Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_072906564.1 BUB13_RS05610 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900142125.1:WP_072906564.1 Length = 452 Score = 411 bits (1056), Expect = e-119 Identities = 207/420 (49%), Positives = 292/420 (69%), Gaps = 6/420 (1%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ ED I PK WYNIIPDL P+ P P D L + P ++ Q+ + +R+I Sbjct: 7 ILPEDRI-PKQWYNIIPDLNGPMAPVVHPGTLQPVTPDDLLPLFPMGLIEQEVSTQRWID 65 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IP+EVR + L+ RP+P+FRA RLE+ L TPA+IY+KYEG +P GSHK NTA+PQAY+ Sbjct: 66 IPDEVR-QILAQWRPSPMFRAHRLEKALGTPAKIYYKYEGVSPAGSHKPNTAVPQAYYNM 124 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 G + + +ETGAGQWG+++ALA M+ ++ T++MVKVS++QKP R+S+MQL+GA+V S Sbjct: 125 LAGTKRIASETGAGQWGSSIALACQMFGLECTVYMVKVSFQQKPYRKSMMQLWGADVIPS 184 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQE 239 P+N T GR +LE + GSLGIA+SEA+E A +E RY +GSVL+ V LHQ+VIG E Sbjct: 185 PSNQTNAGRAVLERDQDSNGSLGIAISEAVEDAATHEDTRYCLGSVLNHVCLHQTVIGLE 244 Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEY 296 Q+D++G+ D++I C GGGSNF G +PF+ +K K R +A P +KG Y Sbjct: 245 AKQQMDMIGDYPDVVIACHGGGSNFAGLGFPFVADKAAGKDLRILAAEPISCPTLTKGVY 304 Query: 297 KYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 +D+ D A + P+ KM TLG D++PP I+AGGLRYHG AP +S L EG++E + + E Sbjct: 305 DFDYGDQAKMAPISKMYTLGHDFMPPGIHAGGLRYHGAAPLVSQLLDEGVIEAKAVGQVE 364 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYES 416 FEAA F +GI+PAPES+HAIRA DEA++A++ + K I+FNLSGHG +D+++Y++ Sbjct: 365 CFEAAVQFARAEGIIPAPESSHAIRAAFDEALQAKEEGKEKTILFNLSGHGHVDMASYDA 424 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: 544 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 452 Length adjustment: 32 Effective length of query: 393 Effective length of database: 420 Effective search space: 165060 Effective search space used: 165060 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