GapMind for Amino acid biosynthesis

 

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

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO356_25355 AO356_25355 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_25355
          Length = 404

 Score =  466 bits (1200), Expect = e-136
 Identities = 225/393 (57%), Positives = 292/393 (74%)

Query: 8   LSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPV 67
           L+R + SAT  +  +  E +A+G  +I L AGEPDFDTP +I++AAI+AI +G T+YT V
Sbjct: 12  LARAQSSATYRIMDRVAERRAQGAKIISLCAGEPDFDTPKHIREAAIEAIGQGHTRYTQV 71

Query: 68  SGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVS 127
           +G+  LREA+A KF++EN LD T   T+V  GGKQ+++NA  ATL+ GD+V++PAPYWVS
Sbjct: 72  AGVRSLREAVAAKFRQENGLDVTWQDTLVCNGGKQVIYNALAATLDEGDQVIVPAPYWVS 131

Query: 128 YPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELK 187
           YPEMV LCGG    V    ++ FKL    LD AITP+T+W + NSPSNP+GA YS EEL+
Sbjct: 132 YPEMVQLCGGESRIVTCDADSGFKLTPAALDAAITPQTRWLILNSPSNPTGAVYSREELQ 191

Query: 188 ALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWR 247
           AL DVL+ HPHV +L DD+YEHL + D  F T  +VEP L  RTLTMNGVSKAYAMTGWR
Sbjct: 192 ALADVLLAHPHVLILADDIYEHLIFDDQVFYTLAQVEPRLASRTLTMNGVSKAYAMTGWR 251

Query: 248 IGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVS 307
           IG+A GP  L++AM+ +QGQQTSGA+SI+Q AA+ AL+GP+DFI  ++ +FQ RRDL+V+
Sbjct: 252 IGFATGPRWLLEAMEKLQGQQTSGASSISQQAALAALDGPKDFIRESRAVFQRRRDLMVA 311

Query: 308 MLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSA 367
           +LN   G++C +P GAFY + SCAGLIG+T+  G+V+ TDED    LL+   VAVVHGSA
Sbjct: 312 LLNATPGLACASPGGAFYAFASCAGLIGRTSSGGRVLHTDEDVAHALLDEADVAVVHGSA 371

Query: 368 FGLGPNFRISYATSEALLEEACRRIQRFCAACR 400
           FGLGP  RI+YA  +A L +AC  I+ FC A R
Sbjct: 372 FGLGPYIRIAYALDDASLRQACEAIRGFCDALR 404


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: 477
Number of extensions: 17
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: 404
Length adjustment: 31
Effective length of query: 369
Effective length of database: 373
Effective search space:   137637
Effective search space used:   137637
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.

Links

Downloads

Related tools

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