GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Burkholderia phytofirmans PsJN

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate BPHYT_RS16770 BPHYT_RS16770 gamma-glutamyl phosphate reductase

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



>FitnessBrowser__BFirm:BPHYT_RS16770
          Length = 423

 Score =  270 bits (691), Expect = 8e-77
 Identities = 150/418 (35%), Positives = 241/418 (57%), Gaps = 12/418 (2%)

Query: 292 DSNARDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGL 351
           D    D+   AR++SR +   S+  +   L  +A  +E +   +K  N  DVA A+E G 
Sbjct: 4   DQYMTDLGRRARQASRAMARASTAAKNAALAAVAQGIERDAALLKEANARDVARAREKGH 63

Query: 352 EESMVARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIV 411
           + + + RL ++   + ++   +R++A + DPIG +        G+ + +   PLGV+ I+
Sbjct: 64  DAAFIDRLTLSDKALKTMVEGLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGII 123

Query: 412 FESRPDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLVTS 470
           +ESRP+  +  A+L ++SGN  +L+GG EA   NA L K+I + + +  +  + + +V +
Sbjct: 124 YESRPNVTIDAAALCLKSGNATILRGGSEALECNAALAKLIGEGLEKAGLPQEAVQVVAT 183

Query: 471 --REEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMA 528
             R  +  L+ + + +D+++PRG   L+ ++ N  ++P++ H DGICHVYVD   D   A
Sbjct: 184 SDRAAVGKLITMTEYVDVIVPRGGKSLIERLMNEARVPMIKHLDGICHVYVDDRADLAKA 243

Query: 529 KRIVSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-- 586
             +  +AK      CN METLLV + +    VL  L    +   V L     A  +L   
Sbjct: 244 LTVCDNAKTHRYGTCNTMETLLVARGIAAE-VLPPLGKLYRDKQVELRVDAAARAVLADA 302

Query: 587 ----IPEA--RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFL 640
               + +A    +  EY A    ++VVE++  AIDHI+ + S HTD IVTEDH+ A  FL
Sbjct: 303 GVGPLVDATEEDWRTEYLAPVLAIKVVENLDAAIDHINTYSSQHTDAIVTEDHDRAMRFL 362

Query: 641 RQVDSAAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698
           R+VDSA+V  NASTRF+DGF FGLGAE+G+S  ++HARGPVG+EGL + ++++ G G+
Sbjct: 363 REVDSASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLKYVVLGHGE 420


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: 598
Number of extensions: 31
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:

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