GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Paraburkholderia bryophila 376MFSha3.1

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate H281DRAFT_00473 H281DRAFT_00473 iron-sulfur cluster-binding protein

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__Burk376:H281DRAFT_00473
          Length = 471

 Score =  300 bits (768), Expect = 1e-85
 Identities = 169/466 (36%), Positives = 267/466 (57%), Gaps = 7/466 (1%)

Query: 9   EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDHAAKNMDTL 68
           +++    + L ++ L+  + K +  + ++RA A   ID  A  A + + ++ A +N+D  
Sbjct: 7   QFKARAGQKLADQRLQQNLTKLSTKFVSARAVAMTAIDFAATRAALKERRNRALENLDVW 66

Query: 69  YAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEED 128
              F+ EA +RGV V  A T  EA  ++  IAR ++ KK IK+KSM  EE  LN  L + 
Sbjct: 67  LETFEREANRRGVTVLFAETTQEAARLVGDIARRHDVKKVIKTKSMVTEEMRLNEVLGQM 126

Query: 129 NVEVIETDLGEWIIQMR-HEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKVA 187
            V+ IETDLGE+I+Q+  +E PSH++ P +H  + ++ADLF++   + +  +I  +   A
Sbjct: 127 GVQSIETDLGEYILQINGNEPPSHIIAPVVHKDKDEIADLFAKTHGRPRLTEIPDMTLEA 186

Query: 188 RRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTL 247
           R+ LR HF +ADMG++G NF +AETG++ LVTNEGN  + T +PRVHVA+ G++K++PTL
Sbjct: 187 RQVLRPHFLSADMGVTGGNFVIAETGSVVLVTNEGNEGMCTVMPRVHVAVTGIEKVLPTL 246

Query: 248 HDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLF 307
            D   ++++LPR+ATGQ  ++Y + + G    E   DG + M++V +D GR  L     F
Sbjct: 247 EDLATAMRLLPRSATGQTTSNYFSLLTGPRG-EGDQDGPEHMYVVLVDGGRTGLIGGD-F 304

Query: 308 SQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCE 367
            ++LRC+RCGAC N CPVY+ VGGH  G +Y G +G +LT  + G DKA +L Q    C 
Sbjct: 305 QEMLRCIRCGACMNHCPVYQKVGGHAYGWVYPGPMGSVLTPSYVGLDKALDLPQAATLCG 364

Query: 368 SCKHICAGGIDLPRLIKEIRARLNEEEGMP----VETTLMGKMLKNRKLFHTLLRFAKWA 423
            C  +C  GI L  L++++R +  E    P        + G M  +  ++  + + A   
Sbjct: 365 ECNSVCPVGIPLSDLLRKLREKQVERRLRPWKERAGLAVWGFMALHPGMYALVTKLAVRV 424

Query: 424 QKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRI 469
            + + G    I  LP   A     + +PA   + FR+ +   R  I
Sbjct: 425 LERLGGSNRSIAKLPLAGAGWTDTRDMPAPVGRTFRELYAAQRSHI 470


Lambda     K      H
   0.321    0.135    0.402 

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: 708
Number of extensions: 37
Number of successful extensions: 4
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: 717
Length of database: 471
Length adjustment: 36
Effective length of query: 681
Effective length of database: 435
Effective search space:   296235
Effective search space used:   296235
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 (21.9 bits)
S2: 53 (25.0 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