Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_073039149.1 BUB04_RS10635 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900129305.1:WP_073039149.1 Length = 453 Score = 403 bits (1035), Expect = e-117 Identities = 201/419 (47%), Positives = 292/419 (69%), Gaps = 5/419 (1%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPE 63 ++ +P+ WYNI+ DLP P+ PP P + + L + P ++ Q+ + +R+I+IPE Sbjct: 9 DESEMPRQWYNILADLPTPMRPPLHPATGEPVKPEDLAPVFPMNLIEQEMSTDRWIEIPE 68 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 V ++Y +I RPTPL+RA+ LE+ L TPA+I++K EG +P GSHK NTA+ QAY+ K G Sbjct: 69 PVLEKY-AIWRPTPLYRARNLEKALGTPAKIFYKNEGVSPPGSHKPNTAVAQAYYNKIFG 127 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 I+ + TETGAGQWG+A+++A M+ ++ ++MVKVSY QKP RR +MQ +GA SP+N Sbjct: 128 IKRLATETGAGQWGSALSMACQMFGLECRVYMVKVSYNQKPYRRLMMQTWGAECIPSPSN 187 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYALKN-EFRYLVGSVLDVVLLHQSVIGQETIT 242 TE GRKIL +P PGSLGIA+SEAIE A+ + E RY +GSVL+ VLLHQ++IG E Sbjct: 188 RTEAGRKILAQDPDSPGSLGIAISEAIEDAVGDPEARYSLGSVLNHVLLHQTIIGLEAQK 247 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAE---IPKFSKGEYKYD 299 Q++ LG D+++GC GGGSNF G PF+ +K + + V +AE P ++G ++YD Sbjct: 248 QMEKLGLYPDVVLGCAGGGSNFAGLCLPFVRDKIHGKDVTVVAAEPTSCPTLTRGPFRYD 307 Query: 300 FPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFE 359 F D+A PL+ M TLG D+VP PI+AGGLRYHG+AP +S L +E ++E R +++ E F Sbjct: 308 FGDTAMTTPLLPMHTLGHDFVPAPIHAGGLRYHGMAPIVSHLLEERLIEARAFDQIETFT 367 Query: 360 AAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418 A + +G +PAPE+ HAI AVV EA+ A++ + KVI+FN SGHG +DL++Y++ + Sbjct: 368 AGVQWARAEGFIPAPETTHAIAAVVQEALRAKEEGKEKVILFNWSGHGYVDLASYDAFL 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: 497 Number of extensions: 24 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: 453 Length adjustment: 32 Effective length of query: 393 Effective length of database: 421 Effective search space: 165453 Effective search space used: 165453 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