GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Pseudomonas fluorescens GW456-L13

Align Phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate PfGW456L13_4494 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Query= reanno::SB2B:6938941
         (308 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4494
          Length = 310

 Score =  177 bits (449), Expect = 3e-49
 Identities = 103/311 (33%), Positives = 168/311 (54%), Gaps = 8/311 (2%)

Query: 4   KLLLLTRENERYRSLLASCHLPELELL---DDNPANIRLAD--IWLAEPGLAAPLVNHAS 58
           ++L+   ++  Y  LL     P+LE+L   D      + AD  +WL +P L A L+    
Sbjct: 2   RVLIAEHDHPVYAQLLREA-APDLEVLTSGDSAELASQAADCPVWLGQPDLLATLLRQGH 60

Query: 59  GLRWMQSTFAGVDLLVKPRQRRDYLLTNVRGIFGPLMSEYLFGYLLARQREHDLYKSQQQ 118
             +W+QST+AG+  L+     R Y LT   GIFG +M+EY+  Y+L  +RE       Q 
Sbjct: 61  QPQWLQSTWAGITPLLADGLPRHYRLTRAVGIFGQVMAEYVLTYMLGHEREVLARLVSQV 120

Query: 119 QKLWLPGSYKTLQGSELLLLGTGSIAKHLAQTAKHFGMKVAGINRSAKATEGFDEVATLE 178
           ++ W     ++L G  +L++GTG I + +AQ    FG+++ G+  SA+    F EV ++ 
Sbjct: 121 ERKWESRQVQSLAGRRVLIVGTGDIGQSVAQFLVPFGVELYGVASSAREQAPFIEVGSMA 180

Query: 179 ALPTLMARADAIASILPSTEATRGILNENILARMKPDAVLFNLGRG-DVLDLDALERQLR 237
            LP L+   D + ++LP+T  T  + +  +  + KP  +  N GRG  V+D D ++  L+
Sbjct: 181 DLPRLVGEVDYVVNLLPNTPDTHDVYDAALFKQFKPTGLFINAGRGVAVVDADLVDA-LK 239

Query: 238 QHPQQQAVLDVFNQEPLPEDHPIWGLGNVIVTPHIAAPSFPEQVAEIFSSNYHKFLLGET 297
           +     AV+DV  QEPLP+ HP W    +++T H +AP+ P  + ++F  N   +  GE 
Sbjct: 240 EGHLAGAVIDVCRQEPLPQRHPFWTAWGLLLTGHSSAPTSPSMMVKLFVENLRAYEAGEA 299

Query: 298 LSHRVNFERGY 308
           L   V+F+RGY
Sbjct: 300 LRGEVDFDRGY 310


Lambda     K      H
   0.320    0.137    0.404 

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: 259
Number of extensions: 15
Number of successful extensions: 1
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: 308
Length of database: 310
Length adjustment: 27
Effective length of query: 281
Effective length of database: 283
Effective search space:    79523
Effective search space used:    79523
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 (21.8 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