Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate WP_053935843.1 WG78_RS00585 arginine N-succinyltransferase
Query= SwissProt::P0AE37 (344 letters) >NCBI__GCF_001294205.1:WP_053935843.1 Length = 338 Score = 346 bits (888), Expect = e-100 Identities = 181/339 (53%), Positives = 234/339 (69%), Gaps = 2/339 (0%) Query: 2 MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61 M IR ++ SD+ L+ LA G G+T+L A+ L+ARI + ++ +G ++ Y FV Sbjct: 1 MRIRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFV 60 Query: 62 LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121 LED TGT+ G IE A+G++D WYNYRVG VHAS+EL +Y L TLFL++D TG+SE Sbjct: 61 LEDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASE 120 Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181 LC+LFL PDWRK+GNG LLS+ RF+FMA F ++F+++V+AEMRGV DE+G SPFW+SLG+ Sbjct: 121 LCSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGR 180 Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241 FF MDF+RADFL G K+FIAELMP +PIYT LS+EAQ IG+VHP T PAR +LE Sbjct: 181 HFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEG 240 Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVE-VAEGQPAQGDFPACLVANENYHHF 300 EGFRY Y+DIFD GP+LE + +RAIR SRL + +A +G P LV+N F Sbjct: 241 EGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVP-WLVSNRKLGSF 299 Query: 301 RVVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCA 339 + L +T P + L LTAA L L GD VR V L A Sbjct: 300 KCALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPLSA 338 Lambda K H 0.321 0.136 0.411 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: 340 Number of extensions: 11 Number of successful extensions: 2 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: 344 Length of database: 338 Length adjustment: 29 Effective length of query: 315 Effective length of database: 309 Effective search space: 97335 Effective search space used: 97335 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 WP_053935843.1 WG78_RS00585 (arginine N-succinyltransferase)
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.3543768.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-142 459.6 0.0 2.9e-142 459.4 0.0 1.0 1 NCBI__GCF_001294205.1:WP_053935843.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001294205.1:WP_053935843.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.4 0.0 2.9e-142 2.9e-142 2 336 .] 3 336 .. 2 336 .. 0.99 Alignments for each domain: == domain 1 score: 459.4 bits; conditional E-value: 2.9e-142 TIGR03244 2 vrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetgkvvGvsai 74 +r ++ sdld+ll+la+ aGvG+t+l a+ ++l++ri+++++s +g + a+++y+fvled tg++vG+s+i NCBI__GCF_001294205.1:WP_053935843.1 3 IRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFVLEDETTGTLVGTSGI 75 7999********************************************************************* PP TIGR03244 75 eaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrkelnGkllskarflfla 147 eaa+G+++++ynyrvg vhas+el+iyk+l tlfl dltgaselC+lfl +++rk+ nG+lls++rflf+a NCBI__GCF_001294205.1:WP_053935843.1 76 EAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASELCSLFLLPDWRKDGNGSLLSRCRFLFMA 148 ************************************************************************* PP TIGR03244 148 efkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkkafiaelmPkfPiyvdllskeaq 220 ef+erfs+++iaemrGvsde+GrsPfWe+lg++ff++df++ad+ls +G+k+fiaelmP +Piy++lls+eaq NCBI__GCF_001294205.1:WP_053935843.1 149 EFPERFSERVIAEMRGVSDENGRSPFWESLGRHFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQ 221 ************************************************************************* PP TIGR03244 221 dvigkvhektkPalalleseGlryqgyvdifdaGptleaevakiravresklvevavaesaaedeaepylvan 293 + ig+vh+ t+Pa++lle eG+ry gyvdifdaGp le+ +++ira+r+s+l + +++ + ++p lv+n NCBI__GCF_001294205.1:WP_053935843.1 222 AAIGEVHPGTRPARKLLEGEGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKG-GVPWLVSN 293 *****************************************************99999998888.9******* PP TIGR03244 294 ekledfrvvlvessldaeelvlsaeeakalkveeGdkvrvval 336 +kl f+ l++++ ++l l+a+ +++l +e+Gd vr v+l NCBI__GCF_001294205.1:WP_053935843.1 294 RKLGSFKCALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPL 336 ****************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (338 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 24.27 // [ok]
This GapMind analysis is from Sep 24 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