Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_4983 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4983 Length = 280 Score = 197 bits (501), Expect = 2e-55 Identities = 103/252 (40%), Positives = 153/252 (60%), Gaps = 2/252 (0%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L+V G++ FGG++AL+ VG + G + +IGPNGAGKT+ FN I+G Y P G+ Sbjct: 14 LLQVQGVTLAFGGVKALTGVGFDVLPGSITAVIGPNGAGKTSLFNTISGFYRPSQGSIRF 73 Query: 69 AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128 G+ + A+ G+ R+FQNI LF MT L+N+ +GRH + + A+ + Sbjct: 74 QGQDITRVPAPQRARLGLGRSFQNIALFRGMTVLDNIKLGRHAHLKTNVLDALLYFGRAR 133 Query: 129 AEEAAIAKRAQE-LLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAG 187 EEA + + +E ++D++ I L YG Q+R+E+ARALA PQ++ LDEP AG Sbjct: 134 REEAELRRDIEERIIDFLEIDHIRHAPVSALPYGLQKRVEMARALAMQPQILMLDEPVAG 193 Query: 188 MNATEKVQLRELIDRIRND-NRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246 MN E + I +R + T+L++EHD+ +VM L D V VL++G+ IA+G PA VQ Sbjct: 194 MNREETEDMARFILDVREEWGVTVLMVEHDMGMVMDLSDHVVVLNFGQVIAQGTPAAVQA 253 Query: 247 NEKVIEAYLGTG 258 N +VI AYLG G Sbjct: 254 NPEVIRAYLGAG 265 Lambda K H 0.319 0.137 0.384 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: 189 Number of extensions: 15 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: 260 Length of database: 280 Length adjustment: 25 Effective length of query: 235 Effective length of database: 255 Effective search space: 59925 Effective search space used: 59925 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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