Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_054340456.1 Nant_RS04530 TRAP transporter substrate-binding protein
Query= reanno::SB2B:6938088 (339 letters) >NCBI__GCF_001305295.1:WP_054340456.1 Length = 327 Score = 451 bits (1159), Expect = e-131 Identities = 223/319 (69%), Positives = 267/319 (83%), Gaps = 3/319 (0%) Query: 23 TVLGFSFGA---VAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQL 79 T L +FGA VA PVEIKFSHVVAENTPKGQMA+KFKELV RL G +V VFP+SQL Sbjct: 9 TTLALAFGAQAAVASPVEIKFSHVVAENTPKGQMAIKFKELVAERLAGRVEVDVFPSSQL 68 Query: 80 FGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLL 139 FGDN L A+LL DVQL APSLSKF++YTK+LQ++DLPFLF+DM+AV+RFQQ GQ LL Sbjct: 69 FGDNKVLEAMLLGDVQLAAPSLSKFQQYTKQLQIYDLPFLFKDMEAVERFQQGPDGQGLL 128 Query: 140 NSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKK 199 +S+ KGLVGLGYLHNGMKQ SA+N + +P DAAG+KFRIM SDV+ AQFEAV A+P+KK Sbjct: 129 SSLESKGLVGLGYLHNGMKQLSASNPIKVPADAAGRKFRIMTSDVLQAQFEAVDAVPLKK 188 Query: 200 PFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPK 259 PFSEVFTLLQT+AIDGQENTWSNIYSKKF+EVQ ITESNHGVLDY++VTS FW SL Sbjct: 189 PFSEVFTLLQTKAIDGQENTWSNIYSKKFFEVQPFITESNHGVLDYLVVTSAEFWMSLDD 248 Query: 260 DKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWS 319 D R +K+++D+A+A GN +A EKANED+Q I+DSKR E++TLT +RQ WV+AM+PVW Sbjct: 249 DLRIELKKALDDAIAYGNGIAAEKANEDKQQIVDSKRSEVITLTDAERQQWVDAMKPVWK 308 Query: 320 QFEDKIGKDLIEAAESANK 338 QFE +IG DLIEAA+++NK Sbjct: 309 QFEAEIGADLIEAAQASNK 327 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: 370 Number of extensions: 5 Number of successful extensions: 1 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: 327 Length adjustment: 28 Effective length of query: 311 Effective length of database: 299 Effective search space: 92989 Effective search space used: 92989 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 24 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