GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PRAI in Desulfovibrio vulgaris Miyazaki F

Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 8502414 DvMF_3120 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)

Query= BRENDA::P16250
         (240 letters)



>FitnessBrowser__Miya:8502414
          Length = 243

 Score =  168 bits (426), Expect = 8e-47
 Identities = 96/236 (40%), Positives = 136/236 (57%), Gaps = 4/236 (1%)

Query: 6   LLPAVDVRDGQAVRLVHGESGTETSYGS-PLEAALAWQRSGAEWLHLVDLDAAF-GTGDN 63
           L PAVD++DG+ VRL  G +  ET +   P   A  WQ  GA+WLH++DLD AF G   N
Sbjct: 3   LFPAVDIKDGRCVRLRQGRADAETVFSDDPAAMARHWQDQGAKWLHVIDLDGAFSGMPAN 62

Query: 64  RALIAEVAQAMDIKVELSGGIRDDDTLAAALATGCTRVNLGTAALETPEWVAKVIAEHGD 123
             LI  +   + + V+L GGIRD+ T  A L  G  R+ +GT ALE P+  A++ A    
Sbjct: 63  FELIRRICADLSVPVQLGGGIRDEATAKAYLDAGVERLIIGTVALEEPDLYARLCATFPG 122

Query: 124 KIAVGLDVRGTTLRGRGWTRDGG-DLYETLDRLNKEGCARYVVTDIAKDGTLQGPNLELL 182
           +I V LD  G  L+ +GW  D G  + + L RL   G A  + TDI +DG   G NL  L
Sbjct: 123 RIGVSLDAEGGRLKTKGWVADSGLTVDDVLPRLLAAGTAFVIYTDIDRDGMQTGVNLSAL 182

Query: 183 KNVCAATDRPVVASGGVSSLDDLRAIAGL-VPAGVEGAIVGKALYAKAFTLEEALE 237
           + +      PV+A+GGV++L+D+RA+  + + + VEGAI G+A+Y     L  A+E
Sbjct: 183 ERLAGMCPVPVIAAGGVATLEDVRALYPMTLTSSVEGAITGRAIYTGTLDLHAAME 238


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: 181
Number of extensions: 16
Number of successful extensions: 6
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: 243
Length adjustment: 23
Effective length of query: 217
Effective length of database: 220
Effective search space:    47740
Effective search space used:    47740
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 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