Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_086509147.1 BZY95_RS06440 amino acid ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >NCBI__GCF_002151265.1:WP_086509147.1 Length = 342 Score = 419 bits (1078), Expect = e-122 Identities = 204/340 (60%), Positives = 263/340 (77%), Gaps = 3/340 (0%) Query: 5 KSTLAVMTAAAVLGVSGFAQAGA-TLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDA 63 K+ ++T+AAVL + + A A TL ++G VQCGVSDGLPGFS PD G+ G+D Sbjct: 5 KNKWLLVTSAAVLALGTASLASANTLQNTIQRGAVQCGVSDGLPGFSAPDDQGEWQGLDV 64 Query: 64 DFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGF 123 D CRAVAAAVFGDA V++ LNA ERFTALQSGE+D+LSRN+T T++RD +GL F G Sbjct: 65 DVCRAVAAAVFGDADAVRYISLNAVERFTALQSGEVDVLSRNTTWTTTRDTTLGLNFTG- 123 Query: 124 ITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSD 183 +T+YDGIGF+ N LGV SA +LDGA IC+Q+GTTTELNV+DYFRANG+++ PI FDTS+ Sbjct: 124 VTFYDGIGFMINRDLGVSSALDLDGAAICVQSGTTTELNVADYFRANGMEFDPIVFDTSE 183 Query: 184 ESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAI 243 ++ E+GRCDVLTSD SQL A R +L+ P V+LPE ISKEPLGPVVR GDD+W I Sbjct: 184 QTVGGYEAGRCDVLTSDTSQLAALRIQLSDPDQSVILPEIISKEPLGPVVRQGDDQWFNI 243 Query: 244 VRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQ 303 V+W+ +A+LNAEE G+T +NV+ E +++ +PD+AR+LG DG YG+ + L +W I+ Q Sbjct: 244 VKWSLFAMLNAEEMGITQENVD-EMRNSDDPDIARLLGQDGNYGEGMGLDANWAYNIISQ 302 Query: 304 VGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 VGNYGE FERN+G G+PL+I+RG+NALW GGIQYAPP+R Sbjct: 303 VGNYGESFERNVGMGSPLQIERGINALWTNGGIQYAPPIR 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: 420 Number of extensions: 17 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: 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 24 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