Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011767164.1 AZO_RS17290 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000061505.1:WP_011767164.1 Length = 280 Score = 192 bits (487), Expect = 8e-54 Identities = 104/241 (43%), Positives = 150/241 (62%), Gaps = 8/241 (3%) Query: 10 PLLQVNGVETYYGN-IRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTG-- 66 P L +N VE Y + I L GV + V +G IV+L+GANGAGKST + +I +A G Sbjct: 16 PYLSINNVEVIYDHVILVLKGVSLEVPQGSIVALLGANGAGKSTTLKSISNLLRAERGDV 75 Query: 67 ---SVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH--FAE 121 S+ F+G + +M +E+ + + Q EGR F +T+ ENL GA ++ + Sbjct: 76 TKGSIEFKGARVDQMTPNELVKRGVIQVMEGRHCFGHLTIEENLLTGAYTRSISRAELKD 135 Query: 122 DVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKG 181 ++EK++ FPRLK R + G SGGEQQM +IGRALMA+P+++LLDEPS+GLAP IV+ Sbjct: 136 NLEKVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEE 195 Query: 182 IFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAY 241 IFE ++ LN E ++ L EQN ALR + Y+M NG++ M G+ K+L N +V+ Y Sbjct: 196 IFEIVKDLNSKERVSFLLAEQNTMVALRYADFGYIMENGRIVMEGAAKDLATNEDVKEFY 255 Query: 242 L 242 L Sbjct: 256 L 256 Lambda K H 0.320 0.137 0.387 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: 190 Number of extensions: 13 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: 247 Length of database: 280 Length adjustment: 25 Effective length of query: 222 Effective length of database: 255 Effective search space: 56610 Effective search space used: 56610 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 (21.8 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