GapMind for catabolism of small carbon sources

 

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

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-15108
         (486 letters)



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

 Score =  367 bits (941), Expect = e-106
 Identities = 199/481 (41%), Positives = 286/481 (59%), Gaps = 14/481 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI GKFVP ++G+ FDN+ P T E +G +A   AA+++LA+ AA  A +  W K +  E
Sbjct: 21  NFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDA-WGKTSVTE 79

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R  ++ K+ D I E  + ++  E+ D GKP   +   DIP A  +F +F+  +R      
Sbjct: 80  RANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEGSM 139

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
           +++D+  + Y    P+GV+G I PWN  +L+  WKLAPA+AAGN +V+KPAE TP    V
Sbjct: 140 SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMV 199

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           L E+  D  +P GV+N+V+G+G    GAAL     +  I+FTG T TG+ IM +A   L 
Sbjct: 200 LVELISDL-LPAGVLNIVNGYG-GEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLI 257

Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306
            ++ ELGGK+PN+ F       D+ LD+ +E  +  +F NQGEVC C SR  +    YE 
Sbjct: 258 PVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIHEDIYEE 316

Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK---RP 363
           F+ + +A+ K +V GDP   +T VGA  S E  +++  Y ++ VEEG  +LTGGK     
Sbjct: 317 FIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVS 376

Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423
           + L+ G+++EPTI+ G  +  RV +EEIFGPVV+V  F TEEE LE  NDT YGL A VW
Sbjct: 377 DDLKDGFYIEPTILKGHNK-MRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVW 435

Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483
           + D    +R    ++AG VWVN +        FGG KQSGIGRE      + Y +  N+ 
Sbjct: 436 SRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNML 495

Query: 484 I 484
           +
Sbjct: 496 V 496


Lambda     K      H
   0.318    0.136    0.404 

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: 602
Number of extensions: 28
Number of successful extensions: 7
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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