Alignments for a candidate for glpD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpD in Pseudomonas stutzeri RCH2

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate GFF1416 Psest_1453 Glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>FitnessBrowser__psRCH2:GFF1416
          Length = 514

 Score =  733 bits (1891), Expect = 0.0
 Identities = 363/502 (72%), Positives = 405/502 (80%)

Query: 5   HTPSAPLAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGL 64
           H   APLAEVYD+AVVGGGING GIAADAAGRGLSVFLCEQ DLA+HTSSASSKL+HGGL
Sbjct: 3   HPLLAPLAEVYDLAVVGGGINGAGIAADAAGRGLSVFLCEQGDLAEHTSSASSKLVHGGL 62

Query: 65  RYLEHYEFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGK 124
           RYLEHYE RLVREALAEREVLLAKAPHIV PLRFVLP+RPHLRP+WMIR GLFLYDHLGK
Sbjct: 63  RYLEHYELRLVREALAEREVLLAKAPHIVTPLRFVLPYRPHLRPSWMIRTGLFLYDHLGK 122

Query: 125 REKLPASRGLRFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCV 184
           REKL  SR LRF   SPLK EI  GFEY+DC VDDARLVVLNA++ARE GAH+H RTRCV
Sbjct: 123 REKLGGSRSLRFGADSPLKDEITHGFEYADCWVDDARLVVLNAMAARELGAHIHPRTRCV 182

Query: 185 SARRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHI 244
           SAR SK LWHLHLER DGS +SIRARALVNA GPWVA FI++ L+Q SP+G+RLIQGSHI
Sbjct: 183 SARSSKALWHLHLERQDGSRFSIRARALVNATGPWVASFIEEQLRQTSPHGMRLIQGSHI 242

Query: 245 IVPKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQ 304
           +VPKLYEG+HAYILQNEDRRIVF  PYL +F++IGTTD EY GDP +V I++ E  YLL 
Sbjct: 243 VVPKLYEGDHAYILQNEDRRIVFITPYLGQFSLIGTTDHEYHGDPTQVRITDAEIDYLLA 302

Query: 305 VVNAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGK 364
           +VNAHFK QL+ ADI +S+AGVRPLCDDESD+PSAITRDYTL+LS   GE PLLSVFGGK
Sbjct: 303 IVNAHFKHQLSRADIRYSYAGVRPLCDDESDQPSAITRDYTLTLSDSAGEGPLLSVFGGK 362

Query: 365 LTTYRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQSVEALTEQLANRYAWLDRELA 424
           LTTYRKLAE+AL QL P F  +   WT  A LPGGE +    AL   L   Y WL   +A
Sbjct: 363 LTTYRKLAEAALAQLAPLFPEMKRPWTHDAALPGGEHLDEPSALAHALCASYPWLPGPIA 422

Query: 425 LRWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLG 484
            RWARTYG+R W LL G +   DLGE  G GL+AREVDYL   EWAQ AEDILWRR+KLG
Sbjct: 423 RRWARTYGSRSWLLLKGTDSLQDLGECFGAGLHAREVDYLMVEEWAQTAEDILWRRTKLG 482

Query: 485 LFLSPSQQVRLGQYLQSEHPHR 506
           LF+ P++   + +YL S    R
Sbjct: 483 LFMQPAEVALVQRYLDSRTAER 504


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: 938
Number of extensions: 40
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: 514
Length adjustment: 35
Effective length of query: 477
Effective length of database: 479
Effective search space:   228483
Effective search space used:   228483
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)
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