Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate AO356_18735 AO356_18735 arginine N-succinyltransferase
Query= SwissProt::P0AE37 (344 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18735 Length = 341 Score = 339 bits (870), Expect = 5e-98 Identities = 173/342 (50%), Positives = 235/342 (68%), Gaps = 2/342 (0%) Query: 2 MVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVFV 61 M++RPV SD+ AL+ LA TG GLT+LPANE L+ R+ A KT++GE + + Y+FV Sbjct: 1 MIVRPVRSSDLPALIALARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFV 60 Query: 62 LEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSSE 121 LED + G V GI AI AVGL +PWYN+RVG V AS+ELN+Y +PTLFL+ND TG+SE Sbjct: 61 LEDDD-GRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSE 119 Query: 122 LCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLGK 181 LC+LFL D+R NG +L+K+R +F+A F F +K++AEMRG+ D++G SPFW+SLG+ Sbjct: 120 LCSLFLHADYRSGLNGRMLAKARLLFIAEFPQLFGNKIIAEMRGMSDDNGRSPFWESLGR 179 Query: 182 RFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLEK 241 FF M+FS+AD+L G G KAFIAELMPK P+YT FLS+ A+ VIGQVHP T PA ++L+ Sbjct: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEGARAVIGQVHPDTEPALSMLKS 239 Query: 242 EGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQGDFPACLVANENYHHFR 301 EGF Y+ Y+DIFD GP +EC+ ++RAIR S+ + +A G P D L+ N R Sbjct: 240 EGFSYQGYVDIFDAGPAVECETGKIRAIRDSQALVLAIGTPGD-DATPFLIHNRKREDCR 298 Query: 302 VVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRLCAEEKT 343 + A L++ L+ +AGD+VR V L A ++ Sbjct: 299 ITAAPARFAAGTLVVDPLTAKRLQLNAGDQVRAVALSAARES 340 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: 363 Number of extensions: 19 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 315 Effective length of database: 312 Effective search space: 98280 Effective search space used: 98280 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 AO356_18735 AO356_18735 (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.28334.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-159 516.5 0.0 1.4e-159 516.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 AO356_18735 arginine N-succinylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 AO356_18735 arginine N-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.3 0.0 1.4e-159 1.4e-159 1 336 [] 2 334 .. 2 334 .. 0.99 Alignments for each domain: == domain 1 score: 516.3 bits; conditional E-value: 1.4e-159 TIGR03244 1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledt 63 ivrpv++sdl+al++la+++G+Glt+lpanee+l++r+ +aek+f+ge+ r++++ylfvled lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 2 IVRPVRSSDLPALIALARSTGTGLTTLPANEERLAHRVGWAEKTFRGEAGRGDADYLFVLED- 63 79************************************************************. PP TIGR03244 64 etgkvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfld 126 ++g+vvG+sai+ avGl+ep+yn+rvg +v+as+elniy++++tlfl+ndltg+selC+lfl+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 64 DDGRVVGISAIAGAVGLREPWYNFRVGLTVSASQELNIYREIPTLFLANDLTGNSELCSLFLH 126 99************************************************************* PP TIGR03244 127 eeyrkelnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfska 189 +yr++lnG++l+kar+lf+aef+++f++kiiaemrG+sd++GrsPfWe+lg++ff+++fs+a lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 127 ADYRSGLNGRMLAKARLLFIAEFPQLFGNKIIAEMRGMSDDNGRSPFWESLGRHFFKMEFSQA 189 *************************************************************** PP TIGR03244 190 dylsgiGkkafiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifd 252 dyl+g+G+kafiaelmPkfP+y+++ls+ a++vig+vh++t+Pal +l+seG+ yqgyvdifd lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 190 DYLTGVGNKAFIAELMPKFPLYTCFLSEGARAVIGQVHPDTEPALSMLKSEGFSYQGYVDIFD 252 *************************************************************** PP TIGR03244 253 aGptleaevakiravresklvevavaesaaedeaepylvanekledfrvvlvessldaeelvl 315 aGp++e+e+ kira+r+s+ +++a++++ +++ +p+l++n+k ed+r+++++++ +a++lv+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 253 AGPAVECETGKIRAIRDSQALVLAIGTPGDDA--TPFLIHNRKREDCRITAAPARFAAGTLVV 313 **************************998665..***************************** PP TIGR03244 316 saeeakalkveeGdkvrvval 336 ++ +ak+l++++Gd+vr val lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18735 314 DPLTAKRLQLNAGDQVRAVAL 334 ******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (336 nodes) Target sequences: 1 (341 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.68 // [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