Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_012964620.1 FERP_RS00405 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000025505.1:WP_012964620.1 Length = 248 Score = 201 bits (510), Expect = 1e-56 Identities = 108/246 (43%), Positives = 156/246 (63%), Gaps = 14/246 (5%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICG-------SPQA 63 +L+ N + +Y N A+ VD+ V +GEIV L G NGAGKSTLM TI G + Sbjct: 1 MLKTNELTVFYENAIAVNNVDIEVEEGEIVGLFGPNGAGKSTLMYTISGIILDKKKKEEM 60 Query: 64 RTGS-------VVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL 116 R G + +E +DIT + ++ A + I PE RR+FP +V+ENL++G L + Sbjct: 61 RGGERITILGRIEYEKKDITFLKPNKRAEMGIILCPERRRVFPESSVVENLKIGGYLRSW 120 Query: 117 KHFAEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAP 176 + ED+EK+F +FP L++ + G LSGGEQQML+I RALMA+PKLLLLDEP LGLAP Sbjct: 121 REVKEDIEKMFEIFPELEKHKNKPAGFLSGGEQQMLAIARALMAKPKLLLLDEPLLGLAP 180 Query: 177 LIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236 L+ K I E ++++ + G+TV + EQ A + R Y++ G ++ SG+ +EL++NP Sbjct: 181 LVQKRIVEVVKRIRDELGVTVLVAEQYARPVFPIIDRGYIIERGTISFSGTSEELMSNPN 240 Query: 237 VRAAYL 242 V+AAYL Sbjct: 241 VKAAYL 246 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: 181 Number of extensions: 6 Number of successful extensions: 2 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: 248 Length adjustment: 24 Effective length of query: 223 Effective length of database: 224 Effective search space: 49952 Effective search space used: 49952 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