Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= uniprot:D8IPI1 (406 letters) >lcl|FitnessBrowser__Dino:3607842 Dshi_1250 ABC transporter related (RefSeq) Length = 351 Score = 291 bits (745), Expect = 2e-83 Identities = 165/364 (45%), Positives = 223/364 (61%), Gaps = 16/364 (4%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M+ I + K Y G V+H +DL I DGEF V +GPSGCGKST+LRMIAGLE+ S G+ Sbjct: 1 MSGITLRGAVKRY-GETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGS 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 + IG V L ER VAMVFQ YALYPHM+V +N+ FGL+ P AEI +V + Sbjct: 60 IHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASE 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L+ L RKP+A+SGGQ+QR AI RAI++ P VFLFDEPLSNLDA+LR ++R +I RL Sbjct: 120 ILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ + T +YVTHDQ+EAMTLAD++++++ GR+ Q G+P ELYR P N+F AGFIG+PAM Sbjct: 180 HKEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 NFL G ++ + H + V + VRP H+ + EP Sbjct: 240 NFLDGRIEN-------DAVHLAGLPPLPVPGAAGRSGPVTVGVRPQHIAL----EPGGD- 287 Query: 301 TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLP-QPGATLTLALDQHELHVFDVES 359 VEL E LG + L R D + + + P G + L+L + +F+ E+ Sbjct: 288 --GYLVELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFEAET 345 Query: 360 GENL 363 G+ L Sbjct: 346 GQRL 349 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: 381 Number of extensions: 16 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: 406 Length of database: 351 Length adjustment: 30 Effective length of query: 376 Effective length of database: 321 Effective search space: 120696 Effective search space used: 120696 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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