Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_001306415.1:WP_054557498.1 Length = 219 Score = 127 bits (319), Expect = 3e-34 Identities = 71/215 (33%), Positives = 118/215 (54%), Gaps = 10/215 (4%) Query: 8 NIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSG---GDILIGE 64 NI+K YG+++ LKG+ I+++ GE + ++G SG GK+TLL ++ L PS I+I Sbjct: 6 NIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSSIMING 65 Query: 65 RSVLGVHPK------DRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118 V + K + +I +FQ + L P + N+ +++ P+A+ + R+ Sbjct: 66 VDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKAKAEVRGRELL 125 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 L + D +P +LSGG++QRVA+ RAL+ NP V DEP NLD++ + + Sbjct: 126 DFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENLHQLFFK 185 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIE 213 L + T V VTH++ E +A R +M DG+I+ Sbjct: 186 LREEFGQTFVIVTHNK-ELANMADRKLIMVDGQIQ 219 Lambda K H 0.320 0.136 0.385 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: 168 Number of extensions: 7 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: 360 Length of database: 219 Length adjustment: 26 Effective length of query: 334 Effective length of database: 193 Effective search space: 64462 Effective search space used: 64462 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: 47 (22.7 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