GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolM in Salinicoccus carnicancri Crm

Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein

Query= SwissProt::Q9WYP3
         (395 letters)



>NCBI__GCF_000330705.1:WP_017549841.1
          Length = 338

 Score =  151 bits (382), Expect = 2e-41
 Identities = 107/356 (30%), Positives = 175/356 (49%), Gaps = 31/356 (8%)

Query: 39  EVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGLTGFPVTLGHEFS 98
           ++ + E+ +P IE   E+I+K+K  GICGSDVH+              T +P  +GHE S
Sbjct: 11  QLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNP-------FTSYPRVIGHEVS 63

Query: 99  GVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCENLNELGFNVDGA 158
           G+V + G EA+          G+ V  E + +CG C  C  G PN C++L   G + DG 
Sbjct: 64  GIVEQVG-EAVTSLAP-----GDLVALEPITYCGECYACRNGQPNVCDSLEVFGVHRDGG 117

Query: 159 FAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLVEPTSVAYNAVIVRGGGIRPGDNVVIL 218
            AEY+K D     +  ++ G    +    A +L+EP ++   A     G +R GD V ++
Sbjct: 118 MAEYLKADEN---NWHKVPGNVSEE----AAALMEPMTIGAQATY--RGDVREGDTVFVI 168

Query: 219 GGGPIGLAAVAILKHAGASKVILSEPSEVRRNLAKELGADHVIDPTKENFVEAVLDYTNG 278
           G GP G+A +   K  GA KV +S+ ++ R + AK +GAD  I P   +  E +   TNG
Sbjct: 169 GAGPTGIACLLQAKQRGA-KVFISDFNQNRLDYAKSIGADATIQPDGVHVEEEINRLTNG 227

Query: 279 LGAKLFLEATGVPQLVWPQIEEVIWRARGINATVAIVARADAKIPLTGEVFQVRRAQIVG 338
             A + ++A G+PQ     +E      R +         +   + LT +  +V  +++  
Sbjct: 228 ELANVVIDAVGLPQTFQQAVELASIAGRVVTLGFNEQPSSIPSLLLTKKELKVAGSRLQT 287

Query: 339 SQGHSGHGTFPRVISLMASG-MDMTKIISKTVSMEEIPEYIKRLQTDKSLVKVTML 393
            Q       FP+VI  +  G +D T+IIS+  SM++I +  + L+ +    +  +L
Sbjct: 288 HQ-------FPKVIDQVGRGEIDPTQIISQRYSMDQIHDAFELLENNPEAARKIVL 336


Lambda     K      H
   0.319    0.138    0.418 

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: 333
Number of extensions: 20
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: 395
Length of database: 338
Length adjustment: 30
Effective length of query: 365
Effective length of database: 308
Effective search space:   112420
Effective search space used:   112420
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: 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