GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Herbaspirillum seropedicae SmR1

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS09050 HSERO_RS09050
           2-aminoadipate aminotransferase
          Length = 398

 Score =  379 bits (973), Expect = e-110
 Identities = 211/396 (53%), Positives = 260/396 (65%), Gaps = 9/396 (2%)

Query: 7   PQNSTWTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLAN 66
           P    W  ++RA+ M  S IREILKVT +P I S AGGLPSP TFPV     A   VL+ 
Sbjct: 6   PAPLQWQFSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFDRVLSQ 65

Query: 67  DGPAALQYAASEGYAPLRQAIADFLPWD---VDADQILITTGSQQALDLIAKVLIDENSR 123
            G  ALQY  ++GY PLR+ IA  L  +   + A+Q+L+ +GSQQ LDL+ KVLIDE S+
Sbjct: 66  QGKMALQYGPTDGYLPLREWIAASLSTNGAQISAEQVLMVSGSQQGLDLLGKVLIDEGSK 125

Query: 124 VLVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNP 183
           VLVETP+YLGALQAF        +V SD+ G+  + ++A  G     AR LY LPNFQNP
Sbjct: 126 VLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAIAGG----ARMLYSLPNFQNP 181

Query: 184 TGRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKV 243
           TGRT+   RR  LV+  A L LPL+ED+PYG L + N P   + + NP G IYMGSFSKV
Sbjct: 182 TGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSMNPSGVIYMGSFSKV 241

Query: 244 LAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYK 303
           L PG+RLG+VVAP+ +  K+ QAKQA DLHT    Q +V E +K  FLD+HVPTIR LY 
Sbjct: 242 LTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGFLDQHVPTIRKLYG 301

Query: 304 QQCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVER-NVAFVPGAA 362
            QC+AML AL Q+       W++P+GGMF+WV LPE + A  LL +AVE+  VAFVPGA 
Sbjct: 302 DQCQAMLDAL-QQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAVEQEKVAFVPGAP 360

Query: 363 FYADNADPRTLRLSFVTSTVEQIATGIAALAAAIRS 398
           FYA+ A   TLRLSFVT   EQI  G+  L   I S
Sbjct: 361 FYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIAS 396


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: 467
Number of extensions: 22
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: 401
Length of database: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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