GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lctB in Methylocella silvestris BL2

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.110) (characterized)
to candidate WP_012592569.1 MSIL_RS18370 electron transfer flavoprotein subunit beta/FixA family protein

Query= BRENDA::H6LBB0
         (264 letters)



>NCBI__GCF_000021745.1:WP_012592569.1
          Length = 283

 Score =  173 bits (439), Expect = 3e-48
 Identities = 99/264 (37%), Positives = 153/264 (57%), Gaps = 7/264 (2%)

Query: 1   MKILVCIKQVPGTSNVEVDPETGVLIRDGVESKLNPYDLFGLETAFRLKEQLGGTITTLS 60
           M ILVCIKQVP ++ + ++P T  ++R GV + +NPYDLF LE A RL++Q GG +T L+
Sbjct: 1   MHILVCIKQVPDSAQIRINPVTQTIMRQGVPTIINPYDLFSLEEALRLRDQFGGEVTVLT 60

Query: 61  MGPMQSKEVLMESFYMGADEGCLLSDRKFGGADVVATSYTLAQG----TKRLGDFDLIIC 116
           MGP  + + L ++  +GAD   LL+DR F G+D +ATS+ L Q     ++  G  D++  
Sbjct: 61  MGPPMASDSLRKALAIGADRAVLLTDRFFAGSDTLATSFALTQAIVKISETFGAPDIVFT 120

Query: 117 GKQTTDGDTAQVGPEMAEFLGIPHVTNVIKILAA--DEKGLTLQMNMEESLEIQRVPYPC 174
           GKQT DGDTAQVGP +A+ L +  +T V KI+    D++ + ++   E  + + +   PC
Sbjct: 121 GKQTIDGDTAQVGPGIAKRLDLLQLTYVAKIVECNPDKREIIVERRSEGGVHVLKTKLPC 180

Query: 175 LITVDKDIYTPRLPSYKRKLDISKNPEIKILTLKDMYDTNEKKYGLSGSPTQVERIFPPE 234
           LIT+ +     R  + K  L  ++  EI   + KD    +  K GL GSPT V+++F P 
Sbjct: 181 LITMLEGSNEVRRGAMKDALRAAR-AEIVTWSAKDAGIADITKCGLKGSPTVVKKVFAPP 239

Query: 235 SNVEKTSFEGDGKVLAKALLGILT 258
              E+  F     V ++    ++T
Sbjct: 240 PRSERAFFVPTADVASQEAENLIT 263


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: 182
Number of extensions: 7
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: 283
Length adjustment: 25
Effective length of query: 239
Effective length of database: 258
Effective search space:    61662
Effective search space used:    61662
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