GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate HSERO_RS06380 HSERO_RS06380 excisionase

Query= BRENDA::Q9I5E3
         (375 letters)



>FitnessBrowser__HerbieS:HSERO_RS06380
          Length = 431

 Score = 89.0 bits (219), Expect = 2e-22
 Identities = 58/189 (30%), Positives = 92/189 (48%), Gaps = 10/189 (5%)

Query: 175 KVMNVSLILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIE 234
           +++ ++L+L A+HE NAS+FT+R  AST + L + V   +  L G  H GA    +E + 
Sbjct: 211 ELIRMALVLCADHELNASSFTSRCVASTDASLRAVVIAGLAGLSGGRH-GATTGRVEALW 269

Query: 235 RFSSPQEATAELLKMLERKDKIMGFGHAIYKDSDPRNEVIKGWSKQLADEVGDKVLFAVS 294
                ++   ++ + L R D + GFGH +Y D DPR   +      L+  +     +A  
Sbjct: 270 DELGTRDVDRKMRERLSRGDDLPGFGHTLYPDGDPRASYL------LSQILPRHSPWAAM 323

Query: 295 EAIDKTMWEQKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANNRI 354
                T+  QK   P+ DF   +    + +P      +F   R+ GW AH  EQR  + +
Sbjct: 324 IDAGITLTGQK---PSVDFALVALRRHLRLPVGAAFGLFALGRSIGWIAHGLEQREQHHL 380

Query: 355 IRPSAEYTG 363
           IRP A Y G
Sbjct: 381 IRPRAVYIG 389



 Score = 25.4 bits (54), Expect = 0.003
 Identities = 13/25 (52%), Positives = 14/25 (56%)

Query: 28  EGAGLTYRGYDVRDLAAAAIFEEVA 52
           +G  L YRG D   LA  A  EEVA
Sbjct: 84  DGGRLFYRGVDALSLAEHASLEEVA 108


Lambda     K      H
   0.319    0.134    0.396 

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: 355
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 375
Length of database: 431
Length adjustment: 31
Effective length of query: 344
Effective length of database: 400
Effective search space:   137600
Effective search space used:   137600
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: 50 (23.9 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