Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease
Query= TCDB::G3LHZ1 (273 letters) >FitnessBrowser__azobra:AZOBR_RS25590 Length = 277 Score = 127 bits (320), Expect = 2e-34 Identities = 74/257 (28%), Positives = 119/257 (46%), Gaps = 4/257 (1%) Query: 20 IIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYINSIIYVVM 79 + + + P W I S K S + WP+ P+L NY IF + + +NS++ Sbjct: 20 VAWAVFPFAWAIVTSLKAGSALF-TVEAWPSQPSLANYAAIFKEQPFGRNILNSLLAASA 78 Query: 80 NTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFGLIDTHI 139 +S+ A+ AAYA R RF G L F +L M P F+L GL + Sbjct: 79 VVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFELVRWLGLYNRIG 138 Query: 140 AVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIASGVGVAG 199 ++ L++ +F +P VW+L FM +PKE++E A +DG ++F+PL+ + G Sbjct: 139 SLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFLPLMGPALAATG 198 Query: 200 FFCFMFSWVELLLARTLTTT---AAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPGALV 256 F+ +W E L A T T T P++ + S + WG + AA V+ +P + Sbjct: 199 LLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAASVVVTVPLIGL 258 Query: 257 IYFVRNYIAKGFALGRV 273 + + I G G V Sbjct: 259 VLLFQRRIVSGLTAGAV 275 Lambda K H 0.330 0.142 0.456 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: 223 Number of extensions: 14 Number of successful extensions: 3 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: 273 Length of database: 277 Length adjustment: 25 Effective length of query: 248 Effective length of database: 252 Effective search space: 62496 Effective search space used: 62496 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