GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Pseudomonas fluorescens FW300-N2E3

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate AO353_04045 AO353_04045 3-ketoacyl-ACP reductase

Query= SwissProt::O93868
         (262 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04045
          Length = 252

 Score =  124 bits (312), Expect = 1e-33
 Identities = 84/260 (32%), Positives = 137/260 (52%), Gaps = 19/260 (7%)

Query: 7   ISFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAY 66
           +   +K II+TGG +G+G +     AA GA +A++  + ++ ++      K  GV+ +AY
Sbjct: 1   MKLTDKVIIITGGCQGLGRSMAEYFAAKGAKLALVDLN-QEKLDQAVAACKAAGVEARAY 59

Query: 67  QCDVSNTDIVTKTIQQIDADLGAISGLIANAGVS----VVK----PATELTHEDFKFVYD 118
            C+V+N + VT  + Q+  D GAI GLI NAG+     ++K      T+++   ++ V D
Sbjct: 60  LCNVANEEQVTHMVAQVAEDFGAIHGLINNAGILRDGLLIKVKDGEMTKMSLAQWQAVID 119

Query: 119 VNVFGVFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSN 178
           VN+ GVF   R VA   ++ +  G+IV  SS+S          G++ Q  Y+++KA  + 
Sbjct: 120 VNLTGVFLCTREVAAKMIELKTGGAIVNISSISRA--------GNVGQTNYSAAKAGVAA 171

Query: 179 LVKGLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAI 238
                A E A  GIRV  ++PG++ T+ T  M  +  +   S IPL R  +PEE+   A 
Sbjct: 172 ATVTWAKELARHGIRVAGIAPGFIETEMTLSMKPEALEKMTSGIPLKRMGKPEEIAHSAA 231

Query: 239 LLLSDHATYMTGGEYFIDGG 258
            +  +   Y TG    +DGG
Sbjct: 232 YIFEN--DYYTGRILEMDGG 249


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: 167
Number of extensions: 14
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: 252
Length adjustment: 24
Effective length of query: 238
Effective length of database: 228
Effective search space:    54264
Effective search space used:    54264
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