Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate AO353_25130 AO353_25130 ABC transporter
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 290 bits (743), Expect = 3e-83 Identities = 165/362 (45%), Positives = 225/362 (62%), Gaps = 15/362 (4%) Query: 1 MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60 M + + +++ G V +L ++L+I GEF+V +G SGCGKSTLL IAGL + G + Sbjct: 1 MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60 Query: 61 FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120 I +R V EP++RG+GMVFQSYALYP M+V N+SFGLK+AK + + +RV R ++I Sbjct: 61 LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120 Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180 LQ+ LL+RKP ELSGGQRQRVA+GRA+ R+ D+ LFDEPLSNLDA LR ++R EI RLH Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240 L +TMIYVTHDQ+EA+TLAD+I V+ G ++Q+ P +Y P + FVAGF+GSP MN Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 Query: 241 FFRGEVEPKDGRSFVRA-----GGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295 F + S V + FD + A T L LG+RPEHV + +A D Sbjct: 241 FLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAADTPLS------LGVRPEHVSL-KAAD 293 Query: 296 GEPTHQAVVDIEEPMGADNLLWL-TFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFD 354 G T +V E +G++ + L T + R + G V L D+G +FD Sbjct: 294 G--TVGVIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGNLHLFD 351 Query: 355 AE 356 A+ Sbjct: 352 AD 353 Lambda K H 0.320 0.137 0.392 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: 387 Number of extensions: 10 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: 361 Length of database: 381 Length adjustment: 30 Effective length of query: 331 Effective length of database: 351 Effective search space: 116181 Effective search space used: 116181 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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