Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_900129305.1:WP_073038605.1 Length = 368 Score = 296 bits (759), Expect = 4e-85 Identities = 162/361 (44%), Positives = 219/361 (60%), Gaps = 20/361 (5%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA+I+ + K F V++ L +A EF+VLVGPSGCGKST LR +AGLE SG I Sbjct: 1 MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 SI G+ +N + P++RDIAMVFQSYALYPHM V +NM FGL + + EI +RV + +E+ Sbjct: 61 SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L I LL R+P +LSGGQRQRVA+GRA+ R LFDEPLSNLDA LR QMR E+ +LH Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 +ST++YVTHDQ+EA TL DRI V+KDG I Q+G P E+Y RP N F+A FIGSP MN Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240 Query: 241 FLEGAVLE--------------KIPWPEAR------KADQILGIRPDAFALNQGPLGTQE 280 FL+ ++E K+P A I GIRP+ G + Sbjct: 241 FLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDVKERPGDALPEG 300 Query: 281 VALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKK 340 V ++D+ E +G + ++ T+ + + + + L +++ K HLFD + Sbjct: 301 VEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFDPE 360 Query: 341 T 341 + Sbjct: 361 S 361 Lambda K H 0.318 0.136 0.383 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: 331 Number of extensions: 10 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: 347 Length of database: 368 Length adjustment: 29 Effective length of query: 318 Effective length of database: 339 Effective search space: 107802 Effective search space used: 107802 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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