Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate AO356_23055 AO356_23055 C4-dicarboxylate ABC transporter
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23055 Length = 322 Score = 148 bits (374), Expect = 2e-40 Identities = 93/295 (31%), Positives = 158/295 (53%), Gaps = 10/295 (3%) Query: 2 RKLLLATTAIAFGLSAAAPAFAEFNDRNIRVSNGINEDHPVGNGIKAMQACLDQKSGGKL 61 R LL+A +AF L+ AA A +++++ + +P ++M L +++ G+L Sbjct: 5 RTLLIAALPLAF-LAQAAHAL------ELKIADIHPKGYPTVMAEESMGKTLTKETNGEL 57 Query: 62 KLTAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGVFDLPFLFANAQEAYTV 121 F GG LG + + + ++ G + S + ++P + VF++PF+F + V Sbjct: 58 TFKYFPGGVLGSEKEVIEQMQVGAIQMSRVSLGIVGPVVPDVNVFNMPFIFRDQAHMRAV 117 Query: 122 LDGDFGDMMNEKLEAA--GLVNLAYWENGFRNLSNSVRPVTKWEDFEGMKVRVMQNNIFL 179 +DGD GD + +++ + GLV LA+ + G RN+ +PV K ED +GMK+RV N +F+ Sbjct: 118 IDGDVGDAILDRITNSEFGLVALAWMDGGTRNIYTK-KPVRKLEDLKGMKIRVQGNPMFI 176 Query: 180 DTFQNLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQKYVTETNHAYTPFL 239 + +GAN M GE+FSAL+T ID EN T+ ++ KY + T H P Sbjct: 177 EMMNAMGANGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHYQNAKYYSLTGHLILPEP 236 Query: 240 FLFSKPIFDSYTPEEQAALRECAVVGRDEERKVIQDLNKKSLEKIKEAGLEVNTL 294 + SK ++ TP++Q +R+ A + EER + + S EK+K AG+E T+ Sbjct: 237 IVMSKITWEKLTPDQQTMVRKAAKAAQAEERALWDQKSTASEEKLKAAGVEFITV 291 Lambda K H 0.317 0.133 0.374 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: 264 Number of extensions: 14 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: 334 Length of database: 322 Length adjustment: 28 Effective length of query: 306 Effective length of database: 294 Effective search space: 89964 Effective search space used: 89964 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 (21.7 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