GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamD in Paraburkholderia bryophila 376MFSha3.1

Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate H281DRAFT_02472 H281DRAFT_02472 Fe-S oxidoreductase

Query= uniprot:Q39TW0
         (387 letters)



>FitnessBrowser__Burk376:H281DRAFT_02472
          Length = 637

 Score =  191 bits (485), Expect = 5e-53
 Identities = 126/396 (31%), Positives = 194/396 (48%), Gaps = 46/396 (11%)

Query: 25  SLKYCYQCGLCDSVCPWNRVRQ-FSMRKIVRQ---GTFGLTE------------------ 62
           S   C QCG C++ CP     Q  + +K+++    G  G T+                  
Sbjct: 246 SFDACVQCGKCEAACPAFAAGQPLNPKKLIQDLVTGMVGGTDAEYAGSPTPGIPVGKHGG 305

Query: 63  ----------IEQEDIWRCSTCGTCPSRCPRGVNQIEAGVAMRRIGAEYDVYPGHVGTIR 112
                     IE E +W C+TC  C   CP  +  ++A V MRR     +      G I 
Sbjct: 306 APGKPLISSLIEAETLWSCTTCRACVQECPMLIEHVDAIVDMRRNQTLVEGTVPGKGPI- 364

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

Query: 171 TAAILNKAGVDFGILGSKESCCGESIRKTGNEELFKRLAKENIKQFIDNGVTKILVSSPH 230
              +LN+AGVD+ +LG  E+  G++ R+ G+E  F+ LAK+ I         KI+ S PH
Sbjct: 423 LVKVLNRAGVDYAVLGGVETDTGDTARRLGDEATFQHLAKKLIDTLSQYSFGKIVTSDPH 482

Query: 231 CYHTFVNEYPEFKVNFEVVFISQYIGQLINEGRLQ---ITGEFAKKVTYHDPCYLGRHNG 287
             H+  NEY      +EV   +  I +L+  G+L    +      K+TYHDPCYLGR+NG
Sbjct: 483 VLHSLRNEYRALGGFYEVQHHTALIDELVASGKLSPRALAAYADSKITYHDPCYLGRYNG 542

Query: 288 IYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGGRIWMETPKEERFADLRIRQAVDVGA 347
             + PR+VL+ + G++++EM  +     CCGGGGG    + P + R  D+RI  A  +GA
Sbjct: 543 ETEAPRRVLKSI-GIKVVEMERHGMRGRCCGGGGGAPLTDIPGKRRIPDIRIDDARGIGA 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: 582
Number of extensions: 30
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 (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