GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Dyella japonica UNC79MFTsu3.2

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase

Query= BRENDA::B6ECN9
         (505 letters)



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

 Score =  226 bits (577), Expect = 1e-63
 Identities = 153/446 (34%), Positives = 236/446 (52%), Gaps = 24/446 (5%)

Query: 45  ATEEDVDMAVKAARSALRRDDWGSTTGAQRAKYLRAIAAKVLEKKPELATLETIDNGKPW 104
           ATE+ +  AVKAA    +   W      +R   L+    +  E++ ELA    ++ GKP 
Sbjct: 42  ATEQAIAAAVKAAEPMRQFKPW------ERQAVLQHCVQRFTERRDELAYALCVEAGKPI 95

Query: 105 FEAASDIDDVVACFEYYADLAEALDSKKQT---EVKLHLDSFKTHVLREPLGVVGLITPW 161
            ++A ++  ++  F   A+  EA+ +  +T   E+   L+ +  +  R PLG V  ITP+
Sbjct: 96  KDSAGEVTRLIETFGIAAE--EAVRTNGETINLEIAKRLNGYHGYTRRVPLGPVSFITPF 153

Query: 162 NYPLLMTTWKVAPALAAGCAAILKPSELASITSLELGEICREVGLPPGALSILTGLGHEA 221
           N+PL +   KVAPA+AAGC  +LKP+E   I +L +GE+  E  LP GA SIL   G  A
Sbjct: 154 NFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAFSILNLDGKHA 213

Query: 222 GSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQLVKPVTLELGGKSPIVV-FDDIHNLDTAV 280
            SPLV  P    ++FTGS   G  + T A    K VTLELGG +  +V  D +  LD  +
Sbjct: 214 -SPLVEDPRFKLLSFTGS-QIGWDLKTRAGH--KKVTLELGGNAACIVDADQLPRLDHVI 269

Query: 281 EWTLFGCFWTNGQICSATSRLIIQETIAPQFLARLLEWTKNIKISDPLEEDCKLGPVISR 340
           E  +FG F+ +GQ C +  R+   E++  +   RL+   K +K  DP +++  LGP+I  
Sbjct: 270 ERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKKETFLGPMIDE 329

Query: 341 GQYEKILKFISTAKDEGATILYGGDRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVL 400
              E++  +I  A+  G  +L GG R     KG  ++ T++ +V    ++ ++EVFGP  
Sbjct: 330 AAAERLHGWIEEARKGGGKVLCGGKR-----KGPMLEATLMENVRGDAKVNRQEVFGPFA 384

Query: 401 CVKTFKTEEEAIELANDTKFGLGAAILSKDLERCERFTKAFQSGIVWINCSQPCFW--QP 458
            +  FK+ +EAI + ND+ +GL A I +  L    R     + G V +N   P F     
Sbjct: 385 LLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVN-DVPSFRVDNM 443

Query: 459 PWGGKKRSGFGRELGEWSLENYLNIK 484
           P+GG K SG GRE   +++E+   I+
Sbjct: 444 PYGGVKLSGAGREGVRYAIEDMTEIR 469


Lambda     K      H
   0.318    0.136    0.421 

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: 538
Number of extensions: 37
Number of successful extensions: 7
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: 505
Length of database: 476
Length adjustment: 34
Effective length of query: 471
Effective length of database: 442
Effective search space:   208182
Effective search space used:   208182
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: 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