Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate PP_1017 PP_1017 mannose/glucose ABC transporter, permease protein
Query= reanno::Smeli:SMc04257 (305 letters) >FitnessBrowser__Putida:PP_1017 Length = 281 Score = 285 bits (728), Expect = 1e-81 Identities = 140/286 (48%), Positives = 197/286 (68%), Gaps = 11/286 (3%) Query: 20 KPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWV 79 KP +LSR + ++ L++ L YL+PL VM++TS K +I GN+ + P IT WV Sbjct: 7 KPVLSLSR--MAIHAVLLIAVLLYLVPLVVMLLTSFKTPEDITTGNLLSWPAVITGIGWV 64 Query: 80 KAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILI 139 KAW +S FWNS+ ITVP+V+IS AI ++NGY L+ WRF+G+ LFF +L+ Sbjct: 65 KAWG---------AVSGYFWNSIMITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLL 115 Query: 140 VGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKA 199 G F+P+Q ++ P L ++G+ T GL++VH ++G+ TL FRN++ +P+ L KA Sbjct: 116 FGCFLPFQTVLLPASFTLGKLGLASTTGGLVLVHVVYGLAFTTLFFRNFYVSIPDALVKA 175 Query: 200 ARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNI 259 AR+DGAGF+TI+ +I+LPMS PI +V +I Q T IWNDFLFGVVF+ + P+TV LNN+ Sbjct: 176 ARLDGAGFFTIFRRIILPMSTPIIMVCLIWQFTQIWNDFLFGVVFSSGDSQPITVALNNL 235 Query: 260 VNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305 VN+ G KEYNV+MAA ++ GL L VY V+G+ FVRG+ AGAVKG Sbjct: 236 VNTSTGAKEYNVDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281 Lambda K H 0.329 0.145 0.450 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: 268 Number of extensions: 9 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: 305 Length of database: 281 Length adjustment: 26 Effective length of query: 279 Effective length of database: 255 Effective search space: 71145 Effective search space used: 71145 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: 48 (23.1 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