GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Pf6N2E2_1764 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1764
          Length = 502

 Score =  248 bits (632), Expect = 5e-70
 Identities = 153/466 (32%), Positives = 234/466 (50%), Gaps = 19/466 (4%)

Query: 41  INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQ---TWRNVNPEER 97
           ING  +      +  +PA +  L G + +A+ D+   A+ +A  AF+    WR + P ER
Sbjct: 29  INGHWLRAGATFEIIDPATELPL-GELDEADADIVGLAVDAARSAFEDRSAWRTMGPSER 87

Query: 98  ANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADA-DTAEAIDFLEYYARQMIELNRGKE 156
             IL K A  +       +  +  E G P   A A + A+ ID   YYA    +L  G  
Sbjct: 88  ERILHKLADELEADSDVLADLIAAELGLPRGAALAFEVAKVIDVFRYYAGFPSKLT-GDT 146

Query: 157 ILSRPGEQNRYFYT-----PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTP 211
           I   P   +  F+      P+GV   I PWN  L +        +  G T+V+KPA    
Sbjct: 147 IEIDPAMDDAEFFAYTTHEPVGVVGAILPWNAPLLVGSWKIAPALAAGCTLVVKPAEDVS 206

Query: 212 VVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAA 271
           +V  +  E+   AGLP GV+N V G GA  G  L++H       FTGS D+G R+Y+ AA
Sbjct: 207 LVILRLAELASKAGLPDGVLNVVTGRGAVTGQALIEHTGIDKFAFTGSTDIGKRIYKAAA 266

Query: 272 VVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKD 331
                 + L RV +E+GGK+ V+V  DAD+   A ++ ++AF  SGQ C +GS+ + H  
Sbjct: 267 ------DRLVRVSLELGGKNPVIVLADADVKAIAPALCMAAFANSGQICVSGSKVMAHAS 320

Query: 332 VYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEGRLMTGGEGD 391
           + +E+L    + AK L  G P + +  +GPV  +K F+++M+YI  G+ EG ++ G    
Sbjct: 321 IANELLGAMASFAKTLVPGSPFDPETVIGPVCSKKQFDRVMAYIRQGETEGNVIIGQRQS 380

Query: 392 SSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITR 451
           +S GF+I PTII DL  ++ ++ EEIFGPV+      D  + +++ N + YGL   +   
Sbjct: 381 TSPGFYINPTIITDLPAQSKLLSEEIFGPVITVETWTDEQNVIDLTNRSAYGLCATIWGS 440

Query: 452 NRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497
           N  HI++  +    G ++ N           P GGF+ SG     G
Sbjct: 441 NHGHIQRLAKRLRTGTVFINSPAFPP--ANIPTGGFRQSGVGRDLG 484


Lambda     K      H
   0.316    0.134    0.388 

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: 612
Number of extensions: 33
Number of successful extensions: 3
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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: 52 (24.6 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