Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate PP_1297 PP_1297 putative amino-acid ABC transporter-binding protein YhdW
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Putida:PP_1297 Length = 342 Score = 596 bits (1537), Expect = e-175 Identities = 296/343 (86%), Positives = 322/343 (93%), Gaps = 1/343 (0%) Query: 1 MKLLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVG 60 MK+LK+TLAV+TAAA LG AQAGATLDAV+KKGFVQCGVSDGLPGFSVPD+ GKIVG Sbjct: 1 MKMLKTTLAVLTAAAALGAVSTAQAGATLDAVKKKGFVQCGVSDGLPGFSVPDAQGKIVG 60 Query: 61 IDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKF 120 IDAD CRAVAAAVFGDATKVKFSQLNAKERFTALQSGE+D+LSRN+T TSSRDAGMGL F Sbjct: 61 IDADVCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEVDVLSRNTTWTSSRDAGMGLVF 120 Query: 121 PGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFD 180 G +TYYDG+GFL N KLGV SAKELDGATICIQAGTTTELNVSD+FRANGLKYTPITFD Sbjct: 121 AG-VTYYDGVGFLVNKKLGVSSAKELDGATICIQAGTTTELNVSDFFRANGLKYTPITFD 179 Query: 181 TSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEW 240 TSDESAKSLESGRCDVLTSDKSQLFAQRSKLA+P +YVVLPETISKEPLGPVVR GD+EW Sbjct: 180 TSDESAKSLESGRCDVLTSDKSQLFAQRSKLAAPTEYVVLPETISKEPLGPVVRKGDEEW 239 Query: 241 LAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQI 300 +IV+WT +A+LNAEEAG+TSKNVEAEAK+TKNPDVAR+LGADGEYGKDLKLPKDWVVQI Sbjct: 240 FSIVKWTLFAMLNAEEAGITSKNVEAEAKATKNPDVARLLGADGEYGKDLKLPKDWVVQI 299 Query: 301 VKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 VKQVGNYGE+FE+NLG+ T L+IDRG+NALWN GGIQYAPPVR Sbjct: 300 VKQVGNYGEVFEKNLGQSTDLKIDRGMNALWNNGGIQYAPPVR 342 Lambda K H 0.315 0.133 0.383 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: 530 Number of extensions: 16 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: 343 Length of database: 342 Length adjustment: 29 Effective length of query: 314 Effective length of database: 313 Effective search space: 98282 Effective search space used: 98282 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: 49 (23.5 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