GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Cupriavidus basilensis 4G11

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Cup4G11:RR42_RS35305
          Length = 401

 Score =  469 bits (1206), Expect = e-137
 Identities = 226/398 (56%), Positives = 289/398 (72%)

Query: 1   MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60
           M  L D L+R+KPS +    Q+ REL+A GRDVIGL AGEPDF+TP +I++AA  A+  G
Sbjct: 1   MLSLTDRLNRIKPSPSSMAGQRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAG 60

Query: 61  ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120
           +T+YT V G  ELR A A+KFKREN LDY A++ IV TG KQ++FNA M T+  GDEV++
Sbjct: 61  KTRYTDVGGTAELRHAAAQKFKRENGLDYAASEIIVSTGAKQVIFNALMCTVQQGDEVIV 120

Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180
           PAPYWVSYP++    GG PVFV  + EN FKL  E+L+RAI+ +T+W + NSP+NPSGAA
Sbjct: 121 PAPYWVSYPDITLFAGGVPVFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAA 180

Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240
           Y+  EL A+ +VL +HPHVWV+TDD+YEHLTY    F T  +  P L  RTLT+NGVSKA
Sbjct: 181 YTRTELVAIAEVLERHPHVWVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKA 240

Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300
           YAMTGWRIGYA  P  LIKAM  +Q Q TSGA ++AQ AA+ AL+GPQDFI  NK +FQ 
Sbjct: 241 YAMTGWRIGYAGAPAPLIKAMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQA 300

Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360
           RRD VV+ L Q  GI C  P GAFYV+ SC  LIG   P G VI + +D+V+ +L+++ +
Sbjct: 301 RRDRVVAALGQVDGIHCQAPAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDL 360

Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAA 398
           AV+ GSA+G+  +FR+S+A S A L+E CRRI+   AA
Sbjct: 361 AVLQGSAYGVDTHFRLSFAASMAQLDEGCRRIEAAAAA 398


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: 486
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