Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_011780137.1 MVAN_RS14695 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000015305.1:WP_011780137.1 Length = 433 Score = 365 bits (937), Expect = e-105 Identities = 191/413 (46%), Positives = 264/413 (63%), Gaps = 10/413 (2%) Query: 8 LPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRD 67 +P +WYN+ +L +P+PP P D L + ++ Q+ E YI+IP+EVR+ Sbjct: 17 VPTHWYNLAAELDEPIPPHLHPGTREPVGPDDLAPLFASALIAQEVASETYIEIPQEVRE 76 Query: 68 RYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127 Y ++ RP+PL RA+R E+ L T A IY KYEG +P GSHK N+A+ QAY+ +G+ + Sbjct: 77 IY-AMWRPSPLIRARRFEKALNTGAHIYVKYEGVSPVGSHKTNSAVAQAYYNHIDGVRKL 135 Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187 TETGAGQWG+A++ A + + ++ ++ V+ SYE KP R +++ YG V++SP+ LTE Sbjct: 136 TTETGAGQWGSALSFAGAQFGLEVEVWQVRASYESKPYRGHLIRTYGGTVHSSPSTLTEA 195 Query: 188 GRKILETNPQHPGSLGIAMSEAIEYALKN-EFRYLVGSVLDVVLLHQSVIGQETITQLDL 246 GR IL +P GSLG+A+SEA+E A + E RY +GSVL+ V+LHQ+VIGQE + QL L Sbjct: 196 GRAILAKDPDTTGSLGMAVSEAVEVAAADPEARYALGSVLNHVVLHQTVIGQEAVAQLAL 255 Query: 247 LGED-ADILIGCVGGGSNFGGFTYPFIGNK----KGKRYIAVSSAEIPKFSKGEYKYDFP 301 + D AD++ GC GGGSN G ++PF+ K R +A A P ++GEY+YD Sbjct: 256 VEPDGADVVFGCAGGGSNLAGLSFPFLREKIHGRSNPRIVAAEPAACPSITRGEYRYDHG 315 Query: 302 DSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAA 361 D AGL PL+KM TLG D+VP PI+AGGLRYHG+AP LS + G+VE ++ + F A Sbjct: 316 DVAGLTPLLKMHTLGMDFVPDPIHAGGLRYHGMAPALSHTVELGLVEGVAISQHDAFAAG 375 Query: 362 KIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNY 414 F QGIVPAPES HAI A A + +V+V LSGHG LDL Y Sbjct: 376 VQFARTQGIVPAPESTHAIAAA---AAHVADDPREQVVVIGLSGHGQLDLPAY 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: 477 Number of extensions: 27 Number of successful extensions: 7 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: 433 Length adjustment: 32 Effective length of query: 393 Effective length of database: 401 Effective search space: 157593 Effective search space used: 157593 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