GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Algiphilus aromaticivorans DG1253

Align Putative alcohol dehydrogenase D; EC 1.1.1.1 (characterized)
to candidate WP_043767718.1 U743_RS09715 alcohol dehydrogenase catalytic domain-containing protein

Query= SwissProt::P9WQB9
         (368 letters)



>NCBI__GCF_000733765.1:WP_043767718.1
          Length = 379

 Score =  249 bits (637), Expect = 7e-71
 Identities = 150/374 (40%), Positives = 205/374 (54%), Gaps = 13/374 (3%)

Query: 3   TTAAVLFEAG--------KPFELMELDLDGPGPGEVLVKYTAAGLCHSDLHLTDGDLPPR 54
           T  AVL E G        +P ++  L+L  PGPGE+ V+  AAG+CHSDL + +G  P  
Sbjct: 5   TRGAVLREMGAAQPYAETRPLKIETLELAPPGPGEIQVRVRAAGICHSDLSVVNGSRPRP 64

Query: 55  FPIVGGHEGSGVIEEVGAGVTRVKPGDHVVCSFIPNCGTCRYCCTGRQNLCDMGATI-LE 113
            P+V GHE +G +E VG  V    PGD VV SF+P CGTC YC  GR  LC  GA     
Sbjct: 65  MPMVLGHEAAGDVEAVGPDVADFAPGDRVVFSFVPACGTCSYCAEGRPVLCVPGAAANSA 124

Query: 114 GCMPDGSFRFH-SQGTDFGAMCMLGTFAERATVSQHSVVKVDDWLPLETAVLVGCGVPSG 172
           G +  G+ R+  S G +      +  FAER  VS  S V++D  LP+E A L GC V +G
Sbjct: 125 GTLLSGARRWRDSDGAECHHHLGVSAFAERTVVSTRSAVRIDPDLPVEIAALFGCAVMTG 184

Query: 173 WGTAVNAGNLRAGDTAVIYGVGGLGINAVQGATAAGCKYVVVVDPVAFKRETALKFGATH 232
            G AVN   +R G++  ++G+GG+G+ A+ GA AAG   VV VDPVA KRE AL  GATH
Sbjct: 185 VGAAVNTAAVRPGESVAVFGMGGVGLAALLGAIAAGAWPVVAVDPVAAKRELALSLGATH 244

Query: 233 AFADAASAAAKVDELTWGQGADAALILVGTVDDEVVSAATAVIGKGGTVVITGLADPAKL 292
                A  A +      G GA  A+  VG+  ++V+  A     +GG  V  GL  P ++
Sbjct: 245 VVDPTAEDAVEAVRAHTGGGAAHAVETVGS--EKVLEQAYFATVRGGQTVTVGLPHPERM 302

Query: 293 TVHVSGTDLTLHEKTIKGSLFGSCNPQYDIVRLLRLYDAGQLMLDELVTTTYNLEQVNQG 352
            + +    L   E+T++GS  GS     D+ R L LY AG+L +D+L+T    L+ +N  
Sbjct: 303 -LSIPAVSLVAEERTLRGSYMGSAVVSRDVPRFLSLYRAGRLPVDKLLTHELALDGINAA 361

Query: 353 YQDLRDGKNIRGVI 366
           +  L   + +R VI
Sbjct: 362 FDRLARAEAVRQVI 375


Lambda     K      H
   0.320    0.138    0.422 

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: 327
Number of extensions: 21
Number of successful extensions: 3
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: 368
Length of database: 379
Length adjustment: 30
Effective length of query: 338
Effective length of database: 349
Effective search space:   117962
Effective search space used:   117962
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 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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