GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Paraburkholderia bryophila 376MFSha3.1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate H281DRAFT_02299 H281DRAFT_02299 aldehyde dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_02299
          Length = 506

 Score =  352 bits (902), Expect = e-101
 Identities = 196/476 (41%), Positives = 278/476 (58%), Gaps = 12/476 (2%)

Query: 23  FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82
           FI GE+     GE F+ +SP+ G     +     AD   A++ A        W + +   
Sbjct: 22  FIGGEWVKPAGGEYFDNVSPITGEPFTSIPRSREADVELALDAAHRA--KAAWGKTSTTD 79

Query: 83  RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142
           R   L R AD +  N++ LA+ ET+D GKP+ ++ + DIP A     + A A+      +
Sbjct: 80  RANILNRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFAGAVRAQEGSI 139

Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202
           +    D +     EP+GVVG I+PWNFP+LMA WKL PALA GN VVLKP+E++P + + 
Sbjct: 140 SEIDDDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASILV 199

Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262
           + +L I+  +PAGVLNV+ G+G   GK LA    +  + FTG T   + +M YA + N+ 
Sbjct: 200 LVEL-IQDLLPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQYASQ-NII 257

Query: 263 RIWLEAGGKSPNIVFADAPDLQAA----AEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
            + LE GGKSPNI FAD  +   +    A    +  A NQGEVCT  SR+L++  I D F
Sbjct: 258 PVTLELGGKSPNIFFADVMNQDDSYFDKALEGFAMFALNQGEVCTCPSRVLIDEKIYDSF 317

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--- 375
           +   ++ +     G+PLD +T +GA    +Q+  +LSY++ G ++GA+ L GG+R     
Sbjct: 318 MERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIGGERNTLSG 377

Query: 376 EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435
           E + G YV+PT+F G  N MRI QEEIFGPV+SV  F T EEA+ IANDT YGL AG+WT
Sbjct: 378 ELSKGYYVKPTVFRG-HNKMRIFQEEIFGPVVSVTTFKTEEEALEIANDTLYGLGAGVWT 436

Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491
            D ++A++  R ++AG VW N Y      A FGG+KQSG GR+     L+ Y + K
Sbjct: 437 RDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTK 492


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: 641
Number of extensions: 38
Number of successful extensions: 7
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: 506
Length adjustment: 34
Effective length of query: 463
Effective length of database: 472
Effective search space:   218536
Effective search space used:   218536
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