GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Cupriavidus basilensis 4G11

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate RR42_RS01280 RR42_RS01280 GMC family oxidoreductase

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Cup4G11:RR42_RS01280
          Length = 559

 Score =  533 bits (1372), Expect = e-156
 Identities = 282/542 (52%), Positives = 358/542 (66%), Gaps = 18/542 (3%)

Query: 3   FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHV-NWA 61
           FDYL+VG GSAGC LA RL+   S +V +LE G  D   L+ TP G AA+LP     N+ 
Sbjct: 5   FDYLVVGGGSAGCALAGRLADSGSDSVAVLETGGHDHHVLVSTPAGCAAMLPRAGSHNYG 64

Query: 62  FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121
           ++T PQPGL GR GYQPRG+ LGGSSS+N MIY RG   D++ W + G +GW +DDVLPY
Sbjct: 65  YRTVPQPGLNGRRGYQPRGRGLGGSSSLNAMIYTRGTPADYDRWASAGCDGWAWDDVLPY 124

Query: 122 FRKSEMHHGGSSE----YHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQ 176
           FR++E +   +      +HGG G L+VS     +   + F+E+A +AG+  N DFNG  Q
Sbjct: 125 FRRAECNERVAGRDDDPWHGGSGPLHVSDLRTPNPFGQRFIEAAQQAGYRRNDDFNGVDQ 184

Query: 177 EGAGYYDVTIRDGRRWSTATAFLK---PVRH-----RSNLTVLTHTHVESIVLLGKQATG 228
           EGAG+Y VT   G RW+ A A+L       H     R NL V+T T V  I   G+ A G
Sbjct: 185 EGAGWYQVTQHGGERWNAARAYLHRGDAADHASNGGRENLAVMTGTQVLRIAFEGRHAVG 244

Query: 229 VQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNL 288
           V   + G    LRAR+EVI+SAGAFGSP LLM+SG+G A+ L   GI   H+LPGVG NL
Sbjct: 245 VVVRLDGRETLLRARREVIVSAGAFGSPQLLMVSGVGPASHLRELGIPVVHDLPGVGANL 304

Query: 289 QDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGL 348
           QDH D+++  +   + L G S+ G  ++   +  Y R R G + SN AEAGAFLK+  GL
Sbjct: 305 QDHLDIIVHKRVAASELFGVSVGGAFRLLAEILRYRRERTGMLTSNFAEAGAFLKSHAGL 364

Query: 349 ERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFL 408
           + PD+QLH V+G  DDH R++  GHG+SCHVCVLRPKS G V LASPD R+AP IDP FL
Sbjct: 365 DEPDLQLHFVVGMADDHMRRIRLGHGYSCHVCVLRPKSRGEVRLASPDIREAPMIDPCFL 424

Query: 409 AHDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGL----HNDEQLIELLRKRTDTIY 464
           +   D+  L+ G RI R I+AQ  +A+FG +++YSA L     +D  +  ++R   DTIY
Sbjct: 425 SDPRDLDGLVAGVRIVRRILAQPQLAAFGGKELYSAHLPADGGDDSAIRAMIRAHADTIY 484

Query: 465 HPIGTCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524
           HP+GTC+MG DE AVVD QLRV G+EGLRVVDASIMPTL+GGNTNA AIMI ERA + I 
Sbjct: 485 HPVGTCRMGMDEYAVVDPQLRVRGVEGLRVVDASIMPTLIGGNTNAPAIMIGERAHDLIR 544

Query: 525 HG 526
           HG
Sbjct: 545 HG 546


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: 965
Number of extensions: 45
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: 559
Length adjustment: 35
Effective length of query: 491
Effective length of database: 524
Effective search space:   257284
Effective search space used:   257284
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