Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3609758 Dshi_3141 ABC transporter related (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Dino:3609758 Length = 352 Score = 306 bits (784), Expect = 6e-88 Identities = 167/317 (52%), Positives = 217/317 (68%), Gaps = 18/317 (5%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 +L + D EFLVL+GPSGCGK+TT+RM+AGLE+ TDG I+IGD+ V P+DRD+AMVFQ Sbjct: 23 SLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEIWIGDRMVNDDLPKDRDVAMVFQ 82 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 NY LYPHMT+ EN+ + L++ G + EI RV AA + LT+FL RKPKALSGGQRQRV Sbjct: 83 NYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQVELTKFLHRKPKALSGGQRQRV 142 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 A+ RAIVR P+VFLMDEPLSNLDAKLRV R ++ L R+L +TTVYVTHDQ EA+T+ D Sbjct: 143 ALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLSRELQITTVYVTHDQIEAMTLAD 202 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDG-DATSGHARIKLS 263 R+AV+K G +QQ+G P E+Y+ PAN+FVAGFIGSPAMNL SV+DG T+G R+ Sbjct: 203 RVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMNLINGSVEDGMFVTTGGTRLVKV 262 Query: 264 PETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFL---YGK- 319 P D R +G R + +++ G+ I + + E G + L +GK Sbjct: 263 PS-------PDRARAILGVRADDMQVHEAGQG---DIDVTIYAFENTGESTLLTVQWGKQ 312 Query: 320 -LVGEGD--LGSSSEDV 333 ++ GD L +DV Sbjct: 313 RVIARGDRHLRKEQDDV 329 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: 368 Number of extensions: 7 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: 352 Length adjustment: 29 Effective length of query: 347 Effective length of database: 323 Effective search space: 112081 Effective search space used: 112081 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