Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PP_1137 PP_1137 high-affinity branched-chain amino acid transporter, ATP binding
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Putida:PP_1137 Length = 233 Score = 245 bits (626), Expect = 5e-70 Identities = 122/235 (51%), Positives = 172/235 (73%), Gaps = 3/235 (1%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +LK + +S YG IQA+ +++E+N+GE+VTLIGANGAGK+T L + G+ A G I Sbjct: 1 MLKFENVSTFYGKIQALHSVNVEINQGEIVTLIGANGAGKSTLLMTLCGSPQAH--SGSI 58 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 +YLG+ L G+ S +++ +A+VPEGR VF R++++ENL MG + +D KG +DK Sbjct: 59 KYLGEELVGQPSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD-KGDYQEQLDKVL 117 Query: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184 +FPRLKER Q GT+SGGEQQMLA+ RALMS PKLLLLDEPS+GL+PI++++IF++I Sbjct: 118 QLFPRLKERYIQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIE 177 Query: 185 NVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 + G+T+ LVEQNA AL+ A R YV+E+G + MQG + +L DP+V+ AYLG Sbjct: 178 QLRRDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVRDAYLG 232 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: 198 Number of extensions: 10 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: 233 Length adjustment: 23 Effective length of query: 218 Effective length of database: 210 Effective search space: 45780 Effective search space used: 45780 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