Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate AZOBR_RS00525 AZOBR_RS00525 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >FitnessBrowser__azobra:AZOBR_RS00525 Length = 405 Score = 133 bits (334), Expect = 1e-35 Identities = 117/365 (32%), Positives = 169/365 (46%), Gaps = 56/365 (15%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP PL+ A+RL E L A+IYFK E TG+HKIN I Q A+ G + ++ ET Sbjct: 61 VGRPNPLYYAERLTEKLGG-AKIYFKREELNHTGAHKINNCIGQILLARRMGKKRIIAET 119 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A ++++M I+M + ++ M+L GA V +T R + Sbjct: 120 GAGQHGVATATVCALFDMPCVIYMGETDIARQQPNVFRMKLLGAEV----VPVTSGARTL 175 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 + AM+EA+ + N + YL+G+ +V QSVIG E Q Sbjct: 176 KD-----------AMNEALRDWVTNVADTYYLIGTAAGPHPYPAMVRDFQSVIGDEVRVQ 224 Query: 244 L-DLLGEDADILIGCVGGGSNFGGFTYPFI---------------GNKKGKRYIAVS-SA 286 + +L G D L+ CVGGGSN G +PF+ G KG A S + Sbjct: 225 MQELEGRLPDSLVACVGGGSNAIGLFHPFLDDPSVQMVAVEAAGHGIDKGPLAHAASITG 284 Query: 287 EIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGI 346 P G Y D G + I+ G D Y GV P S L G Sbjct: 285 GRPGVLHGNRTYLLQDEDGQILEGHSISAGLD------------YPGVGPEHSWLHDIGR 332 Query: 347 VEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGH 406 VE+ ++E +A ++ +GI+PA ESAHA+ +V A + K++ ++V LSG Sbjct: 333 VEYVSATDQETLDAFQLCARTEGIIPALESAHALAEIVKRAPKLPKDH---LMVLCLSGR 389 Query: 407 GLLDL 411 G D+ Sbjct: 390 GDKDI 394 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: 354 Number of extensions: 12 Number of successful extensions: 3 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: 405 Length adjustment: 31 Effective length of query: 394 Effective length of database: 374 Effective search space: 147356 Effective search space used: 147356 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 AZOBR_RS00525 AZOBR_RS00525 (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.22052.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-196 636.2 0.0 1.1e-195 636.1 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS00525 AZOBR_RS00525 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS00525 AZOBR_RS00525 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 636.1 0.0 1.1e-195 1.1e-195 1 384 [. 15 400 .. 15 401 .. 0.99 Alignments for each domain: == domain 1 score: 636.1 bits; conditional E-value: 1.1e-195 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG++v+e+l++ + e+ekay++a++d++f+ ++e lk+y+grp pl++a++l++klggakiy lcl|FitnessBrowser__azobra:AZOBR_RS00525 15 GHFGIYGGRFVAETLMPLILEVEKAYREARADPAFEGAIREQLKQYVGRPNPLYYAERLTEKLGGAKIY 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 +kre+l+htGahkinn +gq+lla+r+GkkriiaetGaGqhGvatat++al+++ c++ymG++d++rq+ lcl|FitnessBrowser__azobra:AZOBR_RS00525 84 FKREELNHTGAHKINNCIGQILLARRMGKKRIIAETGAGQHGVATATVCALFDMPCVIYMGETDIARQQ 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nvfrm+llga+vvpvtsG +tlkda+nealrdWvt+v+dt+y++G+a+GphP+P++vr+fqsvig+ev lcl|FitnessBrowser__azobra:AZOBR_RS00525 153 PNVFRMKLLGAEVVPVTSGARTLKDAMNEALRDWVTNVADTYYLIGTAAGPHPYPAMVRDFQSVIGDEV 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidt..ekhaatlskGkeGvl 274 + q++e egrlPd ++acvGGGsnaiG+f++f++d++v++++vea+G+Gid+ haa+++ G++Gvl lcl|FitnessBrowser__azobra:AZOBR_RS00525 222 RVQMQELEGRLPDSLVACVGGGSNAIGLFHPFLDDPSVQMVAVEAAGHGIDKgpLAHAASITGGRPGVL 290 ***************************************************97678************* PP TIGR00263 275 hGaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipa 343 hG++t+llqdedGqi e hs+saGldypgvgPeh++l+++gr+ey+++td+e+l+a++l++++eGiipa lcl|FitnessBrowser__azobra:AZOBR_RS00525 291 HGNRTYLLQDEDGQILEGHSISAGLDYPGVGPEHSWLHDIGRVEYVSATDQETLDAFQLCARTEGIIPA 359 ********************************************************************* PP TIGR00263 344 lesshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 les+hala ++k apkl+kd+++v+ lsGrGdkd+++va++ lcl|FitnessBrowser__azobra:AZOBR_RS00525 360 LESAHALAEIVKRAPKLPKDHLMVLCLSGRGDKDIFSVAQH 400 **************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (405 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: 10.23 // [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