Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_035219178.1 G491_RS0116420 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000429905.1:WP_035219178.1 Length = 354 Score = 191 bits (485), Expect = 3e-53 Identities = 123/367 (33%), Positives = 194/367 (52%), Gaps = 72/367 (19%) Query: 8 WIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 + + AV +V PL L ++ + + LY +LAL LN+++GY G+ +G+ AFYA+G Sbjct: 14 YAVVAVVWIVSPLFLDNYQTD---VLNTVGLYAILALSLNVILGYGGMFHMGHAAFYAIG 70 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127 AY A++++ G+ T +W +P+A +LA F ++ P + LRGDY Sbjct: 71 AYTTAILSTQF--------------GVPT-MW-TMPIAGILAGVFALIVARPIIHLRGDY 114 Query: 128 LAIVTLGFGEIIRI------------FLNNLDHPVNL-------------TNGPKGLGQI 162 L IVT+G EI+RI FLN + + T GP G Sbjct: 115 LLIVTIGMVEIVRIAIINDAVSSAAKFLNKGFMLLGIQDWALCEKIANASTGGPNG---- 170 Query: 163 DSVKVFGLDLGKRLEVFGFDINSV---TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAI 219 +FG+ +FGF+IN + T Y++L + ++++ + L+ SR GRA + Sbjct: 171 ----IFGV---AAPSIFGFEINGIVNTTHYFFLITAFLAATILLFFLLERSRYGRALRYL 223 Query: 220 REDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMV 279 DEIAA+ G+NT KL AF +GA + G++G +F F+SP SF+ ESV + +V Sbjct: 224 CSDEIAAEGSGVNTSGYKLSAFVIGAFWAGMAGTLFAGKITFISPTSFTFAESVTLFMIV 283 Query: 280 VLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLL 339 +LGG G+IPGVILGA+L+ LPE+ + D R L+ + ++I+M+L Sbjct: 284 ILGGSGYIPGVILGALLVVGLPEIFQ--------------DFQKWRMLVFGIVLVIMMVL 329 Query: 340 RPRGLWP 346 RP+G+ P Sbjct: 330 RPQGIMP 336 Lambda K H 0.328 0.144 0.430 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: 307 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 354 Length adjustment: 29 Effective length of query: 329 Effective length of database: 325 Effective search space: 106925 Effective search space used: 106925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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