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_043529643.1 JH15_RS09320 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000759345.1:WP_043529643.1 Length = 247 Score = 174 bits (441), Expect = 2e-48 Identities = 104/250 (41%), Positives = 145/250 (58%), Gaps = 7/250 (2%) Query: 2 ALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVT 61 A+LE++ L K FG L A DVTL+L GE+ LIGPNGAGK+TL + G P EG + Sbjct: 4 AVLELRNLHKRFGALQATRDVTLDLRPGEIHALIGPNGAGKSTLIGQIAGHIAPDEGQIR 63 Query: 62 LDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAF 121 L + G S + A GLGR+FQ L L+VL NV++A Q + R Sbjct: 64 LSAEDITGLSVAERARRGLGRSFQVSSLADSLSVLRNVMVAV-----QAIQGHSFRFWKP 118 Query: 122 YKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAG 181 + L A + L A+T LS+G++R++E+ ALA P+ L LDEP AG Sbjct: 119 VDRDASLIEPARAAIARMQLSSRADTPVSELSHGERRQVEVACALALNPRALLLDEPMAG 178 Query: 182 MNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIKT 241 + P+ + +LTEL+ +K ++ I+LIEHDM+ V + +R+ VL G +IA GT DEI+T Sbjct: 179 LGPEGSLKLTELLETLK--LEVPILLIEHDMDAVFRLADRVTVLVSGEVIAHGTCDEIRT 236 Query: 242 NKRVIEAYLG 251 + RV EAYLG Sbjct: 237 HPRVREAYLG 246 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: 144 Number of extensions: 6 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: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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