GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2930
          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:

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