Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_03025 AO353_03025 acetylornithine aminotransferase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03025 Length = 406 Score = 768 bits (1984), Expect = 0.0 Identities = 379/406 (93%), Positives = 396/406 (97%) Query: 1 MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 MSVEHAAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH Sbjct: 1 MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 Query: 61 PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120 PALV ALTEQANKLWHVSNVFTNEPALRLAHKL+DATFA+RVFFCNSGAEANEAAFKLAR Sbjct: 61 PALVGALTEQANKLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLAR 120 Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180 RVAHDRFG+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHV +NDL ALK Sbjct: 121 RVAHDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALK 180 Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240 AA+SDKTCAVVLEPIQGEGGVLPA+L+YLQGARELC HNALL+FDEVQTGMGRSG+LFA Sbjct: 181 AAISDKTCAVVLEPIQGEGGVLPADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFA 240 Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID Sbjct: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300 Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360 V+NTPEVLNGV AKHD FKTRLEQIG KYGLFT+VRGLGLLLGCVLS+AWKGKAKD+FNA Sbjct: 301 VVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLFTQVRGLGLLLGCVLSEAWKGKAKDVFNA 360 Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406 AEREGLMILQAGPDVIRFAPSLVVEDADI+ GL+RFERA AKLTQA Sbjct: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFERAVAKLTQA 406 Lambda K H 0.320 0.136 0.400 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: 666 Number of extensions: 8 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate AO353_03025 AO353_03025 (acetylornithine aminotransferase)
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.27095.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-223 725.5 1.0 9.3e-223 725.3 1.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 AO353_03025 acetylornithine amin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 AO353_03025 acetylornithine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.3 1.0 9.3e-223 9.3e-223 1 396 [. 8 403 .. 8 404 .. 1.00 Alignments for each domain: == domain 1 score: 725.3 bits; conditional E-value: 9.3e-223 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqae 65 v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+lv al+eqa+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVGALTEQAN 72 79*************************************************************** PP TIGR03246 66 klwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivaf 130 klwh++n++tnep+lrla+kl+datfad+vffcnsGaeaneaa+klar+va+d++g+ek+ei+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 73 KLWHVSNVFTNEPALRLAHKLIDATFADRVFFCNSGAEANEAAFKLARRVAHDRFGSEKYEIIAA 137 ***************************************************************** PP TIGR03246 131 knsfhGrtlftvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvv 195 nsfhGrtlftv vGGq+kys++f+p+++gi+h+++ndl+alka+isdktcav++epiqGegGv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 138 LNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVKFNDLDALKAAISDKTCAVVLEPIQGEGGVL 202 ***************************************************************** PP TIGR03246 196 padkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGall 260 pad a+l+g+relc +hnallifdevqtG+Gr Gel+ay++yGvtpdiltsak+lGgGfpi a+l lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 203 PADLAYLQGARELCTQHNALLIFDEVQTGMGRSGELFAYQHYGVTPDILTSAKSLGGGFPIAAML 267 ***************************************************************** PP TIGR03246 261 tteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykvf 325 tte+lak+l vGthGttyGGnplacavae+v+d+vnt+e+l+Gvk++h+lf ++le+i+a+y +f lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 268 TTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVVNTPEVLNGVKAKHDLFKTRLEQIGAKYGLF 332 ***************************************************************** PP TIGR03246 326 seirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarle 390 +++rG Gll+G+vl+e+++Gkakd+ naa++eG+++l+aGpdv+rfapslv+e+++i+eGl+r+e lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 333 TQVRGLGLLLGCVLSEAWKGKAKDVFNAAEREGLMILQAGPDVIRFAPSLVVEDADIEEGLERFE 397 ***************************************************************** PP TIGR03246 391 kavekl 396 +av+kl lcl|FitnessBrowser__pseudo3_N2E3:AO353_03025 398 RAVAKL 403 ***987 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.12 // [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