Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate Pf1N1B4_4797 Arginine N-succinyltransferase (EC 2.3.1.109)
Query= SwissProt::P0AE37 (344 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 Length = 344 Score = 316 bits (810), Expect = 5e-91 Identities = 164/334 (49%), Positives = 216/334 (64%), Gaps = 2/334 (0%) Query: 2 MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61 M++RP +D+ AL+ LA G GLT+LPA+ A L+ R+E A KT+ GE + + Y+FV Sbjct: 1 MIVRPATPADLPALLALAHSAGTGLTTLPADAARLTQRLEWAAKTFAGEAERGDADYLFV 60 Query: 62 LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121 LE+ + V GICA+ AVG+ +PWYNYR+G V ASK L + LPTLFL ND TG SE Sbjct: 61 LENDQQEAV-GICALAGAVGMREPWYNYRLGLFVAASKNLGINQQLPTLFLGNDMTGHSE 119 Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181 LC+LFL D R NG LLSK+RF+F+A FR F DKV+AEMRG DE G SPFW+ LG+ Sbjct: 120 LCSLFLHADHRSGLNGRLLSKARFLFLAEFRQHFGDKVIAEMRGYSDEEGVSPFWEGLGR 179 Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241 FF M+F+ AD+L G G K FIAELMPK P+ T L + A+ VIG+VHP T PA +L+ Sbjct: 180 HFFKMNFADADYLTGLGNKTFIAELMPKFPLPTCLLPEAARAVIGRVHPNTEPALGMLKA 239 Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHFR 301 EGF +R+YIDIFDGGP +EC +RA+R S++++++ G P + L+ N + R Sbjct: 240 EGFEHRDYIDIFDGGPLIECATGDIRAVRDSQVLQLSIGTPGE-QAATYLIHNRQFAECR 298 Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLV 335 + A LI+ A L AG VR V Sbjct: 299 ITAAPARVAAGTLIVDAQTAKTLGLSAGSSVRAV 332 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: 371 Number of extensions: 21 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: 344 Length adjustment: 29 Effective length of query: 315 Effective length of database: 315 Effective search space: 99225 Effective search space used: 99225 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 Pf1N1B4_4797 (Arginine N-succinyltransferase (EC 2.3.1.109))
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.8418.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-145 468.6 0.0 5.3e-145 468.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 Arginine N-succinyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 Arginine N-succinyltransferase (EC 2.3.1.109) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.4 0.0 5.3e-145 5.3e-145 1 335 [. 2 333 .. 2 334 .. 0.99 Alignments for each domain: == domain 1 score: 468.4 bits; conditional E-value: 5.3e-145 TIGR03244 1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledte 64 ivrp dl+all+la++aG+Glt+lpa+ ++l++r+e+a k+fage+er++++ylfvle+ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 2 IVRPATPADLPALLALAHSAGTGLTTLPADAARLTQRLEWAAKTFAGEAERGDADYLFVLEN-D 64 79***********************************************************9.7 PP TIGR03244 65 tgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldee 128 +++ vG++a++ avG++ep+ynyr+g v ask+l+i ++l+tlfl nd+tg selC+lfl+ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 65 QQEAVGICALAGAVGMREPWYNYRLGLFVAASKNLGINQQLPTLFLGNDMTGHSELCSLFLHAD 128 77889*********************************************************** PP TIGR03244 129 yrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadyl 192 +r++lnG+llskarflflaef+++f++k+iaemrG+sdeeG sPfWe lg++ff+++f++adyl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 129 HRSGLNGRLLSKARFLFLAEFRQHFGDKVIAEMRGYSDEEGVSPFWEGLGRHFFKMNFADADYL 192 **************************************************************** PP TIGR03244 193 sgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGpt 256 +g+G+k+fiaelmPkfP+ ++ll+++a++vig+vh++t+Pal +l++eG+++++y+difd+Gp+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 193 TGLGNKTFIAELMPKFPLPTCLLPEAARAVIGRVHPNTEPALGMLKAEGFEHRDYIDIFDGGPL 256 **************************************************************** PP TIGR03244 257 leaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvlsaeea 320 +e+ + +iravr+s++++++++++ +++ ++yl++n++++++r+++++++++a++l+++a++a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 257 IECATGDIRAVRDSQVLQLSIGTPGEQA--ATYLIHNRQFAECRITAAPARVAAGTLIVDAQTA 318 ************************9988..99******************************** PP TIGR03244 321 kalkveeGdkvrvva 335 k+l +++G +vr v+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4797 319 KTLGLSAGSSVRAVS 333 ************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (344 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: 9.74 // [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