GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Herbaspirillum seropedicae SmR1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase

Query= BRENDA::Q72LL6
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS09050
          Length = 398

 Score =  337 bits (864), Expect = 4e-97
 Identities = 181/399 (45%), Positives = 256/399 (64%), Gaps = 15/399 (3%)

Query: 3   PLSWSEAFGKGAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILRE 62
           PL W   F + A  +++S IRE+LK+T RP I SFAGGLP+P  FP E    A  R+L +
Sbjct: 8   PLQWQ--FSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFDRVLSQ 65

Query: 63  KGEVALQYSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSP 117
           +G++ALQY PT+GY PLR ++A  +      +  E+VL+ +GSQQ LDL+GKV +DEGS 
Sbjct: 66  QGKMALQYGPTDGYLPLREWIAASLSTNGAQISAEQVLMVSGSQQGLDLLGKVLIDEGSK 125

Query: 118 VLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTG 177
           VL+E PSY+GA+QAF L G +F +VP+ E G   + +E +      R LY +P+FQNPTG
Sbjct: 126 VLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAI--AGGARMLYSLPNFQNPTG 183

Query: 178 GLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFS 237
              P   R +L++     GL ++EDD Y  L +  A LP +  +       GVIY+GSFS
Sbjct: 184 RTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSM----NPSGVIYMGSFS 239

Query: 238 KVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGF-SERLERVRRV 296
           KVL+PG+R+ + VA    + K+ QAKQ  DLHT  L QM+V+E +K+GF  + +  +R++
Sbjct: 240 KVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGFLDQHVPTIRKL 299

Query: 297 YREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALE-ENVAFVPGG 355
           Y ++ QAML AL +  P    +++P+GGMF+W+ LP+ + A  L   A+E E VAFVPG 
Sbjct: 300 YGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAVEQEKVAFVPGA 359

Query: 356 PFFANGGGENTLRLSYATLDREGIAEGVRRLGRALKGLL 394
           PF+AN   +NTLRLS+ T+  E I  GV RLG+ +   L
Sbjct: 360 PFYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIASKL 398


Lambda     K      H
   0.320    0.139    0.403 

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: 485
Number of extensions: 28
Number of successful extensions: 6
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 (21.8 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