GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Cupriavidus basilensis 4G11

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate RR42_RS14595 RR42_RS14595 2-aminoadipate aminotransferase

Query= reanno::acidovorax_3H11:Ac3H11_1358
         (401 letters)



>FitnessBrowser__Cup4G11:RR42_RS14595
          Length = 395

 Score =  426 bits (1094), Expect = e-124
 Identities = 223/386 (57%), Positives = 277/386 (71%), Gaps = 6/386 (1%)

Query: 12  WTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAA 71
           W ++RRA+++  S IREILKVTE+P +IS AGGLPSP TFPV+A   A A + A++  AA
Sbjct: 3   WAISRRAQQLTSSAIREILKVTERPEVISFAGGLPSPATFPVAAMEQAVARIFADNPQAA 62

Query: 72  LQYAASEGYAPLRQAIADFLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPTY 131
           LQYAA+EGY PLR+ IA      VD +++LITTGSQQALDLIAKV+ID  S VLVETP+Y
Sbjct: 63  LQYAATEGYMPLREFIAK--RHAVDVERVLITTGSQQALDLIAKVMIDPGSPVLVETPSY 120

Query: 132 LGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEA 191
           LGALQAF+  EP  V+V  DD+ +L + L  ++  GA   RFLY LPNFQNPTGR M   
Sbjct: 121 LGALQAFSLFEPEFVSVPGDDKSLLPESLTPELTAGA---RFLYALPNFQNPTGRRMPLE 177

Query: 192 RRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRLG 251
           RR ALV  A EL L LVED+PYG+L +       L + NP+G IYMGSFSK+LAPGLRLG
Sbjct: 178 RRQALVARARELGLLLVEDDPYGELSYSGDQLPSLLSMNPDGVIYMGSFSKILAPGLRLG 237

Query: 252 FVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLA 311
           FV+AP  ++ KL QAKQA+DLHTP + QRL  EV++   LD H+PTIR LY  QC+AML 
Sbjct: 238 FVIAPPELHFKLCQAKQASDLHTPSFTQRLAYEVVRDGLLDSHIPTIRTLYAAQCQAMLD 297

Query: 312 ALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPR 371
           +L + M   GV WN P+GGMF+W+ LPEG+ ++E+L +AV RNVA+VPGA FYA N    
Sbjct: 298 SLARHMPE-GVTWNAPEGGMFIWMELPEGLDSMEILQEAVNRNVAYVPGAPFYASNPRRN 356

Query: 372 TLRLSFVTSTVEQIATGIAALAAAIR 397
            LRL+FVT   E+I  G+A L    R
Sbjct: 357 ALRLAFVTVAPERIEQGVAILGTLFR 382


Lambda     K      H
   0.318    0.134    0.392 

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: 17
Number of successful extensions: 4
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: 401
Length of database: 395
Length adjustment: 31
Effective length of query: 370
Effective length of database: 364
Effective search space:   134680
Effective search space used:   134680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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