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) >FitnessBrowser__Dino:3607842 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:
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