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_012965553.1 FERP_RS05235 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000025505.1:WP_012965553.1 Length = 235 Score = 176 bits (446), Expect = 4e-49 Identities = 98/249 (39%), Positives = 149/249 (59%), Gaps = 24/249 (9%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +LEV+ + K FG L A+ +++ + + E +G+IGPNGAGKTTLFN+++G +P+ G V Sbjct: 4 ILEVENVKKKFGELVALENISFSVYDKECLGIIGPNGAGKTTLFNIISGHLKPTAGEVYF 63 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFY 122 +G + G P KIA GL RTFQ +++F++LTV +N + Sbjct: 64 NGERITGMRPSKIAKRGLVRTFQILKVFQNLTVEEN-----------------------F 100 Query: 123 KSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGM 182 ++ + A ++K +L LAKNLS G+ R+L I ALA PK+L LDEP +G+ Sbjct: 101 RAAGIERKDAERIMKELNLHERRNVLAKNLSQGEMRKLNIALALAKNPKVLLLDEPFSGL 160 Query: 183 NPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKTN 242 +P E EL +I +K E +T+++IEH + + ER+ VL YG ++ +GTP+EI + Sbjct: 161 SPAECQELHSVIDHLK-ERGVTLVIIEHKLKELFNHAERVIVLNYGYILCEGTPEEIVQD 219 Query: 243 KRVIEAYLG 251 RVIEAYLG Sbjct: 220 VRVIEAYLG 228 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: 180 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: 254 Length of database: 235 Length adjustment: 24 Effective length of query: 230 Effective length of database: 211 Effective search space: 48530 Effective search space used: 48530 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 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