Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate NP_661098.1 CT0192 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000006985.1:NP_661098.1 Length = 458 Score = 387 bits (994), Expect = e-112 Identities = 194/422 (45%), Positives = 284/422 (67%), Gaps = 7/422 (1%) Query: 1 MVKEDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIK 60 ++ EDE +P+ WYNI DLP P+PPP G D L + P ++ Q+ + ER+I Sbjct: 9 LLSEDE-MPRQWYNIQADLPSPMPPPVGLDGNPIGP-DALAKVFPMNLIEQEVSTERWID 66 Query: 61 IPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAK 120 IPEE+ L + RP+PL+RA+RLE L TPA+IY+K EG +P GSHK NTA+ QA++ + Sbjct: 67 IPEEILG-ILKLWRPSPLYRARRLEAALGTPAKIYYKNEGVSPAGSHKPNTAVAQAWYNR 125 Query: 121 EEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYAS 180 E GI+++ TETGAGQWG+A+A++ + ++ +FMV++S++QKP R+ +M +GA S Sbjct: 126 EFGIKYLTTETGAGQWGSALAMSCKLIGIECKVFMVRISFDQKPFRKIMMNTWGAECIPS 185 Query: 181 PTNLTEYGRKILETNPQHPGSLGIAMSEAIEYAL-KNEFRYLVGSVLDVVLLHQSVIGQE 239 P+ LT GR+ILE +P PGSLGIA+SEAIE A+ +++ RY +GSVL+ V+LHQ++IG E Sbjct: 186 PSPLTAVGRRILEEDPDTPGSLGIAISEAIEQAVERDDTRYALGSVLNHVMLHQTIIGLE 245 Query: 240 TITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK---KGKRYIAVSSAEIPKFSKGEY 296 Q D +G DI+IGC GGGSNF G ++PF+ +K K + IA P ++ Y Sbjct: 246 ARKQFDKIGRYPDIVIGCAGGGSNFAGISFPFLYDKIHGKDVQVIATEPEACPTLTRAPY 305 Query: 297 KYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 YD D A + PL+ M +LG ++PP I+AGGLRYHG+AP +S + G++E + E Sbjct: 306 AYDSGDVAMMTPLLPMHSLGHTFIPPAIHAGGLRYHGMAPLVSHTKQLGLIEATALPQTE 365 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYES 416 +EAA +F +G +PAPE++HAI + EA +A++ + KVI+ N SGHGL+DL Y++ Sbjct: 366 CYEAALLFAHTEGFIPAPETSHAIAQTIREAKQAKEEGKEKVILMNWSGHGLMDLQGYDA 425 Query: 417 MM 418 M Sbjct: 426 YM 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: 521 Number of extensions: 25 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: 458 Length adjustment: 32 Effective length of query: 393 Effective length of database: 426 Effective search space: 167418 Effective search space used: 167418 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