GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Synechococcus elongatus PCC 7942

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate Synpcc7942_0143 Synpcc7942_0143 pyruvate/2-oxoglutarate dehydrogenase complex dehydrogenase (E1) component

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



>FitnessBrowser__SynE:Synpcc7942_0143
          Length = 326

 Score =  279 bits (713), Expect = 8e-80
 Identities = 148/317 (46%), Positives = 208/317 (65%), Gaps = 3/317 (0%)

Query: 8   DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67
           +A+  A+ EEM RD  VFVLGEDVG  GG +K T  LY+++G+ R++DTP+AE+   G+ 
Sbjct: 8   NALRAAIDEEMARDPNVFVLGEDVGHYGGSYKVTKDLYQKYGDFRLLDTPIAENGFTGMA 67

Query: 68  IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127
           +GAAM G+RPI E     F++ A NQI + A  +RY S  +++ PIV R P G G     
Sbjct: 68  VGAAMTGLRPIVEGMNMGFLLLAFNQIANNAM-LRYTSGGNFTIPIVFRGPGGVGRQLGA 126

Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187
            HSQ +EA F   PGLKIV  STPY+AKGLLKAA+RD +PVLFFEH   Y L K ++P +
Sbjct: 127 EHSQRLEAYFHAVPGLKIVACSTPYNAKGLLKAAIRDNNPVLFFEHVLLYNL-KEDLPDE 185

Query: 188 DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEAI 247
           +Y+ P+ KA++ R G D+TV+TY    +  LQA + LEK+G    V+DL ++ P D EAI
Sbjct: 186 EYICPLDKAEIVRPGKDVTVLTYSRMRYHCLQAVKTLEKEGFDPEVIDLISLKPFDFEAI 245

Query: 248 IEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTME 307
             +  KT +V++V E  K G I +E++A I E C  +LDAP+ RL+  DIP  PY   +E
Sbjct: 246 EASVRKTHRVVIVEECMKTGGIAAELSAAIMERCFDELDAPVVRLSSQDIPT-PYNGKLE 304

Query: 308 KYFMVNPDKVEAAMREL 324
              +V P+++ AA+++L
Sbjct: 305 NLTIVQPEQIVAAVKDL 321


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: 303
Number of extensions: 16
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: 326
Length adjustment: 28
Effective length of query: 299
Effective length of database: 298
Effective search space:    89102
Effective search space used:    89102
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