GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcl in Dyella japonica UNC79MFTsu3.2

Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate N515DRAFT_2434 N515DRAFT_2434 (S)-citramalyl-CoA lyase

Query= BRENDA::Q9I562
         (275 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2434
          Length = 321

 Score =  117 bits (292), Expect = 4e-31
 Identities = 95/270 (35%), Positives = 137/270 (50%), Gaps = 12/270 (4%)

Query: 7   RSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTP--EARVL 64
           RS LF PA   ER   A A+ AD  ++DLED+V    K EAR     F    P    R  
Sbjct: 35  RSILFTPALVAERSVNADAADADIALIDLEDSVAAVHKAEARNRAVAFFSRPPITSCRRA 94

Query: 65  VRIN-AAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAA--VASGKPVWPIVESAR 121
           VRIN      G  D LALC        +++PKVES   +  A   +  G  +  I+E+  
Sbjct: 95  VRINNLGSADGLLDLLALCGCPYKPEVVMVPKVESPRDLEIAGSLLGDGVELIAIIETPL 154

Query: 122 GLAALGE-IAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGLAP 180
           G+  +   ++  A +    FG+ D AL     +G +   Q   +AR  L   TR AGL P
Sbjct: 155 GIENISATVSTRARLTATIFGAADFAL----TTGMSIDWQSQHYARSRLATATRGAGLHP 210

Query: 181 PLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRVAE 240
            LD  +  +++  GL  A R AR++G+ G+  +HP QV  I++   PS  +++ ARR+  
Sbjct: 211 -LDSPWFDVRDAEGLTIAARRARELGYSGMGAVHPCQVPIINEIFSPSQDDIDRARRLVA 269

Query: 241 AGA-SGAGVFVVDGEMVDAPVLGRARRLLE 269
           A A  G+G+ ++DG  V AP +  ARRLL+
Sbjct: 270 ASARDGSGICLIDGIAVGAPFIESARRLLQ 299


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: 191
Number of extensions: 16
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: 321
Length adjustment: 26
Effective length of query: 249
Effective length of database: 295
Effective search space:    73455
Effective search space used:    73455
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)

This GapMind analysis is from Sep 17 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