GapMind for catabolism of small carbon sources

 

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

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate GFF4208 HP15_4148 glucose-methanol-choline oxidoreductase

Query= BRENDA::Q76HN6
         (526 letters)



>lcl|FitnessBrowser__Marino:GFF4208 HP15_4148
           glucose-methanol-choline oxidoreductase
          Length = 542

 Score =  485 bits (1248), Expect = e-141
 Identities = 261/528 (49%), Positives = 336/528 (63%), Gaps = 7/528 (1%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62
           FDY++VGAGSAGCVLA+RLSAD   +VC+LEAGP   S  I TP   AA +  +  NWAF
Sbjct: 6   FDYIVVGAGSAGCVLADRLSADGRYSVCVLEAGPGKGSFTIRTPGAFAAHMFIKTYNWAF 65

Query: 63  KTTPQPGL-GGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
              P   L GG+  + PRGK LGGSS INGM+Y+RG ++D+++W+ALGNEGWG+ ++LPY
Sbjct: 66  NARPDQQLRGGQPLFTPRGKGLGGSSLINGMLYVRGQKEDYDEWEALGNEGWGYAEMLPY 125

Query: 122 FRKSEMHHG-GSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEG 178
           F KSE H     + YHG  G LY+       +  S AFV++A + G  Y+ DFNGA QEG
Sbjct: 126 FLKSEHHETLAGTPYHGKGGNLYIGAPETAEYPMSGAFVDAARQTGFPYSSDFNGAEQEG 185

Query: 179 AGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRV 238
            GY+ + I++GRR+  A A+LKP   R NLTVLT   V+ +VL G +A  V+   K S +
Sbjct: 186 VGYFHLNIKNGRRFGVADAYLKPAMSRQNLTVLTEARVKKLVLEGNRAVAVELRHKDSDL 245

Query: 239 HLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCY 298
            L A +E+ILS GA  SP LL LSGIG    LE  GI  RHELPGVG+NLQ+H D  +  
Sbjct: 246 VLNANREIILSGGAINSPQLLQLSGIGDHDALESLGIRCRHELPGVGKNLQEHVDACVLV 305

Query: 299 KSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSV 358
            S   +    SL G +KM      Y   + G +A +  EAG F+K+   + RPD+QLH +
Sbjct: 306 SSRKNNGFTASLGGLLKMVPDTIRYFLSKRGKLAKSITEAGGFIKSSDSVNRPDVQLHML 365

Query: 359 IGTVDDHNR--KLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416
               DD  R  KL    G+S HVCVLRPKS G+V + S DP  AP ID NF A  DD   
Sbjct: 366 PLLFDDSGRDLKLMSNPGYSVHVCVLRPKSSGTVTITSADPFAAPEIDYNFFADPDDCKV 425

Query: 417 LLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475
           ++ G R  R I+A      +   +++  A   +DEQ+IE ++++   +YHP+GTCKMG D
Sbjct: 426 MVDGIRQARRILAAKAFDDYRGEELHPGADRQSDEQIIEKVKEKVGLVYHPVGTCKMGTD 485

Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523
            MAVVD QLRVHG+ GLRVVDASIMP L+ GNTNA  I IAE+AA+ I
Sbjct: 486 RMAVVDPQLRVHGLGGLRVVDASIMPRLISGNTNAPTIAIAEKAADMI 533


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: 867
Number of extensions: 49
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: 542
Length adjustment: 35
Effective length of query: 491
Effective length of database: 507
Effective search space:   248937
Effective search space used:   248937
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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