Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate 3606888 Dshi_0318 cationic amino acid ABC transporter, periplasmic binding protein (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Dino:3606888 Length = 338 Score = 351 bits (900), Expect = e-101 Identities = 181/339 (53%), Positives = 229/339 (67%), Gaps = 3/339 (0%) Query: 5 KSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDAD 64 KS L AAA L +G A TL+ VQ +G V CG+S GL GF+ D+ G+ G D Sbjct: 3 KSVLFGALAAAGLAATG--AAADTLEEVQARGAVNCGISTGLVGFASQDANGEWQGFDVA 60 Query: 65 FCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFI 124 CRAVAAAVFGD T V F+ + + RF L SGEIDML+RN+T T SRD + L+F G I Sbjct: 61 VCRAVAAAVFGDPTAVNFNPVTNQVRFEVLNSGEIDMLARNTTWTFSRDVDLKLEFTG-I 119 Query: 125 TYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDE 184 YYDG GF+ LGV SA ELDGAT+CIQ GTTTELN++D+FRAN + + P+ T+ E Sbjct: 120 NYYDGQGFMVPKALGVSSATELDGATVCIQKGTTTELNLADFFRANNISFEPVPISTASE 179 Query: 185 SAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIV 244 + + +G CDV T+D S L A R+ SP ++VVLPE ISKEPLGP+VR+GD+EW IV Sbjct: 180 AQQQYLAGACDVYTTDASGLAATRASFESPDEHVVLPEIISKEPLGPLVRHGDNEWGDIV 239 Query: 245 RWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQV 304 RWT AL+ AEE GVTS NV A T NP++ R+LG +G G+ L L DW V ++K Sbjct: 240 RWTLNALIAAEELGVTSANVAELAAGTDNPEINRLLGTEGNLGEQLGLSADWAVNVIKAG 299 Query: 305 GNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 GNYGE+FE ++G+ TP+ + RGLNA W GG+ YAPP R Sbjct: 300 GNYGEIFETHIGENTPIGLARGLNAQWTEGGLLYAPPFR 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: 346 Number of extensions: 10 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