Align Rhizopine-binding protein (characterized, see rationale)
to candidate PP_2372 PP_2372 putative Periplasmic sugar-binding protein
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__Putida:PP_2372 Length = 358 Score = 79.0 bits (193), Expect = 2e-19 Identities = 81/275 (29%), Positives = 128/275 (46%), Gaps = 30/275 (10%) Query: 9 SLALSLMLASGAALAD---LRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDAR 65 SL L L L + A A L G+S F W +Y R M A + +++Q+ + R Sbjct: 8 SLCLVLPLVANAQPASVVFLNPGLSTETF---WTSYTR-FMQAAADELGMTLQVQYSERR 63 Query: 66 SDVVKQLSQVESFIS--QKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNR-------- 115 +D+ L+Q + +S Q+ D +V+ A +I + G+ L+ VN Sbjct: 64 ADLT--LTQARAILSAPQRPDYLVLVNEQYVAP-EILRLSRGTGVKLLLVNNGLTASQRL 120 Query: 116 ----RPDDLKLPKGVITVASNDLEAG-QMQMQYLAEKMKGKG--DIVILLGDLANNSTTN 168 +PD P G T+ SND +AG QM LA+ + G D+V G ++ Sbjct: 121 SIEGQPDKYAEPLG--TLMSNDEQAGFQMLHLMLAQLPRDAGPVDLVAFAGVKTTPASQL 178 Query: 169 RTKGVKEVLAKYPGIKIDQEQTGTWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAM 228 R +G++ LA +P +++ Q G W+R + L + + S ND+MA GA Sbjct: 179 RVEGMRRALADFPQVRLRQVVYGGWNRQRAYEQAKQLLERYPATRLVWSANDQMAFGAMQ 238 Query: 229 ALKQAGVEKG-SVLIAGVDGTPDGLRAVKKGDLAV 262 A ++AG G VL A V+ +P+ LRA G L+V Sbjct: 239 AFEEAGHTPGRDVLFAAVNSSPEALRARIDGRLSV 273 Lambda K H 0.315 0.130 0.360 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: 216 Number of extensions: 11 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: 308 Length of database: 358 Length adjustment: 28 Effective length of query: 280 Effective length of database: 330 Effective search space: 92400 Effective search space used: 92400 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 (21.5 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