GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Pseudomonas fluorescens GW456-L13

Align aldehyde dehydrogenase-like protein yneI (characterized)
to candidate PfGW456L13_3880 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)

Query= CharProtDB::CH_024181
         (462 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3880
           Succinate-semialdehyde dehydrogenase [NAD] (EC
           1.2.1.24); Succinate-semialdehyde dehydrogenase
           [NAD(P)+] (EC 1.2.1.16)
          Length = 463

 Score =  612 bits (1578), Expect = e-180
 Identities = 305/459 (66%), Positives = 360/459 (78%)

Query: 3   ITPATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGK 62
           ++  THAISINPATGEQ+   P+     ++ AL  AA GFR WR   ++ RA+ L ++G+
Sbjct: 4   VSSLTHAISINPATGEQIGHYPFESDSALQAALTRAATGFRAWRGKPVEQRAQLLINLGQ 63

Query: 63  ALRARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVI 122
           ALR  ++ MA MIT+EMGKPI QAR E+ K A LC WYAEHGPAML  EPTLVE  +A I
Sbjct: 64  ALRNNAQAMANMITQEMGKPIAQARGEIEKCAQLCQWYAEHGPAMLSPEPTLVEGGKARI 123

Query: 123 EYRPLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIP 182
           EYRPLG ILA+MPWNFP+WQV+RGAVP +LAGN Y+LKHAPNVMG   L+ + FK A  P
Sbjct: 124 EYRPLGPILAVMPWNFPIWQVLRGAVPTLLAGNTYVLKHAPNVMGSTYLLLEAFKQADFP 183

Query: 183 QGVYGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFI 242
           +GV+  +N   DGVS+ I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSDPFI
Sbjct: 184 EGVFEVINVTPDGVSKAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSDPFI 243

Query: 243 VLNDADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRD 302
           VL+DADL+ AVKAAV GRYQNTGQVCAAAKR I+E+GIA  FT +FV A   L +GDP  
Sbjct: 244 VLDDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIAREFTRKFVEATQQLVVGDPLA 303

Query: 303 EENALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAF 362
               +GPMARFDLRDEL  QV  TL +GA LL+GG+K  G GNYY PTVL +VT +MT+F
Sbjct: 304 TTTYIGPMARFDLRDELDQQVRDTLKEGATLLMGGKKAEGPGNYYEPTVLGDVTDQMTSF 363

Query: 363 REEMFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGY 422
           ++E+FGPVA+I  A+DA HALELANDSEFGL+AT++T +   A+QMA+ LE GGVFINGY
Sbjct: 364 KQELFGPVASIITARDAAHALELANDSEFGLTATLYTRNVELAQQMASELETGGVFINGY 423

Query: 423 CASDARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461
            ASD RV+FGGVKKSGFGRELSHFG+ EFCN QTVW DR
Sbjct: 424 SASDPRVSFGGVKKSGFGRELSHFGVREFCNAQTVWLDR 462


Lambda     K      H
   0.319    0.134    0.397 

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: 589
Number of extensions: 14
Number of successful extensions: 1
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: 462
Length of database: 463
Length adjustment: 33
Effective length of query: 429
Effective length of database: 430
Effective search space:   184470
Effective search space used:   184470
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 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, 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