GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Streptacidiphilus oryzae TH49

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_063836871.1 BS73_RS00110 SDR family oxidoreductase

Query= reanno::pseudo5_N2C3_1:AO356_20240
         (272 letters)



>NCBI__GCF_000744815.1:WP_063836871.1
          Length = 345

 Score =  140 bits (354), Expect = 3e-38
 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 2/250 (0%)

Query: 19  LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQAD 78
           L  K   +TGA  GIG+A     A + AR+   DI+    E  A      G    A++ D
Sbjct: 4   LTGKTAFVTGAGSGIGQACALRLAEEGARVAAVDIRLPAAEETAKRIEASGGTAVAVECD 63

Query: 79  VSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFR-DPLEMTEEDWRRCFAIDLDGAWYGC 137
           VS  + + A   R VE  G + V+VN AG+     D +  +E+DW R   +++   +   
Sbjct: 64  VSSGRQVAAAVSRTVEALGALHVIVNAAGILAAEGDVVACSEDDWDRVMGVNVKSMYLIG 123

Query: 138 KAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197
           K  +P+++  G GSI+NIASV     +P    Y  +K  +L LTR + ++YA +G+RVNA
Sbjct: 124 KHGVPEILRAGGGSIVNIASVFGFTALPDECAYDASKGAVLNLTRQMAVQYAKQGIRVNA 183

Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINA 257
           + P   +T L +D      D  AE+       P  R+ +P E+A    FLASD+A F+  
Sbjct: 184 LCPSDCDTPL-LDALLAGGDVEAEKAELAKPIPMGRLARPEEIASGVAFLASDDAAFVTG 242

Query: 258 SCITIDGGRS 267
             + +DGG S
Sbjct: 243 VALPVDGGSS 252


Lambda     K      H
   0.321    0.137    0.419 

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: 192
Number of extensions: 9
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: 272
Length of database: 345
Length adjustment: 27
Effective length of query: 245
Effective length of database: 318
Effective search space:    77910
Effective search space used:    77910
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 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