GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Desulfovibrio vulgaris Hildenborough

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= metacyc::MONOMER-12387
         (496 letters)



>MicrobesOnline__882:208821
          Length = 464

 Score =  163 bits (412), Expect = 1e-44
 Identities = 126/356 (35%), Positives = 175/356 (49%), Gaps = 18/356 (5%)

Query: 74  PAPVRGALVKRFGELLTEHKQDLADLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLY 133
           PA  R A+++R   L+  H + L      E GK  ++++ EV+  ID   +A     QL 
Sbjct: 45  PAHERLAILERLATLMRTHAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLG 104

Query: 134 GRTMPS----ERPGHRLMETWHPLGVVGVISAFNFPVAVWAWNAAVALVCGDTVVWKPSE 189
           GR +P        G        P GVV  ISAFN PV +    A  A   G  V+ KP+ 
Sbjct: 105 GREVPMGLTPASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPAS 164

Query: 190 LTPLNRAACAALLDLAIADAGAPKGLNQVVVGAADVGERLVDSPRVPLVSATGSTRMGRA 249
            TPL+   C  +L L + +AG P+    ++  AA   E+LV  PRV  +S  GS+R+G  
Sbjct: 165 ATPLS---CRNVLRL-MHEAGVPEAWATMLPCAAATAEKLVADPRVAFLSFIGSSRVGWH 220

Query: 250 VGPRVAARFGRTI-LELGGNNAAVVTPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHE 308
           +  ++A   G T  LE GG    V+  SADLD  +   +      AGQ C +++R+    
Sbjct: 221 LRSKLAP--GATCALEHGGAAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPH 278

Query: 309 DIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGE 368
           + A T  ERL AA  +LP GDP +  T VGPL++     R+ E VE A A GGT+  GG 
Sbjct: 279 ETARTFAERLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGG- 337

Query: 369 RQFPDAAPGAYYVRPALVRMPAQ-TAVVREETFAPILYVLTYRDLDEAIRLNNEVP 423
                A        P +V  P Q   + R E F P++ V + RD DEAI   N+VP
Sbjct: 338 -----APLSETLYSPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVP 388


Lambda     K      H
   0.320    0.135    0.406 

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: 519
Number of extensions: 38
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: 496
Length of database: 464
Length adjustment: 34
Effective length of query: 462
Effective length of database: 430
Effective search space:   198660
Effective search space used:   198660
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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