GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS04370
          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:

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