GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Caulobacter crescentus NA1000

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate CCNA_02617 CCNA_02617 histidinol-phosphate aminotransferase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>FitnessBrowser__Caulo:CCNA_02617
          Length = 378

 Score =  211 bits (538), Expect = 2e-59
 Identities = 136/362 (37%), Positives = 199/362 (54%), Gaps = 13/362 (3%)

Query: 10  VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69
           +  +  Y AG  ++E AR  GL  +   KLASNEN LG       A+  A +E   YPD 
Sbjct: 26  LEGVQGYKAGMTLAEAARRTGL--SAFSKLASNENLLGPSPKVAEAVMAAMAEPHIYPDP 83

Query: 70  NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129
           ++  L+AA+  R GV    V +  GS  +++    A +  G SI+ +  +F  Y +  + 
Sbjct: 84  HSDVLRAAIGARLGVSPARVVVSPGSEALIDYVFRAVLHPGDSILLSSPTFPTYEIFGRC 143

Query: 130 LGARAIVVPAV-KYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188
             AR I VP +  +  D+ A+ AA +   +L+ +  PNNPTG  ++    +A L   PR 
Sbjct: 144 AEARIIDVPRLANFDIDVPAVCAAAALGPKLLVLCTPNNPTGNALKAADFQAILAATPRS 203

Query: 189 VVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVS-RTFSKAFGLAGLRVGFAIAQ-PELT 246
            VV +DEAY EY    + +D+ A +  +    VS RTFSKA+GLAGLR+G+ +A  PEL 
Sbjct: 204 TVVFVDEAYREY---HEAFDTFAMLDAWGGPWVSARTFSKAYGLAGLRMGYGVASSPELV 260

Query: 247 DLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDG 306
           D L+R+R PFNV  ++QAAA+AA  D+ +L+++  L      R+    D +G+E+  S  
Sbjct: 261 DYLDRIRPPFNVTAVSQAAALAAWEDQDYLKRTVDLTIAERGRVEAVLDDMGVEHTESHA 320

Query: 307 NFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERT 366
           NFV +R     A        LL QG+I+RP    G   W+RITIG P +N+A IAAL   
Sbjct: 321 NFVFLR---SPAGPEATAAHLLHQGLIIRPTPVAG--GWVRITIGRPADNDALIAALPAA 375

Query: 367 LA 368
           L+
Sbjct: 376 LS 377


Lambda     K      H
   0.318    0.135    0.385 

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: 344
Number of extensions: 16
Number of successful extensions: 5
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: 370
Length of database: 378
Length adjustment: 30
Effective length of query: 340
Effective length of database: 348
Effective search space:   118320
Effective search space used:   118320
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: 50 (23.9 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