Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_900141795.1:WP_074200832.1 Length = 227 Score = 118 bits (295), Expect = 1e-31 Identities = 88/236 (37%), Positives = 134/236 (56%), Gaps = 23/236 (9%) Query: 15 LLEIRDLHKQY--GPLE--VLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 +LE R+L K Y GP E VLKGV L + R V ++GSSGSGK+TLL + L+ G Sbjct: 5 VLEGRNLVKTYRDGPAETPVLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDG 64 Query: 71 QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLL--- 127 ++LL G+ ++ + + ++R M G +Q +L P LTA +NV + LL Sbjct: 65 EVLLLGQPFS-------KLGEAARGRLRNRHM-GFVYQFHHLLPELTAEENVMMPLLIRR 116 Query: 128 KVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEV 187 + + +D+A+ L L+ VGL R H P +LSGG++QRVA+ARA+ P +L DE Sbjct: 117 ESEATARDKALAL----LDAVGLSRRTAHKPSELSGGERQRVALARALVTEPDCVLADEP 172 Query: 188 TSALDPELVGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQG--RIEE 240 T LD +VLS++ L + G +L+VTH++ A + D+ + + G R+EE Sbjct: 173 TGNLDSRSAEQVLSLMDDLNQRFGTALLVVTHDVNIAARM-DRTLTLRDGMIRVEE 227 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: 149 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: 227 Length adjustment: 24 Effective length of query: 241 Effective length of database: 203 Effective search space: 48923 Effective search space used: 48923 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 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