Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::WCS417:GFF2490 (367 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 323 bits (827), Expect = 6e-93 Identities = 178/364 (48%), Positives = 239/364 (65%), Gaps = 13/364 (3%) Query: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 MA +K+ + K F+ +++ L V DKEFVV VGPSGCGKST LR+IAGLEEV+ G I Sbjct: 1 MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60 Query: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 + GR + V P RD+AMVFQ+YALYPHM+V KNM+F L GV + ++ +V +AA I Sbjct: 61 SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120 Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 L + LL+R+P QLSGGQRQRVA+GRAIVR+P+ FLFDEPLSNLDA LRVQMR ELA+LH Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 + LQ+T++YVTHDQ+EAMTLAD++VV+ G+I QVG PLE+Y +PAN FVAGF+G+P M Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240 Query: 241 FLKGKVTRVESQSCEVQLDAGTL-INLPLSGATL---SVGSAVTLGIRPEHL-----EIA 291 FL R+ ++ ++ +D + + +P A V V GIRPE + + Sbjct: 241 FLD---VRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDAL 297 Query: 292 SPGQTTLTVTADVGERLGSDTFCHVITANGEPLTMRIRGDMASQYGETLHLHLDPAHCHL 351 G L DV E +GS+ T T RI ++A + + + L ++ HL Sbjct: 298 PEGVEPLRAEVDVREPIGSEVII-TATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHL 356 Query: 352 FDTD 355 FD + Sbjct: 357 FDPE 360 Lambda K H 0.319 0.136 0.384 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: 12 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: 367 Length of database: 368 Length adjustment: 30 Effective length of query: 337 Effective length of database: 338 Effective search space: 113906 Effective search space used: 113906 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: 49 (23.5 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