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 GFF1732 PGA1_c17560 pyruvate dehydrogenase E1 component subunit beta

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



>FitnessBrowser__Phaeo:GFF1732
          Length = 461

 Score =  261 bits (668), Expect = 2e-74
 Identities = 130/317 (41%), Positives = 200/317 (63%), Gaps = 1/317 (0%)

Query: 8   DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67
           +A+  AM EEM  D  VF++GE+VG   G +K + GL ++FG +RV+DTP+ E   AG+ 
Sbjct: 143 EALRDAMAEEMRGDEDVFLMGEEVGEYQGAYKISQGLLDEFGPKRVIDTPITEHGFAGIA 202

Query: 68  IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127
            GAA  G+RPI E    +F M A++ II+ AAK  Y S      P+V R P G       
Sbjct: 203 TGAAFGGLRPIVEFMTFNFAMQAIDHIINSAAKTLYMSGGQMGAPMVFRGPNGAAARVGA 262

Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187
            HSQ   A +   PGLK+ MP +  DAKGL+K A+RD +PV+F E++  Y         D
Sbjct: 263 QHSQDYAAWYMQIPGLKVAMPYSASDAKGLMKTAIRDNNPVIFLENEILYGKSFDVPKLD 322

Query: 188 DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEAI 247
           DY +P GKA + R+G+D+T++++G+ + +AL+AAE+L +DGISA V+DLRT+ P+D  +I
Sbjct: 323 DYTVPFGKARIWRKGEDVTIVSFGIGMTYALEAAEKLAEDGISAEVIDLRTLRPMDTGSI 382

Query: 248 IEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTME 307
           I++  KT +++ V E   +GS+ S +++++ +     LDAP+    G D+P MPYA  +E
Sbjct: 383 IKSVMKTNRLVTVEEGWPQGSVGSYISSVVMQEAFDYLDAPVITCTGKDVP-MPYAANLE 441

Query: 308 KYFMVNPDKVEAAMREL 324
           K+ +V  D+V  A++++
Sbjct: 442 KHALVTTDEVIEAVKQV 458


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: 418
Number of extensions: 26
Number of successful extensions: 3
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: 461
Length adjustment: 30
Effective length of query: 297
Effective length of database: 431
Effective search space:   128007
Effective search space used:   128007
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: 50 (23.9 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