Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate WP_085219373.1 B9N75_RS03075 ABC transporter ATP-binding protein
Query= reanno::BFirm:BPHYT_RS07685 (263 letters) >NCBI__GCF_900177405.1:WP_085219373.1 Length = 233 Score = 127 bits (320), Expect = 2e-34 Identities = 89/221 (40%), Positives = 126/221 (57%), Gaps = 19/221 (8%) Query: 12 LAVQDIHKRYGDN----EVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQ 67 + ++ + K YG + LKGV L+ +G+ ++++G SGSGKST + + L+ P G Sbjct: 7 IRLKGVTKTYGTGATAFQALKGVDLDVAQGEFLAVMGPSGSGKSTAMNILGCLDVPTGGN 66 Query: 68 IVVDGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVL 127 + G V+T DR D + L R R L VFQ FNL A + LEN VE P+ Sbjct: 67 YLFRGVPVET-LDR-------DQRALLR-RKYLGFVFQGFNLLARTSALEN-VELPLLYR 116 Query: 128 GLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTS 187 G ++E LEKVGLA + P+ LSGGQQQRVAIARA+ +PDV+L DEPT Sbjct: 117 GETKEERHKAGMAALEKVGLADWWDHT-PAELSGGQQQRVAIARAIVTHPDVLLADEPTG 175 Query: 188 ALDPELVGEVLKVMQKL-AEEGRTMIVVTHE---MGFARNV 224 LD E E+++++ L G T+++VTHE FAR++ Sbjct: 176 NLDSERSVEIMELLTDLNRNAGITVLMVTHEPEMAAFARSI 216 Lambda K H 0.318 0.133 0.374 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: 151 Number of extensions: 8 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: 263 Length of database: 233 Length adjustment: 24 Effective length of query: 239 Effective length of database: 209 Effective search space: 49951 Effective search space used: 49951 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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