GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Shewanella oneidensis MR-1

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC 2.3.1.89; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate 203814 SO4745 UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file)

Query= curated2:C4L2D4
         (235 letters)



>FitnessBrowser__MR1:203814
          Length = 454

 Score = 54.3 bits (129), Expect = 4e-12
 Identities = 34/111 (30%), Positives = 57/111 (51%), Gaps = 9/111 (8%)

Query: 91  ARIEPGSFIRDHVQIGNNAVVMMGAVVNIGAVIGDGSMVDMNAVIGARGTLGKNVHLGAG 150
           AR+ PG+ +     IGN   +         AV+G GS     A +G    +G  V++GAG
Sbjct: 327 ARLRPGAELMQDAHIGNFVEMKK-------AVLGVGSKAGHLAYLGD-AQIGAGVNIGAG 378

Query: 151 AVVAGVLEPPSKDPVIIEDGVMIGANAVILEGVRVGENAVVAAGSVVTQDV 201
            +     +  +K   +IED V +G++  ++  V +G+ A + AGS +T+DV
Sbjct: 379 TITCNY-DGANKHLTVIEDNVFVGSDTQLVAPVTIGKGATLGAGSTITRDV 428



 Score = 33.1 bits (74), Expect = 9e-06
 Identities = 42/204 (20%), Positives = 79/204 (38%), Gaps = 22/204 (10%)

Query: 13  IKDAKKETPVKLYVNGQLAGLEIEEAKAFGTDESKLFLTTAERAAAFLEANASVITDSHL 72
           I + K   P +L +N    G+      A  T   +L    A+      +    +I  +H 
Sbjct: 149 IVEQKDANPEQLAINEVNTGIMAVPGNALKTWLDRLSNNNAQGEYYLTD----IIAMAHA 204

Query: 73  EYDRRNSAVPM--LDTTRLNARIEPGSFIRDHVQIGNNAVVMMGAVVNIGA--------V 122
           +    N+A P   ++    N R++     R +       +++ GA +   +         
Sbjct: 205 DGVEINTAQPQSAIEVEGANNRVQLAQLERAYQAREAEKLMIAGANLRDPSRIDIRGEVT 264

Query: 123 IGDGSMVDMNAVIGARGTLGKNVHLGAGAVV--AGVLEPPSKDPVIIEDGVMIGANAVIL 180
           +G   M+D+N +   +  +G NV +GAGA++    + +     P  I +G  +G  A   
Sbjct: 265 VGMDVMIDVNVIFEGKVVIGNNVTIGAGAIIIDTEIADNAEIKPYSIIEGAKLGVAA--- 321

Query: 181 EGVRVGENAVVAAGSVVTQDVPPG 204
                G  A +  G+ + QD   G
Sbjct: 322 ---SAGPFARLRPGAELMQDAHIG 342


Lambda     K      H
   0.315    0.133    0.360 

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: 197
Number of extensions: 11
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 235
Length of database: 454
Length adjustment: 28
Effective length of query: 207
Effective length of database: 426
Effective search space:    88182
Effective search space used:    88182
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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