GapMind for catabolism of small carbon sources

 

Aligments 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 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