GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Paraburkholderia bryophila 376MFSha3.1

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate H281DRAFT_05794 H281DRAFT_05794 Choline dehydrogenase

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Burk376:H281DRAFT_05794
          Length = 550

 Score =  514 bits (1323), Expect = e-150
 Identities = 267/528 (50%), Positives = 351/528 (66%), Gaps = 5/528 (0%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSAD-PSVTVCLLEAGPE-DRSPLIHTPLGLAAILPTR-H 57
           ME+DY+IVGAGS GC LA+RL+ D P  T+ L+EAGP  +R+ L++ P+G+AA++P +  
Sbjct: 1   MEYDYIIVGAGSGGCALASRLADDCPDATIALVEAGPHTNRNLLVNMPVGVAAVVPNKLK 60

Query: 58  VNWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDD 117
            N+ + TTPQPGL GR GYQPRG+  GGSS+IN MIY RGH  D+++W   G +GW + D
Sbjct: 61  TNYGYLTTPQPGLAGRQGYQPRGRGFGGSSAINAMIYTRGHPLDYDEWAESGCDGWSWHD 120

Query: 118 VLPYFRKSEMHHGGSSEYHGGDGELYVSPAN-RHAASEAFVESALRAGHSYNPDFNGATQ 176
           VLPYFR++E +  G+  +HG  G L VS    R+  S  FV++A+ AG+  N DFNG  Q
Sbjct: 121 VLPYFRRAEGNERGADAWHGDSGPLTVSDLRYRNPFSRRFVQAAIEAGYKPNDDFNGPDQ 180

Query: 177 EGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGS 236
           EG G+Y VT RDGRR S A A++   R R+NL  +    V  +V   K+A GV+ +  G 
Sbjct: 181 EGIGFYQVTQRDGRRCSVARAYVYD-RERANLHTIADATVLRVVFEQKRACGVEIVRGGR 239

Query: 237 RVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVL 296
           R  L+AR EV+++AGAF SP LLM SG+G AA L+  GI   H+ P VGQNL DH D  +
Sbjct: 240 REMLKARAEVVVAAGAFNSPQLLMCSGVGPAAHLQAHGIEVLHDAPEVGQNLIDHVDFTI 299

Query: 297 CYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLH 356
             + +     GFS+ G  +M      + RH  G ++SN AEAG FLK+ P LERPD+QLH
Sbjct: 300 NKRVSSIEPTGFSVRGIGRMVPQFATFIRHGRGMLSSNVAEAGGFLKSKPTLERPDLQLH 359

Query: 357 SVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416
                VDDHNR +HWGHG+S HVCVLRP S G+V LAS D R AP IDP F +   D+  
Sbjct: 360 FCAALVDDHNRHMHWGHGYSLHVCVLRPFSRGTVTLASADARAAPVIDPRFFSDSRDLDL 419

Query: 417 LLKGYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDE 476
           L++G ++ R I+    +A  G R++Y+     D QL E + +  DTIYHP+ TC+MG D 
Sbjct: 420 LVEGVQMARRILDAPSLALHGGRELYTRPGQTDAQLREAIARHADTIYHPVATCRMGGDA 479

Query: 477 MAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524
            +VVD QLRV G+ GLR+VDAS+MPTL+GGNTNA  +MI ERAAE IA
Sbjct: 480 ASVVDPQLRVRGVTGLRIVDASVMPTLIGGNTNAPTVMIGERAAELIA 527


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: 884
Number of extensions: 48
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: 550
Length adjustment: 35
Effective length of query: 491
Effective length of database: 515
Effective search space:   252865
Effective search space used:   252865
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