Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__SB2B:6937298 Length = 230 Score = 125 bits (314), Expect = 1e-33 Identities = 78/221 (35%), Positives = 116/221 (52%), Gaps = 12/221 (5%) Query: 4 IHCQALAKHYAGGPP---VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 I QAL K + G L +D+HI EFV ++GPSG GKST++ +I L+ + G Sbjct: 2 ISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSGN 61 Query: 61 LRIGGTVVNDLP------ARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRR 114 + G+ V L R R + VFQ++ L P +S DN+ LR + P + Sbjct: 62 YLLNGSAVGGLSDDALSAVRNREIGFVFQSFHLLPRLSALDNVLLPLRFSETPRGDRQHA 121 Query: 115 VREVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLR 174 + E+ + L L+ +P +SGGQ+QR AIARA++ P++ L DEP LD+K ++ Sbjct: 122 I-ELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTSVEIM 180 Query: 175 GDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQ 215 LH T V VTH++ E A R+I M+DG + Q Sbjct: 181 ALFDELHLS-GQTIVLVTHEE-EVAECAGRIIRMRDGVVQQ 219 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: 215 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: 406 Length of database: 230 Length adjustment: 27 Effective length of query: 379 Effective length of database: 203 Effective search space: 76937 Effective search space used: 76937 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