GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Algiphilus aromaticivorans DG1253

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_052368302.1 U743_RS16290 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000733765.1:WP_052368302.1
          Length = 556

 Score =  585 bits (1508), Expect = e-171
 Identities = 292/522 (55%), Positives = 364/522 (69%), Gaps = 1/522 (0%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           +DY+I+G GSAGCVLANRLS DP  TVCLLEAGP D+SP +  PLG+AA+L +  +NWAF
Sbjct: 2   YDYIIIGGGSAGCVLANRLSEDPETTVCLLEAGPADKSPFVRIPLGMAALLRSPSLNWAF 61

Query: 63  KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122
           +T PQ GLGGR GYQPRGKVLGGSSSIN M+YIRGH+ D++ W   GN GW FD+VLPYF
Sbjct: 62  RTEPQAGLGGRRGYQPRGKVLGGSSSINAMVYIRGHRSDYDGWAEAGNSGWSFDEVLPYF 121

Query: 123 RKSEMHHGGSSEYHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQEGAGY 181
           +++E    G+  +HG  G L V+     HA  + F+ +A   GH    DFNG   EG GY
Sbjct: 122 KRAENQERGADAFHGVGGPLNVADLRSPHAICDDFIAAAEEQGHKRVSDFNGPDMEGVGY 181

Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241
           + VT + G R STA A+L+PV  R NLT++T  +   I + GK+A GV+     +  H+ 
Sbjct: 182 FQVTQQAGDRCSTAKAYLEPVADRPNLTIITEAYATRIDMEGKRAVGVRYRKDDASHHVG 241

Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSN 301
           ARKEV++SAGA  SP LLMLSGIG   EL+  GI   HEL GVG NLQDH D V   KS 
Sbjct: 242 ARKEVLVSAGALQSPQLLMLSGIGPREELDQHGIPICHELAGVGANLQDHLDYVTAVKSP 301

Query: 302 DTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGT 361
               LG SLSGG +M +A+  Y R R G + SN AEAG FL++DP L  PD+QLH  +  
Sbjct: 302 SKEPLGISLSGGWQMLQALRTYRRFRTGKLTSNVAEAGGFLRSDPSLAAPDLQLHFAVAI 361

Query: 362 VDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGY 421
           +DDH RKLH GHG+SCHVC+L PKS G VGL S +P  APRIDP FL+ D+D+  L+KG+
Sbjct: 362 LDDHGRKLHSGHGYSCHVCLLTPKSRGRVGLHSANPMAAPRIDPAFLSEDEDLERLVKGF 421

Query: 422 RITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVVD 481
           R  ++I+    MA    RD+Y+A +  DEQ+   +R+R DT+YHP+GTC+MG+D  AVVD
Sbjct: 422 RRMQEILNAPAMARHRGRDIYTAHVRTDEQIRSAIRQRADTVYHPVGTCRMGRDSDAVVD 481

Query: 482 SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
            QLRVHG+ GLRVVDASIMPT+V GNTNA  IMI E+AAE I
Sbjct: 482 EQLRVHGVAGLRVVDASIMPTVVRGNTNAPTIMIGEKAAEMI 523


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: 889
Number of extensions: 37
Number of successful extensions: 2
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: 556
Length adjustment: 35
Effective length of query: 491
Effective length of database: 521
Effective search space:   255811
Effective search space used:   255811
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