Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_3213 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3213 Length = 236 Score = 199 bits (507), Expect = 3e-56 Identities = 107/234 (45%), Positives = 155/234 (66%), Gaps = 5/234 (2%) Query: 6 LKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHIE 65 L VQ L+ Y G Q ++ + L+ G + ++G NGAGKTT LKA+ G LP + G + Sbjct: 6 LTVQNLTTGYHGFQVLQDLSLQAAPG-ITVIVGPNGAGKTTLLKALAGLLPRT---GTVA 61 Query: 66 YLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWFA 125 G L + V+ LA+V EGR +F +M++ ENL +G + + + A + + F Sbjct: 62 LDGSDLPAMNATACVQRGLALVAEGRQLFPQMTVTENLELGGWLVPSRTR-ADRLAQAFE 120 Query: 126 VFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIRN 185 FPRLKERA Q+AGT+SGGEQQM+A+ARALMS P+LL+LDEPS+GL+P MV+++ +++ Sbjct: 121 DFPRLKERATQLAGTMSGGEQQMVAVARALMSGPRLLMLDEPSLGLAPRMVDELLAIVQR 180 Query: 186 VSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 ++AQG+T+L+VEQN + AL+ A RGYV+E G I G A +L V+ AYLG Sbjct: 181 IAAQGVTVLMVEQNVRKALQIAQRGYVLERGRIVASGAASDLLQSDVVRQAYLG 234 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: 167 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: 241 Length of database: 236 Length adjustment: 23 Effective length of query: 218 Effective length of database: 213 Effective search space: 46434 Effective search space used: 46434 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