GapMind for catabolism of small carbon sources

 

Alignments for a candidate for levDE in Hafnia paralvei ATCC 29927

Align PTS system mannose-specific EIIAB component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_008812475.1 M988_RS15865 PTS N-acetylgalactosamine transporter subunit IIB

Query= CharProtDB::CH_088329
         (323 letters)



>NCBI__GCF_001655005.1:WP_008812475.1
          Length = 160

 Score =  106 bits (265), Expect = 3e-28
 Identities = 54/141 (38%), Positives = 83/141 (58%), Gaps = 1/141 (0%)

Query: 166 LARIDDRLIHGQVATRWTKETNVSRIIVVSDEVAADTVRKTLLTQVAPPGVTAHVVDVAK 225
           + RID+RL+HGQV   WT     + ++V +D+ AAD V++ L+  V   GV      + K
Sbjct: 8   MTRIDNRLVHGQVGVTWTSSLGANLVLVANDDAAADPVQQNLMDMVVADGVQTRYFTLEK 67

Query: 226 MIRVYNNPKYAGERVMLLFTNPTDVERLVEGGVKITSVNVGGMAFRQGKTQVNNAVSVDE 285
            I V +      +++ ++   P DV  LV+GGV I+ VNVG M F +GK Q++  VSV++
Sbjct: 68  TIEVIHKAADR-QKIFIVCKTPQDVLTLVKGGVPISFVNVGNMHFAEGKRQIHKTVSVND 126

Query: 286 KDIEAFKKLNARGIELEVRKV 306
            D  AF++L   G+  EVR+V
Sbjct: 127 SDTAAFRELEKLGVTCEVRRV 147


Lambda     K      H
   0.316    0.133    0.375 

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: 107
Number of extensions: 7
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: 160
Length adjustment: 22
Effective length of query: 301
Effective length of database: 138
Effective search space:    41538
Effective search space used:    41538
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: 46 (22.3 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