Align Monocarboxylate 2-oxoacid-binding periplasmic protein all3028; Extracellular solute-binding protein; Extracytoplasmic solute receptor protein all3028; TRAP transporter monocarboxylate 2-oxoacid-binding subunit P (characterized)
to candidate 3608953 Dshi_2343 TRAP dicarboxylate transporter- DctP subunit (RefSeq)
Query= SwissProt::Q8YSQ6 (364 letters) >FitnessBrowser__Dino:3608953 Length = 361 Score = 229 bits (584), Expect = 9e-65 Identities = 128/325 (39%), Positives = 174/325 (53%), Gaps = 5/325 (1%) Query: 1 MKRREVLNTAAIATATTALVSCTQTNTSSVQAGLPNVRWRMTTSWPKSLGTFIGAETVAK 60 M RR L T+A+ T A S + Q+ M TSWP+ A T Sbjct: 1 MDRRSFLRTSALG-GTAAAASAGLAAPAIAQS---TRTLTMVTSWPRGFAVLDDAATYFN 56 Query: 61 R-VAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAFATSVP 119 V M+ G I A GELV +V DAV AG + H++ YY+IG+ P A+ +VP Sbjct: 57 EAVNAMSGGSLIIEKKAPGELVGAFEVFDAVAAGQADIYHSADYYWIGQHPGYAYFCAVP 116 Query: 120 FGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSDLKGLK 179 FG AQ+ W Y GG ++ A F + + G++G+Q GGWF+ EI S D GL+ Sbjct: 117 FGATAQELTNWYYHDGGQDLHNELGAIFGMHSMQCGNSGSQSGGWFRNEITSAEDFNGLR 176 Query: 180 MRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAAQFYYY 239 R+PGLGGQV+ +LG +VQ +PGGE+Y AL GA+D EWVGP DEK G + A+ YY Sbjct: 177 FRMPGLGGQVLGKLGASVQNIPGGELYQALSSGALDGLEWVGPAADEKAGFQEVAKIYYT 236 Query: 240 PGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTRLLAGG 299 G+ EPG L VNL+ WN L E+Q I A L+Q A+NG AL RL A G Sbjct: 237 AGFHEPGSGLTASVNLDVWNELSPEHQAIMDNAAKATTNYQLSQTLAMNGAALARLQAQG 296 Query: 300 TKLVPYSQEIMQAAQKISFDIFEEN 324 + + + ++ A S ++ +EN Sbjct: 297 VRTLQFPDDVWDAFGAASKEVLDEN 321 Lambda K H 0.317 0.132 0.397 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: 377 Number of extensions: 24 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: 364 Length of database: 361 Length adjustment: 29 Effective length of query: 335 Effective length of database: 332 Effective search space: 111220 Effective search space used: 111220 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