Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6937298 Sama_1468 putative macrolide efflux ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__SB2B:6937298 Length = 230 Score = 169 bits (429), Expect = 5e-47 Identities = 100/221 (45%), Positives = 129/221 (58%), Gaps = 9/221 (4%) Query: 5 LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64 + + + K F GD V+ LR VDIH+ EF+ ++GPSG GKSTL+NII LD PT G Sbjct: 2 ISLQALTKSFRMGDAEVQALRGVDIHIRQNEFVAIMGPSGSGKSTLMNIIGCLDRPTSGN 61 Query: 65 IRIGGKNVVGMPP------RDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118 + G V G+ R+R+I VFQS+ L P LS DN+ L + P+ +RQ Sbjct: 62 YLLNGSAVGGLSDDALSAVRNREIGFVFQSFHLLPRLSALDNVLLPLRFSETPRGDRQHA 121 Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178 I E+ + + LD RP+QLSGGQRQRVA+ RAL +P L L DEP LD+K VE+ Sbjct: 122 I-ELLERVGLGQRLDHRPNQLSGGQRQRVAIARALVNRPTLLLADEPTGALDSKTSVEIM 180 Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQ 219 A LH SG T V VTH++ E RI M+ GVVQQ Sbjct: 181 ALFDELH-LSGQTIVLVTHEE-EVAECAGRIIRMRDGVVQQ 219 Lambda K H 0.318 0.135 0.388 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: 204 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: 355 Length of database: 230 Length adjustment: 26 Effective length of query: 329 Effective length of database: 204 Effective search space: 67116 Effective search space used: 67116 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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