Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate AO353_25630 AO353_25630 arginine N-succinyltransferase
Query= SwissProt::P0AE37 (344 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25630 Length = 344 Score = 310 bits (794), Expect = 3e-89 Identities = 163/336 (48%), Positives = 214/336 (63%), Gaps = 2/336 (0%) Query: 2 MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61 M++RP +D+ AL+ LA G GLT+LPA+ L R+E A KT+ GE +++ Y+FV Sbjct: 1 MIVRPATMNDLPALLALAHSAGAGLTTLPADAGRLRQRLEWAEKTFAGEAERADADYLFV 60 Query: 62 LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121 LE ++ G GICA+ AVGL +PWYNYR+G V ASK L + L TLFL ND TG SE Sbjct: 61 LE-ADNGEAVGICALAGAVGLREPWYNYRMGLFVAASKNLGINQQLLTLFLGNDMTGQSE 119 Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181 LC+LFL R NG LLSK+RF+F+A FR F DKV+AEMRG DE G SPFW+ LG+ Sbjct: 120 LCSLFLHAGHRSGLNGRLLSKARFLFLAEFRQYFGDKVIAEMRGYSDEDGVSPFWEGLGR 179 Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241 FF MDF+ AD+L G G K FIAELMPK P+ T L + A+ IG+VHP T PA +L+ Sbjct: 180 HFFKMDFADADYLTGLGNKTFIAELMPKFPLPTCLLPEAARATIGRVHPNTEPALGMLKA 239 Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHFR 301 EGF +++YIDIFDGGP +EC +RA+R S++++++ G P + L+ N + R Sbjct: 240 EGFEHKDYIDIFDGGPLIECATGDIRAVRDSQVLQLSIGTPGE-QAAVYLIHNRQFADCR 298 Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRL 337 + A LI+ A AL AG VR V L Sbjct: 299 ITAAPARVAAGTLIVDAHTAKALGLTAGASVRAVSL 334 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: 356 Number of extensions: 14 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 AO353_25630 AO353_25630 (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.26635.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-143 462.8 0.0 3.1e-143 462.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 AO353_25630 arginine N-succinylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 AO353_25630 arginine N-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 462.6 0.0 3.1e-143 3.1e-143 1 336 [] 2 334 .. 2 334 .. 0.99 Alignments for each domain: == domain 1 score: 462.6 bits; conditional E-value: 3.1e-143 TIGR03244 1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtet 65 ivrp +dl+all+la++aG Glt+lpa+ +l++r+e+aek+fage+era+++ylfvle ++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 2 IVRPATMNDLPALLALAHSAGAGLTTLPADAGRLRQRLEWAEKTFAGEAERADADYLFVLEA-DN 65 79***********************************************************8.99 PP TIGR03244 66 gkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyr 130 g+ vG++a++ avGl+ep+ynyr+g v ask+l+i ++l tlfl nd+tg+selC+lfl+ +r lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 66 GEAVGICALAGAVGLREPWYNYRMGLFVAASKNLGINQQLLTLFLGNDMTGQSELCSLFLHAGHR 130 9**************************************************************** PP TIGR03244 131 kelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgi 195 ++lnG+llskarflflaef++ f++k+iaemrG+sde+G sPfWe lg++ff++df++adyl+g+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 131 SGLNGRLLSKARFLFLAEFRQYFGDKVIAEMRGYSDEDGVSPFWEGLGRHFFKMDFADADYLTGL 195 ***************************************************************** PP TIGR03244 196 GkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGptleae 260 G+k+fiaelmPkfP+ ++ll+++a++ ig+vh++t+Pal +l++eG+++++y+difd+Gp++e+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 196 GNKTFIAELMPKFPLPTCLLPEAARATIGRVHPNTEPALGMLKAEGFEHKDYIDIFDGGPLIECA 260 ***************************************************************** PP TIGR03244 261 vakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvlsaeeakalkv 325 + +iravr+s++++++++++ +++ + yl++n++++d+r+++++++++a++l+++a++akal + lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 261 TGDIRAVRDSQVLQLSIGTPGEQA--AVYLIHNRQFADCRITAAPARVAAGTLIVDAHTAKALGL 323 ********************9988..99************************************* PP TIGR03244 326 eeGdkvrvval 336 ++G +vr v+l lcl|FitnessBrowser__pseudo3_N2E3:AO353_25630 324 TAGASVRAVSL 334 ********986 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: 10.30 // [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