GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-dehydr in Synechococcus elongatus PCC 7942

Align arogenate dehydrogenase (NADP+) (EC 1.3.1.78) (characterized)
to candidate Synpcc7942_0660 Synpcc7942_0660 arogenate dehydrogenase

Query= BRENDA::P73906
         (279 letters)



>FitnessBrowser__SynE:Synpcc7942_0660
          Length = 323

 Score =  273 bits (698), Expect = 4e-78
 Identities = 143/278 (51%), Positives = 183/278 (65%)

Query: 1   MKIGVVGLGLIGASLAGDLRRRGHYLIGVSRQQSTCEKAVERQLVDEAGQDLSLLQTAKI 60
           M+IG+VGLGLIG SL  D R RGH L+G SR+ +TCE+A+ R +VD A  D ++L  A++
Sbjct: 46  MRIGIVGLGLIGGSLGFDWRDRGHRLLGYSRRPATCERAIARGVVDHASPDPAVLTEAEV 105

Query: 61  IFLCTPIQLILPTLEKLIPHLSPTAIVTDVASVKTAIAEPASQLWSGFIGGHPMAGTAAQ 120
           I L TP+ ++  T+ +L  +  P AIVTDV SVK  I      LW  F+GGHPMAGTA  
Sbjct: 106 IVLATPLGVLETTVRELRDYWHPEAIVTDVGSVKQPIVAALDPLWPRFVGGHPMAGTAEN 165

Query: 121 GIDGAEENLFVNAPYVLTPTEYTDPEQLACLRSVLEPLGVKIYLCTPADHDQAVAWISHL 180
           GI+ A   LF N PYVLTPT+ TDP  +A +  + + LG  +  C PA HD+AVA ISHL
Sbjct: 166 GIEAALRGLFQNRPYVLTPTDQTDPAAIAVVAQLAQELGSVVLHCDPASHDRAVATISHL 225

Query: 181 PVMVSAALIQACAGEKDGDILKLAQNLASSGFRDTSRVGGGNPELGTMMATYNQRALLKS 240
           PV +SA+LIQ C  E D  +  LA  LASSGF DTSRVGGGNPELG MMA YNQ ALL+ 
Sbjct: 226 PVFISASLIQTCLQEPDPAVQTLAATLASSGFCDTSRVGGGNPELGVMMARYNQAALLEQ 285

Query: 241 LQDYRQHLDQLITLISNQQWPELHRLLQQTNGDRDKYV 278
           +  Y+  L++L T I+    P +  +LQQ    R +Y+
Sbjct: 286 IDRYQIQLERLKTAIAAADEPAIAAILQQNQEMRPRYL 323


Lambda     K      H
   0.318    0.135    0.396 

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: 288
Number of extensions: 6
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: 279
Length of database: 323
Length adjustment: 27
Effective length of query: 252
Effective length of database: 296
Effective search space:    74592
Effective search space used:    74592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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