Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_089322784.1 CHB58_RS03800 ornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_900188395.1:WP_089322784.1 Length = 305 Score = 346 bits (887), Expect = e-100 Identities = 169/303 (55%), Positives = 221/303 (72%) Query: 8 RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67 RD + + D T EE+ +L+ + LK QK G+ L+GKTLA+IF+KPSTRTRVSFEV Sbjct: 2 RDFISMLDITKEELKDLLKLTETLKEKQKKGEIFEPLKGKTLALIFEKPSTRTRVSFEVG 61 Query: 68 MAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASVPVI 127 + LGGH +Y++ + QL RGE I DTARVLSRYVD I+ R + + + +L +Y+ VPVI Sbjct: 62 VIQLGGHGIYMDTRSSQLGRGEPIKDTARVLSRYVDGIVIRTFKQERIVELGRYSKVPVI 121 Query: 128 NGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATP 187 N LS+ HPCQ LAD TI E KG+KV ++GDGNNV +S +I G + ATP Sbjct: 122 NALSNEEHPCQILADLFTIKEYCRDFKGLKVAFLGDGNNVCNSWLIGAAMTGINFYAATP 181 Query: 188 EGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKI 247 +GYEP E IK AE+ A + + +DPV+AVK+A+++YTDVWASMGQE E E+RR+I Sbjct: 182 QGYEPSEFYIKKAEEIAKTTSAEIVITNDPVEAVKEANIVYTDVWASMGQEEETEKRREI 241 Query: 248 FRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLA 307 F P+QVN +L+KHAKPD +FMHCLPAHRGEEVT+DVI+S S+VWD+AENRLH QKA+L Sbjct: 242 FMPYQVNSELLKHAKPDVLFMHCLPAHRGEEVTEDVIESCRSIVWDQAENRLHTQKALLT 301 Query: 308 LLL 310 +L+ Sbjct: 302 MLI 304 Lambda K H 0.319 0.134 0.400 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: 287 Number of extensions: 13 Number of successful extensions: 1 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: 317 Length of database: 305 Length adjustment: 27 Effective length of query: 290 Effective length of database: 278 Effective search space: 80620 Effective search space used: 80620 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: 48 (23.1 bits)
Align candidate WP_089322784.1 CHB58_RS03800 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))
# 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/TIGR00658.hmm # target sequence database: /tmp/gapView.16684.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00658 [M=304] Accession: TIGR00658 Description: orni_carb_tr: ornithine carbamoyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-142 457.7 0.0 9.7e-142 457.5 0.0 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089322784.1 CHB58_RS03800 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089322784.1 CHB58_RS03800 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.5 0.0 9.7e-142 9.7e-142 1 303 [. 2 304 .. 2 305 .] 0.99 Alignments for each domain: == domain 1 score: 457.5 bits; conditional E-value: 9.7e-142 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r+++s+ld+++eelk+ll+l+++lk+++kkg+ + lkgktlaliFek+stRtRvsfev++++lG++ + lcl|NCBI__GCF_900188395.1:WP_089322784.1 2 RDFISMLDITKEELKDLLKLTETLKEKQKKGEIFEPLKGKTLALIFEKPSTRTRVSFEVGVIQLGGHGI 70 79******************************************************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 y+++ ++qlgr+e+ikDtarvlsryvd+iv+R++k+e + el +y++vPvin+L+++ehPcqilaDl+t lcl|NCBI__GCF_900188395.1:WP_089322784.1 71 YMDTRSSQLGRGEPIKDTARVLSRYVDGIVIRTFKQERIVELGRYSKVPVINALSNEEHPCQILADLFT 139 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 ike++ ++k++k++++GD+nnv+ns l++aa++G++++ atP+g+ep++ ++kka++iak + +++ +t lcl|NCBI__GCF_900188395.1:WP_089322784.1 140 IKEYCRDFKGLKVAFLGDGNNVCNSWLIGAAMTGINFYAATPQGYEPSEFYIKKAEEIAKTTSAEIVIT 208 ********************************************************************* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dp++avk+a+++ytDvw+smG+ee++e+r +++ pyqvn+ell++akp+v f+hCLPa+rGeevt++v lcl|NCBI__GCF_900188395.1:WP_089322784.1 209 NDPVEAVKEANIVYTDVWASMGQEEETEKRREIFMPYQVNSELLKHAKPDVLFMHCLPAHRGEEVTEDV 277 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 +e+ +siv+d+aenRlh+qka+l++l+ lcl|NCBI__GCF_900188395.1:WP_089322784.1 278 IESCRSIVWDQAENRLHTQKALLTMLI 304 ***********************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (305 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: 10.93 // [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