GapMind for catabolism of small carbon sources

 

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

Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate Pf6N2E2_4704 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF

Query= uniprot:Q39TW0
         (387 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4704
          Length = 649

 Score =  195 bits (495), Expect = 4e-54
 Identities = 120/395 (30%), Positives = 193/395 (48%), Gaps = 47/395 (11%)

Query: 29  CYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGLTE------------------------- 62
           C QCG C++ CP     Q  + +K+++    GL                           
Sbjct: 245 CVQCGKCEAACPAFAAGQPLNPKKLIQDMVVGLAGGTDAKFAGSPYPGKPVGEHGGNPHQ 304

Query: 63  ------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRR-IGAEYDVYPGH-VGTIRNV 114
                 ++ E +W C+TC  C   CP  +  ++A V MRR +  E    P      + N+
Sbjct: 305 PIVNGLVDAETLWSCTTCRACVEECPMMIEHVDAIVDMRRHLTLEKGATPNKGAEVLENL 364

Query: 115 VASLTSEGNSLGGDRTQRGDWAKDLPVKPYAE--GMELLYFTGCYLSYDPRMRKVAAATA 172
           +A+    G + GG    R +WA DL +   +E    ++L++ G   ++D R ++   A  
Sbjct: 365 IATDNPGGFAPGG----RMNWAADLNLNLLSEKKSTDVLFWVGDG-AFDMRNQRTLRAFV 419

Query: 173 AILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPHCY 232
            +L  A +DF +LG +E   G+  R+ G+E  F+ LAK NI+        +I+   PH +
Sbjct: 420 KVLKAAKIDFAVLGLEERDSGDVARRLGDEATFQLLAKRNIQTLAKYSFNRIVTCDPHSF 479

Query: 233 HTFVNEYPEFKVNFEVVFISQYIGQLINEGRLQITGEFAKKVTYHDPCYLGRHNGIYDEP 292
           H   NEY  F  N+ V   S Y+ ++I+ G L +       VTYHDPCYLGR+NG Y+ P
Sbjct: 480 HVLKNEYGAFDGNYLVQHHSTYMAEIIDAGALNLGQHKGDSVTYHDPCYLGRYNGEYEAP 539

Query: 293 RQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGATVLAT 352
           RQVL+ + G+E+ EM  +   S CCGGGGG    + P ++R  D+R+    + GA ++A 
Sbjct: 540 RQVLRAL-GIEVKEMQRSGFRSRCCGGGGGAPITDIPGKQRIPDMRMEDIRETGAELVAV 598

Query: 353 SCPYCITNFTDSSLDLADHEKVEVKDLAEIILEVI 387
            CP C      + L+     +  +KD+AE++ + +
Sbjct: 599 GCPQC-----TAMLEGVVEPRPMIKDIAELVADAL 628


Lambda     K      H
   0.320    0.139    0.427 

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: 611
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 387
Length of database: 649
Length adjustment: 34
Effective length of query: 353
Effective length of database: 615
Effective search space:   217095
Effective search space used:   217095
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: 52 (24.6 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