GapMind for catabolism of small carbon sources

 

Alignments for a candidate for x5p-reductase in Salinicoccus carnicancri Crm

Align Lmo2663 protein (characterized, see rationale)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein

Query= uniprot:Q8Y414
         (343 letters)



>NCBI__GCF_000330705.1:WP_017549841.1
          Length = 338

 Score =  163 bits (412), Expect = 7e-45
 Identities = 107/330 (32%), Positives = 167/330 (50%), Gaps = 9/330 (2%)

Query: 1   MKAVVKTNPGYDQMELKDVEEPQVY-GDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTL 59
           MKA+    PG  Q+ + ++E+P +  GD+V +K+   GICGSD+H + G     + P  +
Sbjct: 1   MKAIQVEKPG--QLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNPFTSYPRVI 58

Query: 60  GHEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGS 119
           GHE SG+V +VG  VTS+  GD V  E     CGEC  C+    N+C +    G   +G 
Sbjct: 59  GHEVSGIVEQVGEAVTSLAPGDLVALE-PITYCGECYACRNGQPNVCDSLEVFGVHRDGG 117

Query: 120 FAEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLL 179
            AE++ + E + H +   +S EAAAL EP+      A  +  +R  DTV V G GP G+ 
Sbjct: 118 MAEYLKADENNWHKVPGNVSEEAAALMEPMTIGA-QATYRGDVREGDTVFVIGAGPTGIA 176

Query: 180 LAQVVKAQGATVIMAGITKDSDRLRLAKELGMDRIVDTLKEDLAEVVLGMTGGYGAERVF 239
                K +GA V ++    + +RL  AK +G D  +      + E +  +T G  A  V 
Sbjct: 177 CLLQAKQRGAKVFISDF--NQNRLDYAKSIGADATIQPDGVHVEEEINRLTNGELANVVI 234

Query: 240 DCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAIDEESIIQREIAYIGSRSQKPSSWIL 299
           D  G      Q + L    G  V +G F E+ ++I    + ++E+   GSR Q    +  
Sbjct: 235 DAVGLPQTFQQAVELASIAGRVVTLG-FNEQPSSIPSLLLTKKELKVAGSRLQ-THQFPK 292

Query: 300 ALDLLANGKIDTDKMITKVYGLDDWREAFE 329
            +D +  G+ID  ++I++ Y +D   +AFE
Sbjct: 293 VIDQVGRGEIDPTQIISQRYSMDQIHDAFE 322


Lambda     K      H
   0.317    0.135    0.392 

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: 312
Number of extensions: 17
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: 343
Length of database: 338
Length adjustment: 28
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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