Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_4630 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4630 Length = 274 Score = 214 bits (544), Expect = 2e-60 Identities = 112/267 (41%), Positives = 164/267 (61%), Gaps = 9/267 (3%) Query: 5 VTNTMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFY 64 +T D +L V+++S++FGG+ A+ D SF K +I A+IGPNGAGK+++ NCI G Y Sbjct: 14 MTTKKIGDVILDVKNISLRFGGVKALTDISFNVKEHEIRAIIGPNGAGKSSMLNCINGVY 73 Query: 65 KPTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKL 124 P G ITF K+ + R E VARTFQN+ LF G++V++N++ ++ Sbjct: 74 TPQDGSITFRGKTFSHM------NSRQVAEMGVARTFQNLALFKGMSVIDNIMTGRN--- 124 Query: 125 MKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIAR 184 +K L + +GP +RE E ++ ++ P G LPYG Q+R+++ R Sbjct: 125 LKIKSNLFLQALRLGPAEREEMAHREKVEHIIDFLEIQAFRKTPVGQLPYGLQKRVDLGR 184 Query: 185 AMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVV 244 A+ P++L LDEP AG+N E + + + E GT+I+LIEHDM VVM+ISD VVV Sbjct: 185 ALAMEPQVLLLDEPMAGMNVEEKQDMCRFILDVNDEFGTTIVLIEHDMGVVMDISDRVVV 244 Query: 245 LEYGQKISDGTPDHVKNDPRVIAAYLG 271 L+YG+KI DGTPD V+N+ VI+AYLG Sbjct: 245 LDYGKKIGDGTPDEVRNNQDVISAYLG 271 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: 202 Number of extensions: 12 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: 292 Length of database: 274 Length adjustment: 26 Effective length of query: 266 Effective length of database: 248 Effective search space: 65968 Effective search space used: 65968 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: 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