Alignments for a candidate for ilvI in Geobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Geobacter lovleyi SZ

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_083768575.1 GLOV_RS05490 thiamine pyrophosphate-binding protein

Query= curated2:O08353
         (599 letters)



>NCBI__GCF_000020385.1:WP_083768575.1
          Length = 564

 Score =  352 bits (904), Expect = e-101
 Identities = 220/573 (38%), Positives = 316/573 (55%), Gaps = 35/573 (6%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           MN AE ++++LE   V  +FG PGGA+     AL+ S +  ++ +HE+ AA  ADGYAR 
Sbjct: 3   MNAAEVIVRSLEKHGVTCVFGVPGGAIESLNTALYKSSISVIVAKHEEGAAFMADGYARV 62

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDA-----L 115
           SG + VC  T+GPGATN++TG+A+A  DS P++ALTGQV T L G  A QE        +
Sbjct: 63  SGVIAVCCSTAGPGATNMITGIASAFGDSIPVIALTGQVSTSLFGKGAIQEFSVQSFGIV 122

Query: 116 GLFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPS 175
            +F  I K++  I    +  E+   A  +A TGR GPVH++LP D+ + ++  D H   S
Sbjct: 123 SIFRQITKYSDIIINENKAGEMISRARRLALTGRKGPVHLNLPADIMKRKVTDDSHERCS 182

Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235
             +++G++         +KKA +L+  AKRP+I+AG G +LS A++ELL+L ELL+IPV 
Sbjct: 183 TTQVLGFD------REAVKKAAQLLLGAKRPVIVAGWGTVLSRADKELLELAELLDIPVA 236

Query: 236 TTLMGKGCISENHPLALGMVGMHGTKPA-NYCLS-ESDVLISIGCRFSDRIT-GDIKSFA 292
           T+   KG +SE HPL+LG++G  G+  A  Y L  + DVL+++G  F++ +T G  K   
Sbjct: 237 TSPKAKGILSEVHPLSLGVLGFAGSPVAKEYILKRDVDVLLAVGTSFNEFVTSGWDKRLL 296

Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352
               +IH+DID  EIGKN  V V I GDA  +L+E++ ++  I      EN  ++ + Q 
Sbjct: 297 PMKSLIHVDIDCNEIGKNYYVHVGIAGDAATVLRELVFEIGRIRKGRRIENTRRKEVEQ- 355

Query: 353 IENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLN--INKNTIITTDVGQNQMWMA 410
                 L K+            K  K +     +I DLN  + KNT+   D G +  W  
Sbjct: 356 -VRAALLVKTR-----------KQNKALYSPHRLIMDLNEALPKNTLYFADNGNSMAWAI 403

Query: 411 HYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAE 470
            Y     P SF    G  +MGF   + IGAK+A  D  V+ + GDG F+MN  E+ T   
Sbjct: 404 RYLTITEPYSFYVGLGFASMGFAVAAPIGAKLAAGDRPVVALVGDGSFLMNGMEVATAVN 463

Query: 471 YNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNE 530
           YNIPV+  I +N  LGMVY  + L          F    D +KLAE+ G +  RI +P E
Sbjct: 464 YNIPVIWVIMNNAMLGMVYHGRKLAGIPEGIPSGFKPV-DHVKLAEALGARGIRITTPGE 522

Query: 531 IN-EALKEAINCDEPYLLDFAIDPSSALSMVPP 562
           IN E + + +    P +LD  IDP      VPP
Sbjct: 523 INRELMDDILAAGVPTVLDVIIDPEE----VPP 551


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: 766
Number of extensions: 41
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: 564
Length adjustment: 36
Effective length of query: 563
Effective length of database: 528
Effective search space:   297264
Effective search space used:   297264
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