GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Caulobacter crescentus NA1000

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate CCNA_02230 CCNA_02230 gluconate 2-dehydrogenase

Query= BRENDA::O58256
         (333 letters)



>FitnessBrowser__Caulo:CCNA_02230
          Length = 319

 Score =  131 bits (329), Expect = 3e-35
 Identities = 88/262 (33%), Positives = 139/262 (53%), Gaps = 16/262 (6%)

Query: 54  ITREVLENAERLKVISCHSAGYDNIDLEEATKRGIYVTKVSGLLSEAVAEFTVGLIINLM 113
           ++R++L    RL +I+C S GYD +D+      GI VT  +GL +  VA+  VGL++   
Sbjct: 62  LSRDMLAEMPRLGLIACVSVGYDGVDVPWCKAHGIAVTHSTGLNAADVADHAVGLVLAAW 121

Query: 114 RKIHYADKFIRRGEWESHAKIWTGFKRIESLYGKKVGILGMGAIGKAIARRLIPFGVKLY 173
           R I   D+ +R G W SHA+          L G+K G++G+G IG+A+A RL  F +K+ 
Sbjct: 122 RGIVEGDQRLRGGHW-SHAE---RMAPRPGLRGRKAGVVGLGHIGEAVAARLKAFDMKVA 177

Query: 174 YWSRHRKVNVEKELKARYMDIDELL---EKSDIVILALPLTRDTYHIINEERVKKLEGK- 229
           +W+   K       +  Y   D L+     SD++I+         H+IN+  ++ +  + 
Sbjct: 178 WWAPRPK-------ETDYPRADSLMALARDSDVLIVCARPDDSNRHLINKPVIEAVGAQG 230

Query: 230 YLVNIGRGALVDEKAVTEAIKQGKLKGYATDVFEKEPVREHELFKYEWETVLTPHYAGLA 289
            +VN+ RG+L+DE A+ +A++ G L   A DVFE+EP            TVLTPH AG  
Sbjct: 231 LIVNVARGSLIDEDALIQALRAGTLGMAALDVFEQEPTPAARWADVP-RTVLTPHTAGAT 289

Query: 290 LEAQEDVGFRAVENLLKVLRGE 311
           L++   +    +ENL +   GE
Sbjct: 290 LDSLPAMVSLTLENLRRYFHGE 311


Lambda     K      H
   0.319    0.139    0.393 

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: 242
Number of extensions: 13
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: 333
Length of database: 319
Length adjustment: 28
Effective length of query: 305
Effective length of database: 291
Effective search space:    88755
Effective search space used:    88755
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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