Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_085931136.1 AZO_RS15300 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000061505.1:WP_085931136.1 Length = 241 Score = 189 bits (481), Expect = 3e-53 Identities = 104/234 (44%), Positives = 150/234 (64%), Gaps = 5/234 (2%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 L++ G+ TYYG L GV+ H+ KGE + L+G NG GK+TL+ T+ G R G V+ Sbjct: 9 LIEAIGLHTYYGASHILHGVNFHIRKGEALGLMGRNGMGKTTLIRTMLGFVNPRAGGVLV 68 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG--AGLDNLKHFAEDVEKIFT 128 G+ +T PT++IARL IA PEGR IFP ++V ENL M AG++ + + D ++ Sbjct: 69 RGQRMTGGPTYKIARLGIAYVPEGRGIFPNLSVRENLNMAARAGVEGQRDWTFD--RVMH 126 Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188 FPRL ER GG LSGGEQQML+IGRALM P LL+LDE + GLAPLIV+ I+ IR+ Sbjct: 127 TFPRLAERINNGGGQLSGGEQQMLTIGRALMTNPDLLILDEATEGLAPLIVREIWRVIRE 186 Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + ++ G+ +V++N A ++ R+ ++V G+V G +E+ NPE+ +L Sbjct: 187 IRDS-GIATVVVDKNHAAVTAITDRSMILVKGQVVFDGPSEEVRNNPELIQKHL 239 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: 207 Number of extensions: 9 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: 241 Length adjustment: 24 Effective length of query: 223 Effective length of database: 217 Effective search space: 48391 Effective search space used: 48391 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