Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Desulfitobacterium hafniense DCB-2

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_015943252.1 DHAF_RS05900 thiamine pyrophosphate-binding protein

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000021925.1:WP_015943252.1
          Length = 591

 Score =  372 bits (956), Expect = e-107
 Identities = 212/592 (35%), Positives = 338/592 (57%), Gaps = 47/592 (7%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M GA+ +   L  + V  ++G PG A+LPFYDA+   ++     RHEQAA   ADGY+RA
Sbjct: 24  MTGAQFLAAFLAKKGVSQIYGIPGAAILPFYDAVRELNMESYNVRHEQAAIFMADGYSRA 83

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +GKVGVC  TSGPGATN +TG+ +A+SDS P++ALTGQVPT LIG D+FQE   + +  P
Sbjct: 84  TGKVGVCAATSGPGATNFLTGLYSAYSDSVPLLALTGQVPTSLIGKDSFQEAPMVEMARP 143

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDID------KHPIP 174
           + K  + ++K   +P I +  +E+A TG+ GP+ +DLP DVQ+  +++D        P P
Sbjct: 144 VTKAAYLVEKAGDLPRILKEGWELATTGKKGPILLDLPLDVQKGLVEVDWSEFDFSPPQP 203

Query: 175 SKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPV 234
            + ++      TI         + ++  AK P +LAGGG++   A E L +  ELL IPV
Sbjct: 204 PRQEIAQDTLNTI---------LSMLYEAKTPTLLAGGGIVQGNAAELLRETAELLQIPV 254

Query: 235 CTTLMGKGCISENHPLALGMVG-MHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT 293
            ++LMGK     +HPL  G+VG M  T   N  + ESD++I++G RF  R TGD + F +
Sbjct: 255 VSSLMGKDAFPNDHPLYGGLVGTMCQTPLGNKTILESDLIINLGGRFDGRGTGDSQRFQS 314

Query: 294 NAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENI--SQ 351
             K++H+++D  E+ ++++ ++ +  D +  L+  +  L            DK  I   Q
Sbjct: 315 GRKVVHVNLDNRELSRHISTELAVAADIRDFLEHFLAFL-----------RDKGFIPTPQ 363

Query: 352 WIENVNSLKKSSIPV---MDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMW 408
             + +  L++  I +     +D +P+KPQ+ + E+        + ++ I+T D G +Q+W
Sbjct: 364 ARQRILDLQEERIRLARRTKFDTLPLKPQQAIAEVREA-----MARDGILTLDCGISQIW 418

Query: 409 MAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTI 468
               F+   PRSFL +G  GTMG+G  +A+GAK+A PD +V+ + GD    M+ QEL T 
Sbjct: 419 ATQLFEAYVPRSFLITGRAGTMGWGLGAALGAKLAYPDRQVVNLLGDASLGMSLQELATA 478

Query: 469 AEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYG 519
           A++NIPVV+ + +N   G++ Q QNL + +R  S +              DF+  A   G
Sbjct: 479 AKHNIPVVVVVLNNSLFGLIRQQQNLLFEQRCISTDLEYENHVQGHSRGLDFVATARGMG 538

Query: 520 IKARRIESPNEINEALKEAINCDEPYLLDFAIDPSSALSMVPPGAKLTNIID 571
           ++A  ++ P++I  AL  A + + PYL++  +DP +  S+   G  LT +++
Sbjct: 539 VEAELVDGPDQIQGALARAFSQNRPYLIEVLVDPLAQCSVSLDGT-LTGVLE 589


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: 752
Number of extensions: 37
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: 599
Length of database: 591
Length adjustment: 37
Effective length of query: 562
Effective length of database: 554
Effective search space:   311348
Effective search space used:   311348
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