Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_110805806.1 C8J30_RS10480 TRAP transporter substrate-binding protein
Query= reanno::SB2B:6938088 (339 letters) >NCBI__GCF_003217355.1:WP_110805806.1 Length = 333 Score = 254 bits (650), Expect = 2e-72 Identities = 137/316 (43%), Positives = 193/316 (61%), Gaps = 1/316 (0%) Query: 22 ATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQLFG 81 A L S A+AEP+ IKFSHVVA +TPKG+ A KF+EL E G V V+PNSQL+ Sbjct: 15 ALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNSQLYK 74 Query: 82 DNNELAALLLNDVQLVAPSLSKFERY-TKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLLN 140 D EL AL L VQ++APSL+KF + +VFDLP++F+D +A+ + Q EAG+ LL+ Sbjct: 75 DKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGEAGKMLLS 134 Query: 141 SMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKKP 200 + KG+ GL + NG K SAN+ L+ P D G K RI S V+ A+ A+GA+P Sbjct: 135 KLEAKGITGLAFWDNGFKIMSANSPLNTPDDFLGLKMRIQSSKVLEAEMNALGAVPQVMA 194 Query: 201 FSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPKD 260 FSEV+ LQT +DG EN SN++++K EVQ H T SNHG L Y ++ ++ FW LP D Sbjct: 195 FSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWDGLPAD 254 Query: 261 KREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWSQ 320 R ++++M E+ N +A E+ + + + E LT E+R AW A+ PV + Sbjct: 255 VRTGLEKAMAESTDYANGIAREENEKALAAMKAAGTTEFHELTAEERAAWEEALAPVADE 314 Query: 321 FEDKIGKDLIEAAESA 336 D+IG + I A ++A Sbjct: 315 MADRIGAETIAAVKAA 330 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: 261 Number of extensions: 10 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: 333 Length adjustment: 28 Effective length of query: 311 Effective length of database: 305 Effective search space: 94855 Effective search space used: 94855 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