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_017359243.1 BA79_RS05245 aldo/keto reductase

Query= SwissProt::O32210
         (276 letters)



>NCBI__GCF_000691145.1:WP_017359243.1
          Length = 281

 Score =  425 bits (1093), Expect = e-124
 Identities = 210/276 (76%), Positives = 238/276 (86%), Gaps = 2/276 (0%)

Query: 1   MPTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGV 60
           M  SL DTV L+NGVEMPWFGLGVFKVE+GN+  ++VKAAI+NGYRSIDTAA+YKNE GV
Sbjct: 1   MVKSLNDTVTLNNGVEMPWFGLGVFKVEDGNQVVDAVKAAIRNGYRSIDTAAVYKNETGV 60

Query: 61  GIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGK--DK 118
           G  IKESGV REELFITSKVWN DQGY+  LAAF+ SL RL LDYLDLYLIHWPG   D 
Sbjct: 61  GKAIKESGVKREELFITSKVWNTDQGYDKALAAFDASLNRLGLDYLDLYLIHWPGPNADT 120

Query: 119 YKDTWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDY 178
           +K+TWRALEKLYKDGK+RAIGVSNF V HLEELLKDAE+ P VNQVEFHP+LT  ELR Y
Sbjct: 121 FKETWRALEKLYKDGKVRAIGVSNFYVQHLEELLKDAEVVPAVNQVEFHPKLTLVELRQY 180

Query: 179 CKGQGIQLEAWSPLMQGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHR 238
            K +GIQ+EAWSPLMQG+LLD++VL +IA ++NKSVAQVILRWDLQ GVVTIPKSI E R
Sbjct: 181 AKEKGIQIEAWSPLMQGKLLDHDVLKEIAAQYNKSVAQVILRWDLQSGVVTIPKSINEER 240

Query: 239 IIENADIFDFELSQEDMDKIDALNKDERVGPNPDEL 274
           I +NADIFDFELSQEDM+KI+ALN +ERVG NP+ +
Sbjct: 241 IKQNADIFDFELSQEDMEKINALNNNERVGSNPETM 276


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: 368
Number of extensions: 21
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: 281
Length adjustment: 25
Effective length of query: 251
Effective length of database: 256
Effective search space:    64256
Effective search space used:    64256
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