Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058859179.1 AS188_RS12835 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_001482365.1:WP_058859179.1 Length = 275 Score = 107 bits (266), Expect = 3e-28 Identities = 70/209 (33%), Positives = 114/209 (54%), Gaps = 12/209 (5%) Query: 25 RALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPTHEIA 84 RALAGV + + +G+ +++IG+NGAGKST++ TI G+ +G+V + D+TR+P H+ A Sbjct: 20 RALAGVSLRLEEGDFLTVIGSNGAGKSTILNTISGTLIPDSGTVRVDDHDVTRLPEHKRA 79 Query: 85 RL--RIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDV---------EKIFTLFPRL 133 R R+ Q P + P MTV +N+ + + + EK+ +L L Sbjct: 80 RYLSRVFQDPM-KGSSPTMTVEQNMAIAYQRGKSRGLVPGLTGARRTLFREKLASLELGL 138 Query: 134 KERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAE 193 + R + G LSGG++Q LS+ A + P++LLLDE + L P + ++ + Sbjct: 139 ENRLGAKVGLLSGGQRQALSLLMATFSEPRILLLDEHTAALDPQRADLVSRLTGEIVAEQ 198 Query: 194 GLTVFLVEQNAFAALRLSHRAYVMVNGKV 222 GLT +V N ALRL +R +M G++ Sbjct: 199 GLTTVMVTHNMEQALRLGNRLIMMHEGRI 227 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: 187 Number of extensions: 9 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: 275 Length adjustment: 25 Effective length of query: 222 Effective length of database: 250 Effective search space: 55500 Effective search space used: 55500 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