Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 272 bits (695), Expect = 1e-77 Identities = 156/363 (42%), Positives = 215/363 (59%), Gaps = 21/363 (5%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M+ I +++H+ G + + + G +VLLGPSGCGKST LR+IAGLE ++ G Sbjct: 1 MSAIQLLNVSRHW-GDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGR 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + IG V LP +R +AMVFQ+YAL+PH++V +NI FGL K P AE ++R+ Sbjct: 60 IMIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVD 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L ALL+RKP +SGGQQQR A+ RA++ +V L DEPLSNLDAKLR ++R +I+ L Sbjct: 120 ILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRAL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 Q L T VYVTHDQ EAM++ADR+ILMQ GRIVQ +P+ELY P FA FIGTP M Sbjct: 180 QQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLR--HAMAVKLAVRPDHVRIAGEREPAA 298 N + ++ A + G R + + L +RP+H+RI E A Sbjct: 240 NLVR-----------LDDARGSVCVAGSRSGTVSVVDSADYVLGIRPEHIRIVPEGWRAV 288 Query: 299 SLTCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVE 358 VE VE LG+ ++L R G + L+ +V GA + L +H+FD + Sbjct: 289 -------VESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFDAK 341 Query: 359 SGE 361 +GE Sbjct: 342 TGE 344 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: 351 Number of extensions: 18 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: 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