Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_012709571.1 NGR_RS26550 ornithine--oxo-acid transaminase
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000018545.1:WP_012709571.1 Length = 401 Score = 440 bits (1131), Expect = e-128 Identities = 212/397 (53%), Positives = 282/397 (71%), Gaps = 4/397 (1%) Query: 6 KSKEIIDQTSHY-GANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKI 64 K+ + +T H GA+NY PL +V++ G +V D EGN Y+D LSAYSAVNQGH HPKI Sbjct: 2 KTTAALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKI 61 Query: 65 IQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWA 124 +A+ +QA K+TLTSRAF NDQL FYE+ A LTG +LPMN+GAEAVE+A+KA R+W Sbjct: 62 FKAMVEQAQKLTLTSRAFRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWG 121 Query: 125 YEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQ 184 YEVKGVA +QAEII C NFHGRT+ V S++ + GFGP PG +++P+GD++A R Sbjct: 122 YEVKGVAADQAEIIVCANNFHGRTIGIVGFSTDPDSHDGFGPFAPGFRIVPFGDIDAFRA 181 Query: 185 AITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFAC 244 AI+ NT AFL EPIQGEAG+++PP G+ E +C + + + DEIQTGLGRTGK A Sbjct: 182 AISENTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAITLVLDEIQTGLGRTGKLLAE 241 Query: 245 DWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLE 304 + + I D+ ++GKAL GG +P+S + ++ E+LGV PG HGSTFGGNPLACA++ A+L+ Sbjct: 242 EHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAIARAALK 301 Query: 305 VLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTE---AARPYCERLKE 361 VL +E + + S +GE F + L I S +I+EVRGRGL + VEL AR YCE LK Sbjct: 302 VLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEAGGARKYCEALKA 361 Query: 362 EGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398 G+L K+TH IR APPL+I+ ++DWA+E+ VL Sbjct: 362 RGILAKDTHGDTIRIAPPLVITAGEVDWALEQFAAVL 398 Lambda K H 0.318 0.136 0.401 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: 468 Number of extensions: 13 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: 401 Length of database: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_012709571.1 NGR_RS26550 (ornithine--oxo-acid transaminase)
to HMM TIGR01885 (rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13))
# 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/TIGR01885.hmm # target sequence database: /tmp/gapView.521635.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01885 [M=402] Accession: TIGR01885 Description: Orn_aminotrans: ornithine--oxo-acid transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-169 549.6 0.0 2.2e-169 549.3 0.0 1.0 1 NCBI__GCF_000018545.1:WP_012709571.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012709571.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 549.3 0.0 2.2e-169 2.2e-169 3 400 .. 6 397 .. 4 399 .. 0.98 Alignments for each domain: == domain 1 score: 549.3 bits; conditional E-value: 2.2e-169 TIGR01885 3 evieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssra 75 ++ie+e+ gahny+pl+vvl+++eG++vwd+eg+ryld lsaysavnqGhchpki ka+veqaqkltl+sra NCBI__GCF_000018545.1:WP_012709571.1 6 ALIETEHLLGAHNYKPLDVVLTRGEGVFVWDIEGNRYLDCLSAYSAVNQGHCHPKIFKAMVEQAQKLTLTSRA 78 6899********************************************************************* PP TIGR01885 76 fyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavisl 148 f nd+++ f e ++ l G kvlpmn+Gaeavetaik +rkWgy++k++++d+a i+++++nfhGrt++++ NCBI__GCF_000018545.1:WP_012709571.1 79 FRNDQLALFYEEIAALTGSHKVLPMNSGAEAVETAIKAVRKWGYEVKGVAADQAEIIVCANNFHGRTIGIVGF 151 ************************************************************************* PP TIGR01885 149 stdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkynv 221 stdp+s+++fGp++p+++ +++++++a++ a++e + +aflvePiqGeaGv+vp gy+ +vrelc+k+ + NCBI__GCF_000018545.1:WP_012709571.1 152 STDPDSHDGFGPFAPGFRIVPFGDIDAFRAAISE---NTVAFLVEPIQGEAGVIVPPAGYFAEVRELCTKHAI 221 *******************************998...899********************************* PP TIGR01885 222 lliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlasa 294 l+ deiqtG++rtGklla ehe + d+ l+GkalsgG+yPvsavl+++ev+ ++kpg+hGst+gGnPla+a NCBI__GCF_000018545.1:WP_012709571.1 222 TLVLDEIQTGLGRTGKLLAEEHEAIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACA 294 ************************************************************************* PP TIGR01885 295 vavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangreawdlclklkekGl 367 +a aal+vl+ee ++e+++++Ge++ + l++++++i++evrG+Gl+ a+ + +++ a + c lk +G+ NCBI__GCF_000018545.1:WP_012709571.1 295 IARAALKVLTEEGMIENSARMGERFMTGLTDIRSNIIREVRGRGLMLAVELVPEA---GGARKYCEALKARGI 364 ****************************************************999...677889********* PP TIGR01885 368 lakptheeiirlaPPlviteeelkeaveiikkv 400 lak+th++ ir+aPPlvit e+++a+e ++ v NCBI__GCF_000018545.1:WP_012709571.1 365 LAKDTHGDTIRIAPPLVITAGEVDWALEQFAAV 397 **************************9988776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (401 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 13.31 // [ok]
This GapMind analysis is from Apr 09 2024. 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