Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085772365.1 B1812_RS15290 ATP-binding cassette domain-containing protein
Query= reanno::Phaeo:GFF1302 (334 letters) >NCBI__GCF_002117405.1:WP_085772365.1 Length = 257 Score = 146 bits (368), Expect = 6e-40 Identities = 90/246 (36%), Positives = 134/246 (54%), Gaps = 9/246 (3%) Query: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 IKL+ V+K++ + V+ + LT+ G T +G SG GKSTLL LI GLE G +RI Sbjct: 2 IKLDKVSKSYDALRVLDDVSLTLAQGCTTAVMGLSGSGKSTLLALIVGLEAPDQGEVRI- 60 Query: 64 GEDATNIPPA-----KRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAA 118 G+D + PA +R + V Q L+PH++ R+NI + G A + +R+ Sbjct: 61 GDD--RMAPASALNLRRRMGYVIQDGGLFPHLTARRNIELMSRELGWRAARRSKRLQELC 118 Query: 119 AALNL-TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEIS 177 + L+R P +LSGGQRQRV++ RA++ +P L DEPL LD R ++ ++ Sbjct: 119 TLTRFPAEALERYPAELSGGQRQRVSLMRALMLDPPILLLDEPLGALDPMTRARLQEDLK 178 Query: 178 ELHKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSP 237 + + L T++ VTHD EA + D IV L G + Q GS +L AP + F+ FI + Sbjct: 179 SIFRTLKKTVVIVTHDVSEAAFLGDTIVFLHQGRVLQQGSFRDLIAAPADPFITEFIRAQ 238 Query: 238 KMNLLT 243 L T Sbjct: 239 ASRLAT 244 Lambda K H 0.320 0.138 0.400 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: 189 Number of extensions: 7 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: 334 Length of database: 257 Length adjustment: 26 Effective length of query: 308 Effective length of database: 231 Effective search space: 71148 Effective search space used: 71148 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 Apr 09 2024. 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