Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_055435910.1 ASC41_RS06935 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21725 (265 letters) >NCBI__GCF_001418085.1:WP_055435910.1 Length = 233 Score = 150 bits (378), Expect = 3e-41 Identities = 94/230 (40%), Positives = 136/230 (59%), Gaps = 14/230 (6%) Query: 15 LLEIRDLHKQY----GPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGG 70 +L+I LHK Y L VLKG+DL+++ G +V ++GSSGSGK+TLL + ML+E G Sbjct: 1 MLKINKLHKSYPIGDSSLHVLKGIDLSVEAGEMVAIMGSSGSGKSTLLNIIGMLDEADEG 60 Query: 71 QILLDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVK 130 + +LD I K + + I +++ + G FQ FNL + AL NV L L + Sbjct: 61 EYILDNVPI-------KNLTEKKAAIYRNKFL-GFIFQSFNLINYKNALDNVALPLY-YQ 111 Query: 131 KLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSA 190 L + E + LE+VGL + H P +LSGGQ+QRVAIARA+A +P L+L DE T A Sbjct: 112 GLKRKERIEKGLFHLEKVGLKDWAHHLPNELSGGQKQRVAIARALAADPKLLLADEPTGA 171 Query: 191 LDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEE 240 LD + E++ I+ L ++G T+L+VTHE A + +IV + G I E Sbjct: 172 LDTKTSHEIMDFIQSLNDEGKTILMVTHEEDIA-SMCKRIVRLKDGVIIE 220 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: 136 Number of extensions: 9 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: 233 Length adjustment: 24 Effective length of query: 241 Effective length of database: 209 Effective search space: 50369 Effective search space used: 50369 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