GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Thiohalospira halophila HL 3

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_093427070.1 BM272_RS01980 hypothetical protein

Query= BRENDA::G4T023
         (295 letters)



>NCBI__GCF_900112605.1:WP_093427070.1
          Length = 292

 Score =  228 bits (581), Expect = 1e-64
 Identities = 132/287 (45%), Positives = 168/287 (58%), Gaps = 6/287 (2%)

Query: 7   TIFGEVLFDHFPDGSRVLGGAPFNVAWHLQAFRQEPHFISRVGQDATGDSVIAAMHKWGM 66
           TIFGEVLFD F D + VLGGAPFNVAWHL+   Q    +SR+G+D  G  +  AM +W +
Sbjct: 9   TIFGEVLFDEFGDHA-VLGGAPFNVAWHLRGLGQPARLVSRMGEDDYGRRIREAMARWDL 67

Query: 67  DMSGLQRDSRHPTGVVDIVIEQGEPAYTIVPEQAYDYID-EDELQDTDRPGLLYHGTLSL 125
           D +GLQRD+ HPTG V + +  GEP Y IV   A+D I+ E  +     PGLLYHGTL+ 
Sbjct: 68  DDAGLQRDTEHPTGRVRVELAAGEPTYEIVTGVAWDAINAEAAVAAVGHPGLLYHGTLAA 127

Query: 126 RQPVSRAALDVLKDAHKGRIFMDVNLREPWWQKDQVLEWLGQADWVKLNHHELAALYPVS 185
           R+  SRAAL+ L+ A    IF+DVNLR PWW++ ++   L  A W+KLN  ELA L    
Sbjct: 128 REGRSRAALEALR-ARADGIFVDVNLRPPWWERHRMAALLDGARWIKLNGDELAELTGAD 186

Query: 186 GDLKADMRRFVELYRLQGLIVTSGKQGAFATDHQGVSCRVTPGEIAQVIDTVGAGDAFAS 245
               A+  R  + +   G++VT G +GA      GV  R     +A   D VGAGDA A+
Sbjct: 187 DAAAAETLR--QRHGATGVLVTRGGEGAELFTESGVE-RAVAAPVAHFEDAVGAGDALAA 243

Query: 246 VMLLGLNLDWPLQITMERAQAFASAMVGQRGATVRDPVFYEPFIAAW 292
           V LLG    W   + + R    ASA+ G RGA   DP FYEPF   W
Sbjct: 244 VFLLGELAGWEAGMRLRRGVELASAVCGLRGAVSDDPDFYEPFRKQW 290


Lambda     K      H
   0.322    0.138    0.432 

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: 287
Number of extensions: 21
Number of successful extensions: 5
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: 295
Length of database: 292
Length adjustment: 26
Effective length of query: 269
Effective length of database: 266
Effective search space:    71554
Effective search space used:    71554
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: 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