GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Dinoroseobacter shibae DFL-12

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__Dino:3607686 Dshi_1095 aldehyde dehydrogenase
           (RefSeq)
          Length = 506

 Score =  294 bits (753), Expect = 4e-84
 Identities = 175/471 (37%), Positives = 256/471 (54%), Gaps = 15/471 (3%)

Query: 15  EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74
           EG       P TG+V+ +IA +SA  V+ A+ AA AA   WG+T+   RA  +LK+AD I
Sbjct: 32  EGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDAWGKTSVTERANIVLKIADRI 91

Query: 75  EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134
           EEN  + A+ E+ + GKP+      +IP  VD FR+FAG  R   G +  E      +  
Sbjct: 92  EENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEG-SMSEIDNDTVAYH 150

Query: 135 RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPA 194
             +PLGVV  I PWN+ ++MAAWKLAPA+AAGNC+VLKP+E TP   + L EL  D+ PA
Sbjct: 151 FHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMVLVELISDLLPA 210

Query: 195 GVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVI 254
           GV+NI+ G G  VG  L    ++  ++ TGS ATG  I+     ++    +ELGGK+P I
Sbjct: 211 GVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLIPVTLELGGKSPNI 270

Query: 255 VF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLK 308
            F      DDA ++  VEG   F  +N G+ CT   R    + IY+  + +  A V  + 
Sbjct: 271 FFKDVMAEDDAFLDKAVEGFVLFA-FNQGEVCTCPSRALIHEDIYEEFIARAIARVKAIV 329

Query: 309 SGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYYAPT 363
            G P    T +G  +S    +++    +     G  +V+TGG+         +G+Y  PT
Sbjct: 330 QGDPRKMETMVGAQASKEQKDKILSYFQIGVEEG-AEVLTGGKVADVSDDLKDGFYIEPT 388

Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423
           +L G      + Q+E+FGPVVSVT F  EE+ +  AND+ YGL + VW++D    +R   
Sbjct: 389 ILKGH-NKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVWSRDQNTCYRFGR 447

Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
            +Q G  WVN +    +    GG K SG G++     L+ Y   ++++V +
Sbjct: 448 GVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNMLVSY 498


Lambda     K      H
   0.317    0.134    0.397 

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: 568
Number of extensions: 32
Number of successful extensions: 4
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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