Alignments for a candidate for dopDH in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Erythrobacter marinus HWDM-33

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_047094308.1 AAV99_RS11885 aldehyde dehydrogenase (NADP(+))

Query= reanno::Korea:Ga0059261_1896
         (524 letters)



>NCBI__GCF_001013305.1:WP_047094308.1
          Length = 518

 Score =  598 bits (1543), Expect = e-175
 Identities = 306/520 (58%), Positives = 380/520 (73%), Gaps = 3/520 (0%)

Query: 3   LTGGLFIGGERRQSDARFHAYDPAAGADIADAGFASASEQDVADACAAAEAAFLPYSTKP 62
           L G  F+ GERR     F A + A G +IA   F  A   D+ADACAAA  A   +++ P
Sbjct: 2   LDGTNFVAGERRSGKTIFRAREAATGLEIAP-DFHEADANDIADACAAAADAQRAFASLP 60

Query: 63  LEARARFLETIADEIEALGDVLIERACRESGLPAARITGERGRTVGQLRLFAKEVRDGAW 122
           L  RA F+  +AD+I+ALGD L +RA RESGLP AR+ GERGRTVGQLRLFA EV  G+W
Sbjct: 61  LSQRATFMRLVADKIDALGDDLTQRAMRESGLPEARLNGERGRTVGQLRLFADEVEHGSW 120

Query: 123 QKLRIDHADRERTPPRPDLRLRMVPLGPVAVFGASNFPLAFSTAGGDTASAFAAGCPVVV 182
           Q+LRIDHAD  RTPP+PDLRLRMVPLGPVAVFGASNFPLAFS AGGDTA+AFAAGC VVV
Sbjct: 121 QRLRIDHADASRTPPKPDLRLRMVPLGPVAVFGASNFPLAFSVAGGDTAAAFAAGCCVVV 180

Query: 183 KGHRAHPGTAELIATAIIRAVETCGMPAGTFGMVNGTSRKVGETLVADPRIQAVGFTGSR 242
           KGH AHPGT+EL+A AI  AV  CG+PAG F ++NGTS  +G  LV+DP I AVGFTGSR
Sbjct: 181 KGHPAHPGTSELVAGAICAAVAECGLPAGVFSLLNGTSNDLGAALVSDPHIAAVGFTGSR 240

Query: 243 GGGEALMRIAAARPRPIPVYAEMAAINPVILMPQALKARGPALAEAFVASLAMGAGQFCT 302
            GG ALM+IAA RP PIPVYAEM+++NPV+LMP  L      LA ++V SL+MGAGQFCT
Sbjct: 241 SGGLALMKIAAERPVPIPVYAEMSSVNPVVLMPARLAEGAEELARSYVGSLSMGAGQFCT 300

Query: 303 NPGLVMGIDGPELDAFVARAGEVLSGQAAQVMLTDGIWEAFESGKAKLAGSAFVTKVAEG 362
           NPG+V+ ++ P L  F+    + L    AQ MLT GI  +F  G  +L+       +  G
Sbjct: 301 NPGIVLAVESPALGQFLDEVAKSLGTVPAQTMLTSGIASSFGEGVDRLSTLPGARLLGSG 360

Query: 363 VEADGPNRGRAALFSVAGKDFLADPVHLHEVFGVSSVVVRCASLEELKAVLGELEGQLTA 422
            E      GRA +++V G+ F A+  + +E+FG  S++V C S+E++KA+L  +EGQLTA
Sbjct: 361 KEG-STACGRAQVYTVDGESFAANEAYSNEIFGPVSIIVTCKSMEQVKAILAGMEGQLTA 419

Query: 423 TLQVDEGDYPEAQALLPVLERTVGRVIANGWPTGVEVTHAMVHGGPYPSTSDPRSTSVGT 482
           TL ++  D+ EA  LLP LE+  GR+IAN WPTGV+VTHAMVHGGP+P+TSD RSTSVGT
Sbjct: 420 TLHMNSDDHAEAAKLLPALEQIAGRIIANSWPTGVDVTHAMVHGGPFPATSDGRSTSVGT 479

Query: 483 LAIDRFLRPVSYQDLPEALLPAALRENAQAGTVARIDGSW 522
           LAIDRFLRPVSYQD+P+ LLP+ALR+ A +G++ RI+G +
Sbjct: 480 LAIDRFLRPVSYQDMPQGLLPSALRD-ASSGSIRRINGQY 518


Lambda     K      H
   0.319    0.135    0.395 

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: 792
Number of extensions: 37
Number of successful extensions: 2
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: 524
Length of database: 518
Length adjustment: 35
Effective length of query: 489
Effective length of database: 483
Effective search space:   236187
Effective search space used:   236187
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 (21.7 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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Protein sequences (fasta format)
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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