Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_092056130.1 BQ4888_RS07930 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900111775.1:WP_092056130.1 Length = 450 Score = 417 bits (1073), Expect = e-121 Identities = 205/419 (48%), Positives = 296/419 (70%), Gaps = 6/419 (1%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ ED I PKYWYN+IPD+P PL P P + + L I P ++ Q+ + +R+I+ Sbjct: 6 LLPEDRI-PKYWYNVIPDMPGPLAPVIHPGTMQPVKPEDLLPIFPMPLIEQEVSQQRWIE 64 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IPE VR+ + I RP+PLFRA RLE+ L TPA+IY+KYEG +P GSHK N+A+PQAYF K Sbjct: 65 IPEPVREIF-RIWRPSPLFRAHRLEKALGTPAKIYYKYEGVSPAGSHKPNSAVPQAYFNK 123 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 G + + TETGAGQWG ++ALA M+ ++ T++MVKVS+ QKP R+S+MQL+GANV S Sbjct: 124 ISGTKRIATETGAGQWGCSIALACQMFGLECTVYMVKVSFAQKPYRKSMMQLWGANVIPS 183 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQE 239 P++ T GR +L +P++ GSLG+A+SEA+E A+ E RY +GSVL+ V LHQ++IG E Sbjct: 184 PSDQTNAGRAMLAKDPENGGSLGLAISEAVEDAVSREDTRYALGSVLNHVCLHQTIIGLE 243 Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEY 296 Q+ + G+ D++IGC GGGSNF G +PF+ +K K R +AV A P ++G Y Sbjct: 244 AKEQMAIAGDYPDVVIGCHGGGSNFAGIGFPFVADKANGKQVRVLAVEPASCPTLTRGVY 303 Query: 297 KYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 +D+ D+A + P+ KM TLG D++PP I+AGGLRYHG +P +S L G++E + ++ Sbjct: 304 AFDYGDTAKMAPVAKMYTLGHDFMPPGIHAGGLRYHGASPLVSQLLAAGVIEAKAVHQLA 363 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYE 415 F+AA +F +GI+PAPES+HAIR +DEA++A++ + K I+FNLSGHG +D++ Y+ Sbjct: 364 CFDAAVLFSRTEGIIPAPESSHAIRGAIDEALQAKEEGKEKTILFNLSGHGHVDMTAYD 422 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: 537 Number of extensions: 25 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: 450 Length adjustment: 32 Effective length of query: 393 Effective length of database: 418 Effective search space: 164274 Effective search space used: 164274 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