GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Acidovorax sp. GW101-3H11

Align 6-phosphofructokinase (EC 2.7.1.11) (characterized)
to candidate Ac3H11_779 Tagatose-6-phosphate kinase (EC 2.7.1.144) / 1-phosphofructokinase (EC 2.7.1.56)

Query= BRENDA::P06999
         (309 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_779
          Length = 318

 Score =  187 bits (476), Expect = 2e-52
 Identities = 121/302 (40%), Positives = 167/302 (55%), Gaps = 3/302 (0%)

Query: 4   IYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGG 63
           + TLTL P+LD AT T Q+ P  KLRC       GGGGINVAR +  LG    A    GG
Sbjct: 4   LITLTLNPALDLATTTAQVAPTHKLRCGPVQRFAGGGGINVARVLHRLGADVLAWALTGG 63

Query: 64  ATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEE 123
           A G  +  LLADE VP A       TR+N  V    +G+++RFV+PG  L   E++   +
Sbjct: 64  AAGAQVQQLLADEGVPTALQAIAGDTRENFSVVETITGQEFRFVLPGPTLQAAEWQACLD 123

Query: 124 QVLEIES-GAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIE 182
            +  + +    L+ SGSLPPG   +   +L  A   +G+R +VD+SG  L+AAL  G + 
Sbjct: 124 ALAALPTPPRWLIASGSLPPGTPDDFYARLARALSGRGVRMVVDTSGPPLAAALQAG-VA 182

Query: 183 LVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVV 242
           LVKP+ +EL  LV + L Q  D   AAQ +V+SG A+ V +SLG QGA+        Q  
Sbjct: 183 LVKPSLRELRELVQQPLEQAADWCAAAQSLVHSGAAETVALSLGEQGAVLATRTGVWQAP 242

Query: 243 PPPVKSQS-TVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDDTQ 301
              + + + T GAGD  + A+   L    +  E +R+GVAAG+AA L+ GT L    D Q
Sbjct: 243 ALNMPATTGTTGAGDCFLAALVWALDRGDAPAEALRWGVAAGAAALLHPGTTLAQAGDLQ 302

Query: 302 KI 303
           ++
Sbjct: 303 RL 304


Lambda     K      H
   0.314    0.131    0.363 

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: 286
Number of extensions: 18
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: 309
Length of database: 318
Length adjustment: 27
Effective length of query: 282
Effective length of database: 291
Effective search space:    82062
Effective search space used:    82062
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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:

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