Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate WP_106713295.1 CU102_RS22265 carbohydrate ABC transporter permease
Query= BRENDA::P68183 (296 letters) >NCBI__GCF_003010955.1:WP_106713295.1 Length = 281 Score = 109 bits (272), Expect = 8e-29 Identities = 93/289 (32%), Positives = 137/289 (47%), Gaps = 25/289 (8%) Query: 15 ITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLIPEQISW--DHWKLA----LGFSVE 68 + HL L+ + I+ P++ + +S+ +T LI + + W D L+ L SV Sbjct: 11 LVHLAALVLLVVILAPVVWLFVMSIS----STPDLIAKPLHWWPDTVDLSRYGVLLSSVA 66 Query: 69 QADGRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIF 128 + G + L+NS+KVAG++ + VAL A+A R P L ++ Sbjct: 67 NSAGEA------FVASLFNSIKVAGMATV--VALIVAVPSAWAVSRTPSVGWSLYAVIAT 118 Query: 129 QMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIA-LHVWTIKGYFETIDSS 187 M P V V LY G LN G+ YL +A W IK F++I Sbjct: 119 YMLPPVALAVPLYMTLAWAGL------LNNVFGLALVYLTILAPFTTWLIKSGFDSIPRE 172 Query: 188 LEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAV 247 +E AA LDGA Q RL+ LPL+ P++A + +F+ A E A L D + TL V Sbjct: 173 IESAATLDGARLDQILRLITLPLAAPVMATAALFAFLLAWDEFFYALLFTSDQRAKTLTV 232 Query: 248 GMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG 296 + + +G A A V++ALP +V L QR L+ GLT+GGVKG Sbjct: 233 AIADLAGGRVSDYGLIATAGVLAALPPLLVGLFMQRALIAGLTSGGVKG 281 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: 230 Number of extensions: 15 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: 281 Length adjustment: 26 Effective length of query: 270 Effective length of database: 255 Effective search space: 68850 Effective search space used: 68850 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: 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