GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Pseudomonas fluorescens FW300-N2E2

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate Pf6N2E2_3131 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= SwissProt::Q9H2A2
         (487 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3131 4-aminobutyraldehyde
           dehydrogenase (EC 1.2.1.19)
          Length = 474

 Score =  315 bits (806), Expect = 3e-90
 Identities = 171/462 (37%), Positives = 265/462 (57%), Gaps = 11/462 (2%)

Query: 28  YDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSRVLNQVADLLEQSLEEF 87
           ++PS G V   +  + + +++AAV++A  AF +WS   P++RS +L ++AD +E   EE 
Sbjct: 22  FNPSLGRVLVEINEASEAQVDAAVRSADAAFEAWSQVPPKDRSLLLLKLADAIEAHGEEL 81

Query: 88  AQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQMDHLGCMHYTVRAPVGV 147
           A+ ES + GK L+ A   +IP     FRFFA +S   +         G      R PVGV
Sbjct: 82  AKLESDNCGKPLSAALNDEIPAIADVFRFFAGASRCMSGSAGGEYLPGHTSMIRRDPVGV 141

Query: 148 AGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLCKLLDKAGVPPGVVNIV 207
              I+PWN PL ++ WKIAPA+AAGNTV+ KPSE T +TA  L +L  +   P GV+N++
Sbjct: 142 IASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRLAELASEI-FPAGVLNVI 200

Query: 208 FGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFEDAN 267
           FG G  VG  LV+HP+V ++S TGS  T   I   ++   K++ +ELGGK P IIF+DA+
Sbjct: 201 FGRGQTVGNPLVTHPKVRMVSLTGSIATGSNIISSTSDSVKRMHMELGGKAPVIIFDDAD 260

Query: 268 LDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEATRKWKVGIPSDPLVSIG 327
           +D  +       F N G+ C    RI+ Q+ IY +F+++   A    K G+ + P   +G
Sbjct: 261 IDAAVEGIRTFGFYNAGQDCTAACRIYAQQGIYEQFVEKLGAAVGSIKYGLQTAPDTEMG 320

Query: 328 ALISKAHLEKVRSYVKRALAEG--AQIWCGEGVDKLSLPARNQAGYFMLPTVITDIKDES 385
            LI+  H ++V ++V+RA+A+     I  G+ VD          G+F  PTV+ D + + 
Sbjct: 321 PLITAQHRDRVAAFVERAIAQPHIRLITGGKAVD--------GNGFFFEPTVLADAQQDD 372

Query: 386 CCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRVHRVAKKLQSGLVWT 445
             +  E+FGPV  V  F  E +V+  AN+  YGLA++VW++++GR HR++ +LQ G  W 
Sbjct: 373 EIVRREVFGPVVSVTSFLDEAQVLAWANDSDYGLASSVWTADIGRAHRLSARLQYGCTWV 432

Query: 446 NCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITVKH 487
           N   +    +P GG K SG G++ +    + +T ++ +  KH
Sbjct: 433 NTHFMLVSEMPHGGQKRSGYGKDMSMYGLEDYTVVRHVMFKH 474


Lambda     K      H
   0.319    0.133    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: 525
Number of extensions: 21
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: 487
Length of database: 474
Length adjustment: 34
Effective length of query: 453
Effective length of database: 440
Effective search space:   199320
Effective search space used:   199320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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