GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Pseudomonas stutzeri RCH2

Align Shikimate kinase 1; SK 1; Shikimate kinase I; SKI; EC 2.7.1.71 (characterized)
to candidate GFF3647 Psest_3714 Shikimate kinase

Query= SwissProt::P0A6D7
         (173 letters)



>FitnessBrowser__psRCH2:GFF3647
          Length = 184

 Score =  177 bits (448), Expect = 1e-49
 Identities = 91/172 (52%), Positives = 121/172 (70%), Gaps = 1/172 (0%)

Query: 1   MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVGWVFDLEGEEGFR 60
           M   +NI L+GPMGAGKSTIGR LA++L + F DSD+EIE+RTGA +  +FD+EGE GFR
Sbjct: 1   MTSLKNIILIGPMGAGKSTIGRLLAKELRLPFKDSDKEIEQRTGASIPLIFDVEGEAGFR 60

Query: 61  DREEKVINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKR 120
           +RE   I EL + +G+VLATGGG+V   E R  L A G V+YL T++++QL RT RD+ R
Sbjct: 61  ERERAAIAELCQLEGVVLATGGGAVLRDENRQALRAGGRVIYLCTSVDQQLERTSRDRNR 120

Query: 121 PLLHVETPPREVLEALANERNPLYEEIADVTIRTDDQSAKVVANQIIHMLES 172
           PLL  +  PR VL AL   R+PLY  IAD+ I TD++  ++V  +I+  L S
Sbjct: 121 PLLQAD-DPRSVLTALMAVRDPLYRSIADIIIETDERPPRLVVMEILDRLAS 171


Lambda     K      H
   0.313    0.132    0.359 

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: 113
Number of extensions: 5
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: 173
Length of database: 184
Length adjustment: 19
Effective length of query: 154
Effective length of database: 165
Effective search space:    25410
Effective search space used:    25410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 44 (21.6 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