GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpF in Klebsiella michiganensis M5al

Align Aconitate-delta-isomerase 1; Itaconic acid/2-hydroxyparaconate biosynthesis cluster protein ADI1; EC 5.-.-.- (characterized)
to candidate BWI76_RS04370 BWI76_RS04370 FldA family protein

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS04370 BWI76_RS04370 FldA family
           protein
          Length = 351

 Score =  243 bits (621), Expect = 5e-69
 Identities = 142/345 (41%), Positives = 200/345 (57%), Gaps = 14/345 (4%)

Query: 5   IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64
           I   + R GTS+G + LA DLP +  +RD  L++IMGSGH L+IDG+GGG+  TSKVAI+
Sbjct: 4   IPCVLMRGGTSKGAFLLADDLPKDIQKRDDCLLAIMGSGHELEIDGIGGGSPQTSKVAII 63

Query: 65  SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124
           S S    E D+DYLF QV + ER VDT PNCGN++  V  FAIE GLV+     T   VR
Sbjct: 64  SQSLSE-EADIDYLFVQVIVNERRVDTTPNCGNMLCAVGGFAIEHGLVEAASPVTR--VR 120

Query: 125 IFNLNSRQASELVIPVYNGRVHYDDIDDMH-MQRPSARVGLRFLDTVGSCTGKLLPTGNA 183
           I N+N+    +  +   +G+V Y+    +  +   +A V L FL+  G+ +G+L PTGN 
Sbjct: 121 IRNVNTNTFIDADVQTPDGKVIYEGDSQIDGVPGRAAPVALTFLNAAGAKSGRLFPTGNR 180

Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243
            D  D ++V+ ID A+P+V I    +G TG E+ + L+ ++ LL  LE +R++AG+ MG 
Sbjct: 181 MDVFDDVRVTCIDMAMPMVVIPAQSLGKTGYESASELDRDSGLLKSLESIRIQAGKAMGF 240

Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303
           GDV+  V+PK  LI P     +   RYF P  CH + A+TGAI  A A  I  ++  E+ 
Sbjct: 241 GDVTNMVIPKPVLISPALSGGSINVRYFMPHNCHKSLAITGAIGLASACIIPKTIANELT 300

Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVP----PENAAQSLVDVA 344
                        I +EHPSG +EV L      PE+   S++  A
Sbjct: 301 KLSGDGI------IKVEHPSGGIEVDLSQTTERPEDIRASVIRTA 339


Lambda     K      H
   0.318    0.133    0.389 

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: 382
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: 443
Length of database: 351
Length adjustment: 31
Effective length of query: 412
Effective length of database: 320
Effective search space:   131840
Effective search space used:   131840
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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