Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Echvi_2909 Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Cola:Echvi_2909 Length = 218 Score = 96.7 bits (239), Expect = 3e-25 Identities = 64/217 (29%), Positives = 110/217 (50%), Gaps = 7/217 (3%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+ G+ YYG++ L GVDV + GEIVS++GA+GAGKSTL+ + A G V Sbjct: 1 MLRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSI 60 Query: 71 EGRDITRMPTHEIARLR---IAQSPEGRRIFPRMTVLENLQMGA--GLDNLKHFAEDVEK 125 + + +T + ++A R + + + P T EN+ + + K+ E ++ Sbjct: 61 DDKSLTALKGDKLAAYRNQEVGFIFQFHNLLPEFTAEENIIIPGLIAKKDEKYLTEKAKE 120 Query: 126 IFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEA 185 + L + +R + LSGGEQQ +++ RAL+ PK++ DEPS L + + E Sbjct: 121 LARLL-GIMDRLGHKPSELSGGEQQRVAVARALINDPKIIFADEPSGNLDTQSAESLHEL 179 Query: 186 IRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222 L + G + +V N A +++ R M +G + Sbjct: 180 FFTLRDRFGQSFVIVTHNQQLA-QMADRMLTMQDGVI 215 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: 118 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: 218 Length adjustment: 23 Effective length of query: 224 Effective length of database: 195 Effective search space: 43680 Effective search space used: 43680 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