Query 046541
Match_columns 94
No_of_seqs 55 out of 57
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 13:09:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046541.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046541hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK04015 DNA/RNA-binding prote 99.4 2.7E-12 5.9E-17 88.2 6.9 65 6-71 25-91 (91)
2 TIGR00285 DNA-binding protein 99.2 6.4E-11 1.4E-15 81.1 6.5 65 5-70 21-87 (87)
3 PF01918 Alba: Alba; InterPro 98.8 1.8E-08 3.9E-13 63.1 5.1 42 3-44 18-67 (70)
4 COG1581 Ssh10b Archaeal DNA-bi 98.4 1.6E-06 3.5E-11 60.2 7.0 67 4-71 23-91 (91)
5 PF12328 Rpp20: Rpp20 subunit 96.1 0.011 2.5E-07 43.0 4.5 42 10-52 61-102 (144)
6 KOG2567 Uncharacterized conser 95.5 0.0046 9.9E-08 47.4 0.5 64 9-72 44-116 (179)
7 TIGR00070 hisG ATP phosphoribo 75.1 1.6 3.6E-05 32.8 1.3 41 9-49 136-179 (182)
8 PRK13583 hisG ATP phosphoribos 71.5 6.2 0.00013 30.9 3.8 40 10-49 160-204 (228)
9 PRK01686 hisG ATP phosphoribos 71.3 3.1 6.7E-05 32.1 2.1 48 3-50 126-186 (215)
10 PF12146 Hydrolase_4: Putative 68.3 7.9 0.00017 24.8 3.2 29 12-40 19-47 (79)
11 PLN02245 ATP phosphoribosyl tr 67.5 9.3 0.0002 32.5 4.3 47 3-49 207-269 (403)
12 PF02780 Transketolase_C: Tran 64.4 8.5 0.00019 25.6 2.9 39 7-45 6-45 (124)
13 PF01634 HisG: ATP phosphoribo 62.1 5.1 0.00011 29.7 1.6 48 3-50 78-138 (163)
14 PRK13584 hisG ATP phosphoribos 58.6 5.8 0.00012 30.7 1.4 41 10-50 133-176 (204)
15 COG3958 Transketolase, C-termi 48.9 18 0.00039 30.1 2.9 33 6-38 188-220 (312)
16 PLN00165 hypothetical protein; 47.6 13 0.00028 25.7 1.6 18 22-39 10-27 (88)
17 PF12695 Abhydrolase_5: Alpha/ 44.1 48 0.001 20.9 3.8 29 13-41 3-31 (145)
18 COG0040 HisG ATP phosphoribosy 43.0 17 0.00036 29.7 1.8 47 3-49 127-186 (290)
19 TIGR03562 osmo_induc_OsmC pero 42.5 77 0.0017 22.3 4.9 52 19-71 51-103 (135)
20 CHL00144 odpB pyruvate dehydro 40.1 27 0.00059 27.9 2.6 32 6-37 197-228 (327)
21 PF13721 SecD-TM1: SecD export 38.8 31 0.00067 23.4 2.4 34 6-39 27-62 (101)
22 PF05137 PilN: Fimbrial assemb 38.1 90 0.0019 18.7 5.8 41 8-48 21-61 (78)
23 PRK10629 EnvZ/OmpR regulon mod 37.9 40 0.00086 24.1 2.9 37 6-43 31-69 (127)
24 PLN02683 pyruvate dehydrogenas 35.0 31 0.00068 28.0 2.2 74 7-81 225-302 (356)
25 smart00344 HTH_ASNC helix_turn 34.4 1.2E+02 0.0027 19.2 4.9 76 5-86 10-89 (108)
26 cd06490 p23_NCB5OR p23_like do 32.5 30 0.00066 22.4 1.5 13 61-73 68-80 (87)
27 PRK11892 pyruvate dehydrogenas 31.9 42 0.00091 28.5 2.6 40 6-45 336-376 (464)
28 PRK10310 PTS system galactitol 31.6 77 0.0017 20.9 3.3 27 12-38 5-33 (94)
29 PRK09212 pyruvate dehydrogenas 31.3 72 0.0016 25.4 3.7 66 6-72 197-263 (327)
30 PRK14459 ribosomal RNA large s 29.6 75 0.0016 26.4 3.6 40 12-51 179-225 (373)
31 COG0096 RpsH Ribosomal protein 27.5 1.7E+02 0.0038 21.4 4.9 20 21-40 29-48 (132)
32 smart00411 BHL bacterial (prok 27.2 46 0.00099 20.9 1.6 17 4-20 33-49 (90)
33 PTZ00182 3-methyl-2-oxobutanat 25.9 1.2E+02 0.0026 24.6 4.2 65 7-72 230-295 (355)
34 PRK05899 transketolase; Review 25.7 53 0.0011 28.2 2.2 32 6-37 506-537 (624)
35 PF01674 Lipase_2: Lipase (cla 25.7 36 0.00078 26.0 1.0 30 10-39 2-32 (219)
36 PTZ00326 phenylalanyl-tRNA syn 24.5 1.2E+02 0.0027 26.4 4.2 37 17-53 30-66 (494)
37 PLN02790 transketolase 24.5 77 0.0017 27.8 2.9 27 11-37 541-567 (654)
38 PRK12753 transketolase; Review 24.4 77 0.0017 27.9 3.0 27 11-37 550-576 (663)
39 PRK10738 hypothetical protein; 24.4 1.8E+02 0.0038 20.4 4.3 26 14-41 40-65 (134)
40 COG3439 Uncharacterized conser 24.3 21 0.00045 25.9 -0.4 18 19-36 36-53 (137)
41 cd03737 SOCS_SOCS3 SOCS (suppr 24.2 33 0.00071 20.5 0.5 10 2-11 30-39 (42)
42 COG0504 PyrG CTP synthase (UTP 24.1 66 0.0014 28.6 2.5 30 15-45 11-41 (533)
43 PF00216 Bac_DNA_binding: Bact 23.5 49 0.0011 20.6 1.2 17 4-20 33-49 (90)
44 PRK10985 putative hydrolase; P 22.6 93 0.002 23.7 2.8 30 12-41 61-92 (324)
45 PLN02853 Probable phenylalanyl 22.0 1.5E+02 0.0032 26.0 4.2 38 16-53 26-63 (492)
46 COG5015 Uncharacterized conser 21.6 57 0.0012 24.2 1.4 15 4-18 50-64 (132)
47 PF09339 HTH_IclR: IclR helix- 21.6 1E+02 0.0022 17.7 2.3 23 17-39 27-49 (52)
48 cd00591 HU_IHF Integration hos 21.6 71 0.0015 19.8 1.7 16 5-20 33-48 (87)
49 smart00418 HTH_ARSR helix_turn 21.5 1.4E+02 0.0031 16.0 2.8 24 17-40 19-42 (66)
50 TIGR00232 tktlase_bact transke 21.5 73 0.0016 27.9 2.3 30 8-37 538-567 (653)
51 PF02302 PTS_IIB: PTS system, 21.4 1.9E+02 0.0041 17.7 3.6 25 13-37 3-29 (90)
52 KOG3379 Diadenosine polyphosph 21.3 1.1E+02 0.0024 23.2 2.9 39 44-82 80-122 (150)
53 COG3119 AslA Arylsulfatase A a 21.3 37 0.0008 28.1 0.4 21 21-41 84-105 (475)
54 TIGR03561 organ_hyd_perox pero 21.3 83 0.0018 21.5 2.1 35 19-53 49-84 (134)
55 PF06418 CTP_synth_N: CTP synt 21.3 57 0.0012 26.7 1.4 30 15-45 11-41 (276)
56 PRK10664 transcriptional regul 21.0 2.1E+02 0.0045 18.8 3.9 48 27-74 31-79 (90)
57 PF12133 Sars6: Open reading f 20.9 53 0.0012 21.5 1.0 8 25-32 8-15 (62)
58 cd07250 HPPD_C_like C-terminal 20.7 84 0.0018 22.7 2.1 43 4-46 73-115 (191)
59 COG4738 Predicted transcriptio 20.6 1.2E+02 0.0025 22.4 2.8 46 23-81 56-101 (124)
60 PLN02234 1-deoxy-D-xylulose-5- 20.5 85 0.0018 28.0 2.5 80 6-86 540-622 (641)
61 PRK10753 transcriptional regul 20.4 2.2E+02 0.0047 18.6 3.9 48 27-74 31-79 (90)
62 PRK00199 ihfB integration host 20.4 2E+02 0.0044 18.5 3.7 40 27-66 32-72 (94)
63 PRK12571 1-deoxy-D-xylulose-5- 20.3 79 0.0017 27.7 2.2 39 6-44 500-539 (641)
64 PF00410 Ribosomal_S8: Ribosom 20.2 1.5E+02 0.0033 20.5 3.2 34 6-43 14-47 (129)
No 1
>PRK04015 DNA/RNA-binding protein albA; Provisional
Probab=99.35 E-value=2.7e-12 Score=88.16 Aligned_cols=65 Identities=29% Similarity=0.386 Sum_probs=57.1
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe--EEEEEEeeeeeeecCCCCCCcccceeEEEEEeec
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL--ASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKA 71 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl--At~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks 71 (94)
|-++.++|.|.|+|.||+.+|+|||||||+-+ +.+++|.+++..+.++ .||...-.+|||+|.|.
T Consensus 25 l~~g~~eV~iKa~G~aIskAV~vaEilk~r~~~~v~v~~I~i~se~i~~~-~g~~~~VS~IEI~l~k~ 91 (91)
T PRK04015 25 FNQGAKEVVIKARGRAISKAVDVAEIVRNRFLPDVEIKEIKIGTEEVTSE-DGRESNVSTIEIVLEKK 91 (91)
T ss_pred HhCCCCeEEEEEeccccchhhhHHHHHHHhccCCeEEEEEEeccEEeecC-CCcEEEEEEEEEEEecC
Confidence 44588999999999999999999999999988 9999999999988553 56666788999999873
No 2
>TIGR00285 DNA-binding protein Alba. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
Probab=99.19 E-value=6.4e-11 Score=81.06 Aligned_cols=65 Identities=28% Similarity=0.376 Sum_probs=53.7
Q ss_pred hhhhhcCcEEEecccchhhHHHHHHHHhhhCCeEE--EEEEeeeeeeecCCCCCCcccceeEEEEEee
Q 046541 5 RYIKQYNDIELTALGMAIPTVVTIAEALKRDGLAS--NIEVKISTVNSKKDDEGRFFQKAKIQIVLGK 70 (94)
Q Consensus 5 r~l~~~~eVeLsALG~AI~tvVtvAEiLK~nglAt--~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~K 70 (94)
.|-++.++|.|.|.|.||+.+|.|||+|+|+-+.. +++|..+|..+.. ..||...-.+|||+|.|
T Consensus 21 ~fn~g~~eV~iKarG~aIskAVdvaeiik~r~~~~v~v~~I~i~te~~~~-~~G~~~~VStIEI~l~~ 87 (87)
T TIGR00285 21 QLNSGADEVIIKARGRAISRAVDVAEIVRNRFIPDIKIKKIKIGTEEIKS-EQGREVNVSTIEIVLAK 87 (87)
T ss_pred HHhCCCCeEEEEEecchhhhHHHHHHHHHHhccCCceEEEEEeccEEeec-CCCceeeEEEEEEEEeC
Confidence 45566899999999999999999999999987754 8888877776533 35676678899999976
No 3
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function. The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
Probab=98.76 E-value=1.8e-08 Score=63.09 Aligned_cols=42 Identities=26% Similarity=0.437 Sum_probs=35.2
Q ss_pred hHhhh-----hhcCcEEEecccchhhHHHHHHHHhhhC---CeEEEEEEe
Q 046541 3 LQRYI-----KQYNDIELTALGMAIPTVVTIAEALKRD---GLASNIEVK 44 (94)
Q Consensus 3 ~Kr~l-----~~~~eVeLsALG~AI~tvVtvAEiLK~n---glAt~kkI~ 44 (94)
+.++| +++++|.|+|+|.||+.+|+||||||++ |+.-+.+++
T Consensus 18 ~~~~L~~~~~~~~~~V~l~g~G~aI~kaI~vaei~K~~~~~~~~qv~~~t 67 (70)
T PF01918_consen 18 ALKLLEGRENGKNDEVVLKGRGKAISKAISVAEILKRRFGEGLYQVNKIT 67 (70)
T ss_dssp HHHHHT-TTHTTCSEEEEEEECCHHHHHHHHHHHHHHHTSTTTEEEEEEE
T ss_pred HHHHHhhhhcCCCCEEEEEEEcHHHHHHHHHHHHHHHhhcCCCEEEEEEe
Confidence 45667 9999999999999999999999999998 555555443
No 4
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=98.38 E-value=1.6e-06 Score=60.24 Aligned_cols=67 Identities=25% Similarity=0.380 Sum_probs=57.3
Q ss_pred HhhhhhcCcEEEecccchhhHHHHHHHHhhhCCe--EEEEEEeeeeeeecCCCCCCcccceeEEEEEeec
Q 046541 4 QRYIKQYNDIELTALGMAIPTVVTIAEALKRDGL--ASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKA 71 (94)
Q Consensus 4 Kr~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl--At~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks 71 (94)
..|-++-+||-|-|=|-|||.+|.+|||++|.=+ +-+|.|.++|..++.+ +||...-.-|||+|.|.
T Consensus 23 t~fn~g~~eViiKARGraIskAVDvaeivRnrf~p~v~ik~Iki~se~~~~~-~gr~~~VS~IeI~L~k~ 91 (91)
T COG1581 23 TQFNEGADEVIIKARGRAISKAVDVAEIVRNRFIPDVQIKDIKIGTEELEGE-DGRTRNVSTIEIVLAKK 91 (91)
T ss_pred HHHHcCCCEEEEEecchhhHhhHhHHHHHHHhcCCCceEEEEEecceeeecC-CCceeeEEEEEEEEecC
Confidence 4678889999999999999999999999998755 6788999998877554 56667789999999874
No 5
>PF12328 Rpp20: Rpp20 subunit of nuclear RNase MRP and P; PDB: 3IAB_B.
Probab=96.07 E-value=0.011 Score=42.98 Aligned_cols=42 Identities=21% Similarity=0.346 Sum_probs=32.9
Q ss_pred cCcEEEecccchhhHHHHHHHHhhhCCeEEEEEEeeeeeeecC
Q 046541 10 YNDIELTALGMAIPTVVTIAEALKRDGLASNIEVKISTVNSKK 52 (94)
Q Consensus 10 ~~eVeLsALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~~~~ 52 (94)
..+|-|+|+|.||.-++.||--++++. -..-.|+|+||.+=|
T Consensus 61 ~~~V~v~gtGkAIeKal~la~~Fq~~~-~~~V~V~TgTV~vvD 102 (144)
T PF12328_consen 61 SEEVTVKGTGKAIEKALSLALWFQRKK-GYKVEVRTGTVEVVD 102 (144)
T ss_dssp -SEEEEEEEGGGHHHHHHHHHHHHHTT----EEEEEEEEEEEE
T ss_pred ccEEEEEeccHHHHHHHHHHHHHhhcC-CeEEEEEeceEEEEE
Confidence 378999999999999999999999984 334468888886433
No 6
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.49 E-value=0.0046 Score=47.44 Aligned_cols=64 Identities=27% Similarity=0.339 Sum_probs=45.1
Q ss_pred hcCcEEEecccchhhHHHHHHHHhhhC--CeEEEEEEeeeee-e-ecCCCCCC-----cccceeEEEEEeecc
Q 046541 9 QYNDIELTALGMAIPTVVTIAEALKRD--GLASNIEVKISTV-N-SKKDDEGR-----FFQKAKIQIVLGKAE 72 (94)
Q Consensus 9 ~~~eVeLsALG~AI~tvVtvAEiLK~n--glAt~kkI~Tstv-~-~~~~~~gr-----~~qKaKIeI~L~Ks~ 72 (94)
.|-+|-+||.|-||.-.|++||||||. ||--..+|+--.+ + -+.-.+|- ..+.+-|-|+|.+.+
T Consensus 44 ~~r~VVfsg~Grai~KTVscaEilKrRipgLhQ~t~l~~~sv~d~W~p~~eGl~pl~vtRhVp~l~IlLS~de 116 (179)
T KOG2567|consen 44 SHRCVVFSGSGRAIVKTVSCAEILKRRIPGLHQVTRLRYTSVEDVWEPTEEGLEPLEVTRHVPMLHILLSLDE 116 (179)
T ss_pred CeeEEEEecCCcceeeeeeHHHHHhhhCcchhhhceeeeeehhhcccccccCccceEEeeccceEEEEEeccc
Confidence 467899999999999999999999974 7777777765433 2 11122331 124577888888754
No 7
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=75.07 E-value=1.6 Score=32.85 Aligned_cols=41 Identities=27% Similarity=0.395 Sum_probs=32.3
Q ss_pred hcCcEEEec-ccc--hhhHHHHHHHHhhhCCeEEEEEEeeeeee
Q 046541 9 QYNDIELTA-LGM--AIPTVVTIAEALKRDGLASNIEVKISTVN 49 (94)
Q Consensus 9 ~~~eVeLsA-LG~--AI~tvVtvAEiLK~nglAt~kkI~Tstv~ 49 (94)
.++.||+.- +|. ||.+.|+-...|+.|||.++..|..|+..
T Consensus 136 l~GsvE~aP~~GlaD~IvDiv~TG~TL~~NgL~~ie~i~~s~a~ 179 (182)
T TIGR00070 136 LNGSVELAPLLGLADAIVDIVSTGTTLRENGLRIIEVILESSAR 179 (182)
T ss_pred CcceeecccCCCceeEEEEEeCCHHHHHHCCCEEeeEEEeeEEE
Confidence 456787743 444 57788888999999999999999988753
No 8
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=71.48 E-value=6.2 Score=30.87 Aligned_cols=40 Identities=20% Similarity=0.137 Sum_probs=31.4
Q ss_pred cCcEEEec-ccch--hhHHHHHHHHhhhCCeEEEE--EEeeeeee
Q 046541 10 YNDIELTA-LGMA--IPTVVTIAEALKRDGLASNI--EVKISTVN 49 (94)
Q Consensus 10 ~~eVeLsA-LG~A--I~tvVtvAEiLK~nglAt~k--kI~Tstv~ 49 (94)
++.||+.- +|+| |-++|+--..||.|||-++. .|..|+..
T Consensus 160 ~GsvElaP~~GlAD~IvDivsTG~TLr~NgL~~i~~~~Il~SsA~ 204 (228)
T PRK13583 160 LGATEGAPANGSAEIIVDITSTGETLRANHLKILSDGVILRSQAC 204 (228)
T ss_pred CCceecccccCcchhhhhhhchhHHHHHCCCEEecCceEEEEEEE
Confidence 56667643 4554 88999999999999999997 88877764
No 9
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=71.29 E-value=3.1 Score=32.12 Aligned_cols=48 Identities=25% Similarity=0.424 Sum_probs=37.2
Q ss_pred hHhhhhhc----------CcEEE-ecccc--hhhHHHHHHHHhhhCCeEEEEEEeeeeeee
Q 046541 3 LQRYIKQY----------NDIEL-TALGM--AIPTVVTIAEALKRDGLASNIEVKISTVNS 50 (94)
Q Consensus 3 ~Kr~l~~~----------~eVeL-sALG~--AI~tvVtvAEiLK~nglAt~kkI~Tstv~~ 50 (94)
+++|++++ +.||+ -.+|+ ||.++|+=-..|+.|||-++..|..|+..+
T Consensus 126 t~~yf~~~gv~~~iv~l~GsvE~aP~~GlAD~IvDivsTG~TLr~NgL~~ie~Il~s~A~L 186 (215)
T PRK01686 126 ARRYFAEKGEQVEIIKLYGSVELAPLVGLADAIVDIVETGNTLRANGLVEVEEIMDISARL 186 (215)
T ss_pred HHHHHHHcCCeEEEEECcCceeeccccCCccEEEEeecChHHHHHCcCEEeeEEEeeEEEE
Confidence 45666654 56676 23454 588999999999999999999999988764
No 10
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=68.29 E-value=7.9 Score=24.78 Aligned_cols=29 Identities=21% Similarity=0.194 Sum_probs=26.5
Q ss_pred cEEEecccchhhHHHHHHHHhhhCCeEEE
Q 046541 12 DIELTALGMAIPTVVTIAEALKRDGLASN 40 (94)
Q Consensus 12 eVeLsALG~AI~tvVtvAEiLK~nglAt~ 40 (94)
-|-+||+|.-+..---+|+-|..+|+++.
T Consensus 19 v~i~HG~~eh~~ry~~~a~~L~~~G~~V~ 47 (79)
T PF12146_consen 19 VVIVHGFGEHSGRYAHLAEFLAEQGYAVF 47 (79)
T ss_pred EEEeCCcHHHHHHHHHHHHHHHhCCCEEE
Confidence 36689999999999999999999999986
No 11
>PLN02245 ATP phosphoribosyl transferase
Probab=67.54 E-value=9.3 Score=32.45 Aligned_cols=47 Identities=21% Similarity=0.285 Sum_probs=35.2
Q ss_pred hHhhhhhcCc--EEEe----------cccc--hhhHHHHHHHHhhhCCeEEEE--EEeeeeee
Q 046541 3 LQRYIKQYND--IELT----------ALGM--AIPTVVTIAEALKRDGLASNI--EVKISTVN 49 (94)
Q Consensus 3 ~Kr~l~~~~e--VeLs----------ALG~--AI~tvVtvAEiLK~nglAt~k--kI~Tstv~ 49 (94)
+++|+++++- |++. .+|+ ||.++|+=-..|+.|||-++. .|..|+..
T Consensus 207 tr~ff~~~Gv~~v~Iv~l~GAvE~AP~lGlADaIvDIVsTGtTLraNgLk~i~~~~Il~S~A~ 269 (403)
T PLN02245 207 GPKFMKDNGFKHVTFSTADGALEAAPAMGIADAILDLVSSGTTLRENNLKEIEGGVVLESQAV 269 (403)
T ss_pred HHHHHHHcCCCeEEEEECcCceecccccCchhhhcchhccHHHHHHCCCEEccCceEEEEEEE
Confidence 5788888876 4443 1344 488999999999999999996 77776654
No 12
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=64.42 E-value=8.5 Score=25.62 Aligned_cols=39 Identities=26% Similarity=0.505 Sum_probs=31.6
Q ss_pred hhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEee
Q 046541 7 IKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVKI 45 (94)
Q Consensus 7 l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~T 45 (94)
+++-.+|-|=+.|.....+..+|+.|+.+|+ +.+-.+++
T Consensus 6 ~~~g~di~iia~G~~~~~al~A~~~L~~~Gi~~~vi~~~~ 45 (124)
T PF02780_consen 6 LREGADITIIAYGSMVEEALEAAEELEEEGIKAGVIDLRT 45 (124)
T ss_dssp EESSSSEEEEEETTHHHHHHHHHHHHHHTTCEEEEEEEEE
T ss_pred EeCCCCEEEEeehHHHHHHHHHHHHHHHcCCceeEEeeEE
Confidence 4667899999999999999999999999985 33444443
No 13
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=62.07 E-value=5.1 Score=29.67 Aligned_cols=48 Identities=23% Similarity=0.357 Sum_probs=36.5
Q ss_pred hHhhhhhcC-cEEEe------------cccchhhHHHHHHHHhhhCCeEEEEEEeeeeeee
Q 046541 3 LQRYIKQYN-DIELT------------ALGMAIPTVVTIAEALKRDGLASNIEVKISTVNS 50 (94)
Q Consensus 3 ~Kr~l~~~~-eVeLs------------ALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~~ 50 (94)
+++|+++++ .+++- ||--||-+.|.--..||.|||-.+..|..|+..+
T Consensus 78 ~~~yf~~~g~~~~ii~l~GsvE~ap~~glAD~IvDiv~TG~TLr~NgL~~i~~i~~s~a~L 138 (163)
T PF01634_consen 78 TRRYFAEKGINVEIIKLSGSVELAPPLGLADAIVDIVETGTTLRANGLKEIETILESSARL 138 (163)
T ss_dssp HHHHHHHCT-EEEEEE-SS-TTHHHHTTSSSEEEEEESSSHHHHHTTEEEEEEEEEEEEEE
T ss_pred HHHHHHHcCCcEEEEEccCCccccCCCCCCCEEEEeccCcHHHHHCCCEEeEEEEEEEEEE
Confidence 578888877 45443 2345677777778889999999999999988753
No 14
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=58.57 E-value=5.8 Score=30.71 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=32.5
Q ss_pred cCcEEEec-ccc--hhhHHHHHHHHhhhCCeEEEEEEeeeeeee
Q 046541 10 YNDIELTA-LGM--AIPTVVTIAEALKRDGLASNIEVKISTVNS 50 (94)
Q Consensus 10 ~~eVeLsA-LG~--AI~tvVtvAEiLK~nglAt~kkI~Tstv~~ 50 (94)
++.|||.- +|+ +|-++|+--..||.|||.++..|..|+..+
T Consensus 133 ~GsvElaP~~GlAD~IvDiv~TG~TLr~NgL~~~e~I~~ssa~L 176 (204)
T PRK13584 133 NGSVELACVVDMVDGIVDIVQTGTTLKANGLVEKQHISDINARL 176 (204)
T ss_pred CCceeeccccCCccEEEEEECccHHHHHCCCEEEEEEEeeEEEE
Confidence 46677631 344 488999999999999999999999988764
No 15
>COG3958 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]
Probab=48.91 E-value=18 Score=30.06 Aligned_cols=33 Identities=24% Similarity=0.536 Sum_probs=29.5
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCeE
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGLA 38 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~nglA 38 (94)
.|+.-.++-|-|-|.=.+.++..|++|+.+|+-
T Consensus 188 vLrdG~D~tiiA~G~mv~~al~AA~~L~~~GIs 220 (312)
T COG3958 188 VLRDGSDLTIIATGVMVAEALEAAEILKKEGIS 220 (312)
T ss_pred EeecCCceEEEecCcchHHHHHHHHHHHhcCCC
Confidence 366778999999999999999999999999963
No 16
>PLN00165 hypothetical protein; Provisional
Probab=47.57 E-value=13 Score=25.72 Aligned_cols=18 Identities=33% Similarity=0.506 Sum_probs=15.1
Q ss_pred hhHHHHHHHHhhhCCeEE
Q 046541 22 IPTVVTIAEALKRDGLAS 39 (94)
Q Consensus 22 I~tvVtvAEiLK~nglAt 39 (94)
++..|-++|-||+||++-
T Consensus 10 vAaSvgaVEalkDQG~cR 27 (88)
T PLN00165 10 VAASVGAVEALKDQGFCR 27 (88)
T ss_pred HHHHHHHHhhccccCeee
Confidence 477888999999999754
No 17
>PF12695 Abhydrolase_5: Alpha/beta hydrolase family; PDB: 3D0K_B 2I3D_B 3DOH_B 3DOI_B 3PFB_A 3S2Z_B 3PFC_A 3QM1_A 3PF8_B 3PF9_A ....
Probab=44.07 E-value=48 Score=20.94 Aligned_cols=29 Identities=28% Similarity=0.269 Sum_probs=25.3
Q ss_pred EEEecccchhhHHHHHHHHhhhCCeEEEE
Q 046541 13 IELTALGMAIPTVVTIAEALKRDGLASNI 41 (94)
Q Consensus 13 VeLsALG~AI~tvVtvAEiLK~nglAt~k 41 (94)
|-+||.|.--.....+++.|-++||+++-
T Consensus 3 v~~HG~~~~~~~~~~~~~~l~~~G~~v~~ 31 (145)
T PF12695_consen 3 VLLHGWGGSRRDYQPLAEALAEQGYAVVA 31 (145)
T ss_dssp EEECTTTTTTHHHHHHHHHHHHTTEEEEE
T ss_pred EEECCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 56888888888889999999999999864
No 18
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=42.97 E-value=17 Score=29.68 Aligned_cols=47 Identities=26% Similarity=0.365 Sum_probs=38.4
Q ss_pred hHhhhhhcC----------cEEEe---cccchhhHHHHHHHHhhhCCeEEEEEEeeeeee
Q 046541 3 LQRYIKQYN----------DIELT---ALGMAIPTVVTIAEALKRDGLASNIEVKISTVN 49 (94)
Q Consensus 3 ~Kr~l~~~~----------eVeLs---ALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~ 49 (94)
+++|+++++ .||+. ||.-||-+.|+--..||-|||..+..|.+|+..
T Consensus 127 ~~~yf~~~g~~~~Ii~l~GsvE~aP~~GlADaIvDivsTG~TLkaNgL~~id~i~~ssa~ 186 (290)
T COG0040 127 ARKYFAEKGIDVEIIKLSGSVELAPALGLADAIVDIVSTGTTLKANGLKEIEVIYDSSAR 186 (290)
T ss_pred HHHHHHHcCceEEEEEccCcEeeccccCccceEEEeecCCHhHHHCCCEEEEEEEeeEEE
Confidence 567777654 46654 566789999999999999999999999998875
No 19
>TIGR03562 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. Pfam model pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress.
Probab=42.53 E-value=77 Score=22.31 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=30.2
Q ss_pred cchhhHHHHHHHHhhhCCeEEEEEEee-eeeeecCCCCCCcccceeEEEEEeec
Q 046541 19 GMAIPTVVTIAEALKRDGLASNIEVKI-STVNSKKDDEGRFFQKAKIQIVLGKA 71 (94)
Q Consensus 19 G~AI~tvVtvAEiLK~nglAt~kkI~T-stv~~~~~~~gr~~qKaKIeI~L~Ks 71 (94)
+.|--..+++.-+|++.|+... .+.. .++++..+..+..+++-++.+.+.-+
T Consensus 51 AlaaC~~~t~~~ia~k~~~~~~-~~~v~a~~~l~~~~~~~~~~~i~v~~~~~~~ 103 (135)
T TIGR03562 51 AHAGCFSMALSAALAEAGFTPE-SLDTTATVTLDKVGGGFAITGIHLTVRAKVP 103 (135)
T ss_pred HHHHHHHHHHHHHHHHCCCCCc-eeEEEEEEEEEecCCceEEEEEEEEEEEEeC
Confidence 3333445888999999999763 3333 34555443222235556666666544
No 20
>CHL00144 odpB pyruvate dehydrogenase E1 component beta subunit; Validated
Probab=40.09 E-value=27 Score=27.88 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=28.4
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL 37 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl 37 (94)
.+++-.+|-|-+.|....++..+|+.|+.+|+
T Consensus 197 v~~~G~ditiia~G~~v~~al~Aa~~L~~~Gi 228 (327)
T CHL00144 197 VVRPGNDITILTYSRMRHHVLQAVKVLVEKGY 228 (327)
T ss_pred EEEcCCCEEEEEccHHHHHHHHHHHHHHhcCC
Confidence 35566799999999999999999999999984
No 21
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=38.80 E-value=31 Score=23.43 Aligned_cols=34 Identities=24% Similarity=0.482 Sum_probs=29.3
Q ss_pred hhhhcCcEEEec--ccchhhHHHHHHHHhhhCCeEE
Q 046541 6 YIKQYNDIELTA--LGMAIPTVVTIAEALKRDGLAS 39 (94)
Q Consensus 6 ~l~~~~eVeLsA--LG~AI~tvVtvAEiLK~nglAt 39 (94)
+..+.|-|++|+ -|..+++...|-..|+.+|..+
T Consensus 27 lyge~pAvqIs~~~~~~~~~~~~~v~~~L~~~~I~~ 62 (101)
T PF13721_consen 27 LYGEDPAVQISASSAGVQLPDAFQVEQALKAAGIAV 62 (101)
T ss_pred ccCCCCcEEEecCCCCccCChHHHHHHHHHHCCCCc
Confidence 345778999999 5888888999999999999876
No 22
>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=38.14 E-value=90 Score=18.67 Aligned_cols=41 Identities=10% Similarity=0.166 Sum_probs=35.5
Q ss_pred hhcCcEEEecccchhhHHHHHHHHhhhCCeEEEEEEeeeee
Q 046541 8 KQYNDIELTALGMAIPTVVTIAEALKRDGLASNIEVKISTV 48 (94)
Q Consensus 8 ~~~~eVeLsALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv 48 (94)
...+.|.|+|....-..+....+-|++.++...-++...+.
T Consensus 21 ~~~~~l~i~G~a~~~~~v~~f~~~L~~~~~f~~v~l~~~~~ 61 (78)
T PF05137_consen 21 INGNTLSISGYADSYQSVAAFLRNLEQSPFFSDVSLSSISR 61 (78)
T ss_pred EeCCEEEEEEEECCHHHHHHHHHHHhhCCCccceEEEEEEe
Confidence 45678999999999999999999999999998777766555
No 23
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=37.93 E-value=40 Score=24.05 Aligned_cols=37 Identities=16% Similarity=0.333 Sum_probs=29.6
Q ss_pred hhhhcCcEEEecc--cchhhHHHHHHHHhhhCCeEEEEEE
Q 046541 6 YIKQYNDIELTAL--GMAIPTVVTIAEALKRDGLASNIEV 43 (94)
Q Consensus 6 ~l~~~~eVeLsAL--G~AI~tvVtvAEiLK~nglAt~kkI 43 (94)
+..+.+-|+||+. |..+++...|-..|+.+|.. .|.|
T Consensus 31 lygedpavQIs~~~~g~~~~~~~~v~~~L~~~gI~-~ksi 69 (127)
T PRK10629 31 LRQQESTLAIRAVHQGASLPDGFYVYQHLDANGIH-IKSI 69 (127)
T ss_pred ccCCCceEEEecCCCCCccchHHHHHHHHHHCCCC-cceE
Confidence 3467889999987 44669999999999999987 3444
No 24
>PLN02683 pyruvate dehydrogenase E1 component subunit beta
Probab=35.02 E-value=31 Score=27.98 Aligned_cols=74 Identities=15% Similarity=0.251 Sum_probs=44.8
Q ss_pred hhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEeeeeeeecCCCCCCcccceeEEEEEeec---cchHHHHhhc
Q 046541 7 IKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKA---EKLEKAVVAT 81 (94)
Q Consensus 7 l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks---~~FD~~~a~~ 81 (94)
++.-.+|-|=+.|.-...+..+||.|+++|+ +.+-..+|-.. ++.+.=-+..++.+..|+++-. ..|-+.+++.
T Consensus 225 ~r~G~dvtIia~G~~v~~Al~Aa~~L~~~GI~v~VId~~~ikP-lD~~~l~~~~~~t~~vvtvEE~~~~GGlGs~Va~~ 302 (356)
T PLN02683 225 EREGKDVTIVAFSKMVGYALKAAEILAKEGISAEVINLRSIRP-LDRDTINASVRKTNRLVTVEEGWPQHGVGAEICAS 302 (356)
T ss_pred EEcCCCEEEEEccHHHHHHHHHHHHHHhcCCCEEEEECCCCCc-cCHHHHHHHHhhcCeEEEEeCCCcCCCHHHHHHHH
Confidence 4555799999999999999999999999884 33333333211 1111111334566666777643 3455544443
No 25
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=34.43 E-value=1.2e+02 Score=19.25 Aligned_cols=76 Identities=20% Similarity=0.218 Sum_probs=48.2
Q ss_pred hhhhhcCcEEEec----ccchhhHHHHHHHHhhhCCeEEEEEEeeeeeeecCCCCCCcccceeEEEEEeeccchHHHHhh
Q 046541 5 RYIKQYNDIELTA----LGMAIPTVVTIAEALKRDGLASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKAEKLEKAVVA 80 (94)
Q Consensus 5 r~l~~~~eVeLsA----LG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks~~FD~~~a~ 80 (94)
++|++++.+-.+. +|..-+++-.--.-|.++|++.- .+..+....-|.+ ..+-+.|.+..++.+|++.+.
T Consensus 10 ~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~-----~~~~~~~~~~g~~-~~~~v~i~~~~~~~~~~v~~~ 83 (108)
T smart00344 10 EELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG-----YTAVINPKKLGLS-VTAFVGVDLESPDKLEEFLEK 83 (108)
T ss_pred HHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec-----eEEEeCHHHcCCC-EEEEEEEEECChhHHHHHHHH
Confidence 3566666544443 67777888888899999999761 1122222223322 367777777666788988877
Q ss_pred ccCCCC
Q 046541 81 TTAPKE 86 (94)
Q Consensus 81 ~~~~~e 86 (94)
-.+-.+
T Consensus 84 l~~~p~ 89 (108)
T smart00344 84 LEKLPE 89 (108)
T ss_pred HhCCcc
Confidence 665443
No 26
>cd06490 p23_NCB5OR p23_like domain found in NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR) and similar proteins. NCB5OR is widely expressed in human organs and tissues and is localized in the ER (endoplasmic reticulum). It appears to play a critical role in maintaining viable pancreatic beta cells. Mice homozygous for a targeted knockout (KO) of the gene encoding NCB5OR develop an early-onset nonautoimmune diabetes phenotype with a non-inflammatory beta-cell deficiency. The role of NCB5OR in beta cells may be in maintaining or regulating their redox status. Proteins in this group in addition contain an N-terminal cytochrome b5 domain and a C-terminal cytochrome b5 oxidoreductase domain. The gene encoding NCB5OR has been considered as a positional candidate for type II diabetes and other diabetes subtypes related to B-cell dysfunction, however variation in its coding region does not appear not to be a major contributor to the pathogenesis of these diseases.
Probab=32.53 E-value=30 Score=22.36 Aligned_cols=13 Identities=46% Similarity=0.626 Sum_probs=10.5
Q ss_pred ceeEEEEEeeccc
Q 046541 61 KAKIQIVLGKAEK 73 (94)
Q Consensus 61 KaKIeI~L~Ks~~ 73 (94)
.-||||.|.|.+.
T Consensus 68 ~~KVEI~L~K~e~ 80 (87)
T cd06490 68 TGKIELVLKKKEP 80 (87)
T ss_pred CceEEEEEEcCCC
Confidence 3499999999764
No 27
>PRK11892 pyruvate dehydrogenase subunit beta; Provisional
Probab=31.85 E-value=42 Score=28.50 Aligned_cols=40 Identities=18% Similarity=0.439 Sum_probs=32.3
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEee
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVKI 45 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~T 45 (94)
.+++-.+|-|-+.|.....+...||+|+.+|+ +.+-..+|
T Consensus 336 v~r~G~DvtIva~G~~v~~Al~Aa~~L~~~GI~~~VIdl~t 376 (464)
T PRK11892 336 IHREGKDVTIVSFSIGMTYALKAAEELAKEGIDAEVIDLRT 376 (464)
T ss_pred EEEcCCCEEEEEccHHHHHHHHHHHHHHhcCCCEEEEECCC
Confidence 45667799999999999999999999999996 44444444
No 28
>PRK10310 PTS system galactitol-specific transporter subunit IIB; Provisional
Probab=31.61 E-value=77 Score=20.86 Aligned_cols=27 Identities=19% Similarity=0.135 Sum_probs=21.3
Q ss_pred cEEEecccchhhHHH--HHHHHhhhCCeE
Q 046541 12 DIELTALGMAIPTVV--TIAEALKRDGLA 38 (94)
Q Consensus 12 eVeLsALG~AI~tvV--tvAEiLK~nglA 38 (94)
-+-.+|-|+|.|+++ .+=++|+++|+-
T Consensus 5 ILvvCgsG~~TS~m~~~ki~~~l~~~gi~ 33 (94)
T PRK10310 5 IIVACGGAVATSTMAAEEIKELCQSHNIP 33 (94)
T ss_pred EEEECCCchhHHHHHHHHHHHHHHHCCCe
Confidence 346788899999985 455999999995
No 29
>PRK09212 pyruvate dehydrogenase subunit beta; Validated
Probab=31.33 E-value=72 Score=25.40 Aligned_cols=66 Identities=12% Similarity=0.252 Sum_probs=43.3
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEeeeeeeecCCCCCCcccceeEEEEEeecc
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKAE 72 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks~ 72 (94)
.+++-.++-|=+.|.....+...||.|+++|+ +.+-.+++-.. ++.+.=-+..++.+-.|+++-.-
T Consensus 197 vl~~G~di~iva~G~~~~~a~eAa~~L~~~Gi~v~vi~~~~l~P-ld~~~i~~~~~~~~~vv~vEe~~ 263 (327)
T PRK09212 197 ILREGSDVTIVTFSIQVKLALEAAELLEKEGISVEVIDLRTLRP-LDTETIIESVKKTNRLVVVEEGW 263 (327)
T ss_pred EEEeCCCEEEEEccHHHHHHHHHHHHHHhcCCcEEEEEEecCCC-CCHHHHHHHHHhCCeEEEEcCCC
Confidence 35556789999999999999999999999986 44444444221 21111123455666666776543
No 30
>PRK14459 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=29.56 E-value=75 Score=26.43 Aligned_cols=40 Identities=23% Similarity=0.386 Sum_probs=31.8
Q ss_pred cEEEecccchhh---HHHHHHHHhhh---CCeEE-EEEEeeeeeeec
Q 046541 12 DIELTALGMAIP---TVVTIAEALKR---DGLAS-NIEVKISTVNSK 51 (94)
Q Consensus 12 eVeLsALG~AI~---tvVtvAEiLK~---nglAt-~kkI~Tstv~~~ 51 (94)
.|-++|+|...- .++.+.++|++ +|+.. ..+|++||+.+-
T Consensus 179 nVvfmGmGEPLlN~d~V~~~i~~l~~~~~~g~gis~r~ITvST~Gl~ 225 (373)
T PRK14459 179 NVVFMGMGEPLANYKRVVAAVRRITAPAPEGLGISARNVTVSTVGLV 225 (373)
T ss_pred EEEEecCCcchhhHHHHHHHHHHHhCcccccCCccCCEEEEECcCch
Confidence 499999999884 48899999998 56655 568999998643
No 31
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=27.52 E-value=1.7e+02 Score=21.36 Aligned_cols=20 Identities=25% Similarity=0.320 Sum_probs=15.8
Q ss_pred hhhHHHHHHHHhhhCCeEEE
Q 046541 21 AIPTVVTIAEALKRDGLASN 40 (94)
Q Consensus 21 AI~tvVtvAEiLK~nglAt~ 40 (94)
|..-...|+++||+.||+-.
T Consensus 29 ~SKl~~~il~vLk~eGYI~~ 48 (132)
T COG0096 29 ASKLKGAILKVLKKEGYIKD 48 (132)
T ss_pred hHHHHHHHHHHHHHcCCcce
Confidence 34556789999999999754
No 32
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=27.21 E-value=46 Score=20.90 Aligned_cols=17 Identities=24% Similarity=0.434 Sum_probs=12.3
Q ss_pred HhhhhhcCcEEEecccc
Q 046541 4 QRYIKQYNDIELTALGM 20 (94)
Q Consensus 4 Kr~l~~~~eVeLsALG~ 20 (94)
...|.+.+.|.|.+||.
T Consensus 33 ~~~L~~g~~V~i~g~G~ 49 (90)
T smart00411 33 TEALKKGEKVELRGFGT 49 (90)
T ss_pred HHHHhCCCeEEEeCcEE
Confidence 34577777888888875
No 33
>PTZ00182 3-methyl-2-oxobutanate dehydrogenase; Provisional
Probab=25.95 E-value=1.2e+02 Score=24.64 Aligned_cols=65 Identities=14% Similarity=0.296 Sum_probs=41.0
Q ss_pred hhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEeeeeeeecCCCCCCcccceeEEEEEeecc
Q 046541 7 IKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKAE 72 (94)
Q Consensus 7 l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks~ 72 (94)
+++-.++-|=+.|.....+..+++.|+.+|+ +.+-.+++-.. ++.+.--+..++.+-.|+++-+-
T Consensus 230 l~~G~di~Iia~Gs~~~~aleAa~~L~~~Gi~v~vI~~~~l~P-ld~e~i~~~~~~~~~IvvvEE~~ 295 (355)
T PTZ00182 230 VREGKDVTIVGYGSQVHVALKAAEELAKEGISCEVIDLRSLRP-WDRETIVKSVKKTGRCVIVHEAP 295 (355)
T ss_pred ecCCCCEEEEEeCHHHHHHHHHHHHHHhCCCcEEEEEEeeCCC-CCHHHHHHHHhcCCEEEEEEeCC
Confidence 5566788999999999999999999998885 33334433211 21111112345566666676543
No 34
>PRK05899 transketolase; Reviewed
Probab=25.73 E-value=53 Score=28.23 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=28.2
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL 37 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl 37 (94)
.+..-++|-|=+.|.-+..+..+|+.|+++|.
T Consensus 506 ~l~~G~dvtiia~G~~v~~al~Aa~~L~~~gi 537 (624)
T PRK05899 506 VLRDDPDVILIATGSEVHLALEAADELEAEGI 537 (624)
T ss_pred EEecCCCEEEEEeCHHHHHHHHHHHHHHhcCC
Confidence 45556899999999999999999999999884
No 35
>PF01674 Lipase_2: Lipase (class 2); InterPro: IPR002918 Lipases or triacylglycerol acylhydrolases hydrolyse ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol and free fatty acids []. This group of lipases has been called class 2 as they are not clearly related to other lipase families, and includes LipA and LipB from Bacillus subtilis [] and uncharacterised proteins from Caenorhabditis.; PDB: 2VTV_B 2X76_A 2X5X_A 2QXU_A 3QMM_A 1I6W_A 3D2C_J 2QXT_B 1R50_A 1T2N_A ....
Probab=25.69 E-value=36 Score=26.04 Aligned_cols=30 Identities=23% Similarity=0.184 Sum_probs=22.2
Q ss_pred cCcEEEecccc-hhhHHHHHHHHhhhCCeEE
Q 046541 10 YNDIELTALGM-AIPTVVTIAEALKRDGLAS 39 (94)
Q Consensus 10 ~~eVeLsALG~-AI~tvVtvAEiLK~nglAt 39 (94)
.|-|-+||.+. +-+..-.+++-|+++||+.
T Consensus 2 ~PVVlVHG~~~~~~~~w~~~~~~l~~~GY~~ 32 (219)
T PF01674_consen 2 RPVVLVHGTGGNAYSNWSTLAPYLKAAGYCD 32 (219)
T ss_dssp --EEEE--TTTTTCGGCCHHHHHHHHTT--C
T ss_pred CCEEEECCCCcchhhCHHHHHHHHHHcCCCc
Confidence 57788999999 8899999999999999985
No 36
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=24.55 E-value=1.2e+02 Score=26.36 Aligned_cols=37 Identities=16% Similarity=0.149 Sum_probs=32.9
Q ss_pred cccchhhHHHHHHHHhhhCCeEEEEEEeeeeeeecCC
Q 046541 17 ALGMAIPTVVTIAEALKRDGLASNIEVKISTVNSKKD 53 (94)
Q Consensus 17 ALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~~~~~ 53 (94)
.+|+....++..+..|+..|++.+.++.+.+..+-++
T Consensus 30 ~~~~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~e 66 (494)
T PTZ00326 30 SLNIDHQKVVGAIKSLESANYITTEMKKSNTWTLTEE 66 (494)
T ss_pred HcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHH
Confidence 5688889999999999999999999999998877554
No 37
>PLN02790 transketolase
Probab=24.48 E-value=77 Score=27.81 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=25.5
Q ss_pred CcEEEecccchhhHHHHHHHHhhhCCe
Q 046541 11 NDIELTALGMAIPTVVTIAEALKRDGL 37 (94)
Q Consensus 11 ~eVeLsALG~AI~tvVtvAEiLK~ngl 37 (94)
++|-|-|.|.-+..++.+|++|+++|+
T Consensus 541 ~dv~iia~G~~v~~Al~Aa~~L~~~gi 567 (654)
T PLN02790 541 PDLILIGTGSELEIAAKAAKELRKEGK 567 (654)
T ss_pred CCEEEEEcCHHHHHHHHHHHHHHhcCC
Confidence 689999999999999999999999886
No 38
>PRK12753 transketolase; Reviewed
Probab=24.38 E-value=77 Score=27.94 Aligned_cols=27 Identities=30% Similarity=0.406 Sum_probs=25.3
Q ss_pred CcEEEecccchhhHHHHHHHHhhhCCe
Q 046541 11 NDIELTALGMAIPTVVTIAEALKRDGL 37 (94)
Q Consensus 11 ~eVeLsALG~AI~tvVtvAEiLK~ngl 37 (94)
++|-|-|.|.-+..++.+||+|+++|+
T Consensus 550 ~dv~iia~Gs~v~~al~Aa~~L~~~gi 576 (663)
T PRK12753 550 PDLILIATGSEVEITLQAAEKLTAEGR 576 (663)
T ss_pred CCEEEEEeCHHHHHHHHHHHHHHhcCC
Confidence 389999999999999999999999885
No 39
>PRK10738 hypothetical protein; Provisional
Probab=24.38 E-value=1.8e+02 Score=20.38 Aligned_cols=26 Identities=15% Similarity=0.114 Sum_probs=18.9
Q ss_pred EEecccchhhHHHHHHHHhhhCCeEEEE
Q 046541 14 ELTALGMAIPTVVTIAEALKRDGLASNI 41 (94)
Q Consensus 14 eLsALG~AI~tvVtvAEiLK~nglAt~k 41 (94)
=|+|||.+. .+++.-+|+++|+-+..
T Consensus 40 lL~aLg~Ct--~i~v~~~l~k~~~~~~~ 65 (134)
T PRK10738 40 VLMAAGGCS--AIDVVSILQKGRQDVVD 65 (134)
T ss_pred HHHHHcCch--HHHHHHHHHHCCCCccc
Confidence 356777765 46788899999976544
No 40
>COG3439 Uncharacterized conserved protein [Function unknown]
Probab=24.33 E-value=21 Score=25.90 Aligned_cols=18 Identities=44% Similarity=0.571 Sum_probs=11.4
Q ss_pred cchhhHHHHHHHHhhhCC
Q 046541 19 GMAIPTVVTIAEALKRDG 36 (94)
Q Consensus 19 G~AI~tvVtvAEiLK~ng 36 (94)
|+-+-+.+.++|+|+++|
T Consensus 36 G~~V~~~id~~e~l~~~g 53 (137)
T COG3439 36 GFKVFTEIDHAEALKNAG 53 (137)
T ss_pred CCeEEEEecHHHHHHhcC
Confidence 555556666666666666
No 41
>cd03737 SOCS_SOCS3 SOCS (suppressors of cytokine signaling) box of SOCS3-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS3, like CIS1 and SOCS1, is involved in the down-regulation of the JAK/STAT pathway. SOCS3 inhibits JAK activity indirectly through recruitment to the cytokine receptors. SOCS3 has been shown to play an essential role in placental development and a non-essential role in embryo development. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=24.22 E-value=33 Score=20.53 Aligned_cols=10 Identities=30% Similarity=1.112 Sum_probs=8.4
Q ss_pred hhHhhhhhcC
Q 046541 2 PLQRYIKQYN 11 (94)
Q Consensus 2 ~~Kr~l~~~~ 11 (94)
|.|.||++|+
T Consensus 30 ~Lk~yL~~Y~ 39 (42)
T cd03737 30 PIKEFLDQYD 39 (42)
T ss_pred HHHHHHHhCC
Confidence 6899999885
No 42
>COG0504 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=24.15 E-value=66 Score=28.63 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=24.0
Q ss_pred EecccchhhHHHHHHHHhhhCCeE-EEEEEee
Q 046541 15 LTALGMAIPTVVTIAEALKRDGLA-SNIEVKI 45 (94)
Q Consensus 15 LsALG~AI~tvVtvAEiLK~nglA-t~kkI~T 45 (94)
+|+||-+|+ +-+++-+||+.||- +..||--
T Consensus 11 vSslGKGi~-aaSlg~lLk~rG~~Vt~~KlDP 41 (533)
T COG0504 11 VSSLGKGIT-AASLGRLLKARGLKVTIQKLDP 41 (533)
T ss_pred ecccccHHH-HHHHHHHHHHCCceEEEEeccc
Confidence 799999996 56899999999994 4556543
No 43
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=23.47 E-value=49 Score=20.60 Aligned_cols=17 Identities=18% Similarity=0.427 Sum_probs=12.3
Q ss_pred HhhhhhcCcEEEecccc
Q 046541 4 QRYIKQYNDIELTALGM 20 (94)
Q Consensus 4 Kr~l~~~~eVeLsALG~ 20 (94)
...|.+.+.|.|.++|.
T Consensus 33 ~~~L~~g~~V~l~g~G~ 49 (90)
T PF00216_consen 33 KEALKEGESVKLPGFGT 49 (90)
T ss_dssp HHHHHTT-EEEETTTEE
T ss_pred HHHHhcCCeEEeeceeE
Confidence 45678888888888885
No 44
>PRK10985 putative hydrolase; Provisional
Probab=22.63 E-value=93 Score=23.70 Aligned_cols=30 Identities=13% Similarity=0.160 Sum_probs=22.6
Q ss_pred cEEEecccchhhH--HHHHHHHhhhCCeEEEE
Q 046541 12 DIELTALGMAIPT--VVTIAEALKRDGLASNI 41 (94)
Q Consensus 12 eVeLsALG~AI~t--vVtvAEiLK~nglAt~k 41 (94)
-|-+||++..... +..+++.|.++|+.++-
T Consensus 61 vll~HG~~g~~~~~~~~~~~~~l~~~G~~v~~ 92 (324)
T PRK10985 61 LVLFHGLEGSFNSPYAHGLLEAAQKRGWLGVV 92 (324)
T ss_pred EEEeCCCCCCCcCHHHHHHHHHHHHCCCEEEE
Confidence 4678999765443 55799999999997763
No 45
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=21.97 E-value=1.5e+02 Score=25.97 Aligned_cols=38 Identities=16% Similarity=0.168 Sum_probs=33.6
Q ss_pred ecccchhhHHHHHHHHhhhCCeEEEEEEeeeeeeecCC
Q 046541 16 TALGMAIPTVVTIAEALKRDGLASNIEVKISTVNSKKD 53 (94)
Q Consensus 16 sALG~AI~tvVtvAEiLK~nglAt~kkI~Tstv~~~~~ 53 (94)
..+|..-..++..+..|+..|++.+.+..+....+-++
T Consensus 26 ~~~g~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~e 63 (492)
T PLN02853 26 ASHGLDHNEVVGVIKSLHGFRYVDAQDIKRETWVLTEE 63 (492)
T ss_pred HHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHH
Confidence 35788899999999999999999999999998887655
No 46
>COG5015 Uncharacterized conserved protein [Function unknown]
Probab=21.65 E-value=57 Score=24.24 Aligned_cols=15 Identities=20% Similarity=0.443 Sum_probs=12.9
Q ss_pred HhhhhhcCcEEEecc
Q 046541 4 QRYIKQYNDIELTAL 18 (94)
Q Consensus 4 Kr~l~~~~eVeLsAL 18 (94)
=+-|+++|+||++++
T Consensus 50 yKqik~np~vefcg~ 64 (132)
T COG5015 50 YKQIKKNPEVEFCGM 64 (132)
T ss_pred HHHHhhCCCeEEEEe
Confidence 367899999999986
No 47
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=21.60 E-value=1e+02 Score=17.75 Aligned_cols=23 Identities=30% Similarity=0.498 Sum_probs=19.7
Q ss_pred cccchhhHHHHHHHHhhhCCeEE
Q 046541 17 ALGMAIPTVVTIAEALKRDGLAS 39 (94)
Q Consensus 17 ALG~AI~tvVtvAEiLK~nglAt 39 (94)
.+|+.-+++-.+-.-|.+.||+.
T Consensus 27 ~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 27 ALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHCcCHHHHHHHHHHHHHCcCee
Confidence 47899999999999999999975
No 48
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=21.55 E-value=71 Score=19.79 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=9.3
Q ss_pred hhhhhcCcEEEecccc
Q 046541 5 RYIKQYNDIELTALGM 20 (94)
Q Consensus 5 r~l~~~~eVeLsALG~ 20 (94)
..|...+.|.|.+||.
T Consensus 33 ~~L~~g~~V~l~~~G~ 48 (87)
T cd00591 33 EALAKGEKVELPGFGT 48 (87)
T ss_pred HHHhCCCeEEEeCCEE
Confidence 4455556666666663
No 49
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=21.54 E-value=1.4e+02 Score=16.03 Aligned_cols=24 Identities=29% Similarity=0.457 Sum_probs=20.4
Q ss_pred cccchhhHHHHHHHHhhhCCeEEE
Q 046541 17 ALGMAIPTVVTIAEALKRDGLASN 40 (94)
Q Consensus 17 ALG~AI~tvVtvAEiLK~nglAt~ 40 (94)
.||...+++-...+-|.++||+..
T Consensus 19 ~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 19 ILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred HHCCCHHHHHHHHHHHHHCCCeee
Confidence 367888899999999999999963
No 50
>TIGR00232 tktlase_bact transketolase, bacterial and yeast. This model is designed to capture orthologs of bacterial transketolases. The group includes two from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous.
Probab=21.48 E-value=73 Score=27.92 Aligned_cols=30 Identities=27% Similarity=0.327 Sum_probs=26.7
Q ss_pred hhcCcEEEecccchhhHHHHHHHHhhhCCe
Q 046541 8 KQYNDIELTALGMAIPTVVTIAEALKRDGL 37 (94)
Q Consensus 8 ~~~~eVeLsALG~AI~tvVtvAEiLK~ngl 37 (94)
.+-++|-|-|.|.-+..+..+|++|+.+|+
T Consensus 538 ~~g~dv~iia~G~~v~~al~Aa~~L~~~Gi 567 (653)
T TIGR00232 538 SKGPDIILIATGSEVSLAVEAAKKLAAENI 567 (653)
T ss_pred cCCCCEEEEEeChHHHHHHHHHHHHHhcCC
Confidence 345799999999999999999999998885
No 51
>PF02302 PTS_IIB: PTS system, Lactose/Cellobiose specific IIB subunit; InterPro: IPR003501 The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This signature is often found downstream of IPR003352 from INTERPRO.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TVM_A 2WY2_D 1IIB_A 2WWV_D 1H9C_A 1E2B_A 2L2Q_A 2KYR_A 3CZC_A 3NBM_A ....
Probab=21.38 E-value=1.9e+02 Score=17.68 Aligned_cols=25 Identities=28% Similarity=0.454 Sum_probs=19.3
Q ss_pred EEEecccchhhHHH--HHHHHhhhCCe
Q 046541 13 IELTALGMAIPTVV--TIAEALKRDGL 37 (94)
Q Consensus 13 VeLsALG~AI~tvV--tvAEiLK~ngl 37 (94)
+-.++=|++.|.++ .+=+.++++|+
T Consensus 3 lvvC~~Gi~TS~~~~~~i~~~~~~~gi 29 (90)
T PF02302_consen 3 LVVCGSGIGTSLMVANKIKKALKELGI 29 (90)
T ss_dssp EEEESSSSHHHHHHHHHHHHHHHHTTE
T ss_pred EEECCChHHHHHHHHHHHHHHHHhccC
Confidence 34677788888887 56788999993
No 52
>KOG3379 consensus Diadenosine polyphosphate hydrolase and related proteins of the histidine triad (HIT) family [Nucleotide transport and metabolism; General function prediction only]
Probab=21.32 E-value=1.1e+02 Score=23.17 Aligned_cols=39 Identities=15% Similarity=0.176 Sum_probs=32.6
Q ss_pred eeeeeeecCCCC-CCcccceeEEEEEeeccch---HHHHhhcc
Q 046541 44 KISTVNSKKDDE-GRFFQKAKIQIVLGKAEKL---EKAVVATT 82 (94)
Q Consensus 44 ~Tstv~~~~~~~-gr~~qKaKIeI~L~Ks~~F---D~~~a~~~ 82 (94)
...|+.++|+.. |..++-.-+-|+=+|..|| |.||.+-+
T Consensus 80 ts~ti~iQDG~~AGQTVpHvHvHIlPR~~gDf~~Nd~IY~~L~ 122 (150)
T KOG3379|consen 80 TSLTIAIQDGPEAGQTVPHVHVHILPRKAGDFGDNDLIYDELD 122 (150)
T ss_pred cceEEEeccccccCcccceeEEEEccccccccccchHHHHHHH
Confidence 346788888876 8899999999999999999 67787765
No 53
>COG3119 AslA Arylsulfatase A and related enzymes [Inorganic ion transport and metabolism]
Probab=21.32 E-value=37 Score=28.07 Aligned_cols=21 Identities=38% Similarity=0.607 Sum_probs=17.0
Q ss_pred hhh-HHHHHHHHhhhCCeEEEE
Q 046541 21 AIP-TVVTIAEALKRDGLASNI 41 (94)
Q Consensus 21 AI~-tvVtvAEiLK~nglAt~k 41 (94)
.+. ++.|+||+||++||.|.-
T Consensus 84 ~l~~~~~Tla~~Lk~~GY~Ta~ 105 (475)
T COG3119 84 GLPDEVPTLAELLKEAGYYTAL 105 (475)
T ss_pred ccCcccchHHHHHHHcCChhhh
Confidence 344 688999999999998843
No 54
>TIGR03561 organ_hyd_perox peroxiredoxin, Ohr subfamily. Pfam model pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein Ohr, or organic hydroperoxide resistance protein.
Probab=21.29 E-value=83 Score=21.46 Aligned_cols=35 Identities=14% Similarity=0.052 Sum_probs=21.6
Q ss_pred cchhhHHHHHHHHhhhCCeEEEEEEe-eeeeeecCC
Q 046541 19 GMAIPTVVTIAEALKRDGLASNIEVK-ISTVNSKKD 53 (94)
Q Consensus 19 G~AI~tvVtvAEiLK~nglAt~kkI~-Tstv~~~~~ 53 (94)
+.|--.++++..++++.|+.+...+. +..+++..+
T Consensus 49 AlasC~~~t~~~~a~~~g~~~~~~~~v~~~~~l~~~ 84 (134)
T TIGR03561 49 GYAACFDGALKLVAGQAKVKLPADAEVTATVGLGKN 84 (134)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCCCcEEEEEEEeccc
Confidence 33444567888999999999742333 344455433
No 55
>PF06418 CTP_synth_N: CTP synthase N-terminus; InterPro: IPR017456 CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism, catalysing the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position []. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found roughly 500 bp upstream of enolase in both beta (Nitrosomonas europaea) and gamma (Escherichia coli) subdivisions of Proteobacterium [].; GO: 0003883 CTP synthase activity, 0006221 pyrimidine nucleotide biosynthetic process; PDB: 2VO1_A 3NVA_B 1VCN_A 1VCO_A 1VCM_A 3IHL_B 2AD5_A 1S1M_B.
Probab=21.26 E-value=57 Score=26.72 Aligned_cols=30 Identities=27% Similarity=0.467 Sum_probs=22.9
Q ss_pred EecccchhhHHHHHHHHhhhCCe-EEEEEEee
Q 046541 15 LTALGMAIPTVVTIAEALKRDGL-ASNIEVKI 45 (94)
Q Consensus 15 LsALG~AI~tvVtvAEiLK~ngl-At~kkI~T 45 (94)
+|+||-+|. +-+++-+||+.|| ++..||--
T Consensus 11 ~SglGKGi~-aaSig~lLk~~G~~V~~~K~DP 41 (276)
T PF06418_consen 11 VSGLGKGIT-AASIGRLLKSRGYKVTMIKIDP 41 (276)
T ss_dssp SSSSSHHHH-HHHHHHHHHCTT--EEEEEEE-
T ss_pred cccccHHHH-HHHHHHHHHhCCeeeeeeeecc
Confidence 689999996 4589999999999 45667655
No 56
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=20.98 E-value=2.1e+02 Score=18.76 Aligned_cols=48 Identities=19% Similarity=0.233 Sum_probs=31.5
Q ss_pred HHHHHhhhCCeEEEEEEeeeeeeecCCCCCC-cccceeEEEEEeeccch
Q 046541 27 TIAEALKRDGLASNIEVKISTVNSKKDDEGR-FFQKAKIQIVLGKAEKL 74 (94)
Q Consensus 27 tvAEiLK~nglAt~kkI~Tstv~~~~~~~gr-~~qKaKIeI~L~Ks~~F 74 (94)
.+.+-|++++-+.+.-.-|..+.-.....|| |...-.|.|-=.+...|
T Consensus 31 ~i~~~L~~~~~v~l~gfG~F~v~~r~aR~grNP~Tge~i~i~a~~~v~F 79 (90)
T PRK10664 31 SVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF 79 (90)
T ss_pred HHHHHHhCCCEEEECCcEEEEEEEeCCccccCCCCCCEEEEcCcccEEE
Confidence 3566788888888888888777766666665 33445666654444444
No 57
>PF12133 Sars6: Open reading frame 6 from SARS coronavirus; InterPro: IPR022736 This entry represents small proteins, typically between 42 to 63 amino acids in length, which are uncharacterised.
Probab=20.89 E-value=53 Score=21.47 Aligned_cols=8 Identities=75% Similarity=0.733 Sum_probs=6.3
Q ss_pred HHHHHHHh
Q 046541 25 VVTIAEAL 32 (94)
Q Consensus 25 vVtvAEiL 32 (94)
-|||||+|
T Consensus 8 qvtiae~l 15 (62)
T PF12133_consen 8 QVTIAEIL 15 (62)
T ss_pred HhhHHHHH
Confidence 48889976
No 58
>cd07250 HPPD_C_like C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS). HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of 4-hydroxyphenylpyruvate to homogentisate (2,5-dihydroxyphenylacetic acid, HG). HmaS converts HPP to 4-hydroxymandelate, a committed step in the formation of hydroxyphenylglycerine, a structural component of nonproteinogenic macrocyclic peptide antibiotics, such as vancomycin. If the emphasis is on catalytic chemistry, HPPD and HmaS are classified as members of a large family of alpha-keto acid dependent mononuclear non-heme iron oxygenases most of which require Fe(II), molecular oxygen, and an alpha-keto acid (typically alpha-ketoglutarate) to either oxygenate or oxidize a third substrate. Both enzymes are exceptions in that they require two,
Probab=20.73 E-value=84 Score=22.75 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=34.7
Q ss_pred HhhhhhcCcEEEecccchhhHHHHHHHHhhhCCeEEEEEEeee
Q 046541 4 QRYIKQYNDIELTALGMAIPTVVTIAEALKRDGLASNIEVKIS 46 (94)
Q Consensus 4 Kr~l~~~~eVeLsALG~AI~tvVtvAEiLK~nglAt~kkI~Ts 46 (94)
-+||..|+.-=++-++..+.++...++-|+.+|+..+..-.+.
T Consensus 73 ~~fl~~~~G~Gv~HIAf~vdDI~~~~~~L~~~Gv~~l~~P~~y 115 (191)
T cd07250 73 QEFLEYYGGAGVQHIALATDDIFATVAALRARGVEFLPIPDNY 115 (191)
T ss_pred HHHHHHhCCCceeEEEEECCCHHHHHHHHHHcCCeeccCchhh
Confidence 4688888666677789999999999999999999877654443
No 59
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=20.62 E-value=1.2e+02 Score=22.41 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=30.1
Q ss_pred hHHHHHHHHhhhCCeEEEEEEeeeeeeecCCCCCCcccceeEEEEEeeccchHHHHhhc
Q 046541 23 PTVVTIAEALKRDGLASNIEVKISTVNSKKDDEGRFFQKAKIQIVLGKAEKLEKAVVAT 81 (94)
Q Consensus 23 ~tvVtvAEiLK~nglAt~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~Ks~~FD~~~a~~ 81 (94)
++|--.-.-|++|||+.+.. .+....|||+.--+ -+-.||++...-
T Consensus 56 PEVSiAMr~Lre~gWV~~R~-------eKKkGKGRPik~Y~------Lt~~~~eIvs~i 101 (124)
T COG4738 56 PEVSIAMRYLRENGWVDERE-------EKKKGKGRPIKLYR------LTVPFDEIVSEI 101 (124)
T ss_pred chhHHHHHHHHHccccchHH-------hcccCCCCCceEEE------ecCcHHHHHHHH
Confidence 34333447899999997642 34467899885443 356788887653
No 60
>PLN02234 1-deoxy-D-xylulose-5-phosphate synthase
Probab=20.54 E-value=85 Score=28.01 Aligned_cols=80 Identities=14% Similarity=0.146 Sum_probs=48.0
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCeEE-EEEEeeeeeeecCCCCCCcccceeEEEEEe--eccchHHHHhhcc
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGLAS-NIEVKISTVNSKKDDEGRFFQKAKIQIVLG--KAEKLEKAVVATT 82 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~nglAt-~kkI~Tstv~~~~~~~gr~~qKaKIeI~L~--Ks~~FD~~~a~~~ 82 (94)
+|.+-.+|-|=|.|.-+..+..+|+.|+++|.-+ +-..++-. .++.+.--...++.+..|+++ ....|-+.+++.-
T Consensus 540 vlreG~dvtIva~G~~v~~Al~AA~~L~~~GI~v~VId~rsik-PlD~~~i~sl~k~~~~vVt~Ee~~~GG~Gs~Va~~l 618 (641)
T PLN02234 540 ILRDGERVALLGYGSAVQRCLEAASMLSERGLKITVADARFCK-PLDVALIRSLAKSHEVLITVEEGSIGGFGSHVVQFL 618 (641)
T ss_pred EEEeCCCEEEEEecHHHHHHHHHHHHHHhcCCCEEEEecCCcC-CCCHHHHHHHHHhCCEEEEECCCCCCcHHHHHHHHH
Confidence 4556679999999999999999999999988532 22222211 111111111223455666665 3467777666655
Q ss_pred CCCC
Q 046541 83 APKE 86 (94)
Q Consensus 83 ~~~e 86 (94)
.+..
T Consensus 619 ~e~~ 622 (641)
T PLN02234 619 ALDG 622 (641)
T ss_pred HHcC
Confidence 4443
No 61
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=20.40 E-value=2.2e+02 Score=18.59 Aligned_cols=48 Identities=21% Similarity=0.272 Sum_probs=32.3
Q ss_pred HHHHHhhhCCeEEEEEEeeeeeeecCCCCCC-cccceeEEEEEeeccch
Q 046541 27 TIAEALKRDGLASNIEVKISTVNSKKDDEGR-FFQKAKIQIVLGKAEKL 74 (94)
Q Consensus 27 tvAEiLK~nglAt~kkI~Tstv~~~~~~~gr-~~qKaKIeI~L~Ks~~F 74 (94)
.+.+-|++.+-+.+.-.-|..+.......|| |.....|.|-=.+...|
T Consensus 31 ~i~~~L~~g~~V~i~gfG~F~v~~r~~R~grNP~Tge~i~i~a~~~v~F 79 (90)
T PRK10753 31 AITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF 79 (90)
T ss_pred HHHHHHHcCCeEEEcCCEEEEEeeeCCccccCCCCCCEEEEcCCccEEE
Confidence 3457788888888888888888776666676 33445566655555544
No 62
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=20.37 E-value=2e+02 Score=18.47 Aligned_cols=40 Identities=15% Similarity=0.155 Sum_probs=27.3
Q ss_pred HHHHHhhhCCeEEEEEEeeeeeeecCCCCCC-cccceeEEE
Q 046541 27 TIAEALKRDGLASNIEVKISTVNSKKDDEGR-FFQKAKIQI 66 (94)
Q Consensus 27 tvAEiLK~nglAt~kkI~Tstv~~~~~~~gr-~~qKaKIeI 66 (94)
.+++-|++.+-+.+..+-|..+.......|| |.....|.|
T Consensus 32 ~i~~~L~~g~~V~l~gfG~F~~~~r~~r~~~np~Tge~i~i 72 (94)
T PRK00199 32 EMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVEL 72 (94)
T ss_pred HHHHHHHcCCeEEEcCCEEEEEEEecCeeccCcCCCCEEEE
Confidence 4567788888888888888888776665564 223444544
No 63
>PRK12571 1-deoxy-D-xylulose-5-phosphate synthase; Provisional
Probab=20.33 E-value=79 Score=27.69 Aligned_cols=39 Identities=13% Similarity=0.331 Sum_probs=31.2
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCe-EEEEEEe
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGL-ASNIEVK 44 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~ngl-At~kkI~ 44 (94)
++.+-.+|-|=|.|.-+..+..+|+.|+++|+ +.+-..+
T Consensus 500 vlr~G~ditIva~G~~v~~aleAa~~L~~~Gi~v~VId~~ 539 (641)
T PRK12571 500 VPREGPDVAILSVGAHLHECLDAADLLEAEGISVTVADPR 539 (641)
T ss_pred EEecCCCEEEEEecHHHHHHHHHHHHHHhcCCCEEEEEcC
Confidence 45556799999999999999999999999886 3344444
No 64
>PF00410 Ribosomal_S8: Ribosomal protein S8; InterPro: IPR000630 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S8 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S8 is known to bind directly to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [], groups eubacterial, algal and plant chloroplast, cyanelle, archaebacterial and Marchantia polymorpha mitochondrial S8; mammalian and plant S15A; and yeast S22 (S24) ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1S1H_H 3O30_O 3O2Z_O 3IZB_H 3U5G_W 3U5C_W 3OTO_H 1AN7_A 2HGR_K 3BBN_H ....
Probab=20.19 E-value=1.5e+02 Score=20.50 Aligned_cols=34 Identities=18% Similarity=0.182 Sum_probs=24.9
Q ss_pred hhhhcCcEEEecccchhhHHHHHHHHhhhCCeEEEEEE
Q 046541 6 YIKQYNDIELTALGMAIPTVVTIAEALKRDGLASNIEV 43 (94)
Q Consensus 6 ~l~~~~eVeLsALG~AI~tvVtvAEiLK~nglAt~kkI 43 (94)
++.++..|.+ -.-.....++++|++.||+--=.+
T Consensus 14 ~~~~~~~v~i----p~sk~~~~il~iL~~eGyI~~f~~ 47 (129)
T PF00410_consen 14 SRARKRFVII----PYSKLNLSILKILKKEGYISGFEI 47 (129)
T ss_dssp HHTTCSEEEE----EHCHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHCCCCEEEe----cccHHHHHHHHHHhhccccceeEe
Confidence 3455666666 346678899999999999865555
Done!