GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctC in Pseudomonas stutzeri RCH2

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate GFF1668 Psest_1706 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::H6LBB1
         (418 letters)



>FitnessBrowser__psRCH2:GFF1668
          Length = 309

 Score =  139 bits (351), Expect = 9e-38
 Identities = 102/323 (31%), Positives = 166/323 (51%), Gaps = 20/323 (6%)

Query: 74  ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTN---ITEKADELLKYGVDK 130
           I V  +H    +   T   +  A+     IG  ++ L+ G+    I E A ++   GV K
Sbjct: 3   ILVIAEHNNAVLAAATLNTVAAAK----AIGGDIHVLVAGSGCGAIGEAAAQI--EGVAK 56

Query: 131 VFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADC 190
           V V D     + + E  A ++ D  +    S +L  AT  G++  PRVAA+      ++ 
Sbjct: 57  VLVADDAAYANQLPENVAPLIADLAKNY--SHVLAAATTNGKNFLPRVAAQLDVDQISEI 114

Query: 191 TILEMKENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDVEMMD 250
             +E  +       RP + GN +A  V  +   +  TVR   F A   VN   G   +  
Sbjct: 115 IAVESADTFK----RPIYAGNAIAT-VQSSAAVKVITVRATGFDA---VNGTGGSAAVEQ 166

Query: 251 IE-KAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIGATVAC 309
           I        +  V E + K    +L+ A+ +V+ GRG++   +   ++  A+K+GA V  
Sbjct: 167 ISGTGDAGKSAFVGEELAKSDRPELTAAKIVVSGGRGMQNGDNFKHLYSLADKLGAAVGA 226

Query: 310 TRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSDPKAPI 369
           +R  ++AG+    +Q+G +G+ V P+L IA+GISGA+Q  AGM++S+ I+AIN D +API
Sbjct: 227 SRAAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPI 286

Query: 370 FNIAHCGMVGDLYEILPELLTMI 392
           F +A  G+VGDL+EI+PEL  ++
Sbjct: 287 FQVADYGLVGDLFEIVPELEKLV 309


Lambda     K      H
   0.319    0.137    0.395 

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: 310
Number of extensions: 15
Number of successful extensions: 2
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: 418
Length of database: 309
Length adjustment: 29
Effective length of query: 389
Effective length of database: 280
Effective search space:   108920
Effective search space used:   108920
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 (21.7 bits)
S2: 49 (23.5 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:

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:

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:

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:

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