Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate GFF250 PGA1_c02620 high-affinity branched-chain amino acid transport ATP-binding protein LivF
Query= uniprot:D8IUY7 (241 letters) >FitnessBrowser__Phaeo:GFF250 Length = 257 Score = 222 bits (566), Expect = 5e-63 Identities = 110/240 (45%), Positives = 167/240 (69%), Gaps = 3/240 (1%) Query: 1 MTTNILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRV 60 M +L ++ L YG I A++G+ L V G++VT++GANGAGK+T LK I+G + + Sbjct: 1 MGAALLDIRNLESFYGPIMAIRGVSLSVQAGQIVTVLGANGAGKSTLLKTISGIMDPEK- 59 Query: 61 EGHIEYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADI 120 G + + G+ ++G++ +V+ + VPEGR VF +S++ENL +GAYT D+ +I D Sbjct: 60 -GSVSFNGEEIQGEEPHRIVRRGIVHVPEGREVFPLLSVEENLTLGAYTRRDQAEIERDR 118 Query: 121 DKWFAVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIF 180 F FP L ER Q AGTLSGG+QQMLA+ R LM P+++LLDEPS+GLSP++V++IF Sbjct: 119 QMVFDYFPILAERRHQEAGTLSGGQQQMLAIGRGLMLRPRIMLLDEPSLGLSPLLVQEIF 178 Query: 181 EVIRNVSA-QGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLG 239 +++ ++ +G+T++LVEQNA++ALE AH GYVME G I M G A ++++ +K+ YLG Sbjct: 179 GILKRLNRDEGVTMMLVEQNARIALELAHVGYVMEIGRIVMDGSADRLMESEDIKSFYLG 238 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: 183 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: 257 Length adjustment: 24 Effective length of query: 217 Effective length of database: 233 Effective search space: 50561 Effective search space used: 50561 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