Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Pf6N2E2_808 Various polyols ABC transporter, permease component 2
Query= reanno::psRCH2:GFF851 (296 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_808 Length = 276 Score = 102 bits (255), Expect = 7e-27 Identities = 89/288 (30%), Positives = 131/288 (45%), Gaps = 23/288 (7%) Query: 12 RLWATHAALLAFVAAIL--FPLLMVISISFRE--GNFATGSLFPENPTLEHWSLALGIPY 67 RL + LA+ AIL FP+ ++ SF+ FAT F PTLE+ Y Sbjct: 8 RLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLEN--------Y 59 Query: 68 THADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLI 127 H + F WNSV I+F ++ L LL++ +AY+ A L ML Sbjct: 60 LHINERSNYFSFA-----WNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLS 114 Query: 128 FQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDAS 187 +M PPV L+ IY L Q G + L + +++ +L + + +W I YF+ I Sbjct: 115 TKMLPPVGVLMPIYLLAKQFGLLDTRLAL-----IVIYTLINLPIVVWMIYTYFKDIPRD 169 Query: 188 LEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSV 247 + EAA +DGAT WQ +LLP++ LA +L+ I E S+ L L+ Sbjct: 170 ILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNE-AFWSLNLTSSKAAPLTA 228 Query: 248 GAQQYLYPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 Y P+ W +A + L+ PI QK +V GL+ G VK Sbjct: 229 LIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 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: 249 Number of extensions: 20 Number of successful extensions: 5 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: 276 Length adjustment: 26 Effective length of query: 270 Effective length of database: 250 Effective search space: 67500 Effective search space used: 67500 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: 47 (22.7 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