Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate WP_028312700.1 H566_RS0119115 ABC transporter
Query= uniprot:A0A0C4Y591 (325 letters) >NCBI__GCF_000482785.1:WP_028312700.1 Length = 312 Score = 398 bits (1022), Expect = e-115 Identities = 203/304 (66%), Positives = 239/304 (78%), Gaps = 1/304 (0%) Query: 21 AAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAKKINPDAKVTVLSA 80 AA A A A + R LK +G+T+GSLGNPYFV +A GAEA AK INP KVT +SA Sbjct: 8 AALALALATAAAGSVQARELKSIGITVGSLGNPYFVTMAKGAEARAKAINPGVKVTAVSA 67 Query: 81 DYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVVAVDVAAAGADATV 140 DYDLNKQF+ ID+FI + VDLIL+NAAD +AIEPAV+KA+KAGI VVAVDV AAGADATV Sbjct: 68 DYDLNKQFTQIDNFISAGVDLILLNAADPKAIEPAVKKAQKAGIAVVAVDVVAAGADATV 127 Query: 141 QTDNTRAGELACAFLAGRLGGRG-NLIIQNGPPVSAVLDRVKGCKMVLGKHPGIHVLSDD 199 QTDN AG+LAC ++ +LG +G N+IIQNGP VSAV+DRV GCK L K P + VLSDD Sbjct: 128 QTDNVAAGKLACKYIVDKLGAKGGNVIIQNGPQVSAVIDRVNGCKAELAKAPSLKVLSDD 187 Query: 200 QDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNRGGILIASVDGAPD 259 QDGKGSREGG+NV Q +LTRFPK+DA+FTINDPQA+G DLAA+QL R GI+I SVDGAPD Sbjct: 188 QDGKGSREGGMNVAQGHLTRFPKVDAIFTINDPQAIGTDLAAKQLGRKGIVITSVDGAPD 247 Query: 260 IEAALKANTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLLPPTLVTRANVNEYK 319 IE ALK NT V+ASASQDPWA A+ AVEIG L++G+ P + L P L+TR NV YK Sbjct: 248 IEVALKGNTQVEASASQDPWAQAQRAVEIGADLLNGKKPPETVIQLAPQLITRDNVAGYK 307 Query: 320 GWAA 323 GWA+ Sbjct: 308 GWAS 311 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: 287 Number of extensions: 6 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: 312 Length adjustment: 27 Effective length of query: 298 Effective length of database: 285 Effective search space: 84930 Effective search space used: 84930 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 Sep 24 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