GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamD in Burkholderia phytofirmans PsJN

Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate BPHYT_RS25200 BPHYT_RS25200 (Fe-S)-binding protein

Query= uniprot:Q39TW0
         (387 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25200 BPHYT_RS25200
           (Fe-S)-binding protein
          Length = 637

 Score =  192 bits (487), Expect = 3e-53
 Identities = 126/396 (31%), Positives = 196/396 (49%), Gaps = 46/396 (11%)

Query: 25  SLKYCYQCGLCDSVCPWNRVRQ-FSMRKIVRQGTFGL----------------------- 60
           S   C QCG C++ CP     Q  + +K+++    G+                       
Sbjct: 246 SFDACVQCGKCEAACPAFAAGQPLNPKKLIQDLVTGMVGGTDAQYAGSPTPGIPVGKHAG 305

Query: 61  --------TEIEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIR 112
                   T IE + +W C+TC  C   CP  +  ++A V MRR     +      G I 
Sbjct: 306 APDKPLISTMIEADTLWSCTTCRACVQECPMLIEHVDAIVDMRRNQTLVEGSVPGKGPI- 364

Query: 113 NVVASLTSEGNSLGGDRTQRGDWAKDLPVKPYAEG--MELLYFTGCYLSYDPRMRKVAAA 170
             +A+L   G+S G D   R DWA DL V+    G  +++L   G   ++D R ++   A
Sbjct: 365 -TLANLRETGSSNGYDIGARYDWAVDLQVQVAQPGRPVDVLLIAG-EGAFDMRYQRTLRA 422

Query: 171 TAAILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPH 230
              +LN+AG+D+ +LG  E+  G++ R+ G+E  F++LA + I         KI+ + PH
Sbjct: 423 LVKVLNRAGIDYAVLGGVETDTGDTARRLGDEATFQQLALKLIGTLSQYSFRKIVTADPH 482

Query: 231 CYHTFVNEYPEFKVNFEVVFISQYIGQLINEGRL--QITGEFA-KKVTYHDPCYLGRHNG 287
             H+  NEY      +EV   +  I QL+  G+L  +    FA +K+TYHDPCYLGR+NG
Sbjct: 483 VLHSLRNEYRALGGFYEVQHHTALIEQLVASGKLTPRAVAAFADRKITYHDPCYLGRYNG 542

Query: 288 IYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGA 347
             + PR++L+ + G++++EM  N     CCGGGGG    + P + R  D+RI  A  VGA
Sbjct: 543 ETEAPRKLLKTI-GIKVVEMERNGMRGRCCGGGGGAPLTDIPGKRRIPDIRIDDAKTVGA 601

Query: 348 TVLATSCPYCITNFTDSSLDLADHEKVEVKDLAEII 383
            ++A  CP C      + L+     + EV D+AE++
Sbjct: 602 EIVAVGCPNC-----TAMLEGVVGPRPEVLDVAELV 632


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: 569
Number of extensions: 33
Number of successful extensions: 7
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: 637
Length adjustment: 34
Effective length of query: 353
Effective length of database: 603
Effective search space:   212859
Effective search space used:   212859
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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