GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Paraburkholderia bryophila 376MFSha3.1

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate H281DRAFT_05658 H281DRAFT_05658 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= BRENDA::P16250
         (240 letters)



>FitnessBrowser__Burk376:H281DRAFT_05658
          Length = 250

 Score =  143 bits (361), Expect = 3e-39
 Identities = 87/229 (37%), Positives = 127/229 (55%), Gaps = 9/229 (3%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           L+PA+D++DGQ VRL  G+    T +   P   A  W   GA  LHLVDL+ AF G   N
Sbjct: 3   LIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVERGARRLHLVDLNGAFAGKPRN 62

Query: 64  ----RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIA 119
               RA+I EV    +I V+L GGIRD +T+   L  G   V +GTAA++ P ++     
Sbjct: 63  EEAIRAIIEEVGG--EIPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLQDACT 120

Query: 120 EHGDKIAVGLDVRGTTLRGRGWTR-DGGDLYETLDRLNKEGCARYVVTDIAKDGTLQGPN 178
             G  I VGLD +   +   GW++  G ++ +   +    GC   + TDI +DG LQG N
Sbjct: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180

Query: 179 LELLKNVCAATDRPVVASGGVSSLDDLRAIAGLVPAGVEGAIVGKALYA 227
           +E    +  A   PV+ASGG+S+L D+ ++  +   G+EG I G+A+Y+
Sbjct: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYS 229


Lambda     K      H
   0.315    0.133    0.385 

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: 164
Number of extensions: 8
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: 240
Length of database: 250
Length adjustment: 24
Effective length of query: 216
Effective length of database: 226
Effective search space:    48816
Effective search space used:    48816
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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