GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3607686
          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:

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