Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate 354190 BT_4664 tryptophan synthase subunit beta (RefSeq)
Query= uniprot:P50383 (425 letters) >FitnessBrowser__Btheta:354190 Length = 456 Score = 385 bits (988), Expect = e-111 Identities = 196/420 (46%), Positives = 278/420 (66%), Gaps = 7/420 (1%) Query: 5 DEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFT-IERYIKIPE 63 +E +P YWYNI D+ PP P + + L I KE+ Q+ + +I+IPE Sbjct: 12 EEEIPHYWYNIQADMVNKPMPPLHPGTKQPLKAEDLYPIFAKELCHQELNQTDAWIEIPE 71 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 +VR+ Y R TPL RA LE+ L TPA IYFK E +P GSHK+N+A+ QAY+ KEEG Sbjct: 72 DVREMY-KYYRSTPLVRAYGLEKALGTPAHIYFKNESVSPIGSHKLNSALAQAYYCKEEG 130 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 + +V TETGAGQWG A++ AA ++ +++ ++ VK+SYEQKP RRSIMQ +GA V SP+ Sbjct: 131 VTNVTTETGAGQWGAALSYAAKVFGLEAAVYQVKISYEQKPYRRSIMQTFGAQVTPSPSM 190 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYA-LKNEFRYLVGSVLDVVLLHQSVIGQETIT 242 T G+ IL +P + GSLG A+SEAIE A + +Y +GSVL V LHQ++IG E Sbjct: 191 STRAGKDILTAHPTYQGSLGTAISEAIELAQMTPNCKYTLGSVLSHVTLHQTIIGLEAEK 250 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK----KGKRYIAVSSAEIPKFSKGEYKY 298 Q+++ GE D++IGC GGGSNFGG ++PF+ + K R++A A PK ++G+++Y Sbjct: 251 QMEMAGEYPDVVIGCFGGGSNFGGISFPFMRHNILEGKKTRFVAAEPASCPKLTRGKFQY 310 Query: 299 DFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIF 358 DF D AG PL+ M TLG ++ P I+AGGLRYHG +S L K+ ++E + + E F Sbjct: 311 DFGDEAGYTPLLPMFTLGHNFAPAHIHAGGLRYHGAGVIVSQLLKDNLMEAVDIQQLESF 370 Query: 359 EAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418 EA +F + +GI+PAPES+HAI A + EA ++ E KVI+FNLSGHGL+D+++Y+ + Sbjct: 371 EAGCLFAQAEGIIPAPESSHAIAAAIREAKACKETGEEKVILFNLSGHGLIDMASYDKYL 430 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: 497 Number of extensions: 21 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: 456 Length adjustment: 32 Effective length of query: 393 Effective length of database: 424 Effective search space: 166632 Effective search space used: 166632 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