Align citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61) (characterized)
to candidate BWI76_RS04555 BWI76_RS04555 citrate/acetate antiporter
Query= BRENDA::Q8VS41 (454 letters) >FitnessBrowser__Koxy:BWI76_RS04555 Length = 451 Score = 820 bits (2117), Expect = 0.0 Identities = 411/454 (90%), Positives = 435/454 (95%), Gaps = 3/454 (0%) Query: 1 MSTTDNAFSATLEPIDTPKTTLKQRWWHIMDNWKVGIVPLPLFLLAGGLIALDCLGGKLP 60 MSTTDNAF AT++PI+TPK LKQRWWHI+DNWKVGI+PLPLFLLAGGLIALDCLGGKLP Sbjct: 1 MSTTDNAFPATIDPINTPKAPLKQRWWHILDNWKVGIIPLPLFLLAGGLIALDCLGGKLP 60 Query: 61 SDIVVMVATLAFFGFACGEFGKRLPVLGKLGAAAICATFIPSALVHYGLLPDVVIESTTK 120 SDIVVMVATLAFFGFACGEFGKRLP+LGKLGAAAICATFIPSALVHYGLLPDVV+ESTTK Sbjct: 61 SDIVVMVATLAFFGFACGEFGKRLPILGKLGAAAICATFIPSALVHYGLLPDVVVESTTK 120 Query: 121 FYKSTNILYLYICCIIVGSIMSMNRTTLIQGFLKIFFPMLCGEVVGMLVGIGVGTLLGME 180 FYKSTNILYLYICCIIVGSIMSMNRTTLIQGF++IFFPMLCGE+VGM+VG+GVGT LG+E Sbjct: 121 FYKSTNILYLYICCIIVGSIMSMNRTTLIQGFMRIFFPMLCGEIVGMVVGVGVGTALGLE 180 Query: 181 PFQVFFFIVLPIMAGGVGEGAIPLSMGYAALMHMEQGVALGRVLPMVMLGSLTAIVISGC 240 PFQVFFFIVLPIMAGGVGEGAIPLS+GYAALMHM+QGVALGRVLPMVMLGSLTAIVI+G Sbjct: 181 PFQVFFFIVLPIMAGGVGEGAIPLSIGYAALMHMDQGVALGRVLPMVMLGSLTAIVIAGG 240 Query: 241 LNQLGKRFPHLTGEGQLMPNRSHETRSLSESEGVSGKTDVGTLASGALLAVLLYMMGMLG 300 LNQLGKRFPHLTGEGQLMPNR +ET + +E GK DV TLASGALLAVLLYM+GMLG Sbjct: 241 LNQLGKRFPHLTGEGQLMPNRRNETHRETPAE---GKMDVTTLASGALLAVLLYMLGMLG 297 Query: 301 HKLIGLPAPVGMLFLAVLLKLANVVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQ 360 K IGLPAPVGMLFLAVLLKL N VSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQ Sbjct: 298 QKTIGLPAPVGMLFLAVLLKLVNGVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQ 357 Query: 361 ELVNAFTLTNLLVIVSTVSALVATGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTA 420 ELVNAFTLTNLLVI+STVSALVATGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILT+ Sbjct: 358 ELVNAFTLTNLLVIISTVSALVATGFLVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTS 417 Query: 421 GNRMSLMPFAQIATRIGGAINVSLGLLFLSHYLA 454 GNRM+LMPFAQIATRIGGAINVSLGLLFLSH+LA Sbjct: 418 GNRMNLMPFAQIATRIGGAINVSLGLLFLSHFLA 451 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: 1024 Number of extensions: 36 Number of successful extensions: 3 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