GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Novosphingobium barchaimii LL02

Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_059153662.1 V474_RS23850 aspartate kinase

Query= SwissProt::A4VFY3
         (476 letters)



>NCBI__GCF_001046635.1:WP_059153662.1
          Length = 484

 Score =  435 bits (1118), Expect = e-126
 Identities = 235/475 (49%), Positives = 308/475 (64%), Gaps = 3/475 (0%)

Query: 2   HTVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVY 61
           H+VEKIGGTSM+    V DN+ +  REGA LY RIFVVSAY+GMT+LLLEHKK+G  GV+
Sbjct: 5   HSVEKIGGTSMAATSTVFDNVLVAGREGADLYNRIFVVSAYAGMTDLLLEHKKSGRAGVH 64

Query: 62  QRFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQK 121
             F   ++ GAWR AL  V   M  +NAE+F+       A+ F+  RI     C+  L +
Sbjct: 65  AHFIRNETPGAWRAALGEVMDAMTVRNAEMFARIESRAEADAFVTKRIAALETCLDDLDR 124

Query: 122 LCAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFE 181
           L A+G F L E +  VREMLA LGEAHSA ++ L L+ RGV+A   DLT W  E     +
Sbjct: 125 LRAHGRFCLKEQMTTVREMLAGLGEAHSAHSTALMLRDRGVDAVFVDLTLWDNEDMRSLD 184

Query: 182 EMISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEF 241
           + I    A  D +R++ + TGY  C  G++  + RGYSE+TF++IA  T AREAIIHKEF
Sbjct: 185 DRIVEALAPIDLARQMPIVTGYAGCEGGMVRRYARGYSEMTFSRIAVLTQAREAIIHKEF 244

Query: 242 HLSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEP 301
           HLSSADP LVG      IGRTNYDVADQL+NLGMEAIHPRA + LR++G+ LR++N F+ 
Sbjct: 245 HLSSADPRLVGEAVARKIGRTNYDVADQLANLGMEAIHPRAGRGLRQSGIPLRVRNTFDR 304

Query: 302 EHGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVVN 361
             GGTLI  DY SE P VEI+ G   V  ++VF+QDM+G+ GYD  I   L +   ++V+
Sbjct: 305 HDGGTLICGDYVSEHPRVEIVTGLSSVQALQVFEQDMVGEKGYDAAILDTLTRHGAWIVS 364

Query: 362 KDSDANSITYYASG--SRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAK 419
           K S+AN+IT+Y SG  S ++    A  IE  +P A VTV  +A+VS IGSDL   G++ +
Sbjct: 365 KSSNANTITHYLSGTDSAQMAGIVAD-IEAHWPGAAVTVQPVAMVSVIGSDLAEPGLVPR 423

Query: 420 TVAALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRALIEPENHGDVIA 474
            + AL  AGI + A+   IR V++Q VV  ED+D A+  LH+ L+E     DV A
Sbjct: 424 ALMALGGAGIGMAAMQHQIRNVDVQFVVAVEDFDPAVRVLHKVLVEGAALTDVKA 478


Lambda     K      H
   0.318    0.133    0.372 

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: 598
Number of extensions: 24
Number of successful extensions: 3
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: 476
Length of database: 484
Length adjustment: 34
Effective length of query: 442
Effective length of database: 450
Effective search space:   198900
Effective search space used:   198900
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 26 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