Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate SMc00676 SMc00676 amino acid-binding periplasmic signal peptide protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Smeli:SMc00676 Length = 331 Score = 350 bits (898), Expect = e-101 Identities = 175/333 (52%), Positives = 224/333 (67%), Gaps = 2/333 (0%) Query: 11 MTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDADFCRAVA 70 M A ++G ATLD V+++G ++CGVS G+ GFS PD G+ G D DFCRAVA Sbjct: 1 MALFATAFLAGTTAQAATLDVVKQRGELRCGVSQGVLGFSAPDDKGEWSGFDIDFCRAVA 60 Query: 71 AAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGFITYYDGI 130 AA G KVK+ L+ KERFTALQSGE+D+LSR +T T SRD +G+ F G + YYDG Sbjct: 61 AATLGSPDKVKYVPLSTKERFTALQSGEVDLLSRQTTWTLSRDTDLGMSFVG-VNYYDGQ 119 Query: 131 GFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSDESAKSLE 190 F+ +GVKS KEL GA++C + GTTTE N++DYF AN ++Y I F+ +D++ ++ Sbjct: 120 AFMVRGDIGVKSVKELSGASVCTETGTTTEQNMADYFSANKIEYQVIAFEKADQTIQAFN 179 Query: 191 SGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAIVRWTGYA 250 SGRCDV ++D S L++QR L P +VVLPE ISKEPLGP VR GDD+W +VRWT +A Sbjct: 180 SGRCDVYSTDASALYSQRLTLNDPDRFVVLPEVISKEPLGPAVRQGDDQWFKVVRWTLFA 239 Query: 251 LLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQVGNYGEM 310 ++ AEE G+T +N A + R LG D E GK L L W Q V VGNYGE+ Sbjct: 240 MIEAEELGITRENA-ASLLESGTAAQKRFLGIDNEAGKALGLDPKWAYQTVAAVGNYGEI 298 Query: 311 FERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 FER+LGK + L IDRGLN LWN GG+ YAPPVR Sbjct: 299 FERHLGKESALRIDRGLNKLWNNGGLIYAPPVR 331 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: 330 Number of extensions: 14 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: 331 Length adjustment: 28 Effective length of query: 315 Effective length of database: 303 Effective search space: 95445 Effective search space used: 95445 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