GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Lentibacillus jeotgali Grbi

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_010529935.1 ON01_RS05120 pyruvate oxidase

Query= SwissProt::P0DP90
         (548 letters)



>NCBI__GCF_000224785.1:WP_010529935.1
          Length = 570

 Score =  234 bits (598), Expect = 5e-66
 Identities = 160/538 (29%), Positives = 276/538 (51%), Gaps = 24/538 (4%)

Query: 1   MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYA 58
           M  ++ V+  L+   +N ++GYPG ++  + +++   G  ++ +  RHE+ AA++A   A
Sbjct: 1   MQASEGVIEILKDWNINHIYGYPGDSVNNLVESIRKAGEAIQFIQVRHEEVAALSASAEA 60

Query: 59  RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118
           + TG  GVC++  GPGA +L+ G+ DA  DS P+V ITGQ+S   +GTD FQEV +  L 
Sbjct: 61  KITGDVGVCLSIGGPGAIHLLNGMYDAKKDSAPMVVITGQISHDLLGTDNFQEVTLERLF 120

Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178
                 +  V S  +L  ++ +AF  A + + G  ++ +P D+ L +   EP  +T+  +
Sbjct: 121 DDVAIFNRRVTSGNQLQPLLKQAFREAYN-QKGVAVLSVPDDVFLETIKQEPLRSTIVPD 179

Query: 179 VTFPHAE--VEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGA 236
           V     +  ++ A   + +A+KP++  G G     A   L  F      P   +L+G G 
Sbjct: 180 VNMTPGKKNIDNAISNIQQAKKPVILAGKGA--LDARDELVAFADKIAAPVVVSLRGKGV 237

Query: 237 VEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAP-HASVIHMDI 295
           +  ++   LG LG  GTK A  A+ E DLLI  G  F  R       F P HAS I +DI
Sbjct: 238 LPDEHRLNLGNLGQIGTKPAYEAMAETDLLILAGTSFPYR------EFLPNHASSIQIDI 291

Query: 296 DPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQ--HCAQLRDEHSWRY-----DHP 348
           +P ++ K    +V L G +   LP L + L   + +Q     Q   ++ W++     +  
Sbjct: 292 NPDKLGKWYPVNVGLAGTVKETLPHLSEQLEDQENRQFLEACQENMKNWWKHIDRLVNAD 351

Query: 349 GDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLP 408
            + +    ++  L D    D +++ DVG    W  + +  T  + F+ SS L TMG GLP
Sbjct: 352 NEQLLGAHVINGLHDFIDDDAILSVDVGNITTWTTRFLRLTN-QQFVISSWLATMGCGLP 410

Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468
            A+ A++  P++ VV I GDG F M + +  T  + QLP+ +++L+N+++GM++  Q+  
Sbjct: 411 GAIAAKLTAPDEQVVAICGDGGFSMVMHDFMTAVKYQLPITVIVLNNEKIGMIKYEQEEM 470

Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSIDE 526
               Y ET L    ++   A+  G  G  +  + ++ +AL +   S+ P ++   I++
Sbjct: 471 GNIPY-ETDLQPF-NYANFANISGGKGFKVKNEKELSSALQSAKESNVPVIVDAEIED 526


Lambda     K      H
   0.320    0.135    0.410 

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: 651
Number of extensions: 29
Number of successful extensions: 6
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: 548
Length of database: 570
Length adjustment: 36
Effective length of query: 512
Effective length of database: 534
Effective search space:   273408
Effective search space used:   273408
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: 53 (25.0 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