GapMind for catabolism of small carbon sources

 

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

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q54HH2
         (324 letters)



>NCBI__GCF_000566685.1:WP_025764552.1
          Length = 323

 Score =  297 bits (761), Expect = 2e-85
 Identities = 151/310 (48%), Positives = 217/310 (70%), Gaps = 5/310 (1%)

Query: 11  DIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSLDEE 70
           D++EAH+RI  +IH+TP++T+  +NEL G  L+FK ENLQK G+FK+RGA NA+ SLD  
Sbjct: 16  DLREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSA 75

Query: 71  ELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCKATLE 130
            L+ G+ THSSGNH QA++ A+ +R +K Y+V+P +AP VK++A+ GYGA++T C+ T E
Sbjct: 76  VLANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPE 135

Query: 131 ARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELME-QVENLDAIITPVGGGGLLSG 189
            RE+   +++ +     IHPF++  V+ GQ T + E++E   E  D ++ PVGGGGLLSG
Sbjct: 136 DREAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSG 195

Query: 190 TCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTVGSLTFPI 249
           T ++A   + N  V  AEP GA D   SL SG IQK      +TIADGLLT +G  TFP+
Sbjct: 196 TALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQK--APYVDTIADGLLTYLGDKTFPV 253

Query: 250 IKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKVGIII 309
           I +    ++LV++ EI  AM+L+WERMK+++EPS A TLAAI++   K   + K+VG+I+
Sbjct: 254 IHKFVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAIIRH--KKLFEGKRVGVIV 311

Query: 310 SGGNVDLSSI 319
           SGGNVDL ++
Sbjct: 312 SGGNVDLGNL 321


Lambda     K      H
   0.315    0.132    0.374 

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: 284
Number of extensions: 14
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: 324
Length of database: 323
Length adjustment: 28
Effective length of query: 296
Effective length of database: 295
Effective search space:    87320
Effective search space used:    87320
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 (21.5 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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