Align LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_008507131.1 BIBO1_RS11580 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A1N7UEH6 (318 letters) >NCBI__GCF_000182725.1:WP_008507131.1 Length = 329 Score = 95.5 bits (236), Expect = 2e-24 Identities = 78/273 (28%), Positives = 126/273 (46%), Gaps = 15/273 (5%) Query: 15 LAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQKEHAADFDMITNGI 74 LAAASA + S D K K+G L EF + K + + ++ Sbjct: 8 LAAASALIATPSLAQDK--KLKIGAAPYGLNAEFMQVWSEALKKHPAVKNGEVELTI--F 63 Query: 75 KNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGIKVVNIDNRLDPDVL 134 D Q + N MI K +AI+ P D +A T ++ ASDAGI VV + R++ D+L Sbjct: 64 DGRYDALVQQEQFNTMITQKFDAIIFVPIDIEAGATAVQAASDAGIPVVGSNTRVNSDLL 123 Query: 135 KSKNLDIPFVGPDNRKGSKLVGDYLAKQLASGDKVGIIEGVPTTTNAQ-QRTAGYKDAM- 192 + +VG D+ + + ++ V I+EG P +AQ R G K A+ Sbjct: 124 AA------YVGSDDTVSGYMEAKDVLDKIGCKGNVVILEG-PIGQSAQISRLEGNKKALA 176 Query: 193 DAAGMKIVSTQSGNWEIDQGQKVASAMLSEYP-DLKALLAGNDNMALGAVSAVRAAG-KA 250 + +K++ Q+ NW + Q + L+ +P + ++ ND MALGA+ A++AA K Sbjct: 177 ECPNVKVLEDQTANWSRAEAQTLMENWLTAHPGQINGVIGQNDEMALGAIEAIKAANLKP 236 Query: 251 GKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQ 283 G + G D I +++G + + A AQ Sbjct: 237 GDFAIAGIDGITDALHAVKEGTMTSILQDANAQ 269 Lambda K H 0.314 0.130 0.349 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: 214 Number of extensions: 12 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: 318 Length of database: 329 Length adjustment: 28 Effective length of query: 290 Effective length of database: 301 Effective search space: 87290 Effective search space used: 87290 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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