Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 290 bits (743), Expect = 3e-83 Identities = 175/371 (47%), Positives = 224/371 (60%), Gaps = 43/371 (11%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L+++ K Y G+ +K +L+IQ EF VFVGPSGCGK+T LRMIAGLE I G Sbjct: 1 MAFLELKNVDKYY-GKLH-AIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGG 58 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 L + R + +VPP RD+AMVFQ+YALYPHMTV +NM+F L+L KV A I +V+ AA Sbjct: 59 QLILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAA 118 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 L++ L R PKALSGGQRQRVA+GR+IVR P+VFL DEPLSNLDA LR R EI Sbjct: 119 DKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIAS 178 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 LH+ L T +YVTHDQ EAMT+ DR+VV+RDG+I+Q TP +Y QP N FVA FIG P Sbjct: 179 LHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQ 238 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MN P +G A A +G+RPE L M Sbjct: 239 MNV----------------------APASLFGQFPAQVA-----EVGIRPEHLQ-----M 266 Query: 301 TTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTI------VARVNPRHVYHVGSSVKLAID 354 + D +L +V +VE +G+E +H + P+ + + R+ R HVG V L D Sbjct: 267 VSPEDGLLAGKVVLVEALGNETLVH--VRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWD 324 Query: 355 LNK-IHIFDAE 364 +K IH FD + Sbjct: 325 DSKHIHYFDTK 335 Lambda K H 0.321 0.138 0.395 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: 397 Number of extensions: 14 Number of successful extensions: 1 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: 384 Length of database: 348 Length adjustment: 30 Effective length of query: 354 Effective length of database: 318 Effective search space: 112572 Effective search space used: 112572 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