GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Dinoroseobacter shibae DFL-12

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__Dino:3607686
          Length = 506

 Score =  334 bits (856), Expect = 5e-96
 Identities = 190/477 (39%), Positives = 278/477 (58%), Gaps = 14/477 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI G++   V G  F+ ++P+ G  + ++A    AD   A++ A A  ++  W + +  +
Sbjct: 22  FIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDA--WGKTSVTE 79

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   +++ AD + +N++ +A  ET D GKPI +++  DIP A     + A  +      +
Sbjct: 80  RANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEGSM 139

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           +   +D +     EP+GVVG I+PWNF +LMA WKL PA+A GN +VLKP+E++P   + 
Sbjct: 140 SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMV 199

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L  +  +PAGVLN++ GYG  VG ALA    +  + FTGST   +++M  A   N+ 
Sbjct: 200 LVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIME-AATVNLI 257

Query: 263 RIWLEAGGKSPNIVFAD--APD---LQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317
            + LE GGKSPNI F D  A D   L  A E      AFNQGEVCT  SR L+   I ++
Sbjct: 258 PVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFV-LFAFNQGEVCTCPSRALIHEDIYEE 316

Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKR---T 374
           F+   +  +K    G+P   +T VGA    +Q + +LSY + G ++GA++L GGK    +
Sbjct: 317 FIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVS 376

Query: 375 LEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434
            +   G Y+EPTI  G  N MR+ QEEIFGPV+SV  F T EEA+ +ANDT YGL AG+W
Sbjct: 377 DDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVW 435

Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
           + D +  ++  R V+AG VWVN Y      A FGG+KQSG GR+     L+ Y + K
Sbjct: 436 SRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 492


Lambda     K      H
   0.316    0.132    0.390 

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: 593
Number of extensions: 36
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: 497
Length of database: 506
Length adjustment: 34
Effective length of query: 463
Effective length of database: 472
Effective search space:   218536
Effective search space used:   218536
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 (21.6 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