Alignments for a candidate for ilvI in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Hydrogenophaga taeniospiralis NBRC 102512

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_068174522.1 HTA01S_RS20055 acetolactate synthase large subunit

Query= curated2:O53554
         (515 letters)



>NCBI__GCF_001592305.1:WP_068174522.1
          Length = 556

 Score =  548 bits (1413), Expect = e-160
 Identities = 296/520 (56%), Positives = 358/520 (68%), Gaps = 11/520 (2%)

Query: 2   NGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARI 61
           NGAQAL+ TLVD GVDVCF NPGTSEMHFVAALD  PRMR +L LFEGVATGAADGYAR+
Sbjct: 3   NGAQALMKTLVDAGVDVCFTNPGTSEMHFVAALDHEPRMRAVLALFEGVATGAADGYARM 62

Query: 62  AGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGT 121
           AG+PAA LLHLG GLGNGLANLHNAR+ RVP+V +VGDHAT+H  YDA L+SDI+ VA  
Sbjct: 63  AGKPAATLLHLGCGLGNGLANLHNARKGRVPVVNIVGDHATFHTVYDAQLQSDIETVARN 122

Query: 122 VS-GWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGAHAA--AGVPAQA 177
           VS G+VR ++  A++  DA  AI A+R    Q+ATLILPADV W +G        +P   
Sbjct: 123 VSPGFVRTSQTTAELCRDAADAITAARGLPGQVATLILPADVSWGEGGEPCPPPPLPQPE 182

Query: 178 AAAPVDVGPVAGVL----RSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTC 233
           AA+   V  +A  +    RSG     L+GG A R PGL AAAR+   +G + L E FPT 
Sbjct: 183 AASDATVSAIAQAISQAARSGGKTAFLLGGQALREPGLLAAARVAAHSGVKLLAEVFPTR 242

Query: 234 LERGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHV 293
           LERGAG+P VER+AY AE A  QL  V+HLVL  A++PVSFFAYPG  SDLVP  C VH 
Sbjct: 243 LERGAGLPPVERIAYLAEMAGVQLAEVQHLVLVDAKAPVSFFAYPGKKSDLVPDTCTVHT 302

Query: 294 LAEP-GGAADALAALADEVAPGTVAP-VAGASRPQLPTGDLTSVSAADVVGALLPERAIV 351
           LA P   A  +L  LA  +      P +  A RP  P G L +      VG LLPE AIV
Sbjct: 303 LASPEQDAVGSLHKLAAALGAAQAQPALQAAQRPGRPRGKLNAAKVCKAVGHLLPEHAIV 362

Query: 352 VDESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAM 411
           +DE+ T G++L   TAGAP HD +TLTGGAIG G+P AVGAA+A P RPVL L  DG+AM
Sbjct: 363 IDEAITSGLMLSAMTAGAPRHDLITLTGGAIGQGLPNAVGAAIACPTRPVLALIGDGTAM 422

Query: 412 YTISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFV 471
           YT+  LW+ ARE L+VT++I+NN +Y +L +EL+RVGA ++ GPKA   LD+  P + F 
Sbjct: 423 YTLQALWTMAREQLNVTSIIFNNASYSVLNVELERVGA-TEAGPKAKSQLDLHGPVLHFA 481

Query: 472 KIAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVP 511
           ++A+GMGV   R TT E+F  AL  A A PGPHLI+ VVP
Sbjct: 482 QLAQGMGVHGVRATTTEDFLKALEYALAHPGPHLIEAVVP 521


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: 737
Number of extensions: 30
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: 556
Length adjustment: 35
Effective length of query: 480
Effective length of database: 521
Effective search space:   250080
Effective search space used:   250080
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