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_011842534.1 RSPH17029_RS18455 TRAP transporter substrate-binding protein
Query= SwissProt::Q8YSQ6 (364 letters) >NCBI__GCF_000015985.1:WP_011842534.1 Length = 351 Score = 191 bits (485), Expect = 3e-53 Identities = 108/327 (33%), Positives = 168/327 (51%), Gaps = 3/327 (0%) Query: 32 AGLPNVRWRMTTSWPKSL-GTFIGAETVAKRVAEMTNGRFKITPFAAGELVPGLQVLDAV 90 A ++RW+M + +L G + VA + + + G ++ + G+L+P +L AV Sbjct: 21 ASAEDLRWKMPIGFGSNLPGLGSPSPWVADMLTKASGGSIEVRVYEPGKLMPAFDILQAV 80 Query: 91 QAGTVECGHTSSYYYIGKSPALAFATSVPFGLNAQQQYAWLYQGGGLAAIQKIYAN--FN 148 G V G+T Y GK PA+ +VPFG+ AW Y G G +Q++YAN +N Sbjct: 81 SDGKVPVGYTWIGYDQGKVPAVPLFAAVPFGMKPWAFTAWYYYGEGHDLLQEVYANAGYN 140 Query: 149 VINFPAGSTGAQMGGWFKKEIKSVSDLKGLKMRIPGLGGQVMSRLGVNVQVLPGGEIYLA 208 V G G + GW+K EI V D +GLK+R GLGG+V+ +LG +V VLP GE++ A Sbjct: 141 VRAQLCGIIGPETAGWYKNEISKVEDYQGLKIRFAGLGGKVIEKLGASVSVLPSGELFQA 200 Query: 209 LDRGAIDAAEWVGPYDDEKLGLNKAAQFYYYPGWWEPGPTLDVLVNLNAWNRLPKEYQEI 268 L+ G IDA E+ P D+ LG + A+F +PGW +P +L+N W++ + + + Sbjct: 201 LETGTIDATEFSMPAIDKALGFGQVAKFNLFPGWHQPFTAQYLLINNAEWDKTTESQKAL 260 Query: 269 FKTATVEANLTMLNQYDALNGEALTRLLAGGTKLVPYSQEIMQAAQKISFDIFEENASKD 328 + A L + + LNG L G E++ + ++ ++ EE A+K+ Sbjct: 261 IEAVCTAAVTRALAEGEFLNGAVLEGFEKEGISAKQIPDEVLAQLKAVTDEVLEEEAAKN 320 Query: 329 AAFKQVYEQWKAFRKQIFAWNRVNELS 355 A FK+VYE F K W LS Sbjct: 321 ADFKRVYESQNEFLKSYRVWEERAYLS 347 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: 369 Number of extensions: 20 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: 351 Length adjustment: 29 Effective length of query: 335 Effective length of database: 322 Effective search space: 107870 Effective search space used: 107870 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 Apr 10 2024. 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