GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Mucilaginibacter mallensis MP1X4

Align Gluconolactonase (characterized, see rationale)
to candidate WP_091375961.1 BLU33_RS17565 SMP-30/gluconolactonase/LRE family protein

Query= uniprot:A0A165IRV8
         (316 letters)



>NCBI__GCF_900105165.1:WP_091375961.1
          Length = 295

 Score =  189 bits (481), Expect = 5e-53
 Identities = 105/281 (37%), Positives = 153/281 (54%), Gaps = 5/281 (1%)

Query: 35  LGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAERAHAPGFIVTLR 94
           LGEG +W+  E  +YWVDI GR  + +DP T  ++ +   + I  +    +    +V L 
Sbjct: 18  LGEGAIWNHMESKLYWVDIEGRLFNVFDPVTNQNRTYNTLKRIGTVVPTNNGQ-VLVALE 76

Query: 95  RGFALFDPATDMAPRYLHQPEPDRAGN-RFNDGKCDAQGRFWAGSMDFACEAPTGALYRY 153
            G A  +  TD    Y    +     N RFNDGKCD +GRFW G+   +       LY  
Sbjct: 77  DGIATIE-LTDGTITYKIDTDIHLMHNKRFNDGKCDHEGRFWVGTHSMSGVREVSELYCI 135

Query: 154 DSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSDLATGTVSNKTLWKH 213
             + +      G +++NG  W+    G+ M++  T  G   +YD D  TG ++NK +   
Sbjct: 136 SENFAMEEKVSGVSISNGIAWNA--DGSLMYYIDTPTGQVVQYDFDRQTGAIANKKVIIT 193

Query: 214 WLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLPVSQVTTCAFGGADL 273
              E G PDGMT D +G LWIA W G+CV   DP T   + +V +P  +V++CAFGG +L
Sbjct: 194 IPEEQGYPDGMTIDNEGMLWIALWDGFCVARFDPQTGEMIHKVAVPAPKVSSCAFGGDNL 253

Query: 274 RTLFISSARVGLTPEQLAAEPLAGALFAVDTDSLGLPAHPF 314
            TL+I++AR  +T E+L   PL+G +FAV TD+ G+PAH F
Sbjct: 254 DTLYITTARAEMTEEELELYPLSGGVFAVKTDAKGMPAHYF 294



 Score = 24.3 bits (51), Expect = 0.004
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 10/52 (19%)

Query: 32  GNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAER 83
           G ++  G+ W+     +Y++          D  TG   ++ FD +  AIA +
Sbjct: 147 GVSISNGIAWNADGSLMYYI----------DTPTGQVVQYDFDRQTGAIANK 188


Lambda     K      H
   0.321    0.137    0.457 

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: 375
Number of extensions: 26
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 316
Length of database: 295
Length adjustment: 27
Effective length of query: 289
Effective length of database: 268
Effective search space:    77452
Effective search space used:    77452
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: 48 (23.1 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