GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctB in Desulfoscipio geothermicus DSM 3669

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate WP_092482220.1 BM299_RS04215 electron transfer flavoprotein subunit beta/FixA family protein

Query= BRENDA::H6LBB0
         (264 letters)



>NCBI__GCF_900115975.1:WP_092482220.1
          Length = 269

 Score =  183 bits (464), Expect = 4e-51
 Identities = 103/263 (39%), Positives = 161/263 (61%), Gaps = 5/263 (1%)

Query: 1   MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGT-ITTL 59
           M I+  +KQVPGT NV+++PETG ++R G ++ +NP D   L  A R+K+Q  GT +T +
Sbjct: 1   MNIVALVKQVPGTDNVKMNPETGTMVRTGKDNVINPLDENALTEALRIKQQTTGTTVTAV 60

Query: 60  SMGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQGTKRLGDFDLIICGKQ 119
           SMGP  +++ L E+  +GADEG LLS R F GAD +AT+  LA   K+L +  +I+CG++
Sbjct: 61  SMGPQTAEKALKEAIALGADEGILLSSRAFAGADTIATARVLAAAVKKLENVSMILCGER 120

Query: 120 TTDGDTAQVGPEMAEFLGIPHVTNVIKILAADEKGLTLQMNMEESLEIQRVPYPCLITVD 179
            TDG+T Q GP +A  LGIP VT V +I   +   + +++ +E   E   +PYP + TV 
Sbjct: 121 ATDGETGQTGPMVAAMLGIPVVTFVKEINVGENTAIVIRI-VENGYEKVEIPYPFMATVV 179

Query: 180 KDIYTPRLPSYKRKLDISKNPEIKILTLKDMYDTNEKKYGLSGSPTQVERIFPPESNVEK 239
           KDI  P  P+   K+  ++   +K+ + +++    + + GL+GSPT+V +IF P+   + 
Sbjct: 180 KDINEPGFPTLSGKVQ-ARETLVKVWSEEEL-GLPKNELGLTGSPTRVVKIFSPKLARDT 237

Query: 240 TSFEGDGKVLAKALL-GILTEKK 261
              + DG   A  +L  +L EKK
Sbjct: 238 RILKHDGSGNAVGILVKLLQEKK 260


Lambda     K      H
   0.316    0.137    0.386 

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: 192
Number of extensions: 6
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: 264
Length of database: 269
Length adjustment: 25
Effective length of query: 239
Effective length of database: 244
Effective search space:    58316
Effective search space used:    58316
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: 42 (22.0 bits)
S2: 47 (22.7 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:

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