GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Pseudomonas fluorescens FW300-N1B4

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Pf1N1B4_1188 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1188
          Length = 484

 Score =  286 bits (732), Expect = 2e-81
 Identities = 152/381 (39%), Positives = 223/381 (58%), Gaps = 2/381 (0%)

Query: 8   KEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMD 66
           +++R    ++L +  LRN       +  + RA +F D  E+  +  + +A +  A   + 
Sbjct: 14  EDFRARAHKALADTQLRNNFRSAMDSLMSKRAASFSDAFEREHLRVLGNAVRARALSKLP 73

Query: 67  TLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLE 126
            L  Q +    + GV VH A T  EAN I+  I R +  ++ IK KSM +EE  +NH L 
Sbjct: 74  DLLEQLEQNLTRNGVTVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEMEMNHVLA 133

Query: 127 EDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKV 186
              +E +E+D+GE+I+Q+ HE PSH++MPAIH +  QVA LF +    +   D+ +L+++
Sbjct: 134 AQGIECLESDMGEFIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVEYTKDVDQLIQI 193

Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246
            R+ LR  F  AD+G+SG NFAVAETGT+ LV NEGN R+ TT+P VH+A+ G++K+V  
Sbjct: 194 GRKVLRQKFFEADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVEN 253

Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306
           L D +  L +L R+A GQ IT+YV  I G  + E  +DG +E+H+V LDNGR     D  
Sbjct: 254 LRDVVPLLSLLTRSALGQPITTYVNMISGPRK-EHELDGPQEVHLVLLDNGRSQAFADSE 312

Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366
             Q L C+RCGAC N CPVY  +GGH  G +Y G IG I+T    G  K  +       C
Sbjct: 313 LRQTLNCIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHMVGLAKVPDHPSASSLC 372

Query: 367 ESCKHICAGGIDLPRLIKEIR 387
            +C  +C   I +P L++ +R
Sbjct: 373 GACGEVCPVKIPIPALLRRLR 393


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: 756
Number of extensions: 32
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: 484
Length adjustment: 37
Effective length of query: 680
Effective length of database: 447
Effective search space:   303960
Effective search space used:   303960
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