GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Pseudomonas simiae WCS417

Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate GFF4112 PS417_21065 3-methylitaconate isomerase

Query= SwissProt::Q937N7
         (396 letters)



>FitnessBrowser__WCS417:GFF4112
          Length = 396

 Score =  682 bits (1760), Expect = 0.0
 Identities = 341/396 (86%), Positives = 365/396 (92%)

Query: 1   MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60
           M HV QIKIPATY+RGGTSKGVFF LQDLPE+AQVPG ARDALL+RVIGSPDPY KQIDG
Sbjct: 1   MAHVAQIKIPATYMRGGTSKGVFFSLQDLPESAQVPGAARDALLLRVIGSPDPYDKQIDG 60

Query: 61  MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120
           MG ATSSTSKTVIL+KSTR DHDVDYLFGQVSID+PFVDWSGNCGNLSAAVG FAISAGL
Sbjct: 61  MGGATSSTSKTVILAKSTRADHDVDYLFGQVSIDKPFVDWSGNCGNLSAAVGSFAISAGL 120

Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180
           VD +R+PHNGVAVVR+WQANIGKTII HVP+T+G VQETGDFELDGVTFPAAEVQLEFMD
Sbjct: 121 VDPARVPHNGVAVVRVWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQLEFMD 180

Query: 181 PAAEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAI 240
           PAAEEEG GG+MFPTGN++DDLEVP VGT KAT+INAGIPTIF+NAE +GYTGTELQ AI
Sbjct: 181 PAAEEEGGGGSMFPTGNLIDDLEVPGVGTFKATLINAGIPTIFINAEDLGYTGTELQGAI 240

Query: 241 NSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAAD 300
           NSD +ALAMFE    YGALRMGLIK++DEAA+RQHTPKVAFV +  DYVASSGK + A D
Sbjct: 241 NSDPKALAMFETVRAYGALRMGLIKHLDEAAQRQHTPKVAFVAKPADYVASSGKAINAGD 300

Query: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVG 360
           VDLLVRALSMGKLHHAMMGTAAVAIGTAAAI GTLVNLAAGG ERNAVRFGHPSGTLRVG
Sbjct: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAISGTLVNLAAGGVERNAVRFGHPSGTLRVG 360

Query: 361 AEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPGDAF 396
           AEA QV+GEW VKKAIMSRSARVLMEG+VRVPGDAF
Sbjct: 361 AEATQVNGEWVVKKAIMSRSARVLMEGFVRVPGDAF 396


Lambda     K      H
   0.317    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: 622
Number of extensions: 20
Number of successful extensions: 1
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: 396
Length of database: 396
Length adjustment: 31
Effective length of query: 365
Effective length of database: 365
Effective search space:   133225
Effective search space used:   133225
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: 50 (23.9 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