GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Burkholderia phytofirmans PsJN

Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate BPHYT_RS21000 BPHYT_RS21000 ornithine cyclodeaminase

Query= BRENDA::O54983
         (313 letters)



>FitnessBrowser__BFirm:BPHYT_RS21000
          Length = 304

 Score =  130 bits (328), Expect = 3e-35
 Identities = 96/304 (31%), Positives = 147/304 (48%), Gaps = 25/304 (8%)

Query: 15  DHLRSSSLL---IPPLEAALANFSKGPDGGVMQPVRTVVPVAKHRGFLGVMPAYSAAEDA 71
           DH+R    +   I  L  ALA    G       PV+  V        + +M A   +   
Sbjct: 7   DHVRRLITMRDAIAELRIALAEHGAG-----RAPVQPRVRTKGEHVSVSMMGAILPSRGV 61

Query: 72  LTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAIATKLLK 131
              K+ + + G  +  VP       LF   +G L++++ G+ +T  RTAAV+ IA+  L 
Sbjct: 62  CGAKVYSTHGGRFDFVVP-------LFSSDDGCLISILHGDALTEFRTAAVTRIASDALA 114

Query: 132 PPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMW--NRTRENAEKFASTVQGDVRVCSS 189
            PG+ VL + G G QA +H     +  S + V +   +   +   +  +     +   S 
Sbjct: 115 RPGARVLAVFGTGRQARAHIRALADGSSIERVLIVGIDHVAQTVAEMQALFPDKLIEASH 174

Query: 190 VQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELMRQA-VLYVD 248
            Q A   ADVI+T T +  P+  G WVKPG  I A+G+S+PD RELDD L+ +A  L V+
Sbjct: 175 AQAAARAADVIVTATRSATPLFDGTWVKPGVFIAAIGSSKPDARELDDALLARANTLVVE 234

Query: 249 SREAALKESGDVLLSGADIFA-----ELGEVISGAK--PAHCEKTTVFKSLGMAVEDLVA 301
           S E A  E+GD+L++   + A     ELG V++  +  P      T+FKSLG  + D+  
Sbjct: 235 SLEQARSEAGDLLMAAPGVVAWDDIIELGAVLANRRIEPRARGDVTIFKSLGFGLADVAL 294

Query: 302 AKLV 305
           A L+
Sbjct: 295 AGLI 298


Lambda     K      H
   0.316    0.131    0.376 

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: 221
Number of extensions: 13
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: 313
Length of database: 304
Length adjustment: 27
Effective length of query: 286
Effective length of database: 277
Effective search space:    79222
Effective search space used:    79222
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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