Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 139 bits (351), Expect = 6e-38 Identities = 87/267 (32%), Positives = 146/267 (54%), Gaps = 6/267 (2%) Query: 9 RAWLL-MLPLLVVMTAVIGWPLVDTVRLSFTDAKLV--GTEGGFVGT-ANYIKMLGGSNF 64 RA+L +LP LVV+ + P + + +S T LV GT F NY ++L + F Sbjct: 24 RAYLAGLLPALVVLGGITLLPGLFLLGVSLTPLSLVNPGTVFDFSDPLGNYRELLRDARF 83 Query: 65 QRALVTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRL 124 +++ + SV ++ G+ ALLLN + R A+RA ++P LP +V A +W++ Sbjct: 84 HNSVLLQLHLSATSVGLQLAAGLGVALLLNVRARFFEAIRAAFLIPMVLPPIVVALIWKI 143 Query: 125 IYNPEYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVP 184 +Y P+ L+ L + GL S + +P A+ A+ VA+ W+ FP L+ LA LQ +P Sbjct: 144 LYTPDVSPLHRLLEEAGL--PVDSLITDPTLAIWAIAVAETWQWFPFTMLMVLATLQLIP 201 Query: 185 RDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANST 244 + A+ +DGA FR +I+ YL L+V + R I++ K F +I+V+T GGP +T Sbjct: 202 DEPLEAARIDGANRRQVFRHIILAYLRPALVVCGLFRLIDSLKAFPLIYVLTNGGPGTAT 261 Query: 245 RTLSILVYQEAFSFQRAGSGASLALIV 271 + + EAF+F G +++A+++ Sbjct: 262 EVTNYYGFIEAFNFSYWGYASAIAVLM 288 Lambda K H 0.326 0.138 0.417 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: 243 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: 293 Length of database: 310 Length adjustment: 27 Effective length of query: 266 Effective length of database: 283 Effective search space: 75278 Effective search space used: 75278 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 (21.7 bits) S2: 48 (23.1 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