GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proB in Acidovorax sp. GW101-3H11

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Ac3H11_704 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_704
          Length = 426

 Score =  274 bits (701), Expect = 6e-78
 Identities = 154/413 (37%), Positives = 243/413 (58%), Gaps = 12/413 (2%)

Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357
           + + A+ +S  +    +  + K L  +A  L  NV  ++ +N  D+  A+ AGL E MV 
Sbjct: 13  LGLQAKTASALMAKAPAAIKNKALKALARLLRENVDALQIDNARDLERARAAGLAEPMVD 72

Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417
           RL ++P  + + A    +LA M D IG +L   +   G+ + +   P+GV  +++ESRP+
Sbjct: 73  RLKLSPKVLETCAEGCEQLAAMPDIIGEILGMKQQPSGIRVGQMRVPIGVFGMIYESRPN 132

Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474
             ++ ASL+I+SGN  +L+GG EA  SN  L K++  A+ E  +    + LV  T RE +
Sbjct: 133 VTIEAASLSIKSGNACILRGGSEAIDSNKALAKLVQQALAEAGLPQDAVQLVQTTDREAV 192

Query: 475 PDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSD 534
             L+ +   +D++IPRG   L+ +I    K+PV+ H DG CH YVD  CD  MA ++  +
Sbjct: 193 GQLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHTYVDDPCDVPMAVKVADN 252

Query: 535 AKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-------I 587
           AK +  + CNA E LLV + +     L ++     + GV + G P +  IL        +
Sbjct: 253 AKTNKYSPCNASEGLLVARGVAAE-FLPKIGAVYAAKGVEMRGCPESLAILQSVAGAQLV 311

Query: 588 PEA-RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSA 646
           P   + ++ EY A   +V++V  +  AI HI+ + S HTD I+T +H  A+ FLR+VDSA
Sbjct: 312 PATEQDWSEEYLAPIISVKIVAGLDEAIAHINHYSSHHTDAILTTNHVHAQRFLREVDSA 371

Query: 647 AVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699
           +V  NASTRF+DGF +GLGAE+G+ST + HARGPVG+EGL + ++++ G+G+V
Sbjct: 372 SVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLKYVVLGEGEV 424


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: 586
Number of extensions: 24
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 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