Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 80.9 bits (198), Expect = 3e-20 Identities = 53/132 (40%), Positives = 75/132 (56%), Gaps = 3/132 (2%) Query: 245 ALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPL 304 A L LT+ +AF+ EI R I++V GQ EAA +LGLR +R VI+PQA++V +PP Sbjct: 87 AAALGLTLNASAFLGEIWRGCIQAVPRGQWEAASALGLRYPGLMRYVILPQAVKVAVPPT 146 Query: 305 TSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQ-TGQAIEVIAITMSVYLAISISISLLM 363 + L K++SLAA IG+ E+ AG ++N T Q V I +Y + +SLL Sbjct: 147 VGFLVQLIKSTSLAAIIGFTELTR--AGQIVNNATFQPFLVFGIVAVLYFLMCWPLSLLS 204 Query: 364 NWYNKRIALIER 375 +R AL R Sbjct: 205 ARLERRYALATR 216 Score = 34.7 bits (78), Expect = 2e-06 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%) Query: 65 VFLIGLLN-TLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQIL 123 +FL+ + TL ++ I I +G +I +AR S + AT Y+++F+ P L+Q+ Sbjct: 10 LFLLSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQLF 69 Query: 124 FWYF 127 +F Sbjct: 70 LVFF 73 Lambda K H 0.328 0.141 0.430 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: 184 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 216 Length adjustment: 26 Effective length of query: 349 Effective length of database: 190 Effective search space: 66310 Effective search space used: 66310 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 (21.8 bits) S2: 47 (22.7 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