GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Caulobacter crescentus NA1000

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_00994 CCNA_00994 oxidoreductase, GMC family

Query= BRENDA::Q76HN6
         (526 letters)



>FitnessBrowser__Caulo:CCNA_00994
          Length = 555

 Score =  415 bits (1066), Expect = e-120
 Identities = 239/542 (44%), Positives = 316/542 (58%), Gaps = 20/542 (3%)

Query: 1   MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDR----------SPLIHTPLGLA 50
           +E DY+IVGAGSAGCVLA RLS +    V LLEAG +DR          + +IH P+G +
Sbjct: 5   IEADYVIVGAGSAGCVLAARLSENGRYKVVLLEAGGDDRPTKNLSQFASNMMIHIPVGYS 64

Query: 51  AILPTRHVNWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGN 110
           + L    VNW F T P PG GGR    PRGKVLGGSSSIN M+Y+RG   D++ W+ LG 
Sbjct: 65  STLKDPKVNWLFTTEPDPGTGGRSHVWPRGKVLGGSSSINAMLYVRGQAADYDGWRQLGC 124

Query: 111 EGWGFDDVLPYFRKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNP 169
           EGW +DDVLPYFRK++    G+ + H   G L V+   + H  SEA +E+  +AG    P
Sbjct: 125 EGWAWDDVLPYFRKAQNQERGACDLHATGGPLNVADMRDAHPISEALIEACDQAGIPRYP 184

Query: 170 DFNGATQEGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGV 229
           D NGA QEGA +Y VT ++G R S+A A+L P   R NL V T+     ++  GK+A GV
Sbjct: 185 DLNGADQEGATWYQVTQKNGARCSSAVAYLHPAMKRPNLRVETNALAGRVLFEGKRAVGV 244

Query: 230 QALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQ 289
           + +  G R    AR EVIL+ GA  SP LL LSG+G+   L   GI    +LPGVG+NLQ
Sbjct: 245 EFMQNGERRAAMARGEVILAGGAINSPQLLQLSGVGAGGLLREHGIEVVADLPGVGENLQ 304

Query: 290 DHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLE 349
           DH  V   Y+    ++     S G ++      Y   R G +  + A   AF K+ P L 
Sbjct: 305 DHYIVAARYRLKSGTVSVNEQSKGGRLAAEAMKYLLFRKGLLTLSAAHVAAFCKSRPDLA 364

Query: 350 RPDIQLHSVIGTVD------DHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRI 403
            PDIQ H +  T+D      +   +L    G +   C LRP+S G + + S DP   P I
Sbjct: 365 GPDIQFHILPATMDLDKLFNEQKMELEGAPGMTIAPCQLRPESRGYIRIKSADPSVYPAI 424

Query: 404 DPNFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGL--HNDEQLIELLRKRTD 461
             N+LA   D   ++ G +  R I  Q  +A +   +M + GL    DEQL++  R+   
Sbjct: 425 FANYLADPLDQEVIVAGLKWARKIGQQPAIAQYVESEM-NPGLEVQTDEQLLDFARQTGS 483

Query: 462 TIYHPIGTCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521
           T+YHP+G+C+MG   MAVVD+QLRV G+EGLRVVDASIMP L+ GNTNA +IMI E+ A+
Sbjct: 484 TLYHPVGSCQMGTGPMAVVDAQLRVRGVEGLRVVDASIMPRLISGNTNAPSIMIGEKGAD 543

Query: 522 WI 523
            I
Sbjct: 544 MI 545


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: 762
Number of extensions: 35
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: 555
Length adjustment: 35
Effective length of query: 491
Effective length of database: 520
Effective search space:   255320
Effective search space used:   255320
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.

Links

Downloads

Related tools

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