Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_027457405.1 K420_RS0106755 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000519045.1:WP_027457405.1 Length = 454 Score = 389 bits (998), Expect = e-112 Identities = 199/420 (47%), Positives = 272/420 (64%), Gaps = 10/420 (2%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPE 63 E E +P +WYN++ D+P P PP P G + + +I P +L Q+ + ER+I IPE Sbjct: 9 EQEEIPTHWYNVVADMPNPPAPPLGPDGNPVPP-EAMGAIFPGPILEQEMSAERWIPIPE 67 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 +VR Y RP PL RA RLE+ L TPA+I+FKYEG +P GSHK N+A+PQAY+ K G Sbjct: 68 DVRQIYAQ-WRPAPLCRALRLEQMLGTPAKIFFKYEGVSPAGSHKPNSAVPQAYYNKLAG 126 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 + + TETGAGQWG+++A A M+ + +FMV VSY+QKP RRS+MQ +GA V+ASPTN Sbjct: 127 TKKLTTETGAGQWGSSIAYAGQMFGLPVRVFMVNVSYQQKPFRRSMMQTWGAEVFASPTN 186 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYALKN-EFRYLVGSVLDVVLLHQSVIGQETIT 242 LT GR L +P GSLG+A+SEA+E A + Y +GSVL+ VLLHQ+VIG E Sbjct: 187 LTNAGRTALAADPDCQGSLGLAISEAVEEAAADPNTCYTLGSVLNHVLLHQTVIGLEAKK 246 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK-------KGKRYIAVSSAEIPKFSKGE 295 Q D +G D++ G GGGS+FGG +PF+ +K R +AV P +KG Sbjct: 247 QFDKIGLYPDVIFGPCGGGSSFGGIAFPFLADKAAGDKRAANLRCVAVEPTSCPTLTKGV 306 Query: 296 YKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNER 355 Y YD+ D++G P++KM TLG D++PP I+AGGLRYHG +P +S L E ++E + Sbjct: 307 YTYDYGDASGYTPIMKMYTLGHDFMPPGIHAGGLRYHGDSPLVSQLFHEKLLEAVAVPQV 366 Query: 356 EIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYE 415 FEA F +GI+PAPES H IRA +DEA+ + E K I+F L+GHG D+++Y+ Sbjct: 367 ATFEAGVQFARAEGIIPAPESCHGIRAAIDEALRCKATGEAKTILFCLTGHGHFDMASYD 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: 521 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