GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Echinicola vietnamensis KMM 6221, DSM 17526

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate Echvi_3562 Echvi_3562 Aldo/keto reductases, related to diketogulonate reductase

Query= SwissProt::O32210
         (276 letters)



>FitnessBrowser__Cola:Echvi_3562
          Length = 319

 Score =  201 bits (512), Expect = 1e-56
 Identities = 120/284 (42%), Positives = 167/284 (58%), Gaps = 36/284 (12%)

Query: 13  NGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKES----G 68
           NG  MP  GLG ++ + G E   +V  AI+ GYR  D A IYKNE+ +G    ++     
Sbjct: 8   NGDTMPIIGLGTWQSKPG-EVYNAVLKAIEIGYRHFDCAYIYKNEKEIGDAFAKAFADGT 66

Query: 69  VAREELFITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWP-------------G 115
           + RE++++TSK+WN+    E  L A E +L+ LQLDYLDLYL+HWP             G
Sbjct: 67  IKREDIWVTSKLWNDSHKPEHVLPALESTLKDLQLDYLDLYLVHWPLALKHGVDFPEENG 126

Query: 116 KDKYKD------TWRALEKLYKDGKIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPR 169
             ++ D      TW A+E L + GK++ IGVSNF++  L+E+L  A+ KP VNQVE HP 
Sbjct: 127 DFEHLDNIPLSTTWAAMEGLLETGKVKHIGVSNFKIEKLKEILASAKSKPEVNQVEMHPF 186

Query: 170 LTQKELRDYCKGQGIQLEAWSPL-----MQGQ-------LLDNEVLTQIAEKHNKSVAQV 217
           L Q+ L DYCK +GI L A++PL      QGQ       LL+N+ +  IA K N + AQV
Sbjct: 187 LPQQGLVDYCKKEGIHLTAYAPLGAAYRTQGQDGVDLPILLENDQVKNIANKLNATTAQV 246

Query: 218 ILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQEDMDKIDAL 261
           +L W++Q  +  IPKS+   RI EN       LSQE+MD+++ L
Sbjct: 247 VLAWNIQRDIAVIPKSVTPSRIEENFKSNLLTLSQEEMDQLNQL 290


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: 276
Number of extensions: 13
Number of successful extensions: 5
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: 319
Length adjustment: 26
Effective length of query: 250
Effective length of database: 293
Effective search space:    73250
Effective search space used:    73250
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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