GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Erythrobacter marinus HWDM-33

Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate WP_047094432.1 AAV99_RS12695 NAD(P)-dependent alcohol dehydrogenase

Query= SwissProt::Q0KDL6
         (366 letters)



>NCBI__GCF_001013305.1:WP_047094432.1
          Length = 354

 Score =  494 bits (1271), Expect = e-144
 Identities = 254/359 (70%), Positives = 292/359 (81%), Gaps = 7/359 (1%)

Query: 5   MKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGHEP 64
           MKAA+FVEPGRI L +KP+PD+GP DAL++ITTTTICGTDVHILKGEYPV KGLTVGHEP
Sbjct: 1   MKAAIFVEPGRIVLGEKPVPDVGPLDALMKITTTTICGTDVHILKGEYPVEKGLTVGHEP 60

Query: 65  VGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYKAT 124
           VG IEKLGSAV G+ EGQRVIAGAI P+  S A+  G  +Q G      GQ G HG+KA 
Sbjct: 61  VGRIEKLGSAVYGFTEGQRVIAGAITPSGTSTASLCGFHAQCG------GQEG-HGWKAI 113

Query: 125 AGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIRIG 184
            GWRFGN IDG QAEY+LVPDA ANL PIPDGL+DEQVLMCPDIMSTGF GAE+  IRIG
Sbjct: 114 GGWRFGNTIDGAQAEYLLVPDAMANLAPIPDGLSDEQVLMCPDIMSTGFGGAESGKIRIG 173

Query: 185 DTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVDEV 244
           DTVAVFAQGPIGL ATAGA + GATTII ++    R+ ++R+MGA  V++F   D VDE+
Sbjct: 174 DTVAVFAQGPIGLFATAGAYMMGATTIIGVESIPARMAMSRQMGATHVVDFSKVDPVDEI 233

Query: 245 MKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGDHK 304
           MK+T GRGVD +IEALG Q+TFE +LRVL+PGGTLSSLGVYS DLTIP  AF+AGLGD+ 
Sbjct: 234 MKITDGRGVDVAIEALGLQSTFEGALRVLRPGGTLSSLGVYSGDLTIPCDAFSAGLGDNH 293

Query: 305 INTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIAI 363
           I T LCPGGKERMRRL+  + SGR+D  ALVTH++ LD IV AY+LFANQR GVLK+AI
Sbjct: 294 IVTTLCPGGKERMRRLMATVASGRIDTKALVTHRFPLDSIVDAYELFANQRGGVLKVAI 352


Lambda     K      H
   0.320    0.138    0.408 

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: 565
Number of extensions: 14
Number of successful extensions: 2
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: 366
Length of database: 354
Length adjustment: 29
Effective length of query: 337
Effective length of database: 325
Effective search space:   109525
Effective search space used:   109525
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: 49 (23.5 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