Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate H281DRAFT_01194 H281DRAFT_01194 amino acid/amide ABC transporter substrate-binding protein, HAAT family (TC 3.A.1.4.-)
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_01194 Length = 383 Score = 306 bits (785), Expect = 5e-88 Identities = 165/365 (45%), Positives = 226/365 (61%), Gaps = 5/365 (1%) Query: 12 AIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKF 71 A+A A +A VKIG AP++G QAHYG D +G ++AIE++N IGGK + F Sbjct: 17 ALAGAPCSYAATPVDVKIGFAAPLTGGQAHYGADFRSGVQLAIEDMNGTNPVIGGKPVHF 76 Query: 72 ELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNP 131 L A+DD ADP+ GT AQKL D V V+GH NSGT+IPA+ +Y G P V AT P Sbjct: 77 VLDAQDDQADPRTGTTVAQKLVDDGVVAVIGHYNSGTSIPAAPIYAKAGTPQVA-MATAP 135 Query: 132 NLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATA 191 + T+ G TTFR++ +D LGA L +AV LK K +AI+DDRTAYGQGVA+ F K A A Sbjct: 136 SYTRLGLPTTFRLLTSDTQLGAVLGDFAVKGLKFKRLAIVDDRTAYGQGVAEEFAKAAKA 195 Query: 192 KGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYF 251 G VV E++T DKA DF AILT IK N DA+FYGG D Q PML+QM L + + Sbjct: 196 AGATVVTEEYTNDKAVDFRAILTKIKQANVDAVFYGGADTQAAPMLKQMRSLAIKST-LL 254 Query: 252 GGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPYT 311 G D + + + K+A A + A GS L++MPGG A+ +Y ++ ++Y+PY Sbjct: 255 GPDMLQSDNLIKIAGEASE--GTLAASEGSPLSQMPGGKAFAERYQKRFNQPVELYAPYA 312 Query: 312 YDATFLIVDAMKRANSVDPKVYTPELAKSSFKGV-TSTIAFEPNGEMKNPAITLYVYKDG 370 YD T + +AMK+A+S DP V+ L ++ KGV TS ++++ G++K +T+Y +G Sbjct: 313 YDGTMAVFNAMKKADSTDPHVFLSALKATNMKGVTTSELSYDQYGDLKYGGVTVYKVVNG 372 Query: 371 KKTPL 375 PL Sbjct: 373 TWKPL 377 Lambda K H 0.315 0.131 0.375 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: 433 Number of extensions: 12 Number of successful extensions: 3 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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: 42 (22.0 bits) S2: 50 (23.9 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