GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Burkholderia phytofirmans PsJN

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__BFirm:BPHYT_RS29875
          Length = 483

 Score =  406 bits (1043), Expect = e-117
 Identities = 218/474 (45%), Positives = 297/474 (62%), Gaps = 6/474 (1%)

Query: 24  INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83
           I+G+     +GE    ++P     +A VA    AD + AV  ARA     VW+ +  A+R
Sbjct: 14  IDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALK--VWNGIRTAER 71

Query: 84  KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143
              L+R A L+R N+EELA LE+LD GKPI      DIP A   + + A   DK+  +V 
Sbjct: 72  ARILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVV 131

Query: 144 PTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRI 203
           P   D L    REPVGVV AIVPWNFPL++  WK+ PALA G ++++KP+E +PLTA+RI
Sbjct: 132 PVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRI 191

Query: 204 AQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKR 263
            +LA+EAG+P GVLN++ G G  VG AL  H  VD + FTGS  + + ++  A   N KR
Sbjct: 192 GELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-GNFKR 250

Query: 264 IWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVV 323
           + LE GGKS N++F DA +L  A  AAAS I FN G+VC+AGSR+L  R + D+ +  + 
Sbjct: 251 VTLELGGKSANLIFPDA-NLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLA 309

Query: 324 EALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYV 383
              K  K G+P   +T++G L+   QM TVL Y+E G  +GA L+ GG R  E   G +V
Sbjct: 310 ARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVGER--GFFV 367

Query: 384 EPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHK 443
           EPT+F  V + MRI+QEEIFGPV SVI F+   +A+ IAN T Y LAAG+W++DI + H+
Sbjct: 368 EPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHR 427

Query: 444 TARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
            AR +RAG+VW+N Y   D+  P+GG   SG GR+    A+E +TE KA W+ +
Sbjct: 428 VARDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAI 481


Lambda     K      H
   0.316    0.132    0.390 

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: 638
Number of extensions: 28
Number of successful extensions: 5
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: 497
Length of database: 483
Length adjustment: 34
Effective length of query: 463
Effective length of database: 449
Effective search space:   207887
Effective search space used:   207887
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 (21.6 bits)
S2: 52 (24.6 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