GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Marino:GFF618
          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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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:

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