Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS00675 AZOBR_RS00675 ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__azobra:AZOBR_RS00675 Length = 229 Score = 105 bits (262), Expect = 8e-28 Identities = 74/219 (33%), Positives = 112/219 (51%), Gaps = 13/219 (5%) Query: 14 WGGVLLLAALMTVALTLAALAV--GAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPEL 71 W V L + V L L LA+ GA VA +L R + Y VFRG P L Sbjct: 7 WDSVPTLLRGVPVTLQLVGLALLFGAGVAFAVALLRLYGNRVTERLMAAYVFVFRGTPLL 66 Query: 72 LVIYLFYFGGSTLVTSVGQL-FGAEGFVGV---PPFVVGALAVGMISGAYQAEVYRSAVL 127 + I+L Y+G +GQ F+ V PF LA+ + +GAY +E+ R A+L Sbjct: 67 VQIFLIYYG-------MGQFELVRSSFLWVYLREPFWCAILALTLNTGAYTSEILRGAIL 119 Query: 128 AVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELL 187 +V +G++EAAR+ GM + RRI++P +R LP GN L +K S+L S L E+ Sbjct: 120 SVPQGQIEAARACGMSRTLLFRRIMMPVAIRQMLPAYGNEVILMVKASSLASTITLLEIT 179 Query: 188 RTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAE 226 ++ + F F+V G++YL++ I++R+ AE Sbjct: 180 GIARKIIAQSFAVFEVFIVAGSIYLLLNFIASRLIRYAE 218 Lambda K H 0.327 0.141 0.403 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: 109 Number of extensions: 5 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: 240 Length of database: 229 Length adjustment: 23 Effective length of query: 217 Effective length of database: 206 Effective search space: 44702 Effective search space used: 44702 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 46 (22.3 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