GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Marinicella litoralis KMM 3900

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_099018731.1 CCS90_RS03360 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_002591915.1:WP_099018731.1
          Length = 526

 Score =  492 bits (1266), Expect = e-143
 Identities = 262/528 (49%), Positives = 345/528 (65%), Gaps = 14/528 (2%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61
           +FDY++VGAGSAGCVLANRLSAD   TV L+EAG  D +P+IH P GLA ++  + +NW 
Sbjct: 3   KFDYIVVGAGSAGCVLANRLSADGKHTVLLVEAGGTDWNPMIHMPAGLAKLVGFKSINWN 62

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           + T P+P L  R  Y PRGKVLGGSSSIN M Y RGH+ D++ W+A GN GWG  DVLPY
Sbjct: 63  YDTEPEPQLNNRKLYWPRGKVLGGSSSINAMCYCRGHRKDYDHWEAQGNAGWGSKDVLPY 122

Query: 122 FRKSEMHHGGSSEYHGGDGELYVSP-ANRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180
           F KSE +    +E+H  DG L VS     +  S+ F+++A  AG+    DFNG  Q G G
Sbjct: 123 FMKSENNQRLKNEFHSQDGLLSVSDHIYTNPLSDVFLDAAAEAGYQRTDDFNGLRQRGFG 182

Query: 181 YYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHL 240
           YY VT ++G+R STA AFLKP + RSNLTV T T  + ++L  K+ATG+     G    L
Sbjct: 183 YYQVTQKNGQRHSTAEAFLKPAKGRSNLTVWTKTLAQKVILKDKKATGLLVKKGGQLQQL 242

Query: 241 RARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL---C 297
           +A KEVILS+GA  SP LLMLSGIG++ EL   GI  +HELPGVG+NLQDH DV L   C
Sbjct: 243 KANKEVILSSGAINSPQLLMLSGIGNSEELAHHGIQCQHELPGVGKNLQDHLDVCLVQHC 302

Query: 298 YKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGL-ERPDIQLH 356
            +      +   LSG          Y   + GP  SN AEAG F ++   + +RPD+Q H
Sbjct: 303 SQDITYDTVNEVLSG--------LKYYLFKKGPGTSNVAEAGGFWQSPMAIDDRPDLQFH 354

Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416
            V   +DDH R    G+G++ H+CVLRP+S G + L S +P   P+I  N+LA + D+  
Sbjct: 355 FVPAMLDDHGRNRLKGNGYTLHMCVLRPESRGEIKLKSANPEDPPQIQANYLAVEHDLKI 414

Query: 417 LLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475
           +++G++I R I A      F   +++  + +  DE++I+ +R + ++IYHPIGTCKMG D
Sbjct: 415 MVEGFKIQRKIFAAKAFDEFRDDEIFPGSEVQTDEEIIDFIRNKAESIYHPIGTCKMGSD 474

Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
           +MAVVD  L+VHGIEGLRVVDAS MPTLV GNTNA  IM+AE+ ++ I
Sbjct: 475 DMAVVDQNLKVHGIEGLRVVDASAMPTLVSGNTNAPTIMMAEKISDVI 522


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: 793
Number of extensions: 36
Number of successful extensions: 5
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: 526
Length adjustment: 35
Effective length of query: 491
Effective length of database: 491
Effective search space:   241081
Effective search space used:   241081
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