GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mcl in Pseudomonas fluorescens FW300-N2E2

Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate Pf6N2E2_1831 Citrate lyase beta chain (EC 4.1.3.6)

Query= BRENDA::A0A172MLA1
         (322 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1831
          Length = 299

 Score =  131 bits (329), Expect = 2e-35
 Identities = 94/296 (31%), Positives = 144/296 (48%), Gaps = 21/296 (7%)

Query: 9   RALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILER 68
           R+LL++P    +F +K+    AD    DLEDSV P +K +AR     A    +  G L+ 
Sbjct: 9   RSLLFVPAHIGKFTEKAHERNADACILDLEDSVAPGQKTQARDAASSAAQNISNRG-LDV 67

Query: 69  AVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHT---LSQLPLSQ 125
            VRIN++DSG  L DL  ++ SP +  +V+PKV SA       +V+ H    L +L   +
Sbjct: 68  LVRINTLDSG-GLLDLQAIV-SPAVCAVVLPKVASA-------EVVRHVALQLDRLETER 118

Query: 126 SASRPPISLLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFA 185
                   +LA +E   +L  L +I  ASP L G+    EDF++   +   P     L+ 
Sbjct: 119 GMDAGQTLILAQIEDVAALPLLDEIATASPRLMGMSLGPEDFSVSAGMEPVPET--LLWP 176

Query: 186 RSAIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQV 245
              +A A R A +      +   +     D S     +Q    G+ LG  G  CIHP QV
Sbjct: 177 NQQVAFACRRAGI------LPFGFPGSIADFSDIPRFRQALVLGRQLGMIGAFCIHPEQV 230

Query: 246 STVQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKK 301
           + + ++F P   EV+++V +      A   GRGA+   GKMID P+  +AR ++ +
Sbjct: 231 AVLNEVFSPGDAEVEYSVALLAEYACAEAEGRGAFAFRGKMIDAPIVARARELLTR 286


Lambda     K      H
   0.316    0.130    0.369 

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: 183
Number of extensions: 7
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: 322
Length of database: 299
Length adjustment: 27
Effective length of query: 295
Effective length of database: 272
Effective search space:    80240
Effective search space used:    80240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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