GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Thiohalomonas denitrificans HLD2

Align isochorismate lyase (EC 4.2.99.21); isochorismate synthase (EC 5.4.4.2) (characterized)
to candidate WP_092996656.1 BLP65_RS10660 anthranilate synthase component I

Query= BRENDA::P9WFX1
         (450 letters)



>NCBI__GCF_900102855.1:WP_092996656.1
          Length = 490

 Score =  150 bits (378), Expect = 1e-40
 Identities = 105/294 (35%), Positives = 151/294 (51%), Gaps = 13/294 (4%)

Query: 156 RHREAIDRLLA-----TGVREVPQSRSVDVSDDPSGFRRR-----VAVAVDEIAAGRYHK 205
           R ++ +DRL+      T V+    S  V   D  SGF +      VA A + IAAG   +
Sbjct: 183 RAQQRLDRLVERMRAITPVQRSGISTEVTEKDFVSGFTQEGFEAAVARAREYIAAGDIMQ 242

Query: 206 VILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRA-DGVVI 264
           V+LS+ + +P+       YR  R  N     + L L G + +G SPE++  VRA DG V 
Sbjct: 243 VVLSQRLSIPYHARPLDLYRALRSLNPSPYMYYLDLEGFQVVGSSPEIL--VRAEDGKVT 300

Query: 265 TEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAAVIDFM 324
             P+AGTR  G+    DR    +L ++ KE+ EH + +     ++  IAE GS  + D M
Sbjct: 301 VRPIAGTRPRGKSEEEDRALEQELLADPKELAEHLMLIDLGRNDVGRIAETGSVQLTDKM 360

Query: 325 TVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDECPRGL 384
            +     V H+ S + A L      M AL A FPA T SG PK   +E I  L+   RG+
Sbjct: 361 VIERYSHVMHIVSNVVADLRDGLTAMDALRATFPAGTVSGAPKIRAMEIIDELEPVKRGV 420

Query: 385 YSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEK 438
           YSGAV  L  +G +D A+ +R A     +  ++AGAGI+ +S P +E+EET  K
Sbjct: 421 YSGAVGYLGWNGNMDTAIAIRTAVIKDEKLHIQAGAGIVYDSVPSKEWEETMNK 474


Lambda     K      H
   0.319    0.135    0.386 

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: 509
Number of extensions: 31
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: 450
Length of database: 490
Length adjustment: 33
Effective length of query: 417
Effective length of database: 457
Effective search space:   190569
Effective search space used:   190569
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: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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