GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Pseudomonas fluorescens FW300-N2E2

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Pf6N2E2_627 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43)

Query= BRENDA::P9WNX3
         (528 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_627
          Length = 325

 Score =  201 bits (511), Expect = 3e-56
 Identities = 122/321 (38%), Positives = 182/321 (56%), Gaps = 9/321 (2%)

Query: 6   VLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLA---AVPEADALLVRSATTVDAEVLAA 62
           V++   L+   +A L  Q +V  ++  D   L+    A+P A  LL  S   +DA +L  
Sbjct: 5   VVLYKALSAQLMARLQAQAQVTLIERLDAQGLVQLREALPSAHGLLGASLK-LDAPLLDL 63

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

Query: 123 SLREHTWKRS---SFSGTEIFGKTVGVVGLGRIGQLVAQR-IAAFGAYVVAYDPYVSPAR 178
            +R   W++S      GT++ GKT+G++G+GRIG+ +AQR    FG  V+ +     PA 
Sbjct: 124 LVRSGGWQQSIGPRHFGTDVHGKTLGIIGMGRIGEALAQRGHFGFGMQVIYHSHSPKPAV 183

Query: 179 AAQLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDE 238
             +      SL+ LL +ADF+ + LP T ET GLID +A A+ +P  I +N +RG +VDE
Sbjct: 184 EQRFNARYCSLETLLQQADFVCLTLPLTAETQGLIDAQAFARMRPESIFINISRGKVVDE 243

Query: 239 AALADAITGGHVRAAGLDVFATEPCT-DSPLFELAQVVVTPHLGASTAEAQDRAGTDVAE 297
            AL DA+  G +R AGLDVF  EP + DSPL +L  VV TPH+G++T E ++       +
Sbjct: 244 TALIDALRNGQIRGAGLDVFEREPLSADSPLLQLDNVVATPHMGSATHETREAMARCAVD 303

Query: 298 SVRLALAGEFVPDAVNVGGGV 318
           ++  ALAGE   + VN G  V
Sbjct: 304 NLLAALAGERPVNLVNAGAWV 324


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: 372
Number of extensions: 18
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: 528
Length of database: 325
Length adjustment: 31
Effective length of query: 497
Effective length of database: 294
Effective search space:   146118
Effective search space used:   146118
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