Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate Ga0059261_3985 Ga0059261_3985 methylmalonyl-CoA epimerase (EC 5.1.99.1)
Query= SwissProt::Q3IZP4 (134 letters) >FitnessBrowser__Korea:Ga0059261_3985 Length = 141 Score = 150 bits (379), Expect = 7e-42 Identities = 72/131 (54%), Positives = 93/131 (70%), Gaps = 3/131 (2%) Query: 2 IGRLNHVAIAVPDLEAAAAQYRNTLGAE-VGAPQDEPDHGVTVIFITLPNTKIELLHPLG 60 +GRLNH+ +A P +EA+ A YR+ +GA+ + AP D P GV V F+ PNT+IEL+ PLG Sbjct: 4 LGRLNHIGVATPSIEASVAFYRDVMGAQTIHAPFDLPAQGVKVCFVDTPNTQIELIEPLG 63 Query: 61 EGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFLH 120 SPI GFL +NPAGG HH+CYEV DI A+ + GA+VL GEP+IGAHG P+ F+H Sbjct: 64 ADSPIHGFLARNPAGGQHHVCYEVPDIHEAKAWFEAKGAKVL--GEPRIGAHGTPIFFVH 121 Query: 121 PKDFNGCLVEL 131 PKD G L E+ Sbjct: 122 PKDMGGVLTEI 132 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: 107 Number of extensions: 9 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: 134 Length of database: 141 Length adjustment: 15 Effective length of query: 119 Effective length of database: 126 Effective search space: 14994 Effective search space used: 14994 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 Ga0059261_3985 Ga0059261_3985 (methylmalonyl-CoA epimerase (EC 5.1.99.1))
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.10499.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-46 142.5 0.0 6.1e-46 142.3 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3985 Ga0059261_3985 methylmalonyl-CoA Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3985 Ga0059261_3985 methylmalonyl-CoA epimerase (EC 5.1.99.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 142.3 0.0 6.1e-46 6.1e-46 1 129 [] 6 134 .. 6 134 .. 0.96 Alignments for each domain: == domain 1 score: 142.3 bits; conditional E-value: 6.1e-46 TIGR03081 1 kldhvaiavkdleeaaklyrdvlGakvsee.eelpeqgvkvvflelgetklellepleedspiakflek 68 +l+h+++a++++e+ +++yrdv+Ga+ ++ +lp qgvkv f++ +t++el+epl+ dspi +fl++ lcl|FitnessBrowser__Korea:Ga0059261_3985 6 RLNHIGVATPSIEASVAFYRDVMGAQTIHApFDLPAQGVKVCFVDTPNTQIELIEPLGADSPIHGFLAR 74 79***********************98886268************************************ PP TIGR03081 69 kkgeGlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129 ++++G hh+++ev di++a + + kg ++l+ epriGahG ++ F+hPkd+gGvL+e++e lcl|FitnessBrowser__Korea:Ga0059261_3985 75 NPAGGQHHVCYEVPDIHEAKAWFEAKGAKVLG-EPRIGAHGTPIFFVHPKDMGGVLTEIME 134 *****************************998.6************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (141 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: 5.24 // [ok]
This GapMind analysis is from Sep 17 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