GapMind for catabolism of small carbon sources

 

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

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q74FW6
         (402 letters)



>NCBI__GCF_000566685.1:WP_025764552.1
          Length = 323

 Score =  211 bits (538), Expect = 2e-59
 Identities = 119/303 (39%), Positives = 176/303 (58%), Gaps = 2/303 (0%)

Query: 7   IQEADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREA 66
           ++EA  R+   + RT L+ S   +E  G  ++FK ENLQ+ GAFKIRGALN M S     
Sbjct: 17  LREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSAV 76

Query: 67  LAKGVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDE 126
           LA G+ T S+GNHAQ +A +A L G+ + + MP + P  KV A R YGA +       ++
Sbjct: 77  LANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPED 136

Query: 127 AYAAAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVAN-ILVPIGGGGLIAGI 185
             A   +   E GA F+HPF+   VM GQ T+  E++++  +  + +L P+GGGGL++G 
Sbjct: 137 REAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSGT 196

Query: 186 ATAIRETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIR 245
           A +      +  +IG E   A  A  SLQ G I + P   T+ADG+ +   G  TFP+I 
Sbjct: 197 ALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQKAPYVDTIADGL-LTYLGDKTFPVIH 255

Query: 246 DLVDEVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTDLSGKTVCVLSGGN 305
             V E+VLV ++EI  A+  + ER KL+VE +GAV LAA++  +      +   ++SGGN
Sbjct: 256 KFVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAIIRHKKLFEGKRVGVIVSGGN 315

Query: 306 IDV 308
           +D+
Sbjct: 316 VDL 318


Lambda     K      H
   0.319    0.137    0.383 

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: 270
Number of extensions: 12
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: 402
Length of database: 323
Length adjustment: 29
Effective length of query: 373
Effective length of database: 294
Effective search space:   109662
Effective search space used:   109662
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 (21.8 bits)
S2: 49 (23.5 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