GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Acidovorax sp. GW101-3H11

Align Aspartate kinase Ask_Ect; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate Ac3H11_4087 Aspartokinase (EC 2.7.2.4)

Query= SwissProt::A4VFY3
         (476 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4087
          Length = 473

 Score =  384 bits (985), Expect = e-111
 Identities = 210/461 (45%), Positives = 296/461 (64%), Gaps = 8/461 (1%)

Query: 3   TVEKIGGTSMSRFEEVLDNIFIGRREGAALYQRIFVVSAYSGMTNLLLEHKKTGEPGVYQ 62
           +VEKIGGTSM+ F +VL +I +   +   +Y RI+VVSAYSG+TN LLEHKKTGE G+Y 
Sbjct: 10  SVEKIGGTSMTAFGDVLRHIML--HDPKRIYGRIYVVSAYSGVTNQLLEHKKTGERGIYA 67

Query: 63  RFADAQSEGAWREALEGVRQRMLAKNAELFSSEYELHAANQFINSRIDDASECMHSLQKL 122
            FA+ +    +++AL  +   +   NA        L  A+ FI+ RI  A E + ++Q +
Sbjct: 68  LFAEGKG---YQDALVNLATSLKKLNAGYADLGLPLDVADAFIDQRIGQAREYLSAMQHV 124

Query: 123 CAYGHFQLSEHLMKVREMLASLGEAHSAFNSVLALKQRGVNARLADLTGWQQEAPLPFEE 182
            A G+    + L+  RE+LAS+GE+HSAFNSV  LK  GV A L DL G+        +E
Sbjct: 125 LASGYLSRHDVLLAAREVLASIGESHSAFNSVEILKANGVKAVLMDLAGFDDNEAWTIDE 184

Query: 183 MISSHFAGFDFSRELVVATGYTHCAEGLMNTFDRGYSEITFAQIAAATGAREAIIHKEFH 242
            I+  F G D S ++VVATGYT   EG+M  FDRGYSE+TF++IA      EA+IHKEFH
Sbjct: 185 RIAHSFKGLDLSDKVVVATGYTKGTEGIMREFDRGYSEVTFSKIAVEVRPAEAVIHKEFH 244

Query: 243 LSSADPNLVGADKVVTIGRTNYDVADQLSNLGMEAIHPRAAKTLRRAGVELRIKNAFEPE 302
           LSSADPNLVG +  + +G TNYDVADQL+++GMEAIHP+AAK +  AG+ +R+KN FEP+
Sbjct: 245 LSSADPNLVGLENAIVVGATNYDVADQLADVGMEAIHPKAAKPMELAGIPIRLKNTFEPD 304

Query: 303 HGGTLISQDYKSEKPCVEIIAGRKDVFGIEVFDQDMLGDIGYDMEISKLLKQLKLYVVNK 362
           H GTLI++D+  E+  VEI+ G   V  IE+ D  M+G +G+D  +  +  + ++  + K
Sbjct: 305 HPGTLITKDFVGERARVEIVTGTDKVTLIEIHDPSMVGTVGFDAGLMNVFCKHEVSYILK 364

Query: 363 DSDANSITYYASGSRKLINRAARLIEEQYPAAEVTVHNLAIVSAIGSDLKVKGILAKTVA 422
            ++ANSI +    S+      A L ++ Y    VT+   AIV  IGS++ + G+LAK   
Sbjct: 365 ATNANSIAHLMWDSQVTPELVAEL-QKDYQV--VTIKPSAIVCTIGSNIGIPGVLAKAAQ 421

Query: 423 ALAEAGISIQAIHQSIRQVEMQCVVNEEDYDAAIAALHRAL 463
           ALA+A +++  + Q++RQV MQ V+  EDY  AI AL+ AL
Sbjct: 422 ALADAQVNVNCVSQTLRQVNMQFVIEREDYKTAIKALNMAL 462


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: 566
Number of extensions: 29
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: 476
Length of database: 473
Length adjustment: 33
Effective length of query: 443
Effective length of database: 440
Effective search space:   194920
Effective search space used:   194920
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 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