Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_093395091.1 BM091_RS08820 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_900114975.1:WP_093395091.1 Length = 264 Score = 261 bits (666), Expect = 1e-74 Identities = 130/247 (52%), Positives = 175/247 (70%) Query: 5 EVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLDG 64 E ++LT FGGL AV + +L L GEL+GLIGPNGAGKTT+FN++TG+ P+ G + Sbjct: 10 EARELTMRFGGLVAVNNFSLTLKGGELMGLIGPNGAGKTTVFNMITGMLVPTSGRIIWQD 69 Query: 65 HLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYKS 124 + G PY+I + G+ RTFQNIRLF DLTV+DNV++++ + + + + L L + Sbjct: 70 EDITGYPPYRITAKGIARTFQNIRLFNDLTVIDNVMVSYHHRLRSSFWHAILGLRKYRAE 129 Query: 125 EKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGMNP 184 E++++ +A+E+L+ L A A L YGQQRRLEI RALAT PK+L LDEPAAGMNP Sbjct: 130 EEQMREEAMEILREVGLAHLAGEKAGALPYGQQRRLEIARALATSPKLLLLDEPAAGMNP 189 Query: 185 QETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTNKR 244 QET EL + +R+I+D F +TI LIEHDM VM + ERI VL+YG IA+GTP+EI+ N Sbjct: 190 QETMELAQFVRKIRDRFNLTIFLIEHDMKFVMGLCERIKVLDYGNTIAEGTPEEIQNNPE 249 Query: 245 VIEAYLG 251 VI+AYLG Sbjct: 250 VIKAYLG 256 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: 202 Number of extensions: 6 Number of successful extensions: 1 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: 264 Length adjustment: 24 Effective length of query: 230 Effective length of database: 240 Effective search space: 55200 Effective search space used: 55200 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 24 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