GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Nitratiruptor tergarcus DSM 16512

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 WP_084275459.1 B8779_RS05065 acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase

Query= curated2:A7HJ58
         (249 letters)



>NCBI__GCF_900176045.1:WP_084275459.1
          Length = 257

 Score = 53.1 bits (126), Expect = 5e-12
 Identities = 36/111 (32%), Positives = 56/111 (50%), Gaps = 3/111 (2%)

Query: 118 IGNNAVIMMGAVINLGAIIGEG-TMIDMNTVIGARARIGKYCHIGAGSVIAGVVEPPSAQ 176
           IG N +I     IN G   G G T+I  N ++ A   +   C IG   ++A       A 
Sbjct: 80  IGKNNIIREFCFINPGTEGGGGKTVIGDNNLLMAYVHVAHDCIIGNNCILANAAT--LAG 137

Query: 177 PVIIEDNVVIGANAVILEGVRVGEHSVVAAGAVVVEDVPPYTVVAGVPAKV 227
            V + D VVIG    I + V +G+++++A  + V +D+PPY +  G  AK+
Sbjct: 138 HVELGDFVVIGGMTPIHQFVHIGDYAMIAGASAVSQDIPPYCLAEGNRAKL 188



 Score = 37.7 bits (86), Expect = 2e-07
 Identities = 26/108 (24%), Positives = 49/108 (45%), Gaps = 2/108 (1%)

Query: 106 IEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSV 165
           I P AI++   +IG N  I   A ++  A+I +   I    +I  + RIG+   +   +V
Sbjct: 2   IHPTAIVKPGAQIGKNVNIGAYAFVSKDAVIEDEVTIMQGAIIDGKTRIGEGTKVFYNAV 61

Query: 166 IAGVVEPPSAQPVIIEDNVVIGANAVILEGVRVGEHSVVAAGAVVVED 213
           +  + +    +   +E  ++IG N +I E   +   +    G  V+ D
Sbjct: 62  VGSIPQDLKFKGEEVE--LIIGKNNIIREFCFINPGTEGGGGKTVIGD 107



 Score = 28.5 bits (62), Expect = 1e-04
 Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 20/82 (24%)

Query: 129 VINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSVIAGVVEPPSAQPVIIEDNVVIGA 188
           +I+  AI+  G  I  N  IGA A + K                      +IED V I  
Sbjct: 1   MIHPTAIVKPGAQIGKNVNIGAYAFVSK--------------------DAVIEDEVTIMQ 40

Query: 189 NAVILEGVRVGEHSVVAAGAVV 210
            A+I    R+GE + V   AVV
Sbjct: 41  GAIIDGKTRIGEGTKVFYNAVV 62



 Score = 27.3 bits (59), Expect = 3e-04
 Identities = 14/58 (24%), Positives = 28/58 (48%)

Query: 111 IIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSVIAG 168
           ++  YV + ++ +I    ++   A +     +    VIG    I ++ HIG  ++IAG
Sbjct: 110 LLMAYVHVAHDCIIGNNCILANAATLAGHVELGDFVVIGGMTPIHQFVHIGDYAMIAG 167


Lambda     K      H
   0.318    0.137    0.375 

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: 211
Number of extensions: 25
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 7
Number of HSP's successfully gapped: 4
Length of query: 249
Length of database: 257
Length adjustment: 24
Effective length of query: 225
Effective length of database: 233
Effective search space:    52425
Effective search space used:    52425
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: 41 (21.6 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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