Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__ANA3:7023042 Length = 367 Score = 150 bits (378), Expect = 8e-41 Identities = 95/275 (34%), Positives = 150/275 (54%), Gaps = 20/275 (7%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 +AD+HCQ + + + GE + ++GPSG GK+T+LRMIAGL G+ Sbjct: 5 IADLHCQIQNHKH-----IKLSAEFSCKAGEVLAVVGPSGGGKTTLLRMIAGLNHPDAGS 59 Query: 61 LRIGGTVVND------LPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRR 114 + G T+ D L ++R++ + Q++ L+P+++ +N+ GL + P +E R Sbjct: 60 IVFGETLWFDHQSRTALTPQQRHIGYMPQHFGLFPNLTALENVVAGLDHI--PKSERIAR 117 Query: 115 VREVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLR 174 ++ +NL L +R P +SGGQ+QR A+ARA+ + PSV L DEP S +D + R +L Sbjct: 118 AKDWLERVNLHGLPDRLPMHLSGGQRQRVALARALAREPSVLLLDEPFSAVDRETRERLY 177 Query: 175 GDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGF 234 ++ RL ++L + VTHD EA+ LAD +IL+ G+++Q G+P E+ PRN A Sbjct: 178 LELARLKEQLLCPVIMVTHDLNEALLLADSMILISQGQMLQQGAPFEVLSRPRNEAVARQ 237 Query: 235 IGTPAMNFLSGTVQRQDGQLFIETAHQRWALTGER 269 +G N G V QD T W GE+ Sbjct: 238 MG--LRNIFDGEVVFQD-----RTKDITWLKFGEQ 265 Lambda K H 0.321 0.137 0.403 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: 293 Number of extensions: 9 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: 406 Length of database: 367 Length adjustment: 30 Effective length of query: 376 Effective length of database: 337 Effective search space: 126712 Effective search space used: 126712 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