Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 169 bits (429), Expect = 7e-47 Identities = 112/303 (36%), Positives = 173/303 (57%), Gaps = 15/303 (4%) Query: 10 ITIGVFVLGYLYCLTQF-PGFASTRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSV 68 + I + +L L ++ F P F + NI + I+A GMTFVIL+ GIDLSVGS+ Sbjct: 25 VGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84 Query: 69 IAFTGVFLAKVIGDFGLSPLLAFPLVLVMGCAFGAFMGLLIDALKIPAFIITLAGMFFLR 128 +A +GV ++ V G+ LA + +G G G+L L + FI+TL M FLR Sbjct: 85 VAVSGV-VSVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLR 143 Query: 129 GVSYLVSEESIPINHPIYDTLSSLAWKIPGGGRLSAMGL---LMLAVVVIGIFLAHRTRF 185 G++Y ++E PI SSL+++ G G L + + +ML V ++ F+ RTRF Sbjct: 144 GMAYTITE-----GQPIVS--SSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFILERTRF 196 Query: 186 GNQVYAIGGNATSANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVEL 245 G +YA+GGNA +A L G+ + +YM++ A LAGI+F+ + AG G EL Sbjct: 197 GRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYEL 256 Query: 246 DAIASVVIGGTLLSGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAI-GILLFIF 304 DAIA+VV+GGT L+GG G ++GTL G I G++ T + ++T++ I GI++ + Sbjct: 257 DAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSV--PFFTQLLIKGIVIILA 314 Query: 305 IAL 307 +A+ Sbjct: 315 VAI 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: 344 Number of extensions: 24 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: 331 Length of database: 339 Length adjustment: 28 Effective length of query: 303 Effective length of database: 311 Effective search space: 94233 Effective search space used: 94233 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 Apr 09 2024. 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