GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Kocuria turfanensis HO-9042

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_157093474.1 AYX06_RS19760 ribokinase

Query= reanno::Smeli:SMc01103
         (299 letters)



>NCBI__GCF_001580365.1:WP_157093474.1
          Length = 393

 Score =  157 bits (396), Expect = 5e-43
 Identities = 116/287 (40%), Positives = 139/287 (48%), Gaps = 26/287 (9%)

Query: 2   ITVFGSINMDLIATTARLPKPGETVAGTDFSTAAGGKGANQALAARRAGASVRMAGAVGS 61
           +TV GSIN+DL A   RLP PGETV G D     GGKGANQA+AA R     RM GAVG 
Sbjct: 109 LTVVGSINVDLTAVCERLPAPGETVIGADLQRQPGGKGANQAVAAARLAGRARMIGAVGD 168

Query: 62  DAFAEGALALLKEAGTDLDLTKTVGEPTGTAHIIVGGDGENVIVVVASANARVSGDDAAN 121
           D      L  L  AG D    + V  PTGTA I V   GEN I V A ANA VS +D + 
Sbjct: 169 DPDGGLLLRHLAAAGVDTTGVRRVPAPTGTALITVDRHGENQITVCAGANAEVSLEDVS- 227

Query: 122 VVAQMSAGDTLMLQLEIPSASVEKALSEAKRRGIRSIINIAPLTPDAARLGRMADIVIAN 181
                +  D ++ QLEI    ++     A+R      +N AP  P  A L    D+VI N
Sbjct: 228 ----FAPEDVVLCQLEI---ELDTVCETARRTPGFFALNAAPARPLPAELVERCDLVIVN 280

Query: 182 ETEFELLAGKAGIAGAEREEAMNGLHAETRQTVIVTLGAEG-VVAIHEGELHRAKGLTIE 240
           ETE+   A    +A AE               V VT GA+G  +  H  ++  A    + 
Sbjct: 281 ETEY---ARIPELADAE--------------LVAVTYGAQGSALYAHGRQIASAPAHEVA 323

Query: 241 PVDTVGAGDTFCGYLAAGLDAGLAFSEALRRAAIAGSLACLKPGAQP 287
            V TVGAGD FC  L   L AGL    ALR A   G+ A     +QP
Sbjct: 324 VVSTVGAGDAFCAALVLALAAGLDHETALRAANAVGAHAVGDASSQP 370


Lambda     K      H
   0.315    0.131    0.356 

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: 327
Number of extensions: 17
Number of successful extensions: 3
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: 299
Length of database: 393
Length adjustment: 29
Effective length of query: 270
Effective length of database: 364
Effective search space:    98280
Effective search space used:    98280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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