Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF1303 PGA1_c13190 ABC transporter permease protein
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__Phaeo:GFF1303 Length = 276 Score = 135 bits (340), Expect = 9e-37 Identities = 90/269 (33%), Positives = 141/269 (52%), Gaps = 25/269 (9%) Query: 3 RLITRCAVWGVGIVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTP-TLENYRQVIGS 61 + I W VG+++ FP+LW +L S KT ++ P FLF TLENY V Sbjct: 10 KAINTALAWAVGLLIF----FPILWTILTSFKTEAQAISDPPVFLFFDWTLENYSVVQER 65 Query: 62 PEVLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGKR--DIQFFLLSLRFLPPVAV 119 + + L NS +I G + +LG + VPAA+ +A VP KR DI ++LS + LP V V Sbjct: 66 SDYMRFLWNSVIIAGGSTILGIIIAVPAAWSMA--FVPSKRTKDILLWMLSTKMLPAVGV 123 Query: 120 AIPLIAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDG----Y 175 P+ +++ +GL D RF ++V +L L I W+ F+ +P EI EAA +DG Sbjct: 124 LYPIYILFIKMGLLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKE 183 Query: 176 GPYAVFWKIALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQE 235 V +A+P A+TLL + +L WNE L LT++ +A L ++++S Sbjct: 184 EILYVLTPMAIPGIASTLL----LNIILAWNEAFWTLNLTAAKAAPLTAFIASYSS---- 235 Query: 236 VPWGVINA---STVLLALPPLIFVGVLSR 261 P G+ A + +A+ P++ +G S+ Sbjct: 236 -PEGLFYAKLSAASTMAIAPILILGWFSQ 263 Lambda K H 0.327 0.142 0.434 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: 239 Number of extensions: 18 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: 270 Length of database: 276 Length adjustment: 25 Effective length of query: 245 Effective length of database: 251 Effective search space: 61495 Effective search space used: 61495 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 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