GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Bacillus altitudinis 41KF2b

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate WP_035702093.1 BA79_RS08060 aldo/keto reductase

Query= SwissProt::O32210
         (276 letters)



>NCBI__GCF_000691145.1:WP_035702093.1
          Length = 279

 Score =  366 bits (939), Expect = e-106
 Identities = 175/276 (63%), Positives = 222/276 (80%), Gaps = 4/276 (1%)

Query: 5   LKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVG--- 61
           L+ T  L+NGV MP FGLGVF+VE G E  E+VK AI+ GYRSIDTA+IY NEEGVG   
Sbjct: 4   LQSTKTLNNGVRMPGFGLGVFQVEEGTELIEAVKTAIQLGYRSIDTASIYGNEEGVGRGI 63

Query: 62  -IGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKDKYK 120
            +G+ E+G+ RE++F+TSKVWN D GYE TL A+E SL++LQLDYLDLYLIHWP + KYK
Sbjct: 64  QLGLAETGLRREDIFVTSKVWNADLGYEATLKAYEDSLKKLQLDYLDLYLIHWPVEGKYK 123

Query: 121 DTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCK 180
           + WRALE LY++GK+RAIGVSNFQ HHL+ELL DA+I P +NQVEFHP+LTQ+ L  Y K
Sbjct: 124 EAWRALETLYREGKVRAIGVSNFQPHHLDELLTDADIIPAINQVEFHPKLTQETLFTYLK 183

Query: 181 GQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRII 240
             GIQ+EAWSPLMQG+LL + ++T++A  ++K+ AQ+ILRWD+Q GV+TIPKS K HR+ 
Sbjct: 184 THGIQMEAWSPLMQGELLHHPLITELAGTYSKTPAQIILRWDVQKGVITIPKSTKAHRLK 243

Query: 241 ENADIFDFELSQEDMDKIDALNKDERVGPNPDELLF 276
           ENADIFDF LS EDM ++  LN+++R+GP+PD   F
Sbjct: 244 ENADIFDFVLSDEDMKRLSDLNENKRIGPDPDNFDF 279


Lambda     K      H
   0.316    0.135    0.397 

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: 316
Number of extensions: 16
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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: 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