Alignments for a candidate for glpD in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpD in Pseudomonas benzenivorans DSM 8628

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_090447978.1 BLS63_RS22200 glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>NCBI__GCF_900100495.1:WP_090447978.1
          Length = 512

 Score =  852 bits (2200), Expect = 0.0
 Identities = 414/504 (82%), Positives = 452/504 (89%)

Query: 9   APLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLE 68
           APLAEVYD+A+VGGGINGVGIAADAAGRGLSVFLCE+ DLAQHTSSASSKLIHGGLRYLE
Sbjct: 9   APLAEVYDLAIVGGGINGVGIAADAAGRGLSVFLCEKDDLAQHTSSASSKLIHGGLRYLE 68

Query: 69  HYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKL 128
           HYEFRLVREALAEREVLLAKAPHIVKPLRF+LPHRPHLRPAWMIRAGLFLYDHLGKREKL
Sbjct: 69  HYEFRLVREALAEREVLLAKAPHIVKPLRFILPHRPHLRPAWMIRAGLFLYDHLGKREKL 128

Query: 129 PASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARR 188
           PASRGLRF   SPLKAEI RGFEYSDC VDDARLVVLNA++AREHGAH+HTRTRCVSARR
Sbjct: 129 PASRGLRFGAGSPLKAEISRGFEYSDCWVDDARLVVLNAMAAREHGAHLHTRTRCVSARR 188

Query: 189 SKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPK 248
           SKGLWHLHLER+DGS YS+RARALVNAAGPWVARFI+DDL+QKSPYGIRLIQGSHI+VP+
Sbjct: 189 SKGLWHLHLERADGSRYSVRARALVNAAGPWVARFIRDDLRQKSPYGIRLIQGSHIVVPR 248

Query: 249 LYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNA 308
           L++GE AYILQNEDRRIVFAIPYL+RFT+IGTTDREYQGDPA+VAISEEE  YLL VVNA
Sbjct: 249 LFDGEQAYILQNEDRRIVFAIPYLERFTLIGTTDREYQGDPAQVAISEEEIDYLLNVVNA 308

Query: 309 HFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTY 368
           HFKQ L+ ADILH++AGVRPLCDDES EPSAITRDYTL+LS   GE PLLSVFGGKLTTY
Sbjct: 309 HFKQPLSRADILHTYAGVRPLCDDESAEPSAITRDYTLALSGHPGEAPLLSVFGGKLTTY 368

Query: 369 RKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELALRWA 428
           RKLAESAL QL P F  +GP+WTA +PLPG EQ++S  AL E L  R+ WL   LA RWA
Sbjct: 369 RKLAESALAQLAPHFPKMGPSWTASSPLPGAEQLESQGALIEALCTRFGWLPTTLARRWA 428

Query: 429 RTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLS 488
            TYG+R W LL  V+ ++DLGEHLGGGLYAREVDYLC+ EWA DA DILWRR+KLGLF++
Sbjct: 429 STYGSRSWLLLKDVHEQSDLGEHLGGGLYAREVDYLCQEEWAMDAADILWRRTKLGLFMT 488

Query: 489 PSQQVRLGQYLQSEHPHRPRVHAA 512
           P QQ RL  YL++EHPH P VH A
Sbjct: 489 PVQQARLTDYLKTEHPHNPEVHVA 512


Lambda     K      H
   0.321    0.136    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: 1015
Number of extensions: 38
Number of successful extensions: 1
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: 512
Length of database: 512
Length adjustment: 35
Effective length of query: 477
Effective length of database: 477
Effective search space:   227529
Effective search space used:   227529
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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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 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