GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Pseudomonas fluorescens FW300-N2C3

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate AO356_07560 AO356_07560 (Fe-S)-binding protein

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07560
          Length = 489

 Score =  293 bits (751), Expect = 1e-83
 Identities = 153/381 (40%), Positives = 225/381 (59%), Gaps = 2/381 (0%)

Query: 8   KEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMD 66
           +++R    ++LD+  LRN       +    RA +F D  E+  +  + +A +  A   + 
Sbjct: 18  EDFRARAHKALDDTQLRNNFRSAMDSLMTKRAASFSDAHEREHLRVLGNAVRARALSKLP 77

Query: 67  TLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLE 126
            L  Q +    + GV VH A T  EAN I+  I R +  ++ IK KSM +EE  +NH LE
Sbjct: 78  DLLEQLETNLTRNGVNVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEMEMNHFLE 137

Query: 127 EDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKV 186
             ++E +E+D+GE+I+Q+ HE PSH++MPAIH +  QVA LF +    +   D+ +L+++
Sbjct: 138 ARDIECLESDMGEYIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEYTKDVDQLIQI 197

Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246
            R+ LR  F  AD+G+SG NFAVAETGT+ LV NEGN R+ TT+P VH+A+ G++K+V  
Sbjct: 198 GRKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVEN 257

Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306
           L D +  L +L R+A GQ IT+YV  I G  + +  +DG +E+H+V LDNGR     D  
Sbjct: 258 LRDVVPLLSLLTRSALGQPITTYVNMISGPRKADE-LDGPQEVHLVLLDNGRSQAFADSE 316

Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366
             Q L C+RCGAC N CPVY  +GGH  G +Y G IG I+T    G  K  +       C
Sbjct: 317 LRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVPDHPSASSLC 376

Query: 367 ESCKHICAGGIDLPRLIKEIR 387
            +C  +C   I +P L++ +R
Sbjct: 377 GACGEVCPVKIPIPALLRRLR 397


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: 758
Number of extensions: 34
Number of successful extensions: 5
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: 489
Length adjustment: 37
Effective length of query: 680
Effective length of database: 452
Effective search space:   307360
Effective search space used:   307360
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