Alignments for a candidate for putA in Haloglycomyces albus DSM 45210

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Haloglycomyces albus DSM 45210

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_025274242.1 HALAL_RS0112015 betaine-aldehyde dehydrogenase

Query= BRENDA::Q65NN2
         (516 letters)



>NCBI__GCF_000527155.1:WP_025274242.1
          Length = 492

 Score =  251 bits (642), Expect = 3e-71
 Identities = 148/457 (32%), Positives = 237/457 (51%), Gaps = 30/457 (6%)

Query: 56  INPANKEEVVGTVSKATQDHAEKAIQAAAKAFET--WRYTDPEERAAVLFRAVAKVRRKK 113
           ++PAN ++ + TV++A  D    A++AA +AF++  WR T   ER   L    ++++ +K
Sbjct: 22  LDPAN-DQPLATVAEADSDDVNAAVKAAREAFDSGPWRQTPASERGDCLRAVASELQNRK 80

Query: 114 HEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGER-NQYVYTP 172
            E + +   + GK   EA+ D  +  +   YYA  M +   G+  ++      ++ VY P
Sbjct: 81  SELTRIESLDTGKTLLEAETDVDDITNVFRYYA-DMADKDSGRVTDTGVPNTVSRIVYEP 139

Query: 173 TGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVV 232
            GV  +I PWN+    M+      +  GNT V+KP+   P+   + V+++E SG+P GVV
Sbjct: 140 IGVCSLIAPWNYPLLQMSWKLAPALAAGNTCVIKPSEVTPLATIELVKIIEASGVPAGVV 199

Query: 233 NFVPGSGAEVGDYLVDHPKTSIITFTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKD 292
           N V G GA  G  + +HP   +++FTG    G RI   AA        +K +  E+GGK+
Sbjct: 200 NLVLGGGATTGAPMTEHPDVDMVSFTGGLHTGKRIMAAAA------ADVKNIALELGGKN 253

Query: 293 TVVVDEDCDIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDEVLKRVIEITESKKVGE 352
             VV  D D E A      ++F  +GQ CSAG+R ++ E + D+ +  V +     K+G 
Sbjct: 254 PNVVFADADFETAVDYALNASFFHSGQVCSAGARLIIEESIKDDFISAVADRARKVKLGR 313

Query: 353 PDSADVYMGPVIDQASFNKIMDYIEIGKEEG-RLVSGGKGDD----SKGYFIEPTIFADL 407
                V +GP++ +    K+ +YI+   +EG  LV GGK  D    + GYF+EPTIF D 
Sbjct: 314 GQDEGVEVGPMVSREHREKVENYIQTAIDEGATLVCGGKRPDDPALTDGYFLEPTIFDDC 373

Query: 408 DPKARLMQEEIFGPVVAFSKVSSFDEALEVANNTEYGLTGAVITKNRDHINRAKQEFHVG 467
           +    +++EE+FGPV++    ++ DEA+ +AN+TEYGL G V T +     R       G
Sbjct: 374 NRDMTIVREEVFGPVLSVETFTTEDEAIALANDTEYGLAGGVWTSDASKAQRVSSAMRHG 433

Query: 468 NLYFNRNCTGAIVGYHPF------GGFKMSGTDSKAG 498
            ++ N         +HP+      GGF  SG   + G
Sbjct: 434 TIWIN--------DFHPYVPQAEWGGFGKSGVGRELG 462


Lambda     K      H
   0.315    0.133    0.382 

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: 627
Number of extensions: 37
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: 516
Length of database: 492
Length adjustment: 34
Effective length of query: 482
Effective length of database: 458
Effective search space:   220756
Effective search space used:   220756
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 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