Alignments for a candidate for adh in Novosphingobium aromaticivorans DSM 12444

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Novosphingobium aromaticivorans DSM 12444

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_010891011.1 SARO_RS17045 aldehyde dehydrogenase family protein

Query= BRENDA::Q402C7
         (499 letters)



>NCBI__GCF_000013325.1:WP_010891011.1
          Length = 501

 Score =  909 bits (2349), Expect = 0.0
 Identities = 449/501 (89%), Positives = 479/501 (95%), Gaps = 2/501 (0%)

Query: 1   MATQLKSAENEYGIKPEYGHFIGGEWVSGDSGKTIDLINPATGAVLTKIQAGNAKDIQRA 60
           MATQL+SAENEYGIK EYGH+IGGEW++GDSGKTIDL+NP+TG VLTKIQAGNAKDI+RA
Sbjct: 1   MATQLRSAENEYGIKSEYGHYIGGEWIAGDSGKTIDLLNPSTGKVLTKIQAGNAKDIERA 60

Query: 61  VAAAKAAFPKWSESSPAERQEILIEVARRLKARHQHYATLETLNNGKPIRESMYFDMPQA 120
           +AAAKAAFPKWS+S P ERQEILIEVARRLKARH HYATLETLNNGKP+RESMYFDMPQ 
Sbjct: 61  IAAAKAAFPKWSQSLPGERQEILIEVARRLKARHSHYATLETLNNGKPMRESMYFDMPQT 120

Query: 121 ISQFEVFAGAAYGLHGQTLDYPDAIGIVHREPLGVCAQIIPWNVPILMMACKIAPALASG 180
           I QFE+FAGAAYGLHGQTLDYPDAIGIVHREPLGVCAQIIPWNVP+LMMACKIAPALASG
Sbjct: 121 IGQFELFAGAAYGLHGQTLDYPDAIGIVHREPLGVCAQIIPWNVPMLMMACKIAPALASG 180

Query: 181 NTVVLKPAETVCLSVIEFFVEMADLLPPGVINVVTGYGADVGEALVTHEDVRKVAFTGSV 240
           NTVVLKPAETVCLSVIEFFVEMADLLPPGVINVVTGYGADVGEALVT  DV KVAFTGS+
Sbjct: 181 NTVVLKPAETVCLSVIEFFVEMADLLPPGVINVVTGYGADVGEALVTSPDVAKVAFTGSI 240

Query: 241 ATARRIIQYASSNIIPQTLELGGKSAHIVCADADIDAAVESATMSTVFNKGEVCLAGSRL 300
           ATARRIIQYAS+NIIPQTLELGGKSAHIVC DADIDAAVESATMSTV NKGEVCLAGSRL
Sbjct: 241 ATARRIIQYASANIIPQTLELGGKSAHIVCGDADIDAAVESATMSTVLNKGEVCLAGSRL 300

Query: 301 FLHQSIQDEFLAKFKVALEGIRQGDPLDFATQLGAQASQMQMDKVQSYLQLATEEGATVL 360
           FLHQSIQDEFLAKFK ALEGIRQGDPLD ATQLGAQAS+MQ DKVQSYL+LATEEGA VL
Sbjct: 301 FLHQSIQDEFLAKFKTALEGIRQGDPLDMATQLGAQASKMQFDKVQSYLRLATEEGAEVL 360

Query: 361 TGGSRNES--LADGHFIKPTVFTNVSNSMRIAREEIFGPVTSVLTWNDEDDMMALANDTT 418
           TGGSR+++  LADG+FIKPTVFTNV+NSMRIA+EEIFGPVTSV+TW+DEDDMM  AN+TT
Sbjct: 361 TGGSRSDAADLADGNFIKPTVFTNVNNSMRIAQEEIFGPVTSVITWSDEDDMMKQANNTT 420

Query: 419 YGLAGGVWTRDISRAHRIARKLETGTVWVNRYYNLKPNMPLGGYKQSGFGREFSHEVLHH 478
           YGLAGGVWT+DI+RAHRIARKLETGTVW+NRYYNLK NMPLGGYKQSGFGREFSHEVL+H
Sbjct: 421 YGLAGGVWTKDIARAHRIARKLETGTVWINRYYNLKANMPLGGYKQSGFGREFSHEVLNH 480

Query: 479 YTQTKSVVINLQEGRVGMFDQ 499
           YTQTKSVV+NLQEGR GMFDQ
Sbjct: 481 YTQTKSVVVNLQEGRTGMFDQ 501


Lambda     K      H
   0.318    0.133    0.390 

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: 901
Number of extensions: 25
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: 499
Length of database: 501
Length adjustment: 34
Effective length of query: 465
Effective length of database: 467
Effective search space:   217155
Effective search space used:   217155
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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