Alignments for a candidate for iolA in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Williamsia sterculiae CPCC 203464

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_076477023.1 BW971_RS04825 gamma-aminobutyraldehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_515
         (500 letters)



>NCBI__GCF_900156495.1:WP_076477023.1
          Length = 500

 Score =  223 bits (568), Expect = 1e-62
 Identities = 145/438 (33%), Positives = 218/438 (49%), Gaps = 7/438 (1%)

Query: 26  VFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRRSRVMFKFKELLDRHHDE 85
           V  PAT  V A ++LA    VD AVA+A  A PAWS  +  +RS V+  F  +LDR    
Sbjct: 30  VIAPATDEVVATMSLATAADVDTAVAAARRALPAWSGATPAQRSTVLLDFARVLDREAHA 89

Query: 86  LA-QIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDNIGGGIDNWNLRQPLG 144
           LA Q +S     +   +  +V   I+ V +  G    L    +        +   R+ +G
Sbjct: 90  LAVQEVSHTGKTIRLASEFDVPGSIDNVTFFAGVARDLVGKATAEYSPDHTSSIRREAVG 149

Query: 145 VCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMARLLTEAGLPDGVFNV 204
           V   +TP+N+P+ + +W    A+ AG   +LKP+E  P  ++ +ARL +EAGLPDGVFNV
Sbjct: 150 VVGSITPWNYPIQMAVWKALPAIAAGCTLVLKPAEITPLTTITLARLASEAGLPDGVFNV 209

Query: 205 VQGDKVAVDALLQ-HPDIEAISFVGSTPIAEYIHQQGTAHGKRVQALGGAKNHMIVMPDA 263
           + G    V A L  HP ++ ++F GST +   +  Q   HG RVQ   G K   +V  DA
Sbjct: 210 LTGTGAEVGAALAGHPGVDLVTFTGSTGVGRQVMAQAAVHGTRVQLELGGKAPFVVFDDA 269

Query: 264 DLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRIDQLKIGNGQQPGTDM 323
           DL+ A    +  +  +AG+ C A + A+    + D+ ++ +   +  +++G+   P TDM
Sbjct: 270 DLEAAVHGAVAGSLINAGQDCTAATRAIVAPALYDDFVSGVAELMAGVRVGDPTDPATDM 329

Query: 324 GPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVGATLFDQVTAEMSIYQ 383
           G L +  H+ KV   +D     G R++  G     PGA    F   TL   V     +Y+
Sbjct: 330 GSLSSRHHREKVAAMVDRARDTGIRVVTGGHVPDGPGA----FYPPTLLADVGEGAEVYR 385

Query: 384 QEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAFARSIKVGMVGINVPI 443
            EIFGPVL +    D   A+       +G   S +TRD   A+  +R I+ G V IN  I
Sbjct: 386 DEIFGPVLTVSSFTDDDDALRRAGDTVYGLAASAWTRDVYRAQRASREIRAGCVWINDHI 445

Query: 444 PVPMAWHSFGGWKRSLFG 461
           P+ ++    GG + S FG
Sbjct: 446 PI-VSEMPHGGLRASGFG 462


Lambda     K      H
   0.321    0.137    0.415 

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: 546
Number of extensions: 30
Number of successful extensions: 4
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: 500
Length of database: 500
Length adjustment: 34
Effective length of query: 466
Effective length of database: 466
Effective search space:   217156
Effective search space used:   217156
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources