Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_3430 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3430 Length = 249 Score = 193 bits (490), Expect = 3e-54 Identities = 107/239 (44%), Positives = 152/239 (63%), Gaps = 10/239 (4%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 LLQ G++ +YG + L VD+ V +GE+V+L+G NGAGKST + T+ G R GS+ F Sbjct: 12 LLQAKGLQAWYGAAQILYDVDLDVRRGEVVALMGRNGAGKSTTLKTLMGMLAKRKGSIQF 71 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDV------- 123 GRD++R H+ ARL + PE RR+F +TV+ENL++G +H+ + Sbjct: 72 MGRDLSRTDPHDAARLGLGFVPEDRRVFTDLTVMENLEVGR--QPARHWPDGTAAPVWTP 129 Query: 124 EKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIF 183 E++F LFP L E + GG +SGGEQQML++ R LM P L+LLDEPS G+AP+IV+ + Sbjct: 130 ERLFKLFPNLGEMPQRPGGRMSGGEQQMLTVARTLMGNPYLVLLDEPSEGVAPVIVEQMA 189 Query: 184 EAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 I +L E +G+++ L EQN A +S RAYV+ G++ S +EL AN EVR AYL Sbjct: 190 HMILELKE-QGVSILLSEQNMHFAELVSDRAYVLEKGQIRYQASMEELAANDEVRRAYL 247 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: 189 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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 17 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