GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Marinobacter adhaerens HP15

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF2856 HP15_2800 glucose-methanol-choline oxidoreductase

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Marino:GFF2856
          Length = 537

 Score =  548 bits (1413), Expect = e-160
 Identities = 286/538 (53%), Positives = 363/538 (67%), Gaps = 14/538 (2%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHV-- 58
           M FDY+IVG GSAG V+A RLS DP V+VCLLEAG +    L   P G+ AI+P      
Sbjct: 1   MIFDYIIVGGGSAGAVMAARLSEDPDVSVCLLEAGGKGDHLLTRAPAGVVAIMPGHGKIN 60

Query: 59  NWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDV 118
           NWA  T  QP L GR G+QPRG+ LGGSS IN M+Y+RGH  D++ W  LG +GWG+DDV
Sbjct: 61  NWALNTEQQPELAGRRGFQPRGRGLGGSSLINAMLYVRGHSADYDGWAELGCDGWGWDDV 120

Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYV-SPANRHAASEAFVESALRAGHSYNPDFNGATQE 177
           LPYFRK+E H GG+SEYHG DG L+V    +    SEAF+E+A   G+  + DFN    E
Sbjct: 121 LPYFRKAECHEGGASEYHGADGPLHVCKQRSPRPISEAFIEAAKERGYPASEDFNTGDNE 180

Query: 178 GAGYYDVTI-----RDGRRWSTATAFLKPV-RHRSNLTVLTHTHVESIVLLGKQATGVQA 231
           G G ++VT      R+G R STA A+L P+   R+NL V+T      I+  GK+A+GV+ 
Sbjct: 181 GVGLFEVTQFHDTERNGERCSTAAAYLYPIIEQRNNLKVVTGARATRILFNGKRASGVEY 240

Query: 232 LIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDH 291
            +KG  +   A +EVILSAGAFGSP LL LSG+G+  ++ P GI   HELPGVG+NLQDH
Sbjct: 241 RLKGQSLTASANREVILSAGAFGSPQLLQLSGVGNPDDILPHGIPMVHELPGVGRNLQDH 300

Query: 292 ADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERP 351
            D +L YKS DT   GFSL+G   M +    +     G +AS  AE  AFLK+DP  ++P
Sbjct: 301 LDFILAYKSADTDNFGFSLTGMKNMLRHSLQWRTDGTGMIASPFAEGAAFLKSDPEQDKP 360

Query: 352 DIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411
           D+QLH V+  V+DH RKLHWGHGFSCHVC LRPKS G V L S DP   P IDPN+L+  
Sbjct: 361 DLQLHFVVSIVEDHARKLHWGHGFSCHVCNLRPKSRGRVFLLSADPMADPGIDPNYLSDP 420

Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH---NDEQLIELLRKRTDTIYHPIG 468
           DD+   +KG +ITR+I+    ++ +   +M+  G+H   +DE+    +R R DTIYHP+G
Sbjct: 421 DDLNLTIKGAKITREILEGPALSPYRQSEMF--GVHDGMSDEEWERHIRARADTIYHPVG 478

Query: 469 TCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIAHG 526
           TCKMG D++AVVDS L+VHG+EGLRVVDAS+MPTL+GGNTNA  IMIAE+ A+ I  G
Sbjct: 479 TCKMGIDDLAVVDSSLKVHGLEGLRVVDASVMPTLIGGNTNAPTIMIAEKNADTIRTG 536


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: 950
Number of extensions: 34
Number of successful extensions: 6
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: 537
Length adjustment: 35
Effective length of query: 491
Effective length of database: 502
Effective search space:   246482
Effective search space used:   246482
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 17 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