GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Pseudomonas fluorescens FW300-N1B4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_5616 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)

Query= BRENDA::A6T8Z5
         (462 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5616
           Succinate-semialdehyde dehydrogenase [NAD] (EC
           1.2.1.24); Succinate-semialdehyde dehydrogenase
           [NAD(P)+] (EC 1.2.1.16)
          Length = 463

 Score =  628 bits (1619), Expect = 0.0
 Identities = 312/463 (67%), Positives = 363/463 (78%), Gaps = 1/463 (0%)

Query: 1   MMNLSA-THAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRR 59
           M N+S+ THA+S+NP  GE +   P+ SE  ++AA++ A AG+  WR  P  +R+ +L  
Sbjct: 1   MTNVSSLTHAISINPANGEQIGYYPFESESALEAALSRAVAGFSLWRSKPAEERSQSLIT 60

Query: 60  IGAALRARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQ 119
           +   LR   E +A MITLEMGKP  QARGE+ K A LC+WYAEHGPAML  E T VE  +
Sbjct: 61  LAKVLRGNAETMANMITLEMGKPTTQARGEIEKCAQLCEWYAEHGPAMLTAEPTQVEGGK 120

Query: 120 AVIEYRPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAA 179
           A IEYRPLG ILAVMPWNFP+WQV+RGAVP L+AGN+Y+LKHAPNVMG A LL E F  A
Sbjct: 121 ARIEYRPLGPILAVMPWNFPIWQVLRGAVPALIAGNTYVLKHAPNVMGCAYLLREAFKQA 180

Query: 180 GLPDGVFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSD 239
             P+GVF  +N T DGVS  I D RIAAVT+TGSVRAG AIGAQAGAALKKCVLELGGSD
Sbjct: 181 DFPEGVFEVINVTPDGVSTAIADPRIAAVTLTGSVRAGMAIGAQAGAALKKCVLELGGSD 240

Query: 240 PFIVLNDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGD 299
           PFIVLNDADLDEAVKAAV GRYQN+GQVCAA+KR I+E GI EAFTRKFV+A   L +GD
Sbjct: 241 PFIVLNDADLDEAVKAAVIGRYQNTGQVCAAAKRLIVEQGIVEAFTRKFVEATRELVVGD 300

Query: 300 PRDEQNYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGM 359
           P     Y+GPMARFDLRDEL +QV  TL+EGATLL+G +K EG+GN++ PTV  +VT  M
Sbjct: 301 PLATDTYIGPMARFDLRDELDRQVQQTLEEGATLLMGGKKAEGSGNFFEPTVFADVTDRM 360

Query: 360 TGFRQELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFL 419
           T F+QELFGPVA++ TARDA HAL LANDSEFGL++T+YT D   A + A ELE GGVF+
Sbjct: 361 TSFKQELFGPVASIITARDAAHALELANDSEFGLASTIYTRDVELAHKLAGELETGGVFI 420

Query: 420 NGYCASDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDRR 462
           NGYCA+D RV FGGVKKSGFGRELSHFG+ EFCNAQTVW DRR
Sbjct: 421 NGYCATDPRVTFGGVKKSGFGRELSHFGVREFCNAQTVWLDRR 463


Lambda     K      H
   0.319    0.133    0.392 

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: 607
Number of extensions: 13
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