Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate WP_086510988.1 BZY95_RS16550 arabinose ABC transporter substrate-binding protein
Query= uniprot:B2SYR6 (332 letters) >NCBI__GCF_002151265.1:WP_086510988.1 Length = 330 Score = 340 bits (872), Expect = 3e-98 Identities = 162/307 (52%), Positives = 223/307 (72%) Query: 23 AQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFTLVKIGAPSGEKVMSAIDNLSAQ 82 AQA D V+IGF+VKQPE+ WF +E + A +E GF +V++ G++V+SAIDNL +Q Sbjct: 24 AQAQDDVRIGFIVKQPEQAWFINEQRAAAERGEELGFRVVRLAGRDGQEVLSAIDNLYSQ 83 Query: 83 KAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVDGAGKPIASVPHMGISAYNIGKQ 142 AQGFVIC PDV+LGP ++ +A G+K++TVDD+ VDG+G+P+ VPH+G+S Y IG+Q Sbjct: 84 GAQGFVICPPDVRLGPAVMNRANQYGMKVITVDDQFVDGSGEPLEGVPHLGMSGYQIGRQ 143 Query: 143 VGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSGATDALIAAGFPKANIVMAPQAK 202 VG+ LAAEI+ RGWD + V A+ +T +LPTA +RT GA+D L+ GFP+ANI APQ Sbjct: 144 VGEALAAEIEARGWDPQQVAALRITNNELPTARERTDGASDVLLEWGFPEANIFDAPQQS 203 Query: 203 TDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVRAAEGRGFKADNMIGIGIGGSDS 262 TDT +AF+AA+ L++ +F+HW+ YALN+E VLG VRA E G A ++IG+GI GS + Sbjct: 204 TDTNSAFSAASPVLSQRSEFEHWIIYALNEESVLGGVRATEQYGLGATDVIGVGINGSGA 263 Query: 263 ALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWITQGKAPPPLTLTTGMLATRDNVAD 322 A EF + +PTGF+GTV +S +HG +T+ +Y WIT+ PP T TTG L TRDN D Sbjct: 264 AFAEFSRSNPTGFHGTVAVSSTQHGRQTAENLYRWITEDVEPPANTETTGTLMTRDNWQD 323 Query: 323 VRQKMGL 329 VR ++GL Sbjct: 324 VRAELGL 330 Lambda K H 0.316 0.133 0.391 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: 350 Number of extensions: 17 Number of successful extensions: 1 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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: 49 (23.5 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