Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 314 bits (804), Expect = 3e-90 Identities = 181/366 (49%), Positives = 241/366 (65%), Gaps = 18/366 (4%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + LR+V K+Y GL + + ++L+I DGEF+++VGPSGCGKSTL+ +AGLE I+ G Sbjct: 1 MAEISLRDVRKSYS-GL-EVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I + ++ + P++RDIAMVFQ+YALYP M+VR+N+A+GL+I K+ AEI+E VAR + Sbjct: 59 EIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L++ LL RKP QLSGGQ+QRVAMGRAL R P +L DEPLSNLDAKLRV+MR ++K Sbjct: 119 KMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKE 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 + + ++TT++YVTHDQ+EAMTL D++ VM G+ +Q TP +IY+ PA FVA FIGSP Sbjct: 179 LQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPA 238 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 MN +P R G AL +GQ R +P AG R++ILGIRPE + A E Sbjct: 239 MNMLPAR-----GLGDALEVAGQ-RLAVP---APAG---RDLILGIRPEHLHPAGPEE-- 284 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPA-VGETLTLQFDPAKVLLFDA 359 P VQ E G D +L D P AP + L + D A + LFDA Sbjct: 285 -PGFELHVQAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDA 343 Query: 360 KTGERL 365 TG RL Sbjct: 344 GTGRRL 349 Lambda K H 0.319 0.138 0.393 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: 19 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: 386 Length of database: 349 Length adjustment: 30 Effective length of query: 356 Effective length of database: 319 Effective search space: 113564 Effective search space used: 113564 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 (21.7 bits) S2: 49 (23.5 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