Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate WP_003542591.1 RL_RS19900 carbohydrate ABC transporter permease
Query= reanno::Phaeo:GFF1303 (276 letters) >NCBI__GCF_000009265.1:WP_003542591.1 Length = 296 Score = 140 bits (354), Expect = 2e-38 Identities = 81/256 (31%), Positives = 138/256 (53%), Gaps = 6/256 (2%) Query: 27 PILWTILTSFKTEAQAISDPPVFLFFDWTLENYSVVQERS-----DYMRFLWNSVIIAGG 81 P++W ++TS K+ A+ PP + TL +Y + + D++RF WNS+ ++ Sbjct: 40 PMIWMLITSIKSGFAAMQFPPQWWPDQPTLASYQKLLDPQNSVGQDFLRFFWNSLFVSTA 99 Query: 82 STILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIYILFIKMGLLDNRF 141 +TIL +I+AVPAA++ + + +L M PAV L P++IL +GL++ Sbjct: 100 TTILSVIVAVPAAYAFSRFTFPGRNFLFFAVLLRNMFPAVIFLVPLFILMRAIGLVNTHA 159 Query: 142 GLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEILYVLTPMAIPGIASTL 201 LV+ + LP+ +W+L ++ IP ++ +AAR+DGAT + + ++ P++ PGI +T Sbjct: 160 SLVLTYLTFGLPLAIWLLKGFYDNIPVQLEQAARIDGATRFQAFILIVMPLSTPGIIATA 219 Query: 202 LLNIILAWNEAFWTLN-LTAAKAAPLTAFIASYSSPEGLFYAKLSAASTMAIAPILILGW 260 + + I AWNE + L+ + L I + S + L AAS M P+++L Sbjct: 220 IYSFIGAWNEYIYAYTFLSKNEQLTLPVGIQRFFSENTTDFPGLMAASFMMSVPVVVLFL 279 Query: 261 FSQKQLVSGLTFGAVK 276 Q+ V LT GAVK Sbjct: 280 VLQRYFVRALTEGAVK 295 Lambda K H 0.327 0.139 0.428 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: 287 Number of extensions: 18 Number of successful extensions: 4 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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