GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Rhodospirillum rubrum ATCC 11170

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_011390757.1 RRU_RS15535 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::Q94AL9
         (477 letters)



>NCBI__GCF_000013085.1:WP_011390757.1
          Length = 443

 Score =  306 bits (783), Expect = 1e-87
 Identities = 178/441 (40%), Positives = 252/441 (57%), Gaps = 12/441 (2%)

Query: 43  LPPFAYTPPPYTGPSADVILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDA 102
           L  F  +  P    SA  +L+KRK     +    Y KPL +V  +  +LFDE+G RYLD 
Sbjct: 7   LNAFDMSDAPTLSDSAQRLLAKRKALFGAASVLFYDKPLELVRAEGCWLFDEAGERYLDV 66

Query: 103 FAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHAIADFSEALASKLPGDLKVVFFT 162
           +  +  V  GHCHP VV  V +Q+ ++   T  YLN AI  ++E L + LP  L  + FT
Sbjct: 67  YNNVPSV--GHCHPHVVAAVADQLAKINTHT-RYLNEAIHRYAERLVATLPPSLSNITFT 123

Query: 163 NSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALN 222
            +G+E+N+LAL +A  Y+G + ++     YHGN AA    +  S  + + +   V     
Sbjct: 124 CTGSESNDLALRLASHYSGGRGVIVTETAYHGNTAAVTEVSPSSA-RDHALAPHVRVVRA 182

Query: 223 PDPYRGVFGSDGEKYAKD----LQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAA 278
           PD YR    +   ++A D    + DL  +G T  ++  + ++I    G+     G+L+ A
Sbjct: 183 PDSYRVAPEALAARFAGDVAAAIADLADHGIT--LSALLVDSIFSSDGVYADPAGFLAEA 240

Query: 279 YDTVKKAGGLFIADEVQSGFARTGN-FWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPE 337
              V + GGLFIADEVQ GF RTG+  WGF+ H V PDIVTM K +GNG P+G V T PE
Sbjct: 241 VAVVHRHGGLFIADEVQPGFGRTGSALWGFQRHGVTPDIVTMGKPMGNGLPMGGVATRPE 300

Query: 338 IAGVLTRR-SYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHE 396
           I         YFNTFGG+  +  AG AVL+VIE E L  NA  VG+YL+E L  L ++  
Sbjct: 301 ILDAFCAEVGYFNTFGGSPAAGAAGSAVLDVIEGEGLMANAEAVGAYLRESLGALAKRFP 360

Query: 397 IIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPL 456
           +IGDVRG GL   VELVSD + KTP+      I++ +++  VLIG  G FGN+ ++ PPL
Sbjct: 361 VIGDVRGAGLFDAVELVSDPEAKTPSPELASAIINGLRQRHVLIGAAGPFGNILKVRPPL 420

Query: 457 CFTKDDADFLVEAMDYSMSKM 477
           CFT+D  D L  A++  ++++
Sbjct: 421 CFTRDQVDILGAALEEVLTEI 441


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: 553
Number of extensions: 29
Number of successful extensions: 6
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: 443
Length adjustment: 33
Effective length of query: 444
Effective length of database: 410
Effective search space:   182040
Effective search space used:   182040
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 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