Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1936 Length = 272 Score = 226 bits (575), Expect = 5e-64 Identities = 116/236 (49%), Positives = 168/236 (71%), Gaps = 3/236 (1%) Query: 5 ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64 +L++Q + AYG I+A++G+ L+V GE+ ++G+NGAGKTT LK I+G + + G I Sbjct: 20 LLRLQNVESAYGPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRK--GSI 77 Query: 65 EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124 E+ GQ + + +V+ L VPEGR VF +S+++NLLMGAYT DK +A DI+ F Sbjct: 78 EFQGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVF 137 Query: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184 FP LKERAAQ AG LSGG+QQMLA++RALM+ P+L+LLDEPS+GLSP + ++IFE++ Sbjct: 138 GYFPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVV 197 Query: 185 NVSAQ-GITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 ++ + G TILLVEQNA +AL A+ GYV+E+G I M+ +++ + +K YLG Sbjct: 198 RINRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYLG 253 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: 184 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: 272 Length adjustment: 24 Effective length of query: 217 Effective length of database: 248 Effective search space: 53816 Effective search space used: 53816 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: 47 (22.7 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