Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate GFF3464 PS417_17735 LacI family transcriptional regulator
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__WCS417:GFF3464 Length = 307 Score = 171 bits (433), Expect = 2e-47 Identities = 103/283 (36%), Positives = 163/283 (57%), Gaps = 7/283 (2%) Query: 1 MIKNTIAIACSTLLLAAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINP 60 M+ T+ + ++ L AA A KP++ +G + ++ NP+FV + E I Sbjct: 3 MLPKTLCLLAVSITLGTAAPAFADAAKPIR-IGASFQEINNPYFVTMKNALEEAGATIG- 60 Query: 61 DAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDV 120 AK+ + +++D++ QV +E+ + +D++++N DS GV AVK A AG+VVVAVD Sbjct: 61 -AKLIITDARHDVSKQVSDVEDMLQKGIDILLINPTDSVGVQSAVKSAHAAGVVVVAVDA 119 Query: 121 AAAG-ADVTVMSDNTMAGAESCKFLAEKLQGKGNVVIVNGPPVSAVMDRVTGCKAEFKKS 179 A G D V S N AG ++C++LA+ + KGN+ I++G V +++RV GCK K Sbjct: 120 QADGPLDSFVGSKNFDAGFQACEYLAKNIGDKGNIAILDGIAVVPILERVRGCKEAVAKH 179 Query: 180 PGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKRSDIK 239 P IKI+S QN RD +T N+L AQP + +F++ND ++GA AI +A D+K Sbjct: 180 PDIKIVS-IQNGKQERDQALTVTENMLQAQPTLKGIFSVNDNGSLGALSAI-EASGLDVK 237 Query: 240 WISGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESVAIGYA 282 +S VDGAP+A +A++ S F A+ AQ P ++ I A Sbjct: 238 LVS-VDGAPEAIKAIQKPGSKFIATSAQYPRDQIRLALGIALA 279 Lambda K H 0.314 0.129 0.360 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: 208 Number of extensions: 18 Number of successful extensions: 6 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: 316 Length of database: 307 Length adjustment: 27 Effective length of query: 289 Effective length of database: 280 Effective search space: 80920 Effective search space used: 80920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 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