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_011613734.1 TERY_RS21355 C4-dicarboxylate ABC transporter
Query= SwissProt::Q8YSQ6 (364 letters) >NCBI__GCF_000014265.1:WP_011613734.1 Length = 368 Score = 524 bits (1349), Expect = e-153 Identities = 242/361 (67%), Positives = 296/361 (81%), Gaps = 2/361 (0%) Query: 1 MKRREVLNTAAIATATTALVSCTQTNTSSVQA-GLPNVRWRMTTSWPKSLGT-FIGAETV 58 MKRR+++N A AT L +C QT T SV LP+V+WRMTTSWP+SL T F GA+T+ Sbjct: 1 MKRRKLINHIATATTVATLAACNQTTTQSVSTDSLPSVKWRMTTSWPRSLDTIFGGAQTI 60 Query: 59 AKRVAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAFATSV 118 RVA MTNGRF IT ++AGE+V GL+VLDAVQ GTV+CGHT+SYYY+GK+ ALAF TSV Sbjct: 61 CDRVAAMTNGRFTITSYSAGEIVGGLEVLDAVQQGTVQCGHTASYYYVGKNSALAFGTSV 120 Query: 119 PFGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSDLKGL 178 PFGL AQQQ AW Y GGGL + K+Y++FN+INFPAG++G QMGGWF++EI +VSDL GL Sbjct: 121 PFGLTAQQQNAWYYHGGGLEIMHKLYSDFNIINFPAGNSGVQMGGWFRQEINTVSDLNGL 180 Query: 179 KMRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAAQFYY 238 MRIPG GG+VM +LGVN QVLPGGEIYLAL+RGA+DAAEWVGPYDD+KLGL KAA++YY Sbjct: 181 SMRIPGFGGEVMKKLGVNAQVLPGGEIYLALERGALDAAEWVGPYDDQKLGLQKAAKYYY 240 Query: 239 YPGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTRLLAG 298 YPGWWEPGPT +V +NLN WN+LPKEYQE+ KT +AN++ML QYDALNG AL L+AG Sbjct: 241 YPGWWEPGPTFEVQINLNEWNKLPKEYQEVLKTVAYQANISMLAQYDALNGVALAELIAG 300 Query: 299 GTKLVPYSQEIMQAAQKISFDIFEENASKDAAFKQVYEQWKAFRKQIFAWNRVNELSYEN 358 GT+L PYSQEI+QAAQK + + +EE A++D FK+VYEQWK FR+QI+ WN +NELS+ Sbjct: 301 GTELRPYSQEILQAAQKAAVEFYEEKATQDTTFKEVYEQWKKFREQIYKWNTINELSFAQ 360 Query: 359 F 359 F Sbjct: 361 F 361 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: 550 Number of extensions: 22 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: 364 Length of database: 368 Length adjustment: 30 Effective length of query: 334 Effective length of database: 338 Effective search space: 112892 Effective search space used: 112892 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