Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate AZOBR_RS25405 AZOBR_RS25405 C4-dicarboxylate ABC transporter
Query= reanno::SB2B:6938088 (339 letters) >FitnessBrowser__azobra:AZOBR_RS25405 Length = 345 Score = 132 bits (331), Expect = 2e-35 Identities = 93/307 (30%), Positives = 147/307 (47%), Gaps = 7/307 (2%) Query: 37 EIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQLFGDNN--ELAALLLNDV 94 E K S V + P + A ++ ELV + G V V+P S L G +N E L + Sbjct: 34 EYKLSVVGSRPIPIAEGAYRWAELVTEKTRGRITVKVYPGSSLVGGDNTREFTGLRQGSI 93 Query: 95 QLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLLNSMSRKGLVGLGYLH 154 L+ S K+ +F LPFLF D A D Q E G+ L + K +V L Sbjct: 94 DLLVNSTINLSPTVKEANLFSLPFLFPDSKAFDAVAQGEPGKALFGILESKQVVPLAVGE 153 Query: 155 NGMKQFS-ANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKKPFSEVFTLLQTRAI 213 NG + S + + P D G K R++ S + F A+GA P + F+++ L T A+ Sbjct: 154 NGFRALSNSKKPVRTPDDLKGLKVRVVGSPIFNDIFTALGANPTQMTFADLQPALSTGAV 213 Query: 214 DGQENTWSNIYSKKFYEV-QTHITESNHGVLDYMLVTSETFWKSLPKDKREIIKQSMDEA 272 DGQEN S + K Y + Q H+T N+ + + ++ W+S + R +++++ +A Sbjct: 214 DGQENPVSLFLAAKLYGLNQKHLTLWNYIADAGLFIANKEVWESWTPEDRALVREAAVQA 273 Query: 273 VALGNKLALEKAN-EDRQLI--LDSKRVELVTLTPEQRQAWVNAMRPVWSQFEDKIGKDL 329 A L+ + EDR + L S V++VT +A+ A RPV+ ++ +G DL Sbjct: 274 AAEFTALSRQGLTAEDRSALTALASHGVQVVTTEQTDVEAFRKATRPVYEKWTQTVGADL 333 Query: 330 IEAAESA 336 + AE A Sbjct: 334 VRKAEEA 340 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: 257 Number of extensions: 16 Number of successful extensions: 5 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: 345 Length adjustment: 29 Effective length of query: 310 Effective length of database: 316 Effective search space: 97960 Effective search space used: 97960 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