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_023434027.1 N177_RS18905 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000496075.1:WP_023434027.1
          Length = 563

 Score =  396 bits (1017), Expect = e-114
 Identities = 227/524 (43%), Positives = 310/524 (59%), Gaps = 6/524 (1%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           EFD+++VGAGSAG VLA+RLSAD +  V +LE G  D S  I  P   +  L  +  +W 
Sbjct: 9   EFDFVVVGAGSAGSVLADRLSADGTNRVLVLEFGGRDNSIYIQMPTAFSIPLGMKRFDWG 68

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           + + P+PGL GR  +Q RGKV+GGSSSING+ Y+RG+  DF++W+  G  GWG+  VLPY
Sbjct: 69  YHSEPEPGLKGRRIHQARGKVIGGSSSINGLAYVRGNAGDFDEWEEHGAAGWGYRHVLPY 128

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEGA 179
           F ++E    G+ EY G  G L  +  N   +    AF+E+  +AG+    D+NG  QEG 
Sbjct: 129 FVRAEDCLYGADEYRGAGGPLGTNNGNNMENPLYRAFIEAGRQAGYGETRDYNGYRQEGF 188

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239
              D+T+R+G R STA A+LKP   R+NL V TH     I+  G++A GV+    G    
Sbjct: 189 CRMDMTVRNGVRCSTANAYLKPAMTRANLDVKTHALTTRILFEGRRAVGVEYRRGGETRR 248

Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299
            +AR EVILSA +F SP LLMLSG+G AA L+  GI   H+LPGVG+NLQDH +V +   
Sbjct: 249 AKARGEVILSASSFNSPKLLMLSGVGPAAHLKSHGIDVLHDLPGVGRNLQDHLEVWVQQL 308

Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359
                 L   L G V  G     +   + G   SN  E+  +++T  GL  PD+Q H + 
Sbjct: 309 CTQPITLNRRL-GLVGQGLIGARWLLTKTGLGISNQFESNGYIRTRAGLRFPDLQYHFLA 367

Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419
           G +    +    G GF  H+   +PKS G V L+S D    P+I  N+L+ ++D      
Sbjct: 368 GAISYDGKPATKGDGFQVHLGHNKPKSRGYVELSSRDAEAQPKIVFNYLSEEEDKEGFRA 427

Query: 420 GYRITRDIIAQTPMASFGLRDMYSAG--LHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477
           G R+TR+I AQ     +   D  S G  +  D+++ + + +  +T YHP G+C+MG DEM
Sbjct: 428 GLRLTREIFAQGAFDPY-RGDELSPGRDVTTDDEIDDWVAETAETAYHPAGSCRMGTDEM 486

Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           AVVD + RVHGIEGLRVVD+SIMPTL  GN NA  IMI E+ A+
Sbjct: 487 AVVDPECRVHGIEGLRVVDSSIMPTLTNGNINAPTIMIGEKGAD 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: 865
Number of extensions: 39
Number of successful extensions: 4
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: 563
Length adjustment: 35
Effective length of query: 491
Effective length of database: 528
Effective search space:   259248
Effective search space used:   259248
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