Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate SMc02118 SMc02118 general L-amino acid-binding periplasmic ABC transporter protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_5402 (343 letters) >FitnessBrowser__Smeli:SMc02118 Length = 341 Score = 396 bits (1018), Expect = e-115 Identities = 191/343 (55%), Positives = 251/343 (73%), Gaps = 4/343 (1%) Query: 3 LLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGID 62 + + L + AAV+G+ A + ATLD V+ KGFVQCGV+ GL GF+ PD++G G D Sbjct: 1 MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD 60 Query: 63 ADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPG 122 D+C+A+AAA+FGD +KVK++ L+AKERF ALQSGE+D+L+RN+T + +RD +G F Sbjct: 61 VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP 120 Query: 123 FITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTS 182 + YYDG GF+ +L VKSA EL GA +C+Q GTTTELN++DYF+AN L+Y P+ F+ Sbjct: 121 -VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKL 179 Query: 183 DESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLA 242 +E + ++GRCDV T+D+S L++ R L+ P D++VLPE ISKEPL P VR GDD+W Sbjct: 180 EEVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFD 239 Query: 243 IVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLG--ADGEYGKDLKLPKDWVVQI 300 IV W YAL+ AEE GVT N+E KST NPDV R LG AD + G DL L +W V I Sbjct: 240 IVSWVHYALVQAEEFGVTQANLEEMKKST-NPDVQRFLGVEADSKIGTDLGLTNEWAVNI 298 Query: 301 VKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343 VK VGNYGE+F+RN+G G+PL+I+RGLNALWN GG+QYAPPVR Sbjct: 299 VKAVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 341 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: 398 Number of extensions: 16 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: 341 Length adjustment: 29 Effective length of query: 314 Effective length of database: 312 Effective search space: 97968 Effective search space used: 97968 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