GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Caulobacter crescentus NA1000

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate CCNA_01603 CCNA_01603 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Caulo:CCNA_01603
          Length = 400

 Score =  212 bits (539), Expect = 2e-59
 Identities = 139/373 (37%), Positives = 205/373 (54%), Gaps = 20/373 (5%)

Query: 23  LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82
           L A   DVI+L+ G+PDF TP ++K AA +AI    T YT   G  EL+ A+    K++ 
Sbjct: 26  LKAAGRDVIALSAGEPDFDTPDNIKNAAIEAIKAGKTKYTDPDGMPELKAAICAKFKREN 85

Query: 83  DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142
              Y   S+I +  G    I  A    L+PGDEVI+P P +  Y  +  L G  PV V+T
Sbjct: 86  GLEYKP-SQIHVAPGGKPVIYNALVATLNPGDEVIIPAPYWVSYPDMTLLAGGTPVSVET 144

Query: 143 TSH-GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNVFVLSD 200
           T+  GFK+T   +E A+TP TK +++  PSNP+G   S  EL++IA  LL+   V+VL+D
Sbjct: 145 TAESGFKITPEALEAAITPKTKWLIINSPSNPSGGAYSRAELQAIADVLLRHPQVWVLTD 204

Query: 201 EIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256
           ++Y  L +D   ++    +   L D+T+ +NG+SK +SMTGWRIG+   P+ + K + K+
Sbjct: 205 DMYEHLVFDDFEFTTIAQVEPKLYDRTLTMNGVSKGYSMTGWRIGYAAGPEPLIKAMGKM 264

Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVKPSGAF 315
                S   SISQ AALEA+    D      + +++R D V   L  + GL    P GAF
Sbjct: 265 ISQTTSNPCSISQWAALEALNGTQDFIKPNAKLFQERRDLVVSMLNQATGLHCPTPEGAF 324

Query: 316 YIFPSIKS-FGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSM 365
           Y++PS     G T+          DF+  LLE  GVA+V G++F      + R+S+A S 
Sbjct: 325 YVYPSCAGLIGKTAPSGKVIESDEDFATELLESEGVAVVHGAAFGL--SPFFRISYATSN 382

Query: 366 DTLREGLDRLELF 378
           + L +   R++ F
Sbjct: 383 EVLEDACSRIQRF 395


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: 346
Number of extensions: 18
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: 393
Length of database: 400
Length adjustment: 31
Effective length of query: 362
Effective length of database: 369
Effective search space:   133578
Effective search space used:   133578
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