GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Dyadobacter tibetensis Y620-1

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q2PGG3
         (331 letters)



>NCBI__GCF_000566685.1:WP_025764552.1
          Length = 323

 Score =  288 bits (738), Expect = 1e-82
 Identities = 147/310 (47%), Positives = 209/310 (67%), Gaps = 6/310 (1%)

Query: 15  IKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQ 74
           ++EAH RI P+IHRTP++TS+ LN ++G  LFFK E LQK GAFK RGA NA+LSLD+  
Sbjct: 17  LREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSAV 76

Query: 75  AAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSS 134
            A G+ THSSGNHA A++ AA ++GI AYIV+P  APK KV  V  YG  + + E T   
Sbjct: 77  LANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPED 136

Query: 135 REEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQE-IDAIVVPISGGGLISGV 193
           RE + ++++ ETG+  IHP+N   ++ GQ T+A E++E   E  D ++ P+ GGGL+SG 
Sbjct: 137 REAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSGT 196

Query: 194 ALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPVVRD 253
           AL+A     +  +I AEP+GA DA  S  +G I   P  +TIADGL   LGD T+PV+  
Sbjct: 197 ALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQKAPYVDTIADGLLTYLGDKTFPVIHK 256

Query: 254 LVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIGIVL 313
            V ++V + + EI+EAM++ +E +K+ VEPSGA+ LAA++      +    + K +G+++
Sbjct: 257 FVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAII-----RHKKLFEGKRVGVIV 311

Query: 314 SGGNVDLGSL 323
           SGGNVDLG+L
Sbjct: 312 SGGNVDLGNL 321


Lambda     K      H
   0.316    0.133    0.380 

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: 281
Number of extensions: 10
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: 331
Length of database: 323
Length adjustment: 28
Effective length of query: 303
Effective length of database: 295
Effective search space:    89385
Effective search space used:    89385
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 (21.6 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