Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_010936730.1 DET_RS05355 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000011905.1:WP_010936730.1 Length = 454 Score = 400 bits (1029), Expect = e-116 Identities = 203/423 (47%), Positives = 294/423 (69%), Gaps = 9/423 (2%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDP-QGAYFSRIDLLRSILPKEVLRQQFTIERYIKIP 62 +++ +P+ WYNI PDLP PLPP P G + D+ +I P ++ Q+F+ ER+I IP Sbjct: 9 QEKDMPQVWYNIQPDLPVPLPPVLHPGTGQPVTPADM-EAIFPMSLIMQEFSPERHIPIP 67 Query: 63 EEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEE 122 EE+ + Y I RPTPL+RA RLE+ L+TPA+I++K E +P GSHK NTA+ QAY+ K+ Sbjct: 68 EELLEIY-KIWRPTPLYRAHRLEKALQTPAKIFYKLEDVSPAGSHKPNTALAQAYYNKKA 126 Query: 123 GIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPT 182 GI+ + TETGAGQWG+++A+A ++++ ++MVKVSY KP RR +M+ +GA+V SP+ Sbjct: 127 GIKRISTETGAGQWGSSLAMACKFFDIECKVYMVKVSYNMKPYRRVMMETWGASVVPSPS 186 Query: 183 NLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQETI 241 T+ GR+ILE +P+ PGSLGIA+SEA+E A+ + +Y +GSVL+ VLLHQ++IGQE Sbjct: 187 PDTKIGREILERDPECPGSLGIAISEAVEDAVTHPGTKYALGSVLNHVLLHQTIIGQEAK 246 Query: 242 TQLDLLGEDADILIGCVGGGSNFGGFTYPFI-----GNKKGKRYIAVSSAEIPKFSKGEY 296 Q+ + DI+IGCVGGGSNFGG PF+ G K R +AV A P +KG Sbjct: 247 KQMAMADCYPDIVIGCVGGGSNFGGIALPFVEDKLNGTHKDTRIMAVEPASCPSLTKGLD 306 Query: 297 KYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 YDF D AG+ P++KM TLG ++PPP++AGGLRYHG++P LS L++ ++E N+ E Sbjct: 307 AYDFGDEAGMTPMMKMFTLGHQFMPPPVHAGGLRYHGMSPLLSHLSRLNLIEATAVNQIE 366 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYES 416 FEA F + +G + APE+ HAIRA +DEA++ R+ E K I+F SGHG +D+++Y+ Sbjct: 367 TFEAGIQFAQTEGFISAPETNHAIRATIDEALKCRETGEAKTILFCHSGHGHVDMASYDL 426 Query: 417 MMK 419 ++ Sbjct: 427 YLR 429 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: 470 Number of extensions: 22 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: 454 Length adjustment: 32 Effective length of query: 393 Effective length of database: 422 Effective search space: 165846 Effective search space used: 165846 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