GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Acidovorax sp. GW101-3H11

Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Ac3H11_2991 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)

Query= metacyc::MONOMER-17424
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2991
          Length = 396

 Score =  251 bits (641), Expect = 2e-71
 Identities = 132/378 (34%), Positives = 223/378 (58%), Gaps = 5/378 (1%)

Query: 3   VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62
           + ++   + DAVR FAQ  + P A   DK  +FP +   +M +LG+ G+ VPEQ+GG+  
Sbjct: 14  LGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAM 73

Query: 63  GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122
           GY+A+ +A+EEI+    +       H+++    I R GNE QK ++L+ L +G  +GA A
Sbjct: 74  GYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALA 133

Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182
           ++EP AGSD  S+K +A  +G +Y+LNGSK +IT+G +A  ++V+A T+PE G RG++AF
Sbjct: 134 MSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAF 193

Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242
           ++     G+ +A+  DKLG   S T ++VF +V+VP  N LG   +G K+ ++ L+  R 
Sbjct: 194 LIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERA 253

Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302
            +    +G+ ++  +    Y ++R+ FG+ + E Q +  ++ADM T +   R      A 
Sbjct: 254 VLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAK 313

Query: 303 L-----RDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVC 357
                  D  R    + +   L+ +E A  +  + +Q  GG GY++++PL R++RD ++ 
Sbjct: 314 NLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLY 373

Query: 358 QIYEGTSDIQRMVIARNL 375
           +I  GTS+I+RM+I R L
Sbjct: 374 EIGAGTSEIRRMLIGREL 391


Lambda     K      H
   0.319    0.134    0.382 

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: 337
Number of extensions: 11
Number of successful extensions: 2
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: 375
Length of database: 396
Length adjustment: 30
Effective length of query: 345
Effective length of database: 366
Effective search space:   126270
Effective search space used:   126270
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.

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