Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_049754194.1 HM1_RS13920 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000019165.1:WP_049754194.1 Length = 462 Score = 408 bits (1049), Expect = e-118 Identities = 202/419 (48%), Positives = 284/419 (67%), Gaps = 5/419 (1%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPE 63 +++ +P WYN+ D+P P P P L + P E+++Q+ + ER+++IPE Sbjct: 21 DEKSIPTAWYNVQADMPNPAEPALHPGTLQPLGPADLTPLFPMELIKQEVSTERWVEIPE 80 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 EVR+ Y RPTP++RA LE+ L TPA+IY+KYEG +P GSHK+NTA+PQAY+ K G Sbjct: 81 EVRELYKQ-WRPTPVYRATGLEKLLDTPAKIYYKYEGTSPAGSHKLNTALPQAYYNKAAG 139 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 I+ + TETGAGQWG+A++LA + + ++ ++MVKVSY QKP R++ MQ+YGA V SP+ Sbjct: 140 IKRLATETGAGQWGSALSLACTFFGLECVVYMVKVSYNQKPYRKAFMQVYGAEVIPSPSM 199 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQETIT 242 T GR++LE NP PGSLGIA+SEA+E A+ E Y +GSVL+ V+LHQ+VIG E Sbjct: 200 RTASGRQVLELNPDSPGSLGIAISEAVEDAVSREDTNYALGSVLNHVILHQTVIGLEAKA 259 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEYKYD 299 QL ++ E D+++GC GGGSNF G +PF+ ++ K R +AV P +KG Y YD Sbjct: 260 QLAMVDEYPDVVLGCCGGGSNFAGIAFPFLADRFQGKKVRLVAVEPDACPTLTKGVYAYD 319 Query: 300 FPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFE 359 + D A L P+ KM TLG D++PP ++GGLRYHG +P +S L EG +E + Y +R IFE Sbjct: 320 YGDLAKLTPVAKMYTLGHDFIPPGFHSGGLRYHGDSPLVSQLYHEGFLEAQAYGQRTIFE 379 Query: 360 AAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418 AA F ++GI+PAPESAHAI + EA A++ E + I+F LSGHG+ DL YE+ + Sbjct: 380 AALAFARSEGIIPAPESAHAIAGAIAEAKAAKEAGEARTILFCLSGHGIFDLGAYEAYL 438 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: 512 Number of extensions: 29 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: 462 Length adjustment: 32 Effective length of query: 393 Effective length of database: 430 Effective search space: 168990 Effective search space used: 168990 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