Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate AZOBR_RS18175 AZOBR_RS18175 sugar ABC transporter
Query= reanno::pseudo5_N2C3_1:AO356_00020 (308 letters) >FitnessBrowser__azobra:AZOBR_RS18175 Length = 295 Score = 134 bits (337), Expect = 3e-36 Identities = 87/271 (32%), Positives = 147/271 (54%), Gaps = 6/271 (2%) Query: 29 VSPSVALLLLWMIVPLAMTVYFSVIRYNLLNPGENEFVGLENFAYFVTDSGFLPGALNTL 88 V+P LL++ PL SV +LL+PG+ +VGL+N+ V D F T Sbjct: 12 VAPVALYLLVFQGYPLVQEFLLSVTSTSLLSPGQQTYVGLDNYRELVFDPEFHQVLRVTA 71 Query: 89 ILVGSVLLISVIFGVLIAALLEASEFFGRGIVRVLLISPFFIMPTVGSLIFKNLIFHPVS 148 + ++ S+ G+L A LL+ + F GRGI R L+ P+ P +LIF +F+ Sbjct: 72 VYTLVCVVASIGLGLLAALLLDGT-FRGRGIARALVTIPWAAPPVAAALIFV-WMFNAQY 129 Query: 149 GILAAVWKFFGAQP--VDWLAH--YPLFSIIVIVSWQWLPFAILLLMTAMQSLDQEQKEA 204 G+ + + +F G V+WL + L +I++ WQ PF+ ++++ A+Q + E +EA Sbjct: 130 GLFSHLAQFLGFAEGGVNWLDEPSFALPAILITTIWQIFPFSSVVILAALQGVPSELREA 189 Query: 205 ARLDGAGALAIFWHLTLPHLARPIAVVVMIETIFLLSVFAEIFTTTNGGPGFASTNLAYL 264 A +DGA L+IF +T P + +A++ ++ T++ L F I+ T GGP + L Sbjct: 190 AVIDGADRLSIFRAVTWPTIRPSVALLTLLITVWSLRRFDVIWLMTQGGPLGETNTLVID 249 Query: 265 IYNQALVQFDVGMASAGGLIAVVIANIAAIV 295 +Y +A V D+G A+A G+I +V+A + +V Sbjct: 250 LYRRAFVYLDLGRAAAVGIIGLVVAILVTLV 280 Lambda K H 0.329 0.142 0.429 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: 263 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 295 Length adjustment: 27 Effective length of query: 281 Effective length of database: 268 Effective search space: 75308 Effective search space used: 75308 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: 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