GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Beijerinckia indica subsp. indica ATCC 9039

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012385734.1 BIND_RS14190 ornithine--oxo-acid transaminase

Query= curated2:Q8ZV07
         (383 letters)



>NCBI__GCF_000019845.1:WP_012385734.1
          Length = 412

 Score =  213 bits (541), Expect = 1e-59
 Identities = 128/374 (34%), Positives = 193/374 (51%), Gaps = 14/374 (3%)

Query: 5   AKYYREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAV 64
           A  Y    + +  G   +++D  G+RY+D  + +     GH +P++V A+K+Q+E +  V
Sbjct: 14  AHNYAPLPVVLSHGQGAFLFDCDGRRYLDMMSAYSAASFGHLHPRLVGALKRQLERLDLV 73

Query: 65  PLNFATPARERFIEEFSKLLPPKFGVVFLQNTGTEAVEVAIKIAKKV--------TRKPT 116
              + T     F E+ ++L           NTG EAVE AIK A++           +  
Sbjct: 74  SRAYHTDTLGPFCEDLARLTG--LDACLPMNTGAEAVETAIKAARRYGYDRLSIPEDQAE 131

Query: 117 IVAFTNSFHGRTMGSLSITWNEKYKKAFEPLYPHVRFGKFNVPHEVDKLIGEDTCCVVVE 176
           I+    +FHGRT   +  + +   ++ F P  P      F     ++  +G  T  V++E
Sbjct: 132 IIVAAGNFHGRTTTIIGFSSDAATRRGFGPFAPGFVLVPFGDAGALEAAVGPRTAAVLIE 191

Query: 177 PIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTA 236
           PIQGE G+    P +L ALR    R G LLIFDEVQ+GFGRTG  +AF+  G +PD    
Sbjct: 192 PIQGEAGIILPPPGYLAALRRLCDRHGILLIFDEVQSGFGRTGRTFAFEHEGAKPDGLIL 251

Query: 237 GKPVAGG-LPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREEDVPGRAE 295
           GK + GG LP+    A+    DVF+PG HGSTF GN + MA A  A  +L+EE +  R+E
Sbjct: 252 GKALGGGLLPVSAFAAKRSLMDVFDPGSHGSTFGGNPLAMAVAREAMHVLQEEHLVERSE 311

Query: 296 RIGAELAKALGDTGSRLAVRVKGMGLMLGLEL---RVKADQFIQPLLERGVMALTAGVNT 352
           ++G  L  AL        + V+G GL  G++L      A +    ++ERGV+       T
Sbjct: 312 KLGGVLLDALRAIDHPAVLAVRGKGLWAGVDLDPALADAKKVCLKMMERGVLTKETHATT 371

Query: 353 LRFLPPYMISKEDV 366
           +RF PP +I++ D+
Sbjct: 372 IRFAPPLVITEADL 385


Lambda     K      H
   0.320    0.138    0.408 

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: 400
Number of extensions: 21
Number of successful extensions: 5
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: 383
Length of database: 412
Length adjustment: 31
Effective length of query: 352
Effective length of database: 381
Effective search space:   134112
Effective search space used:   134112
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 (21.8 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