Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate AZOBR_RS25630 AZOBR_RS25630 ABC transporter
Query= TCDB::Q8DQH8 (254 letters) >FitnessBrowser__azobra:AZOBR_RS25630 Length = 255 Score = 218 bits (556), Expect = 7e-62 Identities = 121/253 (47%), Positives = 164/253 (64%), Gaps = 2/253 (0%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 LL+++ +++ FGG+ AV DVT ++EGELVGLIGPNGAGKTTLFNL++G S GTV Sbjct: 4 LLDIRNVSRRFGGVLAVNDVTGHVDEGELVGLIGPNGAGKTTLFNLISGFTPLSSGTVAF 63 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLI-AFGNHHKQHVFTSFLRLPAF 121 DG ++G ++A LG+ RTFQN+R+F +++V DNV + A G + + F L Sbjct: 64 DGRTISGLKTNQVARLGISRTFQNLRVFPNMSVFDNVSVGAVGALPQGALGALFGSLAGG 123 Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181 E+ + E L+ L A LA NL YGQ++ LEI RALA +P+ L LDEPAAG Sbjct: 124 GARSAEISRRTWEALEAVGLTHVAGELAANLPYGQRKYLEIARALAMQPRFLILDEPAAG 183 Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241 +N ET L + I+R+ +TIML+EHDM LVM + +RI VL GR IA G PD I+ Sbjct: 184 LNDTETRALADFIKRLHGT-GLTIMLVEHDMTLVMSICQRILVLASGRKIADGPPDAIRR 242 Query: 242 NKRVIEAYLGGEA 254 + V+EAYLG +A Sbjct: 243 DPAVLEAYLGVDA 255 Lambda K H 0.319 0.139 0.385 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: 187 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: 254 Length of database: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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