GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas stutzeri RCH2

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1734 Psest_1772 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__psRCH2:GFF1734
          Length = 403

 Score =  150 bits (378), Expect = 8e-41
 Identities = 120/395 (30%), Positives = 191/395 (48%), Gaps = 35/395 (8%)

Query: 19  VSQKARELKAKGRDVIGLGAGEP---DFDTPDNIKKAAIDAIDRGETKYTPVSGIPELRE 75
           V + A+ L+ +G  ++ L  G P    F+ P+ I +  I  +   +  Y+   G+   R+
Sbjct: 20  VLKHAKRLEEEGHRILKLNIGNPAPFGFEAPEEILQDVIRNLPTAQG-YSDSKGLFSARK 78

Query: 76  AIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALC 135
           AI + ++++     +     +G G  +++  +  A LN GDEV+IPAP +  +   V+L 
Sbjct: 79  AIMQYYQQKQVEGVSIEDIYLGNGVSELIVMSMQALLNNGDEVLIPAPDYPLWTAAVSLA 138

Query: 136 GGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMK 195
           GG PV     ++ N+     D+   ITP TK  V  +P+NP+GA Y  E L+ + ++  +
Sbjct: 139 GGKPVHYLCDEQANWWPDLADIKAKITPNTKALVLINPNNPTGAVYPKEVLEGMVELARQ 198

Query: 196 HPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAA--G 253
           H  V + +D++Y+ + Y D    +   + P +    LT NG+SK+Y + G+R G+ A  G
Sbjct: 199 HKLV-LFSDEIYDKILYDDAVHISTASLAPDVL--CLTFNGLSKSYRVAGFRSGWVAISG 255

Query: 254 PLHLIKAMDMIQGQQTSGAASI-----AQWAAVEALNGPQ---DFI---GRNKEIFQGRR 302
           P H  KA   I+G        +     AQ A   AL G Q   D +   GR  E    +R
Sbjct: 256 PKH--KAQSYIEGLDILANMRLCANVPAQHAIQTALGGYQSINDLVLPPGRLLE----QR 309

Query: 303 DLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAV 362
           +    +LN   GISC  P GA Y +P       +  P    I  DE FV +LL +E + +
Sbjct: 310 NRTWELLNDIPGISCVKPMGALYAFP-------RIDPKICPIHNDEKFVLDLLLSEKLLI 362

Query: 363 VHGSAFG--LGPNFRISYATSEALLEEACRRIQRF 395
           V G+AF      +FR+        LE+A  RI  F
Sbjct: 363 VQGTAFNWPWPDHFRVVTLPRVDDLEQAIGRIGNF 397


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: 356
Number of extensions: 19
Number of successful extensions: 4
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: 403
Length adjustment: 31
Effective length of query: 369
Effective length of database: 372
Effective search space:   137268
Effective search space used:   137268
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 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