Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate WP_073037859.1 BUB04_RS05920 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >NCBI__GCF_900129305.1:WP_073037859.1 Length = 399 Score = 355 bits (912), Expect = e-103 Identities = 185/374 (49%), Positives = 248/374 (66%), Gaps = 1/374 (0%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 RA +FQ++ + V + W+L NT NLQ + I +GF FL + A F I + LI Y +++ Sbjct: 27 RAVLFQILVLGVVGLIAWYLISNTVANLQRQKIATGFDFLGKEAAFEIGESLIAYDASNT 86 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 YAR ++G LNT+ V+FIG+++ ILG IG+ARLS NW+IS+LA Y+E ++IP L+Q Sbjct: 87 YARALVVGALNTVKVSFIGIVITVILGTFIGIARLSSNWLISRLAAAYIEFMQDIPVLIQ 146 Query: 122 ILFWYFAVFLSMPGPRAAHNFGDTFFVSSRGLNMPAALVAEGFWPFVISVVLAIVAIVLM 181 + FWY + ++P PR A N F+ +RGL MP + ++ V A + + Sbjct: 147 LFFWYAIFYETLPSPRQALNPMHGVFLCNRGLIMPVPEFHPAYRYVFLAFVAACFLVWGL 206 Query: 182 TRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNFVGGWVLIP 241 RWA KR + TG+ F F V L L + +P + G+P +PEL+GFNF GG L P Sbjct: 207 RRWARKRQDETGKTFPVFRVSLGLLVGLPLAVWMALGSPFSLNVPELRGFNFRGGTTLSP 266 Query: 242 ELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRVII 301 E +AL L L +YTAAF+AE+VR+GI+SVS GQ EAA SLGLR LR VI+PQALRVII Sbjct: 267 EFMALLLGLILYTAAFVAEVVRAGIQSVSKGQREAAMSLGLRPAQVLRLVILPQALRVII 326 Query: 302 PPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISISL 361 PPLTSQ LNL KNSSLA IGYP+ VS+ A T +NQTGQ+IE +A+ M VYL S+S S Sbjct: 327 PPLTSQMLNLTKNSSLAVAIGYPDFVSV-ANTTINQTGQSIEGVALIMVVYLFFSLSTSA 385 Query: 362 LMNWYNKRIALIER 375 MNWYNK++ L+ER Sbjct: 386 FMNWYNKKVKLVER 399 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: 405 Number of extensions: 15 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: 375 Length of database: 399 Length adjustment: 30 Effective length of query: 345 Effective length of database: 369 Effective search space: 127305 Effective search space used: 127305 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: 50 (23.9 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