Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_104913671.1 C3B54_RS05910 ornithine carbamoyltransferase
Query= BRENDA::P0A5M9 (307 letters) >NCBI__GCF_002950575.1:WP_104913671.1 Length = 307 Score = 354 bits (909), Expect = e-102 Identities = 177/307 (57%), Positives = 222/307 (72%) Query: 1 MIRHFLRDDDLSPAEQAEVLELAAELKKDPVSRRPLQGPRGVAVIFDKNSTRTRFSFELG 60 M RHFLRDDD++P EQAE+L LA ++K RPL+GP+ VAVIFDK+STRTR SF +G Sbjct: 1 MTRHFLRDDDVTPEEQAEILSLAGQMKAQRFEHRPLEGPQTVAVIFDKSSTRTRVSFAVG 60 Query: 61 IAQLGGHAVVVDSGSTQLGRDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVI 120 IA LGG +++ + S+QLG ET DTA+VL R V AIVWRT+GQE L+ MA TVPV+ Sbjct: 61 IADLGGTPLIISTASSQLGGKETPADTARVLERMVAAIVWRTYGQEGLEEMADGTTVPVV 120 Query: 121 NALSDEFHPCQVLADLQTIAERKGALRGLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAA 180 NALSD+FHPCQ+LADL T+ E+ G L+ + + GDG +NMA S LL AG+HV +A Sbjct: 121 NALSDDFHPCQLLADLLTMQEKLGTLQDRVVCFSGDGRSNMAQSYLLACAAAGMHVRIAC 180 Query: 181 PEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWTSMGQENDGLDRVK 240 PE F P V A AER A TG SV V D AGADV+VTDTW SMG+E++ + RVK Sbjct: 181 PEQFAPRADVVADAERIALQTGGSVRVGVDPEELVAGADVVVTDTWVSMGKEDEKVQRVK 240 Query: 241 PFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALL 300 F P+Q+ +L+ALA A+ +HCLPA RG E+ +V+DGP S +WDE+ENRLHAQKALL Sbjct: 241 TFTPYQVTDQLMALAKPGALFMHCLPADRGFEVEQSVIDGPQSVIWDESENRLHAQKALL 300 Query: 301 VWLLERS 307 WLLER+ Sbjct: 301 AWLLERA 307 Lambda K H 0.319 0.133 0.387 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: 270 Number of extensions: 9 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: 307 Length of database: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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_104913671.1 C3B54_RS05910 (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.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.714882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-114 366.1 0.0 7.7e-114 365.9 0.0 1.0 1 NCBI__GCF_002950575.1:WP_104913671.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002950575.1:WP_104913671.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 365.9 0.0 7.7e-114 7.7e-114 1 303 [. 3 304 .. 3 305 .. 0.99 Alignments for each domain: == domain 1 score: 365.9 bits; conditional E-value: 7.7e-114 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkg.ktlaliFekrstRtRvsfevaayelGaqvlyln 72 rh+l d+++ee e+l la ++k+++ + ++ l+g +t+a+iF+k+stRtRvsf v++++lG+ +l+++ NCBI__GCF_002950575.1:WP_104913671.1 3 RHFLRDDDVTPEEQAEILSLAGQMKAQRFE---HRPLEGpQTVAVIFDKSSTRTRVSFAVGIADLGGTPLIIS 72 799999*******************99988...899998689******************************* PP TIGR00658 73 keelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgk 145 + ++qlg ke+ +Dtarvl+r+v aiv R+y +e +ee+a+ ++vPv+n+L+d +hPcq+laDllt++eklg+ NCBI__GCF_002950575.1:WP_104913671.1 73 TASSQLGGKETPADTARVLERMVAAIVWRTYGQEGLEEMADGTTVPVVNALSDDFHPCQLLADLLTMQEKLGT 145 ************************************************************************* PP TIGR00658 146 lkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkda 217 l++ + + GD+ n+a+s lla+a G++v++a+Pe++ p+a++v a++ia ++gg++++ dp++ v++a NCBI__GCF_002950575.1:WP_104913671.1 146 LQDRVVCFSGDGrSNMAQSYLLACAAAGMHVRIACPEQFAPRADVVADAERIALQTGGSVRVGVDPEELVAGA 218 ************9************************************************************ PP TIGR00658 218 dviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaen 290 dv++tD+wvsmG+e++k +r+k + pyqv+++l++lakp + f+hCLPa rG ev + v++g++s+++de en NCBI__GCF_002950575.1:WP_104913671.1 219 DVVVTDTWVSMGKEDEKVQRVKTFTPYQVTDQLMALAKPGALFMHCLPADRGFEVEQSVIDGPQSVIWDESEN 291 ************************************************************************* PP TIGR00658 291 Rlhaqkavlkall 303 Rlhaqka+l++ll NCBI__GCF_002950575.1:WP_104913671.1 292 RLHAQKALLAWLL 304 **********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (307 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: 00:00:00.00 # Mc/sec: 16.19 // [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