Align ABC transporter (characterized, see rationale)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__ANA3:7023042 Length = 367 Score = 147 bits (371), Expect = 5e-40 Identities = 88/217 (40%), Positives = 130/217 (59%), Gaps = 14/217 (6%) Query: 28 AGEFVVFVGPSGCGKSTLLRLIAGLDS------ICGGDLLIDGRRVNDLEPRERGVGMVF 81 AGE + VGPSG GK+TLLR+IAGL+ + G L D + L P++R +G + Sbjct: 28 AGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTALTPQQRHIGYMP 87 Query: 82 QSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQILQ---LDKLLQRKPKELSGGQ 138 Q + L+P+++ +N+ GL D ER+ + L+ L L R P LSGGQ Sbjct: 88 QHFGLFPNLTALENVVAGL-----DHIPKSERIARAKDWLERVNLHGLPDRLPMHLSGGQ 142 Query: 139 RQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTHDQVEAM 198 RQRVA+ RA+AREP +LL DEP S +D R ++ E+ARL ++L +I VTHD EA+ Sbjct: 143 RQRVALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIMVTHDLNEAL 202 Query: 199 TLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLG 235 LAD +++++ G++ Q G+P E+ RP + VA +G Sbjct: 203 LLADSMILISQGQMLQQGAPFEVLSRPRNEAVARQMG 239 Lambda K H 0.320 0.137 0.394 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: 285 Number of extensions: 13 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: 381 Length of database: 367 Length adjustment: 30 Effective length of query: 351 Effective length of database: 337 Effective search space: 118287 Effective search space used: 118287 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: 50 (23.9 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