Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__Keio:17422 Length = 406 Score = 555 bits (1431), Expect = e-163 Identities = 270/404 (66%), Positives = 322/404 (79%) Query: 1 MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60 M+ + RA FD ++P YAPA FIPV+G+GSR+WDQ G+E +DFAGGIAVT+LGH H Sbjct: 1 MAIEQTAITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCH 60 Query: 61 PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120 PALV AL Q + +WH+SNVFTNEPALRL RKL++ATFAERV NSG EANE AFKLAR Sbjct: 61 PALVNALKTQGETLWHISNVFTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLAR 120 Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180 YA + P K +IIA N+FHGR+LFTV+VGGQPKYSDGFGPK I HVP+NDL A+K Sbjct: 121 HYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVK 180 Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240 A + D TCAVV+EPIQGEGGV A +L+G R+LCD+H ALLVFDEVQ GMGR G+LFA Sbjct: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFA 240 Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300 YMHYGV PDIL+SAK+LGGGFPI AMLTT EIA G+HG+TYGGNPLA AVA AA D Sbjct: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFD 300 Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360 +INTPEVL+G++AK +RF LQKI Q+Y +F +IRGMGLLIGA L ++KG+ARD L A Sbjct: 301 IINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYA 360 Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 + VMVL A PDV+RFAPSLV++DA+IDEG++RF AVAK+V Sbjct: 361 GAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAKVV 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: 551 Number of extensions: 14 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 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 17422 b3359 (bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI))
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.15959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-209 680.5 0.3 4.2e-209 680.3 0.3 1.0 1 lcl|FitnessBrowser__Keio:17422 b3359 bifunctional acetylornithi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotra # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 680.3 0.3 4.2e-209 4.2e-209 1 397 [] 8 404 .. 8 404 .. 1.00 Alignments for each domain: == domain 1 score: 680.3 bits; conditional E-value: 4.2e-209 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepv 79 ++r++fdev++p+yapa+fipv+g+Gsr+wdq+gkey+dfaGGiav+alGh+hp+lv+alk q+e+lwh++n++tnep+ lcl|FitnessBrowser__Keio:17422 8 ITRATFDEVILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNVFTNEPA 86 79***************************************************************************** PP TIGR03246 80 lrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplp 158 lrl +kl++atfa++v f nsG+eane+a+klar++a ++++ k++i+af+n+fhGr+lftvsvGGq+kys++f+p+p lcl|FitnessBrowser__Keio:17422 87 LRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKP 165 ******************************************************************************* PP TIGR03246 159 egikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymey 237 ++i h+++ndl+a+ka+++d+tcav+vepiqGegGv++a+++fl+glrelcd+h+all+fdevq G+GrtG+l+aym+y lcl|FitnessBrowser__Keio:17422 166 ADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHY 244 ******************************************************************************* PP TIGR03246 238 GvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdele 316 GvtpdiltsakalGgGfpi a+ltt e+a++++ G+hG+tyGGnplacava++ +d++nt+e+leG++++ ++fvd+l+ lcl|FitnessBrowser__Keio:17422 245 GVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKRQRFVDHLQ 323 ******************************************************************************* PP TIGR03246 317 kinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekavek 395 ki+++y+vfs+irG+GlliGa+l+ +y+G+a+d++ a ae+Gv+vl aGpdv+rfapslv+e+++i+eG++r+++av+k lcl|FitnessBrowser__Keio:17422 324 KIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEAGVMVLNAGPDVMRFAPSLVVEDADIDEGMQRFAHAVAK 402 *****************************************************************************99 PP TIGR03246 396 lv 397 +v lcl|FitnessBrowser__Keio:17422 403 VV 404 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (406 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7.68 // [ok]
This GapMind analysis is from Sep 17 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