Alignments for a candidate for leuC in Marinobacter adhaerens HP15

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis