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_RS14180 BWI76_RS14180 hypothetical protein

Query= SwissProt::A0A0U2X0E4
         (443 letters)



>FitnessBrowser__Koxy:BWI76_RS14180
          Length = 361

 Score =  235 bits (599), Expect = 2e-66
 Identities = 143/332 (43%), Positives = 189/332 (56%), Gaps = 10/332 (3%)

Query: 5   IDTTIYRAGTSRGLYFLASDLPAEPSERDAALISIMGSGHPLQIDGMGGGNSLTSKVAIV 64
           I   + R GTS+   FLA DLP +P+ RDA L++ MGS    QIDG+GG + LTSKVAI+
Sbjct: 6   IPCLLMRGGTSKAACFLADDLPVDPASRDAVLLATMGSPDTRQIDGIGGADPLTSKVAII 65

Query: 65  SASTQRSEFDVDYLFCQVGITERFVDTAPNCGNLMSGVAAFAIERGLVQPHPSDTTCLVR 124
             S  R + D+DYLF QV +    VD   NCGN+++ V  FAIERGLV      T   VR
Sbjct: 66  RRSA-RPDADIDYLFAQVNVDRAVVDYGQNCGNILAVVGPFAIERGLVDCVAPLTR--VR 122

Query: 125 IFNLNSRQASELVIPVYNGRVHY-DDIDDMHMQRPSARVGLRFLDTVGSCTGKLLPTGNA 183
           IF  N+ Q +   +P   G V Y  D     +   ++++ L FLD  GS  G LLPTG A
Sbjct: 123 IFMENTGQIAVAEVPCNTGGVEYAGDTRIDGVPGTASKIVLNFLDVAGSSCGALLPTGQA 182

Query: 184 SDWIDGLKVSIIDSAVPVVFIRQHDVGITGSEAPATLNANTALLDRLERVRLEAGRRMGL 243
           SD  DG++V+ ID+ +PVV IR  D+G TG E    L+A+  L  RLE +RL+AG RM L
Sbjct: 183 SDRFDGIEVTCIDNGMPVVLIRASDLGRTGYETREQLDADDELKQRLETIRLQAGPRMNL 242

Query: 244 GDVSGSVVPKLSLIGPGTETTTFTARYFTPKACHNAHAVTGAICTAGAAYIDGSVVCEIL 303
           GDV+   VPK++LI         ++R F P  CH +  V GA+  A A  I GSV     
Sbjct: 243 GDVTQRTVPKMTLIARPRAGGAISSRTFIPHRCHASIGVFGAVSVASACLIPGSV----- 297

Query: 304 SSRASACSASQRRISIEHPSGVLEVGLVPPEN 335
            ++A A       +S+EHP+G   V L   +N
Sbjct: 298 -AQALASLERTPELSVEHPTGEFSVALRLDDN 328


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: 15
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: 361
Length adjustment: 31
Effective length of query: 412
Effective length of database: 330
Effective search space:   135960
Effective search space used:   135960
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