Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 265 bits (677), Expect = 1e-75 Identities = 151/355 (42%), Positives = 205/355 (57%), Gaps = 27/355 (7%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 V+ + + +G+ LV++GPSGCGK+T LR++AGLE VT G I I DVTH+ P R+I+ Sbjct: 18 VRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIAGTDVTHLPPVKRNIS 77 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 MVFQ+YAL+PH+ V EN+ F LK+ DEI +R+ LGL+ L+ KP LSGG Sbjct: 78 MVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGLSGRLDSKPGELSGGM 137 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 +QRVA+GRAI+ V LMDEPLSNLDAKLR R +I +LQR+LG+T +YVTHDQ EA+ Sbjct: 138 QQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRLGITMIYVTHDQVEAM 197 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 TM DRI +++DG + Q +P Y+RPAN FVA FIG+P MN+ G A Sbjct: 198 TMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVPLCPTQGGAA------ 251 Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKL 320 L P D R G RPE L + G+ P + E LGSD+F+ ++ Sbjct: 252 -LEPGGRLLFPGMDPDRYLFGIRPENLRLAESGQ------PAMVTGREYLGSDTFVSCEI 304 Query: 321 VGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIVEGGQHNFSASTGKRL 375 G+ +++VR G+V H G + F A T +R+ Sbjct: 305 HGQ--------------EVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQERV 345 Lambda K H 0.316 0.135 0.380 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: 361 Number of extensions: 17 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: 376 Length of database: 365 Length adjustment: 30 Effective length of query: 346 Effective length of database: 335 Effective search space: 115910 Effective search space used: 115910 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 (21.6 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