GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Snodgrassella alvi wkB2

Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate WP_025331133.1 SALWKB2_RS07905 zinc-dependent alcohol dehydrogenase family protein

Query= SwissProt::Q0KDL6
         (366 letters)



>NCBI__GCF_000600005.1:WP_025331133.1
          Length = 356

 Score =  199 bits (506), Expect = 1e-55
 Identities = 125/365 (34%), Positives = 195/365 (53%), Gaps = 32/365 (8%)

Query: 5   MKAAVFVEPGRIELADKPIPDI-GPNDALVRITTTTICGTDVHILKGEYPVAK------- 56
           MKA V+   G I   ++  P I  P DA++R+T TTICGTD+ I KG+ P  +       
Sbjct: 1   MKAMVYYGAGDIRFEERTKPVIIEPTDAIIRLTRTTICGTDLGIWKGKNPEIEQTAIQKD 60

Query: 57  ----GLTVGHEPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMA 112
               G  +GHE +GIIE+ GSAV  +++G +VI   +        ++ G        L A
Sbjct: 61  GQFNGRILGHEGIGIIEETGSAVKNFKKGDKVIISCV--------SRCGTCENCQKQLYA 112

Query: 113 SGQCGCHGYKATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTG 172
             Q G        GW  G MIDGTQAEYV  P A  +L  +P  L ++  ++  D + T 
Sbjct: 113 HCQSG-------GGWIMGYMIDGTQAEYVRTPFADNSLYRLPANLNEDVAVLLSDALPTA 165

Query: 173 FK-GAENANIRIGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADV 231
            + G +  +++ GDTVA+   GP+G+     A+L   + II ID +D+RL +A+++GA  
Sbjct: 166 HEIGVQYGDVKPGDTVAIVGAGPVGMSCLLTAQLYSPSQIIMIDMDDNRLHMAKELGATQ 225

Query: 232 VLNFRNCDVVDEVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTI 291
           ++N  + D V  V++ TGGRGVD ++EA+G +AT+    RV+K GG L+++GV+   +  
Sbjct: 226 IINSASEDAVARVLEYTGGRGVDCAMEAVGLEATWNICQRVVKEGGHLANVGVHGQSVNF 285

Query: 292 PLSAFAAGLGDHKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLF 351
            L      + +  I T L       M  L+    SG++ +  L TH +  +++  AYD+F
Sbjct: 286 ELEKL--WIKNLTITTGLVNANTTGM--LLKTCCSGKLPMEKLATHHFHFNELEKAYDVF 341

Query: 352 ANQRD 356
            +  D
Sbjct: 342 KHAAD 346


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: 346
Number of extensions: 16
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: 366
Length of database: 356
Length adjustment: 29
Effective length of query: 337
Effective length of database: 327
Effective search space:   110199
Effective search space used:   110199
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.

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