Aligments for a candidate for glpD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for glpD in Cupriavidus basilensis 4G11

Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate RR42_RS16760 RR42_RS16760 FAD-dependent oxidoreductase

Query= SwissProt::Q9SS48
         (629 letters)



>FitnessBrowser__Cup4G11:RR42_RS16760
          Length = 559

 Score =  259 bits (662), Expect = 2e-73
 Identities = 203/591 (34%), Positives = 293/591 (49%), Gaps = 63/591 (10%)

Query: 52  TASVPSRSAQESALIAATASDPLDVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGT 111
           T++ P R A+++ L     S+  D+L++GGG TG+  ALDA  RG RV LVE+ DF+SGT
Sbjct: 17  TSTEPLRLARQAQL-DRLGSETFDILIVGGGVTGAYAALDASLRGYRVALVEKNDFASGT 75

Query: 112 SSRSTKLIHGGVRYLEKAVFNLDYGQLKLVFHALEERKQLIENAPHLCHALPCMTP---- 167
           SS+S+K++HGG+RY+E+       G L LV H+L ER++L  NA HL   LP + P    
Sbjct: 76  SSKSSKMVHGGLRYIEQ-------GNLGLVRHSLLERQRLRRNARHLVQRLPFLFPVMEK 128

Query: 168 --CFDWFEVIYFWMGLKMYDLVAGPRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVV 225
              FD      F   L  YDL  G R   L +  +  E +   PT      ++NL G  +
Sbjct: 129 DGVFDKRLSKAFESLLWTYDLAGGWREGILHQKLTKAEVLSHCPTF----NEENLLGGFM 184

Query: 226 YYDGQMNDSRLNVGLACTAALAGAAVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNS 285
           Y+D +++D+RL + +A TAA  GAAV+NHA+VV  IT +   ++ GA I  +   +E  +
Sbjct: 185 YFDARVDDARLTLNIARTAAFHGAAVVNHAKVVE-ITRNGHGKVDGAII--HAGDREIRA 241

Query: 286 YAKVVVNAAGPFC-DSIRKMIDEDTKPMICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRV 344
            A VVV A G +  D   +   E+    I P+ GVH+ +P         + +P     R 
Sbjct: 242 RAGVVVMATGVWLRDWTGRKKGEEKTLHIRPAKGVHVAIPWLKVRNDCTVTIPVPGRNRR 301

Query: 345 VFMLPWLGRTVAGTTD-------SNTSITSLPEPHEDEIQFILDAISDYLNIKVRRTDVL 397
             +  W   +  GTTD        N   T       +E+ F+LD     L   ++  DVL
Sbjct: 302 ATITRWGNVSYLGTTDEDYEGDLDNVCCT------REELDFLLDGARWALKTDLQAEDVL 355

Query: 398 SAWSGIRPLAMDPTAKSTESISRDHVVFEENPGLVTITGGKWTTYRSMAEDAVDAAIKSG 457
            + +G RPL   P  K+ E I R+H +     GLVTI GGK TT R MAE  +DAA K  
Sbjct: 356 GSIAGCRPLVAPPGGKTLE-IKRNHEIHTAADGLVTIVGGKLTTSRHMAEQTIDAAQK-- 412

Query: 458 QLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQYVRMKKTYGGKVVPGAMDTAAAKHLSHA 517
            L   N C T+   LLG+ G++  +                  V  G +    + HL   
Sbjct: 413 VLGQRNRCQTKSAYLLGAAGYDAQAI-----------------VASGGL----SAHLGER 451

Query: 518 YGSMADRVATIAQEEG-LGKRLAHGHPFLEAEVAYCARHEYCESAVDFIARRCRIAFLDT 576
           YG+ A  V+ I Q +  L   +  G P+ EAE+ Y ARHE   S  D ++RR R   +  
Sbjct: 452 YGTEARFVSDILQADARLQAPIVEGLPYTEAEIVYAARHELAGSVDDVLSRRIRARLMAR 511

Query: 577 DAAARALQRVVEILASEHKWDKSRQKQELQKAKEFLETFKSSKNAQFNDGK 627
           DA+ARA  RV  IL +E    +S   Q++    ++L      K+    D +
Sbjct: 512 DASARAASRVGAILQAELGLSESVVAQQV---NDYLAAVAHEKSVLLGDAQ 559


Lambda     K      H
   0.318    0.133    0.390 

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: 713
Number of extensions: 34
Number of successful extensions: 8
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: 629
Length of database: 559
Length adjustment: 37
Effective length of query: 592
Effective length of database: 522
Effective search space:   309024
Effective search space used:   309024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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