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.

Links

Downloads

Related tools

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:

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:

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:

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:

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