Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate WP_086508159.1 BZY95_RS01105 maltose ABC transporter permease MalG
Query= reanno::psRCH2:GFF851 (296 letters) >NCBI__GCF_002151265.1:WP_086508159.1 Length = 296 Score = 465 bits (1197), Expect = e-136 Identities = 230/296 (77%), Positives = 260/296 (87%) Query: 1 MAMVQPKSARYRLWATHAALLAFVAAILFPLLMVISISFREGNFATGSLFPENPTLEHWS 60 MAMVQP+S R+R A H AL+ F+ ILFPLL+VISISFREGNFATGSL PE +LEHWS Sbjct: 1 MAMVQPRSLRWRKLAAHLALIGFLTLILFPLLLVISISFREGNFATGSLIPERFSLEHWS 60 Query: 61 LALGIPYTHADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAP 120 LALGIP+ ADG+V QPPFPVLLWLWNSVK+A VSS+LI+LLSTTSAYAFARMRF GK P Sbjct: 61 LALGIPWERADGTVVQPPFPVLLWLWNSVKVAIVSSLLIVLLSTTSAYAFARMRFAGKGP 120 Query: 121 ILKSMLIFQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGY 180 ILKSMLIFQMFP VLSLVA+YALFD+LGQ V WLG+N+HGA+IVASLG +ALHIWTIKGY Sbjct: 121 ILKSMLIFQMFPAVLSLVALYALFDRLGQFVGWLGINTHGALIVASLGAVALHIWTIKGY 180 Query: 181 FESIDASLEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDV 240 FESID SLEEAA+VDGA+TWQAF +ILLP+S+PIL VVFILAF+ S+ EYP+ASVLL+D Sbjct: 181 FESIDGSLEEAAMVDGASTWQAFRYILLPLSLPILMVVFILAFVMSIMEYPMASVLLVDE 240 Query: 241 DKLTLSVGAQQYLYPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVKG 296 KLTL+VGAQQYL N WG+FAAAAVLSGLPIT FL CQ+WI+GGLTAGGVKG Sbjct: 241 HKLTLAVGAQQYLADHNQRWGNFAAAAVLSGLPITLAFLICQRWIIGGLTAGGVKG 296 Lambda K H 0.327 0.139 0.433 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: 408 Number of extensions: 13 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: 296 Length of database: 296 Length adjustment: 26 Effective length of query: 270 Effective length of database: 270 Effective search space: 72900 Effective search space used: 72900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 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