GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas fluorescens FW300-N2E2

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf6N2E2_1496 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1496
          Length = 403

 Score =  355 bits (912), Expect = e-102
 Identities = 183/398 (45%), Positives = 244/398 (61%), Gaps = 1/398 (0%)

Query: 3   FLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET 62
           +L+  + RV  SA  A   +A  L+  GRD++ L  GEPDFDTP +IK+AA  AI  G T
Sbjct: 4   YLSKRVQRVSLSANAAAKSRATALREAGRDILDLTTGEPDFDTPTHIKQAAYAAIAAGAT 63

Query: 63  KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122
           KYTP  G+  LR A+ +K   EN LDY     ++  G KQI+FNAF ATL+ GDEV++P 
Sbjct: 64  KYTPTPGVKALRVAVQRKLCTENQLDYPLESIVIANGAKQIIFNAFAATLDDGDEVLVPT 123

Query: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182
           PYW S+P+ V   GG PVF+    E   KL  + L++ I  +T+W + NSP NPSGA YS
Sbjct: 124 PYWPSFPDSVRFNGGEPVFIECGLEQGCKLTPQQLEQHIGERTRWLILNSPGNPSGAVYS 183

Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242
             EL+ L  VL +H HV +L D++YEH+ +        + V P L  R L + GVSK YA
Sbjct: 184 EAELQGLAQVLRRHAHVLILLDELYEHIRFDGRAAQNLLNVAPDLQARCLLVGGVSKTYA 243

Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302
           MTGWRIG+ AGP  L  AM ++Q Q TSGA+S+ Q AA+ A  G  +F+      ++ RR
Sbjct: 244 MTGWRIGFGAGPQALSDAMTVVQSQSTSGASSVGQAAALAAFEGGLEFLPEQVAAYRQRR 303

Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362
           D +VS L   +G+    P G F+V+  CAGL+G+  P G+ +E D D V+ LL+ EGVA 
Sbjct: 304 DGLVSTLRTVEGLEVLEPHGGFFVFVRCAGLLGRYRPDGQRLEHDADVVAYLLD-EGVAG 362

Query: 363 VHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           V GSA+GL P FR+S AT+   + EA RRI   C   R
Sbjct: 363 VAGSAYGLSPWFRLSIATATETVAEAGRRIAHACRQLR 400


Lambda     K      H
   0.318    0.134    0.402 

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: 426
Number of extensions: 19
Number of successful extensions: 2
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: 400
Length of database: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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