Align TRAP-type periplasmic solute-binding protein (characterized, see rationale)
to candidate GFF2035 PGA1_c20680 C4-dicarboxylate-binding periplasmic protein DctP
Query= uniprot:Q930R1 (334 letters) >FitnessBrowser__Phaeo:GFF2035 Length = 333 Score = 140 bits (354), Expect = 3e-38 Identities = 98/333 (29%), Positives = 159/333 (47%), Gaps = 11/333 (3%) Query: 1 MRKLLLATTAIAFGLSAA-APAFAEFNDRNIRVSNGINED-HPVGNGIKAMQACLDQKSG 58 M+ + A TA+A +SA A A + + ++ S+ N D HP G ++ ++++ Sbjct: 1 MKFVTAAATAVALTMSAGTAMAACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMN 60 Query: 59 GKLKLTAFWGGALGGDLQATQALRSGVQEAVVTSSSPLVGIIPALGVFDLPFLFANAQEA 118 G + L + L D + +A+ G + S S +FDLPF+F N Sbjct: 61 GTMCLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAV 120 Query: 119 YTVLDGDFGDMMNEKLEAAGLVNLAYWENGFRNLSNSVRPVTKWEDFEGMKVRVMQNNIF 178 + G M + ++ GL L+YW NG + +S + +P+ D G+K RV +++ Sbjct: 121 DAFQGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSAN-KPLINPSDANGLKFRVQSSDVL 179 Query: 179 LDTFQNLGANATPMAFGEVFSALETKAIDAQENPYVTIDTSKFFEVQKYVTETNHAYTPF 238 + + +G + MAF EV+ AL+ +D QEN + I KFFEVQ VTETNH + Sbjct: 180 VAQMEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDY 239 Query: 239 LFLFSKPIFDSYTP--EEQ--AALRECAVVGRDEERKVIQDLNKKSLEKIKEAGLEVNTL 294 L + S DS P EQ L E E KV N ++ + I +AG V L Sbjct: 240 LVVTSVDWLDSLDPAVREQFLTILGEVTATRNSESTKV----NAEARQSIIDAGGVVREL 295 Query: 295 SAEEQARIREKSMVVYEKHKAEIGAEVVDAILA 327 + E++A E V+E+ ++G +++DA A Sbjct: 296 TPEQRAAWVEAMKPVWEQFAGDVGQDMIDAAQA 328 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: 239 Number of extensions: 13 Number of successful extensions: 3 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: 333 Length adjustment: 28 Effective length of query: 306 Effective length of database: 305 Effective search space: 93330 Effective search space used: 93330 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