Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF3104 Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__psRCH2:GFF3104 Length = 342 Score = 548 bits (1413), Expect = e-161 Identities = 271/340 (79%), Positives = 302/340 (88%), Gaps = 1/340 (0%) Query: 4 LKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDA 63 +KSTLAV+ AA++LG+SG AQAGATLDAVQKKGFVQCG+SDGLPGFS D+ GK GID Sbjct: 4 VKSTLAVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQGIDV 63 Query: 64 DFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGF 123 D CRAVAAAVFGDA+KVK+S L AKERFTALQSGE+D+LSRN+T TSSRDA MGL F G Sbjct: 64 DICRAVAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNFTG- 122 Query: 124 ITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSD 183 +TYYDG GFL N +LGV SAKELDGAT+CIQAGTTTELN+SDYFRANG KYTPIT+DTSD Sbjct: 123 VTYYDGQGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDTSD 182 Query: 184 ESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAI 243 ESAKSLESGRCDVLTSD+SQL+AQR KLA P DYVVLPE ISKEPLGP VR GD+EW I Sbjct: 183 ESAKSLESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWFDI 242 Query: 244 VRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQ 303 VRWT +A+LNAEE GVTS NVE AKSTKNPDVAR+LGA+GEYGKDLKLPKDW VQIVKQ Sbjct: 243 VRWTLFAMLNAEELGVTSANVEEMAKSTKNPDVARLLGAEGEYGKDLKLPKDWAVQIVKQ 302 Query: 304 VGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 VGNYGE+F+RN+G G+ L+I+RGLNALWN GG+QYAPPVR Sbjct: 303 VGNYGEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR 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: 506 Number of extensions: 19 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