Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_900156495.1:WP_083710231.1 Length = 589 Score = 81.3 bits (199), Expect = 7e-20 Identities = 49/126 (38%), Positives = 81/126 (64%), Gaps = 4/126 (3%) Query: 248 LALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPPLTSQ 307 +AL + AA+I EI RSGI+SV GQ EA+R++G ++R V++PQ +R ++P L +Q Sbjct: 440 VALALLAAAYIGEIFRSGIQSVDDGQLEASRAIGFSYRQSMRLVVVPQGVRRVLPALMNQ 499 Query: 308 YLNLAKNSSLAAGIG-YPEMVSLFA-GTVLN-QTGQAIEVIAITMSVYLAISISISLLMN 364 +++L K+SSL +G LFA G LN QTG ++A + +YL ++I ++ L+N Sbjct: 500 FISLIKDSSLVYFLGLLASQRELFAVGRDLNAQTGNLSPLVAAGL-IYLVLTIPLTHLVN 558 Query: 365 WYNKRI 370 + + R+ Sbjct: 559 YIDHRL 564 Score = 44.7 bits (104), Expect = 7e-09 Identities = 20/55 (36%), Positives = 37/55 (67%) Query: 69 GLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQIL 123 GL NTL+++ + +L TILG ++ VA +S++ + A +Y ++FR +P ++ IL Sbjct: 362 GLPNTLILSVVSGVLGTILGMVLAVAGISRSRWLRWPARIYTDIFRGLPAVVVIL 416 Lambda K H 0.328 0.141 0.430 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: 433 Number of extensions: 24 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 589 Length adjustment: 33 Effective length of query: 342 Effective length of database: 556 Effective search space: 190152 Effective search space used: 190152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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