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_011779810.1 MVAN_RS13025 urea ABC transporter ATP-binding protein UrtD
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000015305.1:WP_011779810.1 Length = 277 Score = 150 bits (380), Expect = 2e-41 Identities = 104/255 (40%), Positives = 147/255 (57%), Gaps = 20/255 (7%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 LEV+ LT F G AV DV L L +G+L LIGPNGAGKTT+ + +TG+ P+ G+V Sbjct: 26 LEVRGLTVDFDGFKAVSDVDLTLFQGDLRFLIGPNGAGKTTVIDAITGLV-PATGSVNKS 84 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLR----LP 119 G L GK ++IA G+GRTFQ +F+ LTVL N+ IA G + V+T R LP Sbjct: 85 GVELLGKKVHQIARRGVGRTFQTASVFEQLTVLQNLDIAAG--AGRSVWTLLRRRNGVLP 142 Query: 120 AFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPA 179 A +AL + + L A+ A L++GQ++ LEI L +L LDEP Sbjct: 143 AI--------EQALHTIGLTHL---ADKPAGVLAHGQKQWLEIGMLLVQNADVLLLDEPV 191 Query: 180 AGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 AGM+ +E E L+RRI E T++++EHDM+ + + VL G++IA+G+ E+ Sbjct: 192 AGMSAEEREETGNLLRRIGAE--RTVVVVEHDMDFMRAFATSVTVLARGQVIAEGSVTEV 249 Query: 240 KTNKRVIEAYLGGEA 254 + N +V E YLG A Sbjct: 250 QANPKVQEVYLGTAA 264 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: 174 Number of extensions: 7 Number of successful extensions: 4 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: 277 Length adjustment: 25 Effective length of query: 229 Effective length of database: 252 Effective search space: 57708 Effective search space used: 57708 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