Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_017616633.1 CDO52_RS13840 carbohydrate ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >NCBI__GCF_002263495.1:WP_017616633.1 Length = 315 Score = 238 bits (607), Expect = 2e-67 Identities = 119/233 (51%), Positives = 167/233 (71%), Gaps = 7/233 (3%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P R TL+NYA +L G SF N++ ++VPSTV+ ++IAA AAYA AWM FPGR L Sbjct: 90 PSRLTLENYAGLLDNEGFVASFFNTILISVPSTVLIVVIAALAAYAFAWMEFPGRDWLFL 149 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265 VVGLLVVPLQ++LIP+ Q+Y +G + + G+ L H GFGLP AI+LLRN+ A Sbjct: 150 GVVGLLVVPLQVALIPIAQVYGPLGIYGSIP-----GVVLFHVGFGLPFAIFLLRNFFAA 204 Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325 +PR+++E+AR+DG + IF ++ILPL PA+AS AIFQFLW WNDLLVA+VF + + Sbjct: 205 IPRDLLEAARMDGGKELTIFRRVILPLGGPAIASLAIFQFLWVWNDLLVALVFADSANQP 264 Query: 326 LVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVK 378 +T L + + G N +++++ AF+++VVPL+VFFA QRY V+G++AG+VK Sbjct: 265 --MTVALQSEMRQFGANIDVISSGAFLSMVVPLLVFFAFQRYFVQGVMAGAVK 315 Score = 50.1 bits (118), Expect = 9e-11 Identities = 22/45 (48%), Positives = 30/45 (66%) Query: 12 AVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSR 56 A+ + ++L+ L W LPT GL +SSLR A SGWWT L++ SR Sbjct: 48 AIQVLLVLVGLFWLLPTLGLFVSSLRSPQDNASSGWWTVLAAPSR 92 Lambda K H 0.324 0.139 0.418 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: 299 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 380 Length of database: 315 Length adjustment: 29 Effective length of query: 351 Effective length of database: 286 Effective search space: 100386 Effective search space used: 100386 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 49 (23.5 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