GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas simiae WCS417

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF3717 PS417_19025 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__WCS417:GFF3717
          Length = 401

 Score =  360 bits (924), Expect = e-104
 Identities = 175/398 (43%), Positives = 253/398 (63%)

Query: 3   FLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGET 62
           FL+D +  + PS +IA +    EL+A+GRD++    GEPDFDTP +I  AA  A+  G+T
Sbjct: 4   FLSDRVLGIAPSPSIAANALVTELRAQGRDIVNFTVGEPDFDTPAHILAAASQAMHNGDT 63

Query: 63  KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPA 122
            YT  +G   LR+AI  K +++N+L Y   + + G GGK ++++A  ATLN GDEV++  
Sbjct: 64  HYTSTTGTLALRQAICLKLQQDNDLAYGLDEVVAGCGGKHVIYHALAATLNRGDEVIVHT 123

Query: 123 PYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYS 182
           PYWVSYP++  L   TPV +P  +   FKL  + L++AIT +TKW + NSP+NPSGA Y+
Sbjct: 124 PYWVSYPDIARLNDATPVIIPGDESLGFKLSPDALEQAITARTKWVILNSPNNPSGAVYN 183

Query: 183 HEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYA 242
             EL AL  VL +HPHV ++ D++YEH  YG  R      + P L  RTL +NG SK YA
Sbjct: 184 ETELLALAQVLRRHPHVLIMADEIYEHFIYGRARHVPLTRLAPDLKPRTLIVNGASKGYA 243

Query: 243 MTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRR 302
           MTGWR+G+ AGP  LI A+  +  Q T+  +S++Q AAV A  G Q  I   +E +Q RR
Sbjct: 244 MTGWRLGFGAGPAWLIAAIAKLLSQTTTCPSSLSQAAAVAAFTGDQAPIAAMREEYQQRR 303

Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362
             ++++L    G+SC  P+GAFYV+ + +GL+GK  P G  +++D   V  LL   G+A 
Sbjct: 304 ARMLALLADIPGLSCTPPDGAFYVFANVSGLMGKLTPQGDRLDSDTQLVDYLLRDYGLAT 363

Query: 363 VHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           V G+A+G+ P  R+S+A+S  ++EE CRR++  C   R
Sbjct: 364 VSGAAYGMSPYVRLSFASSSEVIEEGCRRLKDACRDLR 401


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: 438
Number of extensions: 16
Number of successful extensions: 1
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: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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