GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuC in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF2264 Psest_2309 aconitate hydratase 2

Query= curated2:B2V844
         (431 letters)



>lcl|FitnessBrowser__psRCH2:GFF2264 Psest_2309 aconitate hydratase 2
          Length = 875

 Score =  102 bits (253), Expect = 6e-26
 Identities = 115/470 (24%), Positives = 192/470 (40%), Gaps = 67/470 (14%)

Query: 2   GMTITEKIIAAHAGRDY---VEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPN 58
           G T+ +K++    G      V PG     K+    + D T P+   +L+    D      
Sbjct: 387 GFTLAQKMVGRACGLPEGKGVRPGTYCEPKMTTVGSQDTTGPMTRDELK----DLACLGF 442

Query: 59  KIALVMDHF-----FP-PKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGF 112
              LVM  F     +P P D+ +   +    DF       +   G   G++H+ L     
Sbjct: 443 SADLVMQSFCHTAAYPKPIDVNTHHTLP---DFIMNRSGVSLRPGD--GIIHSWLNR--M 495

Query: 113 VVPGDLVIGADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKW 172
           ++P  +  G DSHT    GI   S   GS  +A+  ATG   L +PES+   F  + Q  
Sbjct: 496 LLPDTVGTGGDSHTRFPIGI---SFPAGSGLVAFAAATGVMPLDMPESVLVRFKGQMQPG 552

Query: 173 VGGKDFV-----------LTVIGKIGVDGALYKAMEYQGEAIRALDIDNRLTIANMAIEA 221
           +  +D V           L  + K G    ++     + E +  L ++    +++ + E 
Sbjct: 553 ITLRDLVHAIPYYAIQQGLLTVEKKGKKN-IFSGRILEIEGLNQLTVEQAFELSDASAER 611

Query: 222 GGKSGIIE-PDEKTVDWVRKRTN---------------------------REFKLYKSDP 253
                 I+ P++   ++++                                + KL ++D 
Sbjct: 612 SAAGCTIKLPEDSIAEYLKSNITMLRWMISEGYGDARTLERRAQAMEAWLADPKLLEADK 671

Query: 254 DAKYCCEYEFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDLRIAA 312
           DA+Y    E D +++ EPV+  P+ P + + +S VAG  ID+VFIGSC    +   R A 
Sbjct: 672 DAEYAAVIEIDLAEVKEPVLCAPNDPDDARLLSTVAGEKIDEVFIGSCMT-NIGHFRAAG 730

Query: 313 AILKSKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHMGILA 372
            +L   K     R  + P +     Q   EG   I   AG  +    C  C+G    +  
Sbjct: 731 KLLDKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARV-Q 789

Query: 373 EGEVCLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKY 422
            G   +STS RNF  R+G   + VYL+S  +AA ++++G++    E  +Y
Sbjct: 790 TGSTVVSTSTRNFPNRLG-DATNVYLASAELAAVASIIGKLPTVAEYMEY 838


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: 855
Number of extensions: 44
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 431
Length of database: 875
Length adjustment: 37
Effective length of query: 394
Effective length of database: 838
Effective search space:   330172
Effective search space used:   330172
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 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