GapMind for Amino acid biosynthesis

 

Aligments for a candidate for proB in Marinobacter adhaerens HP15

Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate GFF618 HP15_601 gamma-glutamyl phosphate reductase

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



>lcl|FitnessBrowser__Marino:GFF618 HP15_601 gamma-glutamyl phosphate
           reductase
          Length = 418

 Score =  275 bits (702), Expect = 4e-78
 Identities = 148/404 (36%), Positives = 240/404 (59%), Gaps = 7/404 (1%)

Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361
           AR ++  +   ++  R + LL  A+AL+A    +   N  D+   +E GL+ +M+ RL +
Sbjct: 14  ARAAATGVARSTTAVRNQALLATAEALDAAREELALANGKDLQMGRENGLDAAMLDRLEL 73

Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421
           TP +I ++   +R++A + DPIG +        G+ + K   PLGV+ I++ESRP+  V+
Sbjct: 74  TPQRIDTMIEGLRQVASLPDPIGAITDMNYRPSGIQVGKMRVPLGVIGIIYESRPNVTVE 133

Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET---VGGKLIGLVTSREEIPDLL 478
            ASL ++SGN  +L+GG E+  SN  + + ++  + +         +   T R  + +L+
Sbjct: 134 AASLCLKSGNATILRGGSESIHSNQAIARCLSAGLAKAGLPENAVQVIKTTDRAAVGELI 193

Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538
            + D +D+++PRG   L+ +I    ++PV+ H DG+CHVY+D   D + A ++  +AK  
Sbjct: 194 TMPDYVDVIVPRGGKGLIERISRDARVPVIKHLDGVCHVYIDSHADPEKALKVAINAKTH 253

Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-IPEARS--FNH 595
               CN METLLV  ++ ++ +L  L  A    GV L G  R   I+  + EA    +  
Sbjct: 254 RYGTCNTMETLLVDAEIAED-ILPLLAQAFVEKGVELRGCERTRAIVEGVVEATEADWEA 312

Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655
           EY A    V VV+ + GAI HI+R+ S HTD I+TE++  A  F+ +VDS++V  NASTR
Sbjct: 313 EYLAPVLAVRVVDGLEGAIAHINRYSSQHTDSIITENYTRARRFITEVDSSSVMVNASTR 372

Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699
           F+DGF +GLGAE+G+ST +IHARGPVG+EGL + ++++ G G +
Sbjct: 373 FADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKYVVFGDGHI 416


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: 602
Number of extensions: 21
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: 418
Length adjustment: 36
Effective length of query: 681
Effective length of database: 382
Effective search space:   260142
Effective search space used:   260142
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.

Links

Downloads

Related tools

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