GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Pseudomonas putida KT2440

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PP_3376 PP_3376 putative phosphonate dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>FitnessBrowser__Putida:PP_3376
          Length = 320

 Score =  198 bits (504), Expect = 2e-55
 Identities = 120/316 (37%), Positives = 184/316 (58%), Gaps = 9/316 (2%)

Query: 6   VLIADKLAPSTVAALGDQVEVRWVDGPDRD---KLLAAVPEADALLVRSATTVDAEVLAA 62
           +++  +L+   +A L D+VEV WVD    D   +L  A+P A  LL  S   +DA +L  
Sbjct: 5   IVLYKRLSDDLMARLQDRVEVTWVDTTQPDALARLRDALPGAHGLLGASLR-LDASLLDL 63

Query: 63  APKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAADA 122
           AP+L++V+   VG+DN D+   + RGV++ N P     + A+   AL+LA +R++     
Sbjct: 64  APQLEVVSSVSVGVDNYDIAELSRRGVMLTNTPDVLTETTADTGFALILATARRVVELAN 123

Query: 123 SLREHTWKRS---SFSGTEIFGKTVGVVGLGRIGQLVAQRIAA-FGAYVVAYDPYVSPAR 178
            +R+  W+ +   +  G+++ GKT+G+VG+GRIG+ +A+R AA FG  V+ +     P  
Sbjct: 124 WVRDGRWQANLGPAHFGSDVHGKTLGIVGMGRIGEALARRAAAGFGMRVLYHSQRAKPEV 183

Query: 179 AAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDE 238
            A+      SLD+LL +ADF+ + +P +  T GLI    LA  KP  I+VN +RG +VDE
Sbjct: 184 EARYAACQCSLDELLQQADFVCLTVPLSASTEGLIGARELALMKPDAILVNISRGRVVDE 243

Query: 239 AALADAITGGHVRAAGLDVFATEPC-TDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAE 297
            AL +A+    +R AGLDVF  EP   DSPL +L  VV TPH+G++T E +        +
Sbjct: 244 QALIEALRARRIRGAGLDVFVHEPLPIDSPLLQLDNVVATPHIGSATEETRQAMARCAVD 303

Query: 298 SVRLALAGEFVPDAVN 313
           ++  ALAGE   + VN
Sbjct: 304 NLLSALAGERPVNLVN 319


Lambda     K      H
   0.317    0.133    0.370 

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: 351
Number of extensions: 19
Number of successful extensions: 5
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: 528
Length of database: 320
Length adjustment: 31
Effective length of query: 497
Effective length of database: 289
Effective search space:   143633
Effective search space used:   143633
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: 50 (23.9 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