GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuC in Pseudomonas putida KT2440

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate PP_2112 PP_2112 aconitate hydratase 1

Query= curated2:Q9WYC7
         (418 letters)



>lcl|FitnessBrowser__Putida:PP_2112 PP_2112 aconitate hydratase 1
          Length = 913

 Score = 94.4 bits (233), Expect = 1e-23
 Identities = 78/247 (31%), Positives = 109/247 (44%), Gaps = 43/247 (17%)

Query: 25  LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHASP-----SPRKELSNSQKM 79
           LA +  AMA+ G  P  IN    +           L IDH+       +P+    N    
Sbjct: 100 LAAMRAAMAKAGGDPQRINPLSPVD----------LVIDHSVMVDRYGTPQAFAENVDIE 149

Query: 80  MREFGKEM-----GVKVFD------AGDGISHQILAE--------------KYVKPGDLV 114
           M+  G+       G   FD       G GI HQ+  E               Y  P  LV
Sbjct: 150 MQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQVNLEYLGRTVWTREADGRTYAFPDTLV 209

Query: 115 AGADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDI 173
            G DSHT    GLG  G G+G  +      LGQ     +PE I   + GKL++G+ A D+
Sbjct: 210 -GTDSHTTMINGLGVLGWGVGGIEAEAAM-LGQPVSMLIPEVIGFKLTGKLREGITATDL 267

Query: 174 ILEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFL 233
           +L + ++L   G   K +EF+G  +  + + DR TI+NMA E GA  G  P D+ T ++L
Sbjct: 268 VLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFPVDQVTLDYL 327

Query: 234 KKMGREE 240
           +  GR E
Sbjct: 328 RLSGRPE 334



 Score = 35.4 bits (80), Expect = 7e-06
 Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 13/116 (11%)

Query: 308 IALKILEKH-GKHPDVRLIVGPASRKVYMDALEKGIIKKFVELGAAVIPPGCGPCVGIHM 366
           +A K LEK   + P V+  + P S+ V       G+     +LG  ++  GC  C+G + 
Sbjct: 469 VAKKALEKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIG-NS 527

Query: 367 GVLGDG-ERVLSTQ----------NRNFKGRMGNPNAEIYLASPATAAATAVTGYI 411
           G L +  E+ + +           NRNF+GR+       +LASP    A A+ G +
Sbjct: 528 GPLDEAIEKAIGSADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSV 583


Lambda     K      H
   0.318    0.137    0.395 

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: 820
Number of extensions: 44
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 418
Length of database: 913
Length adjustment: 37
Effective length of query: 381
Effective length of database: 876
Effective search space:   333756
Effective search space used:   333756
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.

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