GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Dechlorosoma suillum PS

Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate Dsui_0219 Dsui_0219 anthranilate synthase component I

Query= curated2:Q73XV3
         (450 letters)



>FitnessBrowser__PS:Dsui_0219
          Length = 491

 Score =  141 bits (355), Expect = 5e-38
 Identities = 84/252 (33%), Positives = 129/252 (51%), Gaps = 1/252 (0%)

Query: 187 YRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGGIRA 246
           ++  VA A   I  G   +V+LS+ +  PF+    S YR  R  N     +         
Sbjct: 221 FKQAVAKAKEYITEGDIMQVVLSQRMTKPFSASPLSLYRALRTLNPSPYMYYFDFEDFHV 280

Query: 247 VGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVRSSL 306
           VG SPE++  +  D V V  P+AGTR  G     D    +DL ++ KEI EH   +    
Sbjct: 281 VGASPEILTRLEGDTVTV-RPIAGTRKRGATPEEDAALAEDLLADQKEIAEHVQLLDLGR 339

Query: 307 QEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTASGIP 366
            ++  +A+ G+  +T+ M++     V H+ S V G+L      +D L+A FPA T SG P
Sbjct: 340 NDVGRVAQTGSVKLTERMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAP 399

Query: 367 KAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGIIEES 426
           K   +E I  L+   RG+Y GA+  +  +G +D A+ +R A   DG+  ++AGAGI+ +S
Sbjct: 400 KVRAMEIIDELEPVKRGIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADS 459

Query: 427 TPEREFEETCEK 438
            P  E++ET  K
Sbjct: 460 DPTSEWQETQNK 471


Lambda     K      H
   0.318    0.135    0.391 

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: 427
Number of extensions: 22
Number of successful extensions: 2
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: 450
Length of database: 491
Length adjustment: 33
Effective length of query: 417
Effective length of database: 458
Effective search space:   190986
Effective search space used:   190986
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: 51 (24.3 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