GapMind for catabolism of small carbon sources

 

Aligments for a candidate for 1pfk in Klebsiella michiganensis M5al

Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate BWI76_RS17175 BWI76_RS17175 6-phosphofructokinase II

Query= curated2:P23354
         (318 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS17175 BWI76_RS17175
           6-phosphofructokinase II
          Length = 310

 Score =  118 bits (295), Expect = 2e-31
 Identities = 89/281 (31%), Positives = 132/281 (46%), Gaps = 6/281 (2%)

Query: 7   TVTLNPAIDQTIQLDRLQPGAVHRASSVRNDAGGKGINVAACLADWGSQVAALGVLGVGN 66
           T+TL P++D   Q  ++ P    R S+   + GG GINVA  +   G    A+  +G   
Sbjct: 6   TLTLAPSLDSATQTPQIYPEGKLRCSAPVFEPGGGGINVARAITFLGGSATAIFPVGGAT 65

Query: 67  AGVFEALFRERGITDHCHRVAGDTRTNLKLVEAQVNETTDINLPGLQLGQAHLQGVADHL 126
                AL  +  +          TR NL +      E     +PG  L    L+ + + +
Sbjct: 66  GEHLTALLTDEHVPVDTVETHDWTRQNLHVHVNASGEQYRFVMPGAALTADELRLIEEKV 125

Query: 127 APLLRAGLPVVLSGSLPAGLPEDSWAQLQAQASAAGARVLLDTSGAPLVAALAAAPVAMP 186
             +    L +V+SGSLP G+  ++  QL   A   G R ++D+SG  L AAL    + + 
Sbjct: 126 LTIAPGSL-LVISGSLPPGISVENLTQLVKNAQRHGLRCIVDSSGDALAAALDVGNIEL- 183

Query: 187 YAVKPNRHELEAWTGHPLGDHAALTAAAHALIARG-IQLVVISMGTEGALFVQRDQQLIA 245
             VKPN+ EL A     L     +  AA  LI  G +Q VV+S+G +GAL V  D  +  
Sbjct: 184 --VKPNQKELSALVQRDLSQPDDVRLAAQELIRSGKVQRVVVSLGAQGALGVDADGSVQV 241

Query: 246 RPPRLAQGSSVGAGDAMVAGLAAALLDDATELEQCARLATA 286
            PP +   S+VGAGD+MV  +   L ++A+ LE   R   A
Sbjct: 242 VPPPMKSQSTVGAGDSMVGAMTLRLAENAS-LEDMVRFGVA 281


Lambda     K      H
   0.318    0.132    0.383 

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: 180
Number of extensions: 5
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: 318
Length of database: 310
Length adjustment: 27
Effective length of query: 291
Effective length of database: 283
Effective search space:    82353
Effective search space used:    82353
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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