Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate WP_045580738.1 AL072_RS08275 methylmalonyl-CoA epimerase
Query= SwissProt::Q3IZP4 (134 letters) >NCBI__GCF_001305595.1:WP_045580738.1 Length = 134 Score = 219 bits (558), Expect = 1e-62 Identities = 107/133 (80%), Positives = 114/133 (85%) Query: 1 MIGRLNHVAIAVPDLEAAAAQYRNTLGAEVGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60 MIG+LNHVAI VPDL AA A YR+TLGA V P D HGVTV+F+TLPNTKIELLHP G Sbjct: 1 MIGKLNHVAIVVPDLPAATALYRDTLGAAVSQPVDLAPHGVTVVFVTLPNTKIELLHPFG 60 Query: 61 EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120 E SPIAGFLEKNP+GGIHHICYEV+DILAARDR+K GARVLG GEPKIGAH KPVLFLH Sbjct: 61 EKSPIAGFLEKNPSGGIHHICYEVDDILAARDRMKAQGARVLGDGEPKIGAHDKPVLFLH 120 Query: 121 PKDFNGCLVELEQ 133 PKDF G LVELEQ Sbjct: 121 PKDFCGTLVELEQ 133 Lambda K H 0.319 0.141 0.421 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: 147 Number of extensions: 5 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: 134 Length of database: 134 Length adjustment: 15 Effective length of query: 119 Effective length of database: 119 Effective search space: 14161 Effective search space used: 14161 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: 42 (20.8 bits)
Align candidate WP_045580738.1 AL072_RS08275 (methylmalonyl-CoA epimerase)
to HMM TIGR03081 (mce: methylmalonyl-CoA epimerase (EC 5.1.99.1))
# 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/TIGR03081.hmm # target sequence database: /tmp/gapView.1599097.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03081 [M=129] Accession: TIGR03081 Description: metmalonyl_epim: methylmalonyl-CoA epimerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-51 160.1 0.0 2.1e-51 160.0 0.0 1.0 1 NCBI__GCF_001305595.1:WP_045580738.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001305595.1:WP_045580738.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 160.0 0.0 2.1e-51 2.1e-51 1 129 [] 4 133 .. 4 133 .. 0.99 Alignments for each domain: == domain 1 score: 160.0 bits; conditional E-value: 2.1e-51 TIGR03081 1 kldhvaiavkdleeaaklyrdvlGakvseeeelpeqgvkvvflelgetklellepleedspiakflekkkgeG 73 kl+hvai v+dl +a++lyrd+lGa+vs+ +l+ +gv+vvf+ l +tk+ell+p +e+spia+flek++ +G NCBI__GCF_001305595.1:WP_045580738.1 4 KLNHVAIVVPDLPAATALYRDTLGAAVSQPVDLAPHGVTVVFVTLPNTKIELLHPFGEKSPIAGFLEKNPSGG 76 79*********************************************************************** PP TIGR03081 74 lhhialevddieaaletlkekgvrllde.epriGahGkkvaFlhPkdtgGvLielee 129 +hhi++evddi aa + +k +g r+l++ ep+iGah k+v FlhPkd G L+ele+ NCBI__GCF_001305595.1:WP_045580738.1 77 IHHICYEVDDILAARDRMKAQGARVLGDgEPKIGAHDKPVLFLHPKDFCGTLVELEQ 133 **************************988**************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (134 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: 6.69 // [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