GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas fluorescens FW300-N2E2

Align Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized)
to candidate Pf6N2E2_1004 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= SwissProt::Q6CEE9
         (278 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1004
          Length = 252

 Score =  126 bits (317), Expect = 4e-34
 Identities = 82/249 (32%), Positives = 134/249 (53%), Gaps = 12/249 (4%)

Query: 31  LKGKVASITGSSSGIGFAVAEAFAQAGADVAIWYNSKPSDEKAEYLSKTYGVRSKAYKCA 90
           L  KVA +TG   GIG A+AE FA+ GA V +    +P   K + +         A    
Sbjct: 15  LHNKVALVTGGGMGIGRAIAELFAEEGATVIVGDVHQPEPYKNDSVV--------AKHLD 66

Query: 91  VTNAKQVETTIQTIEKDFGKIDIFIANAGIPWTAGPMIDVPNNEEWDKVVDLDLNGAYYC 150
           V+  +  E  +  + ++ GK+D+ + NAG+  +  P ID    ++W++V+D++ NG +Y 
Sbjct: 67  VSKLEDWELLVAEVVREHGKVDVLVNNAGLVGSYLP-IDEITLDDWNRVIDINQNGVFYG 125

Query: 151 AKYAGQIFKKQGYGSFIFTASMSGHIVNIPQMQACYNAAKCAVLHLSRSLAVEW-AGFAR 209
            +    + K+Q  GS +  +S+ G IV    + A Y A+K AV  +S++ A+ + A   R
Sbjct: 126 MRTVVPVMKRQHAGSIVNVSSIWG-IVGASGVSA-YQASKAAVRMMSKNAALSYVANGIR 183

Query: 210 CNTVSPGYMATEISDFIPRDTKEKWWQLIPMGREGDPSELAGAYIYLASDASTYTTGADI 269
            N++ PG + T + D    D         PM R  DP E+A A ++LASD +++ TGA++
Sbjct: 184 VNSLHPGLVETPMIDRQAADITAAVVAATPMKRAADPKEIAYAALFLASDEASFITGAEL 243

Query: 270 LVDGGYCCP 278
           +VDGGY  P
Sbjct: 244 VVDGGYTTP 252


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: 162
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: 278
Length of database: 252
Length adjustment: 25
Effective length of query: 253
Effective length of database: 227
Effective search space:    57431
Effective search space used:    57431
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 17 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