GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Psychromonas ossibalaenae JAMM 0738

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_019615352.1 G327_RS0113660 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000381745.1:WP_019615352.1
          Length = 561

 Score =  427 bits (1098), Expect = e-124
 Identities = 232/528 (43%), Positives = 322/528 (60%), Gaps = 10/528 (1%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           ++DY+IVGAGSAGCVLANRLSAD    V LLE G  D+S  I  P  L+  + T+   W 
Sbjct: 5   QYDYIIVGAGSAGCVLANRLSADSGNKVLLLETGGSDKSIFIQMPTALSIPMNTKKYAWQ 64

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           F+T  +P L  R  + PRGKVLGGSSSINGM+Y+RGH  DF++WQ  G + W +   LPY
Sbjct: 65  FETEAEPFLDNRRMHCPRGKVLGGSSSINGMVYVRGHARDFDEWQQAGAQNWDYAHCLPY 124

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEGA 179
           F+K+E    G ++Y G  G L V+  N  ++   +AFV + + AG+    D+N   QEG 
Sbjct: 125 FKKAETWSFGGNDYRGESGPLAVNNGNNMKNPLYQAFVNAGVDAGYLATADYNAGQQEGF 184

Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239
           G   +T+++G RWSTA A+L+P   R NLTV+TH  V  ++L GK A GV    KG    
Sbjct: 185 GPMHMTVKNGVRWSTANAYLRPAMKRDNLTVITHALVHKVLLEGKTAVGVSYESKGQLTE 244

Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299
           LR  KEV+LSAG+ GSPH+L LSGIG+A  L   GI   HELPGVG+NLQDH +    +K
Sbjct: 245 LRCNKEVLLSAGSIGSPHILQLSGIGAADTLAQAGIEQVHELPGVGENLQDHLEFYFQFK 304

Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYAR---HRNGPVASNCAEAGAFLKTDPGLERPDIQLH 356
                L   SL+G +     +F   R   +++G  A+N  E+  F+++  GLE PD+Q H
Sbjct: 305 ----CLKPISLNGKIDPLNKLFIGTRWILNKSGLGATNHFESCGFIRSKAGLEWPDLQYH 360

Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416
            +   +    ++   GHGF  H+   +PKS G V + S + R AP+I  N+L+H DD+  
Sbjct: 361 FLPAAMRYDGKEAFAGHGFQVHIGHNKPKSRGRVKVVSSNARTAPQIQFNYLSHQDDIEG 420

Query: 417 LLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475
                R+TR+II Q  +  + G        +  D+++   +R   ++ YHP  +C+MG+D
Sbjct: 421 FRACVRLTREIINQPGLDEYRGEEIQPGLAVQTDQEIDSFVRSSVESAYHPSCSCRMGED 480

Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
            M+VV+S+ +VHGIEGLRVVD+SI PT+  GN N+  IM AERAA+ I
Sbjct: 481 AMSVVNSETKVHGIEGLRVVDSSIFPTIPNGNLNSPTIMTAERAADII 528


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: 823
Number of extensions: 33
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: 561
Length adjustment: 35
Effective length of query: 491
Effective length of database: 526
Effective search space:   258266
Effective search space used:   258266
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