Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF3033 PGA1_c30820 putative ABC transporter permease protein
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__Phaeo:GFF3033 Length = 320 Score = 121 bits (304), Expect = 2e-32 Identities = 69/220 (31%), Positives = 122/220 (55%), Gaps = 7/220 (3%) Query: 90 YTVLFRKPTFLLMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLM 149 Y+ F + L LN I+T I +IQV+V + AAYA AKL+F R+ +F + + +L+ Sbjct: 102 YSKAFTEAPLLRYLLNGIIVTGSIFLIQVVVALPAAYALAKLKFWGREAVFGLVLFCLLI 161 Query: 150 PLQVTLVPNYILLRKLDMIGSFLSVILPGGFSAFGVVLLRQYMRGIPDECCEAAMIDGAG 209 P+ +P YI+L KL + ++ ++++P S FG+ L+RQ+ +PD+ +AA +DG G Sbjct: 162 PVHAIALPLYIMLAKLGLTNTYAALVVPWTISVFGIFLMRQFFMTVPDDLIDAARMDGMG 221 Query: 210 YLKTFTKIILPQCKSIIASLAILAFIDNWNMVEQPLIFLS---DSAKYPLSVYLAYINEG 266 +++LP + + AI + + +WN P I ++ D PL + + +G Sbjct: 222 EFSIVWRVMLPTAIPALLAFAIFSIVAHWNDYFWPRIVVTGNRDLFTPPLGL-REFKGDG 280 Query: 267 D---LGLAFASGVLYMIPTVLIYLYGEKYFVEGIQLTGIK 303 D G A+ + + P ++ +L +K F+EGI L+G+K Sbjct: 281 DGSYFGPMMATATVIVTPLIVAFLLAQKRFIEGITLSGMK 320 Lambda K H 0.331 0.147 0.425 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: 196 Number of extensions: 13 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: 303 Length of database: 320 Length adjustment: 27 Effective length of query: 276 Effective length of database: 293 Effective search space: 80868 Effective search space used: 80868 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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