Align Ethylmalonyl-CoA/methylmalonyl-CoA epimerase; EC 5.1.99.-; EC 5.1.99.1 (characterized)
to candidate CCNA_02011 CCNA_02011 methylmalonyl CoA epimerase
Query= SwissProt::Q3IZP4 (134 letters) >FitnessBrowser__Caulo:CCNA_02011 Length = 139 Score = 145 bits (365), Expect = 3e-40 Identities = 73/132 (55%), Positives = 91/132 (68%), Gaps = 3/132 (2%) Query: 1 MIGRLNHVAIAVPDLEAAAAQYRNTLGA-EVGAPQDEPDHGVTVIFITLPNTKIELLHPL 59 MIG+LNHV +A P ++ + YR+ LGA + P+ GV V F+ LPN++IEL+ P Sbjct: 1 MIGKLNHVGVATPSIDESVKMYRDLLGATSITDKWAMPEQGVWVCFVNLPNSQIELIEPY 60 Query: 60 GEGSPIAGFLEKNPAGGIHHICYEVEDILAARDRLKEAGARVLGSGEPKIGAHGKPVLFL 119 GE SPI GFL KNP GG HHIC+EVE+I ARD L GA VL GEP+IGAHG ++F+ Sbjct: 61 GEKSPIHGFLAKNPKGGQHHICFEVENIYEARDALVAKGATVL--GEPRIGAHGTLIIFV 118 Query: 120 HPKDFNGCLVEL 131 HPKD G LVEL Sbjct: 119 HPKDMGGMLVEL 130 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: 110 Number of extensions: 8 Number of successful extensions: 3 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: 139 Length adjustment: 15 Effective length of query: 119 Effective length of database: 124 Effective search space: 14756 Effective search space used: 14756 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 CCNA_02011 CCNA_02011 (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.18522.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-47 146.8 0.0 2.8e-47 146.7 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02011 CCNA_02011 methylmalonyl CoA epi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02011 CCNA_02011 methylmalonyl CoA epimerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 146.7 0.0 2.8e-47 2.8e-47 1 129 [] 4 132 .. 4 132 .. 0.97 Alignments for each domain: == domain 1 score: 146.7 bits; conditional E-value: 2.8e-47 TIGR03081 1 kldhvaiavkdleeaaklyrdvlGa.kvseeeelpeqgvkvvflelgetklellepleedspiakflekkkge 72 kl+hv++a+++++e +k+yrd+lGa +++++ ++peqgv v f++l ++++el+ep +e+spi +fl+k++++ lcl|FitnessBrowser__Caulo:CCNA_02011 4 KLNHVGVATPSIDESVKMYRDLLGAtSITDKWAMPEQGVWVCFVNLPNSQIELIEPYGEKSPIHGFLAKNPKG 76 79**********************84689999***************************************** PP TIGR03081 73 GlhhialevddieaaletlkekgvrlldeepriGahGkkvaFlhPkdtgGvLielee 129 G hhi++ev++i +a + l kg +l+ epriGahG ++F+hPkd+gG+L+el+e lcl|FitnessBrowser__Caulo:CCNA_02011 77 GQHHICFEVENIYEARDALVAKGATVLG-EPRIGAHGTLIIFVHPKDMGGMLVELME 132 ************************9998.6************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (129 nodes) Target sequences: 1 (139 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: 5.01 // [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