GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Dyella japonica UNC79MFTsu3.2

Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate N515DRAFT_0916 N515DRAFT_0916 Sugar or nucleoside kinase, ribokinase family

Query= SwissProt::P26420
         (307 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0916
          Length = 312

 Score = 91.7 bits (226), Expect = 2e-23
 Identities = 91/306 (29%), Positives = 135/306 (44%), Gaps = 31/306 (10%)

Query: 4   KIWVLGDAVVDLLPDG------------EGRLLQCPGGAPANVAVGVARLGGDSGFIGRV 51
           ++ V+G+  VDL+  G                L  PG +    A+G+ARLG    F GR+
Sbjct: 8   RVLVVGEVNVDLVLKGLHAEPAPGQEVLADDFLMTPGSSSMICAMGLARLGNAVAFHGRL 67

Query: 52  GDDPFGRFMRHTLAQEQVDVNYMRLDAAQRTSTVVVDLDSHGERTFTFMVRPSADLFLQP 111
           G D +G +    L    +DV  ++ +AA RT  + V L +  +R+        A L  + 
Sbjct: 68  GADAWGSYCLDALRDAGIDVASLQPEAALRTG-ITVSLSTPRDRSLVTFSGAIAALRAED 126

Query: 112 EDLPPFAAGQWLHVCSIALSAEPSRSTTFAALEAIKRAGGYVSFDPNIRSD-LWQDPQDL 170
                 A    LHV S  L  +  R+         ++AG  +S DP    +  W D  DL
Sbjct: 127 VSDALLAGAGHLHVSSFYLQ-KALRADIRQLFARARKAGLTLSLDPGFDPEQRWGD--DL 183

Query: 171 RDCLDRALALADAIKLSEEELAFISGSDDIVSGIARL-NARFQPTLLLVTQGKAGVQAAL 229
           R  L+      D    +EEEL  ++G + +   +A L N R   TL++  +G+ G     
Sbjct: 184 RGVLED----VDVFLPNEEELRALTGENHVRKALAALDNGR---TLIVAKRGRQGCAVLH 236

Query: 230 RGQVSHFPARPVVAVDTTGAGDAFVAGLLAGLAAHGIPDNLAALAPDLALAQTCGALATT 289
            G++   PA  V AVD+TGAGD+F AG L      G+P     L   L     CG+L+T 
Sbjct: 237 DGKLLVAPALAVEAVDSTGAGDSFDAGFLHAW-LRGLP-----LRDCLRWGNACGSLSTR 290

Query: 290 AKGAMT 295
             G  T
Sbjct: 291 GIGGTT 296


Lambda     K      H
   0.321    0.137    0.406 

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: 200
Number of extensions: 10
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: 307
Length of database: 312
Length adjustment: 27
Effective length of query: 280
Effective length of database: 285
Effective search space:    79800
Effective search space used:    79800
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