GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcl in Mesorhizobium ciceri WSM1271

Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate YP_004134379.1 Mesci_6210 citryl-CoA lyase

Query= BRENDA::Q9I562
         (275 letters)



>NCBI__GCF_000185905.1:YP_004134379.1
          Length = 270

 Score =  169 bits (428), Expect = 6e-47
 Identities = 115/264 (43%), Positives = 149/264 (56%), Gaps = 9/264 (3%)

Query: 10  LFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPEARVLVRINA 69
           LFVP +RPER  KA  SGAD VI+DLEDAV  G K  AR  +  +      A ++VRINA
Sbjct: 11  LFVPGSRPERFAKADNSGADAVILDLEDAVAPGDKDRAREVVVAYAAMLKSA-IVVRINA 69

Query: 70  AEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAA--VASGKPVWPIVESARGLAALG 127
           A  P H  D+   R   GV  ++LPK E    +   A  +A    V  +VESA GLA L 
Sbjct: 70  AGTPWHEADIDAVRRLEGV-SVMLPKAERPEDIADMAKHMARSVSVIALVESAVGLANLP 128

Query: 128 EIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGLAPPLDGVYP 187
            I A +G+  ++FGS+D +LDL    G       L  AR  ++ ++R AG A P+DGV  
Sbjct: 129 AILATSGIVAVAFGSVDFSLDL----GCAHDRLTLLAARNEIVWRSRAAGRAAPIDGVTT 184

Query: 188 AIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRVAEAGASGAG 247
            + +     +  R A  MGFGG L IHP Q+EPI     PS  E+ WAR +  A +SG  
Sbjct: 185 DLSSPEITEDDARHAMKMGFGGKLAIHPRQIEPIRVAFRPSDKEIIWARDIVGAASSGEA 244

Query: 248 VFVVDGEMVDAPVLGRARRLLERA 271
           V  V+GEMVD PV+ RAR++L RA
Sbjct: 245 V-QVNGEMVDRPVIERARQVLRRA 267


Lambda     K      H
   0.320    0.137    0.394 

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: 188
Number of extensions: 13
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: 275
Length of database: 270
Length adjustment: 25
Effective length of query: 250
Effective length of database: 245
Effective search space:    61250
Effective search space used:    61250
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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