Alignments for a candidate for glpA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpA in Desulfovibrio vulgaris Hildenborough

Align anaerobic glycerol-3-phosphate dehydrogenase subunit A (EC 1.1.5.3) (characterized)
to candidate 207410 DVU1940 anaerobic glycerol-3-phosphate dehydrogenase, A subunit, putative

Query= ecocyc::ANGLYC3PDEHYDROGSUBUNITA-MONOMER
         (542 letters)



>MicrobesOnline__882:207410
          Length = 516

 Score =  376 bits (965), Expect = e-108
 Identities = 219/535 (40%), Positives = 291/535 (54%), Gaps = 27/535 (5%)

Query: 9   SDVIIIGGGATGAGIARDCALRGLRVILVERHDIATGATGRNHGLLHSGARYAVTDAESA 68
           + V+IIG GATG G+ARD ALRG+  IL+++ D+  GA+G NHGLLHSG RY  TD  +A
Sbjct: 3   TQVLIIGAGATGTGVARDLALRGVDCILIDQRDVNAGASGGNHGLLHSGGRYVFTDPHAA 62

Query: 69  RECISENQILKRIARHCVEPTNGLFITLPEDDLSFQATFIRACEEAGISAEAIDPQQARI 128
            EC +E  ILKRIA  C+E T G F+ +  DD ++ + F   C +AG+    +D  +AR 
Sbjct: 63  AECKAEGDILKRIAPQCIEETGGYFVAVEGDDPAYASDFPGYCAKAGVPCREVDAHEARR 122

Query: 129 IEPAVNPALIGAVKVPDGTVDPFRLTAANMLDAKEHGAVILTAHEVTGLIREGATVCGVR 188
            EPA+  +     +V D +VDPF+L+  N+ DA  HG   L    V G   E   +   R
Sbjct: 123 NEPAIAESTFAVYEVEDASVDPFKLSLENVADAGRHGGRYLRYTRVLGFDMERGRIVAAR 182

Query: 189 VRNHLTGETQALHAPVVVNAAGIWGQHIAEYADLRIRMFPAKGSLLIMDHRINQHVINRC 248
           V +  +G    + A   V AAG W   I   A   + +  AKG+LL+   R+   VINR 
Sbjct: 183 VEDMRSGREYRIVADEYVVAAGAWSGGITAMAGCHVDIVYAKGTLLVTQTRMAHRVINRL 242

Query: 249 RKPSDADILVPGDTISLIGTTSLRIDYNEIDDNRVTAEEVDILLREGEKLAPVMAKTRIL 308
           R P D DILVPG T+S++GTTSLR++    DD R T  EVD+ + EG  + P +A  R +
Sbjct: 243 RTPGDGDILVPGGTVSVLGTTSLRVE--SPDDVRPTVAEVDVNINEGMGMVPSLADARFI 300

Query: 309 RAYSGVRPLVASDDDPSG--RNVSRGIVLLDHAERDGLDGFITITGGKLMTYRLMAEWAT 366
           RAY+GVRPLV S   PSG  R  SRG VLLDH E DG+   +TI GGKL TYRLMAE A 
Sbjct: 301 RAYAGVRPLVRS-GKPSGSDRAASRGFVLLDH-EEDGVHNLVTIAGGKLTTYRLMAERAA 358

Query: 367 DAVCRKLGNTRPCTTADLALPGSQEPAEVTLRKVISLPAPLRGSAVYRHGDRTPAWLSEG 426
           D VC +LG + PC TA   +  S E            P  L+    +R+ DR        
Sbjct: 359 DLVCERLGVSAPCLTAVRPISPSDEAEWAE-------PGVLQKQNWWRNHDRDD------ 405

Query: 427 RLHRSLVCECEAVTAGEVQYAVENLNVNS----LLDLRRRTRVGMGTCQGELCACRAAGL 482
                L+CECE V    V   +      +    LL +  R+RVG G+CQG  C  R    
Sbjct: 406 ----YLLCECEIVPKSGVDSIIATFKDEAEPPRLLAIGLRSRVGKGSCQGAFCGARITAH 461

Query: 483 LQRFNVTTSAQSIEQLSTFLNERWKGVQPIAWGDALRESEFTRWVYQGLCGLEKE 537
           +    +    + ++ L  FL  RWKG +PI WG    ++E    +Y GL G+E E
Sbjct: 462 MHDRRIIEGREGLDGLREFLGARWKGQRPILWGAQFNQAELKEALYFGLVGMELE 516


Lambda     K      H
   0.320    0.136    0.403 

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: 769
Number of extensions: 35
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: 542
Length of database: 516
Length adjustment: 35
Effective length of query: 507
Effective length of database: 481
Effective search space:   243867
Effective search space used:   243867
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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Protein sequences (fasta format)
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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