GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Psychrobacter cryohalolentis K5

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme

Query= BRENDA::Q2PGG3
         (331 letters)



>NCBI__GCF_000013905.1:WP_011513321.1
          Length = 326

 Score =  300 bits (769), Expect = 2e-86
 Identities = 159/311 (51%), Positives = 204/311 (65%), Gaps = 9/311 (2%)

Query: 17  EAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQAA 76
           EAH+RIKPYIHRTPVLTS  LN ++G  +FFKCE  QK GAFK RGA NAV  L  E A 
Sbjct: 18  EAHERIKPYIHRTPVLTSRFLNELAGCEMFFKCENFQKAGAFKVRGASNAVFGLSDEDAK 77

Query: 77  KGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSSRE 136
            GV THSSGNHA +LS AA  +GIP  +V+P  AP+ K   V  YGG +   E + +SRE
Sbjct: 78  NGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITECEPSTTSRE 137

Query: 137 EIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEI----DAIVVPISGGGLISG 192
           E+ +KV  ETG   +HPYND R+I+GQ T + E LEQ++EI    D +V PI GGG+ISG
Sbjct: 138 EVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAPIGGGGMISG 197

Query: 193 VALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPVVR 252
             L   ++ P ++I AAEP  ADDAA+S  AG II     NT+ADGL+  L DLTW  V 
Sbjct: 198 TCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHIIADDAPNTVADGLKVPLKDLTWHFVS 257

Query: 253 DLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIGIV 312
           + V D++T  E EI+EAMK+ +  +K+ +EPS A+ LA +L N           K +G++
Sbjct: 258 NYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILKNK-----DVFAGKKVGVI 312

Query: 313 LSGGNVDLGSL 323
           ++GGNVDL  L
Sbjct: 313 ITGGNVDLDKL 323


Lambda     K      H
   0.316    0.133    0.380 

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: 320
Number of extensions: 16
Number of successful extensions: 3
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: 331
Length of database: 326
Length adjustment: 28
Effective length of query: 303
Effective length of database: 298
Effective search space:    90294
Effective search space used:    90294
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 (21.6 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