GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Novosphingobium aromaticivorans DSM 12444

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_011906689.1 SARO_RS18085 aminotransferase

Query= BRENDA::P9WPZ5
         (397 letters)



>NCBI__GCF_000013325.1:WP_011906689.1
          Length = 393

 Score =  258 bits (659), Expect = 2e-73
 Identities = 168/392 (42%), Positives = 218/392 (55%), Gaps = 19/392 (4%)

Query: 3   VSRLRP-YA---TTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYP 58
           + RL P YA    T+F  MS LA  +GA+NLGQGFPDE  PP +L+A   A A   +QYP
Sbjct: 5   LQRLHPVYAGMPVTIFEHMSGLARELGAINLGQGFPDEAPPPALLEALSRAAAERSHQYP 64

Query: 59  PGPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPF 118
           P  G   LRRA+A       G++   E+ V+VT GATEA+A A+L  V PG EVLL  P 
Sbjct: 65  PMAGIPELRRAVAGFYAWTQGLEVGAES-VIVTSGATEAVACAILAAVAPGDEVLLFSPA 123

Query: 119 YDSYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSA 178
           YD+Y+P++  AG   V VPL P    +  D  A+  AVTPRTRAL++N P NPTG V + 
Sbjct: 124 YDAYAPLIRRAGGVPVFVPLSPPH--WRYDEAAIVAAVTPRTRALVLNDPLNPTGTVAAD 181

Query: 179 TELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTG 238
           TELA IA + V  +L+ I DEV+E++ FD  RH  L    GMA RTI I SA K+F  TG
Sbjct: 182 TELAMIASLCVRHDLIAICDEVWENVRFDGRRHRSLLALPGMARRTIKIGSAGKIFGATG 241

Query: 239 WKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRL 298
           WK+GW     ++ A +  A Q+L++      Q AVA  L+ + A  A         R  L
Sbjct: 242 WKVGWMVAAPDMAAVLARAHQFLTFTTAPMLQWAVAQGLE-DPALAAGCTARWAETRGVL 300

Query: 299 AAGLTEIGFAVHDSYGTYFLCADPRPLG--YDDSTEFCAALPEKVGVAAIPMSAFCDPAA 356
              L   GF V D+  T+F C D    G   DD T F      + GVA+IP+SA  +   
Sbjct: 301 IEALGRRGFTVLDTTATWFTCIDLAASGIALDDRT-FSDRAVREAGVASIPLSALWE--- 356

Query: 357 GQASQQADVWNHLVRFTFCKRDDTLDEAIRRL 388
           G A+ +      +VR   CK +  L EA+ RL
Sbjct: 357 GDAAPEG-----IVRLCHCKPEAMLLEAMDRL 383


Lambda     K      H
   0.321    0.135    0.405 

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: 471
Number of extensions: 28
Number of successful extensions: 4
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: 397
Length of database: 393
Length adjustment: 31
Effective length of query: 366
Effective length of database: 362
Effective search space:   132492
Effective search space used:   132492
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 (21.9 bits)
S2: 50 (23.9 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