GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisB in Klebsiella michiganensis M5al

Align imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (EC 4.2.1.19; EC 3.1.3.15) (characterized)
to candidate BWI76_RS18935 BWI76_RS18935 bifunctional imidazole glycerol-phosphate dehydratase/histidinol phosphatase

Query= ecocyc::IMIDPHOSPHADEHYDHISTIDPHOSPHA-MONOMER
         (355 letters)



>FitnessBrowser__Koxy:BWI76_RS18935
          Length = 355

 Score =  639 bits (1648), Expect = 0.0
 Identities = 311/355 (87%), Positives = 330/355 (92%)

Query: 1   MSQKYLFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPELLKLQKAGYKLVMITNQDGLG 60
           M+QK+LFIDRDGTLISEPP DFQVDRFDKLAFEP VIP LLKLQ+ GYKLVMITNQDGLG
Sbjct: 1   MTQKFLFIDRDGTLISEPPVDFQVDRFDKLAFEPQVIPALLKLQQEGYKLVMITNQDGLG 60

Query: 61  TQSFPQADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAM 120
           T S PQ +FDGPHNLMMQIF SQGV FDEVLICPHLPAD CDCRKPK +LV  +L +  M
Sbjct: 61  TASLPQDEFDGPHNLMMQIFASQGVNFDEVLICPHLPADNCDCRKPKTRLVLPWLEQGVM 120

Query: 121 DRANSYVIGDRATDIQLAENMGITGLRYDRETLNWPMIGEQLTRRDRYAHVVRNTKETQI 180
           D A+SYVIGDRATDIQLA+NMGITGLRYDRE L+WP I EQLTRRDRYAHV R TKETQ+
Sbjct: 121 DTAHSYVIGDRATDIQLADNMGITGLRYDREQLDWPTICEQLTRRDRYAHVERITKETQV 180

Query: 181 DVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALG 240
           DV+VWLDREGGSKI+TGVGFFDHMLDQIATHGGFR+E+NV GDLYIDDHHTVEDTGLALG
Sbjct: 181 DVKVWLDREGGSKISTGVGFFDHMLDQIATHGGFRLEVNVGGDLYIDDHHTVEDTGLALG 240

Query: 241 EALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEH 300
           EALK+ALGDKRGI RFGFVLPMDECLARCALDISGRPHLEYKA+FTYQRVGDLSTEM+EH
Sbjct: 241 EALKLALGDKRGIGRFGFVLPMDECLARCALDISGRPHLEYKADFTYQRVGDLSTEMVEH 300

Query: 301 FFRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355
           FFRSLSYTM VTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRV+GDTLPSSKGVL
Sbjct: 301 FFRSLSYTMAVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVQGDTLPSSKGVL 355


Lambda     K      H
   0.322    0.140    0.420 

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: 579
Number of extensions: 14
Number of successful extensions: 3
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: 355
Length of database: 355
Length adjustment: 29
Effective length of query: 326
Effective length of database: 326
Effective search space:   106276
Effective search space used:   106276
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 (21.9 bits)
S2: 49 (23.5 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