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 GFF4026 Psest_4099 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component
Query= SwissProt::Q8YSQ6 (364 letters) >FitnessBrowser__psRCH2:GFF4026 Length = 367 Score = 291 bits (745), Expect = 2e-83 Identities = 157/366 (42%), Positives = 218/366 (59%), Gaps = 7/366 (1%) Query: 1 MKRREVLNTAAIATATTALVSCTQT----NTSSVQAGLP--NVRWRMTTSWPKSL-GTFI 53 MKRR + AA AT L C N A P W+M T+WPK+ G Sbjct: 1 MKRRHLFGAAAALLATLGLAGCNDDKKVENAGQQAASEPAKTYTWKMVTAWPKNYPGLGT 60 Query: 54 GAETVAKRVAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALA 113 AE +A RV M++GR I +AAGELVP L+V DAV GT E GH ++YY+ GK P Sbjct: 61 AAERLADRVKVMSDGRLTIKVYAAGELVPALEVFDAVSRGTAELGHGAAYYWKGKVPTAQ 120 Query: 114 FATSVPFGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVS 173 F TSVPFGL+A + AWL +G G ++ YA F V G+TG QMGGW+ KEI ++ Sbjct: 121 FFTSVPFGLSAIEMNAWLSRGEGQKFWEEAYAPFGVKPMVVGNTGMQMGGWYNKEINALG 180 Query: 174 DLKGLKMRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKA 233 DL+GLK+R+PGLGG+V++RLG LPGGE++ AL GAIDA +WV PY+D GL+KA Sbjct: 181 DLRGLKIRMPGLGGEVLARLGATTVNLPGGEVFTALQTGAIDATDWVSPYNDLAFGLHKA 240 Query: 234 AQFYYYPGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALT 293 A++YYYPGW EP L++LVN A + LP++ Q I AT A+ M++ Y N AL Sbjct: 241 AKYYYYPGWQEPQAVLELLVNQKAMDTLPEDLQAILTEATRAASRDMMDDYVYNNALALE 300 Query: 294 RLLAGGTKLVPYSQEIMQAAQKISFDIFEENASKDAAFKQVYEQWKAFRKQIFAWNRVNE 353 +L G +L + E++ A Q+ S + E A++ +++ KAF++Q+ + ++E Sbjct: 301 QLKQQGVELKRFPDEVLDAMQEQSELVLGELAAQSELNGRIWASMKAFQEQVKPMHEISE 360 Query: 354 LSYENF 359 N+ Sbjct: 361 KELYNW 366 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: 411 Number of extensions: 21 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: 364 Length of database: 367 Length adjustment: 30 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 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