Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_02332 H281DRAFT_02332 L-arabinose-binding protein
Query= uniprot:B2SYR6 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_02332 Length = 334 Score = 341 bits (875), Expect = 1e-98 Identities = 172/329 (52%), Positives = 229/329 (69%), Gaps = 2/329 (0%) Query: 3 RRIFLT-LAAAATGVLFNAPVAQAAD-PVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFT 60 RR+ LT +AAAA F A ++ AD P+K+GFLVK PE+ WF +E K A ++ GF+ Sbjct: 6 RRLTLTAIAAAAIAAPFAAQLSAHADQPLKVGFLVKMPEQAWFINEQKAATALGQKDGFS 65 Query: 61 LVKIGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVD 120 +V IG P GEKV+SAIDNL AQ A+GFVIC PDV+LGP I A+AK +K +TVDD+LVD Sbjct: 66 VVNIGTPDGEKVLSAIDNLGAQGAKGFVICAPDVRLGPAIQARAKRYNMKFVTVDDQLVD 125 Query: 121 GAGKPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSG 180 +GKP+A+VPH+G+SA+ IG QVG ++ E+K+RGW ++VGA+ +T +LPTA RT G Sbjct: 126 SSGKPLANVPHLGMSAFKIGNQVGQAISDEMKRRGWKPEEVGALRITNYELPTAKLRTDG 185 Query: 181 ATDALIAAGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVR 240 AT+ L+A GF K NI APQ TD E FNA++ L K+P K WV +ALN+E VLG VR Sbjct: 186 ATETLLAGGFKKENIFDAPQKTTDDEGGFNASSPVLAKHPNIKKWVIFALNEESVLGGVR 245 Query: 241 AAEGRGFKADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWITQ 300 A E A ++IG+GI G+ A EF+K PTGFYGT+ +S HG+E++ + +WI Sbjct: 246 ATEQLHIPAADVIGVGINGAGEAFAEFQKKEPTGFYGTIAVSSTMHGKESTENLVEWIKD 305 Query: 301 GKAPPPLTLTTGMLATRDNVADVRQKMGL 329 GK PP T TTG L R N DVR+++G+ Sbjct: 306 GKQPPADTQTTGKLMVRGNWQDVRKELGI 334 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: 368 Number of extensions: 15 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: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 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 17 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