GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Azorhizobium caulinodans ORS 571

Align 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized)
to candidate WP_043879531.1 AZC_RS17440 homocitrate synthase

Query= curated2:Q8RCF9
         (384 letters)



>NCBI__GCF_000010525.1:WP_043879531.1
          Length = 399

 Score =  311 bits (796), Expect = 3e-89
 Identities = 164/368 (44%), Positives = 218/368 (59%)

Query: 7   KPVYIVDTTLRDGEQTAGVVFANNEKIRIAQMLDEIGIDQLEVGIPTMGGDEKETVAKIA 66
           +  ++ DTTLRDGEQ  GV F   EKI IA  L   G+ ++E G P MG +E ET+  I 
Sbjct: 14  RTAFLNDTTLRDGEQAPGVAFTRKEKIEIAAALAAAGVPEIEAGTPAMGDEEVETIRSIV 73

Query: 67  KLGLKASIMAWNRAVVKDVQESLECGVDAVAISISTSDIHIEHKLKKTRQWVLDSMTEAV 126
            L L   +MAW R    D+  ++  GV  V +SI TSD  +  KL K R W L  + E V
Sbjct: 74  SLNLPTRVMAWCRMSEDDLMAAVAAGVKIVNVSIPTSDRQLAGKLGKDRAWALGRVAEVV 133

Query: 127 RFAKKEGVYVSVNAEDASRTDMNFLIEFARCAKQAGADRLRFCDTVGFLDPFKTYEMVKA 186
             A++ G  V+V  ED+SR D +FL   A  AK AGA RLR  DT+G LDPF TY +V+ 
Sbjct: 134 TLARRLGFEVAVGGEDSSRADPDFLCRLAETAKAAGAFRLRLADTLGVLDPFGTYALVRR 193

Query: 187 IKDAVDIEIEMHTHNDFGMATANALAGVKAGAKFVGVTVNGLGERAGNAALEEVVMALKY 246
           +    DIE+E H H+D G+ATAN LA V  GA+   VTV GLGERAGNAALEEV +AL+ 
Sbjct: 194 VAATTDIELEFHAHDDLGLATANTLAAVMGGARHASVTVAGLGERAGNAALEEVAIALRQ 253

Query: 247 VYKMDLGIDTSRFREISEYVALASGRPLPPSKAIVGKNVFAHESGIHVDGALKNPYTYEV 306
             + + GI  +  + ++E V  A+ RP+P  KAIVG +VF HESGIHV G LK+  TYE 
Sbjct: 254 TARAETGIAPAALKPLAELVCGAAARPVPRGKAIVGADVFTHESGIHVSGLLKDRATYEA 313

Query: 307 FDPQEVGLERQIVIGKHSGTAALINKFKEYGRVLTEEEANLLLPHVRKMAIQLKRPLFDK 366
            +P+  G    +V+GKHSG AA+     + G  +       +L  VR  A++ K  +  +
Sbjct: 314 LNPELFGRGHTVVLGKHSGLAAVEKALADEGITVDAVRGRAILDRVRAFAVRTKENVSRE 373

Query: 367 ELMYLYED 374
            L+  Y+D
Sbjct: 374 TLLRFYQD 381


Lambda     K      H
   0.318    0.135    0.379 

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: 355
Number of extensions: 12
Number of successful extensions: 1
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: 384
Length of database: 399
Length adjustment: 31
Effective length of query: 353
Effective length of database: 368
Effective search space:   129904
Effective search space used:   129904
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: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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