
T ss_pred CCHHHHHHHHHHHCCCCC
T ss_conf 114887999998589888
No 6
>pfam05763 DUF835 Protein of unknown function (DUF835). The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=9.09 E-value=1.3e+02 Score=14.73 Aligned_cols=18 Identities=39% Similarity=0.601 Sum_probs=12.9
Q ss_pred CCCCCCCCEEEEEEEECC
Q ss_conf 800201120123012249
Q 537021.9.peg.1 28 NPVDINGMRSFVFWITNV 45 (45)
Q Consensus 28 npvdingmrsfvfwitnv 45 (45)
||-.+...-.-++|+|++
T Consensus 32 ~P~~~~~~~~~viWlT~~ 49 (136)
T pfam05763 32 NPEKWRELYIPVIWITKV 49 (136)
T ss_pred CHHHHHCCCCEEEEEECC
T ss_conf 979973559707998416
No 7
>PRK13266 Thf1-like protein; Reviewed
Probab=9.07 E-value=1.5e+02 Score=14.42 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHCCCC
Q ss_conf 986033655786333800
Q 537021.9.peg.1 13 KVFSQSKRLFLEFFLNPV 30 (45)
Q Consensus 13 kvfsqskrlflefflnpv 30 (45)
...|.|||.|.+.|--|+
T Consensus 5 ~TVsDsKr~F~~~~p~pI 22 (224)
T PRK13266 5 RTVSDSKRAFHAAFPRVI 22 (224)
T ss_pred CCHHHHHHHHHHHCCCCC
T ss_conf 114887999998589888
No 8
>pfam11264 ThylakoidFormat Thylakoid formation protein. THF1 is localized to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling. THF1 is also thought to have a role in chloroplast and leaf development. THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis.
Probab=9.00 E-value=1.5e+02 Score=14.44 Aligned_cols=16 Identities=38% Similarity=0.598 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHCCCC
Q ss_conf 6033655786333800
Q 537021.9.peg.1 15 FSQSKRLFLEFFLNPV 30 (45)
Q Consensus 15 fsqskrlflefflnpv 30 (45)
.|.|||.|.+.|--|+
T Consensus 2 VsDsKr~F~~~~p~pI 17 (216)
T pfam11264 2 VSDSKRAFHAAYPRPI 17 (216)
T ss_pred CCHHHHHHHHHCCCCC
T ss_conf 0157999998589888
No 9
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=8.53 E-value=85 Score=15.72 Aligned_cols=15 Identities=40% Similarity=0.789 Sum_probs=11.5
Q ss_pred HHHCCCCCCCCCEEE
Q ss_conf 633380020112012
Q 537021.9.peg.1 24 EFFLNPVDINGMRSF 38 (45)
Q Consensus 24 efflnpvdingmrsf 38 (45)
+|+|||--|..|+.|
T Consensus 11 ~~~lN~~~IE~ie~~ 25 (67)
T COG1582 11 EFWLNAHHIETIEAF 25 (67)
T ss_pred CEEECHHHHHHHHCC
T ss_conf 025378784432216
No 10
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain; InterPro: IPR014089 This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised , , . In most species this protein is bifunctional, existing as fused alpha-beta domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs. .
Probab=7.91 E-value=1.3e+02 Score=14.84 Aligned_cols=10 Identities=50% Similarity=0.737 Sum_probs=0.0
Q ss_pred HCCCCCCCC-C
Q ss_conf 338002011-2
Q 537021.9.peg.1 26 FLNPVDING-M 35 (45)
Q Consensus 26 flnpvding-m 35 (45)
+-|||||-| |
T Consensus 347 ~~NPVD~~GsD 357 (457)
T TIGR02717 347 IKNPVDVLGSD 357 (457)
T ss_pred CCCCCEEEECC
T ss_conf 78751255227
Done!