Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate AO353_01535 AO353_01535 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01535 Length = 242 Score = 181 bits (458), Expect = 2e-50 Identities = 95/230 (41%), Positives = 148/230 (64%), Gaps = 4/230 (1%) Query: 2 ALIQMLG---FGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIG 58 AL+Q LG F +G+G +LL + MTV L++ +L + + G + A+AKLS + LR+ Sbjct: 4 ALLQTLGLSGFSLKGFGPLLLEGSWMTVKLSILSLLLSVLLGLIGASAKLSSVKLLRIPA 63 Query: 59 DIYTTVFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQ 118 +YTT+ RGVP+L+++ L ++ T +TS + G E ++ + PF G + +G I GAY Sbjct: 64 QLYTTLIRGVPDLVLMLLIFYSLQTWLTSFTEALGWE-YIEINPFAAGIITLGFIYGAYF 122 Query: 119 AEVYRSAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALI 178 E +R A+LAV RG++EAA + G+ R ++ PQ++RFALPGIGN W + LK +AL+ Sbjct: 123 TETFRGAILAVPRGQMEAATAYGLSRAQRFRFVVFPQMMRFALPGIGNNWMVILKATALV 182 Query: 179 SVTGLAELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAH 228 S+ GLA+L++ +Q A S++Q F F V+ +YL++TS SN V E H Sbjct: 183 SIIGLADLVKAAQDAGKSSYQLFFFLVLAALIYLVITSASNYVLRWLERH 232 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: 116 Number of extensions: 7 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: 242 Length adjustment: 23 Effective length of query: 217 Effective length of database: 219 Effective search space: 47523 Effective search space used: 47523 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