Alignments for a candidate for ilvI in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Herbaspirillum seropedicae SmR1

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate HSERO_RS19735 HSERO_RS19735 acetolactate synthase

Query= curated2:O53554
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS19735
          Length = 518

 Score =  382 bits (982), Expect = e-110
 Identities = 233/519 (44%), Positives = 301/519 (57%), Gaps = 17/519 (3%)

Query: 3   GAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARIA 62
           GA AL   L+D GVD CFANPGT+E+  V  L++ P++R ++ L E V TGAADGY R+ 
Sbjct: 6   GAHALWAGLLDQGVDTCFANPGTTELDLVRGLESFPKLRCVVALQENVCTGAADGYGRML 65

Query: 63  GRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGTV 122
           GRPA+ LLHLGPG  NG+ANLHNARRAR P+V ++GDH ++H  YDAPL SDI+++A  V
Sbjct: 66  GRPASTLLHLGPGFANGIANLHNARRARTPIVNIIGDHTSWHLPYDAPLSSDIESLAHPV 125

Query: 123 SGWVRRTEAAADV-GADAEAAIAASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAAAP 181
           SGWV R    AD+  A AE+   ++ +G Q +TLI PAD  ++D A A+     +     
Sbjct: 126 SGWVHRITGTADIAAAAAESVRQSTAAGGQGSTLIFPADFQYADMAEASPAAATEKDTGQ 185

Query: 182 VD---VGPVAGVLRSGEPAMMLIGGDATRGPGL-----TAAARIVQATGARWLCETFPTC 233
            D          L+  +  + L+GG      GL      A ARI    G     ETFP  
Sbjct: 186 ADDYRADQALARLQGAQRVVFLLGGGGEES-GLGARAQRAVARIAAHIGCSVYAETFPAR 244

Query: 234 LERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHV 293
            ERG G+P+ +RL YF E A   LD    +VL GA  P+++F Y G PS LV A   +  
Sbjct: 245 AERGQGLPSFDRLPYFPEPARKVLDDADLVVLVGALPPITYFGYVGHPSALV-APERLLT 303

Query: 294 LAEPG-GAADALAALADEV-APGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIV 351
           ++ PG  AA  +  LAD + AP  V P    + P LP G+LT    A V+   LPERAIV
Sbjct: 304 ISLPGRPAAGRVEQLADALGAPAYVTP--QHALPPLPEGELTPQKIAAVLARELPERAIV 361

Query: 352 VDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAM 411
             E  TCG      +  A  H  LT TGGAIG G+P A+GAAVA PDR V+ L SDGS  
Sbjct: 362 SVEGGTCGYPFYAVSDAARPHTVLTNTGGAIGQGLPVALGAAVACPDRTVVGLLSDGSTQ 421

Query: 412 YTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFV 471
           YTI  LWS A EN  V  +I  N  Y ILR EL+R GA    G +A  +  +  P +D+V
Sbjct: 422 YTIQTLWSLAHENARVVVLIAANHQYAILRNELRRDGA--PLGERAAQMTALDHPRIDWV 479

Query: 472 KIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
            +A+  GVPA R  T ++    L+AAFA  GP LI++ +
Sbjct: 480 GLAQSYGVPASRAETAQQLQQQLQAAFAGTGPALIEMAL 518


Lambda     K      H
   0.318    0.134    0.402 

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: 636
Number of extensions: 24
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: 515
Length of database: 518
Length adjustment: 35
Effective length of query: 480
Effective length of database: 483
Effective search space:   231840
Effective search space used:   231840
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis