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 Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate GFF1219 PGA1_c12350 acetolactate synthase, catabolic

Query= curated2:P37251
         (574 letters)



>FitnessBrowser__Phaeo:GFF1219
          Length = 554

 Score =  173 bits (439), Expect = 1e-47
 Identities = 158/555 (28%), Positives = 240/555 (43%), Gaps = 30/555 (5%)

Query: 6   QVDSASAECTQTMSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILPRHEQ 65
           + +SA+A  T  +  A +L + L        FG PGG VL + D L  +G+   L +HE 
Sbjct: 3   ETNSAAAAATDPLRAADVLAQRLYAAGCRHAFGMPGGEVLTLVDALTKAGISFHLAKHEN 62

Query: 66  GAIHAAEGYARVSGKPGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDA 125
            A    EG     G P +++AT GPGA N V  +A+A  D +P++V TG V  +   +  
Sbjct: 63  SAGFMGEGVYHSDGAPVILVATLGPGALNGVNVVANAHQDRVPMLVLTGCVDAAEAATYT 122

Query: 126 FQEADILGITMPVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEF 185
            Q  D   +  P+TK +Y++   E    I  +A  IAT  R GPV ID+P  VA      
Sbjct: 123 HQVLDHQAVFAPITKATYRL-NAEAAGVIADKALRIATQPRNGPVHIDVPISVADAP--- 178

Query: 186 SYDHEMNLPGYQPTTEPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQ 245
           +  H   L   +  T+P    + +    ++ A +PV + G   +   A   L+ + E  Q
Sbjct: 179 AGPHRPYLAPAR-ATQPQPADLAQARAWLAEADRPVAVVGLDAVAEDAGASLRAFLEHYQ 237

Query: 246 IPVAHTLLGLGGFPADHPLFLGMAGMHGTYTANM--ALHECDLLISIGARFDDRVTGNLK 303
           IP   +    G  P DHPL LG AG+      ++   L E DL++++G  +D      ++
Sbjct: 238 IPFVTSYKAKGILPEDHPLCLGGAGLSPLADRHLLPLLREADLILALG--YDPI---EMR 292

Query: 304 HFARNA----KIAHIDIDPAEIGKIMKT-QIPVVGDSKIVLQELIKQDGKQSDSSEWKKQ 358
              RNA    +   IDI   +    M T  + VV      L+ L        D+ +    
Sbjct: 293 PGWRNAWDCSRQRVIDICAEDNTHYMHTASLTVVAGLAPSLRALTVGAQLADDAPQGN-- 350

Query: 359 LAEWKEEYPLWYVDNEEEGFK------PQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFY 412
            A W +  P    D     F       P  +I         + +   D G H++  +Q +
Sbjct: 351 -AHWPDGQPEAARDALAAAFAADADWGPAAIIAECQATLPADTLATADSGAHRILLSQMW 409

Query: 413 PFQKADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNL 472
              +    + S GL TMG  +P AIG +LAE   TVV+  GD GF M   EL    EL +
Sbjct: 410 HCYEPRALIQSSGLCTMGCAVPMAIGRKLAEPQRTVVSFSGDAGFLMVAGELSTAAELGV 469

Query: 473 PVKVVILNNACLGMVRQWQEIFYEERYSESKF-ASQPDFVKLSEAYGIKGIRISSEAEAK 531
               V+  +A L ++   Q    + R   +       DF  +  A+G  G+R+   A  +
Sbjct: 470 APIFVVFVDASLALIDLKQR---QRRLDNAGVDFGLHDFAAMGRAFGGNGVRVRDRASLR 526

Query: 532 EKLEEALTSREPVVI 546
             L EA  +    VI
Sbjct: 527 AALSEAQQAERFTVI 541


Lambda     K      H
   0.317    0.135    0.391 

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: 683
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 574
Length of database: 554
Length adjustment: 36
Effective length of query: 538
Effective length of database: 518
Effective search space:   278684
Effective search space used:   278684
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 (21.6 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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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