Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1937 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1937 Length = 279 Score = 201 bits (512), Expect = 1e-56 Identities = 107/267 (40%), Positives = 164/267 (61%), Gaps = 4/267 (1%) Query: 9 MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68 M++DTLL ++LS++FGG++A+N+ SF+ +RG++ LIGPNGAGKTTVFN I+ Y PT Sbjct: 1 MTNDTLLSAQNLSVRFGGVLAVNNVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYTPTT 60 Query: 69 GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128 G I + G L P ++ +ARTFQNI LF +VL NLL+ +H + + Sbjct: 61 GTIAYAGPGGAMLPLTDQPPHKVASLG-IARTFQNIELFEHASVLHNLLIGRHTQQHSSL 119 Query: 129 GYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188 + V + +A E E ++ DL D LPYG ++ +E+ARA+CT Sbjct: 120 WAEMFFTRKVREGEIQAREKAEQI---IDFLDLQHYRDTMVAGLPYGVRKVVELARALCT 176 Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248 P+LL LDEP++GLN E+ + ++ I+ E G ++L++EHDMS+V ++SD V+ + G Sbjct: 177 EPKLLLLDEPSSGLNVEETDDMAFWIQDIQHELGITVLMVEHDMSLVSKVSDRVLAMNQG 236 Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDE 275 + ++ GTP V+ P V+ AYLG D+ Sbjct: 237 EVVAMGTPREVQTHPGVVEAYLGTIDD 263 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: 209 Number of extensions: 11 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: 279 Length adjustment: 26 Effective length of query: 266 Effective length of database: 253 Effective search space: 67298 Effective search space used: 67298 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