Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 147 bits (372), Expect = 3e-40 Identities = 88/213 (41%), Positives = 120/213 (56%), Gaps = 8/213 (3%) Query: 29 GEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIR------IDGEDATNIPPAKRGLAMVFQ 82 GE VGPSG GKSTL+R+IAGL SG IR E + P +R L V Q Sbjct: 29 GEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQRHLGYVPQ 88 Query: 83 SYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNLTDYLDRRPGQLSGGQRQRV 142 + L+P+M+ N+ + IP E+ R + +NL DR P LSGGQRQRV Sbjct: 89 HFGLFPNMTALANVVAALDH--IPKAERVARAKDWLERVNLHGLPDRLPANLSGGQRQRV 146 Query: 143 AIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRLATTMIYVTHDQVEAMTMAD 202 A+ RA+ REP L DEP S +D R + LE++ L ++LA +I VTHD EA+ +AD Sbjct: 147 ALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDLNEALLLAD 206 Query: 203 KIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIG 235 +++++ G + Q GSP E+ PRN VA +G Sbjct: 207 RMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239 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: 245 Number of extensions: 11 Number of successful extensions: 2 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: 369 Length adjustment: 29 Effective length of query: 305 Effective length of database: 340 Effective search space: 103700 Effective search space used: 103700 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: 49 (23.5 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