Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_900105005.1:WP_090273343.1 Length = 404 Score = 554 bits (1427), Expect = e-162 Identities = 268/399 (67%), Positives = 321/399 (80%) Query: 7 QVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKA 66 QV RADFDR MVPNYAP IPVRG+GSR+WDQ GRE ID AGGIAV SLGHAHP LV+A Sbjct: 6 QVNRADFDRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEA 65 Query: 67 LTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDV 126 LTEQAQ++WHVSN+ TNEPALRLA KLV ATFA++V NSGAEANEAAFKLARR+A+D Sbjct: 66 LTEQAQKLWHVSNIMTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQ 125 Query: 127 YGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDK 186 GP K+EIIA SNSFHGRTLFTV+VGGQPKYS GFGP GI+HVPYND+ AL+A IS++ Sbjct: 126 SGPDKHEIIACSNSFHGRTLFTVSVGGQPKYSQGFGPAISGISHVPYNDIAALEAQISER 185 Query: 187 TCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGV 246 TCAVV+EP+QGEGGV+PA YL+ R LCD++NALL+FDEVQSGMGR G+L+AYMH GV Sbjct: 186 TCAVVVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGV 245 Query: 247 VPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPE 306 PDIL+SAK +GGGFPI AMLT +A LSVGTHG+TYGGNPL AVAE LD+INTP+ Sbjct: 246 APDILTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQ 305 Query: 307 VLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAV 366 VLDGV + + + L+ + E G+F EIRG GLLIGA L + W+G+A V+ A++E + Sbjct: 306 VLDGVGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGL 365 Query: 367 MVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLVR 405 +VLQA DVVR APSL+I +A+I E L R A+ +L++ Sbjct: 366 LVLQAGADVVRLAPSLIIPEADIREALGRMRAALLRLIK 404 Lambda K H 0.318 0.135 0.394 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: 544 Number of extensions: 15 Number of successful extensions: 1 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: 406 Length of database: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 WP_090273343.1 BLU11_RS10765 (aspartate aminotransferase family protein)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))
# 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.carbon/TIGR03246.hmm # target sequence database: /tmp/gapView.525849.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03246 [M=397] Accession: TIGR03246 Description: arg_catab_astC: succinylornithine transaminase family 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-205 669.1 0.1 1.2e-205 668.9 0.1 1.0 1 NCBI__GCF_900105005.1:WP_090273343.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900105005.1:WP_090273343.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.9 0.1 1.2e-205 1.2e-205 1 396 [. 7 402 .. 7 403 .. 0.99 Alignments for each domain: == domain 1 score: 668.9 bits; conditional E-value: 1.2e-205 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgng 73 v+r++fd +mvp+yap ++ipvrg+Gsr+wdq+g+eyid+aGGiavn+lGhahp+lveal+eqa+klwh++n NCBI__GCF_900105005.1:WP_090273343.1 7 VNRADFDRLMVPNYAPVEMIPVRGDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVSNI 79 79*********************************************************************** PP TIGR03246 74 ytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGG 146 +tnep+lrla klv atfadkv f nsGaeaneaa+klar++a+d+ g++k+ei+a+ nsfhGrtlftvsvGG NCBI__GCF_900105005.1:WP_090273343.1 80 MTNEPALRLADKLVAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKHEIIACSNSFHGRTLFTVSVGG 152 ************************************************************************* PP TIGR03246 147 qakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifd 219 q+kys++f+p ++gi+h++ynd++al+a+is++tcav+vep+qGegGv+pa+ ++lk++r+lcd++nallifd NCBI__GCF_900105005.1:WP_090273343.1 153 QPKYSQGFGPAISGISHVPYNDIAALEAQISERTCAVVVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFD 225 ************************************************************************* PP TIGR03246 220 evqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvl 292 evq+G+GrtG+lyaym+ Gv+pdiltsak++GgGfpi a+lt +++a +l+vGthG+tyGGnpl+cavae+vl NCBI__GCF_900105005.1:WP_090273343.1 226 EVQSGMGRTGKLYAYMHSGVAPDILTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVL 298 ************************************************************************* PP TIGR03246 293 dlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaG 365 d++nt+++l+Gv +r++++++ l + ++ vfseirG+GlliGavl e+++G+a +++++a+eeG+lvl+aG NCBI__GCF_900105005.1:WP_090273343.1 299 DIINTPQVLDGVGERQAQLTAGLRILADELGVFSEIRGQGLLIGAVLAERWRGQAGQVMRLAQEEGLLVLQAG 371 ************************************************************************* PP TIGR03246 366 pdvvrfapslvieeeeikeGlarlekavekl 396 +dvvr+apsl+i+e++i e l r+ a+ +l NCBI__GCF_900105005.1:WP_090273343.1 372 ADVVRLAPSLIIPEADIREALGRMRAALLRL 402 *************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (404 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.49 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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