GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Xanthobacter autotrophicus Py2

Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_012114728.1 XAUT_RS13770 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>NCBI__GCF_000017645.1:WP_012114728.1
          Length = 400

 Score =  595 bits (1534), Expect = e-175
 Identities = 286/398 (71%), Positives = 332/398 (83%)

Query: 1   MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60
           M+ ++ AL R+KPS TIA+S KARELKA GRD++ L AGEPDFDTP+NIK+AAI AI RG
Sbjct: 1   MSLISSALKRIKPSQTIAISNKARELKAAGRDIVALSAGEPDFDTPENIKEAAIAAIRRG 60

Query: 61  ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120
           ETKYT V GIPEL+ AI +KFKREN+LDY  +Q  VGTGGKQ+LFNA +AT++ GDEV+I
Sbjct: 61  ETKYTAVDGIPELKAAICRKFKRENDLDYKPSQVTVGTGGKQVLFNALVATVDAGDEVLI 120

Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180
           PAPYWVSYP++V  CGG PV V T  E+NFKL+ + L+ AITPKTKW +FNSPSNPSGAA
Sbjct: 121 PAPYWVSYPDIVEFCGGKPVPVMTTIEDNFKLRPDVLEAAITPKTKWLIFNSPSNPSGAA 180

Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240
           YS +ELKALTDVL+K+P VW+LTDDMYEHL Y DF+F TP +VEP LY RTLTMNGVSKA
Sbjct: 181 YSFDELKALTDVLVKYPQVWILTDDMYEHLVYDDFKFVTPAQVEPKLYNRTLTMNGVSKA 240

Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300
           Y MTGWRIGYAAGP  LIKAM  +Q Q TS  +SIAQWAA+EAL+GPQDFI  N ++F+ 
Sbjct: 241 YCMTGWRIGYAAGPEALIKAMGTLQSQSTSNPSSIAQWAALEALDGPQDFIAANNKVFKE 300

Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360
           RRDLVVSMLNQAKG+ CP PEGAFYV+PSCAG IGKT P G  I +DEDF ++LLE EGV
Sbjct: 301 RRDLVVSMLNQAKGLHCPKPEGAFYVFPSCAGTIGKTTPGGVTIASDEDFATQLLEAEGV 360

Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCAA 398
           AVVHGSAFGLGP FRISYAT+ + LEEACRRIQRFC +
Sbjct: 361 AVVHGSAFGLGPAFRISYATATSDLEEACRRIQRFCGS 398


Lambda     K      H
   0.318    0.134    0.402 

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: 617
Number of extensions: 21
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 Jul 25 2024. The underlying query database was built on Jul 25 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