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_011841980.1 RSPH17029_RS14865 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000015985.1:WP_011841980.1 Length = 233 Score = 167 bits (424), Expect = 1e-46 Identities = 100/252 (39%), Positives = 135/252 (53%), Gaps = 19/252 (7%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 M+LLE + L +HFGGL A+ V +L GE+ LIGPNGAGK+TL LL+G GT+ Sbjct: 1 MSLLEARGLVRHFGGLRAIDGVDFDLAAGEIHALIGPNGAGKSTLVGLLSGRIPAQAGTI 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 DG + + G+ FQ +F LT DNV +A Sbjct: 61 RFDGRDITRLPAHARVGCGIAYAFQITSVFPRLTTFDNVALAVQR--------------- 105 Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180 ++L A L L G+A LA LSYG QR LEI LA P++L LDEP Sbjct: 106 --TGARDLAAATEAALARVGLSGEAGQLAGTLSYGHQRLLEIAMGLALAPRLLILDEPTQ 163 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 G+ E L+R + E +T++LIEH+M +VM++ +RI VL GR++AQGTP EI+ Sbjct: 164 GLASGEIESFMTLVRSLVPE--VTVLLIEHNMEVVMDLAQRITVLNAGRVLAQGTPAEIQ 221 Query: 241 TNKRVIEAYLGG 252 ++ V AYLGG Sbjct: 222 ADRAVQAAYLGG 233 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: 168 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: 233 Length adjustment: 23 Effective length of query: 231 Effective length of database: 210 Effective search space: 48510 Effective search space used: 48510 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: 46 (22.3 bits)
This GapMind analysis is from Apr 10 2024. 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