Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate WP_013684673.1 ARCVE_RS10115 tryptophan synthase subunit beta
Query= BRENDA::Q97TX6 (429 letters) >NCBI__GCF_000194625.1:WP_013684673.1 Length = 386 Score = 157 bits (396), Expect = 7e-43 Identities = 138/413 (33%), Positives = 193/413 (46%), Gaps = 62/413 (15%) Query: 25 LPEELPPPQDPTGKSLELLKEVLPSKVLELEFAKERYVKIPDEVLERYLQV--GRPTPII 82 +PE L PP K+ E LK+ EF KE L+ YL+V GRPTP+ Sbjct: 11 IPEVLMPPLKELEKAYEELKD-------SEEFKKE---------LDYYLRVYAGRPTPLY 54 Query: 83 RAKRLEEYLGNNIKIYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETGAGQWGSS 142 AK L E +G KIYLK E ++G+HKIN+ L AK + ETGAGQ G + Sbjct: 55 FAKNLTEKVGG-AKIYLKREDLLHSGAHKINNTLGQALLAKYMGKNRLIAETGAGQHGVA 113 Query: 143 VALASALFRMKAHIFMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLLAKDSNHP 202 A+A ALF MK I+M + + M++ GAEVHP S G + L KD Sbjct: 114 TAIAGALFGMKTEIYMGSEDVERQKPNVFRMKLLGAEVHPVDS-----GSKTL-KD---- 163 Query: 203 GSLGIAISDAVEYAHKNGGKYVVGSVVNSDIM------FKTIAGMEAKKQ-MELIGEDPD 255 ++ A+ D V A Y++GSVV F+++ G E KKQ +E+ G PD Sbjct: 164 -AINEALRDWV--ATFENTHYLIGSVVGPHPYPTMVRDFQSVIGQETKKQILEVEGCLPD 220 Query: 256 YIIGVVGGGSNYAALAYPFLGDELR--------SGKVRRKYIASGSSEVPKMTKGVYKYD 307 I+ VGGGSN + YPF+ D++R G K+ AS + + G+ Y Sbjct: 221 CIVACVGGGSNAIGIFYPFVKDKVRLIGVEAAGEGIETGKHSASLGAGKKGVLHGMLSYF 280 Query: 308 YPDTAKLLPMLKMYTIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARDYSQEESFK 367 D A GL Y GV P + L G + + E++ K Sbjct: 281 LQDE------------DGQIATTHSVAAGLDYPGVGPEHAYLKESGRAEYVAVTDEQALK 328 Query: 368 WAKLFSELEGYIPAPETSHALPILAEIAEEAKKSGERKTVLVSFSGHGLLDLG 420 S+ EG IPA E++HA+ EIA+E ++ + ++V+ SG G DLG Sbjct: 329 AFAELSKAEGIIPALESAHAVAYAMEIAKEMQRD---EIIVVNLSGRGDKDLG 378 Lambda K H 0.316 0.135 0.392 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: 442 Number of extensions: 25 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: 429 Length of database: 386 Length adjustment: 31 Effective length of query: 398 Effective length of database: 355 Effective search space: 141290 Effective search space used: 141290 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_013684673.1 ARCVE_RS10115 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00263.hmm # target sequence database: /tmp/gapView.15567.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00263 [M=385] Accession: TIGR00263 Description: trpB: tryptophan synthase, beta subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-203 661.7 0.4 2.1e-203 661.5 0.4 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013684673.1 ARCVE_RS10115 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684673.1 ARCVE_RS10115 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 661.5 0.4 2.1e-203 2.1e-203 2 383 .. 2 382 .. 1 384 [. 0.99 Alignments for each domain: == domain 1 score: 661.5 bits; conditional E-value: 2.1e-203 TIGR00263 2 kfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiyl 70 kfgefGGq++pevl++ l+elekaye++k+ eefkkel+++l+ yagrptpl+faknl++k+ggakiyl lcl|NCBI__GCF_000194625.1:WP_013684673.1 2 KFGEFGGQFIPEVLMPPLKELEKAYEELKDSEEFKKELDYYLRVYAGRPTPLYFAKNLTEKVGGAKIYL 70 69******************************************************************* PP TIGR00263 71 kredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqkl 139 kredllh+Gahkinn+lgqallak++Gk+r+iaetGaGqhGvata+a+al+g++ e+ymG+edverqk+ lcl|NCBI__GCF_000194625.1:WP_013684673.1 71 KREDLLHSGAHKINNTLGQALLAKYMGKNRLIAETGAGQHGVATAIAGALFGMKTEIYMGSEDVERQKP 139 ********************************************************************* PP TIGR00263 140 nvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevk 208 nvfrm+llga+v+pv+sGsktlkda+nealrdWv++ e+thy++Gs+vGphP+P++vr+fqsvig+e+k lcl|NCBI__GCF_000194625.1:WP_013684673.1 140 NVFRMKLLGAEVHPVDSGSKTLKDAINEALRDWVATFENTHYLIGSVVGPHPYPTMVRDFQSVIGQETK 208 ********************************************************************* PP TIGR00263 209 eqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGa 277 +qile eg lPd ++acvGGGsnaiGif++f++d+ v+ligvea+G+Gi+t kh+a+l +Gk+GvlhG+ lcl|NCBI__GCF_000194625.1:WP_013684673.1 209 KQILEVEGCLPDCIVACVGGGSNAIGIFYPFVKDK-VRLIGVEAAGEGIETGKHSASLGAGKKGVLHGM 276 *********************************98.********************************* PP TIGR00263 278 ktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipales 346 +++lqdedGqi ++hsv+aGldypgvgPeha+l+e+graey+a+tde+al+a+ lsk eGiipales lcl|NCBI__GCF_000194625.1:WP_013684673.1 277 LSYFLQDEDGQIATTHSVAAGLDYPGVGPEHAYLKESGRAEYVAVTDEQALKAFAELSKAEGIIPALES 345 ********************************************************************* PP TIGR00263 347 shalaaleklapklkkdeivvvnlsGrGdkdletvak 383 +ha+a+++++a+++++dei+vvnlsGrGdkdl v++ lcl|NCBI__GCF_000194625.1:WP_013684673.1 346 AHAVAYAMEIAKEMQRDEIIVVNLSGRGDKDLGIVME 382 ********************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (386 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.87 // [ok]
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