GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Shewanella sp. ANA-3

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::Q9S795
         (501 letters)



>lcl|FitnessBrowser__ANA3:7025944 Shewana3_3092 succinate
           semialdehyde dehydrogenase (RefSeq)
          Length = 482

 Score =  301 bits (770), Expect = 4e-86
 Identities = 172/482 (35%), Positives = 260/482 (53%), Gaps = 14/482 (2%)

Query: 8   RQLFIDGEWREPILKKRIPIVNPATEEVIGDIPAATTEDVDVAVNAARRALSRNKGKDWA 67
           +Q +I+G+W +   K+ + I NPAT  VI  +P     +   A+ AA  AL       W 
Sbjct: 11  QQCYINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPA-----WR 65

Query: 68  KAPGAVRAKYLRAIAAKVNERKTDLAKLEALDCGKPLDEAVWDMDDVAGCFEFYADLAEG 127
                 R   LR     +NE   DLA +   + GKPL EA  ++   A   E++A+    
Sbjct: 66  ALTAKERGVKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAE---- 121

Query: 128 LDAKQKAPVSLP--MESFKSYVLKQPLGVVGLITPWNYPLLMAVWKVAPSLAAGCTAILK 185
            +AK+    ++P      +  V+KQP+GV   ITPWN+P  M   K AP+LAAGCT ++K
Sbjct: 122 -EAKRVYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK 180

Query: 186 PSELASVTCLELADICREVGLPPGVLNVLTGFGSEAGAPLASHPGVDKIAFTGSFATGSK 245
           P+     T L LA +    G+P GV +V+TG     G  + S+P V K++FTGS   G K
Sbjct: 181 PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIK 240

Query: 246 VMTAAAQLVKPVSMELGGKSPLIVFDDVDLDKAAEWALFGCFWTNGQICSATSRLLVHES 305
           +M   A  +K +S+ELGG +P IVFDD ++D A E A+   +   GQ C   +R+ V   
Sbjct: 241 LMEQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG 300

Query: 306 IASEFIEKLVKWSKNIKISDPMEEGCRLGPVVSKGQYEKILKFISTAKSEGATILHGGSR 365
           +  EF  KL      +K+ + + EG   GP+++    EK+   +  A S+GAT++ GG  
Sbjct: 301 VYDEFARKLSIAVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGK- 359

Query: 366 PEHLEKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFASEDEAIELANDSHYGLGAAV 425
             H   G F EPT++T+V +SM++ REE FGP+  +  F   D+ I+ AND+ +GL A  
Sbjct: 360 -PHSLGGNFFEPTVLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYF 418

Query: 426 ISNDTERCDRISEAFEAGIVWINCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQV 485
              D     +++EA E G+V +N        AP+GG+K SG GRE  ++G++ YL +K +
Sbjct: 419 YGRDISLVWKVTEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEYLEIKYI 478

Query: 486 TL 487
            +
Sbjct: 479 CM 480


Lambda     K      H
   0.318    0.135    0.416 

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: 614
Number of extensions: 22
Number of successful extensions: 4
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: 501
Length of database: 482
Length adjustment: 34
Effective length of query: 467
Effective length of database: 448
Effective search space:   209216
Effective search space used:   209216
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