GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Pseudomonas fluorescens FW300-N2E3

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate AO353_06495 AO353_06495 gamma-glutamyl phosphate reductase

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



>FitnessBrowser__pseudo3_N2E3:AO353_06495
          Length = 423

 Score =  273 bits (698), Expect = 1e-77
 Identities = 151/404 (37%), Positives = 240/404 (59%), Gaps = 6/404 (1%)

Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360
           AAR++SR +   S+  + + LL  ADAL+     + A NELD+A+ +  GLE +M+ RL 
Sbjct: 15  AARDASRVIGRASTAQKNRALLAAADALDNARAELTAANELDLAAGRANGLEPAMLERLA 74

Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420
           +TP +I  +   +R++A + DP+G +   +    G+ + K   PLGV+ I++ESRP+  +
Sbjct: 75  LTPARIDGMIVGLRQVAALPDPVGAIRDMSYRPSGIQVGKMRVPLGVVGIIYESRPNVTI 134

Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDL 477
             ASL ++SGN  +L+GG EA  SN  +   I   + E  +   ++ +V  T R  +  L
Sbjct: 135 DAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEAGLPAAVVQVVETTDRAAVGAL 194

Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537
           + + + +D+++PRG   L+ ++    ++PV+ H DGICHVYV    +   A+RI  +AK 
Sbjct: 195 ITMPEYVDVIVPRGGKGLIERVSRDARVPVIKHLDGICHVYVSAHAELPKAQRIAFNAKT 254

Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595
                C AMETLLV + + +   L  +    +  GV L G  R   I+++  A    ++ 
Sbjct: 255 YRYGICGAMETLLVDQAVAKQ-FLPAMAEQFREKGVELRGCERTRAIIDVVAATEEDWST 313

Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655
           EY A   ++ VV+ +  AI+HI+ +GS HTD IV+E    A  F+ +VDSA+V  N  T 
Sbjct: 314 EYLAPILSILVVDGLDQAIEHINHYGSHHTDSIVSEHQGEARRFVAEVDSASVMINTPTC 373

Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699
           F+DGF +GLGAE+G+ST ++HARGPVG+EGL   ++I+ G GQ+
Sbjct: 374 FADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYIVVGDGQL 417


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: 607
Number of extensions: 19
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: 423
Length adjustment: 36
Effective length of query: 681
Effective length of database: 387
Effective search space:   263547
Effective search space used:   263547
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: 53 (25.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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