GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Herbaspirillum seropedicae SmR1

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate HSERO_RS08715 HSERO_RS08715 2-dehydro-3-deoxygluconokinase

Query= SwissProt::Q0JGZ6
         (323 letters)



>FitnessBrowser__HerbieS:HSERO_RS08715
          Length = 308

 Score =  140 bits (354), Expect = 3e-38
 Identities = 103/314 (32%), Positives = 153/314 (48%), Gaps = 18/314 (5%)

Query: 5   SELVVSFGEMLIDFVPTVAGVSLAEAPA-FVKAPGGAPANVAIAVARLGGGAAFVGKLGD 63
           S+ ++++GE +++F   +      +AP  F++  GG  +N AIA AR G  +A++  +GD
Sbjct: 2   SKTILAYGEAMVEFNQRI------DAPRQFLQGYGGDTSNFAIAAARQGAASAYLSAVGD 55

Query: 64  DEFGRMLAAILRDNGVDDGGVVFDAGARTALAFVTLRADGEREFMFYRNPSADMLLTHAE 123
           D FG+ L A+ +   VD   V    G  T + FVT  A G   F + R  SA        
Sbjct: 56  DHFGQDLLALWQREEVDVRHVAIAPGGSTGIYFVTHDAAG-HHFHYRRAGSAASAYQAKA 114

Query: 124 LNVELIKRAAVFHYGSISL-IAEPCRSAHLRAMEIAKEAGALLSYDPNLREALWPSREEA 182
           L +E I  A   H   ISL I+E    A L AM  A+ +G   S D NLR  LWP  E A
Sbjct: 115 LPLEAIAAAGALHLSGISLAISESACEAGLAAMAHARASGVTTSLDTNLRLRLWP-LERA 173

Query: 183 RTKILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYAR 242
           R ++   +   DI   S  ++  LTG++   D +V +L    +KL+   LG +GC     
Sbjct: 174 RARMEEAFRLCDICLPSWEDVSLLTGLED-RDAIVDRLLSYGVKLVAFKLGKEGCYVATS 232

Query: 243 DFRGAVPSYKVQQVDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANACGAITAT 302
           D R  V  Y V  +D TGAGD F GA +  ++    +         A ++AN   A++ T
Sbjct: 233 DQRRMVAPYPVDSLDATGAGDCFGGAFMAELMAGRDAF-------AAARYANVAAALSTT 285

Query: 303 KKGAIPSLPTEVEV 316
             GA+  +P   +V
Sbjct: 286 GYGAVEPIPRRAQV 299


Lambda     K      H
   0.320    0.136    0.388 

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: 238
Number of extensions: 15
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: 323
Length of database: 308
Length adjustment: 27
Effective length of query: 296
Effective length of database: 281
Effective search space:    83176
Effective search space used:    83176
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