Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0842 Dsui_0842 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__PS:Dsui_0842 Length = 593 Score = 186 bits (472), Expect = 1e-51 Identities = 110/260 (42%), Positives = 156/260 (60%), Gaps = 16/260 (6%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL+ E ++ +FGGL+A D + + G++ ALIGPNGAGK+T+FNCI+G P+ G I+F Sbjct: 345 LLQAEGVTKRFGGLVANKDMALTVQAGEVMALIGPNGAGKSTMFNCISGVNPPSEGRISF 404 Query: 74 NQKSGKQYLLERLPDFRITKEAR--VARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 L + + AR ++RTFQ++RL SG+TVLEN+ + H L Y Sbjct: 405 --------LGQPVAGLEARDIARLGLSRTFQHVRLLSGMTVLENVAIGAH--LRGRHNYL 454 Query: 132 ILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPE 191 GL + E A + A +E+ L + D AG L G QR +EIARA+ P Sbjct: 455 AAGL---RLERAEEARLLAEAARQIERVGLAEHMFDAAGSLALGKQRIIEIARALAADPC 511 Query: 192 LLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKI 251 LL LDEPAAGL E L LL+ +R E G ILL+EHDM VM ++D VVV+E+G+K+ Sbjct: 512 LLLLDEPAAGLRYLEKQALAELLRKLRGE-GMGILLVEHDMDFVMGLADRVVVMEFGEKL 570 Query: 252 SDGTPDHVKNDPRVIAAYLG 271 ++G P+ ++ +P V+ AYLG Sbjct: 571 AEGLPEEIQKNPAVLEAYLG 590 Lambda K H 0.318 0.136 0.386 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: 431 Number of extensions: 15 Number of successful extensions: 4 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: 292 Length of database: 593 Length adjustment: 31 Effective length of query: 261 Effective length of database: 562 Effective search space: 146682 Effective search space used: 146682 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 (21.7 bits) S2: 50 (23.9 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