GapMind for catabolism of small carbon sources

 

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

Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate N515DRAFT_4224 N515DRAFT_4224 coniferyl-aldehyde dehydrogenase

Query= BRENDA::P51648
         (485 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4224 N515DRAFT_4224
           coniferyl-aldehyde dehydrogenase
          Length = 456

 Score =  270 bits (690), Expect = 8e-77
 Identities = 161/431 (37%), Positives = 234/431 (54%), Gaps = 11/431 (2%)

Query: 23  RLQQLEALRRMVQEREKDILTAIAADLC-KSEFNVYSQEVITVLGEIDFMLENLPEWVTA 81
           R ++L AL  ++ E   +I  AI  D   +        EV   L  I   L +   W+  
Sbjct: 16  RARRLRALNDLIGEHRGEIADAIHQDFGGRPAQETDLLEVFPSLSAIRHALAHGRRWMKP 75

Query: 82  KPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIAAGNAVIIKPSELSE 141
           +     +L M     I+PQPLGVV II  WNYP  L   P++ A+AAGN V++K SE + 
Sbjct: 76  RRSWPGLLFMPARNEIRPQPLGVVGIIVPWNYPLFLAAGPMVDALAAGNRVMVKMSEYTP 135

Query: 142 NTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNTAVGKIVMEAAAKHL 201
             + + A+L  +Y   +   V+ G  +         FDH+ +TG+TAVG+ VM AA+ +L
Sbjct: 136 QFSALFAQLAARYFKPEEVCVVTGDADVAQAFSALPFDHLLFTGSTAVGRHVMRAASANL 195

Query: 202 TPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYILCEASLQNQIVWKI 261
           TPVTLELGGKSP  +           RI  GK  N GQTCIAPDY+L   +  ++ V   
Sbjct: 196 TPVTLELGGKSPAIVGPGARFANAVERILVGKLFNAGQTCIAPDYVLLPRAQVDEFVAAA 255

Query: 262 KETVKEFYGENIKESPDYERIINLRHFKRILSL-----LEGQKIA-FGGETDE-ATRYIA 314
           ++     Y + ++ +  Y  II+ R ++R+ +L      +G K+   G ETD+   R + 
Sbjct: 256 RDVAARLYPQPVR-NEQYASIISERQYQRLAALRDDAARDGAKLTLLGDETDDIQRRRMT 314

Query: 315 PTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLALYVFSHNHKLIKRM 374
           P +LT V     VMQEEIFGP+LP+VP  ++++AI ++     PLALY+F  +  L+ R+
Sbjct: 315 PALLTGVSESMAVMQEEIFGPLLPLVPYDDIEQAIAYVAAHPHPLALYLFEEDGALVDRV 374

Query: 375 IDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSHQRPCLLKSLKREG 434
           +  T++GGVT ND + H   +  PFGGVG SG G YHG+  F TFSH +  + +  +  G
Sbjct: 375 LARTTAGGVTINDTLYHIAQHDLPFGGVGPSGSGGYHGEAGFRTFSHLK-SVFRQARVNG 433

Query: 435 ANKLRYPPNSQ 445
           A  L  PP  Q
Sbjct: 434 AGLLN-PPYGQ 443


Lambda     K      H
   0.321    0.139    0.411 

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: 460
Number of extensions: 13
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: 485
Length of database: 456
Length adjustment: 33
Effective length of query: 452
Effective length of database: 423
Effective search space:   191196
Effective search space used:   191196
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 (21.9 bits)
S2: 51 (24.3 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