GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Thiohalospira halophila HL 3

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_093428290.1 BM272_RS08145 threonine ammonia-lyase, biosynthetic

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_900112605.1:WP_093428290.1
          Length = 504

 Score =  195 bits (495), Expect = 2e-54
 Identities = 104/301 (34%), Positives = 166/301 (55%), Gaps = 3/301 (0%)

Query: 19  RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78
           R+   A +TP+  ++ ++     +VF K E+ Q + ++K RGA N +  L   QR  GV+
Sbjct: 13  RVYDVARETPLDPATGLSNRLGNQVFLKREDLQPVFSYKLRGAYNKIIHLAPEQRARGVI 72

Query: 79  TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138
             S+GNHAQ +ALSA+ LGIPA+I+MP   P+ K+ A +  G +++++    D+      
Sbjct: 73  AASAGNHAQGVALSARRLGIPARIVMPKTTPDIKIEAVRALGAEIVLHGSSYDEAFAHCM 132

Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELFEEV-GPLDALFVCLGGGGLLSGSALAARH 197
           +I+E  G+  IPPYD P V+AGQGT A EL  +   PL+A+FV +GGGGLL+G +   R 
Sbjct: 133 QIAEEAGMAFIPPYDDPDVIAGQGTVAMELARQAPQPLEAVFVPVGGGGLLAGVSAYFRA 192

Query: 198 FAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDI 257
             P   + GVEP        +   G  V +      ADG   + +G   F I++E VD++
Sbjct: 193 LYPGVRIIGVEPADAPTLHSALAAGERVQLPQVGIFADGVAVRRIGEEPFRILRESVDEV 252

Query: 258 LTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKE--KLKNKRIGIIISGGNVDIE 315
           + VS + +   +K      + + EP G LS A  +   E  +L+   +  ++SG N++ +
Sbjct: 253 VLVSTDAICAAIKDIFDNTRSIAEPAGALSVAGLKQYVENHRLEGANLAAVVSGANINFD 312

Query: 316 R 316
           R
Sbjct: 313 R 313


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: 351
Number of extensions: 15
Number of successful extensions: 2
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: 504
Length adjustment: 31
Effective length of query: 292
Effective length of database: 473
Effective search space:   138116
Effective search space used:   138116
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