GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Brucella inopinata BO1

Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate WP_008505361.1 BIBO1_RS08590 glucose 1-dehydrogenase

Query= SwissProt::Q6CEE9
         (278 letters)



>NCBI__GCF_000182725.1:WP_008505361.1
          Length = 246

 Score =  141 bits (355), Expect = 2e-38
 Identities = 91/245 (37%), Positives = 131/245 (53%), Gaps = 6/245 (2%)

Query: 32  KGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCAV 91
           K KV  +TG +SGIG A A AF + GA V I   S    + A+ L+  +  ++   K  V
Sbjct: 4   KDKVVIVTGGASGIGEATARAFIREGAKVVIADFSDHGQQLADELAGAHE-QALFIKTDV 62

Query: 92  TNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYCA 151
            + K V+  I    +++G++DI  ANAGI   A   ID  +   W K +D++L G Y C 
Sbjct: 63  ADTKAVQALIVRTVENYGRLDIMFANAGI--AADAPIDELDEAAWQKTIDINLTGVYLCD 120

Query: 152 KYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGF-ARC 210
           KYA    + QG G  +   S+  H+         Y AAK  V  L+++LA+++     R 
Sbjct: 121 KYAIDQMRSQGGGVIVNCGSIHSHVGK--SGVTAYAAAKGGVKLLTQTLAIDYGPQNIRV 178

Query: 211 NTVSPGYMATEISDFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTYTTGADIL 270
           N V PGY+ T +   IP D K+    L PMGR G   E+A A ++LASD +++  GA +L
Sbjct: 179 NAVCPGYIDTPLLKNIPDDKKQALVALHPMGRLGRAEEVANAVLFLASDEASFVNGASLL 238

Query: 271 VDGGY 275
           VDGGY
Sbjct: 239 VDGGY 243


Lambda     K      H
   0.317    0.132    0.409 

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: 165
Number of extensions: 9
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: 278
Length of database: 246
Length adjustment: 25
Effective length of query: 253
Effective length of database: 221
Effective search space:    55913
Effective search space used:    55913
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