Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_086511129.1 BZY95_RS17245 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::psRCH2:GFF857 (371 letters) >NCBI__GCF_002151265.1:WP_086511129.1 Length = 380 Score = 412 bits (1060), Expect = e-120 Identities = 212/367 (57%), Positives = 265/367 (72%), Gaps = 5/367 (1%) Query: 1 MASVTLRDICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDL 60 MA++ L DI K +D T + + +DL++ D EFVVFVGPSGCGKSTLLR+IAGLE TSGD+ Sbjct: 1 MATLQLHDIVKRFDDTEVIKGVDLEVNDREFVVFVGPSGCGKSTLLRMIAGLESATSGDI 60 Query: 61 LIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEI 120 LID R+N++ P +R + MVFQSYALYPHMTV +NM F LKLA V K E +R+V A I Sbjct: 61 LIDGVRMNEVGPAERGLAMVFQSYALYPHMTVEDNMGFSLKLAGVPKEERRRKVREAASI 120 Query: 121 LQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLH 180 LQL+ LLERKPK LSGGQRQRVAIGR +VR P +FLFDEPLSNLDA LRVQMRIE+ARLH Sbjct: 121 LQLEPLLERKPKALSGGQRQRVAIGRAIVRNPSIFLFDEPLSNLDAALRVQMRIELARLH 180 Query: 181 QRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMN 240 + + +TMIYVTHDQ+EAMT+ADKIVVL G + QVG P+ LYH+P+NRFVAGF+GSP+MN Sbjct: 181 EELDATMIYVTHDQIEAMTMADKIVVLQGGVVEQVGSPMELYHHPRNRFVAGFIGSPKMN 240 Query: 241 FVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDEADFTFHG 300 F+EV +SA+ V + LP G T+PVDGS + D LTLGIRPEH + + + G Sbjct: 241 FLEVERVSAAATGVEVRLPDGDTCTVPVDGSGLD-DDALTLGIRPEHLQLDPQGPLS--G 297 Query: 301 QITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCHLFRENGEAC 360 +I V ERLG LY+ ++ ++T+ DGN+ G++ G + D HLF G A Sbjct: 298 RIEVIERLGGVTSLYVRMQ--NTLVTVSADGNVDSRVGDSLRFGFERDCAHLFDGEGLAL 355 Query: 361 TRHYREP 367 R P Sbjct: 356 PSLARHP 362 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: 451 Number of extensions: 14 Number of successful extensions: 4 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: 380 Length adjustment: 30 Effective length of query: 341 Effective length of database: 350 Effective search space: 119350 Effective search space used: 119350 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: 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