Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 295 bits (755), Expect = 1e-84 Identities = 172/372 (46%), Positives = 228/372 (61%), Gaps = 12/372 (3%) Query: 1 MADIHCQALAKHYAGGP-PVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59 MA + + Y GG P + LDL I DGEF+VL+GPSGCGKST LRM+AGLED++ G Sbjct: 1 MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60 Query: 60 TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119 +RIG V LP ++R++AMVFQNYALYPHM+V DN+ F L+ AEI +V E A Sbjct: 61 AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120 Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179 +L+L L+RKP+A+SGGQ+QR A+ RAI++ P VFL DEPLSNLDAKLR R I Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180 Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239 L +RL TTVYVTHDQ+EAMT+ DRV +++DG + Q +P +Y P NLF AGFIG+PA Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240 Query: 240 MNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHA--MAVKLAVRPDHVRIAGEREPA 297 MN + + G F E+ Q ++ + +A V + VRP+H+ I G E Sbjct: 241 MNLVEVPI-TDGGVKFGESVVQ---VSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGG 296 Query: 298 A-SLTCPVSVELVEILGADALL--TTRCGDQT--LTALVPADRLPQPGATLTLALDQHEL 352 V+V +VE LGAD + + + G +T L V +P G L + E Sbjct: 297 GEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGET 356 Query: 353 HVFDVESGENLS 364 HVF +G+ LS Sbjct: 357 HVFSTSTGKRLS 368 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: 400 Number of extensions: 13 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: 369 Length adjustment: 30 Effective length of query: 376 Effective length of database: 339 Effective search space: 127464 Effective search space used: 127464 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 Apr 09 2024. 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