Alignments for a candidate for ilvI in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Hydrogenovibrio halophilus DSM 15072

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_019895085.1 A377_RS0104925 acetolactate synthase large subunit

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000384235.1:WP_019895085.1
          Length = 547

 Score =  315 bits (806), Expect = 4e-90
 Identities = 198/562 (35%), Positives = 303/562 (53%), Gaps = 41/562 (7%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M  A+  ++ LE E VE +FG PG   +   DAL  SD+  +  RHEQ AA  AD Y R 
Sbjct: 1   MKAAKRFVQCLENEGVEFVFGVPGEENMDILDALLDSDIRFITCRHEQGAAFMADVYGRI 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G+ GVC+ T GPGATNLVTGVA A+ D SP+VA+ GQ  T  +  ++ Q +D + LF P
Sbjct: 61  TGRAGVCLSTLGPGATNLVTGVADANMDRSPIVAIAGQAATTRLHKESHQVVDLVSLFKP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHP-IPSKVKL 179
           I K+  Q+ +   +PE+ R AF++AQ  +PG   ID P+++QE+       P +P+++ L
Sbjct: 121 ISKYATQVLEPETLPEVVRKAFKLAQAEKPGASFIDFPENIQEMLTPETPLPVVPTRLSL 180

Query: 180 IGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239
             +        + +K+A ++I  AKRP+IL G GV  + A++++    E   IP+  T M
Sbjct: 181 ADH--------KLLKQAAQIIDQAKRPMILVGNGVARANASKQVQAFAEHRQIPLVNTFM 232

Query: 240 GKGCISE-NHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAK-- 296
            KG +    +PL++G  G+      N   + SDV+I +G    D +      +  N +  
Sbjct: 233 AKGSVPHYKNPLSMGTTGLQKGDYENGGFANSDVVICVG---FDMVEYHPHLWNPNREHT 289

Query: 297 IIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENV 356
           I+HID   AE+  +   DV +VG+    LK + + L           ND           
Sbjct: 290 IVHIDTCAAEVDYSYMPDVELVGNIGRNLKALSEHL---------PANDTP------PQP 334

Query: 357 NSLKKSSIPVMDYDD----IPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412
             L+++ I  MD  +     P+KPQKI+ +L   +D     K+ I   DVG ++MWMA +
Sbjct: 335 FPLRQAMIAEMDQFENDQAWPLKPQKIIWDLRTAMD-----KDAIAICDVGAHKMWMARF 389

Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472
           F+ + P + + S G  +MG   P A+GAK+A PD  V+ +TGD G MMN QEL T     
Sbjct: 390 FRAEQPNTCIISNGFASMGIALPGAVGAKLAHPDKAVVAVTGDAGLMMNVQELETALREQ 449

Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532
            P+VI I+++   G++ +W+     +R   ++F   PDF+  A+S+G    RIES +++ 
Sbjct: 450 TPIVILIWNDSQYGLI-EWKQKRRFQRSAYIDFKN-PDFVTFAQSFGATGVRIESADQLL 507

Query: 533 EALKEAINCDEPYLLDFAIDPS 554
            ALK AI      L+D  +D S
Sbjct: 508 PALKTAIATPTVTLIDCPVDYS 529


Lambda     K      H
   0.319    0.137    0.405 

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: 748
Number of extensions: 27
Number of successful extensions: 7
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: 599
Length of database: 547
Length adjustment: 36
Effective length of query: 563
Effective length of database: 511
Effective search space:   287693
Effective search space used:   287693
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 (21.7 bits)
S2: 53 (25.0 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