GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Nocardioides daejeonensis MJ31

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_110207115.1 DNK54_RS11370 ribokinase

Query= reanno::acidovorax_3H11:Ac3H11_3034
         (350 letters)



>NCBI__GCF_003194585.1:WP_110207115.1
          Length = 310

 Score = 46.6 bits (109), Expect = 9e-10
 Identities = 82/276 (29%), Positives = 108/276 (39%), Gaps = 53/276 (19%)

Query: 78  RGLHDAGVALAAPTPVRAPSAL--------ALAALDAEG-KASYSFYRDGVADRQVTAAA 128
           +G + A  A  A   VR   A+        ALA L AE    S      GVA    T  A
Sbjct: 41  KGANAAVAAARAGAEVRYVGAVGADDLGTGALAELVAENIDVSGVVVEPGVA----TGTA 96

Query: 129 LTAACSALPELQVVATGCLALVAQDAALYLPWLAAQRAAGRMVVVDANLRL----SAVDD 184
           L     A      VA G  A+V+ ++   +  LA  R     V+V   + +    +AV+ 
Sbjct: 97  LIVVDHAGENQIAVAAGANAVVSPESVRQV--LARSRGWATCVLVSTEIPMDAVVAAVET 154

Query: 185 ADAYR-------ANVMAALQHAHLIKVSD----------DDLEALAIPGANALERAHFLQ 227
           A AY        A V A L  A L+ +S           D   AL  P   +LE      
Sbjct: 155 ARAYDLPCVLNPAPVAAGL--AGLVSMSPVLTPNQGELRDLCRALGEPDETSLEAMASAV 212

Query: 228 QQTQAQWLALTLGPNGAWLLQRDGLAVHAREEAPITVVDTVGAGDCFLAGLITAWLAGPE 287
             +    +A+TLG +G  +   DG   H        VVDT GAGD F  G++ A LA  E
Sbjct: 213 AHSSKAAVAVTLGADGVMVADPDGSTCHIPAAPVAEVVDTTGAGDTF-NGVLAAALASGE 271

Query: 288 -------RGEDALAL-------RAGGLTAPVTEARL 309
                  RG  A ++       RAG  TA V +A L
Sbjct: 272 TISGAVRRGVAAASISVGSAGARAGMPTAEVIDAAL 307


Lambda     K      H
   0.320    0.133    0.392 

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: 250
Number of extensions: 13
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: 350
Length of database: 310
Length adjustment: 28
Effective length of query: 322
Effective length of database: 282
Effective search space:    90804
Effective search space used:    90804
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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