Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_078715769.1 B5D49_RS00915 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900167125.1:WP_078715769.1 Length = 449 Score = 383 bits (984), Expect = e-111 Identities = 194/416 (46%), Positives = 278/416 (66%), Gaps = 8/416 (1%) Query: 8 LPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRD 67 +P WYN PDLP PL PP DP+ D L I P ++ Q+ + +R+I IP+ V D Sbjct: 15 MPTQWYNPQPDLPTPLAPPLDPETHEPVTPDQLGVIFPTSLIEQEMSQDRWIPIPQPVLD 74 Query: 68 RYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127 Y + RPTPL RA+ LE+ + RI++K E +P GSHK NTA+PQAYF EG++ + Sbjct: 75 AY-RLWRPTPLIRARNLEKAIGAKCRIFYKDESVSPAGSHKPNTAVPQAYFNMTEGVKRL 133 Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187 TETGAGQWGTA++ A S + M T++MVKVSYE KP R+ +++ YG+ V+ SP+ LT Sbjct: 134 STETGAGQWGTALSFACSQFGMDCTVYMVKVSYEMKPYRQILIRNYGSTVHPSPSELTRT 193 Query: 188 GRKILETNPQHPGSLGIAMSEAIE-YALKNEFRYLVGSVLDVVLLHQSVIGQETITQLDL 246 G ++L +P GSLG+A+SEA+E A ++ +Y +GSVL+ VL+HQ+++G ET QL Sbjct: 194 GAEMLRRDPGCKGSLGLAISEAVEDAATHDDTKYTLGSVLNHVLVHQTIVGLETEQQLAE 253 Query: 247 LGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEYKYDFPDS 303 G D L+GCVGGGSNF G PF+ K + ++A P ++GEY+YD+ D Sbjct: 254 QGLKPDHLVGCVGGGSNFAGLVLPFLRRKLDGENIHFVASEPRACPSLTRGEYRYDYGDM 313 Query: 304 AGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKI 363 A L PL+KM TLG ++P PI+AGGLRYHG AP L L +EG+++ R Y + + F+AA++ Sbjct: 314 ARLTPLMKMHTLGHAFMPAPIHAGGLRYHGDAPILCNLMEEGLIDARSYFQTDCFDAARL 373 Query: 364 FIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMMK 419 F++ QG +PAPE++HAI+A +D A EA + +VF SGHG+LDL++Y++ +K Sbjct: 374 FLQTQGFLPAPETSHAIKAAIDVAKEAGPDEN---VVFLYSGHGMLDLASYDAYLK 426 Lambda K H 0.318 0.138 0.403 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: 496 Number of extensions: 28 Number of successful extensions: 5 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: 425 Length of database: 449 Length adjustment: 32 Effective length of query: 393 Effective length of database: 417 Effective search space: 163881 Effective search space used: 163881 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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