GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Pseudomonas fluorescens GW456-L13

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737
          Length = 496

 Score =  323 bits (827), Expect = 1e-92
 Identities = 186/464 (40%), Positives = 255/464 (54%), Gaps = 11/464 (2%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALK-GAWGRMSLAQRVEVLYAVADGINRRFDD 82
           +P     + +  +A    V+ AV ++  A K G W  +  A R  +L      +    ++
Sbjct: 38  NPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSLRPADRERILLNFTRLVEEHAEE 97

Query: 83  FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEM--PTPDGVGAINYAV 140
               E    GK +++AR +D+       +  +     +  + F++  P P G     +  
Sbjct: 98  LAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKIEGQTFDVSIPLPPGAKFTAFTK 157

Query: 141 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPP 200
           R PVGVV  I PWN PLL+  WK+ PALA G TV++KP+ ETP TA  L E+   AG+P 
Sbjct: 158 REPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKPAMETPLTAMRLAELALEAGIPA 217

Query: 201 GVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAA 260
           GV+NVV G G  S G  LT HP V+ ++FTG T  G+++  A  +     SLELGGKN  
Sbjct: 218 GVFNVVTGGGA-SVGGVLTQHPLVSKVSFTGSTAVGKSVGVACMENMTRFSLELGGKNPM 276

Query: 261 IVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320
           IV AD D++KA++G +     N GQVC    R YV R I D+FV  L      M +G   
Sbjct: 277 IVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSIHDQFVEALAAAVSSMPIGAGM 336

Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKG-GAWVQPTIWTGL 379
           +    + PL+S++ ++ VL + + A + GA VVTGG      E L+G G +VQPTI   +
Sbjct: 337 NCDAAINPLVSRKQQQSVLKHIELARQQGARVVTGG------ELLEGDGFFVQPTILADI 390

Query: 380 GDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVG 439
                VAREE+FGP   VMPFD E+ VI  ANDN YGLA  +WT +L +A  +   IE G
Sbjct: 391 DHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLWTNDLGKAMNLVPRIEAG 450

Query: 440 IAWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483
             WVN+  L D    FGG KQSG+GRE G   +E YTELK+VCI
Sbjct: 451 TVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVCI 494


Lambda     K      H
   0.318    0.135    0.406 

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: 569
Number of extensions: 24
Number of successful extensions: 3
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: 485
Length of database: 496
Length adjustment: 34
Effective length of query: 451
Effective length of database: 462
Effective search space:   208362
Effective search space used:   208362
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