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 WP_092349289.1 BLU87_RS12855 ABC transporter substrate-binding protein
Query= SwissProt::Q8YSQ6 (364 letters) >NCBI__GCF_900107645.1:WP_092349289.1 Length = 364 Score = 310 bits (795), Expect = 3e-89 Identities = 154/356 (43%), Positives = 219/356 (61%), Gaps = 4/356 (1%) Query: 3 RREVLNTAAIATATTALVSCTQTNTSSVQAGLPNVRWRMTTSWPKSLGTF-IGAETVAKR 61 RR+ L A ATA A + T ++ W+M T+WP GA+ +A+ Sbjct: 6 RRDFLKKATAATAVAA--TATTIGAPAIVRAEKTYNWKMVTTWPPHFPLLGEGADKLAEM 63 Query: 62 VAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAFATSVPFG 121 + M+ GR I + GELVP LQ DAV G VE GH ++YY+ GKSPA F +VPFG Sbjct: 64 IRTMSGGRLNIQVYGGGELVPALQAFDAVSQGMVEMGHGAAYYWAGKSPAAQFFAAVPFG 123 Query: 122 LNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSDLKGLKMR 181 +NAQ AWLY GGG+ + +Y+ FN+ PAG+TG QMGGWF +EIKS+ D KGLKMR Sbjct: 124 MNAQAMNAWLYAGGGMKLWEDVYSKFNLKPLPAGNTGVQMGGWFNREIKSMDDFKGLKMR 183 Query: 182 IPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAAQFYYYPG 241 IPGLGG+V+S+ G + GGE+Y L+RG IDA EWVGPY+D +G K A++YYYPG Sbjct: 184 IPGLGGKVLSKAGGTAVLSAGGELYTNLERGVIDATEWVGPYNDYMMGFYKVAKYYYYPG 243 Query: 242 WWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTRLL-AGGT 300 W E G L+ VN +A+ LP++ Q I AT+ +N+ +L + +A N L ++L G Sbjct: 244 WHEAGSVLESFVNKSAYEALPEDLQAIVTNATIASNMWVLCESEAKNNIYLDKMLKEEGV 303 Query: 301 KLVPYSQEIMQAAQKISFDIFEENASKDAAFKQVYEQWKAFRKQIFAWNRVNELSY 356 L + +++ +K S ++ EE + D ++VY+ +KAF+KQ AW++++E Y Sbjct: 304 ILKKFPADVISQLRKYSVEVLEEAVANDPESQKVYDSFKAFQKQQLAWSKISEQPY 359 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: 433 Number of extensions: 22 Number of successful extensions: 4 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: 364 Length adjustment: 29 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 24 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