Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate WP_047094318.1 AAV99_RS11970 ABC transporter ATP-binding protein
Query= uniprot:Q88GX0 (260 letters) >NCBI__GCF_001013305.1:WP_047094318.1 Length = 240 Score = 151 bits (382), Expect = 1e-41 Identities = 89/217 (41%), Positives = 126/217 (58%), Gaps = 7/217 (3%) Query: 20 LIRIEGLNKHYG----AFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQG 75 LI +EG+ K +G AF L+ +D+++ G+ + + GPSGSGKST + + L+V G Sbjct: 6 LIELEGITKTFGKGPAAFQALKGVDMKIDRGDFVAIMGPSGSGKSTTMNILGCLDVPTDG 65 Query: 76 SIQVDGIDLAATTREAAQV--RSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAE 133 + GI++ A TR+ + R +G VFQ FNL + L+N L P RG ++K Sbjct: 66 IFRFRGIEVQALTRDQRSLLRRRYLGFVFQGFNLLARTTALENVEL-PLLYRGETKKQRR 124 Query: 134 ERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAE 193 A L KVG+ A P++LSGGQQQRVAIARAL P ++L DEPT LD E E Sbjct: 125 IAAERSLDKVGLLPWASHTPAELSGGQQQRVAIARALVTDPDVLLADEPTGNLDTERSLE 184 Query: 194 VLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEG 230 ++++L L+ TG+T+L VTHE A V F +G Sbjct: 185 IMELLTDLSDTGITVLMVTHEEEMAEYARTIVHFRDG 221 Lambda K H 0.322 0.137 0.395 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: 145 Number of extensions: 6 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: 260 Length of database: 240 Length adjustment: 24 Effective length of query: 236 Effective length of database: 216 Effective search space: 50976 Effective search space used: 50976 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 (21.9 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