Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_011383337.1 AMB_RS04560 C4-dicarboxylate ABC transporter
Query= reanno::SB2B:6938088 (339 letters) >NCBI__GCF_000009985.1:WP_011383337.1 Length = 337 Score = 245 bits (625), Expect = 1e-69 Identities = 134/323 (41%), Positives = 190/323 (58%), Gaps = 2/323 (0%) Query: 12 LFTLGKASLLATVL-GFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYK 70 L TL ++ A VL G + A+P+ IKFSHVVA +TPKG+ A FK+L E R G K Sbjct: 3 LGTLIAGAIAACVLAGSAMAQQAQPIVIKFSHVVAPDTPKGKGAEYFKKLAEERTKGRVK 62 Query: 71 VSVFPNSQLFGDNNELAALLLNDVQLVAPSLSKFERY-TKKLQVFDLPFLFEDMDAVDRF 129 V V+PNSQL+ D E+ AL L VQ++APSL+KF K+ +VFDLP++F D + Sbjct: 63 VEVYPNSQLYKDKEEMEALQLGAVQMLAPSLAKFGPLGVKEFEVFDLPYIFPSKDVLRSV 122 Query: 130 QQSEAGQQLLNSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQF 189 G LL + KG++GL Y NG K SAN + P D G K RI S V+ A+ Sbjct: 123 TGGPVGASLLKKLEGKGIIGLAYWDNGFKIMSANKPIKAPSDLKGVKMRIQSSKVLDAEM 182 Query: 190 EAVGAIPVKKPFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVT 249 A+GA+P FSEV+ LQT +DG EN SN+Y++K +EVQ H T +NHG L Y ++ Sbjct: 183 RALGALPQVMAFSEVYQALQTGVVDGTENPPSNMYTQKMHEVQKHATMTNHGYLGYAVIV 242 Query: 250 SETFWKSLPKDKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQA 309 ++ FW+ LP D R ++ +M EA N +A + ++ + + S + E + + +A Sbjct: 243 NKKFWEGLPADIRATLEGAMSEASVFANAIAQTENDDAVKAMKASGKTEFHDPSAAEIEA 302 Query: 310 WVNAMRPVWSQFEDKIGKDLIEA 332 W A+ PV E ++GKDLIE+ Sbjct: 303 WRKALLPVHKDMEGRVGKDLIES 325 Lambda K H 0.316 0.132 0.368 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: 294 Number of extensions: 12 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: 339 Length of database: 337 Length adjustment: 28 Effective length of query: 311 Effective length of database: 309 Effective search space: 96099 Effective search space used: 96099 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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