GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuC in Synechococcus elongatus PCC 7942

Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= curated2:O27439
         (419 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0903 Synpcc7942_0903
           bifunctional aconitate hydratase 2/2-methylisocitrate
           dehydratase
          Length = 861

 Score =  111 bits (278), Expect = 7e-29
 Identities = 116/452 (25%), Positives = 193/452 (42%), Gaps = 58/452 (12%)

Query: 4   TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63
           T+++K++ RA G   V  G      +    + D TGP++ +  + +     +  + ++  
Sbjct: 373 TLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTGPMTRDEMKELA-CLGFSADLVMQS 431

Query: 64  FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123
           F H          + H  + DF+ ++G        +G+ H  L     ++P  V  G DS
Sbjct: 432 FCHTAAYPKPVDIKTHKTLPDFIAQRG-GVALKPGDGIIHSWLNRM--LLPDTVGTGGDS 488

Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVIL 179
           HT        F  GI    GS  +A   A G +   +PE++     G L+  +  +DV+ 
Sbjct: 489 HT-------RFPLGISFPAGSGLVAFAAAIGAMPLDMPESVLVRFTGSLQPGITLRDVVN 541

Query: 180 NIIGRVGADGATYMACE-----FAG-----ETVAEMSVSDRMVLSNMAIEMGGKTGIVEP 229
            I  +    G   ++ E     F+G     E + ++ +     L++   E       ++ 
Sbjct: 542 AIPYQAIQQGLLTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDATAERSCAGSTIKL 601

Query: 230 DEKTL------------NYVRR------------RSGKPW----RVFKTDPDAPSLSVME 261
            E T+            N + R            R  + W    ++   D DA   +V+E
Sbjct: 602 SEDTVAEYLRSNVALMKNMIARGYEDSRTLARRIRQMEDWLANPQLLSADEDAEYAAVIE 661

Query: 262 VDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAILKNRKVS 320
           +++ +L EP +ACP++ DNVK ++EV G  I ++F+GSC    +   R AA +L+     
Sbjct: 662 INLDELTEPILACPNDPDNVKKLSEVAGDPIHEIFIGSCMT-NIGHYRAAAKVLEGEGQV 720

Query: 321 DSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGEVSLSTS 380
              R+ + P +R    R  +EG    F  AGA +  P C  C+G     V       STS
Sbjct: 721 GG-RLWICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCSLCMGNQ-ARVADNTTVFSTS 778

Query: 381 NRNFRGRQGSPEAEVYLSSAAVAAASAVKGSI 412
            RNF  R G   A+VYL SA +AA  A+ G I
Sbjct: 779 TRNFNNRMGK-GAQVYLGSAELAAVCALLGRI 809


Lambda     K      H
   0.318    0.135    0.396 

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: 790
Number of extensions: 49
Number of successful extensions: 4
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: 419
Length of database: 861
Length adjustment: 37
Effective length of query: 382
Effective length of database: 824
Effective search space:   314768
Effective search space used:   314768
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