Alignments for a candidate for ilvI in Bradyrhizobium sp. BTAi1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Bradyrhizobium sp. BTAi1

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012044691.1 BBTA_RS21905 acetolactate synthase large subunit

Query= curated2:O53554
         (515 letters)



>NCBI__GCF_000015165.1:WP_012044691.1
          Length = 553

 Score =  509 bits (1311), Expect = e-148
 Identities = 279/517 (53%), Positives = 353/517 (68%), Gaps = 8/517 (1%)

Query: 2   NGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARI 61
           NGAQALI TL + GV VCF NPGTSEMHFVAALD+   MR +L LFEGVATGAADGYAR+
Sbjct: 3   NGAQALIRTLANAGVRVCFTNPGTSEMHFVAALDSAAEMRAVLCLFEGVATGAADGYARM 62

Query: 62  AGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGT 121
            G PAA LLHLG GLGNGLANLHNAR+ +VP+V +VGDHATYH KYDA L+SDI+ VA  
Sbjct: 63  TGMPAATLLHLGCGLGNGLANLHNARKGKVPVVNIVGDHATYHVKYDAQLQSDIETVARN 122

Query: 122 VS-GWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGA--HAAAGVPAQA 177
           VS  +V  ++  +++  DA AA+ A+ S   Q+ATLILPADV W +G     A  +    
Sbjct: 123 VSPNFVWTSQVTSELCRDAVAAVKAACSWPGQVATLILPADVSWGEGGVPEPAPVIEPPP 182

Query: 178 AAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237
           AA    V  VA  +++G  + +L+GG A     L AAARI    G +   ETFPT ++RG
Sbjct: 183 AADDATVTEVADTIKAGGRSAILLGGTALHEESLLAAARIAATCGVKVYAETFPTRMQRG 242

Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297
           AG+PAV+R+AY AE A+ QL  +  L+L  A++PVSFFAYPG  S L P  C+V  L+ P
Sbjct: 243 AGLPAVDRIAYLAEMASIQLREIDTLILVDAKAPVSFFAYPGKKSYLAPDNCKVLTLSTP 302

Query: 298 G-GAADALAALADEV-APGTVAPVAGASRPQLPTGD-LTSVSAADVVGALLPERAIVVDE 354
              AA +L  LA  + A     P+A  +RP  P G+ LT+      VG LLPE AI++DE
Sbjct: 303 AQDAAGSLKKLAAALQAESATPPLAPPARPGRPRGNKLTAEKVCKAVGHLLPENAILIDE 362

Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414
           + + G++L + TAGAP HD +TLTGGAIG G+P A+GAA+A PDRPV+ L  DGS+MYTI
Sbjct: 363 AISSGLMLSKFTAGAPRHDLITLTGGAIGQGLPNAIGAAIACPDRPVIALIGDGSSMYTI 422

Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474
             LW+ ARE L+VT +I+NN +Y +L +EL+RVGA    GPKA   LD+  P + F +IA
Sbjct: 423 QSLWTIAREQLNVTAIIFNNASYSVLNVELERVGA-ERIGPKARAQLDLHGPVLKFAQIA 481

Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVP 511
           +GMGV A R TT +E  DAL +A   PGPHLI+ VVP
Sbjct: 482 DGMGVRATRATTPDELTDALASALKRPGPHLIEAVVP 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: 651
Number of extensions: 23
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: 553
Length adjustment: 35
Effective length of query: 480
Effective length of database: 518
Effective search space:   248640
Effective search space used:   248640
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 10 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