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.
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:
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