GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Streptacidiphilus oryzae TH49

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate WP_037577835.1 BS73_RS31830 hypothetical protein

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>NCBI__GCF_000744815.1:WP_037577835.1
          Length = 379

 Score =  197 bits (501), Expect = 5e-55
 Identities = 134/334 (40%), Positives = 178/334 (53%), Gaps = 20/334 (5%)

Query: 9   IYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIVSAST 68
           + R GTS+G YFLA DLPA+P+ER+A L+ IMGS  P QIDG+GG + LTSKVA+VSAS 
Sbjct: 14  LMRGGTSKGGYFLAGDLPADPAERNALLLRIMGSPDPRQIDGLGGAHPLTSKVAVVSASA 73

Query: 69  QRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVRIFNL 128
             +  DVDYLF QV +    V  A NCGNL++GV  FAIERGLV     +T   VRI  L
Sbjct: 74  DPAA-DVDYLFLQVAVDAPDVSDAQNCGNLLAGVGPFAIERGLVAAEEGETP--VRIRML 130

Query: 129 NSRQASELVIPVYNGRVHY-DDIDDMHMQRPSARVGLRFLDTV------GSCTGKLLPTG 181
           N+ Q +   I     RV Y  D     +   +A V L F D+           G LLPTG
Sbjct: 131 NTGQLATARIRTPGRRVRYAGDTTTPGVPGTAAPVVLEFGDSAADSPHSADAGGGLLPTG 190

Query: 182 NASD-WIDGLKVSIIDSAVPVVFIRQHD---VGITGSEAPATLNANTALLDRLERVRLEA 237
           N  D  + G++ +++D+ +PVV +   D    G+ G E P  L A+  L  R+  +R  A
Sbjct: 191 NVVDELLPGVRATLVDAGMPVVLLDVEDFAEFGLRGDETPEQLEADEKLAARIAALRSAA 250

Query: 238 GRRMGLGDVSGSVVPKLSLIG-PGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDG 296
              MGL   + + VPKL+L+  P T   T   R F P   H A  V  A+  A    + G
Sbjct: 251 MPLMGLDPATATTVPKLTLVSPPRTPGGTVATRSFIPVRAHAAIGVVAAVSVASGLLLKG 310

Query: 297 SVVCEILSSRASACSASQRRISIEHPSGVLEVGL 330
           S        R +    S   + +EHP+G L+V +
Sbjct: 311 ST-----GRRHAEFPPSGEPLRLEHPTGHLDVAI 339


Lambda     K      H
   0.318    0.133    0.389 

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: 462
Number of extensions: 20
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: 443
Length of database: 379
Length adjustment: 31
Effective length of query: 412
Effective length of database: 348
Effective search space:   143376
Effective search space used:   143376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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