Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__Putida:PP_1722 Length = 329 Score = 224 bits (571), Expect = 2e-63 Identities = 133/328 (40%), Positives = 190/328 (57%), Gaps = 8/328 (2%) Query: 1 MGQIKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTI 60 M + ++ + K++ V +D IE GEF +GPSGCGKSTLLR IAGL + SG I Sbjct: 1 MSFVSVQKLQKSYAGSPVFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSGQI 60 Query: 61 RIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAA 120 +DG D + P KRG+ MVFQSYAL+P+M+V +N+AF ++M + ADE + R+ Sbjct: 61 LLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVLEL 120 Query: 121 LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH 180 + L + R P QLSGGQ QRVA+ R++V P L DEPLS LDA +R +R +I + Sbjct: 121 VELGKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRAIQ 180 Query: 181 KRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMN 240 + L T I+VTHDQ EA+TM+D+I ++ G I Q G LY AP ++F AGFIG+ N Sbjct: 181 RELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIGN--YN 238 Query: 241 LLTGPQAA----QHNAATIGIRPEHLSISETEGMWAGTIGVSEHLGSDTFFHVQCDAFDD 296 LL A+ + A+ + IRPE +++ E G + LG+ + V+ + Sbjct: 239 LLDADSASRLLQRPVASRLAIRPESITLGE-HGELDAEVRSHSLLGNVIRYRVRVREVEL 297 Query: 297 PLTVRASGELDL-GYGERVFLTPDMTHL 323 + V DL G+RV ++ D T L Sbjct: 298 VVDVLNRSPADLHADGKRVSVSIDPTAL 325 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: 268 Number of extensions: 10 Number of successful extensions: 1 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: 329 Length adjustment: 28 Effective length of query: 306 Effective length of database: 301 Effective search space: 92106 Effective search space used: 92106 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