Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_4983 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4983 Length = 280 Score = 195 bits (495), Expect = 1e-54 Identities = 113/266 (42%), Positives = 164/266 (61%), Gaps = 18/266 (6%) Query: 14 LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73 LL+V+ +++ FGG+ A+ F+ G ITA+IGPNGAGKT++FN I+GFY+P+ G I F Sbjct: 14 LLQVQGVTLAFGGVKALTGVGFDVLPGSITAVIGPNGAGKTSLFNTISGFYRPSQGSIRF 73 Query: 74 NQKSGKQYLLERLPDFRITKEARVA--RTFQNIRLFSGLTVLENLLVAQHNKLMKASGYT 131 + + R+P + AR+ R+FQNI LF G+TVL+N+ + +H L Sbjct: 74 QGQD-----ITRVP---APQRARLGLGRSFQNIALFRGMTVLDNIKLGRHAHLKTN---V 122 Query: 132 ILGLIGVGPYKREAAEA---IELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188 + L+ G +RE AE IE + D I A P LPYG Q+R+E+ARA+ Sbjct: 123 LDALLYFGRARREEAELRRDIEERIIDFLEIDHIRHA--PVSALPYGLQKRVEMARALAM 180 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 P++L LDEP AG+N E+ + + +R E G ++L++EHDM +VM++SDHVVVL +G Sbjct: 181 QPQILMLDEPVAGMNREETEDMARFILDVREEWGVTVLMVEHDMGMVMDLSDHVVVLNFG 240 Query: 249 QKISDGTPDHVKNDPRVIAAYLGVED 274 Q I+ GTP V+ +P VI AYLG D Sbjct: 241 QVIAQGTPAAVQANPEVIRAYLGAGD 266 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: 195 Number of extensions: 10 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: 280 Length adjustment: 26 Effective length of query: 266 Effective length of database: 254 Effective search space: 67564 Effective search space used: 67564 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