Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 273 bits (698), Expect = 6e-78 Identities = 162/360 (45%), Positives = 223/360 (61%), Gaps = 25/360 (6%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + K + G + +DL I GEF+V +GPSGCGKST+LR+IAGLE I GG+ Sbjct: 1 MAYLQLRGIEKFF-GEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGS 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L + G + D P+ +R++AMVFQ+YALYPHMSVY+N++F L+ K ID +V+ A Sbjct: 60 LMLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAAR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +LNL L+R P+ +SGGQ+QR AI RAI++ P VFLFDEPLSNLDA LR Q R +I +L Sbjct: 120 ILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ L TT+YVTHDQ+EAMTLADRV++++DG I Q G+P ELY P N F A FIGTP M Sbjct: 180 HRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 N + Q Q A A+ + +RP+++ + R A+ Sbjct: 240 NVVPVDKLPQPVQQQAPAAPAGAAVGA-------------IGLRPENITV---RTTGAT- 282 Query: 301 TCPV--SVELVEILGADALL--TTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 PV V+L+E LGA+ L+ TT G Q ++ L + G ++L +D + H FD Sbjct: 283 --PVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDL-RVGDAVSLDIDASQAHWFD 339 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: 361 Number of extensions: 17 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: 406 Length of database: 350 Length adjustment: 30 Effective length of query: 376 Effective length of database: 320 Effective search space: 120320 Effective search space used: 120320 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: 50 (23.9 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