Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 538 bits (1385), Expect = e-157 Identities = 266/404 (65%), Positives = 312/404 (77%) Query: 1 MSAPHAQVERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAH 60 M+ + RA FD ++P YAPA FIPV+G+GSRVWDQ G+E +DFAGGIAVT+LGH H Sbjct: 1 MATEQPAITRATFDEVILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCH 60 Query: 61 PALVKALTEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLAR 120 PALV AL EQ +++WH SNVFTNEPALRL RKLVDATFA+RV NSG EANE AFKLAR Sbjct: 61 PALVAALHEQGEKLWHTSNVFTNEPALRLGRKLVDATFADRVVFMNSGTEANETAFKLAR 120 Query: 121 RYANDVYGPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK 180 Y + P K +IIA N+FHGR+LFTV+VGGQPKYSDGFGPK I HVP+NDL A+K Sbjct: 121 HYTVTRHSPYKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIVHVPFNDLHAVK 180 Query: 181 AAISDKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFA 240 A + D TCAVV+EPIQGEGGV A +L+G R LCD+H ALLVFDEVQ GMGR G LFA Sbjct: 181 AVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGRTGSLFA 240 Query: 241 YMHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALD 300 YMHYGV PDIL+SAK+LGGGFPI AMLTT +IA G+HG+TYGGNPLA AV AA D Sbjct: 241 YMHYGVTPDILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAVGGAAFD 300 Query: 301 VINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNA 360 +INTPEVLDGV AK E F LQ+I + +F +IRGMGLLIGA L ++ GKARD L A Sbjct: 301 LINTPEVLDGVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYA 360 Query: 361 AEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 A + VMVL A PDV+RF PSLVIDD++I EG+ RF +AV +++ Sbjct: 361 AAEAGVMVLNAGPDVMRFVPSLVIDDSDIAEGMARFAQAVERVL 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: 545 Number of extensions: 21 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 BWI76_RS26000 BWI76_RS26000 (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.15394.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-208 677.3 0.3 4e-208 677.1 0.3 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS26000 BWI76_RS26000 aspartate aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 677.1 0.3 4e-208 4e-208 1 396 [. 8 403 .. 8 404 .. 1.00 Alignments for each domain: == domain 1 score: 677.1 bits; conditional E-value: 4e-208 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlg 71 ++r++fdev++p+yapa+fipv+g+Gsrvwdq+gkey+dfaGGiav+alGh+hp+lv+al+eq+eklwh++ lcl|FitnessBrowser__Koxy:BWI76_RS26000 8 ITRATFDEVILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWHTS 78 79********************************************************************* PP TIGR03246 72 ngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftv 142 n++tnep+lrl +klvdatfad+v f nsG+eane+a+klar++++ ++++ k++i+af+n+fhGr+lftv lcl|FitnessBrowser__Koxy:BWI76_RS26000 79 NVFTNEPALRLGRKLVDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKTKIIAFHNAFHGRSLFTV 149 *********************************************************************** PP TIGR03246 143 svGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhn 213 svGGq+kys++f+p+p++i h+++ndl+a+ka+++d+tcav+vepiqGegGv++a+++fl+glr+lcd+h+ lcl|FitnessBrowser__Koxy:BWI76_RS26000 150 SVGGQPKYSDGFGPKPADIVHVPFNDLHAVKAVMDDHTCAVVVEPIQGEGGVTAATPEFLQGLRDLCDQHQ 220 *********************************************************************** PP TIGR03246 214 allifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnpla 284 all+fdevq G+GrtG+l+aym+yGvtpdiltsakalGgGfpi a+ltt+++a++++ G+hG+tyGGnpla lcl|FitnessBrowser__Koxy:BWI76_RS26000 221 ALLVFDEVQCGMGRTGSLFAYMHYGVTPDILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLA 291 *********************************************************************** PP TIGR03246 285 cavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaa 355 cav ++ +dl+nt+e+l+Gv ++ elfv++l++i+ar+++fs+irG+GlliGa+l+ +y+Gka+d++ aaa lcl|FitnessBrowser__Koxy:BWI76_RS26000 292 CAVGGAAFDLINTPEVLDGVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAELKPQYHGKARDFLYAAA 362 *********************************************************************** PP TIGR03246 356 eeGvlvliaGpdvvrfapslvieeeeikeGlarlekavekl 396 e+Gv+vl aGpdv+rf pslvi++++i+eG+ar+++ave++ lcl|FitnessBrowser__Koxy:BWI76_RS26000 363 EAGVMVLNAGPDVMRFVPSLVIDDSDIAEGMARFAQAVERV 403 **************************************997 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.23 // [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