Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 300 bits (768), Expect = 4e-86 Identities = 173/343 (50%), Positives = 213/343 (62%), Gaps = 34/343 (9%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 NL+I DGEF+V VGPSGCGKST LR LAGLE V+ G I IG +DVT V P DRD+AMVFQ Sbjct: 23 NLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADRDLAMVFQ 82 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 +YALYPHMTV ENM F +K+ G D +R+ EAA L L ++L+RKP LSGGQRQRV Sbjct: 83 SYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQLSGGQRQRV 142 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 A+GRAIV+NP VFL DEPLSNLDAKLRVQ R ++ L ++LG T +YVTHDQ EA+TM D Sbjct: 143 AIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHDQVEAMTMAD 202 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARIKLSP 264 +I VL G ++QVG+P +LY +P + FVA FIGSPAMN+ + V D +S Sbjct: 203 KIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFSSDVGLQD---------ISL 253 Query: 265 ETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKLVGEG 324 + AA +G RPE +EI+P+G D I + E LG +S LY L G Sbjct: 254 DASAAF---------VGCRPEHIEIVPDG---DGHIAATVHVKERLGGESLLYLGLKG-- 299 Query: 325 DLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIVEGGQHNF 367 GQIV R + G+ R H F Sbjct: 300 -----------GGQIVARVGGDDETKVGAAVSLRFSRHRLHQF 331 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: 384 Number of extensions: 21 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: 376 Length of database: 338 Length adjustment: 29 Effective length of query: 347 Effective length of database: 309 Effective search space: 107223 Effective search space used: 107223 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 Sep 17 2021. 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