Query gi|254780449|ref|YP_003064862.1| hypothetical protein CLIBASIA_01670 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 459
No_of_seqs 4 out of 6
Neff 1.6
Searched_HMMs 39220
Date Sun May 29 16:39:54 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780449.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam09796 QCR10 Ubiquinol-cyto 55.2 5.3 0.00014 20.0 1.0 25 266-290 31-55 (64)
2 KOG2757 consensus 49.0 6.2 0.00016 19.6 0.5 26 89-114 9-34 (411)
3 cd00693 secretory_peroxidase S 34.0 23 0.00057 15.9 1.5 32 357-388 250-282 (297)
4 PRK01622 OxaA-like protein pre 32.6 23 0.0006 15.7 1.4 26 85-110 54-79 (266)
5 TIGR00463 gltX_arch glutamyl-t 31.5 10 0.00026 18.2 -0.6 104 226-366 341-456 (600)
6 cd03013 PRX5_like Peroxiredoxi 30.9 18 0.00045 16.6 0.5 58 281-342 75-135 (155)
7 KOG1626 consensus 30.0 33 0.00083 14.8 1.8 60 287-356 168-227 (279)
8 TIGR00515 accD acetyl-CoA carb 29.8 16 0.0004 16.9 0.1 39 216-259 13-51 (292)
9 PRK08745 ribulose-phosphate 3- 27.3 23 0.00058 15.8 0.6 20 333-352 196-215 (223)
10 pfam11190 DUF2976 Protein of u 26.1 43 0.0011 14.0 1.8 37 78-114 45-82 (87)
11 PRK10140 putative acetyltransf 25.5 37 0.00095 14.4 1.4 29 420-448 118-146 (162)
12 COG4759 Uncharacterized protei 25.0 41 0.001 14.1 1.5 109 6-114 112-244 (316)
13 TIGR00016 ackA acetate kinase; 24.1 42 0.0011 14.1 1.5 126 312-442 37-192 (416)
14 KOG4407 consensus 23.9 23 0.00059 15.8 0.1 100 278-402 1218-1317(1973)
15 TIGR02013 rpoB DNA-directed RN 23.6 35 0.00088 14.6 0.9 40 404-445 1144-1186(1449)
16 pfam09187 DUF1950 Domain of un 23.3 49 0.0013 13.6 1.7 18 345-362 4-21 (119)
17 TIGR02094 more_P_ylases alpha- 23.1 51 0.0013 13.5 3.3 121 228-364 336-472 (618)
18 KOG3926 consensus 22.7 31 0.0008 14.9 0.6 32 362-393 257-288 (332)
19 PRK02463 OxaA-like protein pre 22.4 48 0.0012 13.7 1.5 22 87-108 56-77 (307)
20 COG0218 Predicted GTPase [Gene 22.4 50 0.0013 13.6 1.6 55 320-374 126-185 (200)
21 cd01763 Sumo Small ubiquitin-r 22.0 51 0.0013 13.5 1.6 24 326-349 47-70 (87)
22 pfam10950 DUF2775 Protein of u 21.8 21 0.00053 16.1 -0.5 76 296-393 4-82 (108)
No 1
>pfam09796 QCR10 Ubiquinol-cytochrome-c reductase complex subunit (QCR10). The QCR10 family of proteins are a component of the ubiquinol-cytochrome c reductase complex (also known as complex III or cytochrome b-c1 complex). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. This subunit (QCR10) is required for stable association of the iron-sulfur protein with the complex.
Probab=55.15 E-value=5.3 Score=19.99 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 7777533456675408654433222
Q gi|254780449|r 266 FIEKLAHTTKAIDKKIPFIGNQWRD 290 (459)
Q Consensus 266 ~i~~~~~~t~ai~~k~p~~~~~~~~ 290 (459)
|.+-.-.--+.|.+|||++|..|++
T Consensus 31 F~~~vP~vq~dil~KIP~~g~~~~~ 55 (64)
T pfam09796 31 FFSGVPRFQDDILQKIPVFGSYWER 55 (64)
T ss_pred HHCCCCHHHHHHHHHCCCCCCHHCC
T ss_conf 6057714899998727754310034
No 2
>KOG2757 consensus
Probab=48.96 E-value=6.2 Score=19.59 Aligned_cols=26 Identities=27% Similarity=0.326 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 77441057665102577877877788
Q gi|254780449|r 89 GNYGWGIVGAISDAALLIPVVGYGAR 114 (459)
Q Consensus 89 gnygwg~~g~isd~all~~~~~y~~~ 114 (459)
-||+||-.|.-|-||-|+---+++.+
T Consensus 9 k~Y~WGk~G~~S~varlaaa~d~~~~ 34 (411)
T KOG2757 9 KQYAWGKKGSESLVARLAAAGDPSFQ 34 (411)
T ss_pred EECCCCCCCCHHHHHHHHHCCCCCCC
T ss_conf 10354566808899999872898534
No 3
>cd00693 secretory_peroxidase Secretory peroxidases. Horseradish peroxidase and related secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants, where they have been implicated in hydrogen peroxide detoxification, auxin catabolism and lignin biosynthesis and stress response. Class III peroxidases contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=33.97 E-value=23 Score=15.85 Aligned_cols=32 Identities=22% Similarity=0.436 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHH-CCCHHHHHHHHHHHHCHH
Q ss_conf 68854644556542-040222268999872600
Q gi|254780449|r 357 AKNPKQLQLISSYA-NQSIFADSVVHLMQSIPE 388 (459)
Q Consensus 357 ~kN~e~~QLISSYA-nQ~IF~qsyi~L~sehPe 388 (459)
.-|++.+.+...|| +|.-|...|..-|...-+
T Consensus 250 ~~d~~T~~~V~~~A~~~~~F~~~Fa~AmvKmg~ 282 (297)
T cd00693 250 FSDPRTRAIVKRYANNQNAFFEDFAKSMVKMGN 282 (297)
T ss_pred HCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHC
T ss_conf 659409999999851978999999999999847
No 4
>PRK01622 OxaA-like protein precursor; Validated
Probab=32.55 E-value=23 Score=15.74 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=16.0
Q ss_pred HHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 64157744105766510257787787
Q gi|254780449|r 85 EFKKGNYGWGIVGAISDAALLIPVVG 110 (459)
Q Consensus 85 efkkgnygwg~~g~isd~all~~~~~ 110 (459)
.+--|||||+|+-..-=+-++.-|..
T Consensus 54 ~~~~gnyGlaIIl~TiivRlil~PL~ 79 (266)
T PRK01622 54 HHIHGSYGIAIIIVTLIIRSLMIPLA 79 (266)
T ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 87588499999999999999998702
No 5
>TIGR00463 gltX_arch glutamyl-tRNA synthetase; InterPro: IPR004526 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of E. coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure . ; GO: 0000166 nucleotide binding, 0004818 glutamate-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006424 glutamyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=31.50 E-value=10 Score=18.17 Aligned_cols=104 Identities=26% Similarity=0.329 Sum_probs=56.5
Q ss_pred HCCCCCCCCCHHHHHCC--CCHH---HHHHHHCCCCCCHHHCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC
Q ss_conf 00124544310222101--2202---345531032100010004677775334566754086544332223321343133
Q gi|254780449|r 226 QLSKSTPQGIWTKALTK--ADPA---LESIYQRGKIFSNTIKNNAFIEKLAHTTKAIDKKIPFIGNQWRDINTAHSEFKM 300 (459)
Q Consensus 226 ~~~~~~~~~~~tka~~~--~~~~---~~~~~~~~~~~s~tik~~~~i~~~~~~t~ai~~k~p~~~~~~~~~~~~~~e~~~ 300 (459)
-+++|.-|||--+.+.- -||- |-.+-.||- +.-||-+=|--||-.--|++-.
T Consensus 341 Lsts~~~~~i~~g~y~GnWDDpRLpTlRa~rRRG~-----------------~pEai~~~~~~~G~~~nd~~~s------ 397 (600)
T TIGR00463 341 LSTSSIKKGIVRGDYSGNWDDPRLPTLRAVRRRGI-----------------KPEAIREFMLSIGVKRNDVKLS------ 397 (600)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCCCC-----------------CHHHHHHHHHHCCCCEEEEEEE------
T ss_conf 21034541101265124656888630233211788-----------------1578999999719961244312------
Q ss_pred CHHCCHHHHHHHHHHHCCCCHHHHHH--CCCCEEEEEECCEECCCC--HH-HHHHHHHHHHCCCHHH--HHHH
Q ss_conf 11207167878887725651124441--147247997094542000--89-9999998550688546--4455
Q gi|254780449|r 301 VPLSDQTLFRDFQGLCGKNIDNQFIL--DLNRASFIFNGKKLARDN--SA-EAIQKLMNQFAKNPKQ--LQLI 366 (459)
Q Consensus 301 ~~~~~~~~frdf~~l~g~n~dn~fll--D~NrasFIvNgkkIsvdN--~~-~mL~~l~k~f~kN~e~--~QLI 366 (459)
++-|-+- |+-++ +++|+.||+|-.||.+-+ +- +--.++--.-|++||+ +.||
T Consensus 398 -----------w~~lYA~---Nk~~id~~A~Ryffi~~PvKl~~~gse~Pq~~~~~~~P~hp~~Pe~Ger~l~ 456 (600)
T TIGR00463 398 -----------WKNLYAL---NKKIIDKKARRYFFIWNPVKLEIEGSELPQEKKIVERPLHPDNPEVGERKLI 456 (600)
T ss_pred -----------HHHHHHH---HHHHCCCCCCCEEEEECCEEEEEECCCCCCCCCHHCCCCCCCCCCCCCEEEE
T ss_conf -----------5677662---3554032468038888888999856768878712117776778874555798
No 6
>cd03013 PRX5_like Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5 suggests that it may have an important antioxidant role in organelles that are major sources of reactive oxygen species (ROS), as well as a role in the control of signal transduction. PRX5 has been shown to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. As with all other PRXs, the N-terminal peroxidatic cysteine of PRX5 is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Human PRX5 is able to resolve this intermediate by forming an intramolecular disulfide bond with its C-terminal cysteine (the resolving cysteine), which can then be reduced by TRX, just like an atypical 2-cys PRX. This resolving cysteine, however, is not conserved in other members of the subfamily. In such cases
Probab=30.91 E-value=18 Score=16.57 Aligned_cols=58 Identities=17% Similarity=0.307 Sum_probs=34.1
Q ss_pred CCCCCCCCCCCCCCHHHCCCCHHCCHHHHHHHHHHHCCCCHHHH---HHCCCCEEEEEECCEECC
Q ss_conf 86544332223321343133112071678788877256511244---411472479970945420
Q gi|254780449|r 281 IPFIGNQWRDINTAHSEFKMVPLSDQTLFRDFQGLCGKNIDNQF---ILDLNRASFIFNGKKLAR 342 (459)
Q Consensus 281 ~p~~~~~~~~~~~~~~e~~~~~~~~~~~frdf~~l~g~n~dn~f---llD~NrasFIvNgkkIsv 342 (459)
=||.-+.|+.-+-+...++|+.-.+ ++|--.+|-..|..- -.-..|+.||+++++|-.
T Consensus 75 D~fv~~AW~~~~~~~~~i~~lsD~~----~~f~~~lGl~~d~~~~g~g~Rs~R~a~iv~dg~I~~ 135 (155)
T cd03013 75 DPFVMKAWGKALGAKDKIRFLADGN----GEFTKALGLTLDLSAAGGGIRSKRYALIVDDGKVKY 135 (155)
T ss_pred CHHHHHHHHHHHCCCCCEEEEECCC----HHHHHHHCCEECCCCCCCCCCCEEEEEEEECCEEEE
T ss_conf 9999999999609877359954674----799997298062567878002100899999998999
No 7
>KOG1626 consensus
Probab=30.01 E-value=33 Score=14.79 Aligned_cols=60 Identities=22% Similarity=0.349 Sum_probs=45.2
Q ss_pred CCCCCCCCHHHCCCCHHCCHHHHHHHHHHHCCCCHHHHHHCCCCEEEEEECCEECCCCHHHHHHHHHHHH
Q ss_conf 3222332134313311207167878887725651124441147247997094542000899999998550
Q gi|254780449|r 287 QWRDINTAHSEFKMVPLSDQTLFRDFQGLCGKNIDNQFILDLNRASFIFNGKKLARDNSAEAIQKLMNQF 356 (459)
Q Consensus 287 ~~~~~~~~~~e~~~~~~~~~~~frdf~~l~g~n~dn~fllD~NrasFIvNgkkIsvdN~~~mL~~l~k~f 356 (459)
..+||+.-..-||.+----...|||++---||+. -.|.|+|.-.+.+-+-+.+|+-|.-.
T Consensus 168 ~~ndi~DV~~~~Pg~L~~tr~wFr~YKiPdGKpe----------N~faf~~~f~n~~~A~~iIk~t~d~w 227 (279)
T KOG1626 168 EYNDIEDVEKLFPGLLEATRRWFRDYKIPDGKPE----------NKFAFVGDFLNKKFALDIIKETHDLW 227 (279)
T ss_pred HHCCHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC----------CCHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 3155788877676138999999997478789973----------10100244457588999999999999
No 8
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit; InterPro: IPR000438 Fatty acid synthesis involves a set of reactions, commencing with carboxylation of acetyl-CoA to malonyl-CoA. This is an irreversible reaction, catalysed by the acetyl-CoA carboxylase complex (6.4.1.2 from EC); a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase and two non-identical carboxyl transferase subunits (alpha and beta) in a 2:2 association . The reaction involves two steps: Biotin carrier protein + ATP + HCO_3^- = Carboxybiotin carrier protein + ADP + P_i Carboxybiotin carrier protein + Acetyl-CoA = Malonyl-CoA + Biotin carrier protein In the first step, biotin carboxylase catalyses the carboxylation of the carrier protein to form an intermediate. Next, the transcarboxylase complex transfers the carboxyl group from the intermediate to acetyl-CoA forming malonyl-CoA.; GO: 0003989 acetyl-CoA carboxylase activity, 0006633 fatty acid biosynthetic process, 0009317 acetyl-CoA carboxylase complex.
Probab=29.82 E-value=16 Score=16.86 Aligned_cols=39 Identities=26% Similarity=0.514 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHCCCCHHHHHHHHCCCCCCH
Q ss_conf 56555431110012454431022210122023455310321000
Q gi|254780449|r 216 VEESISKINSQLSKSTPQGIWTKALTKADPALESIYQRGKIFSN 259 (459)
Q Consensus 216 ~~~~~~~~~~~~~~~~~~~~~tka~~~~~~~~~~~~~~~~~~s~ 259 (459)
.|..|.++.|.-+++.|.|.|||. |+-+.+.-+-.+++|
T Consensus 13 aePP~~~~~~~~~~~~~~g~wtKC-----p~C~~~~Y~keL~~n 51 (292)
T TIGR00515 13 AEPPVLKLRSTRKAEVPEGVWTKC-----PKCGQLLYTKELQRN 51 (292)
T ss_pred CCCCCCCCCCCCCCCCCCCCEECC-----CHHHHHHHHHHHHCC
T ss_conf 678777888885335788730014-----424344346653035
No 9
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=27.29 E-value=23 Score=15.82 Aligned_cols=20 Identities=15% Similarity=0.320 Sum_probs=8.2
Q ss_pred EEEECCEECCCCHHHHHHHH
Q ss_conf 99709454200089999999
Q gi|254780449|r 333 FIFNGKKLARDNSAEAIQKL 352 (459)
Q Consensus 333 FIvNgkkIsvdN~~~mL~~l 352 (459)
||.-....+-++..+++++|
T Consensus 196 ~V~GSaiF~~~d~~~~i~~l 215 (223)
T PRK08745 196 FVAGSAIFNAPDYAQVIAQM 215 (223)
T ss_pred EEECHHHHCCCCHHHHHHHH
T ss_conf 99741775799999999999
No 10
>pfam11190 DUF2976 Protein of unknown function (DUF2976). This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=26.08 E-value=43 Score=14.00 Aligned_cols=37 Identities=32% Similarity=0.541 Sum_probs=23.5
Q ss_pred CCHHHHHHHCCCCCCCHHHHHHHHHH-HHHHHHHHHHH
Q ss_conf 00011776415774410576651025-77877877788
Q gi|254780449|r 78 PIYGTYREFKKGNYGWGIVGAISDAA-LLIPVVGYGAR 114 (459)
Q Consensus 78 piygt~~efkkgnygwg~~g~isd~a-ll~~~~~y~~~ 114 (459)
-.++||.|...|.-+||-.|+.--+. .|+..+-|+..
T Consensus 45 ~ai~ty~ei~~GK~~W~~fg~~viVGviLlv~viwLlt 82 (87)
T pfam11190 45 AALGTYNEIRDGKKTWGDFGAIVIVGVVLLVFVIWLVT 82 (87)
T ss_pred HHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf 99978999972612088631378768599999999985
No 11
>PRK10140 putative acetyltransferase YhhY; Provisional
Probab=25.49 E-value=37 Score=14.41 Aligned_cols=29 Identities=28% Similarity=0.225 Sum_probs=23.9
Q ss_pred CEEEEECCCCCCHHHHCCEEEEEEECCCC
Q ss_conf 10133000125414315516999867898
Q gi|254780449|r 420 TKVQAVDKIAGKPLKEYGLKISGILSPDK 448 (459)
Q Consensus 420 sdl~~~n~~~gkkyk~yGIKaSgILSpdk 448 (459)
..|...|..+.++|+.||-+.+|+|....
T Consensus 118 l~V~~~N~~Ai~Ly~k~GF~~eG~~~~~~ 146 (162)
T PRK10140 118 LTVFVDNAPAIKVYKKYGFEIEGTGKKYA 146 (162)
T ss_pred EEEECCCHHHHHHHHHCCCEEEEEEHHEE
T ss_conf 99986999999999988998998870118
No 12
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.96 E-value=41 Score=14.14 Aligned_cols=109 Identities=17% Similarity=0.172 Sum_probs=61.2
Q ss_pred HHHCCCCCCCC----CHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHCCCC-CEEE---------------EEECC
Q ss_conf 43206888872----0889898886302344323334--4779999987412233-1001---------------33000
Q gi|254780449|r 6 INKYFPPNNNI----ERKEIADKLIKNISIVDKTMDV--LPLYHQVRELTQNKAS-TEQV---------------IDIST 63 (459)
Q Consensus 6 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~---------------~~~~~ 63 (459)
+.+.++|.++. .+..+.|-|+-+-+-+|+...- -|+|+|+|.--.++.- .-.| ||...
T Consensus 112 l~l~~~~~~l~~~~~~~~h~RdiLVCTHgn~D~cCarfG~P~Y~~~r~~~a~l~~~~lRvWq~SHfgGHrFAPTlidlP~ 191 (316)
T COG4759 112 LALLLQGKELAQFDIYPQHTRDILVCTHGNVDVCCARFGYPFYQQLRAQYADLNLENLRVWQSSHFGGHRFAPTLIDLPQ 191 (316)
T ss_pred HHHHCCCCCCHHHCCCHHHHCEEEEECCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCHHHCCCC
T ss_conf 98750874423330231120158995478721566640858999998764330345347997425576525731421878
Q ss_pred HH--HHHHEEEEEEHHCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 01--0211110000000001177641577441057665102577877877788
Q gi|254780449|r 64 KV--KDVAVDVAVSMIPIYGTYREFKKGNYGWGIVGAISDAALLIPVVGYGAR 114 (459)
Q Consensus 64 ~~--~~~~~~~~~~mipiygt~~efkkgnygwg~~g~isd~all~~~~~y~~~ 114 (459)
-- -....+.-.+.+---|.++++|+++-|||++-..-.+|--.+-..+|-.
T Consensus 192 GqyyG~Ld~~~~~~l~~r~gdvk~L~~~YRGWg~L~~~~QI~Erei~~~~GW~ 244 (316)
T COG4759 192 GQYYGHLDPESLDSLLTRTGDVKQLKPFYRGWGGLPKFEQIAEREIWMQHGWD 244 (316)
T ss_pred CCEEEECCHHHHHHHHHCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCHH
T ss_conf 75212258899999985067566640120677678789999999999984656
No 13
>TIGR00016 ackA acetate kinase; InterPro: IPR004372 Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate.; GO: 0016301 kinase activity, 0016774 phosphotransferase activity carboxyl group as acceptor, 0006082 organic acid metabolic process.
Probab=24.08 E-value=42 Score=14.06 Aligned_cols=126 Identities=25% Similarity=0.286 Sum_probs=74.6
Q ss_pred HHHHHCCCCHHHHHHCCCCEEEE-EEC-C----EECCCCHHHHHHHHHHHHCC--CHHHHHHHHHHHC--------CCHH
Q ss_conf 88772565112444114724799-709-4----54200089999999855068--8546445565420--------4022
Q gi|254780449|r 312 FQGLCGKNIDNQFILDLNRASFI-FNG-K----KLARDNSAEAIQKLMNQFAK--NPKQLQLISSYAN--------QSIF 375 (459)
Q Consensus 312 f~~l~g~n~dn~fllD~NrasFI-vNg-k----kIsvdN~~~mL~~l~k~f~k--N~e~~QLISSYAn--------Q~IF 375 (459)
.+|||- .+-++-.+-..+ .+| + +.+..+.+++|+.+.+++.+ +.+-+++-++-+- -..|
T Consensus 37 ~~Gl~e-----~i~~~~~~~~~~n~~g~~~~~~~~~~~~h~~A~~~~~~~L~~~~~~~i~~~l~eI~~IGHRvVHGG~~f 111 (416)
T TIGR00016 37 LSGLVE-----RIFLANARIKTVNENGGKKEEELLAIADHQEAVKFILNTLTNQSDKKIIKLLSEIDLIGHRVVHGGEKF 111 (416)
T ss_pred HHHHHH-----HHCCCCCEEEEEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECEEEECCCCC
T ss_conf 998872-----222775157777525774311221201189999999999874013322122012006302257276432
Q ss_pred HHHHH---HHHHHCHHHHHHHCCCCCCEEEEEE-------EEECCEEEE--EEECCCEEE--EECCCCCCHHHHCCEEEE
Q ss_conf 22689---9987260033331136873069999-------860766999--983231013--300012541431551699
Q gi|254780449|r 376 ADSVV---HLMQSIPEFAKYASKSGSASKFTAK-------TLTNGEVAF--TAKYTTKVQ--AVDKIAGKPLKEYGLKIS 441 (459)
Q Consensus 376 ~qsyi---~L~sehPe~~kYq~Ks~Sr~sY~~n-------tL~DG~V~F--tAk~~sdl~--~~n~~~gkkyk~yGIKaS 441 (459)
.+|++ +-+.++-++.+++|+|||+..-.+. -++++-|+- ||=-|+--+ |+|-.--+.|+++|||-=
T Consensus 112 ~~Svi~t~e~~~~I~~~~~LAPLHNpa~l~gIe~~~~~~~~~~~k~VaVFDTaFHqTip~eayLYalPy~~y~~~giRrY 191 (416)
T TIGR00016 112 TDSVIITDEVIKKIKDISELAPLHNPAHLDGIEAALKLKVLPKAKNVAVFDTAFHQTIPEEAYLYALPYSWYKEHGIRRY 191 (416)
T ss_pred CCCEEECHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHCCCEEC
T ss_conf 22255368999999989850686781247999999972036788716886386365777511024451899986494010
Q ss_pred E
Q ss_conf 9
Q gi|254780449|r 442 G 442 (459)
Q Consensus 442 g 442 (459)
|
T Consensus 192 G 192 (416)
T TIGR00016 192 G 192 (416)
T ss_pred C
T ss_conf 6
No 14
>KOG4407 consensus
Probab=23.90 E-value=23 Score=15.79 Aligned_cols=100 Identities=19% Similarity=0.334 Sum_probs=55.8
Q ss_pred HHHCCCCCCCCCCCCCCHHHCCCCHHCCHHHHHHHHHHHCCCCHHHHHHCCCCEEEEEECCEECCCCHHHHHHHHHHHHC
Q ss_conf 54086544332223321343133112071678788877256511244411472479970945420008999999985506
Q gi|254780449|r 278 DKKIPFIGNQWRDINTAHSEFKMVPLSDQTLFRDFQGLCGKNIDNQFILDLNRASFIFNGKKLARDNSAEAIQKLMNQFA 357 (459)
Q Consensus 278 ~~k~p~~~~~~~~~~~~~~e~~~~~~~~~~~frdf~~l~g~n~dn~fllD~NrasFIvNgkkIsvdN~~~mL~~l~k~f~ 357 (459)
--++--....|||+|..-+-.|| +||..-.-+-+|.-|-|..++||-. ---||-..|.+|..-.|
T Consensus 1218 ~~~v~~~DdrWrDvNVVSSLLK~-------F~RkLPepL~t~~~Y~~FIEAnrk~--------~~l~Rl~~Lr~l~~~LP 1282 (1973)
T KOG4407 1218 LSKVESLDDRWRDVNVVSSLLKM-------FLRKLPEPLLTDKLYPFFIEANRKS--------THLNRLHKLRNLLRKLP 1282 (1973)
T ss_pred CHHHHCCCCCHHHHHHHHHHHHH-------HHHHCCCCCCCCCCHHHHHHHCCCC--------CHHHHHHHHHHHHHHCC
T ss_conf 00111146410236799999999-------9985872003542003466512344--------67889999999998677
Q ss_pred CCHHHHHHHHHHHCCCHHHHHHHHHHHHCHHHHHHHCCCCCCEEE
Q ss_conf 885464455654204022226899987260033331136873069
Q gi|254780449|r 358 KNPKQLQLISSYANQSIFADSVVHLMQSIPEFAKYASKSGSASKF 402 (459)
Q Consensus 358 kN~e~~QLISSYAnQ~IF~qsyi~L~sehPe~~kYq~Ks~Sr~sY 402 (459)
..+ |---+|+. --+.-..++-|.++..|+ |-+-.|
T Consensus 1283 rhh--------YETlKfLi-~HL~~Vt~nsdvNkMEpr-NLAI~F 1317 (1973)
T KOG4407 1283 RHH--------YETLKFLI-VHLSEVTKNSDVNKMEPR-NLAIMF 1317 (1973)
T ss_pred CCH--------HHHHHHHH-HHHHHHHCCCCCCCCCCC-CEEEEE
T ss_conf 551--------78899999-999987425643435654-226773
No 15
>TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=23.55 E-value=35 Score=14.62 Aligned_cols=40 Identities=33% Similarity=0.489 Sum_probs=21.5
Q ss_pred EEEEECCEEEEEEECCC---EEEEECCCCCCHHHHCCEEEEEEEC
Q ss_conf 99860766999983231---0133000125414315516999867
Q gi|254780449|r 404 AKTLTNGEVAFTAKYTT---KVQAVDKIAGKPLKEYGLKISGILS 445 (459)
Q Consensus 404 ~ntL~DG~V~FtAk~~s---dl~~~n~~~gkkyk~yGIKaSgILS 445 (459)
=-+|..|+.+.|--|-+ ++++=||-||- |-|=|| +|=|||
T Consensus 1144 GDeLppGV~~~VkVYiA~KRKiqvGDKMAGR-HGNKGv-vSkIlP 1186 (1449)
T TIGR02013 1144 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGR-HGNKGV-VSKILP 1186 (1449)
T ss_pred CCCCCCCCEEEEEEEEEECCCCCCCCCCCCC-CCCCEE-EEEECC
T ss_conf 8878765236889988861205888843555-578415-655245
No 16
>pfam09187 DUF1950 Domain of unknown function(DUF1950). Members of this family pertain to a set of functionally uncharacterized hypothetical eukaryotic proteins.
Probab=23.33 E-value=49 Score=13.58 Aligned_cols=18 Identities=33% Similarity=0.361 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHCCCHHH
Q ss_conf 899999998550688546
Q gi|254780449|r 345 SAEAIQKLMNQFAKNPKQ 362 (459)
Q Consensus 345 ~~~mL~~l~k~f~kN~e~ 362 (459)
++||-|+.||++|--...
T Consensus 4 rAemYQ~yMkqiPIP~~~ 21 (119)
T pfam09187 4 RAEMYQEYMKQIPIPAKR 21 (119)
T ss_pred HHHHHHHHHHHCCCCCCC
T ss_conf 799999999839988667
No 17
>TIGR02094 more_P_ylases alpha-glucan phosphorylases; InterPro: IPR011834 This family consists of known phosphorylases, and homologues believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related families: Glycogen/starch/alpha-glucan phosphorylase and Glycosyl transferase, family 35.; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=23.08 E-value=51 Score=13.48 Aligned_cols=121 Identities=25% Similarity=0.404 Sum_probs=82.1
Q ss_pred CCCCCCCCHHHHHCCCCHHHHH----------HHHCCCCCCHHHCHHHHHHHHHHHHHHHH---HHCCCCCCCCCCCCCC
Q ss_conf 1245443102221012202345----------53103210001000467777533456675---4086544332223321
Q gi|254780449|r 228 SKSTPQGIWTKALTKADPALES----------IYQRGKIFSNTIKNNAFIEKLAHTTKAID---KKIPFIGNQWRDINTA 294 (459)
Q Consensus 228 ~~~~~~~~~tka~~~~~~~~~~----------~~~~~~~~s~tik~~~~i~~~~~~t~ai~---~k~p~~~~~~~~~~~~ 294 (459)
+.-.++.+|.+--.-.|-.|=+ -|-|.|+...-.++-+..+.+..+..-.| -.+=.||=--|=
T Consensus 336 ~~~~~~~~w~~~~~iPDeeLW~~h~~~K~~Li~~ir~~~~~~~~~~~~~~~~~~~~~~~lD~~~p~~LtIGFARRf---- 411 (618)
T TIGR02094 336 EDLASEEIWEAIDDIPDEELWEVHLKLKAELIDYIRRRLREQLLRRGADAAELKATDRLLDAKSPDVLTIGFARRF---- 411 (618)
T ss_pred ECCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCEECHHHCC----
T ss_conf 0478767998741189689999999989999999999999988850368668888864146457885252212227----
Q ss_pred HHHCCCCHHCCHHHHHHHHHHHCCCCHHHHHHC-CCCEE-EEEECCEECCCCHHHH-HHHHHHHHCCCHHHHH
Q ss_conf 343133112071678788877256511244411-47247-9970945420008999-9999855068854644
Q gi|254780449|r 295 HSEFKMVPLSDQTLFRDFQGLCGKNIDNQFILD-LNRAS-FIFNGKKLARDNSAEA-IQKLMNQFAKNPKQLQ 364 (459)
Q Consensus 295 ~~e~~~~~~~~~~~frdf~~l~g~n~dn~fllD-~Nras-FIvNgkkIsvdN~~~m-L~~l~k~f~kN~e~~Q 364 (459)
+-|||-.| +|||-.-| ..-++| ..|-- |||-||-=--|+.-|. ||+. -+|.+.|||+-
T Consensus 412 -AtYKRa~L----lf~D~eRL------~~il~~n~~RPVQ~vFAGKAHP~D~~GK~~Iq~i-~~~s~~Pef~g 472 (618)
T TIGR02094 412 -ATYKRATL----LFRDLERL------KRILNNNPERPVQIVFAGKAHPADEAGKELIQRI-VEFSKRPEFRG 472 (618)
T ss_pred -CCCCCHHH----HCCCHHHH------HHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHH-HHHHHCCCCCC
T ss_conf -60026132----20777899------9983568888568897155679975458999999-99862778576
No 18
>KOG3926 consensus
Probab=22.69 E-value=31 Score=14.90 Aligned_cols=32 Identities=22% Similarity=0.162 Sum_probs=27.7
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHCHHHHHHH
Q ss_conf 64455654204022226899987260033331
Q gi|254780449|r 362 QLQLISSYANQSIFADSVVHLMQSIPEFAKYA 393 (459)
Q Consensus 362 ~~QLISSYAnQ~IF~qsyi~L~sehPe~~kYq 393 (459)
..|||+|-.-|.=..|-|-+|---+|-.-+|+
T Consensus 257 ~~~l~l~k~~q~dWkqmyf~L~r~yg~keqya 288 (332)
T KOG3926 257 HTILILSKKGQKDWKQMYFQLRRTYGVKEQYA 288 (332)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHH
T ss_conf 88630321121049999999998638588888
No 19
>PRK02463 OxaA-like protein precursor; Provisional
Probab=22.39 E-value=48 Score=13.66 Aligned_cols=22 Identities=18% Similarity=0.046 Sum_probs=12.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 1577441057665102577877
Q gi|254780449|r 87 KKGNYGWGIVGAISDAALLIPV 108 (459)
Q Consensus 87 kkgnygwg~~g~isd~all~~~ 108 (459)
--|||||+|+-..-=+-++..|
T Consensus 56 ~g~nyG~aIIl~TiiIRlillP 77 (307)
T PRK02463 56 LGLGFGLAIIIVTIIVRTLILP 77 (307)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
T ss_conf 3877338999999999999983
No 20
>COG0218 Predicted GTPase [General function prediction only]
Probab=22.38 E-value=50 Score=13.55 Aligned_cols=55 Identities=18% Similarity=0.267 Sum_probs=37.5
Q ss_pred CHHHHHHCCCCEEEEEECC--EECCCCHH---HHHHHHHHHHCCCHHHHHHHHHHHCCCH
Q ss_conf 1124441147247997094--54200089---9999998550688546445565420402
Q gi|254780449|r 320 IDNQFILDLNRASFIFNGK--KLARDNSA---EAIQKLMNQFAKNPKQLQLISSYANQSI 374 (459)
Q Consensus 320 ~dn~fllD~NrasFIvNgk--kIsvdN~~---~mL~~l~k~f~kN~e~~QLISSYAnQ~I 374 (459)
..++|+.+......|+-+| ||+.+..+ +++++.++..++....+++.||.+.+++
T Consensus 126 em~~~l~~~~i~~~vv~tK~DKi~~~~~~k~l~~v~~~l~~~~~~~~~~~~~ss~~k~Gi 185 (200)
T COG0218 126 EMIEFLLELGIPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGI 185 (200)
T ss_pred HHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCH
T ss_conf 999999975998699997110377467888999999984689886643999865454489
No 21
>cd01763 Sumo Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=22.02 E-value=51 Score=13.48 Aligned_cols=24 Identities=21% Similarity=0.728 Sum_probs=18.9
Q ss_pred HCCCCEEEEEECCEECCCCHHHHH
Q ss_conf 114724799709454200089999
Q gi|254780449|r 326 LDLNRASFIFNGKKLARDNSAEAI 349 (459)
Q Consensus 326 lD~NrasFIvNgkkIsvdN~~~mL 349 (459)
++.+.+.|+|||..|+-+.....|
T Consensus 47 ~~~~~~rF~fdG~ri~~~~TP~~L 70 (87)
T cd01763 47 LSMNSVRFLFDGQRIRDNQTPDDL 70 (87)
T ss_pred CCCCCEEEEECCEECCCCCCHHHC
T ss_conf 980025998999694899997794
No 22
>pfam10950 DUF2775 Protein of unknown function (DUF2775). This eukaryotic family of proteins has no known function.
Probab=21.78 E-value=21 Score=16.06 Aligned_cols=76 Identities=18% Similarity=0.196 Sum_probs=50.2
Q ss_pred HHCCCCHHCCHHHHHHHHHHHCCCCHHHHHHCCCCEEEEEECCEECCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHH
Q ss_conf 43133112071678788877256511244411472479970945420008999999985506885464455654204022
Q gi|254780449|r 296 SEFKMVPLSDQTLFRDFQGLCGKNIDNQFILDLNRASFIFNGKKLARDNSAEAIQKLMNQFAKNPKQLQLISSYANQSIF 375 (459)
Q Consensus 296 ~e~~~~~~~~~~~frdf~~l~g~n~dn~fllD~NrasFIvNgkkIsvdN~~~mL~~l~k~f~kN~e~~QLISSYAnQ~IF 375 (459)
.||.++-.-||-+-...|||+-... +.+.-.--+ ..+.|+++||.+--+|.|-...+-
T Consensus 4 g~ywk~~mkd~~mpe~i~gll~~~~---------------------~~~~~t~~~-~~k~~v~dFEPrP~~s~Y~dnd~~ 61 (108)
T pfam10950 4 GEYWKDVMKDQDMPEAIQGLLNAKN---------------------IKPSKTHAK-KEKGAIGDFEPRPNVSAYDDNDIK 61 (108)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCC---------------------CCCCCHHHH-HHCCCCCCCCCCCCCEECCCCCCC
T ss_conf 7899998637876189997762165---------------------577508888-611310236889862002677533
Q ss_pred ---HHHHHHHHHHCHHHHHHH
Q ss_conf ---226899987260033331
Q gi|254780449|r 376 ---ADSVVHLMQSIPEFAKYA 393 (459)
Q Consensus 376 ---~qsyi~L~sehPe~~kYq 393 (459)
.++++++|-.-|++-.|-
T Consensus 62 ~ke~k~~~~dfEPrPniSaY~ 82 (108)
T pfam10950 62 NKEKKSFVEDFEPKPNISAYG 82 (108)
T ss_pred CCCCCCCCCCCCCCCCCEEEC
T ss_conf 143200003567588630224
Done!