Alignments for a candidate for ilvI in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Nitriliruptor alkaliphilus DSM 45188

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_052667645.1 NITAL_RS18575 acetolactate synthase large subunit

Query= curated2:O53554
         (515 letters)



>NCBI__GCF_000969705.1:WP_052667645.1
          Length = 519

 Score =  605 bits (1560), Expect = e-177
 Identities = 326/519 (62%), Positives = 377/519 (72%), Gaps = 7/519 (1%)

Query: 1   MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60
           MNGA ALI TLV   VDVCF NPGTSEMHFVAALD VP MRG+L LFEGVATGAADGYAR
Sbjct: 1   MNGANALIRTLVGADVDVCFTNPGTSEMHFVAALDDVPEMRGVLALFEGVATGAADGYAR 60

Query: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120
           IAGRPAAVLLHLGPGLGNGLANLHNARRA  P+V +VGDHA  HK+ DAPLESDI+ VA 
Sbjct: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRAATPVVNIVGDHALPHKQLDAPLESDIETVAR 120

Query: 121 TVSGWVRRTEAAADVGAD-AEAAIAASRSGSQIATLILPADVCWSDGAHAAAGV-PAQAA 178
            VS WVR + + ADVG D AEA  AA  S  Q+ATLILPADV W DG   A  V PA   
Sbjct: 121 NVSSWVRTSTSTADVGRDAAEAVAAAIGSPGQVATLILPADVSWGDGGVVADPVAPAGRR 180

Query: 179 AAPVD-VGPVAGVLRSGEPAMMLIGGDATRGP-GLTAAARIVQATGARWLCETFPTCLER 236
             P D +   A  LRSGE  ++L+GGDA   P  + AAA I QA+GA  L E FPT L R
Sbjct: 181 GVPADTITGAAKALRSGEATLILVGGDALADPTAVDAAATIAQASGAAILAEVFPTRLAR 240

Query: 237 GAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAE 296
           G G+  ++RL Y +E A+ QL GV+HL+L GA  PV+FFAYP  PS LVP G EVH+LA 
Sbjct: 241 GQGVAPLDRLGYLSEAASQQLAGVRHLILVGAEEPVTFFAYPDKPSRLVPEGTEVHMLAG 300

Query: 297 PGGAA-DALAALADEVAPGTVAPVAGASRP-QLPTGDLTSVSAADVVGALLPERAIVVDE 354
              AA DALAALADE+    VAP   A  P Q PTG L + +A+  VGALLPE AIVVDE
Sbjct: 301 ASDAAGDALAALADELGCAGVAPPRPAGEPSQRPTGQLDAWTASLAVGALLPEGAIVVDE 360

Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414
           + T  + LP  TA +P HDWLTLTGG+IGYG+PAAVGAA+AAPDR VL L++DGSAMYTI
Sbjct: 361 AVTSSLSLPMTTAASPRHDWLTLTGGSIGYGLPAAVGAAIAAPDRKVLALQADGSAMYTI 420

Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474
             LW+ ARE LDVT V+YNN +Y+IL++ELQRVGA +  GP A DL D+ RP +DF ++A
Sbjct: 421 QSLWTMAREELDVTVVLYNNASYEILKMELQRVGADT-TGPAAADLFDLGRPRLDFTELA 479

Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVPSL 513
            GMGVPA R TT +EF   L AA A PGP L++ ++P L
Sbjct: 480 RGMGVPATRATTADEFTVQLEAALATPGPSLVEAMIPKL 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: 724
Number of extensions: 39
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: 515
Length of database: 519
Length adjustment: 35
Effective length of query: 480
Effective length of database: 484
Effective search space:   232320
Effective search space used:   232320
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