Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_028316557.1 G491_RS0125530 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000429905.1:WP_028316557.1 Length = 458 Score = 398 bits (1023), Expect = e-115 Identities = 205/424 (48%), Positives = 290/424 (68%), Gaps = 11/424 (2%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ EDE +P+ WYNI+ D+ + PP P G S D L + P ++ Q+ + ER+I Sbjct: 7 LLTEDE-MPRQWYNILADIK--MNPPLGPDGNPVSP-DQLAPVFPMNLIEQEVSQERWID 62 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IP+EV D Y ++ RP+PL RA RLE+ L TPARIYFK EG +P GSHK NTA+PQAY+ K Sbjct: 63 IPQEVMDIY-TLWRPSPLVRATRLEKALGTPARIYFKNEGVSPAGSHKPNTAVPQAYYNK 121 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 E GI+ + TETGAGQWG+A++ A + + ++ T++MV++S++QKP R+S+M ++G AS Sbjct: 122 EFGIKKITTETGAGQWGSALSFACAQFGLQCTVYMVRISFDQKPYRKSMMGVWGGKCIAS 181 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKN---EFRYLVGSVLDVVLLHQSVIG 237 P+ LT+ GR LE +P PGSLGIA+SEA+E A+ + E RY +GSVL+ V+LHQ+VIG Sbjct: 182 PSTLTKAGRDALERDPNTPGSLGIAISEAVEAAVSDETGETRYSLGSVLNHVMLHQTVIG 241 Query: 238 QETITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYI---AVSSAEIPKFSKG 294 E QL+ +GE DI+IGC GGGSNF G +PF +K +++ V A P +K Sbjct: 242 LEAKKQLEKVGEYPDIVIGCAGGGSNFAGLAFPFAQDKINGKHVEIYPVEPAACPTLTKA 301 Query: 295 EYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNE 354 + YD D AG PL+ M +LG +VP PI+AGGLRYHG+APT+S L EG+++ + N+ Sbjct: 302 PFVYDHGDVAGYTPLLPMHSLGHAFVPAPIHAGGLRYHGMAPTVSQLVDEGLMDAKSVNQ 361 Query: 355 REIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNY 414 + +EA IF ++G +PAPE+ HAI V+ EA +A++ + KVI+FN SGHG LDL Y Sbjct: 362 LDCYEAGLIFARSEGHIPAPETTHAIAQVIKEANKAKEEGKEKVILFNWSGHGALDLGAY 421 Query: 415 ESMM 418 E + Sbjct: 422 EKYL 425 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: 509 Number of extensions: 22 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: 458 Length adjustment: 32 Effective length of query: 393 Effective length of database: 426 Effective search space: 167418 Effective search space used: 167418 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