GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydrogenase; EC 1.1.1.85; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH (uncharacterized)
to candidate GFF838 HP15_817 3-isopropylmalate dehydrogenase

Query= curated2:B0RIP4
         (355 letters)



>FitnessBrowser__Marino:GFF838
          Length = 384

 Score =  240 bits (613), Expect = 4e-68
 Identities = 159/384 (41%), Positives = 212/384 (55%), Gaps = 33/384 (8%)

Query: 1   MPRTISLAVVPGDGIGPEVVHEALRVLREAVPADVSLDT--TQYPFGAGHFLET-GQILT 57
           M +T  +AV PGDGIGPEVV EA+R L E + A   LD   T++P+ +  + E  G+ + 
Sbjct: 1   MAQTTRIAVTPGDGIGPEVVAEAVRCL-ETLRAKHGLDLEWTRFPWPSHAWHEEHGESMP 59

Query: 58  DSDLAALAQHDAILLGAVGG----DPRDARLAGGIIERGLLLKLRFAFDHYINLRPTALL 113
              LA L ++DAILLGA+G     D  D  L    I    LL +R  FD ++  RP  LL
Sbjct: 60  ADALAQLQKYDAILLGALGDPGPMDDPDRYLLPDSISLAPLLDMRKGFDQWVCERPARLL 119

Query: 114 PGVASPLA--APGQVDFVVVREGTEGPYAGNGGVLRRGTEHEIATEVSVNTAHGVERTVR 171
           PG    LA      +D +V+RE +EG Y   GG LR+GT  E+AT++ V T    +R +R
Sbjct: 120 PGARQYLADERAKDIDMLVIRENSEGEYVSQGGRLRKGTPDEVATQMEVFTRKATDRIIR 179

Query: 172 FAFELAEKRDRKRVT--------------------LVHKTNVLTFAGSLWQRTVDRVAAE 211
           + FE A  R   RV+                    LV K N L + G ++    D ++ E
Sbjct: 180 YGFEQARNRAADRVSEGRTRTFRTLDGRTCESQVCLVTKRNALRYWGDMYTEAFDEISKE 239

Query: 212 HPDVTVDYLHVDATMIFLVTDPSRFDVIVSDNLFGDIITDLAAAISGGIGLAASGNVNPT 271
           +PDV   +  VDA  +  V  P  FDV+V+ NL GDI+TDLAA +SGG+G+A S N+NPT
Sbjct: 240 YPDVATHHELVDAACMKFVQSPWAFDVVVASNLQGDILTDLAAVLSGGMGVAPSCNLNPT 299

Query: 272 GA-FPSMFEPVHGSAPDIAGQQKADPTAAILSVALLLDHLGLSE-AAARVSAAVSDDLAA 329
               PSMFEP HGSAPDIAGQ  ADPTA + + A +L+ LG  + A A     + D +AA
Sbjct: 300 DPDMPSMFEPTHGSAPDIAGQGLADPTAMLFTAARMLEWLGRKDPAIAAAGKELFDAVAA 359

Query: 330 -RATGDAAPRSTAEVGDAILRALS 352
             A    + R T E+G AI   LS
Sbjct: 360 DLAENSGSRRGTHEIGSAICERLS 383


Lambda     K      H
   0.319    0.136    0.389 

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: 377
Number of extensions: 23
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 355
Length of database: 384
Length adjustment: 30
Effective length of query: 325
Effective length of database: 354
Effective search space:   115050
Effective search space used:   115050
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: 49 (23.5 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