Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 288 bits (736), Expect = 2e-82 Identities = 154/364 (42%), Positives = 223/364 (61%), Gaps = 16/364 (4%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 M+ + +++ K Y G V+H +DL + DGEF V +GPSGCGKST+LRM+AGLE+ + GT Sbjct: 1 MSGVTLESVIKRY-GQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGT 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 +RIGG V L +R V+MVFQ YALYPHM+V +N+ FGL+ A +I +V E + Sbjct: 60 IRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L L+ L+RKP+A+SGGQ+QR AI RAI++ P VFLFDEPLSNLDA+LR ++R +I RL Sbjct: 120 ILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ + T +YVTHDQ+EAMTLAD++++++ GRI Q G+P ELYR P N F AGFIG+P+M Sbjct: 180 HKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 NF+ G VQ E + + + + V + +RP+H+ + L Sbjct: 240 NFIRGRVQGG------EVVSDGLVHSVSKTASAQEGQEVLIGLRPEHLELRPGSSHRVDL 293 Query: 301 TCPV-SVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVES 359 T + V ++G D + + D G + L +D + +FD ++ Sbjct: 294 TESLGGVSYAHLIGPDG--------EKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDAKT 345 Query: 360 GENL 363 L Sbjct: 346 EARL 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: 362 Number of extensions: 13 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: 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 24 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