Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Ga0059261_0238 Ga0059261_0238 tryptophan synthase, beta subunit
Query= uniprot:P50383 (425 letters) >FitnessBrowser__Korea:Ga0059261_0238 Length = 403 Score = 133 bits (334), Expect = 1e-35 Identities = 113/365 (30%), Positives = 169/365 (46%), Gaps = 58/365 (15%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+PL+ A+RL + A+IYFK E TG+HKIN I Q A G + ++ ET Sbjct: 61 VGRPSPLYFAERLTRHYGG-AKIYFKREELNHTGAHKINNCIGQILLAIRMGKKRIIAET 119 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A + + + TIFM E++ M+L GA Sbjct: 120 GAGQHGVATATVCARFGLPCTIFMGAKDIERQQPNVFRMKLLGA---------------- 163 Query: 192 LETNPQHPGSLGI--AMSEAIE--YALKNEFRYLVGSVL------DVVLLHQSVIGQETI 241 E P GS + AM+EA+ A ++ Y++G+ ++V QSVIG E+ Sbjct: 164 -EVRPVTSGSQSLKDAMNEALRDWVATVHDTFYIIGTAAGPHPYPELVRDFQSVIGTESR 222 Query: 242 TQ-LDLLGEDADILIGCVGGGSNFGGFTYPFIGNK-----------KG---KRYIAVSSA 286 Q L+ G D+LI VGGGSN G +PF+ + KG + A + Sbjct: 223 AQMLEAEGRLPDLLIAAVGGGSNAIGLFHPFLDDNDVAMVGVEAAGKGIDTSEHAASLTG 282 Query: 287 EIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGI 346 P G Y D G + I+ G D Y G+ P S L + G Sbjct: 283 GAPGILHGNKTYLLQDEDGQITEAHSISAGLD------------YPGIGPEHSWLHESGR 330 Query: 347 VEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGH 406 VE+ + + +A ++ + +GI+PA ES+HA+ A+ +A E + K+I+ N+SG Sbjct: 331 VEYLPVTDTQALDAFQLCCKLEGIIPALESSHALAALEHKARELPSD---KIILVNVSGR 387 Query: 407 GLLDL 411 G D+ Sbjct: 388 GDKDI 392 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: 376 Number of extensions: 20 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: 403 Length adjustment: 31 Effective length of query: 394 Effective length of database: 372 Effective search space: 146568 Effective search space used: 146568 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: 50 (23.9 bits)
Align candidate Ga0059261_0238 Ga0059261_0238 (tryptophan synthase, beta subunit)
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.2048.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-198 643.6 0.0 6.5e-198 643.4 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0238 Ga0059261_0238 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0238 Ga0059261_0238 tryptophan synthase, beta subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 643.4 0.0 6.5e-198 6.5e-198 1 384 [. 15 398 .. 15 399 .. 1.00 Alignments for each domain: == domain 1 score: 643.4 bits; conditional E-value: 6.5e-198 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg+fGG+yv+e+l++ + +le++y+ ak+d++f++e++ l+k+y+grp+pl+fa++l++++ggakiy lcl|FitnessBrowser__Korea:Ga0059261_0238 15 GHFGQFGGRYVAETLMPLILDLEREYRAAKADPAFQAEFDGLMKHYVGRPSPLYFAERLTRHYGGAKIY 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 +kre+l+htGahkinn +gq+lla r+GkkriiaetGaGqhGvatat++a++gl c+++mGa+d+erq+ lcl|FitnessBrowser__Korea:Ga0059261_0238 84 FKREELNHTGAHKINNCIGQILLAIRMGKKRIIAETGAGQHGVATATVCARFGLPCTIFMGAKDIERQQ 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nvfrm+llga+v pvtsGs++lkda+nealrdWv++v+dt+y++G+a+GphP+Pe+vr+fqsvig+e lcl|FitnessBrowser__Korea:Ga0059261_0238 153 PNVFRMKLLGAEVRPVTSGSQSLKDAMNEALRDWVATVHDTFYIIGTAAGPHPYPELVRDFQSVIGTES 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++q+le+egrlPd +ia+vGGGsnaiG+f++f++d++v+++gvea+GkGidt++haa+l+ G +G+lhG lcl|FitnessBrowser__Korea:Ga0059261_0238 222 RAQMLEAEGRLPDLLIAAVGGGSNAIGLFHPFLDDNDVAMVGVEAAGKGIDTSEHAASLTGGAPGILHG 290 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 +kt+llqdedGqi+eahs+saGldypg+gPeh++l+e+gr+ey +td++al+a++l++k eGiipale lcl|FitnessBrowser__Korea:Ga0059261_0238 291 NKTYLLQDEDGQITEAHSISAGLDYPGIGPEHSWLHESGRVEYLPVTDTQALDAFQLCCKLEGIIPALE 359 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 sshalaale+ a +l+ d+i++vn+sGrGdkd+ tva+a lcl|FitnessBrowser__Korea:Ga0059261_0238 360 SSHALAALEHKARELPSDKIILVNVSGRGDKDIYTVAQA 398 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (403 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 10.45 // [ok]
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