GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Klebsiella michiganensis M5al

Align 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58) (characterized)
to candidate BWI76_RS27945 BWI76_RS27945 2-oxo-3-deoxygalactonate kinase

Query= BRENDA::A6TFZ6
         (292 letters)



>FitnessBrowser__Koxy:BWI76_RS27945
          Length = 291

 Score =  448 bits (1152), Expect = e-131
 Identities = 218/292 (74%), Positives = 256/292 (87%), Gaps = 1/292 (0%)

Query: 1   MTARYIAIDWGSTNLRAWLYQGEECLESRQSEAGVTRLNGRSPAAVLAEITQHWRDGATP 60
           MT+RYIAIDWGSTNLRAWLYQ ++CLESRQS AGVTRLNG SPAAV +EIT+ WRDGATP
Sbjct: 1   MTSRYIAIDWGSTNLRAWLYQDDQCLESRQSAAGVTRLNGESPAAVFSEITRGWRDGATP 60

Query: 61  VVMAGMVGSNVGWKIAPYLPLPAAFSDIGQQLTAVGDNIWIIPGLCVSRDDNHNVMRGEE 120
            V+AGMVGSNVGWK+APYLP+P  FS IGQQLT+VGD +WIIPGL VSRD N NVMRGEE
Sbjct: 61  AVLAGMVGSNVGWKVAPYLPVPVDFSAIGQQLTSVGDKVWIIPGLSVSRDANQNVMRGEE 120

Query: 121 TQLLGARALAPSSVYVMPGTHCKWVLADRRQIHDFRTVLTGELHHLLLQLSLVGAGLPPQ 180
           TQLLGAR +APSS+YVMPGTHCKWV ADR+QI+DFRTV+TGELH+LLL+ SLVGAGLP Q
Sbjct: 121 TQLLGARMIAPSSIYVMPGTHCKWVQADRQQINDFRTVMTGELHYLLLRHSLVGAGLPEQ 180

Query: 181 ETSAAAFAAGLQRGINNPAVLPQLFEVRASHVLGALPREQVSEFLSGLLIGAEVATLSDT 240
            ++  AF AGL+RG+++P +LP+LFEVRASHVLG+LPREQV EFLSGLLIGAEVATLS+ 
Sbjct: 181 VSAPGAFNAGLERGLHSPDILPRLFEVRASHVLGSLPREQVGEFLSGLLIGAEVATLSER 240

Query: 241 FAGQQAISLVAGSSLTSRYQQAFAAIGREVSAVAGDTAFQTGIRSIAYAVAN 292
           F   Q +++V G +L +RYQQA +AIGR+ + V+GD AFQTG+RSI +AVAN
Sbjct: 241 FRDPQ-VTIVGGEALANRYQQALSAIGRQTTVVSGDNAFQTGVRSIIHAVAN 291


Lambda     K      H
   0.319    0.133    0.397 

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: 366
Number of extensions: 8
Number of successful extensions: 2
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: 292
Length of database: 291
Length adjustment: 26
Effective length of query: 266
Effective length of database: 265
Effective search space:    70490
Effective search space used:    70490
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 (21.8 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:

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