Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_042441347.1 TX73_RS24405 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000195775.1:WP_042441347.1 Length = 309 Score = 411 bits (1056), Expect = e-119 Identities = 206/301 (68%), Positives = 232/301 (77%), Gaps = 1/301 (0%) Query: 4 RHFTDLSTVSEGDLRFMLDDAVVRKARLKAG-ERTRPLEGKVLAMIFDKPSTRTRVSFDV 62 RHF DL+ + +LR ML AV KA+ KA + +PL GK LAMIFDKPSTRTRVSFDV Sbjct: 7 RHFLDLTELPTSELRNMLSAAVAMKAKRKANADGEKPLAGKTLAMIFDKPSTRTRVSFDV 66 Query: 63 GMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVPV 122 GMRQLGGE+IMLTG EMQLGR ETIADTA+VLSR+VD IMIR +H+ LLEL NATVPV Sbjct: 67 GMRQLGGESIMLTGAEMQLGRGETIADTARVLSRFVDIIMIRILNHEALLELAANATVPV 126 Query: 123 INGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVAV 182 INGLT +HPCQ+MAD+MTFEEHRGP+ G+TIAWTGD NNVL S A+ RF F LN+A Sbjct: 127 INGLTRKSHPCQVMADVMTFEEHRGPIKGRTIAWTGDDNNVLASFAHAAQRFEFKLNIAT 186 Query: 183 PEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSPY 242 P P++ DW KA G + PEEAV ADCVVTD WVSMG + HN+ PY Sbjct: 187 PPQLSPSKALRDWIKASGAAITIGTDPEEAVRGADCVVTDTWVSMGDKDGEHRHNLLKPY 246 Query: 243 QVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCLG 302 QVNAKLM+ A DA+FMHCLPAHRGEEVTDEVIDGP SVVFDEAENRLHAQK +LAWCLG Sbjct: 247 QVNAKLMSLAHKDAIFMHCLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKGILAWCLG 306 Query: 303 A 303 A Sbjct: 307 A 307 Lambda K H 0.320 0.133 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: 378 Number of extensions: 14 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: 303 Length of database: 309 Length adjustment: 27 Effective length of query: 276 Effective length of database: 282 Effective search space: 77832 Effective search space used: 77832 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_042441347.1 TX73_RS24405 (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.13637.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-117 378.5 0.0 1.3e-117 378.3 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_042441347.1 TX73_RS24405 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_042441347.1 TX73_RS24405 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.3 0.0 1.3e-117 1.3e-117 1 303 [. 7 305 .. 7 306 .. 0.98 Alignments for each domain: == domain 1 score: 378.3 bits; conditional E-value: 1.3e-117 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgke.ekklkgktlaliFekrstRtRvsfevaayelGaqv 68 rh+l+l++l ++el+++l a +k+++k++ ek l gktla+iF+k+stRtRvsf+v++ +lG+++ lcl|NCBI__GCF_000195775.1:WP_042441347.1 7 RHFLDLTELPTSELRNMLSAAVAMKAKRKANADgEKPLAGKTLAMIFDKPSTRTRVSFDVGMRQLGGES 75 8**************************9998775889******************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDll 137 ++l e+qlgr+e+i+Dtarvlsr+vd+i++R +he + ela +a+vPvingLt ++hPcq++aD++ lcl|NCBI__GCF_000195775.1:WP_042441347.1 76 IMLTGAEMQLGRGETIADTARVLSRFVDIIMIRILNHEALLELAANATVPVINGLTRKSHPCQVMADVM 144 ********************************************************************* PP TIGR00658 138 tikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklel 206 t +e+ g +k+ ++++ GD nnv s+ aa + +++++atP++l+p++++ ++ k++g+ +++ lcl|NCBI__GCF_000195775.1:WP_042441347.1 145 TFEEHRGPIKGRTIAWTGDDNNVLASFAHAAQRFEFKLNIATPPQLSPSKALRDWI----KASGAAITI 209 *************************************************9998876....67******* PP TIGR00658 207 tedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtde 275 dp++av++ad ++tD+wvsmG+++ + +r +llkpyqvn +l++la+++++f+hCLPa+rGeevtde lcl|NCBI__GCF_000195775.1:WP_042441347.1 210 GTDPEEAVRGADCVVTDTWVSMGDKDGE-HRHNLLKPYQVNAKLMSLAHKDAIFMHCLPAHRGEEVTDE 277 ***********************98765.89************************************** PP TIGR00658 276 vlegeasivfdeaenRlhaqkavlkall 303 v++g++s+vfdeaenRlhaqk++l+++l lcl|NCBI__GCF_000195775.1:WP_042441347.1 278 VIDGPQSVVFDEAENRLHAQKGILAWCL 305 ************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (309 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 7.91 // [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