Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate GFF2914 PS417_14910 C4-dicarboxylate ABC transporter
Query= reanno::SB2B:6938088 (339 letters) >FitnessBrowser__WCS417:GFF2914 Length = 327 Score = 343 bits (879), Expect = 5e-99 Identities = 170/317 (53%), Positives = 225/317 (70%), Gaps = 1/317 (0%) Query: 22 ATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQLFG 81 AT+ A+P+ IKF+HVVAENTPKGQ AL FK+L + RLPG KV V+PNS LFG Sbjct: 12 ATLFAAGLAQAADPIVIKFAHVVAENTPKGQGALLFKKLAQERLPGRVKVEVYPNSSLFG 71 Query: 82 DNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLLNS 141 D E+ ALLL DVQ++APSL+KFE+YT+++Q++DLPFLF D+ AVDRFQ ++ G+ LL + Sbjct: 72 DGKEMEALLLGDVQMLAPSLAKFEQYTQQVQIYDLPFLFNDLAAVDRFQAAQ-GKALLTA 130 Query: 142 MSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKKPF 201 M K ++GL Y HNG+KQ S+N AL P DA G KFR+ S V+ QF+A+ A P K F Sbjct: 131 MQDKNILGLAYWHNGLKQLSSNKALHEPKDARGLKFRVQASSVLEEQFKAIRANPRKMSF 190 Query: 202 SEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPKDK 261 +EV+ LQT ++G ENTWSN S+K EVQ + TESNHG++DYM++T+ TFW LP D Sbjct: 191 AEVYQGLQTGTVNGTENTWSNYESQKVNEVQKYFTESNHGLIDYMVITNATFWNGLPPDI 250 Query: 262 REIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWSQF 321 R ++Q M E NK A +Q I+D+K E++ LTPEQRQ W AMRPVW +F Sbjct: 251 RSTLEQIMVEVTVEVNKQAEALNQSAKQKIIDAKTSEIIELTPEQRQLWREAMRPVWQKF 310 Query: 322 EDKIGKDLIEAAESANK 338 E +IG DLI+AA+++N+ Sbjct: 311 EGEIGADLIKAADASNQ 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: 275 Number of extensions: 7 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: 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 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