GapMind for catabolism of small carbon sources

 

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

Align Fructokinase-1; Fructokinase I; OsFKI; EC 2.7.1.4 (characterized)
to candidate N515DRAFT_3101 N515DRAFT_3101 ribokinase

Query= SwissProt::Q0JGZ6
         (323 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3101
          Length = 297

 Score = 84.0 bits (206), Expect = 4e-21
 Identities = 95/320 (29%), Positives = 134/320 (41%), Gaps = 40/320 (12%)

Query: 4   RSELVVSFGEMLIDFVPTVAGVS-LAEAPAFVKAPGGAPANVAIAVARLGGGAAFVGKLG 62
           R  +V S    L+   P  AG         F+  PGG  AN A+A ARLG     +G LG
Sbjct: 3   RVVVVGSINMDLVTLAPRFAGPGETVLGERFLTVPGGKGANQAVAAARLGAEVTLIGALG 62

Query: 63  DDEFGRMLAAILRDNGV--DDGGVVFDAGARTALAFVTLRADGEREFMFYRNPSADMLLT 120
           DD FG  L   L   G+  D    + D G+ TA   V   A GE E +     +A +   
Sbjct: 63  DDTFGEQLREGLAREGIALDYVSRIDDCGSGTASITV---AGGENEIIVVPAANARVTPA 119

Query: 121 HAELNVELIKRAAVFHYGSISLIAEPCRSAHLRAMEI---AKEAGALLSYDPNLREALWP 177
             E   + I RA                 A L  MEI   + EA   L +   +   L P
Sbjct: 120 QVEAATDAIARA----------------DAVLVQMEIPLESVEATLRLGHRLGVPVILNP 163

Query: 178 SREEARTKILSIW-DQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQG 236
           +  +   K+ + W   A  V  ++ EL  L G D+ +D     L R     +++T G +G
Sbjct: 164 APAQ---KLPTEWLKLARYVTPNQHELAILLGADAQQD--FRALMRQAPGPVVLTRGGEG 218

Query: 237 CKYYARDFRGAVPSYKVQQVDTTGAGDAFVGALLRRIVQDPSSLQDQKKLEEAIKFANAC 296
             Y           + V  VDTTGAGD F GAL         ++   + L +A++ A A 
Sbjct: 219 AWYREDGEPTHQSGFAVDVVDTTGAGDTFNGAL---------AVFLHEGLPQAVRKACAA 269

Query: 297 GAITATKKGAIPSLPTEVEV 316
            A++ T+ GA   +PT VE+
Sbjct: 270 AALSVTRLGAQGGMPTRVEL 289


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: 230
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: 323
Length of database: 297
Length adjustment: 27
Effective length of query: 296
Effective length of database: 270
Effective search space:    79920
Effective search space used:    79920
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