Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_077279759.1 B1C78_RS13820 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_002000365.1:WP_077279759.1 Length = 452 Score = 416 bits (1068), Expect = e-120 Identities = 207/423 (48%), Positives = 292/423 (69%), Gaps = 7/423 (1%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ E+EI P +WYN++ D+P P PP P G S ++L +I P +L Q+ + ER+I Sbjct: 7 LLDENEI-PTHWYNVMADMPNPPAPPLGPDGKPVSP-EMLGAIFPPGILEQEMSTERWIP 64 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IP+EVR+ L + RP+PL+RA RLE L TPA+IY+KYEG +P GSHK N+A+ QAY+ + Sbjct: 65 IPDEVRE-ILRLWRPSPLYRAHRLEAALGTPAKIYYKYEGVSPAGSHKPNSAVAQAYYNR 123 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 E GI + TETGAGQWG+++ALA M+ ++ ++MVKVSY+QKP RRS+M+ +GA V AS Sbjct: 124 EAGIRRLTTETGAGQWGSSIALAGQMFGLEVRVYMVKVSYDQKPFRRSMMETWGAEVLAS 183 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYAL-KNEFRYLVGSVLDVVLLHQSVIGQE 239 PT++TE GRKIL +P PGSLGIA+SEA+E A + + Y +GSVL+ V+LHQ++IGQE Sbjct: 184 PTDMTESGRKILAQDPNSPGSLGIAISEAVEEAASRPDTNYALGSVLNHVVLHQTIIGQE 243 Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEY 296 Q + +G+ D + GGGSNFGG +PF+ +K + R +AV P ++G Y Sbjct: 244 VKKQFEKVGDYPDAIFAPCGGGSNFGGAAFPFLADKAAGREVRLVAVEPTSCPTLTRGHY 303 Query: 297 KYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 YDF DS GL PL+ M TLG D+VPP I+AGGLRYHG +P +S L KEG++E + Sbjct: 304 AYDFGDSVGLTPLMLMYTLGHDFVPPGIHAGGLRYHGDSPLVSQLYKEGLIEAVAVPQIA 363 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYES 416 F+A F +GI+PAPES HAIRA +DEA+ ++ E + + FNLSGHG D+++++ Sbjct: 364 TFDAGVQFARTEGIIPAPESCHAIRACIDEALRCKEAGEARTLFFNLSGHGHFDMASFDK 423 Query: 417 MMK 419 + Sbjct: 424 YFR 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: 538 Number of extensions: 23 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: 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 09 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