GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Herbaspirillum seropedicae SmR1

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase

Query= SwissProt::H3ZPL1
         (417 letters)



>FitnessBrowser__HerbieS:HSERO_RS09050
          Length = 398

 Score =  314 bits (805), Expect = 3e-90
 Identities = 169/410 (41%), Positives = 252/410 (61%), Gaps = 17/410 (4%)

Query: 10  KLEAPTLDYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITK 69
           KLE P    +  FS++A  MK+S IRE+LK+    D+ S AGGLP+P TFPVE +     
Sbjct: 2   KLENPA-PLQWQFSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFD 60

Query: 70  EVLEKHAAQALQYGTTKGFTPLRLALAEWMRERYDI---PISKVDIMTTSGSQQALDLIG 126
            VL +    ALQYG T G+ PLR    EW+          IS   ++  SGSQQ LDL+G
Sbjct: 61  RVLSQQGKMALQYGPTDGYLPLR----EWIAASLSTNGAQISAEQVLMVSGSQQGLDLLG 116

Query: 127 RVFINPGDIIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKV 186
           +V I+ G  ++VE P+YL ALQAF  Y  +F  +P D+ G+  + +E             
Sbjct: 117 KVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAI-------AGGA 169

Query: 187 KIVYTIPTFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDE 246
           +++Y++P FQNP G T+  +RR +L+E  ++    ++ED+PYG L Y   P+  + + + 
Sbjct: 170 RMLYSLPNFQNPTGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSMNP 229

Query: 247 EGRVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGY 306
            G VIY+G+FSK+L PG R+G++ A    I K+E AKQ+ DL T   +Q++ ++ ++ G+
Sbjct: 230 SG-VIYMGSFSKVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGF 288

Query: 307 LDKHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAV 366
           LD+H+P I + Y  +  AML AL+++ P    W+KPEGGMF+W TLPE ID   +L +AV
Sbjct: 289 LDQHVPTIRKLYGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAV 348

Query: 367 -AKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415
             + VA+VPG  F+A+   KNT+RL+F  VP E+IR G++RL + I  ++
Sbjct: 349 EQEKVAFVPGAPFYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIASKL 398


Lambda     K      H
   0.318    0.137    0.398 

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: 444
Number of extensions: 23
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: 417
Length of database: 398
Length adjustment: 31
Effective length of query: 386
Effective length of database: 367
Effective search space:   141662
Effective search space used:   141662
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.

Links

Downloads

Related tools

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