GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Azospirillum brasilense Sp245

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate AZOBR_RS22250 AZOBR_RS22250 pyruvate dehydrogenase E1 component beta subunit

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



>lcl|FitnessBrowser__azobra:AZOBR_RS22250 AZOBR_RS22250 pyruvate
           dehydrogenase E1 component  beta subunit
          Length = 465

 Score =  267 bits (683), Expect = 3e-76
 Identities = 136/317 (42%), Positives = 204/317 (64%), Gaps = 3/317 (0%)

Query: 8   DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67
           +A+  AM EEM RD  VF++GE+V +  G +K + GL ++FG +RV+DTP+ E   AG+G
Sbjct: 146 EALRDAMAEEMRRDPTVFLMGEEVAQYQGAYKVSQGLLQEFGADRVIDTPITEIGFAGLG 205

Query: 68  IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127
           +GAA  G+RPI E    +F + A++ I++ AAK  Y S     CPIV R P G     A 
Sbjct: 206 VGAAFRGLRPIVEFMTFNFALQAIDHIVNSAAKTLYMSGGQMGCPIVFRGPNGAAARVAA 265

Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVP-A 186
            HSQ     +A+ PGLK+V P +  D KGL+K+A+RD +PV+F E++  Y     EVP +
Sbjct: 266 QHSQDFTPWYASIPGLKVVAPYSASDFKGLMKSAIRDPNPVIFLENEILYGQ-SFEVPES 324

Query: 187 DDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKEA 246
           +D+++PIG+A ++R G D+T+  + L V +AL AA+ LEKDGISA V+DLRT+ PLD E 
Sbjct: 325 EDFIVPIGRAKIRRAGTDVTITAHSLMVSYALAAADLLEKDGISAEVIDLRTIRPLDTET 384

Query: 247 IIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAPTM 306
           I+ +  KT +++ V E      I +E++A++ E     LDAP+ R+ G D+P MPYA  +
Sbjct: 385 IVNSVKKTNRLVTVEEAWPTCGIGAELSALMMEQAFDYLDAPVIRVTGLDVP-MPYAANL 443

Query: 307 EKYFMVNPDKVEAAMRE 323
           EK  + +PD++  A ++
Sbjct: 444 EKLVLPSPDRIAEAAKK 460


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: 412
Number of extensions: 24
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: 465
Length adjustment: 30
Effective length of query: 297
Effective length of database: 435
Effective search space:   129195
Effective search space used:   129195
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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