Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_092481696.1 BM299_RS01495 TrpB-like pyridoxal phosphate-dependent enzyme
Query= uniprot:P50383 (425 letters) >NCBI__GCF_900115975.1:WP_092481696.1 Length = 451 Score = 420 bits (1080), Expect = e-122 Identities = 209/416 (50%), Positives = 292/416 (70%), Gaps = 6/416 (1%) Query: 8 LPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRD 67 +P+ WYN++ D+P PP P + L +I P E+++Q+ + ER+I IPEEV+ Sbjct: 13 MPRQWYNVMADMPNLPKPPLHPATQKPVGPEDLSAIFPMELIKQEVSTERWIDIPEEVQK 72 Query: 68 RYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHV 127 Y + RP+PL RA+RLE+ L TPA+I++KYEG +P GSHK+NTA+PQAY+ K+EGI + Sbjct: 73 IY-RLWRPSPLCRARRLEKALDTPAKIFYKYEGVSPAGSHKLNTAVPQAYYNKKEGINRL 131 Query: 128 VTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEY 187 TETGAGQWG A++ A + + M+ +FMVKVSYEQKP RRS+MQ++G++V SP+N T Sbjct: 132 TTETGAGQWGVALSQACNFFGMECRVFMVKVSYEQKPYRRSMMQIFGSSVVPSPSNETAA 191 Query: 188 GRKILETNPQHPGSLGIAMSEAIEYALKNE-FRYLVGSVLDVVLLHQSVIGQETITQLDL 246 GRK+L +P PGSLGIA+SEA+E A + E Y +GSVL+ V+LHQ+VIGQE Q+ Sbjct: 192 GRKVLAADPDSPGSLGIAISEAVEVAAQREDTNYALGSVLNHVILHQTVIGQEAKEQMAK 251 Query: 247 LGEDADILIGCVGGGSNFGGFTYPFIGNKKGK----RYIAVSSAEIPKFSKGEYKYDFPD 302 GE +I+IGC GGGSNF G +PF+ +K + R IA + P ++G + YDF D Sbjct: 252 AGEYPNIVIGCCGGGSNFAGTAFPFVYDKLVRGAKIRLIAAEPSSCPTLTRGRFGYDFGD 311 Query: 303 SAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAK 362 AGL PL+ M TLG +++PP I+AGGLRYHG +P +S L +GI+E ++ IFE A Sbjct: 312 VAGLTPLLSMYTLGSEFMPPSIHAGGLRYHGDSPLVSQLLHDGIIEATALDQTSIFEGAI 371 Query: 363 IFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418 +F ++GIVPAPESAHAI+ ++EA+ A++ E + I+F LSGHGLLDL +Y+ M Sbjct: 372 MFARSEGIVPAPESAHAIQCAINEALAAKEAGEARTILFTLSGHGLLDLPSYDKFM 427 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: 483 Number of extensions: 26 Number of successful extensions: 6 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: 451 Length adjustment: 32 Effective length of query: 393 Effective length of database: 419 Effective search space: 164667 Effective search space used: 164667 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