Align Arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 7023381 Shewana3_0611 arginine succinyltransferase (RefSeq)
Query= reanno::ANA3:7023381 (339 letters) >lcl|FitnessBrowser__ANA3:7023381 Shewana3_0611 arginine succinyltransferase (RefSeq) Length = 339 Score = 676 bits (1745), Expect = 0.0 Identities = 339/339 (100%), Positives = 339/339 (100%) Query: 1 MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60 MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL Sbjct: 1 MLIIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDKPFDEGYL 60 Query: 61 MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120 MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA Sbjct: 61 MVLEDTATREVVGTCAIEAAVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGA 120 Query: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL Sbjct: 121 AELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRFGETVIAEMRGVSDSDGNSPFYCWL 180 Query: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL Sbjct: 181 QKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNTRPALSLL 240 Query: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY 300 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY Sbjct: 241 QAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESDKQFIVSNTQLANY 300 Query: 301 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM Sbjct: 301 RATSACLAVDDKTEQVVISPELAEGLLLAKGDQIRILAM 339 Lambda K H 0.322 0.138 0.401 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: 539 Number of extensions: 9 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: 339 Length of database: 339 Length adjustment: 28 Effective length of query: 311 Effective length of database: 311 Effective search space: 96721 Effective search space used: 96721 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate 7023381 Shewana3_0611 (arginine succinyltransferase (RefSeq))
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))
# 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/TIGR03244.hmm # target sequence database: /tmp/gapView.21665.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03244 [M=336] Accession: TIGR03244 Description: arg_catab_AstA: arginine N-succinyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-141 455.4 0.0 5.2e-141 455.3 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7023381 Shewana3_0611 arginine succinylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023381 Shewana3_0611 arginine succinyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.3 0.0 5.2e-141 5.2e-141 1 335 [. 3 338 .. 3 339 .] 0.97 Alignments for each domain: == domain 1 score: 455.3 bits; conditional E-value: 5.2e-141 TIGR03244 1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfagele.raeegylfvledtetgkvvGvsaiea 76 i+rp++ d+++l+++a+e+G+G+tslp+n +ll+++i+rae sf + ++ + +egyl+vledt+t +vvG++aiea lcl|FitnessBrowser__ANA3:7023381 3 IIRPIQAGDFESLYQIAEESGHGFTSLPVNADLLRHKIARAEASFVKVIDkPFDEGYLMVLEDTATREVVGTCAIEA 79 79*********************************************9651579*********************** PP TIGR03244 77 avGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflflaefkerf 153 avG+e++fy+yr+g+ v +s+++++ +++etl+l++d+tga+elCtlfl+e yrk++nG++ls++rflfla++ +rf lcl|FitnessBrowser__ANA3:7023381 80 AVGMEDAFYHYRLGTEVYHSEQIEVRNEVETLTLCHDYTGAAELCTLFLREGYRKGNNGRMLSRSRFLFLAQHAKRF 156 ***************************************************************************** PP TIGR03244 154 skkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhekt 230 ++++iaemrGvsd +G+sPf+ +l+k+f +df +adylsg+Gkkaf+ae+mP+ P+yv+ll++eaq+vig+vh++t lcl|FitnessBrowser__ANA3:7023381 157 GETVIAEMRGVSDSDGNSPFYCWLQKNFLGIDFIQADYLSGLGKKAFMAEMMPRNPVYVCLLPEEAQKVIGEVHTNT 233 ***************************************************************************** PP TIGR03244 231 kPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvess 307 +Pal ll++eG+r +gyvdifd+Gpt+e+++++iravres+l++v ++e ++d ++++v+n++l+++r++ + ++ lcl|FitnessBrowser__ANA3:7023381 234 RPALSLLQAEGFRCRGYVDIFDGGPTVECRLTDIRAVRESRLLTVDIGEMPESD--KQFIVSNTQLANYRATSACLA 308 **************************************************9999..99*************986554 PP TIGR03244 308 ..ldaeelvlsaeeakalkveeGdkvrvva 335 ++e++v+s+e a+ l + +Gd++r++a lcl|FitnessBrowser__ANA3:7023381 309 vdDKTEQVVISPELAEGLLLAKGDQIRILA 338 33889***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (339 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: 00:00:00.01 # Mc/sec: 7.61 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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