GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ketodeoxyribonate-cleavage in Dinoroseobacter shibae DFL-12

Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate 3610094 Dshi_3475 protein of unknown function DUF849 (RefSeq)

Query= reanno::WCS417:GFF1426
         (310 letters)



>FitnessBrowser__Dino:3610094
          Length = 279

 Score =  122 bits (306), Expect = 1e-32
 Identities = 94/301 (31%), Positives = 145/301 (48%), Gaps = 31/301 (10%)

Query: 5   RPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRPSQDP 64
           +P II  A+TG++ T S +P +PIT  E  ++   A EAGA+I H H R+ +D  PS DP
Sbjct: 4   KPCIICVAITGSVATKSANPAVPITVAEQVESTHEAFEAGASICHAHVRN-DDETPSSDP 62

Query: 65  ALFAEFLPQI-KAASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGLYEM 123
             FA     + K    ++I  +TGG    G E     ++  +P++ASL +GS NF     
Sbjct: 63  EKFARLQEGLQKHCPGMIIQFSTGGRSGAGRER--GGMLPLRPDMASLTVGSNNF----- 115

Query: 124 LNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYTAAH 183
                                R++ N    +  + +    +    EIE +D+ H++ AA 
Sbjct: 116 -------------------PTRVYENPPDLVDWLASEMRAHEVIPEIEAFDLSHIHHAAL 156

Query: 184 FLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLF-GSDYVWSILGAGRGQIPL 242
               G L    +IQ V G++  +    E     R T +RL  G+++  + +GA   QI +
Sbjct: 157 MHRDGRLATRPYIQFVMGVKNAMPVDRETFDFYRATVERLLPGAEWCGAAIGA--SQIVM 214

Query: 243 ATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREILGL 302
               ++ G +AR GLED++      LA SNA  VRR+  +       VA P +AREILGL
Sbjct: 215 NEWCVAEGGHARTGLEDNVRLDRETLAPSNAALVRRVVELCNQYERPVADPAQAREILGL 274

Query: 303 K 303
           +
Sbjct: 275 R 275


Lambda     K      H
   0.321    0.138    0.416 

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: 239
Number of extensions: 14
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: 310
Length of database: 279
Length adjustment: 26
Effective length of query: 284
Effective length of database: 253
Effective search space:    71852
Effective search space used:    71852
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 (21.9 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