GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Streptacidiphilus oryzae TH49

Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate WP_037571123.1 BS73_RS09750 1-phosphofructokinase family hexose kinase

Query= curated2:Q833W9
         (313 letters)



>NCBI__GCF_000744815.1:WP_037571123.1
          Length = 305

 Score =  157 bits (397), Expect = 3e-43
 Identities = 100/297 (33%), Positives = 152/297 (51%), Gaps = 10/297 (3%)

Query: 1   MIVTVTMNPSIDISYLLDHLKLDTVNRTSQVTKTPGGKGLNVTRVIHDLGGDVIATGVLG 60
           MI+TVT N ++D+SY L  L+    NR   V +  GGKG+NV RV+H LG  V+A G+ G
Sbjct: 1   MILTVTPNAALDVSYHLPELRPGEENRVRSVRERAGGKGVNVARVLHALGEPVLAAGLAG 60

Query: 61  GFHGAFIANELKKANIPQAFTSIKEETRDSIAIL--HEGNQTEILEAGPTVSPEEISNFL 118
           G  G  I +EL  + +P+A T +  E+R ++A++    G  T + E G  V+  E + F 
Sbjct: 61  GLTGRRIRDELAASGVPEALTEVTAESRRTVAVVATERGEATGLWEPGAEVAAGEWTRFR 120

Query: 119 ENFDQLIKQAEIVTISGSLAKGLPSDFYQELVQKAHAQEVKVLLDTSGDSLRQVLQGPWK 178
             + +L+ +   V + GSL  G P D Y +L   A A  V  LLD  G++L   L     
Sbjct: 121 AAYRELLARTRAVALCGSLPPGAPGDAYAQLGADARAAGVPWLLDADGEALAAGLAA--G 178

Query: 179 PYLIKPNLEELEGLLGQDFSENPLAAVQTALTKPMFAGIEWIVISLGKDGAIAKHHDQFY 238
           P L+KPN  EL  + G    +  LA  +  L      G   +V+SLG +G +A   +  +
Sbjct: 179 PDLVKPNAAELRRVAGD--GDGELAGAERLLA----LGARAVVVSLGAEGMLAVTPEGAW 232

Query: 239 RVKIPTIQAKNPVGSGDATIAGLAYGLAKDAPAAELLKWGMAAGMANAQERMTGHVD 295
           R   P +   N  G+GDA +A L+ G+A+  P  + ++  +A   A     + G  D
Sbjct: 233 RAAPPRVVHGNATGAGDAAVAALSRGVARGLPWQDRVRDAVALSAAAVASPVAGGYD 289


Lambda     K      H
   0.315    0.134    0.378 

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: 272
Number of extensions: 17
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: 313
Length of database: 305
Length adjustment: 27
Effective length of query: 286
Effective length of database: 278
Effective search space:    79508
Effective search space used:    79508
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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