GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Cupriavidus basilensis 4G11

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate RR42_RS35305 RR42_RS35305 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Cup4G11:RR42_RS35305
          Length = 401

 Score =  207 bits (528), Expect = 3e-58
 Identities = 135/376 (35%), Positives = 209/376 (55%), Gaps = 20/376 (5%)

Query: 18  RKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLY 77
           ++   L A   DVI LT G+PDF TP H++ AA +A+    T YT   G  ELR A    
Sbjct: 21  QRVRELRAAGRDVIGLTAGEPDFETPAHIREAAWRAMQAGKTRYTDVGGTAELRHAAAQK 80

Query: 78  MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137
            K++   +Y A SEII++TGA Q I  A    +  GDEVI+P P +  Y  I    G  P
Sbjct: 81  FKRENGLDY-AASEIIVSTGAKQVIFNALMCTVQQGDEVIVPAPYWVSYPDITLFAGGVP 139

Query: 138 VIVDTTS-HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NV 195
           V V   + +GFKLT   +E A++  T+ ++L  P+NP+G   +  EL +IA +L+   +V
Sbjct: 140 VFVACQAENGFKLTPEELERAISARTRWLILNSPNNPSGAAYTRTELVAIAEVLERHPHV 199

Query: 196 FVLSDEIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251
           +V++D+IY  LTYD   +      A  L+ +T+ ING+SK+++MTGWRIG+  AP  + K
Sbjct: 200 WVMTDDIYEHLTYDGAAFVTLAQAAPSLKARTLTINGVSKAYAMTGWRIGYAGAPAPLIK 259

Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVK 310
            ++K+   + S A++++Q AA+ A+    D     +  ++ R D V   L  + G+    
Sbjct: 260 AMVKLQSQSTSGANAVAQAAAIAALDGPQDFIAANKAVFQARRDRVVAALGQVDGIHCQA 319

Query: 311 PSGAFYIFPSIK----------SFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360
           P+GAFY+F S +          S   +S D+   +L+   +A++ GS++    + + RLS
Sbjct: 320 PAGAFYVFASCEALIGARTPHGSVIRSSDDWVNWVLDSQDLAVLQGSAYGV--DTHFRLS 377

Query: 361 FACSMDTLREGLDRLE 376
           FA SM  L EG  R+E
Sbjct: 378 FAASMAQLDEGCRRIE 393


Lambda     K      H
   0.319    0.135    0.388 

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: 316
Number of extensions: 13
Number of successful extensions: 7
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: 393
Length of database: 401
Length adjustment: 31
Effective length of query: 362
Effective length of database: 370
Effective search space:   133940
Effective search space used:   133940
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: 50 (23.9 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