GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Escherichia coli BW25113

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate 16478 b2373 hypothetical protein (NCBI)

Query= BRENDA::P9WG39
         (547 letters)



>FitnessBrowser__Keio:16478
          Length = 564

 Score =  219 bits (559), Expect = 2e-61
 Identities = 166/552 (30%), Positives = 270/552 (48%), Gaps = 22/552 (3%)

Query: 1   MSTDTAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTA 60
           MS        MH   +I   LK + IDT++ + G  +  +    + EGIR I  RHEQ+A
Sbjct: 1   MSDQLQMTDGMH---IIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSA 57

Query: 61  AFAAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRA--PALRWGMGS 118
            +AA     +T+ PG+    + PG  NG++A+A A  N  P++++ G +    +    G 
Sbjct: 58  GYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGD 117

Query: 119 LQEIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD-HAFSMSS 177
            +E+D +    P A+ A      ++ G+ + +A++ +VS   G  ++D P +  A +M  
Sbjct: 118 YEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEK 177

Query: 178 DNGRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEE 235
           D      +      P   P   ++  A  LL+ A+RP+I+ G    +  A+  L   +E 
Sbjct: 178 DEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIES 237

Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFGGV-FGSTTQ 294
             IP L   MA+G++   H L+ + ARS AL  ADV ++VG  +++ L  G   + + TQ
Sbjct: 238 AQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQ 297

Query: 295 LIVADRVEPAR-EHPRPVAAGLYGDLTAT----LSALAGSGGTDHQGWIEELATAETMAR 349
            I  D +EP   +  RP+A  + GD+ ++    L+ L  +  T    W + L   +    
Sbjct: 298 FIQLD-IEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNA 356

Query: 350 DLEKAELVDDRIPLHPMRVYAELAALL--ERDALVVIDAGDFGSYAGRMIDSYLPGCWLD 407
                +L  D  PL+     + +  +L   +D  +V +  +    A  +ID Y P   LD
Sbjct: 357 QKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLD 416

Query: 408 SGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNG 467
            G +G +G G GYA+ A +      VV ++GD AFGFSGME +T+ R+N+ V  VI NNG
Sbjct: 417 CGTWGVMGIGMGYAIGASVTSGS-PVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNG 475

Query: 468 IWGLEKHPMEALYGYSVVA--ELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASG 525
             G+ +     L G    +  +L    RYD+++ A  G G  V+   ELR AL     S 
Sbjct: 476 --GIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSR 533

Query: 526 LPAVVNVLTDPS 537
            P ++NV+ DP+
Sbjct: 534 KPTIINVVIDPA 545


Lambda     K      H
   0.319    0.135    0.405 

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: 715
Number of extensions: 35
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: 547
Length of database: 564
Length adjustment: 36
Effective length of query: 511
Effective length of database: 528
Effective search space:   269808
Effective search space used:   269808
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 (21.8 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