GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroL in Pseudomonas fluorescens FW300-N2E3

Align Shikimate kinase 1; SK 1; Shikimate kinase I; SKI; EC 2.7.1.71 (characterized)
to candidate AO353_12500 AO353_12500 shikimate kinase

Query= SwissProt::P0A6D7
         (173 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_12500
          Length = 172

 Score =  174 bits (441), Expect = 7e-49
 Identities = 88/167 (52%), Positives = 117/167 (70%), Gaps = 1/167 (0%)

Query: 5   RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVGWVFDLEGEEGFRDREE 64
           RN+ LVGPMGAGKSTIGR LA++L + F DSD+EIE RTGA++ W+FD EGE GFRDRE+
Sbjct: 2   RNLILVGPMGAGKSTIGRLLAKELRLPFKDSDKEIELRTGANIPWIFDKEGEPGFRDREQ 61

Query: 65  KVINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLH 124
            +I EL    G+VLATGGG+V     R  L A G VVYL  ++E+Q+ RT RD+ RPLL 
Sbjct: 62  AMIAELCALDGVVLATGGGAVMREANRRALHAGGRVVYLHASVEQQVGRTARDRNRPLLR 121

Query: 125 VETPPREVLEALANERNPLYEEIADVTIRTDDQSAKVVANQIIHMLE 171
              P + + + LA  R+PLY EIAD+ + TD++  ++V   I+  L+
Sbjct: 122 TADPAKTLRDLLA-LRDPLYREIADLVVETDERPPRMVVLDILERLQ 167


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: 119
Number of extensions: 4
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: 172
Length adjustment: 18
Effective length of query: 155
Effective length of database: 154
Effective search space:    23870
Effective search space used:    23870
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