GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Methanoculleus horonobensis T10

Align 6-deoxy-5-ketofructose 1-phosphate synthase (EC 2.2.1.11) (characterized)
to candidate WP_067073672.1 MCUHO_RS04020 aldolase

Query= BRENDA::Q58980
         (310 letters)



>NCBI__GCF_001602375.1:WP_067073672.1
          Length = 306

 Score =  373 bits (957), Expect = e-108
 Identities = 181/301 (60%), Positives = 233/301 (77%), Gaps = 4/301 (1%)

Query: 13  DVKVPLTVPEDRKEEYIKNYLELTKRTGNVMLFAGDQKIEHLNDDFFGEGIAKDDASPEH 72
           D+++PL VP + +E Y +NY ++T  TG +MLFAGDQK+EHLNDDF+GEGI  DDA PEH
Sbjct: 6   DIRIPLDVPSEEQERYRENYRKITHGTGRLMLFAGDQKVEHLNDDFYGEGIHPDDADPEH 65

Query: 73  LFNIASKGKICGFATQLGLIARYGMDYKKIPYIVKINSKTHLVKT--RDPISRALVHVKD 130
           LF IA + +I  FATQLG+IARYG DY+ +PY+VK+NSKTHLVKT  RDP+S  L  V+ 
Sbjct: 66  LFRIADRARIGVFATQLGMIARYGEDYRDVPYLVKLNSKTHLVKTAQRDPLSSELHLVRQ 125

Query: 131 VVDLKENSGLKILGVGYTIYPGSEYEHIMFEEASRVILEAHKHGLIAIIWSYPRGKNVKD 190
           VVDL++ +GL ILGVGYTIY GSEYE +M  +A++++  AH +GLI ++W YPRGK VKD
Sbjct: 126 VVDLRDRTGLAILGVGYTIYLGSEYEPMMLFQAAQIVNNAHANGLITVLWMYPRGKAVKD 185

Query: 191 EKDPHLIAGAAGVAACLGADFVKVNYPKCDN--PAERFKEAVLAAGRTGVLCAGGKSIEP 248
           E+DPHLIAGAAGVAA LG+DFVKVN PK  +   A   +EAV A GRTGV+CAGG   + 
Sbjct: 186 ERDPHLIAGAAGVAATLGSDFVKVNPPKAGDRIDAALLREAVAAGGRTGVVCAGGSHADA 245

Query: 249 EKFLKQIWEQINISGARGNATGRNIHQKPLDAAIRMCNAIYAITIEGKSLEEALKIYYGD 308
            +FL+Q+ +QI++ G  GNATGRNIHQ+PLD A+R CNAI AIT++   ++EA+ IY G 
Sbjct: 246 PEFLQQLHDQIHVGGTLGNATGRNIHQRPLDEAVRFCNAISAITLDDAGVDEAVGIYEGG 305

Query: 309 R 309
           +
Sbjct: 306 K 306


Lambda     K      H
   0.319    0.139    0.408 

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: 336
Number of extensions: 14
Number of successful extensions: 3
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: 310
Length of database: 306
Length adjustment: 27
Effective length of query: 283
Effective length of database: 279
Effective search space:    78957
Effective search space used:    78957
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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