Alignments for a candidate for ilvI in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Caulobacter crescentus NA1000

Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate CCNA_00397 CCNA_00397 acetolactate synthase

Query= curated2:O53554
         (515 letters)



>FitnessBrowser__Caulo:CCNA_00397
          Length = 512

 Score =  464 bits (1195), Expect = e-135
 Identities = 263/514 (51%), Positives = 316/514 (61%), Gaps = 6/514 (1%)

Query: 1   MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60
           MNGA ALI TL D GV  CFANPGTSEM FV+ALD  PRMR +L LFEGVATGAADGY R
Sbjct: 1   MNGADALITTLADNGVTACFANPGTSEMQFVSALDREPRMRSVLCLFEGVATGAADGYGR 60

Query: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120
           +AG+PA  LLHLGPG  NG ANLHNARRA  P+V V+GDHATYH+ +DAPL SDI A+A 
Sbjct: 61  MAGKPACTLLHLGPGYANGAANLHNARRAFTPVVNVIGDHATYHRDFDAPLNSDIAALAA 120

Query: 121 TVSGWVRRTEAAADVG-ADAEAAIAASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAA 179
             S WV+  E A  VG   AEA IAA  +    A L+LPAD  W++       V   A A
Sbjct: 121 PNSVWVKSAETADSVGPLAAEAIIAAYGTPGGNACLVLPADAAWNEATVKGPMVTPPAFA 180

Query: 180 AP--VDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237
           AP    V  VA  L      ++L+G  A     L AA R+  A G R L +TF     RG
Sbjct: 181 APDAASVEAVAKALGGATKPVLLLGSGACGEAALAAAGRLA-AHGVRVLTDTFTARQARG 239

Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVL-AE 296
            G    ++L YF E A   LDGV  +VL   ++PV+FFAYP  PS LVP GC V  L   
Sbjct: 240 EGRFRPDKLPYFGELALKDLDGVDLIVLVATQTPVAFFAYPDRPSVLVPEGCSVETLCGR 299

Query: 297 PGGAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDESN 356
              AA AL ALAD +      PV   + P  P G L + +    +   +P   I+ D++ 
Sbjct: 300 EVDAAAALNALADALGAPAAGPVETYAAPDAPAGRLDAWAIGAAIARHMPTDTIISDDAV 359

Query: 357 TCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTISG 416
           T G+ +   T  A AHDWL+LTGGAIG GIP A+GAAVA PDR VL L  DG+ MYT+ G
Sbjct: 360 TAGLPIFTQTKAARAHDWLSLTGGAIGQGIPLAIGAAVACPDRKVLALTGDGAGMYTVQG 419

Query: 417 LWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIAEG 476
           LW+  RE LDVT V++ N AY IL IEL R GAG +PGP A  LLD+  P +D+VK+AEG
Sbjct: 420 LWTVVREKLDVTVVVFANHAYRILGIELGRTGAG-NPGPAAAKLLDLGDPRIDWVKLAEG 478

Query: 477 MGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
           +G+ A RV T E F +A   A A PGP LI+  +
Sbjct: 479 LGMAAERVATAEAFEEAFARAMATPGPRLIEAAM 512


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: 613
Number of extensions: 25
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: 512
Length adjustment: 35
Effective length of query: 480
Effective length of database: 477
Effective search space:   228960
Effective search space used:   228960
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