Alignments for a candidate for ilvI in Rhizobium etli CFN 42

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhizobium etli CFN 42

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011428581.1 RHE_RS27855 hypothetical protein

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000092045.1:WP_011428581.1
          Length = 541

 Score =  226 bits (576), Expect = 2e-63
 Identities = 173/563 (30%), Positives = 273/563 (48%), Gaps = 44/563 (7%)

Query: 5   EAMIKALEAEKVEILFGYPGGALLPFYDALHHS-DLIHLL-TRHEQAAAHAADGYARASG 62
           +A+ ++L A  ++ +FG PG  +  F DAL+ + D I  + TRHEQ AA+ A GYA+++G
Sbjct: 9   QAITRSLVAHGIDTIFGIPGAHMYDFNDALYDAGDKIRFIHTRHEQGAAYMAYGYAKSTG 68

Query: 63  KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQ--EI-DALGLFM 119
           ++G      GPG  N    + TA+  ++P++ +TG + + LIG    Q  E+ D L    
Sbjct: 69  RIGAYTVVPGPGVLNSGAALCTAYGANAPVLCITGNIMSHLIGRGRGQLHELPDQLATMR 128

Query: 120 PIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDV-QELELDIDKHPIPSKVK 178
            I K   +I    +   +         +GR GP  ++ P DV  +   +ID       V+
Sbjct: 129 GITKTAERINHPSEAGTVMAGLVAKMLSGRQGPGAVEAPWDVFGQSAPEID-------VR 181

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
           +    P    +P QI  A  LI+ A  P+I+ GGG   + A+ E+  L ELL  PV +  
Sbjct: 182 VGARVPHPAVNPNQIAAAAALISGASNPMIMVGGGA--ADASAEIAALAELLQAPVTSHR 239

Query: 239 MGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298
            GKG + ++HP+ L  V       A     + DVLI IG R   +     K      KII
Sbjct: 240 SGKGIVPDDHPIYLNFVA------AYEYWKKVDVLIGIGSRLELQFMR-WKWLPKGLKII 292

Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358
            ID+DP E+ + +  D+ IV  A+   + +          D+   + +E+ ++    +N 
Sbjct: 293 RIDVDPTEMVR-LKPDLGIVAAARDGTQALA---------DAVAGSRREDRTREFAELND 342

Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418
             KS           ++PQ  +  L A+ + L   ++     ++ Q        F    P
Sbjct: 343 EAKSRFSA-------VQPQ--LGYLQAIREALP--RDGFFVEEISQMGFTARFAFPVYGP 391

Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478
           R +++ G    +GFGF +A+G KVA PD  VI ++GDGGFM   QEL T  ++ I VV  
Sbjct: 392 RQYVTCGYQDNLGFGFNTALGVKVAHPDKAVISVSGDGGFMFGVQELATAVQHKIAVVAI 451

Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538
           +F+N   G V + Q   Y  R    +    PDF+ L ES+GI++ R  SP E+   L+ A
Sbjct: 452 VFNNSAYGNVLRDQKQTYKGRTLGSDLTN-PDFVALGESFGIRSFRATSPEELKNILETA 510

Query: 539 INCDEPYLLDFAIDPSSALSMVP 561
           +  DEP L++  ++  S  S  P
Sbjct: 511 LALDEPVLIEVPVEKGSEASPWP 533


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: 736
Number of extensions: 44
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: 541
Length adjustment: 36
Effective length of query: 563
Effective length of database: 505
Effective search space:   284315
Effective search space used:   284315
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