Alignments for a candidate for glpD in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpD in Paraburkholderia phymatum STM815

Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate WP_012399839.1 BPHY_RS02095 glycerol-3-phosphate dehydrogenase

Query= CharProtDB::CH_091834
         (512 letters)



>NCBI__GCF_000020045.1:WP_012399839.1
          Length = 511

 Score =  542 bits (1397), Expect = e-159
 Identities = 277/483 (57%), Positives = 343/483 (71%), Gaps = 7/483 (1%)

Query: 14  VYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHYEFR 73
           +YD+ VVGGGING GIA DAAGR LSV LCEQ DLA HTSSAS+KLIHGGLRYLE+ EF 
Sbjct: 6   IYDLLVVGGGINGAGIARDAAGRSLSVLLCEQDDLAAHTSSASTKLIHGGLRYLEYREFG 65

Query: 74  LVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGKREKLPASRG 133
           LVR+AL ERE LL  APHI+ PLRFV+PH P LRPAW+IRAGLFLYDHL +RE LP S G
Sbjct: 66  LVRKALQERETLLRAAPHIMWPLRFVMPHMPDLRPAWLIRAGLFLYDHLARRELLPGSHG 125

Query: 134 L---RFTGSSPLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSARRSK 190
           +   +     PL   I+RGF YSD  VDDARLVVLNA+ A EHGA + TRT+ V A R+ 
Sbjct: 126 IDMRKHPAGQPLVDSIKRGFVYSDGWVDDARLVVLNALDAHEHGATILTRTKLVGAARAN 185

Query: 191 GLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLK--QKSPYGIRLIQGSHIIVPK 248
           G WH  L R+DGS+ ++RAR++ NAAGPWV   ++  L   Q++ Y +RL++GSHI+V +
Sbjct: 186 GEWHAQLLRADGSVTTVRARSIANAAGPWVGELLRGPLSRGQETNYSVRLVKGSHIVVRR 245

Query: 249 LYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVVNA 308
           L+E +HAYI QN D+RI+FAIPY   FT+IGTTD EY+GDP++VAI   ET YL   +N 
Sbjct: 246 LFEHDHAYIFQNPDKRIIFAIPYERDFTLIGTTDLEYKGDPSQVAIDASETQYLCDSINR 305

Query: 309 HFKQQLAAADILHSFAGVRPLCDDE-SDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLTT 367
           +F+Q +A  D+  +++GVRPL +DE +D PSA+TRDY L L A  GE PLLSVFGGK+TT
Sbjct: 306 YFRQHIAPRDVYWTYSGVRPLLEDENADNPSAVTRDYRLELDAPAGEAPLLSVFGGKITT 365

Query: 368 YRKLAESALTQLQPFFANLGPAWTAKAPLPGGEQMQS-VEALTEQLANRYAWLDRELALR 426
           +RKLAE A+  L     +   AWTA  PLPGG+  ++  E    Q A  + WL   LA R
Sbjct: 366 FRKLAEEAVDDLARALRHDKRAWTAGVPLPGGDIARADFERFAAQFAQHHTWLPATLARR 425

Query: 427 WARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGLF 486
           +AR YGTR  R++      ADLG+    GLY  E+ YL + EWA  A D+LWRRSKLGL 
Sbjct: 426 YARAYGTRAERVIGDARSLADLGQQFAPGLYEAELRYLRETEWATTARDVLWRRSKLGLH 485

Query: 487 LSP 489
           + P
Sbjct: 486 VEP 488


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: 786
Number of extensions: 34
Number of successful extensions: 5
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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