Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate GFF2997 HP15_2941 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >FitnessBrowser__Marino:GFF2997 Length = 452 Score = 416 bits (1069), Expect = e-121 Identities = 201/418 (48%), Positives = 288/418 (68%), Gaps = 6/418 (1%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPE 63 E+ +PKYWYN+ DLP+PLP P L + P ++ Q+ T ER I+IPE Sbjct: 8 EESQMPKYWYNLQADLPEPLPAVLHPGTQQPVGPSDLEPLFPMALIEQEVTTEREIEIPE 67 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 VRD Y ++ RP PL+RA RLE+ L TPA+I++KYEG +P GSHK NTAIPQA++ +E G Sbjct: 68 PVRDVY-NLWRPAPLYRAHRLEKALGTPAKIFYKYEGVSPAGSHKPNTAIPQAFYNREAG 126 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 I + TETGAGQWGT+++ A S++++ T+F V+VSY QKP RR++M+ YGA ASP+ Sbjct: 127 IRTLTTETGAGQWGTSLSFAGSLFDIDVTVFQVRVSYNQKPYRRAVMETYGAKCVASPSE 186 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYALKN-EFRYLVGSVLDVVLLHQSVIGQETIT 242 LTE+GRK+L P H GSLGIA+SEA+E A+++ +Y +GSVL+ VLLHQS+IG E + Sbjct: 187 LTEFGRKVLAETPDHTGSLGIAISEAVELAVQDPNTKYALGSVLNHVLLHQSIIGLEAMQ 246 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK----KGKRYIAVSSAEIPKFSKGEYKY 298 Q+++ D+++GC GGGSNF G +PF+G+ + R +AV + P ++G+Y Y Sbjct: 247 QMEMADCWPDVIVGCTGGGSNFAGIAFPFMGHALRGGEKSRIVAVEPSACPTLTRGKYAY 306 Query: 299 DFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIF 358 D+ D+A + PL KM TLG + PP +AGGLRYHG+AP +S + G+ + Y +RE F Sbjct: 307 DYGDTAHMTPLTKMHTLGSGFTPPGFHAGGLRYHGMAPLVSHAKELGLFDAVSYTQRECF 366 Query: 359 EAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYES 416 EA +F +N+GIVPAPE+ HA++ +DEA+ ++ + +VI+FNL GHG D++ Y S Sbjct: 367 EAGVLFAKNEGIVPAPEANHAVKGAIDEALRCKREGKEEVILFNLCGHGHFDMAAYTS 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: 487 Number of extensions: 27 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