Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_052892752.1 PATSB16_RS19085 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= uniprot:Q1MCU2 (292 letters) >NCBI__GCF_001931675.1:WP_052892752.1 Length = 598 Score = 190 bits (483), Expect = 6e-53 Identities = 109/263 (41%), Positives = 158/263 (60%), Gaps = 10/263 (3%) Query: 12 DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71 + +L V +FGGL+A+ND SF+ K G+I LIGPNGAGK+T FN +TG + T G I Sbjct: 340 EVILDVRAARKEFGGLVAVNDVSFQVKAGEIVGLIGPNGAGKSTTFNLVTGVLQATSGEI 399 Query: 72 TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 TF+ + +++L I K + RTFQ++RL ++VLEN+ + H + + Sbjct: 400 TFHGER-----IDKLASREIVKRG-IGRTFQHVRLLPTMSVLENVAIGAHLRDRQGLRRR 453 Query: 132 ILGLIGVGPYKREAAEAIEL---ARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188 G + + + AE L A +E+ L + + AG L G QR LEIARA+ Sbjct: 454 PQGGVWSSVLRLDRAEEAMLMHEAARQIERVGLGEHMYEEAGSLALGQQRILEIARALAC 513 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 P LL LDEPAAGL +E L LL+ + ++ G S+LL+EHDM VM ++DH+VV+E+G Sbjct: 514 DPTLLLLDEPAAGLRYKEKQALAELLRKL-SDEGMSVLLVEHDMDFVMNLTDHLVVMEFG 572 Query: 249 QKISDGTPDHVKNDPRVIAAYLG 271 KI++G P+ V+ DP V+ AYLG Sbjct: 573 TKIAEGLPEDVQKDPAVLEAYLG 595 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: 397 Number of extensions: 19 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: 598 Length adjustment: 31 Effective length of query: 261 Effective length of database: 567 Effective search space: 147987 Effective search space used: 147987 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 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