GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pseudomonas fluorescens FW300-N2E2

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Pf6N2E2_3131 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3131
          Length = 474

 Score =  321 bits (822), Expect = 4e-92
 Identities = 178/466 (38%), Positives = 269/466 (57%), Gaps = 6/466 (1%)

Query: 15  INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74
           ING  ++ + G    V NP+ G V+  + +   A+   A+ +AD A  AW  +  K+RS 
Sbjct: 7   INGHLVNGE-GPGQAVFNPSLGRVLVEINEASEAQVDAAVRSADAAFEAWSQVPPKDRSL 65

Query: 75  KLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIPG 133
            L +  + +  + ++LA+L +   GKPL+ A   EI   A    +FA  ++ + G     
Sbjct: 66  LLLKLADAIEAHGEELAKLESDNCGKPLSAALNDEIPAIADVFRFFAGASRCMSGSAGGE 125

Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193
           + P    ++ + P+GV A+I PWN+P  M+  K  PALAAG T+VLKP+ QTP +AL L 
Sbjct: 126 YLPGHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSEQTPLTALRLA 185

Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253
           ELA     PAGVL+V+ G    VG  L  +  VR +S TGS   G  ++   +  +K++ 
Sbjct: 186 ELASEI-FPAGVLNVIFGRGQTVGNPLVTHPKVRMVSLTGSIATGSNIISSTSDSVKRMH 244

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313
           +ELGG AP I+FDDAD+D AVEG     + N GQ C  A RIY Q G+Y+ F EKL AAV
Sbjct: 245 MELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQQGIYEQFVEKLGAAV 304

Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSK-GAKVLSGGKLIEGN--FFEPTI 370
             +K G      T  GPLI  +   +V   +E A+++   ++++GGK ++GN  FFEPT+
Sbjct: 305 GSIKYGLQTAPDTEMGPLITAQHRDRVAAFVERAIAQPHIRLITGGKAVDGNGFFFEPTV 364

Query: 371 LVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEA 430
           L D  +   + + E FGP+  +  F DEA+V+A +ND+++GLAS  +  D+ R  R++  
Sbjct: 365 LADAQQDDEIVRREVFGPVVSVTSFLDEAQVLAWANDSDYGLASSVWTADIGRAHRLSAR 424

Query: 431 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476
           L+YG   +NT  +     P GG K SG G++ S YG+EDY  ++++
Sbjct: 425 LQYGCTWVNTHFMLVSEMPHGGQKRSGYGKDMSMYGLEDYTVVRHV 470


Lambda     K      H
   0.317    0.134    0.384 

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: 553
Number of extensions: 18
Number of successful extensions: 5
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: 480
Length of database: 474
Length adjustment: 33
Effective length of query: 447
Effective length of database: 441
Effective search space:   197127
Effective search space used:   197127
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 (21.6 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:

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