GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA' in Paucidesulfovibrio gracilis DSM 16080

Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 (characterized)
to candidate WP_078715827.1 B5D49_RS01240 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase

Query= SwissProt::Q6LZE3
         (272 letters)



>NCBI__GCF_900167125.1:WP_078715827.1
          Length = 266

 Score =  323 bits (828), Expect = 2e-93
 Identities = 147/259 (56%), Positives = 202/259 (77%)

Query: 9   NVGKLIRLERIFDKKSEKTVIIPMDHGVSSGPLDGIKDMRITTNAVADGGANAVLGHKGL 68
           ++GK IRLERIF++ + +T+++PMDHGV+ GP++GI+DMR   + V +GGANAVL HKG 
Sbjct: 2   HIGKAIRLERIFNRNTHRTIVVPMDHGVTVGPIEGIEDMREAVSRVVEGGANAVLEHKGN 61

Query: 69  VRHGHRGYGRDIGLIIHMSAGTSISPDPNKKVIVTTVEDAMRMGADAVSLHVNVGAESDF 128
           VR GHR  GRD+GLI+H+SA T +SP PN K +V +VEDA+ +GADAVS+H+N+G +++ 
Sbjct: 62  VRCGHRAEGRDVGLIVHLSASTCLSPRPNYKGLVASVEDAVCLGADAVSVHLNLGDDNET 121

Query: 129 EMYRDLGLISETCEHWGMPLIAMMYPRGPKIKDEKDPEVVAHAARLGAELGADIIKTNYT 188
           +M RD+G ++     WGMPL+AM+Y RGPK+KDE DP VVAH AR+G ELGAD++K NYT
Sbjct: 122 DMLRDVGRVATDAARWGMPLLAMVYARGPKVKDEYDPAVVAHCARVGTELGADVVKVNYT 181

Query: 189 GDPDTFKEVVKGCPAPIVIAGGPKTNTDEEFLQMVKDAMHAGGKGVASGRNVFQHKDVKG 248
           GDPD+F  V   C  P+VIAGGPK ++  EFLQMV+D++ AGG G++ GRNVFQH  V  
Sbjct: 182 GDPDSFSRVTGACCIPVVIAGGPKMDSTGEFLQMVRDSLMAGGAGLSVGRNVFQHPRVTK 241

Query: 249 ITSAICKIVHEDVEVEEAL 267
           +  A+  +VHED++V+EA+
Sbjct: 242 LVQALSMVVHEDMQVDEAV 260


Lambda     K      H
   0.317    0.137    0.398 

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: 322
Number of extensions: 11
Number of successful extensions: 1
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: 272
Length of database: 266
Length adjustment: 25
Effective length of query: 247
Effective length of database: 241
Effective search space:    59527
Effective search space used:    59527
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: 47 (22.7 bits)

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

Links

Downloads

Related tools

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