Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013403237.1 CALHY_RS06835 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000166355.1:WP_013403237.1 Length = 256 Score = 125 bits (315), Expect = 6e-34 Identities = 81/255 (31%), Positives = 132/255 (51%), Gaps = 24/255 (9%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L++ V +G I AL V++ + KG I+ LIG NGAGK+T+ I G TG + F Sbjct: 1 MLRIKNVTVNFGGIVALNNVNIDIEKGAIIGLIGPNGAGKTTVFNVISGIYNPNTGRIEF 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMG----------AGLDNLKHF- 119 DIT T++++ L I+++ + R+F ++V++N+++ + F Sbjct: 61 SNYDITYKKTYQVSALGISRTFQNIRLFKELSVIDNVKISFHKNISYNLFDAIFRTSKFL 120 Query: 120 ---------AEDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEP 170 AE++ KIF L+ E+ + L GEQ+ L I RAL PKLLLLDEP Sbjct: 121 KEEEQNHKKAEELLKIFGLY----EKRFELAKNLPYGEQRKLEIVRALATSPKLLLLDEP 176 Query: 171 SLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKE 230 + G+ P + + + I+ + E LT+ L+E + + + + YV+ G+V G+ E Sbjct: 177 AAGMNPQETQELKKLIKFIKERFDLTILLIEHDMSVVMDICEKIYVLDYGEVIAVGTPVE 236 Query: 231 LLANPEVRAAYLEGG 245 + NP V AYL G Sbjct: 237 VKNNPRVIEAYLGEG 251 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: 144 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: 256 Length adjustment: 24 Effective length of query: 223 Effective length of database: 232 Effective search space: 51736 Effective search space used: 51736 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