Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate BWI76_RS07665 BWI76_RS07665 ABC transporter substrate-binding protein
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__Koxy:BWI76_RS07665 Length = 311 Score = 107 bits (267), Expect = 4e-28 Identities = 91/297 (30%), Positives = 143/297 (48%), Gaps = 22/297 (7%) Query: 33 SAAAQRPLK-KVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVLSADYDLNKQFSHI 91 S AAQ K + + + SL NPY+ + A GA AK++ + T+LS D+ KQ I Sbjct: 17 SFAAQAAEKGTIMIMVNSLDNPYYASEAKGASEKAKELG--YQTTILSHGEDVKKQNELI 74 Query: 92 DSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAGADATVQT---DNTRAG 148 D+ I KV I+++ AD+ A A+ KA+KAGI VV ++ D ++ +N +AG Sbjct: 75 DTAIGKKVQGIILDNADSTASVAAIEKAKKAGIPVVLINREIPVDDIALEQITHNNFQAG 134 Query: 149 ELACAFLAGRLGGRG-------NLIIQNGPPVSAVLDRVKGCKMVLGKHPGIHVLSDDQD 201 ++ +G NL N + R K V+ ++P + V QD Sbjct: 135 SEVANVFVEKMAEKGKYAELTCNLADNN------CVTRSKSFHQVIDQYPDM-VSVAKQD 187 Query: 202 GKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGILIASVDGAPDIE 261 KG+ G +M L P + V N P A+GA A + NR +++ +DG+ D Sbjct: 188 AKGTLIDGKRIMDSILQAHPDVKGVICGNGPVALGAIAALKAANRNDVVVVGIDGSNDER 247 Query: 262 AALKANTLVQASASQDPWAIARTAV-EIGVGLMHGQAPANRTVLLPPTLVTRANVNE 317 A+KA TL QA+ AIA V ++ L G+ PA + V+ L+T+ N ++ Sbjct: 248 DAVKAGTL-QATVMLQAQAIAAQGVTDLDNYLQKGEKPAKQRVMFRGILITQDNADK 303 Lambda K H 0.318 0.132 0.377 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: 177 Number of extensions: 10 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: 325 Length of database: 311 Length adjustment: 27 Effective length of query: 298 Effective length of database: 284 Effective search space: 84632 Effective search space used: 84632 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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