Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_055437631.1 ASC41_RS15790 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_001418085.1:WP_055437631.1 Length = 220 Score = 134 bits (337), Expect = 2e-36 Identities = 87/227 (38%), Positives = 135/227 (59%), Gaps = 12/227 (5%) Query: 15 LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74 +++ ++HK Y L VLKGV++ +++G VV+++GSSG+GKTTLL+ + L+ Sbjct: 1 MIKAENIHKYYDDLHVLKGVNVHIKKGEVVSIVGSSGAGKTTLLQILGTLDTISK----T 56 Query: 75 DGESIGYHEVNGKRVRH-SEKVIAQHR-AMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132 D S+ +NGK + SEK +A+ R G FQ L P TA++NV + +KK Sbjct: 57 DDSSL---IINGKNISSLSEKQLAKFRNEHIGFIFQFHQLLPEFTAIENVCIPAF-IKKT 112 Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192 K EA A++ L+ +GL R +H P +LSGG+QQRVA+ARA+ NPSL+ DE + LD Sbjct: 113 PKAEATKRAKELLDFLGLSHRYNHKPNELSGGEQQRVAVARALINNPSLIFADEPSGNLD 172 Query: 193 PELVGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRI 238 E + S+ L ++ G T ++VTH A +++D+ + M G I Sbjct: 173 SESAENLHSLFFKLRDEFGQTFVIVTHNEELA-DLADRKLVMVDGVI 218 Lambda K H 0.319 0.135 0.379 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: 120 Number of extensions: 8 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: 265 Length of database: 220 Length adjustment: 23 Effective length of query: 242 Effective length of database: 197 Effective search space: 47674 Effective search space used: 47674 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: 46 (22.3 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