GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Azospirillum brasilense Sp245

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate AZOBR_RS04075 AZOBR_RS04075 gamma-glutamyl phosphate reductase

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



>FitnessBrowser__azobra:AZOBR_RS04075
          Length = 426

 Score =  273 bits (699), Expect = 1e-77
 Identities = 155/408 (37%), Positives = 238/408 (58%), Gaps = 15/408 (3%)

Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360
           AAR ++ +L  + S  + + L   A A+ A    I+A N+ DVA+A++ GL   M+ RL 
Sbjct: 21  AARAAAAELATVPSPSKDQALRAAAAAIRARKAEIQAANDADVAAAKDRGLAGPMIERLA 80

Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420
           +   +I ++A  +  +AD  DPIG V+ +    +GL +++   PLGV+ I++ESRP+   
Sbjct: 81  LNDARIEAMAKGLEDIADFPDPIGGVIAEWTRPNGLAIQRVRVPLGVIGIIYESRPNVTA 140

Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAI-----PETVGGKLIGLV--TSREE 473
               L ++SGN  +L+GG E+ RS+  +   + D +     PE      I LV  T R  
Sbjct: 141 DAGGLCLKSGNAAILRGGSESIRSSHAIAACLADGLRAAGLPEAA----IQLVPTTDRAA 196

Query: 474 IPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533
           +  +L + D ID+++PRG   L+ +I   ++IPV+ H DG   VYVD   D + A+++V 
Sbjct: 197 VGHMLTMRDFIDVIVPRGGKSLIQRIAEESRIPVIKHLDGNNTVYVDAGADPEKARKVVM 256

Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKI---LNIPEA 590
           +AK+   + C A ETLLV + +  +A+L  L+  L   G  + G   A  +   +    A
Sbjct: 257 NAKMRRTSICGAAETLLVDRKIA-DAMLPVLVKDLLDAGCAVRGDAAAQAVDPRVTAVTA 315

Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650
             ++ E+        VV+ V GAIDHI+RHGS HTD IVTED   AE FL+++DS  V  
Sbjct: 316 EDWDTEFLDAIIACGVVDGVDGAIDHINRHGSHHTDAIVTEDPAAAERFLQRIDSGIVLW 375

Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698
           NAST+F+DG  FG+GAE+G+ST + HARGPVG E L + ++++RG GQ
Sbjct: 376 NASTQFADGGEFGMGAEIGISTDKFHARGPVGAEQLTSYKYVVRGDGQ 423


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: 621
Number of extensions: 23
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: 426
Length adjustment: 36
Effective length of query: 681
Effective length of database: 390
Effective search space:   265590
Effective search space used:   265590
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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