Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc04256 (361 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 205 bits (522), Expect = 1e-57 Identities = 127/298 (42%), Positives = 180/298 (60%), Gaps = 12/298 (4%) Query: 1 MTSV--SVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDG 58 MTS+ SV DL + G +L ++LD++ GE + LLG SG GK+TLL IAGL S G Sbjct: 1 MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60 Query: 59 QIFIKDRNVTWEEPK------DRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEK 112 I I ++ V K R +G VFQSYAL+P TV +N+++GLK+ K+P EI + Sbjct: 61 SIRIGEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQ 120 Query: 113 RVKRASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSEL 172 RV+ L + L +R P +LSGGQ+QRVA+ R+LV + V L DEPLSNLDAKLR E Sbjct: 121 RVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEA 180 Query: 173 RVEIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAG 232 R+ +++L L + + VTHDQ EA+ +AD++ ++K GVI+Q P +Y AP++LFVA Sbjct: 181 RIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAE 240 Query: 233 FIGSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV 290 F+G + N G V DG S R G + + T L+ G + +R E +K+ Sbjct: 241 FMG--ANNTISGLVTDVDGDS-ARIEGNGWALRG-RLRTPLKAGDRATAVVRLEKIKL 294 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: 321 Number of extensions: 12 Number of successful extensions: 2 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: 353 Length adjustment: 29 Effective length of query: 332 Effective length of database: 324 Effective search space: 107568 Effective search space used: 107568 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 Apr 09 2024. 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