Align Monocarboxylic acid transporter (characterized)
to candidate WP_011383956.1 AMB_RS07815 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_000009985.1:WP_011383956.1 Length = 561 Score = 406 bits (1044), Expect = e-117 Identities = 229/543 (42%), Positives = 325/543 (59%), Gaps = 39/543 (7%) Query: 23 ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 I +FV+F+ T+ + T + DFY G +G QNGLAIAGDY+SAASFLGI Sbjct: 44 IIMFVIFVGATLGITYWAAGRTKTAADFYAAGGGITGFQNGLAIAGDYMSAASFLGISAL 103 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 + +GYDG ++S+G+ V W + L L+AE LRN+G++T ADV +RL + P+R AA G+L Sbjct: 104 VYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKYTFADVCGYRLARTPIRTFAATGSL 163 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 V +FYLI QM GAG L+ +L + V IVG +M+ YV GGM TT+VQ+IK Sbjct: 164 IVVIFYLIGQMVGAGQLIKLLFGMD----YVYAVMIVGALMMVYVTFGGMVATTWVQIIK 219 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262 A LL+GG + + L A+E H I+ P GA Sbjct: 220 ACLLLGGATFIAFGVMSQFGFSFEKLFVKAIEVHPKK----------VAIMAP----GAL 265 Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322 +T +D ISL +AL GTAGLPH+LMRF+TVP A+EARKSV +A IG FY++T ++G+ Sbjct: 266 VTNPVDAISLGMALMFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYILTFIIGF 325 Query: 323 GAAALV--GPDRV------IAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374 GA +V P+ + + G N AA LA +GG++F+ ISAVAFAT+LAVV+G Sbjct: 326 GAITMVATNPEYLTKGLGSLDLKGGNNMAAVWLAHAIGGNLFLGFISAVAFATILAVVSG 385 Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434 L + ++A+ HD+Y +VI +GQ+TE ++V VS+I + +G+I+++LG++ QNVAF+VA Sbjct: 386 LTLAGASAISHDLYASVIMHGQATEGKEVTVSKIASICLGVIAVLLGLVFEKQNVAFIVA 445 Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494 L F+VAASAN P ++ S++W T GAV GL+ +++++ LS AV G Sbjct: 446 LTFSVAASANFPVLVLSMFWGGLTTRGAVLGGMIGLLMSVIMVVLSKAVWVQSF----GF 501 Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE------MEVRSLTGVGVEKA 548 IFP P L S+P AF W+ +++ DN AE +RS TG+G E A Sbjct: 502 KAEIFPFAYPALFSVPAAFFFSWLFSIM---DNSPSAQAERAAYEAQSIRSETGLGAEGA 558 Query: 549 VDH 551 H Sbjct: 559 ASH 561 Lambda K H 0.324 0.138 0.393 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: 704 Number of extensions: 32 Number of successful extensions: 6 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: 551 Length of database: 561 Length adjustment: 36 Effective length of query: 515 Effective length of database: 525 Effective search space: 270375 Effective search space used: 270375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 53 (25.0 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