Alignments for a candidate for ilvI in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Phaeobacter inhibens BS107

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate GFF1906 PGA1_c19360 acetolactate synthase isozyme, large subunit

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__Phaeo:GFF1906
          Length = 601

 Score =  302 bits (773), Expect = 3e-86
 Identities = 183/569 (32%), Positives = 290/569 (50%), Gaps = 38/569 (6%)

Query: 4   AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63
           AE ++  L    VE +FG  G   +    AL  S +  +  RHEQ A+HAAD YAR +G+
Sbjct: 16  AEHIVDFLGRRNVEHVFGLCGHTNIAVLAALADSPIDFITVRHEQIASHAADAYARVTGR 75

Query: 64  VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALG------L 117
             V +    PG TN  TGVA A  D  PMV + G +PT   G    QE++         +
Sbjct: 76  ASVVLSHLSPGLTNCATGVANAALDCVPMVVIAGDIPTHYYGKHPHQEVNLHADAAQWEI 135

Query: 118 FMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKV 177
           + P VK  +++ +   + EI   AF +A++G+PGPV +++P D+    +  D        
Sbjct: 136 YRPFVKRAWRVDRADLMAEILEKAFHLAESGQPGPVLVNVPMDIFSEVISSDTFD----- 190

Query: 178 KLIGYNPTTIGHPRQ----IKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIP 233
             I  N  T+  P       ++ +  +A+AK P+   GGG+LL+ A+ E+ +    + +P
Sbjct: 191 -RIASNTKTLVKPSMDDETARRIVSGLAAAKDPVAYIGGGILLAQASAEIEEFATHMGLP 249

Query: 234 VCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDR--------IT 285
           +  +LMGKG + ++HPL +GM G  GT+  N     +DV+ ++G RF +          T
Sbjct: 250 IAHSLMGKGAVRDDHPLVMGMTGFWGTELVNQTCLNADVVFAVGTRFKEADCSSWYPGYT 309

Query: 286 GDIKSFATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND 345
            +I +   + K+IHIDI+P EIG+N   ++ +V DAK  L+ + +    +          
Sbjct: 310 FNIGAKGNDTKVIHIDIEPQEIGRNYPTEIGVVADAKAALRVLTRVAKDMYPDGFNRTEK 369

Query: 346 KENISQWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQN 405
           K  I+ + E+    K S++ +      P+ P++I+ +    + D     + IITTDVG N
Sbjct: 370 KAEIAAFRED---FKASNVEMQTSAAFPMMPERILADTRIALPD-----DAIITTDVGWN 421

Query: 406 QMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQEL 465
           +  +   F   TP S L+ GG  TMGFG P+AIGAK+A P+  V+ + GDGGF  N   L
Sbjct: 422 KNGVGQQFDILTPGSILTPGGFATMGFGPPAAIGAKLAAPERVVLSLVGDGGFGQNPSML 481

Query: 466 GTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGA------PDFIKLAESYG 519
            T  E N+ ++  + +N   G +   Q   YG    +   G A      P + ++A +YG
Sbjct: 482 ATAVELNLGIIWLVMNNNAFGTIAGLQKAHYGLTYGTTFPGSAAAPTNGPGYAEIARAYG 541

Query: 520 IKARRIESPNEINEALKEAINCDEPYLLD 548
            +  RI S +E+  AL+ AI   +P +LD
Sbjct: 542 AEGIRISSADELLPALQAAIASGKPTVLD 570


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: 844
Number of extensions: 42
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: 601
Length adjustment: 37
Effective length of query: 562
Effective length of database: 564
Effective search space:   316968
Effective search space used:   316968
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 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