GapMind for catabolism of small carbon sources

 

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

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= SwissProt::P42236
         (488 letters)



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

 Score =  276 bits (705), Expect = 2e-78
 Identities = 175/488 (35%), Positives = 256/488 (52%), Gaps = 15/488 (3%)

Query: 7   QNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRK 66
           ++ Y NFI G++V    G       P    ++VG +  S+A DVE A+ AA+ AK AW K
Sbjct: 16  KDRYDNFIGGKFVPPVEGRYFDNVTPI-TGEVVGQIARSSAADVELALDAAHAAKDAWGK 74

Query: 67  LTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAK-GETARGIAILRYYAGEGMR 125
            +  ER   + K AD +E+ L+ IA   T + GK + E    +    +   RY+AG    
Sbjct: 75  TSVTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRG 134

Query: 126 KTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185
           + G +    D D + +    PLGVVG I PWNF + +  WK+APA+  GN +V+KPA +T
Sbjct: 135 QEGSM-SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQT 193

Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245
                 ++    +  LPAGV+N+V G G  VG  LA  D +  + FTGS   G+ I +AA
Sbjct: 194 PAAIMVLVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAA 252

Query: 246 LARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299
                   LE+GGK+P      V+  DDA L+ A E  +  AF   G+ CT  SR ++  
Sbjct: 253 TVNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAFNQ-GEVCTCPSRALIHE 311

Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGE 359
            IYE F  + + R K I  GD  K +  +G  ASK Q D  LSY + G +EGA +L GG+
Sbjct: 312 DIYEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGK 371

Query: 360 KLE-NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418
             + +   ++G+Y++P I     ++M + QEEIFGPV+++    + EEAL +AND  +GL
Sbjct: 372 VADVSDDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGL 430

Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478
            A +++ +      F   + AG V +N   A     A FGG KQS    RE  +   D +
Sbjct: 431 GAGVWSRDQNTCYRFGRGVQAGRVWVNNYHA-YPAHAAFGGYKQSGI-GRENHKMMLDHY 488

Query: 479 TAIKTVFV 486
              K + V
Sbjct: 489 QQTKNMLV 496


Lambda     K      H
   0.315    0.132    0.374 

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: 582
Number of extensions: 32
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: 488
Length of database: 506
Length adjustment: 34
Effective length of query: 454
Effective length of database: 472
Effective search space:   214288
Effective search space used:   214288
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 (21.5 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