GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Synechococcus elongatus PCC 7942

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate Synpcc7942_0931 Synpcc7942_0931 UDP-N-acetylglucosamine acyltransferase

Query= SwissProt::O34981
         (236 letters)



>FitnessBrowser__SynE:Synpcc7942_0931
          Length = 268

 Score = 51.6 bits (122), Expect = 2e-11
 Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 2/111 (1%)

Query: 104 VEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGSVLAGVIEPPSA 163
           V IGD   I    +IN  +  GE T+I  + +L     V  NC +    V++  +    A
Sbjct: 81  VRIGDRNRIREYVTINRATKAGEATVIGNDNLLMAYVHVAHNCILHNRIVISNAVS--LA 138

Query: 164 KPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVVAGTPAK 214
             +V+E   VIG  + + + V VG+ A++   + V  DV PY +V G PA+
Sbjct: 139 GHIVVESGAVIGGMSGLHQFVHVGRNAMIGGMSRVERDVPPYMLVEGNPAR 189



 Score = 34.3 bits (77), Expect = 2e-06
 Identities = 31/110 (28%), Positives = 47/110 (42%), Gaps = 8/110 (7%)

Query: 92  ARIEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAG 151
           A I PGA I   V+IG  AVI  G  + IG+     T +  + V+ G   +G+   I  G
Sbjct: 9   AIIAPGAEIHPSVQIGPYAVI--GEHVRIGA----HTTVGAHAVIDGWTEIGEENRIFPG 62

Query: 152 SVLAGVIEPPSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVND 201
           + +   +E    K       V IG    + E VT+ +        ++ ND
Sbjct: 63  AAIG--LESQDKKTDGSLSVVRIGDRNRIREYVTINRATKAGEATVIGND 110


Lambda     K      H
   0.313    0.134    0.364 

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: 174
Number of extensions: 14
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 6
Number of HSP's successfully gapped: 2
Length of query: 236
Length of database: 268
Length adjustment: 24
Effective length of query: 212
Effective length of database: 244
Effective search space:    51728
Effective search space used:    51728
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: 46 (22.3 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