Alignments for a candidate for ilvH in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvH in Pseudomonas simiae WCS417

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate GFF1617 PS417_08225 acetolactate synthase

Query= curated2:P37251
         (574 letters)



>FitnessBrowser__WCS417:GFF1617
          Length = 571

 Score =  275 bits (702), Expect = 5e-78
 Identities = 179/556 (32%), Positives = 284/556 (51%), Gaps = 20/556 (3%)

Query: 34  EMIFGYP--GGAVLPIYDKLYNSGLVHILP-RHEQGAIHAAEGYARVSGKP--GVVIATS 88
           ++++GY   GG +  + D +   G   ++   HEQGA  AA   +R +     GV + TS
Sbjct: 15  KVLYGYELIGGMITHLVDSINQLGKTKLVSVHHEQGAAFAASAVSRATHHEVLGVALGTS 74

Query: 89  GPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSD------AFQEADILGITMPVTKHS 142
           GPGATNL+TG+AD  +DS P +  TGQV T  +  +       FQE D + +   +TK++
Sbjct: 75  GPGATNLITGIADCWLDSHPCLFLTGQVNTYELKGERNIRQQGFQELDSVALVSSITKYA 134

Query: 143 YQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPTTEP 202
           YQVR  ++L   +++A  +A  GRPGPVL+DIP D+   + + +      LP  Q    P
Sbjct: 135 YQVRHVDELLPCLQKAIDLAREGRPGPVLLDIPMDIQRTDIDDAAVSAFLLPCAQQIAAP 194

Query: 203 -NYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLGLGGFPAD 261
                +  +  A++ A+ P+IL G G ++        N  E   IP   +L G    PA 
Sbjct: 195 LQAADLETISNALACARNPLILLGGGAVNTPNFAHWLNQLETSGIPYVASLKGAEKIPAS 254

Query: 262 HPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NLKHFARNAKIAHIDIDPAE 320
              +LGM G +GT  AN A+  CD L+ +G+R D R TG   + FAR AK+  ID+   +
Sbjct: 255 AN-YLGMLGAYGTRAANHAVQNCDFLLVLGSRLDVRQTGAKPEDFARKAKVFQIDLMEGQ 313

Query: 321 IGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVDNEEE-GFK 379
           +   +K     V +      +    + +++  + W    A+ + ++   +VD   +    
Sbjct: 314 LNNRVKAHASYVMELNTFFADFPLCEVQEN--AAWNAWAADLRADFDQSFVDEYTDWSVS 371

Query: 380 PQKLIEYIHQFTKGEAI-VATDVGQHQMWSAQFYPFQKADKWVTSGGLGTMGFGLPAAIG 438
           P  +   +   TKG  +    DVG +QMW+A             SGGLGTMGF +PAAIG
Sbjct: 372 PFVICSTLGALTKGHGVDFVADVGNNQMWAAHTLRLSPGQSMHHSGGLGTMGFAIPAAIG 431

Query: 439 AQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGMVRQWQEIFYEER 498
           A  A  +  V+ + GDGG Q+ +QELD+I    LPV +++LNN  LGMVR +QE+++E R
Sbjct: 432 ACNAG-NKPVIVITGDGGAQLNIQELDIIARDQLPVLIIVLNNHSLGMVRGFQEMYFEGR 490

Query: 499 YSESKF-ASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVIDVRVASEEKVF 557
            S + +      F  + EAYGI    +S+  E   ++   + S  P +I++ +    +  
Sbjct: 491 NSSTYWNGYTSQFKAIGEAYGISSTVVSTHEEFAAQVGMFIESPRPALIELMMPDARECR 550

Query: 558 PMVAPGKGLHEMVGVK 573
           P +  G+ + + +  K
Sbjct: 551 PRLEFGRSIDQQLPEK 566


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: 757
Number of extensions: 39
Number of successful extensions: 8
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: 574
Length of database: 571
Length adjustment: 36
Effective length of query: 538
Effective length of database: 535
Effective search space:   287830
Effective search space used:   287830
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Protein sequences (fasta format)
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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, or view the source code, or see 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