GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Lutibaculum baratangense AMV1

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_023432295.1 N177_RS10510 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000496075.1:WP_023432295.1
          Length = 554

 Score =  413 bits (1061), Expect = e-119
 Identities = 232/534 (43%), Positives = 318/534 (59%), Gaps = 19/534 (3%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60
           +E D++IVGAGSAGC LA+RLS D   +V ++E G  D  P IH P  L+  +     +W
Sbjct: 5   LEADFVIVGAGSAGCALAHRLSEDGRHSVLVIEGGGTDWGPFIHMPAALSYPMNMNRYDW 64

Query: 61  AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120
            F+T P+P LGGR    PRGKVLGGSSSINGM+Y+RGH  DF+ W+A G +GWGF D+LP
Sbjct: 65  GFRTAPEPHLGGRRLAVPRGKVLGGSSSINGMVYVRGHACDFDGWEADGAKGWGFADILP 124

Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPDFNGATQEGA 179
           Y+ K E  HGG + + G DG L+V+    R+    AFVE+   AG+    D+NG  QEG 
Sbjct: 125 YYLKLETSHGGEAGWRGSDGPLHVTRGPRRNPLYHAFVEAGKEAGYGETADYNGHRQEGF 184

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239
           G  ++T+  GRRWS A A+L+    R N+ V+ ++ V  +V+   +ATGV+   +G    
Sbjct: 185 GPMEMTVWGGRRWSAANAYLRRAWKRKNVRVMANSFVRRVVIENGRATGVEIGARGVERT 244

Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299
           +RAR+EVILSA +  SP LLMLSGIG A  L   GI  + + PGVG+NLQDH ++ L  +
Sbjct: 245 VRARREVILSASSINSPKLLMLSGIGGADALRKLGIEVKADRPGVGRNLQDHLEIYLQAE 304

Query: 300 S-------NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPD 352
           S          +LLG +L G          +   + G  ASN  E+ AF+++  G+  PD
Sbjct: 305 SLKPVTLYRYNNLLGKALVGA--------QWLFTKTGLGASNQFESAAFIRSKAGVSYPD 356

Query: 353 IQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDD 412
           IQ H +   V          HGF  HV  +R KS G V L SP+P  AP I  N+++H +
Sbjct: 357 IQYHFLPLAVRYDGTSAVKAHGFQVHVGPMRSKSRGHVALTSPEPEAAPEILFNYMSHAE 416

Query: 413 DVATLLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCK 471
           D        R+TR+I+ Q  M  + G   M      +DE L E +R+  ++ YHP GTC+
Sbjct: 417 DWEDFRACIRLTREILRQPAMKDYLGREIMPGPDATDDEALDEFVREEVESAYHPCGTCR 476

Query: 472 MG--QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           MG  +D +AVVD + RV G+EGLRVVD+SI P +  GN NA +IM+ E+AA+ I
Sbjct: 477 MGAAEDPLAVVDPECRVIGVEGLRVVDSSIFPRITNGNLNAPSIMVGEKAADHI 530


Lambda     K      H
   0.319    0.137    0.419 

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: 853
Number of extensions: 49
Number of successful extensions: 6
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: 526
Length of database: 554
Length adjustment: 35
Effective length of query: 491
Effective length of database: 519
Effective search space:   254829
Effective search space used:   254829
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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