Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS28570 AZOBR_RS28570 amino acid ABC transporter ATPase
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__azobra:AZOBR_RS28570 Length = 241 Score = 229 bits (584), Expect = 4e-65 Identities = 121/236 (51%), Positives = 168/236 (71%), Gaps = 4/236 (1%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L V LSV+YG I+A++G+ + V GE+V LIGANGAGK++ L+ ITG +PA+ G + Sbjct: 1 MLTVADLSVSYGPIRALRGVSIRVGAGEIVALIGANGAGKSSLLRGITGLVPAT---GRV 57 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQ-IAADIDKW 123 + G+P+ G + + V +AM PEGR +FT ++ ENLL+G + + Q IAA+ID++ Sbjct: 58 TFDGRPIDGLSTPQRVALGVAMAPEGRQIFTDQTVHENLLLGGHLLRGRPQRIAANIDRF 117 Query: 124 FAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVI 183 +A+FPRL ER Q+AGTLSGGEQQMLA+ARALM+ PKLL+LDEPS+GL+PI+ IF + Sbjct: 118 YALFPRLLERRDQIAGTLSGGEQQMLAIARALMTEPKLLILDEPSLGLAPIITADIFRTL 177 Query: 184 RNVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 + G+TILLVEQ A AL A R YV+E G I ++G A + DPR++ AYLG Sbjct: 178 VGLRRDGMTILLVEQMANQALAIADRAYVLEGGSIVLEGVAATLRRDPRIREAYLG 233 Lambda K H 0.317 0.134 0.365 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: 180 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: 241 Length of database: 241 Length adjustment: 23 Effective length of query: 218 Effective length of database: 218 Effective search space: 47524 Effective search space used: 47524 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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