Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 172 bits (435), Expect = 1e-47 Identities = 112/297 (37%), Positives = 169/297 (56%), Gaps = 12/297 (4%) Query: 14 VFVLGYLYCLTQFPGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTG 73 VF+L + F + R +IL + GI+AVGMT+VIL+ GIDLSVGS++AF G Sbjct: 30 VFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAG 89 Query: 74 VFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLRGVSYL 133 + A V G L A + G G G ++ L IP F+ TL + RG++++ Sbjct: 90 LCSAMVATQ-GYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFI 148 Query: 134 VSEESIPINHPIYDTLSSLAWKIPGGGRLSAMG--LLMLAVVVIGIFLAHR-TRFGNQVY 190 +++ S PI D A+ G G++ +G +++ AVV + ++ R T +G VY Sbjct: 149 LNDGS-----PITDLPD--AYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVY 201 Query: 191 AIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIAS 250 A+GGN SA GI R +Y++S LA LAG+V S T + AGV ELDAIA+ Sbjct: 202 AVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAA 261 Query: 251 VVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIAL 307 VVIGGT LSGG G+++GTLFG + G+I +N G +SS++ ++A G+++ + + Sbjct: 262 VVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLG-VSSYYQQVAKGLIIVFAVLI 317 Lambda K H 0.329 0.145 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: 335 Number of extensions: 31 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: 331 Length of database: 325 Length adjustment: 28 Effective length of query: 303 Effective length of database: 297 Effective search space: 89991 Effective search space used: 89991 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: 49 (23.5 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