Align Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized)
to candidate WP_041457309.1 AVA_RS26830 ornithine--oxo-acid transaminase
Query= SwissProt::P38021 (401 letters) >NCBI__GCF_000204075.1:WP_041457309.1 Length = 400 Score = 495 bits (1274), Expect = e-144 Identities = 233/395 (58%), Positives = 308/395 (77%), Gaps = 3/395 (0%) Query: 7 SKEIIDQTSHYGANNYHPLPIVISEALGAWVKDPEGNEYMDMLSAYSAVNQGHRHPKIIQ 66 +++ I+ YGA+NYHPL +VI++ G WV D EG +Y+D LSAYSA+NQGH HPKI+Q Sbjct: 3 TQDYIELEQQYGADNYHPLDVVITKGEGVWVWDIEGKKYLDFLSAYSALNQGHCHPKILQ 62 Query: 67 ALKDQADKITLTSRAFHNDQLGPFYEKTAKLTGKEMILPMNTGAEAVESAVKAARRWAYE 126 A+ QA ++TLTSRAF NDQLG FY+K +++G +LPMN+GAEAVE+A+KA R+WAY+ Sbjct: 63 AMIKQAQQVTLTSRAFRNDQLGKFYQKLCQISGLPKVLPMNSGAEAVETAIKAIRKWAYK 122 Query: 127 VKGVADNQAEIIACVGNFHGRTMLAVSLSSEEEYKRGFGPMLPGIKLIPYGDVEALRQAI 186 VKG+ +NQAEII C NF GRT+ +S S+EE+Y+ GFGP+ G K+IP+GD +AL QAI Sbjct: 123 VKGIPENQAEIIVCSNNFSGRTISLISFSTEEQYQDGFGPLTTGFKVIPFGDAQALEQAI 182 Query: 187 TPNTAAFLFEPIQGEAGIVIPPEGFLQEAAAICKEENVLFIADEIQTGLGRTGKTFACDW 246 TPNTAAFL EPIQGE GI++PP GFL++A IC+ +VL + DEIQTGLGRTGK FA + Sbjct: 183 TPNTAAFLVEPIQGEGGIIVPPHGFLKQAEQICRHHHVLLVFDEIQTGLGRTGKMFAHQY 242 Query: 247 DGIVPDMYILGKALGGGVFPISCIAADREILGVFNPGSHGSTFGGNPLACAVSIASLEVL 306 + + PD +GKAL GG +PIS + E++G+F PG HGSTFGGNPLA A+ IA+L+VL Sbjct: 243 ENVKPDGITVGKALSGGFYPISAFISTEEVMGIFQPGDHGSTFGGNPLAAAIGIAALDVL 302 Query: 307 EDEKLADRSLELGEYFKSELESIDSPVIKEVRGRGLFIGVEL---TEAARPYCERLKEEG 363 +EKL +++L+LGEYF +L+SI+S IKEVRG+GL IG+EL AR +C+ L +EG Sbjct: 303 IEEKLPEKALKLGEYFIEKLQSIESTYIKEVRGKGLLIGMELYPEAGGARRFCKALAKEG 362 Query: 364 LLCKETHDTVIRFAPPLIISKEDLDWAIEKIKHVL 398 LL KET D VIRFAPPL+IS++++DWA+EKI+ VL Sbjct: 363 LLAKETRDNVIRFAPPLVISEDEIDWALEKIERVL 397 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: 499 Number of extensions: 12 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: 400 Length adjustment: 31 Effective length of query: 370 Effective length of database: 369 Effective search space: 136530 Effective search space used: 136530 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_041457309.1 AVA_RS26830 (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.4204.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-170 553.7 0.0 1.2e-170 553.5 0.0 1.0 1 lcl|NCBI__GCF_000204075.1:WP_041457309.1 AVA_RS26830 ornithine--oxo-acid Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_041457309.1 AVA_RS26830 ornithine--oxo-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 553.5 0.0 1.2e-170 1.2e-170 1 401 [. 3 397 .. 3 398 .. 0.99 Alignments for each domain: == domain 1 score: 553.5 bits; conditional E-value: 1.2e-170 TIGR01885 1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkl 69 ++++iele++yga nyhpl+vv++k+eG+ vwd+egk+yldflsaysa+nqGhchpki++a+++qaq++ lcl|NCBI__GCF_000204075.1:WP_041457309.1 3 TQDYIELEQQYGADNYHPLDVVITKGEGVWVWDIEGKKYLDFLSAYSALNQGHCHPKILQAMIKQAQQV 71 6899***************************************************************** PP TIGR01885 70 tlssrafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnf 138 tl+sraf nd++g+f ++++++ G kvlpmn+Gaeavetaik rkW+yk+k+ipe++a i+++++nf lcl|NCBI__GCF_000204075.1:WP_041457309.1 72 TLTSRAFRNDQLGKFYQKLCQISGLPKVLPMNSGAEAVETAIKAIRKWAYKVKGIPENQAEIIVCSNNF 140 ********************************************************************* PP TIGR01885 139 hGrtlavislstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddg 207 Grt+++is st+++ +++fGp++ ++k i++++++ale+a++ + aaflvePiqGe G++vp +g lcl|NCBI__GCF_000204075.1:WP_041457309.1 141 SGRTISLISFSTEEQYQDGFGPLTTGFKVIPFGDAQALEQAITP---NTAAFLVEPIQGEGGIIVPPHG 206 ****************************************9987...9********************* PP TIGR01885 208 ylkkvrelckkynvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmlt 276 +lk+++++c++++vll+ deiqtG++rtGk++a+++e+vkPd +++GkalsgG+yP+sa ++ +evm + lcl|NCBI__GCF_000204075.1:WP_041457309.1 207 FLKQAEQICRHHHVLLVFDEIQTGLGRTGKMFAHQYENVKPDGITVGKALSGGFYPISAFISTEEVMGI 275 ********************************************************************* PP TIGR01885 277 ikpgehGstygGnPlasavavaalevlkeeklaeraeklGeelreelkklkkeivkevrGkGllnaivi 345 ++pg+hGst+gGnPla+a+ +aal+vl eekl e+a klGe + e+l++++++ +kevrGkGll ++ + lcl|NCBI__GCF_000204075.1:WP_041457309.1 276 FQPGDHGSTFGGNPLAAAIGIAALDVLIEEKLPEKALKLGEYFIEKLQSIESTYIKEVRGKGLLIGMEL 344 ********************************************************************* PP TIGR01885 346 deskangreawdlclklkekGllakptheeiirlaPPlviteeelkeaveiikkvl 401 +++ a c l+++Gllak+t++++ir+aPPlvi+e+e+++a+e i++vl lcl|NCBI__GCF_000204075.1:WP_041457309.1 345 YPEA---GGARRFCKALAKEGLLAKETRDNVIRFAPPLVISEDEIDWALEKIERVL 397 *999...678899**************************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (400 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: 11.11 // [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