Align Arginine N-succinyltransferase subunit alpha; ARUAI; EC 2.3.1.109; AOST; AST (uncharacterized)
to candidate AO356_18730 AO356_18730 arginine N-succinyltransferase
Query= curated2:P80357 (338 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18730 Length = 339 Score = 571 bits (1472), Expect = e-168 Identities = 288/339 (84%), Positives = 312/339 (92%), Gaps = 1/339 (0%) Query: 1 MLVMRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYF 60 MLVMRPAQ ADL +VQRLAADSP+GVTSLPDD ERL DKI ASEASFAAEVS+NGEESYF Sbjct: 1 MLVMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYF 60 Query: 61 FVLEDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGN 120 FVLED+A+G+L GCSAIVASAG+SEPFYSFRNETFVHASR L IHNKIHVLS CHDLTGN Sbjct: 61 FVLEDTATGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGN 120 Query: 121 SLLTSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAV 180 SLLTSFYV +LV S ++ELNSRGRLLF+ASHPERFAD+VV EIVGYSDE G+SPFW+A+ Sbjct: 121 SLLTSFYVVPELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAI 180 Query: 181 GRNFFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDIL 240 GRNFFDLNY AE+L GLKSRTFLAELMPHYPIYVPLLPDAAQE+MGQVHPRAQITFDIL Sbjct: 181 GRNFFDLNYAAAERLCGLKSRTFLAELMPHYPIYVPLLPDAAQEAMGQVHPRAQITFDIL 240 Query: 241 MREGFETDNYIDIFDGGPTLHARTSGIRSIAQSRVVPVKIGEAPK-SGRPYLVTNGQLQD 299 MREGFETD+YIDIFDGGPTLHAR SGIRSIAQSRVVPVKIGE K +GR YLV N QLQD Sbjct: 241 MREGFETDHYIDIFDGGPTLHARVSGIRSIAQSRVVPVKIGEPVKGAGRQYLVANAQLQD 300 Query: 300 FRAVVLDLDWAPGKPVALSVEAAEALGVGEGASVRLVAV 338 +RAV+L+LD+APGKPV L +EAAEALGVGEGASVRLVAV Sbjct: 301 YRAVLLELDYAPGKPVTLDMEAAEALGVGEGASVRLVAV 339 Lambda K H 0.319 0.135 0.387 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: 445 Number of extensions: 9 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate AO356_18730 AO356_18730 (arginine N-succinyltransferase)
to HMM TIGR03245 (aruF: arginine/ornithine succinyltransferase, alpha subunit (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/TIGR03245.hmm # target sequence database: /tmp/gapView.18665.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03245 [M=336] Accession: TIGR03245 Description: arg_AOST_alph: arginine/ornithine succinyltransferase, alpha subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-170 552.5 0.0 2.8e-170 552.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 AO356_18730 arginine N-succinylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 AO356_18730 arginine N-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 552.3 0.0 2.8e-170 2.8e-170 1 336 [] 3 339 .] 3 339 .] 0.99 Alignments for each domain: == domain 1 score: 552.3 bits; conditional E-value: 2.8e-170 TIGR03245 1 vvrParladldaierlaresaigvtslPadrekleekiaqsessfaaevsfsgeesylfvled 63 v+rPa++adl +++rla++s+igvtslP+d e+l +kia+se sfaaevsf+geesy+fvled lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 3 VMRPAQMADLGEVQRLAADSPIGVTSLPDDVERLSDKIAASEASFAAEVSFNGEESYFFVLED 65 79************************************************************* PP TIGR03245 64 setgkllGtasivasaGyaePfysyrndtlvhasrelkvnnkihvlslsheltGksllasfyv 126 ++tgkl+G+++ivasaGy+ePfys+rn+t+vhasrelk++nkihvls +h+ltG+sll+sfyv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 66 TATGKLAGCSAIVASAGYSEPFYSFRNETFVHASRELKIHNKIHVLSQCHDLTGNSLLTSFYV 128 *************************************************************** PP TIGR03245 127 dpelreaeaaellsrarllfiaaererfasrviaellGvsdeaGesPfWdaiGrkffdldfaa 189 pel+++ + el+sr+rllf+a+++erfa++v++e++G sde+G+sPfWdaiGr+ffdl++aa lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 129 VPELVGSPWSELNSRGRLLFVASHPERFADSVVTEIVGYSDENGDSPFWDAIGRNFFDLNYAA 191 *************************************************************** PP TIGR03245 190 verasglksktfiaelmPsyPiyvpllpdeaqealgqvheraelafdlllreGfeadryidif 252 +er++glks+tf+aelmP+yPiyvpllpd+aqea+gqvh+ra+++fd+l+reGfe+d+yidif lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 192 AERLCGLKSRTFLAELMPHYPIYVPLLPDAAQEAMGQVHPRAQITFDILMREGFETDHYIDIF 254 *************************************************************** PP TIGR03245 253 dgGpvleaeldrlktvkksrekpvkieeaatgg.stylvsnglledfravladlavvdGkalr 314 dgGp+l+a++++++++++sr++pvki e +g ++ylv+n +l+d+ravl++l+ ++Gk+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 255 DGGPTLHARVSGIRSIAQSRVVPVKIGEPVKGAgRQYLVANAQLQDYRAVLLELDYAPGKPVT 317 ****************************999888***************************** PP TIGR03245 315 lkadaaealgvseGdavrlval 336 l+++aaealgv+eG++vrlva+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18730 318 LDMEAAEALGVGEGASVRLVAV 339 *******************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.15 // [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