GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA 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)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_225
          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:

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