GapMind for catabolism of small carbon sources

 

Aligments 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_225 Putative benzaldehyde dehydrogenase oxidoreductase protein (EC 1.2.1.28)

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_225 Putative benzaldehyde
           dehydrogenase oxidoreductase protein (EC 1.2.1.28)
          Length = 492

 Score =  244 bits (623), Expect = 5e-69
 Identities = 150/465 (32%), Positives = 245/465 (52%), Gaps = 21/465 (4%)

Query: 38  PLIINGERVT--------TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTW 89
           P  ING++          +  ++   NP   +QL+     +  DL + A Q+A +A   W
Sbjct: 8   PYAINGDQYINGTWRAGRSARRLDDRNPFNGEQLLEMPLASIADL-DDAYQAAQKAQAAW 66

Query: 90  RNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMI 149
             ++P +R   L K A +I+ R+ E   WL+HE+G    +A  +    ++ +       +
Sbjct: 67  AQLHPTQRGAQLEKLAQVIQNRREEIIDWLIHESGSTRIKASMEWQFTLNLVRECTTMPM 126

Query: 150 ELNRGKEILS-RPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPAS 208
           ++  G+ + S +PGEQ+  F  P+GV   ISPWNF L + + + V  +  GNT+VLKPAS
Sbjct: 127 QVE-GRILTSYKPGEQSFVFREPLGVVGVISPWNFPLYLSMRSVVPALALGNTIVLKPAS 185

Query: 209 TTPVVAAKFV-EVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLY 267
            T V     +  + E+AG P+G +N V G+G+E+GD  V+HP  SLI+FTGS DVG    
Sbjct: 186 DTAVTGGLLIAHLFEEAGFPEGSLNVVVGAGSEIGDAFVEHPVPSLISFTGSTDVG---- 241

Query: 268 ERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAV 327
                +  G  H+KRV +E+GG   +VV  DAD+D+AA + +V  F   GQ C + +R +
Sbjct: 242 RNVGRIATGGKHIKRVALELGGNAPLVVLDDADIDVAAHAAVVGRFLHQGQICMSVNRVI 301

Query: 328 IHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMT 386
           + + +Y +         +NL  GDPT  D  +GPV+++   + ++  ++  +  G + + 
Sbjct: 302 VDRSLYADFASLVAERVRNLKTGDPTKADTVIGPVVNQSQLDGLLRKLDGARSAGLKQLC 361

Query: 387 GGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTG 446
           GG    ++G  +   +  ++  +  + ++E FGP++    A +  HAL +AN +EYGL+ 
Sbjct: 362 GG---PASGLVLPAHVFGEVGADQELARDETFGPLLPLLVAENETHALALANASEYGLSS 418

Query: 447 AVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491
           AV TR+ A      R    G  + N + T       PFGG K SG
Sbjct: 419 AVFTRDMARGLNFARGIVAGMTHIN-DITVDDQPNAPFGGEKNSG 462


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: 630
Number of extensions: 32
Number of successful extensions: 6
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: 492
Length adjustment: 34
Effective length of query: 481
Effective length of database: 458
Effective search space:   220298
Effective search space used:   220298
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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