GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argB in Klebsiella michiganensis M5al

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate BWI76_RS23220 BWI76_RS23220 amino-acid N-acetyltransferase

Query= BRENDA::Q9X2A4
         (282 letters)



>FitnessBrowser__Koxy:BWI76_RS23220
          Length = 443

 Score =  139 bits (350), Expect = 1e-37
 Identities = 92/286 (32%), Positives = 150/286 (52%), Gaps = 11/286 (3%)

Query: 2   RIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHG 61
           R + V     ++PYI    GKTFVI  GG A++ +N   + + DI LL   GI+ ++V+G
Sbjct: 6   RTELVEGFRHSVPYINAHRGKTFVIMLGGEAIEHDNFS-SIVNDIGLLHSLGIRLVVVYG 64

Query: 62  GGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEM---VLVGKINKEIVMNLNLHGGRAV 118
             P I   + +   EPV+    RVTD KT+E+V+    +L  +I   + M+LN    +  
Sbjct: 65  ARPQIDANLAEHRHEPVYHKQTRVTDAKTLELVKQAAGMLQLEITARLSMSLNNTPLQGA 124

Query: 119 GICGKDSKLIVAEKETKHGDIGYV--GKVKKVNPEILHALIENDYIPVIAPVGIGEDGHS 176
            I       I+A+       + Y   G++++++ E +H  ++N  I ++ PV +   G S
Sbjct: 125 HINVVSGNFIIAQPLGVDDGVDYCHSGRIRRIDEEAIHRQLDNGAIVLMGPVAVSVTGES 184

Query: 177 YNINADTAAAEIAKSLMAEKLILLTDVDGVL-KDGKLISTLTPDEA----EELIRDGTVT 231
           +N+ ++  A ++A  L AEK+I      GV  +DG+++  L P+EA    EE+  D   +
Sbjct: 185 FNLTSEEIATQLAIKLKAEKMIGFCSSQGVYNQDGEIVPELFPNEAQARVEEIEADEDYS 244

Query: 232 GGMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277
            G +  +  AV A R GV   H+I+      +L E+FSR GIGT I
Sbjct: 245 SGTVRFLRGAVKACRSGVRRCHLISYQENGTLLQELFSRDGIGTQI 290


Lambda     K      H
   0.318    0.140    0.393 

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: 284
Number of extensions: 21
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: 282
Length of database: 443
Length adjustment: 29
Effective length of query: 253
Effective length of database: 414
Effective search space:   104742
Effective search space used:   104742
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: 49 (23.5 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