GapMind for catabolism of small carbon sources

 

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

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_03016 H281DRAFT_03016
           aldehyde dehydrogenase (acceptor)
          Length = 483

 Score =  402 bits (1032), Expect = e-116
 Identities = 215/474 (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  IDGKRLPPGTGEYSVNINPATEEPIAHVAQGSAADVDTAVRAARAALK--VWNGIKAAER 71

Query: 84  KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143
              L R A L+R N++ELA LE+LD GKPI      D+P A   + + A   DK+  +V 
Sbjct: 72  GRILSRLAGLMRANLDELAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKINGQVV 131

Query: 144 PTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRI 203
           P   D L    REPVGVV AIVPWNFPL++  WK+ PALA G ++++KP+E +PL+A+RI
Sbjct: 132 PVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLSALRI 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++AG  +GA L+ GG R  E   G +V
Sbjct: 310 ARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVDAGRSEGASLVTGGGRIGER--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: 640
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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