GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Marinobacter adhaerens HP15

Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= curated2:O27439
         (419 letters)



>FitnessBrowser__Marino:GFF2253
          Length = 864

 Score =  110 bits (275), Expect = 2e-28
 Identities = 119/466 (25%), Positives = 200/466 (42%), Gaps = 76/466 (16%)

Query: 4   TVSEKILARASGKDR---VEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKI 60
           T+++K++ +A G +    V         +    + D TGP++ +  + +     +  + +
Sbjct: 382 TLAQKMVGKACGLEEGKGVRPNTYCEPHMTTVGSQDTTGPMTRDELKDLA-CLGFQADLV 440

Query: 61  VVIFDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVG 120
           +  F H          +    M DF+  +G  +     +G+ H  L     ++P  V  G
Sbjct: 441 MQSFCHTAAYPKPVDVEMQHTMPDFIRTRGGVSLRP-GDGIIHSWLNRM--LLPDTVGTG 497

Query: 121 TDSHTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKD 176
            DSHT        F  GI    GS  +A   ATG +   +PE++    +G+++  +  +D
Sbjct: 498 GDSHT-------RFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGEMQPGITLRD 550

Query: 177 VILNI---------------------IGRV-GADGATYMACEFAGE-------------- 200
           ++  I                      GR+   +G  ++  E A E              
Sbjct: 551 LVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELSDASAERSAAGCT 610

Query: 201 ------TVAEMSVSDRMVLSNMAIEMGGKTGIVEPDEKTLNYVRRRSGKPW----RVFKT 250
                 +VAE   S+  +L  M  E  G       D +TL   R +  + W    ++ + 
Sbjct: 611 INLSEDSVAEYLRSNITMLRWMIAEGYG-------DPRTLER-RAQQMEEWLADPKLMRA 662

Query: 251 DPDAPSLSVMEVDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRD 309
           D DA    V+E+D++D+ EP V CP++ D+ K ++EV G ++D+VF+GSC    +   R 
Sbjct: 663 DKDAEYAHVIEIDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMT-NIGHFRA 721

Query: 310 AAAILKNRKVSDSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGL 369
           A  +L+  K   S R+ + P ++    + ++EG    +  AG     P C  C+G     
Sbjct: 722 AGKLLEQHKGPLSTRLWMSPPTKMDQAQLMEEGYFNTYGTAGVRTEMPGCSLCMGNQ-AR 780

Query: 370 VGPGEVSLSTSNRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415
           V P    LSTS RNF  R G   A VYL+SA +AA  AV G +  P
Sbjct: 781 VAPKSTVLSTSTRNFPNRLGD-GANVYLTSAELAAVGAVLGKLPSP 825


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: 821
Number of extensions: 55
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: 2
Length of query: 419
Length of database: 864
Length adjustment: 37
Effective length of query: 382
Effective length of database: 827
Effective search space:   315914
Effective search space used:   315914
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