GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Rhodobacter maris JA276

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_097068497.1 CRO22_RS02400 beta-ketoacyl-ACP reductase

Query= SwissProt::Q6CEE9
         (278 letters)



>NCBI__GCF_900217815.1:WP_097068497.1
          Length = 240

 Score =  119 bits (298), Expect = 6e-32
 Identities = 79/242 (32%), Positives = 126/242 (52%), Gaps = 9/242 (3%)

Query: 34  KVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCAVTN 93
           +VA +TG + GIG A++ A  +AG  V   Y    +DE A   +   G+  K  K +V +
Sbjct: 3   RVALVTGGTRGIGAAISMALKEAGYTVVANYAG--NDEAAREFTHVTGI--KTVKWSVAD 58

Query: 94  AKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYCAKY 153
               E  I+ IE + G ID+ + NAGI  T        + E+WD+V+  +LNG +     
Sbjct: 59  YTGCEDGIRQIEDEVGPIDVLVNNAGI--TRDAPFHKMSREQWDQVIGTNLNGLFNMTHP 116

Query: 154 AGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEWAGFA-RCNT 212
                +++ +G  I  +S++G      Q+   Y+AAK   +  +++LA E A      N 
Sbjct: 117 LWNGMRERKFGRIINISSINGQKGQFGQVN--YSAAKAGDIGFTKALAQEGARSGITVNA 174

Query: 213 VSPGYMATEISDFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTYTTGADILVD 272
           + PGY+ATE+   +P   +E     IP+GR G+P E+A   ++LASD + + TGA   V+
Sbjct: 175 ICPGYIATEMVMAVPEKVRESIIATIPVGRLGEPDEIARTVVFLASDQAGFITGATFTVN 234

Query: 273 GG 274
           GG
Sbjct: 235 GG 236


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: 171
Number of extensions: 7
Number of successful extensions: 3
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: 240
Length adjustment: 24
Effective length of query: 254
Effective length of database: 216
Effective search space:    54864
Effective search space used:    54864
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