Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 298 bits (764), Expect = 1e-85 Identities = 177/356 (49%), Positives = 223/356 (62%), Gaps = 28/356 (7%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 V+ F+L I D EFLVL+GPSGCGK+TT+RM+AGLE + G I+IGD+ V + P+DRD+A Sbjct: 19 VEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEIWIGDRMVNALDPKDRDVA 78 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 MVFQ+Y LYP+M V EN+ F LK+ + E RV A+A + L +FL RKP ALSGGQ Sbjct: 79 MVFQSYGLYPNMNVYENIRFPLKVRKVPEVEHEARVMRASAMVELDDFLHRKPAALSGGQ 138 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 RQRVA+ RAIVR P VFLMDEPLSNLDAKLRV TR QI L +L VTT+YVTHDQ EA+ Sbjct: 139 RQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNLSHELQVTTIYVTHDQIEAM 198 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 T+ DR+ V+ G +QQVG P E+YDRPAN FVA FIGSPAMNL +V DG T R+ Sbjct: 199 TLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPAMNLMEGAVTDG--TFHGDRV 256 Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDSFLYGKL 320 ++ + AA GR+T+GFR E +++ +D I + +E LG + + Sbjct: 257 AIAGLSGAA------GRVTLGFRAEDAQVV----DSDGQIAAPVYSMELLGDATMV---- 302 Query: 321 VGEGDLGSSSEDVPESGQIVVRAAPNAAPAP-GSVFHARIVEGGQHNFSASTGKRL 375 V G +V AP A G+ RI G H F A TG L Sbjct: 303 -----------TVKAGGTLVAVKAPKEFRAEIGAPVQIRIPTGICHLFDAQTGVHL 347 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: 370 Number of extensions: 11 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: 347 Length adjustment: 29 Effective length of query: 347 Effective length of database: 318 Effective search space: 110346 Effective search space used: 110346 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