GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Pseudomonas stutzeri RCH2

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate GFF1262 Psest_1295 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::W0PFQ7
         (399 letters)



>FitnessBrowser__psRCH2:GFF1262
          Length = 398

 Score =  541 bits (1393), Expect = e-158
 Identities = 262/397 (65%), Positives = 321/397 (80%)

Query: 3   TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62
           +LF+AVE+APRDPILGLNE +NADTR  KVNLGVGVYY++ G+IPLL+AV EAE  R+ A
Sbjct: 2   SLFSAVEMAPRDPILGLNEAFNADTRPNKVNLGVGVYYNEEGRIPLLRAVVEAEHARIAA 61

Query: 63  HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122
           +A RGYLPIEGI  Y+   Q+LLFG DS +I +GR +T QALGGTGALK+GADFLK+L P
Sbjct: 62  NAPRGYLPIEGIAAYDAAVQKLLFGNDSSLIAEGRVVTTQALGGTGALKVGADFLKRLLP 121

Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182
           D+ V IS+PSWENHRALFE AGF V+ YSYYDA+ HG++  G    +K +P  SI+VLHA
Sbjct: 122 DAVVAISNPSWENHRALFESAGFPVQNYSYYDASNHGIDRAGLLQDLKNLPPRSIVVLHA 181

Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242
           CCHNPTGVD + E W+QI  +++ ++ VPF+DIAYQGFG  ++EDAA VRLFA+ GM+ F
Sbjct: 182 CCHNPTGVDLNLEDWKQILEVLRAQDHVPFIDIAYQGFGDSIEEDAAAVRLFAESGMTFF 241

Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302
           +SSSFSKSFSLYGERVGAL++VT S +E++RVLSQ+KRVIRTNYSNPPTHG  +VA +LN
Sbjct: 242 VSSSFSKSFSLYGERVGALSMVTQSREESARVLSQVKRVIRTNYSNPPTHGATIVASVLN 301

Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362
           +PEL A WE+EL +MR RIRE+R  + ++L A G K DF+FV AQRGMFSYSGLT EQVE
Sbjct: 302 SPELRAMWEAELGEMRSRIRELRLSMVEQLTAKGAKTDFSFVAAQRGMFSYSGLTAEQVE 361

Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399
           RLR E G+YA+++GRIC AALN  NI  V  AI  VL
Sbjct: 362 RLRVEFGVYAISTGRICAAALNRSNIGHVTDAIVQVL 398


Lambda     K      H
   0.318    0.134    0.385 

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: 475
Number of extensions: 13
Number of successful extensions: 1
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: 399
Length of database: 398
Length adjustment: 31
Effective length of query: 368
Effective length of database: 367
Effective search space:   135056
Effective search space used:   135056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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