Aligments for a candidate for glpD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for glpD in Pseudomonas stutzeri RCH2

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate GFF2721 Psest_2775 Glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>lcl|FitnessBrowser__psRCH2:GFF2721 Psest_2775 Glycerol-3-phosphate
           dehydrogenase
          Length = 511

 Score =  743 bits (1917), Expect = 0.0
 Identities = 364/495 (73%), Positives = 423/495 (85%), Gaps = 1/495 (0%)

Query: 10  PLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEH 69
           P++E+YDVAV+GGGINGVGIAADAAGRGLSVFLCE+ DLA HTSSASSKLIHGGLRYLEH
Sbjct: 7   PVSELYDVAVIGGGINGVGIAADAAGRGLSVFLCERDDLASHTSSASSKLIHGGLRYLEH 66

Query: 70  YEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLP 129
           YEFRLVREALAERE+LLAKAPHIVKP+RFVLPHRPHLRPAWMIRAGLFLYD+LG R+KLP
Sbjct: 67  YEFRLVREALAEREMLLAKAPHIVKPMRFVLPHRPHLRPAWMIRAGLFLYDNLGMRKKLP 126

Query: 130 ASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRS 189
           ASRGLRF   SPLK  I RGFEYSDC VDDARLVVLNA++ARE GAH+HTRT+C+SA+R+
Sbjct: 127 ASRGLRFGSESPLKPVITRGFEYSDCWVDDARLVVLNAMAAREKGAHIHTRTQCLSAKRA 186

Query: 190 KGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIVPKL 249
            G+WH+ L+R DGS +S+RA+ALVNAAGPWVA+FI ++L+Q+SPYGIRLIQGSHIIVPKL
Sbjct: 187 GGIWHVELQREDGSRFSLRAKALVNAAGPWVAQFIGENLQQRSPYGIRLIQGSHIIVPKL 246

Query: 250 YEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNAH 309
           YEGE AYI+QNEDRRIVFAIPYLDR+TMIGTTDREY+GDPAKV+ISEEE AY+L V N H
Sbjct: 247 YEGEQAYIMQNEDRRIVFAIPYLDRYTMIGTTDREYRGDPAKVSISEEEIAYVLGVANTH 306

Query: 310 FKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTTYR 369
           F++QL   DI+H+FAGVRPLCDDESD PSA+TRDYTLSL+A   + PLLSVFGGKLTTYR
Sbjct: 307 FRKQLEPRDIVHTFAGVRPLCDDESDNPSAVTRDYTLSLAAEEKQAPLLSVFGGKLTTYR 366

Query: 370 KLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELALRWAR 429
           KLAESA+ QL+PFF  +G +WTA+A LPGGE M + +ALTE+L  +   L   LA RWA 
Sbjct: 367 KLAESAMAQLKPFFPAMGGSWTAQAALPGGEDMSTADALTEELVAKVQGLKLPLAKRWAT 426

Query: 430 TYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLFLSP 489
            YG RVWR+L   +    LGE LG  LYA+EV+YL + EWA   +DILWRR+KLGL  S 
Sbjct: 427 LYGNRVWRMLGEAHSLDALGEDLGQQLYAQEVEYLRREEWATQVDDILWRRTKLGLAFSE 486

Query: 490 SQQVRLGQYLQSEHP 504
            ++ RL +YL +E P
Sbjct: 487 PEKARLARYL-AERP 500


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: 895
Number of extensions: 22
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: 511
Length adjustment: 35
Effective length of query: 477
Effective length of database: 476
Effective search space:   227052
Effective search space used:   227052
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 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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