Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_011427048.1 RHE_RS19705 ornithine--oxo-acid transaminase
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000092045.1:WP_011427048.1 Length = 399 Score = 444 bits (1142), Expect = e-129 Identities = 212/398 (53%), Positives = 280/398 (70%), Gaps = 3/398 (0%) Query: 4 LSKSKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPK 63 ++ S+++I GANNY PL +V++ G V D +GN Y+D LSAYSAVNQGH HPK Sbjct: 1 MNTSEKLIATEQRLGANNYKPLDVVLTRGEGVHVWDTDGNRYLDCLSAYSAVNQGHCHPK 60 Query: 64 IIQALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRW 123 I+ A+ +QA ++TLTSRAF NDQL YE+ A LTG ILPMN+GAEAVE+A+KA R+W Sbjct: 61 ILAAMVEQAGRLTLTSRAFRNDQLAYLYEELAALTGSHKILPMNSGAEAVETAIKAVRKW 120 Query: 124 AYEVKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALR 183 YEVKGV + QAEII C NFHGRT+ +S S++ + + GFGP PG + IP+GD EA Sbjct: 121 GYEVKGVPEGQAEIIVCADNFHGRTLSIISFSTDPDARTGFGPYTPGFRTIPFGDAEAFA 180 Query: 184 QAITPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFA 243 AI NT A L EPIQGEAG++IPP G+ +C NV I DEIQTGLGRTGK A Sbjct: 181 AAINSNTVAALIEPIQGEAGVIIPPAGYFSRIRELCTANNVTLILDEIQTGLGRTGKLLA 240 Query: 244 CDWDGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASL 303 + +GI D+ ++GKAL GG +P+S + ++ E+LGV PG HGSTFGGNPLACAV+ +L Sbjct: 241 EEHEGIEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARTAL 300 Query: 304 EVLEDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVEL---TEAARPYCERLK 360 +VL +E + + + E+G+YF L SI S ++++VRGRGL + +EL AR YC LK Sbjct: 301 KVLVEEGMIENAAEMGDYFLEGLRSIRSNIVRDVRGRGLMMAIELEPEAGGARQYCHALK 360 Query: 361 EEGLLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398 E GLL K+THD IR APPL+I++E +DWA+ +I+ + Sbjct: 361 ERGLLAKDTHDHTIRLAPPLVITREQVDWAVSQIEKTI 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: 445 Number of extensions: 10 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: 399 Length adjustment: 31 Effective length of query: 370 Effective length of database: 368 Effective search space: 136160 Effective search space used: 136160 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_011427048.1 RHE_RS19705 (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.aa/TIGR01885.hmm # target sequence database: /tmp/gapView.14333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-172 558.6 0.0 3.9e-172 558.4 0.0 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011427048.1 RHE_RS19705 ornithine--oxo-acid Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011427048.1 RHE_RS19705 ornithine--oxo-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 558.4 0.0 3.9e-172 3.9e-172 1 401 [. 4 398 .. 4 399 .] 0.98 Alignments for each domain: == domain 1 score: 558.4 bits; conditional E-value: 3.9e-172 TIGR01885 1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkl 69 se++i++e++ ga+ny+pl+vvl+++eG++vwd++g+ryld lsaysavnqGhchpki++a+veqa +l lcl|NCBI__GCF_000092045.1:WP_011427048.1 4 SEKLIATEQRLGANNYKPLDVVLTRGEGVHVWDTDGNRYLDCLSAYSAVNQGHCHPKILAAMVEQAGRL 72 6889***************************************************************** PP TIGR01885 70 tlssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnf 138 tl+sraf nd+++ + e ++ l G k+lpmn+Gaeavetaik +rkWgy++k++pe +a i+++++nf lcl|NCBI__GCF_000092045.1:WP_011427048.1 73 TLTSRAFRNDQLAYLYEELAALTGSHKILPMNSGAEAVETAIKAVRKWGYEVKGVPEGQAEIIVCADNF 141 ********************************************************************* PP TIGR01885 139 hGrtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddg 207 hGrtl++is stdp++r++fGpy+p++++i+++++ea+ a+++ + +a l+ePiqGeaGv++p g lcl|NCBI__GCF_000092045.1:WP_011427048.1 142 HGRTLSIISFSTDPDARTGFGPYTPGFRTIPFGDAEAFAAAINS---NTVAALIEPIQGEAGVIIPPAG 207 *****************************************999...5566689*************** PP TIGR01885 208 ylkkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmlt 276 y+ ++relc+ +nv li deiqtG++rtGklla ehe++ d+ l+GkalsgG+yPvsavl+++ev+ + lcl|NCBI__GCF_000092045.1:WP_011427048.1 208 YFSRIRELCTANNVTLILDEIQTGLGRTGKLLAEEHEGIEADVTLIGKALSGGFYPVSAVLSNSEVLGV 276 ********************************************************************* PP TIGR01885 277 ikpgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivi 345 +kpg+hGst+gGnPla+ava al+vl ee ++e+a+++G+ + e l++++++iv++vrG+Gl+ ai + lcl|NCBI__GCF_000092045.1:WP_011427048.1 277 LKPGQHGSTFGGNPLACAVARTALKVLVEEGMIENAAEMGDYFLEGLRSIRSNIVRDVRGRGLMMAIEL 345 ********************************************************************* PP TIGR01885 346 deskangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401 ++++ a + c lke+Gllak+th++ irlaPPlvit+e++++av+ i+k++ lcl|NCBI__GCF_000092045.1:WP_011427048.1 346 EPEA---GGARQYCHALKERGLLAKDTHDHTIRLAPPLVITREQVDWAVSQIEKTI 398 ***9...678899***************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (399 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: 8.09 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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