GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Magnetospirillum magneticum AMB-1

Align UDP-glucose 4-epimerase; EC 5.1.3.2; Galactowaldenase; UDP-galactose 4-epimerase (uncharacterized)
to candidate WP_011382485.1 AMB_RS00195 nucleoside-diphosphate sugar epimerase

Query= curated2:Q56623
         (328 letters)



>NCBI__GCF_000009985.1:WP_011382485.1
          Length = 318

 Score =  229 bits (584), Expect = 7e-65
 Identities = 130/311 (41%), Positives = 179/311 (57%), Gaps = 4/311 (1%)

Query: 12  ILLTGSTGFVGTNLVKSLTLKSDYIVKSAVRHAVNKDDGLLFEVGDINASTDFELPLKNT 71
           +L+TG+ GFVG  L + L     ++  +        D       G + A  ++   L+  
Sbjct: 3   VLVTGANGFVGQPLCRRLAELGHHVAGAVRGQPYLPDCVERRPAGRLVADGNWSAALEGM 62

Query: 72  TVVVHCAARAHVMDDKEAEPLTLYREVNTAGTVNLAKQAIDSGVKRFIFISSIKVNGEGT 131
             VVH AAR HVM D   +PL  +R  N AGT+ LA+QA  +G+   +F+SSIK NGE T
Sbjct: 63  QAVVHLAARVHVMHDASHDPLAEFRAANGAGTLRLAEQAAQAGIGHLVFLSSIKANGEET 122

Query: 132 LVGCPFKTEDNHAPEDDYGLSKSEAEKQLVALAKDSSMEVVIIRPTIVYGPGVKANFASL 191
               PF    N AP D YG+SK EAE+ L  +A  + + V ++RP +VYGPGVK NF +L
Sbjct: 123 -THTPFGPL-NAAPVDPYGISKLEAEQGLAEIAARTGLAVTVLRPPLVYGPGVKGNFRAL 180

Query: 192 MRLVSKGIPLPFGSITQNKRSLVSINNLVDLIVTCIDHPKAANQ--VFLVSDGHDVSTAE 249
           +RLV++G+PLP G  T N+RSL+ + NLVD I   +D P    Q  VF + D    STA+
Sbjct: 181 IRLVNRGLPLPLGCCTHNRRSLIGLGNLVDAIRAVLDQPPHPGQCRVFTLCDAEAPSTAD 240

Query: 250 MVRELAIALDKPTWQLPVPIWCYKLFGKLFGKSDIVDRLTGTLQVDISHTKETLGWKPPQ 309
           +VR LA AL +P   LP+P+   +L   L GK   + RLT +L+VD S     +GW PP+
Sbjct: 241 LVRSLARALGRPARLLPIPVGLMRLGAGLLGKGAAIQRLTASLEVDGSALAAAIGWVPPE 300

Query: 310 TLQEGFKQTAQ 320
           TL EG   TA+
Sbjct: 301 TLDEGLTATAR 311


Lambda     K      H
   0.318    0.134    0.388 

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: 256
Number of extensions: 9
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: 328
Length of database: 318
Length adjustment: 28
Effective length of query: 300
Effective length of database: 290
Effective search space:    87000
Effective search space used:    87000
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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