Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate WP_086511158.1 BZY95_RS17250 carbohydrate ABC transporter permease
Query= BRENDA::P68183 (296 letters) >NCBI__GCF_002151265.1:WP_086511158.1 Length = 272 Score = 93.2 bits (230), Expect = 6e-24 Identities = 69/210 (32%), Positives = 105/210 (50%), Gaps = 8/210 (3%) Query: 87 NSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFDR 146 NSV VA S + + ++ AYA A + L ML +M P V LV +Y +F Sbjct: 70 NSVVVAFGSTLLALLIAIPAAYAMAFLPTRRTKATLLWMLSTKMLPPVGVLVPIYLIFRD 129 Query: 147 LGEYIPFIGLNTHGGVIFAY-LGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRL 205 LG L+T G+I Y L + + VW + +F+ + + EA +DGA+ +Q Sbjct: 130 LGL------LDTRSGLIIVYTLMNLPIVVWMLYTFFKDLPRDILEAGRMDGASTFQEVVY 183 Query: 206 VLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWGDFAA 265 +LLPL++P +A +LS I + E SL L N+ L + + +P+ W +A Sbjct: 184 LLLPLTLPGIASTGLLSVILSWNEA-FWSLNLTSSNAAPLTAYIASFSSPEGLFWAKLSA 242 Query: 266 AAVMSALPITIVFLLAQRWLVNGLTAGGVK 295 A+ M+ PI I L Q+ +V GLT G VK Sbjct: 243 ASTMAIAPILIFGWLTQKQMVRGLTFGAVK 272 Lambda K H 0.328 0.141 0.435 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: 229 Number of extensions: 14 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: 296 Length of database: 272 Length adjustment: 26 Effective length of query: 270 Effective length of database: 246 Effective search space: 66420 Effective search space used: 66420 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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