GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Psychrobacter cryohalolentis K5

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q54HH2
         (324 letters)



>NCBI__GCF_000013905.1:WP_011513321.1
          Length = 326

 Score =  302 bits (773), Expect = 8e-87
 Identities = 154/316 (48%), Positives = 210/316 (66%), Gaps = 8/316 (2%)

Query: 8   TLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSL 67
           TL D+ EAH+RI+ YIH+TPVLT+  +NELAG E++FKCEN QK G+FK+RGA NA+F L
Sbjct: 12  TLDDMLEAHERIKPYIHRTPVLTSRFLNELAGCEMFFKCENFQKAGAFKVRGASNAVFGL 71

Query: 68  DEEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCKA 127
            +E+   GV THSSGNH  +LSYA+  R + C VV+P  AP  K  A+ GYG  +T+C+ 
Sbjct: 72  SDEDAKNGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITECEP 131

Query: 128 TLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENL----DAIITPVGG 183
           +  +RE    ++  +     +HP+++ +VIAGQ T S E +EQ+E +    D ++ P+GG
Sbjct: 132 STTSREEVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAPIGG 191

Query: 184 GGLLSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTVG 243
           GG++SGTC+T  +L P++K++AAEPL ADD  RS  +G I       PNT+ADGL   + 
Sbjct: 192 GGMISGTCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHI--IADDAPNTVADGLKVPLK 249

Query: 244 SLTFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIK 303
            LT+  +      ++  TE+EI  AMKL W  MKIIIEPS A  LA ILK   KD    K
Sbjct: 250 DLTWHFVSNYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILKN--KDVFAGK 307

Query: 304 KVGIIISGGNVDLSSI 319
           KVG+II+GGNVDL  +
Sbjct: 308 KVGVIITGGNVDLDKL 323


Lambda     K      H
   0.315    0.132    0.374 

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: 329
Number of extensions: 14
Number of successful extensions: 4
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: 324
Length of database: 326
Length adjustment: 28
Effective length of query: 296
Effective length of database: 298
Effective search space:    88208
Effective search space used:    88208
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 (21.5 bits)
S2: 48 (23.1 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