GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5616
          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 (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