Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_110207179.1 DNK54_RS11795 ornithine--oxo-acid transaminase
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_003194585.1:WP_110207179.1 Length = 406 Score = 403 bits (1036), Expect = e-117 Identities = 197/392 (50%), Positives = 265/392 (67%), Gaps = 3/392 (0%) Query: 11 IDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQALKD 70 I + + A+NYHPLP+VI++A GA V D +G Y+D L+AYSAVN GHR+P++ Sbjct: 14 IAEVERHAAHNYHPLPVVIADAEGATVVDIDGRRYLDCLAAYSAVNFGHRNPRLTAVAHA 73 Query: 71 QADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYEVKGV 130 Q D++TLTSRAFH+ LGPF A+L GKEM+LPMNTGAEAVES +K AR+W YEVKGV Sbjct: 74 QLDRLTLTSRAFHSAALGPFCSALAELAGKEMVLPMNTGAEAVESGIKVARKWGYEVKGV 133 Query: 131 ADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAITPNT 190 A ++A I+ GNFHGRT VS S + + G+GP PG + +PYGD A+ +AI +T Sbjct: 134 ATDRANIVVAHGNFHGRTTTIVSFSDDPDAFTGYGPFTPGFRSVPYGDAAAVAEAIDDDT 193 Query: 191 AAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDWDGIV 250 A L EPIQGEAG++IPP +L + + +VL I DEIQ+GLGRTG TFACD G+ Sbjct: 194 VAVLLEPIQGEAGVIIPPGDYLPQVRDVTAARDVLLIVDEIQSGLGRTGATFACDLVGVT 253 Query: 251 PDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVLEDEK 310 PD+Y+LGKALGGG+ P+S + D ++LGV PG HGSTFGGNPLA AV +A +E+L + Sbjct: 254 PDLYLLGKALGGGIVPVSAVVGDADVLGVLRPGQHGSTFGGNPLAAAVGLAVVELLATGE 313 Query: 311 LADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVELTEA---ARPYCERLKEEGLLCK 367 + R+ LGE + L + + VR GL+ GV++ A AR CER+ G+L K Sbjct: 314 MQLRAKTLGESLREGLTAYLGHGLTAVRSVGLWAGVDVDPAAGTAREVCERMMRGGVLAK 373 Query: 368 ETHDTVIRFAPPLIISKEDLDWAIEKIKHVLR 399 +TH +R APPL++++ +LD A+ + LR Sbjct: 374 DTHGQTVRLAPPLVVTEAELDRAVAALGSALR 405 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: 461 Number of extensions: 21 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: 406 Length adjustment: 31 Effective length of query: 370 Effective length of database: 375 Effective search space: 138750 Effective search space used: 138750 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_110207179.1 DNK54_RS11795 (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.802402.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-142 461.4 0.0 1.3e-142 461.2 0.0 1.0 1 NCBI__GCF_003194585.1:WP_110207179.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003194585.1:WP_110207179.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.2 0.0 1.3e-142 1.3e-142 4 400 .. 13 403 .. 10 405 .. 0.98 Alignments for each domain: == domain 1 score: 461.2 bits; conditional E-value: 1.3e-142 TIGR01885 4 vieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlssraf 76 +i+ e+++ahnyhplpvv++ aeGa+v d++g+ryld l+aysavn Gh p++ ++ q ++ltl+sraf NCBI__GCF_003194585.1:WP_110207179.1 13 AIAEVERHAAHNYHPLPVVIADAEGATVVDIDGRRYLDCLAAYSAVNFGHRNPRLTAVAHAQLDRLTLTSRAF 85 5677789****************************************************************** PP TIGR01885 77 yndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavisls 149 ++ ++g f +++l G ++vlpmntGaeave++ik+arkWgy++k++++d+a i++a+gnfhGrt +++s s NCBI__GCF_003194585.1:WP_110207179.1 86 HSAALGPFCSALAELAGKEMVLPMNTGAEAVESGIKVARKWGYEVKGVATDRANIVVAHGNFHGRTTTIVSFS 158 ************************************************************************* PP TIGR01885 150 tdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckkynvl 222 dp++ +++Gp++p++++++y++++a+ ea+++ + +a+l+ePiqGeaGv++p +yl +vr++ +vl NCBI__GCF_003194585.1:WP_110207179.1 159 DDPDAFTGYGPFTPGFRSVPYGDAAAVAEAIDD---DTVAVLLEPIQGEAGVIIPPGDYLPQVRDVTAARDVL 228 *******************************99...677899******************************* PP TIGR01885 223 liadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPlasav 295 li+deiq G++rtG +a++ +v Pd+ llGkal+gG++Pvsav++d +v+ +++pg+hGst+gGnPla+av NCBI__GCF_003194585.1:WP_110207179.1 229 LIVDEIQSGLGRTGATFACDLVGVTPDLYLLGKALGGGIVPVSAVVGDADVLGVLRPGQHGSTFGGNPLAAAV 301 ************************************************************************* PP TIGR01885 296 avaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivideskangreawdlclklkekGll 368 +a +e+l ++ ra+ lGe+lre l++ + ++ vr Gl +++ +d+ + +a ++c +++ G+l NCBI__GCF_003194585.1:WP_110207179.1 302 GLAVVELLATGEMQLRAKTLGESLREGLTAYLGHGLTAVRSVGLWAGVDVDPAA---GTAREVCERMMRGGVL 371 ****************************************************99...8999************ PP TIGR01885 369 akptheeiirlaPPlviteeelkeaveiikkv 400 ak+th++ +rlaPPlv+te el++av + ++ NCBI__GCF_003194585.1:WP_110207179.1 372 AKDTHGQTVRLAPPLVVTEAELDRAVAALGSA 403 ************************99887665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (406 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: 00:00:00.00 # Mc/sec: 17.58 // [ok]
This GapMind analysis is from Sep 24 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