Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate SM_b21095 SM_b21095 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Smeli:SM_b21095 Length = 290 Score = 75.1 bits (183), Expect = 2e-18 Identities = 39/118 (33%), Positives = 73/118 (61%), Gaps = 1/118 (0%) Query: 244 LALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVIIPP 303 +A L L + A+ +E+VRSG+ SV GQ EAAR++G+ LR++++PQA+RV++PP Sbjct: 154 VAAVLGLGISQGAYTSEVVRSGLLSVDSGQYEAARTIGMTQMKMLRRIVLPQAMRVMVPP 213 Query: 304 LTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361 + ++ + + K +SLA+ I Y E++ A + + +E++ + YL + +S+ Sbjct: 214 VGNEVIGMVKLTSLASVIQYSEILH-NAQIIYFANTRVLELLLVASFWYLLVVSVLSI 270 Score = 60.1 bits (144), Expect = 7e-14 Identities = 30/80 (37%), Positives = 45/80 (56%) Query: 47 FGIAQHLIDYTEADSYARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLA 106 F + Q Y +A L GL NTLL+T + L +LG +I + R+S N ++S +A Sbjct: 48 FSVGQIEWSYVRDFLFAPAILAGLYNTLLMTVAAMGLGIVLGVVIAIMRISGNPVLSLIA 107 Query: 107 TVYVEVFRNIPPLLQILFWY 126 Y+ VFR P LLQ++ W+ Sbjct: 108 IGYIWVFRGAPALLQLMLWF 127 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: 265 Number of extensions: 12 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: 290 Length adjustment: 28 Effective length of query: 347 Effective length of database: 262 Effective search space: 90914 Effective search space used: 90914 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: 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