GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Algiphilus aromaticivorans DG1253

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_043772030.1 U743_RS11935 threonine ammonia-lyase, biosynthetic

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_000733765.1:WP_043772030.1
          Length = 510

 Score =  212 bits (540), Expect = 1e-59
 Identities = 117/308 (37%), Positives = 181/308 (58%), Gaps = 7/308 (2%)

Query: 19  RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78
           R+   A +TP+  +  ++     ++  K E+ Q + +FK RGA N ++QL+EA+R  GV+
Sbjct: 13  RVYDVAIRTPLSPAPRLSARIGNKLLLKREDLQPVHSFKLRGAFNRIAQLSEAERAKGVV 72

Query: 79  TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138
             S+GNHAQ +AL+A+ LG  A I+MP   P+ KV A +G+GG+V+++    D+    A 
Sbjct: 73  CASAGNHAQGVALAARTLGCTAWIVMPRTTPQIKVDAVRGFGGKVVLHGDAYDEASAHAA 132

Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVG-----PLDALFVCLGGGGLLSGSAL 193
           +I E  G T IPPYD P V+AGQGT A+E+ E++      PLD +FVC+GGGGLL+G A 
Sbjct: 133 KIVEERGATYIPPYDDPLVIAGQGTIAREIVEQLAEAGEKPLDVIFVCVGGGGLLAGVAA 192

Query: 194 AARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEK 253
             +  +P  +V GVEPE  +   ++   G  V +      ADG   +  G   F + +  
Sbjct: 193 YIKAVSPTTKVIGVEPEDSDCMGRALAAGRRVILPQVGLFADGVAVRQAGKEPFRVARAC 252

Query: 254 VDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGN 311
           VD +LTVS +E+   ++      + V EP G L+ A A+  A++   ++KR+G I+SG N
Sbjct: 253 VDAMLTVSIDEICAAVRDVFYENRSVPEPAGALAVAGAKRWALETGARDKRLGAIVSGAN 312

Query: 312 VDIERYAH 319
           V+ +R  H
Sbjct: 313 VNFDRLRH 320


Lambda     K      H
   0.318    0.135    0.384 

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: 335
Number of extensions: 15
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: 323
Length of database: 510
Length adjustment: 31
Effective length of query: 292
Effective length of database: 479
Effective search space:   139868
Effective search space used:   139868
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: 50 (23.9 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