Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate BWI76_RS13550 BWI76_RS13550 polar amino acid ABC transporter inner membrane subunit
Query= reanno::Smeli:SMc02120 (384 letters) >FitnessBrowser__Koxy:BWI76_RS13550 Length = 308 Score = 105 bits (263), Expect = 1e-27 Identities = 83/272 (30%), Positives = 140/272 (51%), Gaps = 28/272 (10%) Query: 135 RIPYKGLNALLLLVALPI-LSAILLPGGW----FGLTYVETPLWGGLMVTLVLSFVGIAV 189 R P + + A L L+AL + + ++ W F + + + GL TL+L+ + A+ Sbjct: 13 RYPLRAVGAALALLALAVVIQSVAFNPRWEWGVFARWFFDPVILEGLGQTLLLTLLATAL 72 Query: 190 SLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA----------SVMLPLFL 239 S+ LG LLAL R S+ ++ L +I + R +PLI VL + S+ +P Sbjct: 73 SVILGGLLALARLSSSWLLSSLAWGYIWLFRSLPLIVVLIILYNFSYLYDRLSIGIPFTG 132 Query: 240 PQGVTFD------KFLRALIGVSLFASAYMAEVVRGGLQAIPKGQYEGADSLGLSFWQKM 293 +F+ +F A++G++L SAY AE++RGG + GQYE A +LGL ++ Sbjct: 133 ISWASFETINVLGQFSTAVVGLTLVQSAYTAEIIRGGFLGVDHGQYEAAAALGLPASRRT 192 Query: 294 GFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFSDTNWATAVTPLTG 353 I+LPQAL+ ++P N I L K T++V ++ M +L +++ ++ T V P Sbjct: 193 LRIILPQALRTILPAGFNEIISLAKGTAMVYVLAMPELFYTIQMIYNRTQ---EVIP--- 246 Query: 354 LIFAGFVFWLFCFG-MSRYSGFMERLLDRSQR 384 L+ G ++L +S +ER L RS+R Sbjct: 247 LLMVGAAWYLVITSVLSLIQFLVERGLARSER 278 Lambda K H 0.329 0.144 0.454 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: 302 Number of extensions: 11 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: 384 Length of database: 308 Length adjustment: 29 Effective length of query: 355 Effective length of database: 279 Effective search space: 99045 Effective search space used: 99045 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