Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate SMa2309 SMa2309 ABC transporter permease
Query= reanno::Phaeo:GFF2752 (280 letters) >FitnessBrowser__Smeli:SMa2309 Length = 273 Score = 145 bits (365), Expect = 1e-39 Identities = 81/258 (31%), Positives = 138/258 (53%), Gaps = 2/258 (0%) Query: 24 LIALFPVFVILVNSFKTRKAIFRDPL-GLPTSDTFSLVGYQTVLKQGDFFLYFQNSMIVT 82 +I L P+F +++ SF++ + L G PT + + Y V Q YF NS+++T Sbjct: 16 IIWLAPLFAVILTSFRSMADVMSGNLWGWPT-EIAVVENYTAVFTQTPMAGYFLNSLVIT 74 Query: 83 VVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELMVDTGLVNT 142 + S+ VL +A F LA YRF GNM++ G +P +I + + +LMV L +T Sbjct: 75 IPSVIGVLSLSTLAGFVLARYRFPGNMVIFALFVGGNFLPHQIMMIPVRDLMVRLNLYDT 134 Query: 143 LTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPLVRPAMAT 202 TALI+ + A A + F+ + D+L A R +G + + +V+PLVRPA A Sbjct: 135 TTALIIFHVAFQTGFATLFMRNFIAALPDELFQAARAEGATPFQTLIHVVVPLVRPAWAA 194 Query: 203 VAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLSALSMAILPVMVL 262 +A+ IWND ++ ++L ++ K +T G G++V+ WN + + + +P +V+ Sbjct: 195 LAILLFTFIWNDYFWAVVLTVSDNVKPVTAGLANLRGEWVSAWNLISAGTIIVAVPPVVM 254 Query: 263 YVIFSRQLIRGITSGAVK 280 + + + I G+T GAVK Sbjct: 255 FFLMQKHFIAGLTMGAVK 272 Lambda K H 0.330 0.143 0.414 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: 196 Number of extensions: 9 Number of successful extensions: 1 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: 280 Length of database: 273 Length adjustment: 25 Effective length of query: 255 Effective length of database: 248 Effective search space: 63240 Effective search space used: 63240 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: 47 (22.7 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