Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_025765140.1 X939_RS0120435 ornithine--oxo-acid transaminase
Query= BRENDA::Q98TS5 (439 letters) >NCBI__GCF_000566685.1:WP_025765140.1 Length = 419 Score = 519 bits (1337), Expect = e-152 Identities = 250/405 (61%), Positives = 318/405 (78%), Gaps = 4/405 (0%) Query: 39 SSEYVFDRESKYGAHNYHPLPVALERGKGVYVWDVEGRRYFDFLSAYSAVNQGHCHPKIL 98 +S+ D E ++GAHNY P+ V L +G+GV+VWDVEG+ Y DFLSAYSAV+QGHCHPKI+ Sbjct: 12 TSQQAIDLELRFGAHNYKPMSVVLNKGRGVHVWDVEGKEYLDFLSAYSAVSQGHCHPKII 71 Query: 99 DALKSQADKLTLTSRAFYNDVLGEYEEYITKIFGYNKVLPMNTGVEGGETACKLARKWAY 158 AL +QA KLTLTSRAFYND LG E+Y+ + FGY+KVL MN+GVE GETA KL RKWAY Sbjct: 72 QALINQAQKLTLTSRAFYNDQLGPCEQYMAEYFGYDKVLMMNSGVEAGETALKLTRKWAY 131 Query: 159 TVKGIPKYKAQIIFAAGNFWGRTMSAISSSTDPSSYEGFGPFMPGFKIIPYNDLPALERA 218 VKG+P +A++++ +GNFWGRT++A+SSSTDPSS +GPF+PGF+IIPYNDL ALE Sbjct: 132 KVKGVPTDQAKMVYVSGNFWGRTLAAVSSSTDPSSTTHYGPFLPGFQIIPYNDLEALESC 191 Query: 219 LQ-DPNVAAFMVEPIQGEAGVIVPDEGYLTGVRQLCTAHNVLFIADEVQTGLARTGKMLA 277 + DPN+A FMVEPIQGEAGV+VP EGYL GVR LCT + VLFIADEVQTG+ RTGK LA Sbjct: 192 FKSDPNIAGFMVEPIQGEAGVVVPHEGYLQGVRNLCTQYQVLFIADEVQTGIGRTGKKLA 251 Query: 278 VDHENVRPDLVILGKALSGGVYPVSAVLCDDEVMLTIKPGEHGSTYGGNPLGCRVAMASL 337 D E V+PD+++LGKALSGGV+PVSA L +DEVMLTI PGEHGST+GGNPL C VA+A+L Sbjct: 252 CDWEGVKPDILVLGKALSGGVFPVSAALANDEVMLTILPGEHGSTFGGNPLACAVAVAAL 311 Query: 338 EVIEEEKLAENANXMGELLRAEL--MKTPSDIVTAVRGKGLLNAIVIKQSKDCD-AWKVC 394 +V+EEE LA NA MG++ R+ + ++ ++ VRGKGLLNAIVI S++ D A +C Sbjct: 312 KVVEEEDLAANAEAMGQIFRSRMHDLQKQCSLIEIVRGKGLLNAIVINDSEESDTANTLC 371 Query: 395 LRLRDNGLLAKPTHGDIIRLAPPLTIKEDEIRECSEIIHKTLLSF 439 ++ + GLL KPTHG+ IR APPL I +++ + +II + + F Sbjct: 372 YQMMEKGLLCKPTHGNKIRFAPPLVINAEQMNQACDIIAEVFIQF 416 Lambda K H 0.318 0.136 0.404 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: 534 Number of extensions: 12 Number of successful extensions: 4 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: 439 Length of database: 419 Length adjustment: 32 Effective length of query: 407 Effective length of database: 387 Effective search space: 157509 Effective search space used: 157509 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_025765140.1 X939_RS0120435 (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.2128128.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-198 643.9 0.0 5e-198 643.7 0.0 1.0 1 NCBI__GCF_000566685.1:WP_025765140.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000566685.1:WP_025765140.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 643.7 0.0 5e-198 5e-198 1 400 [. 13 412 .. 13 414 .. 0.99 Alignments for each domain: == domain 1 score: 643.7 bits; conditional E-value: 5e-198 TIGR01885 1 seevieleekygahnyhplpvvlskaeGakvwdvegkryldflsaysavnqGhchpkivkalveqaqkltlss 73 s+++i+le ++gahny+p+ vvl+k++G++vwdvegk+yldflsaysav+qGhchpki++al++qaqkltl+s NCBI__GCF_000566685.1:WP_025765140.1 13 SQQAIDLELRFGAHNYKPMSVVLNKGRGVHVWDVEGKEYLDFLSAYSAVSQGHCHPKIIQALINQAQKLTLTS 85 689********************************************************************** PP TIGR01885 74 rafyndvfgefaeyvtklfGydkvlpmntGaeavetaiklarkWgykkkkipedkalilsaegnfhGrtlavi 146 rafynd++g +++y++++fGydkvl+mn+G+ea+eta+kl+rkW+yk+k++p+d+a+++ ++gnf+Grtla++ NCBI__GCF_000566685.1:WP_025765140.1 86 RAFYNDQLGPCEQYMAEYFGYDKVLMMNSGVEAGETALKLTRKWAYKVKGVPTDQAKMVYVSGNFWGRTLAAV 158 ************************************************************************* PP TIGR01885 147 slstdpesrenfGpyvpnvkkieynnlealeealeeagekvaaflvePiqGeaGvvvpddgylkkvrelckky 219 s stdp+s++++Gp++p+++ i+yn+leale+ +++ ++++a+f+vePiqGeaGvvvp++gyl+ vr+lc++y NCBI__GCF_000566685.1:WP_025765140.1 159 SSSTDPSSTTHYGPFLPGFQIIPYNDLEALESCFKS-DPNIAGFMVEPIQGEAGVVVPHEGYLQGVRNLCTQY 230 ***********************************9.************************************ PP TIGR01885 220 nvlliadeiqtGiartGkllaveheevkPdivllGkalsgGvyPvsavladkevmltikpgehGstygGnPla 292 +vl+iade+qtGi+rtGk la+++e+vkPdi++lGkalsgGv+Pvsa la++evmlti pgehGst+gGnPla NCBI__GCF_000566685.1:WP_025765140.1 231 QVLFIADEVQTGIGRTGKKLACDWEGVKPDILVLGKALSGGVFPVSAALANDEVMLTILPGEHGSTFGGNPLA 303 ************************************************************************* PP TIGR01885 293 savavaalevlkeeklaeraeklGeelreelkklkk..eivkevrGkGllnaivideskangreawdlclklk 363 +avavaal+v++ee+la +ae +G+++r+++++l+k ++++ vrGkGllnaivi++s+ ++ +a lc +++ NCBI__GCF_000566685.1:WP_025765140.1 304 CAVAVAALKVVEEEDLAANAEAMGQIFRSRMHDLQKqcSLIEIVRGKGLLNAIVINDSE-ESDTANTLCYQMM 375 **********************************774579******************9.999********** PP TIGR01885 364 ekGllakptheeiirlaPPlviteeelkeaveiikkv 400 ekGll kpth++ ir+aPPlvi e++++a++ii++v NCBI__GCF_000566685.1:WP_025765140.1 376 EKGLLCKPTHGNKIRFAPPLVINAEQMNQACDIIAEV 412 **********************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (419 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: 20.42 // [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