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_RS20795 BPHYT_RS20795 sorbosone dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS20795
          Length = 502

 Score =  369 bits (947), Expect = e-106
 Identities = 208/476 (43%), Positives = 292/476 (61%), Gaps = 5/476 (1%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI+G+     +GE     SP  G  +       + D N AV +AR  F+ G WS+L+  +
Sbjct: 23  FIDGKDYAGNTGEFVTRKSPGHGVPVTATPRACVDDLNAAVASARRAFDDGRWSRLSGEQ 82

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L++ A L+R  VE LA LETL+ GKPIG S   +I  AA    + A     V+ + 
Sbjct: 83  RATVLLKTARLIRDKVETLAYLETLESGKPIGQSRG-EINAAAGIWEYAAGLARVVHGDS 141

Query: 143 APT-PHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201
             T   D  GL  R+P+GVVG + PWNFP  +   +L   LA G + V+KP+E +  T +
Sbjct: 142 HDTLGADLFGLTVRQPIGVVGIVTPWNFPFFILSERLPFVLAAGCTAVVKPAELTSTTTL 201

Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261
           ++A L  EAG+P GV+NV+ G G  VG+ALA HMDVD + FTGST + + ++  AG  NM
Sbjct: 202 KLAALLTEAGLPDGVVNVVTGLGAVVGQALAEHMDVDMMSFTGSTPVGRSVLAAAG-GNM 260

Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321
           K++ LE GGK+P IVFADA DL  AA+A A  I FN G+ C +GSRL+V RS++++ +  
Sbjct: 261 KKVGLELGGKNPQIVFADA-DLDDAADAIAFGICFNAGQCCVSGSRLVVHRSVEEELVAR 319

Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGT 381
           V    +  + G+PLD    VGA+V+ +Q + +  +I+AG +DGA+L+ GG+ T       
Sbjct: 320 VKAVFEKVRVGDPLDASNHVGAIVEARQFDKIRGFIDAGRRDGAQLVHGGEST-SHGERF 378

Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441
           +++PT+F  V     +AQEEIFGPVLSV +FDT EEA+ +AN  PYGLAA IWT D+  A
Sbjct: 379 FIQPTLFRNVQPQSALAQEEIFGPVLSVTSFDTFEEAIQLANGVPYGLAASIWTRDLQGA 438

Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497
             + R V+AG +WVN    G    P GG KQSG GR+   + +E+YTELK+  ++L
Sbjct: 439 ISSFREVQAGRIWVNCTITGGPEMPIGGVKQSGIGRETGRYGVEEYTELKSVHVQL 494


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: 666
Number of extensions: 33
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: 502
Length adjustment: 34
Effective length of query: 463
Effective length of database: 468
Effective search space:   216684
Effective search space used:   216684
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