Align L-arabinose-binding periplasmic protein; Short=ABP; Flags: Precursor (characterized, see rationale)
to candidate SM_b20508 SM_b20508 sugar ABC transporter substrate-binding protein
Query= uniprot:B2SYR6 (332 letters) >FitnessBrowser__Smeli:SM_b20508 Length = 327 Score = 436 bits (1122), Expect = e-127 Identities = 224/326 (68%), Positives = 251/326 (76%), Gaps = 1/326 (0%) Query: 4 RIFLTLAAAATGVLFNAPVAQAADPVKIGFLVKQPEEPWFQDEWKFAEIAAKEKGFTLVK 63 R +A A T +F A A AAD VKIGF+VKQPEEPWFQDEWKFA+ AAKEKGFTLVK Sbjct: 2 RFIKAVALAGTVAIFAATSAFAAD-VKIGFIVKQPEEPWFQDEWKFADEAAKEKGFTLVK 60 Query: 64 IGAPSGEKVMSAIDNLSAQKAQGFVICTPDVKLGPGIVAKAKADGLKMMTVDDRLVDGAG 123 IGA GEKV SAIDNL AQ AQGF+ICTPDVKLGPGIVAKA A+ LK+MTVDDRLV+ G Sbjct: 61 IGAQDGEKVQSAIDNLGAQGAQGFIICTPDVKLGPGIVAKAAANDLKLMTVDDRLVNADG 120 Query: 124 KPIASVPHMGISAYNIGKQVGDGLAAEIKKRGWDMKDVGAIDVTYEQLPTAHDRTSGATD 183 PI VPHMGISA IG+ VG+ + AEIKKRGWDMK+VGAI V+Y+QLPTA DR GA Sbjct: 121 SPIEDVPHMGISATKIGEAVGEAIVAEIKKRGWDMKEVGAIRVSYDQLPTAVDRVEGALS 180 Query: 184 ALIAAGFPKANIVMAPQAKTDTENAFNAANIALTKNPQFKHWVAYALNDEGVLGAVRAAE 243 L A GFP+AN+ APQAKTDTE A NAA + L KN K WVA LNDE VLGAVRA E Sbjct: 181 VLKANGFPEANVFDAPQAKTDTEAALNAATVVLNKNAGIKKWVAVGLNDEAVLGAVRATE 240 Query: 244 GRGFKADNMIGIGIGGSDSALNEFKKPSPTGFYGTVIISPKRHGEETSTLMYDWITQGKA 303 G AD+MIGIGIGG+DSA+NEFKKPS TGF+GTVIISPKRHG ET+ MY+WI GK Sbjct: 241 TVGIPADSMIGIGIGGADSAINEFKKPSATGFFGTVIISPKRHGYETALNMYEWIANGKE 300 Query: 304 PPPLTLTTGMLATRDNVADVRQKMGL 329 P L LT G LA RDN VR+++G+ Sbjct: 301 PEKLILTAGQLALRDNYEAVRKELGI 326 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: 427 Number of extensions: 21 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: 327 Length adjustment: 28 Effective length of query: 304 Effective length of database: 299 Effective search space: 90896 Effective search space used: 90896 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