Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_028584457.1 G494_RS0110165 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000429965.1:WP_028584457.1 Length = 235 Score = 258 bits (658), Expect = 1e-73 Identities = 129/233 (55%), Positives = 173/233 (74%), Gaps = 1/233 (0%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L++ ++TYYGNI+AL +D+ V GEI++LIGANGAGKST +M+I G R+G ++F Sbjct: 1 MLELRNIDTYYGNIQALHQIDLTVEAGEIITLIGANGAGKSTTLMSISGISPPRSGEIIF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH-FAEDVEKIFTL 129 +G+ I +P ++I L I+Q PEGR IFP +TV ENL MGA L N K A+D+E ++ L Sbjct: 61 KGKPIHELPANKIVTLGISQVPEGRHIFPELTVAENLDMGAFLRNDKRGIADDLEYLYDL 120 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FP L++R Q GG LSGGEQQML+I RALMA P+LLLLDEPS+GLAPL+ K IFE I K+ Sbjct: 121 FPILRKRRNQPGGNLSGGEQQMLAISRALMAHPQLLLLDEPSMGLAPLVTKQIFEIIEKI 180 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 N + T+FLVEQNA AL+++HR YV+ NG++TM +LLAN +V+ AYL Sbjct: 181 NREQNTTIFLVEQNANLALQIAHRGYVLENGRITMHDQADKLLANKDVQKAYL 233 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: 205 Number of extensions: 5 Number of successful extensions: 2 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: 235 Length adjustment: 23 Effective length of query: 224 Effective length of database: 212 Effective search space: 47488 Effective search space used: 47488 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: 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