Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Dsui_1054 Dsui_1054 pyridoxal-phosphate dependent TrpB-like enzyme
Query= uniprot:P50383 (425 letters) >FitnessBrowser__PS:Dsui_1054 Length = 454 Score = 405 bits (1040), Expect = e-117 Identities = 203/420 (48%), Positives = 285/420 (67%), Gaps = 10/420 (2%) Query: 4 EDEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPE 63 E +P +WYNI+ DL P PP P G + + + I P +L Q+ + +R+I IP+ Sbjct: 9 EQNEIPTHWYNIVADLKTPPVPPLGPDGQPATP-EQMGVIFPGAILEQEMSDQRWIPIPQ 67 Query: 64 EVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEG 123 EVR+ Y + RP PL RA RLE+ L T A+IY+KYEG +P GSHK N+A+PQA++ K+ G Sbjct: 68 EVREIY-RLWRPAPLVRAVRLEQALGTTAKIYYKYEGVSPAGSHKPNSAVPQAFYNKQAG 126 Query: 124 IEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTN 183 I+ + TETGAGQWG++++ A M+ + ++MVKVSY+QKP RR +MQ +GA V+ASP+ Sbjct: 127 IKRLTTETGAGQWGSSISFAGQMFGLPVRVYMVKVSYDQKPYRRLMMQTWGAEVFASPSE 186 Query: 184 LTEYGRKILETNPQHPGSLGIAMSEAIEYAL-KNEFRYLVGSVLDVVLLHQSVIGQETIT 242 LT+ GR L NP + GSLG+A+SEA+E A + + Y +GSVL+ VLLHQ+++G E Sbjct: 187 LTQTGRAALAENPDNQGSLGLAISEAVEEAASRPDTNYTLGSVLNHVLLHQTIVGLEAKK 246 Query: 243 QLDLLGEDADILIGCVGGGSNFGGFTYPFIGNK-------KGKRYIAVSSAEIPKFSKGE 295 Q D +GE D++IG GGGS+FGG +PF+ +K + R +AV P +KG Sbjct: 247 QFDKIGEYPDVVIGPCGGGSSFGGIAFPFLADKAAGDKRAENLRCLAVEPTSCPTLTKGA 306 Query: 296 YKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNER 355 Y YDF D++G PL+KM TLG D++PP I+AGGLRYHG +P +S + EG+VE ++ Sbjct: 307 YAYDFGDASGFTPLMKMYTLGHDFMPPGIHAGGLRYHGASPLVSQVVHEGLVEPVAVSQL 366 Query: 356 EIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYE 415 FEA F +GI+PAPES HAIRA +DEA++A+ E KVI+FNL+GHG D+S+YE Sbjct: 367 ATFEAGVQFARAEGIIPAPESCHAIRAAIDEALKAKVTGEPKVILFNLTGHGHFDMSSYE 426 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: 504 Number of extensions: 18 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: 454 Length adjustment: 32 Effective length of query: 393 Effective length of database: 422 Effective search space: 165846 Effective search space used: 165846 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