GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7025944
          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 (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