GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Pseudomonas fluorescens FW300-N2C3

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate AO356_05050 AO356_05050 glutamate-pyruvate aminotransferase

Query= BRENDA::D2Z0I0
         (402 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05050
          Length = 405

 Score =  442 bits (1138), Expect = e-129
 Identities = 216/386 (55%), Positives = 282/386 (73%), Gaps = 5/386 (1%)

Query: 7   FPKVKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHG 66
           F ++ +LP YVF +  ELK   RR GEDI+DL MGNPD     HI++KL  VA R + HG
Sbjct: 10  FARIDRLPPYVFNITAELKMAARRRGEDIIDLSMGNPDGATPPHIVEKLVTVAQREDTHG 69

Query: 67  YSASKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGDTVIVPN 126
           YS SKGIPRLR+AI  +YK RY V++DPE  AI+TIG+KEG +HLMLA L+ GDTV+VPN
Sbjct: 70  YSTSKGIPRLRRAISRWYKDRYEVDIDPETEAIVTIGSKEGLAHLMLATLDQGDTVLVPN 129

Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186
           P+YPIH Y  +I G    SVP++P  DF +   R     I+ S  KPK ++L FP NPT 
Sbjct: 130 PSYPIHIYGAVIAGAQVRSVPLVPGVDFFDELERA----IRGSIPKPKMMILGFPSNPTA 185

Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246
            CV+L+FF+ V+ LAKQ  + ++HD AYAD+ +DG+  PSI+QV GA D+AVE +++SK 
Sbjct: 186 QCVELDFFERVIALAKQYDVLVIHDLAYADIVYDGWKAPSIMQVPGAKDIAVEFFTLSKS 245

Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTPIQVASIIALESPYEVVEKNREIYRR 306
           ++MAGWR+ F+VGN  L+  LA +KSY DYG FTP+QVA+I ALE   + V    E YR+
Sbjct: 246 YNMAGWRIGFMVGNPELVNALARIKSYHDYGTFTPLQVAAIAALEGDQQCVRDIAEQYRQ 305

Query: 307 RRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVG-MNSLDFSLFLLREAKVAVSPGIGFG 365
           RR+VLV+GL+ +GW V+ PK SM+VWAK+PE    + SL+F+  LL EAKV VSPG+GFG
Sbjct: 306 RRNVLVKGLHELGWMVENPKASMYVWAKIPEAYAHLGSLEFAKKLLAEAKVCVSPGVGFG 365

Query: 366 EYGEGYVRFALVENEHRIRQAVRGIK 391
           EYG+ +VRFAL+EN+ RIRQAVRGI+
Sbjct: 366 EYGDDHVRFALIENQDRIRQAVRGIR 391


Lambda     K      H
   0.322    0.141    0.425 

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: 557
Number of extensions: 28
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: 402
Length of database: 405
Length adjustment: 31
Effective length of query: 371
Effective length of database: 374
Effective search space:   138754
Effective search space used:   138754
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 (21.9 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