GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Neptunomonas antarctica S3-22

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_054339706.1 Nant_RS00625 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_001305295.1:WP_054339706.1
          Length = 533

 Score =  430 bits (1105), Expect = e-125
 Identities = 232/522 (44%), Positives = 308/522 (59%), Gaps = 2/522 (0%)

Query: 4   DYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAFK 63
           DY+IVGAGSAGCVLANRLSADP+  V LLEAG ED  P IH P+G    +     +W FK
Sbjct: 9   DYIIVGAGSAGCVLANRLSADPNNRVLLLEAGGEDTYPWIHIPIGYIYTMNNPKTDWCFK 68

Query: 64  TTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYFR 123
           T    GL GR    PRGKVLGGSSSINGMIY+RG + D++ W +LGN+GW +D+VLPYF+
Sbjct: 69  TQADAGLNGRALNYPRGKVLGGSSSINGMIYMRGQKQDYDHWASLGNKGWSWDEVLPYFK 128

Query: 124 KSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQEGAGYY 182
           KSE H+ G+S+ HG  GE  V          + F ++A   G     DFN    EG  Y+
Sbjct: 129 KSEDHYSGASDMHGSGGEWRVEEQRLSWEVLDGFRQAAAETGIPSIDDFNTGDNEGFSYF 188

Query: 183 DVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLRA 242
            V  + GRRWS+A  FL P++HR NLT++T  HV+ + ++ K   G+   I G   +   
Sbjct: 189 QVNQKKGRRWSSARGFLDPIKHRPNLTIITKAHVDRLHIVNKTVIGIAFDINGMPSYAGV 248

Query: 243 RKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYKSND 302
            KE++L AG+  SP +L  SGIG+   L+   I   H+LPGVG+NLQDH  V   +K  +
Sbjct: 249 NKEILLCAGSVISPVILQRSGIGNTDLLKQHKIDVVHDLPGVGENLQDHLQVRAVFKVKN 308

Query: 303 TSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVIGTV 362
           T  L    +      K +FDYA  R GP +   ++ G F K+    E  +++ H    + 
Sbjct: 309 TLTLNEQANSLFGKMKMVFDYAFFRRGPFSMAPSQLGGFAKSSAEYETANLEYHIQPLSC 368

Query: 363 DDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLKGYR 422
           +     LH     +  VC LRPKS G + L S DP  AP I PN+L+H +D        +
Sbjct: 369 EKLGDPLHTFPAITASVCNLRPKSRGHIRLRSKDPYAAPIITPNYLSHKEDKQVAADALK 428

Query: 423 ITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAVVD 481
           +TR I        +   +      +++DE LI+       TI+HP+GTCKMG D+M+VVD
Sbjct: 429 LTRRICQANAFKKYQPEEFKPGLAINSDEDLIKAAGDIATTIFHPVGTCKMGSDQMSVVD 488

Query: 482 SQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
            QL+V+GIE LRVVDASIMPT+  GNTN+  IMIAE+AAE I
Sbjct: 489 YQLKVYGIERLRVVDASIMPTITSGNTNSPTIMIAEKAAEMI 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: 719
Number of extensions: 30
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: 533
Length adjustment: 35
Effective length of query: 491
Effective length of database: 498
Effective search space:   244518
Effective search space used:   244518
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.

Links

Downloads

Related tools

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