GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Ruegeria conchae TW15

Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_010439728.1 G7G_RS0106455 aspartate aminotransferase family protein

Query= BRENDA::B1XNF8
         (418 letters)



>NCBI__GCF_000192475.1:WP_010439728.1
          Length = 438

 Score =  208 bits (529), Expect = 3e-58
 Identities = 147/432 (34%), Positives = 224/432 (51%), Gaps = 47/432 (10%)

Query: 26  HTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHIS 85
           HT    PVA A GEGC L D+ G+ YLD      +C LGH++  +++AV  Q++++    
Sbjct: 8   HTKSELPVA-AGGEGCYLIDSTGRRYLDCGDAAVSC-LGHSNETVVKAVQQQVEQIAFAH 65

Query: 86  NLYYIPEQG-ALAQWIVEHSCAD--KVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142
             +   E   ALA+ ++EH+  D  +V+F + G+EA EAAIKL R+Y +  +   E+  +
Sbjct: 66  TGFMTSEPAEALAELLIEHAPGDLDRVYFVSGGSEATEAAIKLARQY-YLETGQPERRHV 124

Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPL----------------PDGFAYVPYNDIRA 186
           ++ + S+HG TL  ++A G    +  F P+                P+G +   Y    A
Sbjct: 125 IARRQSYHGNTLGALSAGGNEWRRAQFAPMLIEMTHIAPCYEYAEKPEGESSYDYGQRVA 184

Query: 187 LEEAITDIDEGNRRVAAIMLEALQGEG-GVRPGDVEYFKAVRRICDENGILLVLDEVQVG 245
            E     +  G   V A M E + G   G  P    YFK +R ICD+ G+LL+LDEV  G
Sbjct: 185 NELEAEILRLGPNTVMAFMAEPVVGATLGAVPAVEGYFKRIREICDQYGVLLILDEVMCG 244

Query: 246 VGRTGKYWGYENLGIEPDIFTSAKGLAGGI-PIGAMMCKDSC--AVFNPG---EHASTFG 299
           +GRTG  +  ++ G+ PDI   AKGL  G  PIGAM+C      A+ N     +H  T+ 
Sbjct: 245 MGRTGHLFACDHDGVAPDILCIAKGLGAGYQPIGAMLCSARIYDAIQNGSGFFQHGHTYI 304

Query: 300 GNPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEI 359
           G+P + AAALAVV  L Q +L       GE+L++ L T   ++P+  D+RG GL  G+E+
Sbjct: 305 GHPVATAAALAVVTELTQNDLPLRAALMGEKLQSALTTAFGQHPHVGDIRGRGLFRGIEL 364

Query: 360 KADLEL---------TSIEVVKAAMEKGLLLAPA--------GPKVLRFVPPLIVSAAEI 402
            A+ E           + ++ KAA  +GL+  P         G  +L   PP I+   +I
Sbjct: 365 VANRETKTPFDPALGVAGKIKKAAFAEGLICYPMSGTRDGQHGDHIL-LAPPFIIEGKQI 423

Query: 403 NEAIALLDQTLA 414
           +E +A LD+ ++
Sbjct: 424 DELVAKLDRAIS 435


Lambda     K      H
   0.319    0.136    0.406 

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: 436
Number of extensions: 26
Number of successful extensions: 8
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: 418
Length of database: 438
Length adjustment: 32
Effective length of query: 386
Effective length of database: 406
Effective search space:   156716
Effective search space used:   156716
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 26 2024. The underlying query database was built on Jul 25 2024.

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