GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Pseudomonas fluorescens GW456-L13

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate PfGW456L13_2522 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= uniprot:A0A2E7P8M8
         (258 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2522
          Length = 248

 Score =  103 bits (256), Expect = 4e-27
 Identities = 80/249 (32%), Positives = 119/249 (47%), Gaps = 16/249 (6%)

Query: 5   LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64
           LQ+KV +VTGGASGIG A   + +AEGA  +          F     GL        L++
Sbjct: 4   LQNKVAVVTGGASGIGLACVRRFSAEGAQVIGLDIGSAPADF----PGL-----FMTLDV 54

Query: 65  QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL-DAGRNEFVASLERNLIHYYVMAHY 123
           +DEA+  + + E + RFGR+D LVN AGV D   +       +   ++ NL    + + Y
Sbjct: 55  RDEAQVQQVMQEVISRFGRIDVLVNAAGVADQGSVTQTTTANWQRVMDINLTGSMLTSKY 114

Query: 124 CVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALI 182
            +  +   R G+I+NV S   L G      Y  SKG    LTR  A       +RVN L 
Sbjct: 115 ALASMVEQRNGSIINVGSIFGLQGCDGNVAYNVSKGGINQLTRSMAIDYGYANIRVNGLC 174

Query: 183 PAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQ 242
           P  + TP+      +     +   A  +   +  R    EE+A++A+FL S  +S  +GQ
Sbjct: 175 PGLIETPM-----TSMVRDNDAFHAFFASQHMLNRSGQPEEVANVALFLASDEASFVSGQ 229

Query: 243 WVFVDGGYT 251
            + VDGG++
Sbjct: 230 MIAVDGGFS 238


Lambda     K      H
   0.318    0.134    0.394 

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: 139
Number of extensions: 12
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: 258
Length of database: 248
Length adjustment: 24
Effective length of query: 234
Effective length of database: 224
Effective search space:    52416
Effective search space used:    52416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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