Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_091519694.1 BM253_RS04260 phosphate ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_900115115.1:WP_091519694.1 Length = 248 Score = 103 bits (258), Expect = 4e-27 Identities = 74/243 (30%), Positives = 124/243 (51%), Gaps = 13/243 (5%) Query: 3 QIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGL-----ETPTS 57 ++ +L FG+ + ++S+ + E L+GPSGCGKST LR + + + Sbjct: 4 KLSAENLNISFGEKHVLKNISVSFAEHEITALIGPSGCGKSTLLRSFNRMHDLFPDAKIN 63 Query: 58 GDIYIGG-DHMNYRVPQN---RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDE 113 G +++ D + VP + I MVFQ +P ++ +NI +GL+ + E + Sbjct: 64 GSLHLEELDLYDRHVPVTEIRKRIGMVFQKANPFPK-SIYENIAYGLKINNLPCNKEVVQ 122 Query: 114 RVVEVAETLG-IADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAE 172 + +E A + + L LSGGQQQR+ + RA+ PEV LMDEP S LD + Sbjct: 123 KALEEAYLWDEVKNDLKMPATRLSGGQQQRLCIARAVALRPEVILMDEPCSALDPVSTLK 182 Query: 173 MRTELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVA 232 + +++L+ + T V VTHN +A +AD+ M GE+++ + E ++ P N A Sbjct: 183 IEELIKHLKKK--YTIVIVTHNMQQAQRIADKTVFMYLGEVKEEGTTDEIFNHPKNEMTA 240 Query: 233 EFI 235 +I Sbjct: 241 NYI 243 Lambda K H 0.317 0.135 0.386 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: 174 Number of extensions: 9 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: 383 Length of database: 248 Length adjustment: 27 Effective length of query: 356 Effective length of database: 221 Effective search space: 78676 Effective search space used: 78676 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 (21.6 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