Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013403238.1 CALHY_RS06840 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000166355.1:WP_013403238.1 Length = 234 Score = 267 bits (682), Expect = 2e-76 Identities = 139/235 (59%), Positives = 179/235 (76%), Gaps = 2/235 (0%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+VNG++ YYG I+AL V + V KGEIV+LIGANGAGKSTL+ TI G + RTGS+ F Sbjct: 1 MLKVNGIDVYYGAIQALFSVSLDVQKGEIVTLIGANGAGKSTLLKTISGLIRPRTGSIYF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH-FAEDVEKIFTL 129 E DIT+ + EI +L I+ PEGRR+FP MTVLENL++GA L K ED++K+F Sbjct: 61 EDIDITKKSSMEIVKLGISHVPEGRRVFPEMTVLENLELGAYLRKDKQGIKEDLKKVFER 120 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 FPRL ER Q GTLSGGEQQML+IGRALM+RPKLLLLDEPS+GLAP++V IF+ I+++ Sbjct: 121 FPRLYERKNQLAGTLSGGEQQMLAIGRALMSRPKLLLLDEPSMGLAPILVTEIFKIIKEI 180 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 N ++G T+ L+EQNA AL ++ RAYV+ GK+ +SG KE+ ANPEV+ AYL G Sbjct: 181 N-SQGTTILLIEQNAHMALSIADRAYVIETGKIVLSGDAKEIAANPEVKKAYLGG 234 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: 213 Number of extensions: 6 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: 234 Length adjustment: 23 Effective length of query: 224 Effective length of database: 211 Effective search space: 47264 Effective search space used: 47264 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