Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= reanno::Marino:GFF3099 (404 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 810 bits (2091), Expect = 0.0 Identities = 404/404 (100%), Positives = 404/404 (100%) Query: 1 MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG 60 MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG Sbjct: 1 MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG 60 Query: 61 LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY 120 LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY Sbjct: 61 LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY 120 Query: 121 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL 180 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL Sbjct: 121 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL 180 Query: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY Sbjct: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240 Query: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT Sbjct: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300 Query: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG 360 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG Sbjct: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG 360 Query: 361 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA Sbjct: 361 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLTA 404 Lambda K H 0.318 0.137 0.406 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: 782 Number of extensions: 19 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: 404 Length of database: 404 Length adjustment: 31 Effective length of query: 373 Effective length of database: 373 Effective search space: 139129 Effective search space used: 139129 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate GFF3099 HP15_3042 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase 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.2113.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-205 668.9 0.1 1.4e-205 668.7 0.1 1.0 1 lcl|FitnessBrowser__Marino:GFF3099 HP15_3042 bifunctional N-succiny Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.7 0.1 1.4e-205 1.4e-205 1 396 [. 6 402 .. 6 403 .. 0.99 Alignments for each domain: == domain 1 score: 668.7 bits; conditional E-value: 1.4e-205 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngyt 75 v+re fdevmvp+yap+++ipvrgeGsr+wdqeg+e+id+ GGiav++lGh+hp lv al++qaek+whl+n++t lcl|FitnessBrowser__Marino:GFF3099 6 VSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMT 80 78************************************************************************* PP TIGR03246 76 nepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqaky 150 nep+lrlak l d tfa++vff+nsGaeaneaa+klar++a++++g+ek+ei++fknsfhGrtlftvsvGGq+ky lcl|FitnessBrowser__Marino:GFF3099 81 NEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKY 155 *************************************************************************** PP TIGR03246 151 sedfaplpegikhaayndlealkalis.dktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtG 224 e+f+p p+gi+ha++ndle++k+lis +ktca++vepiqGegGv+p d+afl+glr+lcd+ +all+fdevq+G lcl|FitnessBrowser__Marino:GFF3099 156 LEGFEPAPGGIHHAEFNDLESVKKLISkEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSG 230 **************************7479********************************************* PP TIGR03246 225 vGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntae 299 vGr G++yay+ yGv+pdil+sak+lGgGfp+ a+ltt ++a++l vGthG+tyGGn lacava++v+d+v+++e lcl|FitnessBrowser__Marino:GFF3099 231 VGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPE 305 *************************************************************************** PP TIGR03246 300 lleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfaps 374 +l+Gvk+r++++ + + i++ry vf+e+rG Gll+G+vlte+++Gkakd++na eeGv+vl+aG++v+r+aps lcl|FitnessBrowser__Marino:GFF3099 306 ILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPS 380 *************************************************************************** PP TIGR03246 375 lvieeeeikeGlarlekavekl 396 l+i+e +i+ l+r+e av+kl lcl|FitnessBrowser__Marino:GFF3099 381 LIIPEPDIELALERFEAAVKKL 402 *******************987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.52 // [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