GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Pseudomonas fluorescens FW300-N1B4

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Pf1N1B4_2688 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)

Query= metacyc::AT2G39800-MONOMER
         (717 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688
          Length = 415

 Score =  272 bits (695), Expect = 3e-77
 Identities = 150/404 (37%), Positives = 241/404 (59%), Gaps = 6/404 (1%)

Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360
           AARE+SR +   S+  + + L   A+AL+A    + A NELD+A+ +  GLE +++ RL 
Sbjct: 7   AAREASRVIGRASTAQKNRALQAAANALDAARAELTAANELDLAAGRANGLEPALLERLA 66

Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420
           +TP +I  +   +R++A + DP+G +   +    G+ + K   PLGV+ I++ESRP+  +
Sbjct: 67  LTPERIDGMIVGLRQVAALPDPVGAIRDMSYRPSGIQVGKMRVPLGVIGIIYESRPNVTI 126

Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDL 477
             ASL ++SGN  +L+GG EA  SN  +   I   + E  +   ++ +V  T R  +  L
Sbjct: 127 DAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEAGLPAAVVQVVETTDRAAVGAL 186

Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537
           + + + +D+++PRG   L+ ++    ++PV+ H DGICHVYV    D   A+RI  +AK 
Sbjct: 187 ITMPEYVDVIVPRGGRGLIERVSRDARVPVIKHLDGICHVYVSAHADLPKAQRIAFNAKT 246

Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595
                C AMETLLV + + ++  L  +   L+  GV L G  R   I+    A    ++ 
Sbjct: 247 YRYGICGAMETLLVDQAVAKD-FLPSMAAQLREKGVELRGCERTRAIIEAVAATEEDWHT 305

Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655
           EY A   ++ VV+ +  AI+HI+++GS HTD IV+E+      F+ +VDS++V  N  T 
Sbjct: 306 EYLAPILSIRVVDGLDQAIEHINKYGSHHTDSIVSENLADTRRFVAEVDSSSVMINTPTC 365

Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699
           F+DGF +GLGAE+G+ST ++HARGPVG+EGL   ++I+ G GQ+
Sbjct: 366 FADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYIVVGDGQL 409


Lambda     K      H
   0.318    0.135    0.378 

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: 600
Number of extensions: 22
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: 717
Length of database: 415
Length adjustment: 35
Effective length of query: 682
Effective length of database: 380
Effective search space:   259160
Effective search space used:   259160
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 (21.7 bits)
S2: 52 (24.6 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