GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Microvirga lotononidis WSM3557

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_009763905.1 MICLODRAFT_RS21385 threo-3-hydroxy-L-aspartate ammonia-lyase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_000262405.1:WP_009763905.1
          Length = 335

 Score =  396 bits (1018), Expect = e-115
 Identities = 195/316 (61%), Positives = 245/316 (77%)

Query: 7   LPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALS 66
           LPTY+DV +A+ RI   A++TPVLTS T ++     +FFK ENFQ+ GAFKFRGA NA++
Sbjct: 19  LPTYEDVVAAARRIDGVAHRTPVLTSRTADERTGGRLFFKAENFQRGGAFKFRGAYNAIA 78

Query: 67  QLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMY 126
           +L+   +K GV+ FSSGNHAQAIA + ++  +P  IIMP DAP  KVAATKGYGG+V++Y
Sbjct: 79  RLSPDAKKRGVVAFSSGNHAQAIAYAGQLQEVPTVIIMPQDAPAMKVAATKGYGGEVVLY 138

Query: 127 DRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGG 186
           DRYK+DRE + +++S+  GLT+IPPYDH  V+AGQGTA KEL EEVGPLD L VC+GGGG
Sbjct: 139 DRYKEDREAIGRKLSQERGLTLIPPYDHEDVIAGQGTATKELIEEVGPLDMLLVCVGGGG 198

Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246
           LL+GSALA++  +P+C +YGVEPEAGND QQSFR GSIV I  P TIADGAQT ++GN T
Sbjct: 199 LLAGSALASKALSPDCRIYGVEPEAGNDAQQSFRTGSIVKIPVPTTIADGAQTTYVGNKT 258

Query: 247 FSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGII 306
           F I++   DDILTVSD +L+D ++F+  RMKIVVEPTGCL+ AAA       K+KR+GII
Sbjct: 259 FPIMRAFADDILTVSDTQLVDTMRFFVERMKIVVEPTGCLAAAAALHGIVPCKDKRVGII 318

Query: 307 ISGGNVDIERYAHFLS 322
           ISGGNVD    A FL+
Sbjct: 319 ISGGNVDPRALAGFLA 334


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: 330
Number of extensions: 5
Number of successful extensions: 1
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: 335
Length adjustment: 28
Effective length of query: 295
Effective length of database: 307
Effective search space:    90565
Effective search space used:    90565
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: 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