Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate SM_b20854 SM_b20854 sugar uptake ABC transporter permease
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Smeli:SM_b20854 Length = 331 Score = 192 bits (487), Expect = 1e-53 Identities = 111/303 (36%), Positives = 170/303 (56%), Gaps = 10/303 (3%) Query: 33 ITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSI-SQIGMVSCTMMFCLASRDFDLS 91 + + + IF+V+ A + D F + N+L + + S G+++ M+F + +R DLS Sbjct: 23 VQRFGTLAIFLVLVAVATWWSDSFLTRGNLLNVLRQVASTAGIMAVGMLFVILTRGIDLS 82 Query: 92 VGSTVAFAGVL----CAMVLNATGNTFIAIVAAVAAGGVIGFVNGAVIAYLRINALITTL 147 VGS +A VL CAM+ TG T ++ G G V G IAYLR+ + + +L Sbjct: 83 VGSVMALGSVLTGYFCAMLGYGTGATIFLVLLC---GAACGLVTGGFIAYLRLPSFVMSL 139 Query: 148 ATMEIVRGLGFIVSHGQAVGVSSD--TFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQT 205 A M + RGL I+S G+ + +S F + G G+ P+ + +I GV+LN T Sbjct: 140 AMMAVARGLSLIISEGRPIPLSDAGAAFSSFGSGFVLGIPQPVILMFAIYIAGGVVLNFT 199 Query: 206 VYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGF 265 +GR AIG N EA RL+GI V R V +++I G + LAG+I ASR G G Sbjct: 200 RFGRVITAIGSNEEAVRLSGIAVPRYIVAVYVISGLLAGLAGIIAASRTGVGSAQVGIGA 259 Query: 266 ELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAA 325 ELNVI+A V+GG SL+GG+ + ++G L+MG + N+MNL + ++Q + GAI++ A Sbjct: 260 ELNVIAAVVIGGASLMGGKGGVINTLLGALVMGIITNIMNLAGVPGYHQQVYMGAIIVVA 319 Query: 326 VLL 328 +LL Sbjct: 320 MLL 322 Lambda K H 0.326 0.139 0.396 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: 336 Number of extensions: 27 Number of successful extensions: 6 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: 338 Length of database: 331 Length adjustment: 28 Effective length of query: 310 Effective length of database: 303 Effective search space: 93930 Effective search space used: 93930 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 (21.7 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