GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Flavobacterium sp. LM5

Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_078210872.1 BXU11_RS02295 hydroxyacid dehydrogenase

Query= curated2:A1RYE4
         (339 letters)



>NCBI__GCF_002017945.1:WP_078210872.1
          Length = 315

 Score =  167 bits (423), Expect = 3e-46
 Identities = 106/301 (35%), Positives = 165/301 (54%), Gaps = 30/301 (9%)

Query: 29  HESKDWPPSREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLKVISTYSVGFDHIDIPEA 88
           H   D+  S+E +   I+D   ++     KID   +D A NL+ I+    G + ID   A
Sbjct: 25  HNEADFTSSKEAVEDKIKDYHGIVIRSRFKIDKNFIDKATNLRFIARVGAGLESIDCEYA 84

Query: 89  TKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVEADKIIRTGQWDKPWNPYFLTGPELK 148
             + I +   P    +AV+E ++G+IL++  ++ +AD  IR GQW++  N     G EL 
Sbjct: 85  LSKNIALIAAPEGNRNAVSEHSLGMILSLFNKLNQADAEIRKGQWNRESN----RGHELD 140

Query: 149 GKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVIPNMEFTD-----LDTLLE 203
           GKT+G++G G +G A AK+L  FDV++L YDI         +PN+  T+     L+ L +
Sbjct: 141 GKTVGIIGYGNMGKAFAKKLRGFDVEVLCYDI---------LPNVGDTNAKQVTLEELQQ 191

Query: 204 KSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARGPVVDTEALVKALKEGWIAGAA 263
           K+D++S+H+P T ET  ++N + +     + +LINT+RG  V T  LV+AL+ G I GA 
Sbjct: 192 KADVLSLHIPWTPETDKMVNADFIASFSNSFWLINTSRGKNVVTADLVQALESGKILGAG 251

Query: 264 LDVFEQEPL-------PPNHP-----LTKFDNVVLAPHIASATIEARQRMAELAARNLIA 311
           LDV E E L         N P     L K   V+L+PHIA  T E+ +R+A++    + A
Sbjct: 252 LDVLEYEKLSFETLFQDKNTPEAFDYLLKSPKVLLSPHIAGWTFESHERLAQVIVDKIKA 311

Query: 312 V 312
           +
Sbjct: 312 L 312


Lambda     K      H
   0.319    0.137    0.404 

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: 260
Number of extensions: 10
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: 339
Length of database: 315
Length adjustment: 28
Effective length of query: 311
Effective length of database: 287
Effective search space:    89257
Effective search space used:    89257
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 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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