GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_0903
          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:

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