GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS22250
          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:

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