GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Dyella japonica UNC79MFTsu3.2

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase

Query= metacyc::MONOMER-15732
         (497 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA
           reductase
          Length = 476

 Score =  218 bits (554), Expect = 5e-61
 Identities = 148/457 (32%), Positives = 228/457 (49%), Gaps = 13/457 (2%)

Query: 43  TGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSRLRPRERQNLLWRLADLMERDARQLAE 102
           +G+V   V   DA+  ++A+ AA +A +  P  + +P ERQ +L            +LA 
Sbjct: 28  SGKVATRVAVPDAKATEQAIAAAVKAAE--PMRQFKPWERQAVLQHCVQRFTERRDELAY 85

Query: 103 LECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREA 162
             C+  GK    +   +V   I+     A  A +  G T+   +    N  +HG+ RR  
Sbjct: 86  ALCVEAGKPIKDS-AGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNG-YHGYTRRVP 143

Query: 163 IGVVGAIVAWNFPLLLACWKLGPALATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVF 222
           +G V  I  +NFPL L   K+ PA+A GC  VLKPA+ TP+  L + E++ E   P G F
Sbjct: 144 LGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAF 203

Query: 223 NVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMP 282
           +++   G +A + L   P    L+FTGS     L  +A      +VTLELGG +  IV  
Sbjct: 204 SILNLDGKHA-SPLVEDPRFKLLSFTGSQIGWDLKTRA---GHKKVTLELGGNAACIVDA 259

Query: 283 D--ANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRKHFDNVVADIAGIANGMKLGNGLDP 340
           D    L           F+  GQ C +  R+Y H   +D +   +     G+K G+    
Sbjct: 260 DQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKK 319

Query: 341 AVQMGPLISAKQQDRVTGYIELGRELGATVACGGEGFGPGYFVKPTVIVDVDQRHRLVQE 400
              +GP+I     +R+ G+IE  R+ G  V CGG+  GP   ++ T++ +V    ++ ++
Sbjct: 320 ETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKRKGP--MLEATLMENVRGDAKVNRQ 377

Query: 401 EIFGPVLVAMPFDDLDEVIGMANDNPYGLGASIWSNDLAAVHRMIPRIKSGSVWVN-CHS 459
           E+FGP  +  PF  LDE I M ND+ YGL A I+++ LA   R    ++ G V VN   S
Sbjct: 378 EVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVNDVPS 437

Query: 460 ALDPALPFGGYKMSGVGREVGAAAIEHYTELKSVLIK 496
                +P+GG K+SG GRE    AIE  TE++ ++++
Sbjct: 438 FRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMVMR 474


Lambda     K      H
   0.320    0.137    0.413 

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: 496
Number of extensions: 26
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: 497
Length of database: 476
Length adjustment: 34
Effective length of query: 463
Effective length of database: 442
Effective search space:   204646
Effective search space used:   204646
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: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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