GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Phaeobacter inhibens BS107

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate GFF445 PGA1_c04560 putative fumarate lyase

Query= curated2:Q9I6Q8
         (459 letters)



>FitnessBrowser__Phaeo:GFF445
          Length = 449

 Score =  249 bits (637), Expect = 1e-70
 Identities = 165/440 (37%), Positives = 233/440 (52%), Gaps = 15/440 (3%)

Query: 7   NQLFDAYFMAAPMRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAACRAELY 66
           +QL+ + F A  +  +FSD   ++ ML  E ALA+A+ + G++P  + A I  A      
Sbjct: 8   SQLYASLFSAGDVSRLFSDSAEIRAMLLVEGALAKAQGKLGLIPEDSAAAIGRAVMEVAL 67

Query: 67  DPLALAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQLRRAL 126
           DP AL +A    G     LV AL  ++ A   E  +YVH GATSQD MDS L+L+LR+AL
Sbjct: 68  DPGALTQAAGQNGVPVPGLVSALRDEMNA--PEHAQYVHWGATSQDIMDSALMLRLRQAL 125

Query: 127 ALLEQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHRQRLRE 186
           A +E DL  L   L+D A+ HA+ P+A RT+ Q ATP + G  +A     L    + L  
Sbjct: 126 AAVETDLLILLTQLSDMADTHANLPMAARTYGQLATPTSFGAVVAAWGQPLAALLEELPT 185

Query: 187 LRPRLLVLQFGGASGTLAALGEQALPVAAALAEELGLALPEQPWHTQRDRLVEFASVLGL 246
           LR   L++   GA+GT +ALG +A  + A LA  L L  P + WHT R  ++  A  L  
Sbjct: 186 LRQTCLLVSLSGAAGTSSALGPKASELRAELAAGLSLVDPHRSWHTDRSPVLRIADWLTR 245

Query: 247 VAGSLGKFGRDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATRAPGLV 306
              SL K G D   L Q+   E+        G SSTMP K+NPV+++ LIA A++A   +
Sbjct: 246 ACTSLSKLGTDCLALRQSGIDEL---TTITAGASSTMPQKQNPVAASALIALASQATAQL 302

Query: 307 STLFAAMPQEHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRRNLGLT 366
           S L  A   +H+R    W  EW +LP++    A A + A+ + +GL  DA++M RNL   
Sbjct: 303 SALHHAAAHQHQRDGASWFGEWLSLPQIVFCAASAARTAVSMTKGLAPDAKQMLRNLHAA 362

Query: 367 HGLVLAEAVSIALARRIGREAAHHLVEQCCRRAVEQRRELRAVLGEEARVSAELSGDELD 426
           +G + AEA+S ALA ++ R  A   V+  C +A +Q   L+ V        A L   ELD
Sbjct: 363 NGTIYAEALSFALAEQMRRGEAQAAVKDLCVKAAQQGVPLQEV--------AALQFPELD 414

Query: 427 R--LLDPAHYLGQARAWVER 444
              L D    LG A    +R
Sbjct: 415 HATLFDATRQLGSATYEAQR 434


Lambda     K      H
   0.320    0.133    0.386 

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: 439
Number of extensions: 16
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: 459
Length of database: 449
Length adjustment: 33
Effective length of query: 426
Effective length of database: 416
Effective search space:   177216
Effective search space used:   177216
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: 51 (24.3 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