GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Cupriavidus basilensis 4G11

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate RR42_RS04465 RR42_RS04465 aspartate aminotransferase

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



>FitnessBrowser__Cup4G11:RR42_RS04465
          Length = 371

 Score =  555 bits (1429), Expect = e-163
 Identities = 276/363 (76%), Positives = 313/363 (86%)

Query: 5   FGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELG 64
           FGP YVRAI+PY+AGKPISEVAREFGL E+TIVKLASNENPLGMPESA+ A+A A ++LG
Sbjct: 8   FGPEYVRAISPYVAGKPISEVAREFGLVESTIVKLASNENPLGMPESARTAIAAAVADLG 67

Query: 65  RYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYA 124
           RYPDAN F LK ALS R+ VP DW+TLGNGSNDILEIAAHA V+ G+SIVYA++SFAVYA
Sbjct: 68  RYPDANGFALKGALSARFDVPPDWLTLGNGSNDILEIAAHALVKPGESIVYAEHSFAVYA 127

Query: 125 LATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDK 184
           LATQ +GARAI V A  YGHDLDAM  A++ DTRL+F+ANPNNPTGTF+   ++E FL K
Sbjct: 128 LATQEVGARAIEVKARDYGHDLDAMAVAIAPDTRLVFIANPNNPTGTFLPAAEIETFLAK 187

Query: 185 VPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPE 244
           VP  VVVVLDEAY EYL   ++YDSIAWVR+YPNLLVSRTFSKA+GLAGLR+G+A+AQP 
Sbjct: 188 VPADVVVVLDEAYNEYLDDAQQYDSIAWVRKYPNLLVSRTFSKAYGLAGLRIGYAVAQPA 247

Query: 245 LTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPS 304
           LTDLLNR+RQPFNVN+LAQAAA+AAL D AFL++SA LN  G  +L  AFD+LGL+YVPS
Sbjct: 248 LTDLLNRIRQPFNVNSLAQAAAVAALGDAAFLQRSAELNRAGKAQLVAAFDRLGLQYVPS 307

Query: 305 DGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364
            GNFVLVRVG DD AG RVNL LLKQGVIVRPVGNY LPQWLRITIGLPEEN AFIAALE
Sbjct: 308 SGNFVLVRVGRDDGAGARVNLALLKQGVIVRPVGNYNLPQWLRITIGLPEENAAFIAALE 367

Query: 365 RTL 367
           + L
Sbjct: 368 KAL 370


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: 540
Number of extensions: 15
Number of successful extensions: 1
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: 371
Length adjustment: 30
Effective length of query: 340
Effective length of database: 341
Effective search space:   115940
Effective search space used:   115940
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