GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Pseudomonas fluorescens FW300-N1B4

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910
          Length = 430

 Score =  216 bits (549), Expect = 2e-60
 Identities = 138/423 (32%), Positives = 212/423 (50%), Gaps = 11/423 (2%)

Query: 61  ILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVE 120
           +L +R +F+   +   +  PL I   +   L+D  G+RYLD   GI V+N GH HP VV 
Sbjct: 11  LLRQRDQFVPRGLVTAH--PLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVA 68

Query: 121 PVINQIKRLQHPTVLYLNHA-IADFSEALASKLPGD--LKVVFFTNSGTEANELALMMAK 177
            V  Q++++ H     + +    D ++ L   + G    K  FFT SG EA E A+ +A+
Sbjct: 69  AVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFT-SGAEAVENAVKIAR 127

Query: 178 LYTGCQDIVAVRNGYHGNAAATMGATGQSM---WKFNVVQNSVHHALNPDPYRGVFGSDG 234
            +T    ++A R G+HG        TG S      F      V H   P+ YRGV     
Sbjct: 128 AHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSDMA 187

Query: 235 EKYAKDLQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEV 294
            K   +L  L        +A  I E +QG GG +     +L A      K G + I DE+
Sbjct: 188 LKALDEL--LATQVAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEI 245

Query: 295 QSGFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGN 354
           Q+GF RTG ++GF+   + PD+VT+AK +  G PL  VV   EI           T+GGN
Sbjct: 246 QTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGN 305

Query: 355 SVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVS 414
           ++S  A LAV+   E+E+L      +G  L+E L +L+ ++  IGDVRG G ML +EL+ 
Sbjct: 306 ALSCAAALAVIEAYEQEQLLARGEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELIK 365

Query: 415 DRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMDYSM 474
           D   +TP       ++D+ +  G+L+ K G + NV R   PL  ++   D  ++ +D ++
Sbjct: 366 DDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQILDAAL 425

Query: 475 SKM 477
           +++
Sbjct: 426 ARV 428


Lambda     K      H
   0.320    0.136    0.403 

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: 501
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: 477
Length of database: 430
Length adjustment: 33
Effective length of query: 444
Effective length of database: 397
Effective search space:   176268
Effective search space used:   176268
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 (21.8 bits)
S2: 51 (24.3 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