Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012103405.1 CKL_RS14905 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000016505.1:WP_012103405.1 Length = 460 Score = 365 bits (938), Expect = e-105 Identities = 191/417 (45%), Positives = 281/417 (67%), Gaps = 8/417 (1%) Query: 5 DEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIE-RYIKIPE 63 +E +P+ WYN+ D+ + P +P ++ + L ++ +E+ +Q+ + RY+ IPE Sbjct: 12 EEEIPRKWYNLRADMKEQHEPYINPGTMKPAKAEDLYAVFCEELAKQEMDDKTRYVDIPE 71 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 EV + Y I RP+PL RA LE+ L TPA+IY+K+EG +GSHK+N+A+ Q Y+AK++G Sbjct: 72 EVLNFY-KIYRPSPLCRAYNLEKALDTPAKIYYKFEGNNTSGSHKLNSAVAQVYYAKKQG 130 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 I + TETGAGQWGTA++ A + + + T++MVKVS +QKP R++IM+ +GA V SP++ Sbjct: 131 ITSLTTETGAGQWGTALSEACAYFEIPLTVYMVKVSSQQKPYRKAIMETFGAKVIPSPSD 190 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQETIT 242 TE GR IL NP GSLG A+SEAIE+A+K E RY++GSVL+ VLLHQS+IG ET Sbjct: 191 TTEAGRAILAKNPNTGGSLGCAISEAIEHAVKTENCRYVLGSVLNQVLLHQSIIGLETKA 250 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKR----YIAVSSAEIPKFSKGEYKY 298 ++ + DI+IGC GGGSN GG PF+ +K ++ +IAV A P ++G+Y Y Sbjct: 251 AMEKIDTYPDIVIGCAGGGSNLGGLIAPFMQDKLTEKANPYFIAVEPASCPSLTRGKYAY 310 Query: 299 DFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIV-EWREYNEREI 357 DF D+ + PL KM TLG +++P +AGGLRYHG++P LS L +G + E R + I Sbjct: 311 DFCDTGKITPLAKMYTLGCEFIPSANHAGGLRYHGMSPILSKLYHDGYMDEARAVEQTRI 370 Query: 358 FEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNY 414 F+AA +F + + I+PAPES+HAIR +DEA++ ++ E K I+F L+G G D+ Y Sbjct: 371 FDAAALFAKYETILPAPESSHAIRVAIDEALKCKETGEAKTILFGLTGTGYFDMQAY 427 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: 474 Number of extensions: 21 Number of successful extensions: 6 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: 460 Length adjustment: 32 Effective length of query: 393 Effective length of database: 428 Effective search space: 168204 Effective search space used: 168204 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