Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058859405.1 AS188_RS14300 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_001482365.1:WP_058859405.1 Length = 624 Score = 90.1 bits (222), Expect = 1e-22 Identities = 73/237 (30%), Positives = 125/237 (52%), Gaps = 18/237 (7%) Query: 12 LQVNGVETYYGNIRA-----LAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTG 66 L + GVE +G+ A L G+D+ V G+ V+++G +G+GKSTL + S G Sbjct: 361 LVLAGVEAAHGDPAAGAPTVLRGIDLRVPAGQHVAVVGPSGSGKSTLAALLVRSMDPVAG 420 Query: 67 SVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG------AGLDNLKHFA 120 SV +G D+ R+ + R +A + +F +V EN+++G A ++ A Sbjct: 421 SVSLDGHDL-RLLSLATVRGSVALLLQDSVLF-HGSVRENIRLGRPGATDAEVEQAARAA 478 Query: 121 EDVEKIFTLFPRLKERHA-QRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIV 179 + + FPR + +RG T+SGG++Q L+I RAL+ +++LDE + GL P Sbjct: 479 Q-AHGFVSAFPRGYDTPVGERGSTVSGGQRQRLAIARALLRDAPVVVLDEATTGLDPEAA 537 Query: 180 KGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236 + + A+R+L G T V +A AL + R + +G++ + G+ ELLA+P+ Sbjct: 538 REVVAALRRL--VRGRTSLAVTHDAALALS-ADRVLWLQDGRILLDGTPAELLADPD 591 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: 345 Number of extensions: 16 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: 624 Length adjustment: 30 Effective length of query: 217 Effective length of database: 594 Effective search space: 128898 Effective search space used: 128898 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: 50 (23.9 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