Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF194 PGA1_c01980 glutamate/glutamine/aspartate/asparagine-binding protein BztA
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Phaeo:GFF194 Length = 338 Score = 342 bits (877), Expect = 8e-99 Identities = 169/334 (50%), Positives = 227/334 (67%), Gaps = 1/334 (0%) Query: 10 VMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRAV 69 ++ A + G++ A A TLD V+ +G + CGV+ GL GF+ P++ G+ G D CRAV Sbjct: 6 ILGALTIAGLAAGAAAAGTLDDVKARGKLNCGVTTGLVGFAAPNANGEWEGFDVAVCRAV 65 Query: 70 AAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYYDG 129 AAAV GD+T V+F K RFTAL SGEIDML+RN+T T SRD + +F G + YYDG Sbjct: 66 AAAVLGDSTAVEFVPTTGKTRFTALASGEIDMLARNTTWTFSRDVDLKFEFVG-VNYYDG 124 Query: 130 IGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKSL 189 GF+ +LGV SAKELDGAT+CIQ GTTTELN++D+FR+N + Y P+ +T+ E+ + Sbjct: 125 QGFMVPKELGVSSAKELDGATVCIQTGTTTELNLADFFRSNNISYEPVPIETNAEAQQQY 184 Query: 190 ESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTGY 249 +G CDV T+D S L A R+ P +V+LPE ISKEPLGP+VR+GD EW +VRW+ Sbjct: 185 LAGACDVYTTDASGLAATRATFDDPSAHVLLPEIISKEPLGPLVRHGDHEWGDVVRWSLN 244 Query: 250 ALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGNYGE 309 AL+ AEE GVTS N+ A T+NP++ R+LG +G G+ L L DW + GNYGE Sbjct: 245 ALVAAEELGVTSANIGEMAAGTENPEINRLLGTEGTLGEMLGLSADWAKNAIGAGGNYGE 304 Query: 310 MFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 +F +N+G+ TP+ + RGLNA W GG+ YAPP R Sbjct: 305 VFAKNIGEDTPIGLARGLNAQWTEGGLLYAPPFR 338 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: 390 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: 338 Length adjustment: 28 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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