GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0379
          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 (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