GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Planktomarina temperata RCA23

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_044051092.1 RCA23_RS15620 threonine ammonia-lyase IlvA

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_000738435.1:WP_044051092.1
          Length = 411

 Score =  152 bits (384), Expect = 1e-41
 Identities = 94/311 (30%), Positives = 160/311 (51%), Gaps = 8/311 (2%)

Query: 11  DDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNE 70
           +  A A+ER+++    TP+  +  ++  + A+++ K E+   + ++K RGA NA+ +  +
Sbjct: 6   NQAAEATERMRQLFPATPLQRNDHLSNVYDADIWLKREDLSPVRSYKLRGAFNAMGK--Q 63

Query: 71  AQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGG---QVIMYD 127
           A +   V   S+GNHAQ +A   + L     I MP+  PE K+  T+ +GG   QV +  
Sbjct: 64  ADKDVFVCA-SAGNHAQGVAYVCRHLQKKGVIFMPVTTPEQKIRKTRLFGGAWVQVQLVG 122

Query: 128 RYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVC-LGGGG 186
            Y DD  + ++      G   + P+D P V+ GQ T   E+ E++G    +FV  +GGGG
Sbjct: 123 DYFDDTLRASQAYCAEVGGHFLSPFDDPDVIEGQATVTYEMLEQLGRSPDVFVVPVGGGG 182

Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246
           L S +       AP  E++ VEP  G     + + G+ + ++   T  DGA    +G  T
Sbjct: 183 LSSSARRLLSERAPETEIFYVEPSGGKSLAAAVQAGAPIALEQVDTFVDGAAVAKMGVNT 242

Query: 247 FSIIKE-KVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGI 305
           F+ +K    D +L + ++ +   +        IV+EP G L+  A + +K+K+K K +  
Sbjct: 243 FAALKGIDADHVLDIPEDRICTTILDMLNTEGIVLEPAGALALDALKDLKDKIKGKTVVC 302

Query: 306 IISGGNVDIER 316
           + SGGN D ER
Sbjct: 303 VSSGGNFDFER 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: 287
Number of extensions: 21
Number of successful extensions: 6
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: 411
Length adjustment: 29
Effective length of query: 294
Effective length of database: 382
Effective search space:   112308
Effective search space used:   112308
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