GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pseudomonas stutzeri RCH2

Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate GFF4021 Psest_4094 Aspartokinases

Query= SwissProt::A4VFY3
         (476 letters)



>FitnessBrowser__psRCH2:GFF4021
          Length = 476

 Score =  912 bits (2357), Expect = 0.0
 Identities = 466/476 (97%), Positives = 470/476 (98%)

Query: 1   MHTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGV 60
           MHTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGV
Sbjct: 1   MHTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGV 60

Query: 61  YQRFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQ 120
           YQRFADAQ+EGAWREALE VRQRML KNAELFSSEYELHAANQFINSRIDDASECMHSLQ
Sbjct: 61  YQRFADAQNEGAWREALEQVRQRMLEKNAELFSSEYELHAANQFINSRIDDASECMHSLQ 120

Query: 121 KLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPF 180
           KLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPF
Sbjct: 121 KLCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPF 180

Query: 181 EEMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKE 240
           EEMI+SHFAGFD SRELVVATGYTHCAEGLMNT+DRGYSEITFAQIAAATGA EAIIHKE
Sbjct: 181 EEMIASHFAGFDLSRELVVATGYTHCAEGLMNTYDRGYSEITFAQIAAATGAHEAIIHKE 240

Query: 241 FHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFE 300
           FHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFE
Sbjct: 241 FHLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFE 300

Query: 301 PEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVV 360
           PEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDI +DMEISKLLKQLKLYVV
Sbjct: 301 PEHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDISHDMEISKLLKQLKLYVV 360

Query: 361 NKDSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKT 420
           NKDSDANSITYYASGSRKLINRAARLIEE YPAAEVTVHNLAIVSAIGSDLKVKGILAKT
Sbjct: 361 NKDSDANSITYYASGSRKLINRAARLIEEHYPAAEVTVHNLAIVSAIGSDLKVKGILAKT 420

Query: 421 VAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIAAA 476
           VAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIAAA
Sbjct: 421 VAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIAAA 476


Lambda     K      H
   0.318    0.133    0.372 

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: 845
Number of extensions: 24
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: 476
Length of database: 476
Length adjustment: 33
Effective length of query: 443
Effective length of database: 443
Effective search space:   196249
Effective search space used:   196249
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: 51 (24.3 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