GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisF in Pedobacter sp. GW460-11-11-14-LB5

Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate CA265_RS19260 CA265_RS19260 imidazole glycerol phosphate synthase subunit HisF

Query= curated2:Q4FNT7
         (251 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS19260 CA265_RS19260 imidazole
           glycerol phosphate synthase subunit HisF
          Length = 255

 Score =  151 bits (381), Expect = 1e-41
 Identities = 84/236 (35%), Positives = 142/236 (60%), Gaps = 4/236 (1%)

Query: 1   MLKNRIIPCLDV-KNGRVVKGINFVDLKDAGDPVEQAKIYSDGGADEICFLDITASKENR 59
           MLK+R+IP L + ++G +VK   F   K  GDP+   +I++    DE+  LDI ASK  R
Sbjct: 1   MLKHRVIPALLLNQHGGLVKTTKFAAPKYIGDPLNAMRIFNTKEVDELMVLDIDASKLKR 60

Query: 60  DTIYDVVERTSKKCFVPLTVGGGVRGVEDINKLLNCGADKVSINTAAVQSPEMIIESSKK 119
           +  Y ++E+ + +CF+PL  GGG++ ++   K+   G +K+ + TA ++  +++ +   +
Sbjct: 61  EPNYGLIEQFAGECFMPLCYGGGIKTIDQAYKIFKLGVEKICLQTAVLEDLDLVRDLVAR 120

Query: 120 FGSQCIVVAIDAKKNG-DKWEVFTHGGRNNTNIDAIEFAKKMEDNGAGELLVTSMDRDGT 178
           FGS  IVV++D KK+   + ++F      N N + I + K+  D GAGE+L+ ++D+DGT
Sbjct: 121 FGSSAIVVSVDVKKDWLQRPKLFKSSEGKNANENWISYIKQAVDAGAGEILLNAVDKDGT 180

Query: 179 QIGYDNDLMFKISSTVNIPIIASGGVGNLDHLVDGIRLGNASAVLAASIF-HYGTH 233
             G D  L+ + S  ++ P+IA GG+G+L  + D +  G ASAV A + F  +G H
Sbjct: 181 LQGSDLTLIKQASGEISAPLIALGGIGSLKDIKDAVDAG-ASAVAAGAFFVFHGPH 235


Lambda     K      H
   0.317    0.136    0.392 

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: 192
Number of extensions: 11
Number of successful extensions: 4
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: 251
Length of database: 255
Length adjustment: 24
Effective length of query: 227
Effective length of database: 231
Effective search space:    52437
Effective search space used:    52437
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: 46 (22.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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