Align citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61) (characterized)
to candidate RR42_RS29530 RR42_RS29530 malate permease
Query= BRENDA::Q8VS41 (454 letters) >FitnessBrowser__Cup4G11:RR42_RS29530 Length = 451 Score = 507 bits (1306), Expect = e-148 Identities = 254/448 (56%), Positives = 333/448 (74%), Gaps = 8/448 (1%) Query: 9 SATLEPIDTPKTTLKQR-----WWHIMDNWKVGIVPLPLFLLAGGLIALDCLGGKLPSDI 63 S TL P + +T +K R WW +M+ +++GI+PLP++++ LIA + GK+P +I Sbjct: 5 SHTLPPAEAQQTAIKPRFWPEGWWKLME-FRIGIIPLPVYVILLALIAGFAVTGKVPGEI 63 Query: 64 VVMVATLAFFGFACGEFGKRLPVLGKLGAAAICATFIPSALVHYGLLPDVVIESTTKFYK 123 + +A LAFFGF C E GKRLP++ +GAAAI ATFIPSAL +Y LLP ++ TT+F K Sbjct: 64 SMAIAVLAFFGFTCAEIGKRLPIIRNIGAAAIFATFIPSALTYYHLLPKPILSLTTEFTK 123 Query: 124 STNILYLYICCIIVGSIMSMNRTTLIQGFLKIFFPMLCGEVVGMLVGIGVGTLLGMEPFQ 183 STN LYL+I IIVGSI+SM+R LIQGF+KIF P+ G + +VG VGT LG+ Sbjct: 124 STNFLYLFIASIIVGSILSMDRRVLIQGFIKIFIPLAVGSIAAGIVGTAVGTALGLGAHH 183 Query: 184 VFFFIVLPIMAGGVGEGAIPLSMGYAALMHMEQGVALGRVLPMVMLGSLTAIVISGCLNQ 243 FF+IV+PIMAGGVGEGAIPLS+GY+ ++H+ QG +VLP VMLGSLTAI++SG L++ Sbjct: 184 TFFYIVVPIMAGGVGEGAIPLSIGYSEILHLPQGDLFAQVLPPVMLGSLTAIILSGVLDK 243 Query: 244 LGKRFPHLTGEGQLMPNRSHETRSLSESEGVSGKTDVGTLASGALLAVLLYMMGMLGHKL 303 +GKRFPHLTGEG+L E + E + G DV +A+ + A+ LY++G++ L Sbjct: 244 VGKRFPHLTGEGRLQVGEEDEMDPVQEE--IRGHIDVTHIAAAGITAITLYLLGLMCRNL 301 Query: 304 IGLPAPVGMLFLAVLLKLANVVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQELV 363 GLPAPV MLFLAVL+K+ VSP LQEG+ +VYKFF TAVTYP+LFA+GVA+TPW +L+ Sbjct: 302 FGLPAPVAMLFLAVLVKITRAVSPPLQEGAFVVYKFFSTAVTYPLLFAIGVAMTPWDKLI 361 Query: 364 NAFTLTNLLVIVSTVSALVATGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTAGNR 423 AFTL N++ IV+TV+ L+ TGF+V + + MHPID AIV+ C SGQGGTGDVAILTA NR Sbjct: 362 AAFTLANIVTIVATVTTLMGTGFVVARMLKMHPIDTAIVNACHSGQGGTGDVAILTAANR 421 Query: 424 MSLMPFAQIATRIGGAINVSLGLLFLSH 451 M+LMPFAQIATRIGGAI V+L L+ L+H Sbjct: 422 MTLMPFAQIATRIGGAIVVTLTLIVLAH 449 Lambda K H 0.326 0.142 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 739 Number of extensions: 38 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 454 Length of database: 451 Length adjustment: 33 Effective length of query: 421 Effective length of database: 418 Effective search space: 175978 Effective search space used: 175978 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory