GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Novosphingobium barchaimii LL02

Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_059153062.1 V474_RS19410 glucose 1-dehydrogenase

Query= reanno::Phaeo:GFF1301
         (257 letters)



>NCBI__GCF_001046635.1:WP_059153062.1
          Length = 260

 Score =  215 bits (548), Expect = 6e-61
 Identities = 126/254 (49%), Positives = 157/254 (61%), Gaps = 4/254 (1%)

Query: 4   LSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTARAEATAAQI---GAAAIAVELD 60
           L+GK AL+TGAA GI    A AYA +GAR+V AD +   AEATAA I   G  A A+  D
Sbjct: 3   LTGKIALVTGAASGISREIAHAYAEQGARIVCADRNGEAAEATAAAIRSAGGQAEALRCD 62

Query: 61  VTDQASIDRALSRTVECFGGLDILINNAAVFTAAPLVEVTREAYQRTFDINVSGTLFMMQ 120
           +T QA  D A+S      GGLDIL+N A +  A PL++VT +++Q  FDINV+G  FM+Q
Sbjct: 63  ITSQADRDAAVSMATSFDGGLDILVNGAGILQAQPLLDVTPDSFQSVFDINVTGLFFMLQ 122

Query: 121 AAAQQMITQGTGGKIINMASQAGRRGEPLVSVYCATKAAVISLTQSAGLNLISHGINVNA 180
           A+A+ MI  G  G+IIN+AS AGR+G      Y A+KAAVIS+TQSAG  L  H I VNA
Sbjct: 123 ASARAMIAAGRSGRIINLASIAGRQGIGTSVQYSASKAAVISITQSAGQALAPHNICVNA 182

Query: 181 IAPGVVDGEHWDGVDAF-FAKYEGKAPGQKKAEVAQSVPYGRMGTAADLTGMAVFLASED 239
           IAPG V    W  + A   A     A  +    + Q V  GR+    D+ G A+FLA E 
Sbjct: 183 IAPGFVQTAMWREIQAMAVAGSAAIAAEEFNDGIVQQVAKGRLADPGDMVGAALFLAGEG 242

Query: 240 ADYVVAQTYNVDGG 253
           A+YVV QT NVDGG
Sbjct: 243 AEYVVGQTINVDGG 256


Lambda     K      H
   0.317    0.130    0.365 

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: 176
Number of extensions: 11
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: 257
Length of database: 260
Length adjustment: 24
Effective length of query: 233
Effective length of database: 236
Effective search space:    54988
Effective search space used:    54988
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 (21.7 bits)
S2: 47 (22.7 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