Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 7025948 Shewana3_3096 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__ANA3:7025948 Length = 378 Score = 115 bits (287), Expect = 2e-30 Identities = 70/230 (30%), Positives = 127/230 (55%), Gaps = 6/230 (2%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 LL++ V + ++RA+ V + +NKGEI +L+G +G+GKSTL+ + G + +G + Sbjct: 20 LLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIFL 79 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNL--KHFAEDVEKIFT 128 +G DIT +P +E + QS +FP MTV +N+ G D L + V+++ Sbjct: 80 DGEDITDLPPYERPINMMFQS---YALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLK 136 Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188 L +++ ++ LSGG++Q +++ R+L RPKLLLLDEP L + + + + Sbjct: 137 LV-HMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVE 195 Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVR 238 + E G+T +V + A+ ++ R +M +G + +GS ++ +P R Sbjct: 196 ILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSR 245 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: 227 Number of extensions: 14 Number of successful extensions: 4 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: 378 Length adjustment: 27 Effective length of query: 220 Effective length of database: 351 Effective search space: 77220 Effective search space used: 77220 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: 48 (23.1 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