GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Cupriavidus basilensis 4G11

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate RR42_RS04460 RR42_RS04460 chorismate mutase

Query= SwissProt::P27603
         (365 letters)



>FitnessBrowser__Cup4G11:RR42_RS04460
          Length = 379

 Score =  332 bits (852), Expect = 8e-96
 Identities = 169/358 (47%), Positives = 235/358 (65%), Gaps = 6/358 (1%)

Query: 6   QLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHIM 65
           +L  LR +ID+LD  +L +++ RA+ A +V  VK     K   A  +RPERE  V++ + 
Sbjct: 27  ELTPLREQIDTLDRELLAMLNRRAQLALDVGEVK-----KKYGAPVFRPERELQVIRKVQ 81

Query: 66  ELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPMA 125
             N GPL ++ +A ++RE+MS+C  LE+PL VA+LGP GTFS+ A   HFGH V   P  
Sbjct: 82  GANPGPLLDDSVAAIWREVMSACRGLEKPLEVAFLGPAGTFSEQALYAHFGHEVSGVPCP 141

Query: 126 AIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGET 185
           +IDEVFR V AG V +GVVPVENSTEGAV+ TLD FL+  + I GE+ L++HH+L+    
Sbjct: 142 SIDEVFRAVEAGTVEYGVVPVENSTEGAVSRTLDLFLQTSLKISGEIALKVHHNLMASSP 201

Query: 186 TKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAA 245
                +T + +HAQ+LAQC+ WL A+YP++ER AVSSNA+AA+    +   AAIAG+ AA
Sbjct: 202 DMKG-VTVVRAHAQALAQCQHWLTANYPHLERQAVSSNAEAARMASEDPTVAAIAGESAA 260

Query: 246 QLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPFHS 305
             Y L  +   I+D P N TRF +IG  E  P+G D+TS+I+S+ NK GA+++LL P   
Sbjct: 261 NRYHLHLVRTHIQDDPHNRTRFAVIGRYETEPSGSDQTSMILSVPNKAGAVYQLLAPLAD 320

Query: 306 NGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363
           NG+ + R E+RP+RSG W Y F++D  GH  D  +   LE++   A   KVLGSYP +
Sbjct: 321 NGVSMCRFESRPARSGAWEYYFYVDVEGHQHDASVARALEELRRNAAYFKVLGSYPSS 378


Lambda     K      H
   0.319    0.133    0.390 

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: 332
Number of extensions: 8
Number of successful extensions: 3
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: 365
Length of database: 379
Length adjustment: 30
Effective length of query: 335
Effective length of database: 349
Effective search space:   116915
Effective search space used:   116915
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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