GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Paraburkholderia bryophila 376MFSha3.1

Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate H281DRAFT_00856 H281DRAFT_00856 2-keto-3-deoxygluconate kinase

Query= reanno::Cup4G11:RR42_RS28860
         (311 letters)



>FitnessBrowser__Burk376:H281DRAFT_00856
          Length = 311

 Score =  400 bits (1027), Expect = e-116
 Identities = 200/301 (66%), Positives = 235/301 (78%), Gaps = 3/301 (0%)

Query: 4   DILAFGEALVEFNQQPDDPSRYLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLL 63
           +ILA GEA++EFNQ   D   YLQGFGGDTSNFCIAAARQGAR G++SAVG D FG  L+
Sbjct: 10  EILALGEAMIEFNQSAKDEPNYLQGFGGDTSNFCIAAARQGARTGFVSAVGADHFGRLLI 69

Query: 64  ALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHRFDYLRSGSAASHYSHENLPHHAIAEA 123
            LW +E+VDT  VR+D  A TGVYFV+H   GH FDYLR+GSAAS Y+  +LP  AIA A
Sbjct: 70  DLWEREQVDTALVRVDPHASTGVYFVSHGPDGHAFDYLRAGSAASRYAPRDLPLDAIAAA 129

Query: 124 RYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGIMREAFAL 183
           + +H+SGISLAIS SACDA L A+ HAR  G QV+ DTNLRL+LW L RAR +M EA   
Sbjct: 130 KVIHLSGISLAISLSACDAALEAITHARANGVQVSFDTNLRLKLWPLNRARAVMLEAIRQ 189

Query: 184 TDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTLVPPYTV 243
           TD+CLPSWDD+T LTGL  RD IVD+LL  G  +VALKLG+EG+Y+ATP+ R +VP + V
Sbjct: 190 TDICLPSWDDVTELTGLTGRDEIVDFLLSHGPRVVALKLGKEGSYIATPDERRVVPGHVV 249

Query: 244 RPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPIPS---IETVL 300
             VDATGAGDCFGG+F+ARL  GDDPF+AARYANVAAALST GYGAVAPIPS   +E +L
Sbjct: 250 NAVDATGAGDCFGGAFIARLVEGDDPFEAARYANVAAALSTQGYGAVAPIPSRAAVERIL 309

Query: 301 A 301
           A
Sbjct: 310 A 310


Lambda     K      H
   0.321    0.136    0.409 

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: 356
Number of extensions: 6
Number of successful extensions: 1
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: 311
Length of database: 311
Length adjustment: 27
Effective length of query: 284
Effective length of database: 284
Effective search space:    80656
Effective search space used:    80656
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 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