GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuC in Pseudomonas simiae WCS417

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF2930 PS417_14990 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= curated2:B2V844
         (431 letters)



>lcl|FitnessBrowser__WCS417:GFF2930 PS417_14990 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 869

 Score =  101 bits (251), Expect = 1e-25
 Identities = 127/474 (26%), Positives = 195/474 (41%), Gaps = 75/474 (15%)

Query: 2   GMTITEKIIAAHAGRDY---VEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPN 58
           G T+ +K++    G      V PG     K+    + D T P+   +L+    D      
Sbjct: 381 GFTLAQKMVGKACGLPEGKGVRPGTYCEPKMTTVGSQDTTGPMTRDELK----DLACLGF 436

Query: 59  KIALVMDHF-----FP-PKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGF 112
              LVM  F     +P P D+ +   +    DF    G  +   G   G++H+ L     
Sbjct: 437 STDLVMQSFCHTAAYPKPIDVTTHHTLP---DFIMTRGGVSLRPGD--GIIHSWLNR--M 489

Query: 113 VVPGDLVIGADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKW 172
           ++P  +  G DSHT    GI   S   GS  +A+  ATG   L +PES+   F  K +  
Sbjct: 490 LLPDTVGTGGDSHTRFPMGI---SFPAGSGLVAFAAATGVMPLDMPESILVRFKGKMKPG 546

Query: 173 VGGKDFV-----------LTVIGKIGVDGALY-KAMEYQGEAIRALDIDNRLTIANMAIE 220
           +  +D V           L  + K G   A   + +E +G     L+    L+ A+    
Sbjct: 547 ITLRDLVHAIPYYAIQSGLLTVEKKGKKNAFSGRILEIEGLNDLTLEQAFELSDASAERS 606

Query: 221 AGG------KSGIIE-----------------PDEKTVD--------WVRKRTNREFKLY 249
           A G      K  I E                  D +T++        WV+       +L 
Sbjct: 607 AAGCTIKLSKESITEYLNSNITLLRWMIGEGYGDPRTLERRAQAMEAWVKNP-----ELM 661

Query: 250 KSDPDAKYCCEYEFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDL 308
           ++D DA+Y    E D ++I EP++  P+ P + + +S VAG  ID+VFIGSC    +   
Sbjct: 662 EADADAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMT-NIGHF 720

Query: 309 RIAAAILKSKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHM 368
           R A  +L+  K     R  + P +     Q   EG   I   AG  +    C  C+G   
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780

Query: 369 GILAEGEVCLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKY 422
            +     V +STS RNF  R+G   + VYL+S  +AA ++ LGR+   +E   Y
Sbjct: 781 RVEPNSTV-VSTSTRNFPNRLG-DGANVYLASAELAAVASTLGRLPTVEEYMGY 832


Lambda     K      H
   0.319    0.137    0.407 

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: 852
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 431
Length of database: 869
Length adjustment: 37
Effective length of query: 394
Effective length of database: 832
Effective search space:   327808
Effective search space used:   327808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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