Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058929664.1 AU252_RS04340 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_001484605.1:WP_058929664.1 Length = 257 Score = 180 bits (456), Expect = 3e-50 Identities = 94/228 (41%), Positives = 145/228 (63%), Gaps = 2/228 (0%) Query: 15 NGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRD 74 N V Y + L G ++ KGE++ +IG NGAGKSTL+ + G + +G+VV G+D Sbjct: 24 NLVAGYLPGVNILNGCNIEARKGELIGIIGPNGAGKSTLLKAMFGLVKVHSGTVVVRGQD 83 Query: 75 ITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFPRLK 134 IT + +++ + + P+ +F +T+ EN+QMG K FAE + + +LFP L Sbjct: 84 ITGLKANKLVTMGVGFVPQNNNVFATLTIEENMQMGM-FQRPKDFAERFDFVTSLFPELG 142 Query: 135 ERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEG 194 +R AQR G+LSGGE+QM+++GRALM P +LLLDEPS GL+P+ F + ++N A G Sbjct: 143 KRRAQRAGSLSGGERQMVAMGRALMMEPAVLLLDEPSAGLSPVKQDETFLRVHEINRA-G 201 Query: 195 LTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 ++V +VEQNA L++ RAYV+ G+ +G+G+EL+ +P+V YL Sbjct: 202 VSVIMVEQNARRCLQICDRAYVLDQGRDAYTGTGRELMKDPKVIQLYL 249 Lambda K H 0.320 0.137 0.387 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: 167 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: 247 Length of database: 257 Length adjustment: 24 Effective length of query: 223 Effective length of database: 233 Effective search space: 51959 Effective search space used: 51959 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