GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Pedobacter sp. GW460-11-11-14-LB5

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate CA265_RS18860 CA265_RS18860 alpha-ketoacid dehydrogenase subunit beta

Query= metacyc::MONOMER-11684
         (327 letters)



>FitnessBrowser__Pedo557:CA265_RS18860
          Length = 328

 Score =  270 bits (689), Expect = 5e-77
 Identities = 136/325 (41%), Positives = 210/325 (64%), Gaps = 3/325 (0%)

Query: 1   MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60
           M  + + +A+  AM EEM +D RVF+LGE+V    G +K + G+ ++FG +R++DTP+AE
Sbjct: 1   MREIQFREALREAMSEEMRKDDRVFLLGEEVAEYNGAYKVSQGMLDEFGAKRIIDTPIAE 60

Query: 61  SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120
              AG+  GAA  G+ PI E    +F + A++QII+ AAKI   S   +SCP+V R P G
Sbjct: 61  LGFAGIATGAATAGLIPIVEFMTFNFSLVAIDQIINGAAKILSMSGGQFSCPMVFRGPTG 120

Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180
                   HSQ+ E  FAN PGLK+V+P+TPYDAKGLLK ++ D+DPV+F E +  Y   
Sbjct: 121 NAGQLGAQHSQNFENWFANTPGLKVVVPATPYDAKGLLKQSIIDQDPVIFMESEVMYG-D 179

Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYG-LCVHFALQAAERLEKDGISAHVVDLRTV 239
           KG+VPA++Y + +GKA+V ++G D+T++T+G +       A E L K+GI+  V+DLRTV
Sbjct: 180 KGDVPAEEYYIELGKANVTKQGTDVTIVTFGKMLTRVVNPAVEELTKEGINVEVIDLRTV 239

Query: 240 YPLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPA 299
            P+D + II +  KT ++++V E     S+  E+A ++ +H    LDAP+ R+   D+P 
Sbjct: 240 RPIDYDTIIASVKKTNRLVVVEEAWPLASLSGEIAFMVQKHAFDYLDAPVLRITCADVP- 298

Query: 300 MPYAPTMEKYFMVNPDKVEAAMREL 324
           +PY+PT+    + N ++V  A++E+
Sbjct: 299 LPYSPTLIAASLPNAERVVKAVKEV 323


Lambda     K      H
   0.319    0.136    0.392 

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: 281
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: 327
Length of database: 328
Length adjustment: 28
Effective length of query: 299
Effective length of database: 300
Effective search space:    89700
Effective search space used:    89700
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 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