GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Pedobacter sp. GW460-11-11-14-LB5

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase

Query= BRENDA::O59791
         (323 letters)



>FitnessBrowser__Pedo557:CA265_RS15860
          Length = 416

 Score =  175 bits (444), Expect = 2e-48
 Identities = 105/316 (33%), Positives = 164/316 (51%), Gaps = 3/316 (0%)

Query: 4   NLVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALN 63
           N   P   D  SAS+R+K    +TP+  ++ ++  + A ++ K E+ Q + ++K RGA N
Sbjct: 2   NTTTPNTLDFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYN 61

Query: 64  ALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGG-- 121
            +S L +     GV+  S+GNHAQ +A S K LGI   I MP   P+ KV  T  +GG  
Sbjct: 62  KISSLPQDALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDN 121

Query: 122 -QVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFV 180
            +V++     DD  K A   S  +  T IPP+D   V+ GQ T   E++E++  LD + +
Sbjct: 122 VEVVLVGDTFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIVM 181

Query: 181 CLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQ 240
            +GGGGL SG +   +   P  ++ GVEP        +   G    ++      DGA  +
Sbjct: 182 PVGGGGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVK 241

Query: 241 HLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKN 300
            +G+ T+   KE +D +  + + ++   +        IVVEP G LS AA   +K+++  
Sbjct: 242 RIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITG 301

Query: 301 KRIGIIISGGNVDIER 316
           K +  I+SGGN DIER
Sbjct: 302 KTVVCIVSGGNNDIER 317


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: 300
Number of extensions: 18
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: 416
Length adjustment: 30
Effective length of query: 293
Effective length of database: 386
Effective search space:   113098
Effective search space used:   113098
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 17 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