GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS19260
          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 (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