GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudovibrio axinellae Ad2

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase

Query= SwissProt::O93868
         (262 letters)



>NCBI__GCF_001623255.1:WP_068003992.1
          Length = 263

 Score =  112 bits (281), Expect = 6e-30
 Identities = 87/254 (34%), Positives = 121/254 (47%), Gaps = 13/254 (5%)

Query: 12  KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVS 71
           K  IVTGG +GIG A  +     GA V +I  + + A E  ++   EFG     + CDV 
Sbjct: 6   KVAIVTGGAQGIGYAIAQRFLEDGAKV-MISDADERAGEAAQEALSEFGHVAFCH-CDVG 63

Query: 72  NTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAV 131
               V   +     + G I  L+ NAGV+       L+ +DF  V  VN+ G F   +AV
Sbjct: 64  VRLDVRNMVANTLDEFGDIDVLVNNAGVTAAGDFLTLSEDDFDRVLQVNLKGAFLCSQAV 123

Query: 132 AKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLT---QVFYNSSKAACSNLVKGLAAEWA 188
           A+  ++K ++G        +  IIN SS+N  L    QV Y  SK   + L    A   A
Sbjct: 124 ARHMVEKIEEGG------SAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNVSAVALA 177

Query: 189 SAGIRVNALSPGYVNTD--QTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHAT 246
             GIRVN + PG + TD  +    D+   +   S  PL R  QP E+ G A  L SD A+
Sbjct: 178 KYGIRVNGIGPGSIETDMLKAVVQDESKMNKVLSRTPLGRLGQPSEIAGVASFLASDDAS 237

Query: 247 YMTGGEYFIDGGQL 260
           Y++G   F DG +L
Sbjct: 238 YVSGQTIFADGARL 251


Lambda     K      H
   0.317    0.130    0.372 

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: 142
Number of extensions: 7
Number of successful extensions: 4
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: 262
Length of database: 263
Length adjustment: 25
Effective length of query: 237
Effective length of database: 238
Effective search space:    56406
Effective search space used:    56406
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 (21.7 bits)
S2: 47 (22.7 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