Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3454 PS417_17680 ABC transporter
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__WCS417:GFF3454 Length = 231 Score = 176 bits (446), Expect = 4e-49 Identities = 100/232 (43%), Positives = 140/232 (60%), Gaps = 5/232 (2%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L V + +YY L GV + VN GE+V+L+G NGAGK+T + +I G R G + F Sbjct: 1 MLIVENIHSYYDKSHVLEGVSLTVNPGELVTLLGRNGAGKTTTLRSILGIICPRKGQIHF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130 G+ + EIAR +A PE R IF +TV ENL++ K +E ++ +F Sbjct: 61 NGQALVGQKIFEIARQGLALVPENRGIFRLLTVEENLRIATR----KTSRWQLEDVYGMF 116 Query: 131 PRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLN 190 PRLKER G LSGGEQQML+I RAL+ PKLL+LDEP+ GLAP+IV + + +RK+ Sbjct: 117 PRLKERRKNAGHALSGGEQQMLAIARALLNDPKLLILDEPTEGLAPVIVDELVKILRKVK 176 Query: 191 EAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242 + +GL V LVEQN +L+ R YV+ G+V GS + A+P ++ YL Sbjct: 177 D-DGLPVLLVEQNLMVCDKLADRHYVLEQGRVVYEGSAEAFRADPTIKNRYL 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: 176 Number of extensions: 4 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: 231 Length adjustment: 23 Effective length of query: 224 Effective length of database: 208 Effective search space: 46592 Effective search space used: 46592 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 17 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