Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 296 bits (759), Expect = 5e-85 Identities = 172/363 (47%), Positives = 225/363 (61%), Gaps = 14/363 (3%) Query: 1 MASVTLRDICKSYDG--TPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58 MA+VT + Y G P +DL+I DGEF+V VGPSGCGKST LR++AGLED+ +G Sbjct: 1 MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60 Query: 59 DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118 + I + V LPPKDR + MVFQ+YALYPHMTVA+NM F LK+A V+K EI+ +VE A Sbjct: 61 AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120 Query: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178 +IL L + L+RKPK LSGGQRQRVA+GR +VREP+VFL DEPLSNLDA LRV R +IA Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180 Query: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238 L +R+ T +YVTHDQVEAMT+ D++ VL G + QV P ++Y P N FVAGF+GSP Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240 Query: 239 MNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGD-PLTLGIRPEHFVMPDEA--- 294 MN VEV + S ++ G A + GD +T+G+RPEH + Sbjct: 241 MNLVEVPITDGGVKFG----ESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGG 296 Query: 295 --DFTFHGQITVAERLGQYNLLYLTLERLQDVITLC--VDGNLRVTEGETFAAGLKADKC 350 D + V E LG +Y + + + I L V G +G+ +A + Sbjct: 297 GEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGET 356 Query: 351 HLF 353 H+F Sbjct: 357 HVF 359 Lambda K H 0.322 0.139 0.405 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: 403 Number of extensions: 19 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: 371 Length of database: 369 Length adjustment: 30 Effective length of query: 341 Effective length of database: 339 Effective search space: 115599 Effective search space used: 115599 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 (21.9 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