GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Pseudomonas stutzeri RCH2

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF1235 Psest_1268 Aspartate/tyrosine/aromatic aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__psRCH2:GFF1235
          Length = 382

 Score =  166 bits (419), Expect = 1e-45
 Identities = 106/360 (29%), Positives = 178/360 (49%), Gaps = 8/360 (2%)

Query: 24  VAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKAD 83
           +A     ++L+ G PDF  P  ++ A    +      Y P  G   LR+ V   +     
Sbjct: 20  LAADTGALNLSQGFPDFDGPEALREAVAGHVMAGHNQYAPMTGLPALREQVAAKVAGLYG 79

Query: 84  FNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTT 143
            + DA +E+ IT GA+QAI  A + ++ PGDEVI+  P Y  YEP + L G   +    +
Sbjct: 80  RDVDAAAEVTITPGATQAIFCAIQAVIRPGDEVIVFDPCYDSYEPSVQLAGGVCIHQQLS 139

Query: 144 SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIY 203
              F++  + + DA+TP T+ +VL  P NP+G  +  ++L  +AAL++ R++++LSDE+Y
Sbjct: 140 LPDFRIDWQRLADAITPRTRMIVLNTPHNPSGALIDADDLDRLAALIRERDIYLLSDEVY 199

Query: 204 SELTYD-RPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYN 260
             L +D R H S+  +  L  +  VI+   K++ +TGW+ G++ AP  ++  + KVHQY 
Sbjct: 200 EHLVFDGREHASVLRHDELYQRAFVISSFGKTYHVTGWKTGYVVAPPMLSVELRKVHQYV 259

Query: 261 VSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDVVKPSGAFYIFPS 320
                +  Q A  + +    +    +   Y+ + D   D L        + +G ++    
Sbjct: 260 SFTGVTPLQWALADFMAAHPEHLAELPAFYQAKRDLFCDLLAGSRFSFTRAAGTYFQLAD 319

Query: 321 IKSFGMTSFDFSMA--LLEDAGVALVPGSSFSTYGEG---YVRLSFACSMDTLREGLDRL 375
             +      D +MA  L  + GVA +P S F  +       VR  FA   +TLR+  +RL
Sbjct: 320 YSAIRPDLDDVAMAEWLTREHGVACIPISVFYQHPPANLRLVRFCFAKREETLRQAAERL 379


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: 349
Number of extensions: 19
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: 393
Length of database: 382
Length adjustment: 30
Effective length of query: 363
Effective length of database: 352
Effective search space:   127776
Effective search space used:   127776
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 Apr 09 2024. The underlying query database was built on Apr 09 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