GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas fluorescens FW300-N1B4

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Pf1N1B4_4425 Aspartate aminotransferase (EC 2.6.1.1)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4425
          Length = 403

 Score =  368 bits (944), Expect = e-106
 Identities = 187/397 (47%), Positives = 254/397 (63%), Gaps = 1/397 (0%)

Query: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63
           L+  + RV  SA  A   +A  L+  GRD++ L  GEPDFDTP++IK+AA  AI  G TK
Sbjct: 5   LSKRVQRVSLSANAAAKSQATALREAGRDILDLTIGEPDFDTPEHIKQAAYAAIAGGATK 64

Query: 64  YTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAP 123
           YTP  G+  LR A+ +K ++EN+LDY     ++  G KQI+FNAF ATL+ GD+V++P P
Sbjct: 65  YTPTPGVKALRIAVQRKLRQENHLDYPLESIVIANGAKQIIFNAFAATLDDGDQVLVPTP 124

Query: 124 YWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSH 183
           YW S+P+ V   GG PVF+        KL AE L++ I  +T+W + N P NPSGA YS 
Sbjct: 125 YWPSFPDSVRFNGGEPVFIECGLAQGCKLTAEQLEQYIGERTRWLILNGPGNPSGAVYSA 184

Query: 184 EELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAM 243
            EL+AL +VL +HP V +L D++YEH+ +      + + V P L  R L + GVSK YAM
Sbjct: 185 AELQALAEVLRRHPQVLILLDELYEHIRFDGRPAQSLLSVAPDLQSRCLLVGGVSKTYAM 244

Query: 244 TGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRD 303
           TGWRIG+ AGP  L  AM ++Q Q TSGA+S+ Q AA+ A +G  DF+      +Q RRD
Sbjct: 245 TGWRIGFGAGPQALANAMTVVQSQSTSGASSVGQAAALAAFDGGLDFLRSQVAAYQQRRD 304

Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363
           L+VS L +  G+    P+G F+V+  CAGL+G+  P G+ ++TD D V+ LLE EGVA V
Sbjct: 305 LLVSALRKVDGLEVLEPQGGFFVFIRCAGLLGRYRPDGQRLQTDADVVAYLLE-EGVAGV 363

Query: 364 HGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
            GSA+GL P FR+S AT+   + EA RRI + C   R
Sbjct: 364 AGSAYGLSPWFRLSIATATETVAEAGRRIAQACGQLR 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: 419
Number of extensions: 13
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.

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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