GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Phaeobacter inhibens BS107

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate GFF2283 PGA1_c23150 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta

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



>FitnessBrowser__Phaeo:GFF2283
          Length = 331

 Score =  275 bits (704), Expect = 9e-79
 Identities = 140/324 (43%), Positives = 205/324 (63%), Gaps = 2/324 (0%)

Query: 1   MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60
           M  ++   A+N A+ EEM RD  VF++GEDV   G  FK  +GL E+FG ERV+DTP+AE
Sbjct: 1   MREITLSQAVNEALAEEMRRDETVFIIGEDVAEAGTPFKVLSGLVEEFGTERVVDTPIAE 60

Query: 61  SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120
               G+ +GAAM G RP+ ++ F DFI   ++Q+ ++AAK  Y S    S P+V+R   G
Sbjct: 61  PGFMGLAVGAAMTGTRPVVDLMFGDFIYLIMDQLCNQAAKTHYMSGGKMSAPLVLRTNMG 120

Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180
                A  HSQS+ A+ A+ PGLK+ MPS+ Y+AKGL+K A+RD +PV+ FE K  Y   
Sbjct: 121 ATRRSAAQHSQSLHALVAHIPGLKVAMPSSAYEAKGLMKTAIRDNNPVVIFEDKLMYN-D 179

Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240
           K  VP +++++P G+A++KR G+DIT+I     V     AAE L K+GI A V+D RT+ 
Sbjct: 180 KAPVPEEEFLIPFGEANIKRAGNDITLIATSSMVQVCEAAAEILAKEGIDAEVIDPRTIV 239

Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300
           PLD+E +I +A KT +V++V E  +   I  E+A  I+E   + LDAP+ R+   D+P +
Sbjct: 240 PLDEETLIASAKKTSRVIVVDEGHQSYGITGEIAGRINEKAFYHLDAPVLRMGAMDVP-V 298

Query: 301 PYAPTMEKYFMVNPDKVEAAMREL 324
           P++P +E   +  P+ V A  R+L
Sbjct: 299 PFSPALEDITVPTPEAVAANARKL 322


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: 270
Number of extensions: 12
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: 327
Length of database: 331
Length adjustment: 28
Effective length of query: 299
Effective length of database: 303
Effective search space:    90597
Effective search space used:    90597
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: 49 (23.5 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