GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS09050
          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:

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