Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate PP_3816 PP_3816 Polyamine ABC transporter, permease protein
Query= reanno::Koxy:BWI76_RS01820 (296 letters) >FitnessBrowser__Putida:PP_3816 Length = 269 Score = 65.1 bits (157), Expect = 2e-15 Identities = 61/200 (30%), Positives = 97/200 (48%), Gaps = 19/200 (9%) Query: 88 SIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMF-PAVLSLVALYALFDR 146 S+KVA +T I V L A+A R RFPG+ LL G+ M P V+ VA+YALF + Sbjct: 73 SLKVAVLTTIAAVLLGLPSAFALVRGRFPGRE-LLYGLFTMPMIVPLVIIAVAVYALFLK 131 Query: 147 LGQYVPFVGLNTHGGVIFAY-----MGGIALHVWTIKGYFETIDGSLEEAAALDGATPWQ 201 LG + G +FA+ + + + +I + D S+E+AA + GA+ Q Sbjct: 132 LG----------YTGTLFAFVVSHVIVALPFTIISIINSLKLFDQSIEDAAVICGASRLQ 181 Query: 202 AFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWG 261 A V P P + + +F+ + EV V S+++ + TL V M L Q+ Sbjct: 182 AIFKVTFPAIRPGMIAGGLFAFLVSWDEV-VLSVMMASPDLQTLPVKMWTTLR-QDLSPV 239 Query: 262 DFAAAAVLSAIPITVVFLLA 281 A+ +L + + V+F+ A Sbjct: 240 IAVASTLLIGLSLLVMFIAA 259 Lambda K H 0.328 0.141 0.438 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: 256 Number of extensions: 19 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: 296 Length of database: 269 Length adjustment: 26 Effective length of query: 270 Effective length of database: 243 Effective search space: 65610 Effective search space used: 65610 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 (21.8 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