GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Halomonas xinjiangensis TRM 0175

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043526943.1 JH15_RS03245 choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>NCBI__GCF_000759345.1:WP_043526943.1
          Length = 563

 Score =  363 bits (931), Expect = e-104
 Identities = 213/527 (40%), Positives = 300/527 (56%), Gaps = 8/527 (1%)

Query: 2   EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHVN 59
           E+DY+I+GAGSAG VLA RL+ D  V+V LLEAG  D      T  P  LA  L  +  N
Sbjct: 6   EYDYIIIGAGSAGNVLATRLTEDADVSVLLLEAGGPDYRFDFRTQMPAALAYPLQGKRYN 65

Query: 60  WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDDV 118
           WAF+T P+P +  R     RGK LGGSS INGM Y+RG+  D++ W +  G E W + + 
Sbjct: 66  WAFETDPEPYMNDRRMECGRGKGLGGSSLINGMCYLRGNALDYDSWAKQPGLEDWNYLEC 125

Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVSPANR--HAASEAFVESALRAGHSYNPDFNGATQ 176
           LPYF+++E    G + YHGG+G + V+      +    AF+++ + AG+    D NG  Q
Sbjct: 126 LPYFKRAETRDIGPNTYHGGEGPVSVATPKEGNNELYGAFIQAGIEAGYPATEDVNGYQQ 185

Query: 177 EGAGYYD-VTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKG 235
           EG G  D  T  +GRR STA  +L   + R NLT+ TH   + I+  GK+A GV    KG
Sbjct: 186 EGFGPMDRTTTPNGRRASTARGYLDVAKRRDNLTIETHAVTDRILFEGKRAVGVAYARKG 245

Query: 236 SRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVV 295
           +   +RAR+EV+L  GA  SP +L+ SG+G+A  L+   I   H+LPGVG+NLQDH ++ 
Sbjct: 246 AAQEVRARREVLLCGGAIASPQILLRSGVGNAEHLKEYDIPVVHDLPGVGENLQDHLEMY 305

Query: 296 LCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL 355
           + Y+     +  +         K   ++     G  +SN  EA  F++T+     P++Q 
Sbjct: 306 IQYECT-KPISFYPALKWYNQPKIGAEWLFFGTGIGSSNQFEAAGFIRTNDDEAWPNLQY 364

Query: 356 HSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVA 415
           H +   +  + +     HGF  HV  +R  S G + L S DP  AP I  N+++   D  
Sbjct: 365 HFLPIAISYNGKSAVQAHGFQAHVGSMRSMSRGRIRLTSKDPNAAPSILFNYMSEQKDWE 424

Query: 416 TLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQ 474
                 R+TR+IIAQ  M  +  R++     +  DE+L E +R+  +T YHP G+CKMG 
Sbjct: 425 EFRDAIRLTREIIAQPAMDPYRGREISPGPNVQTDEELDEFVRQHAETAYHPSGSCKMGY 484

Query: 475 DEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           D+MAVVD   RVHG+E LRV+DASIMP +  GN NA  IMIAE+ A+
Sbjct: 485 DDMAVVDGAGRVHGLENLRVIDASIMPVITTGNLNAPTIMIAEKMAD 531


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: 876
Number of extensions: 45
Number of successful extensions: 7
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