GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Sinorhizobium medicae WSM419

Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate YP_001328819.1 Smed_3160 class I and II aminotransferase

Query= metacyc::MONOMER-21143
         (387 letters)



>NCBI__GCF_000017145.1:YP_001328819.1
          Length = 410

 Score =  230 bits (587), Expect = 5e-65
 Identities = 128/390 (32%), Positives = 208/390 (53%), Gaps = 13/390 (3%)

Query: 4   AKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGY 63
           A  +  +G      + A A  ++ +GKP+I LG G+PDF TP HV  AA  A+  G   Y
Sbjct: 15  ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPDHVKQAASDAIHRGETKY 74

Query: 64  VLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPA 123
              +G  E ++A+  K ++      + + + +  G K  ++ A+    +PG E++ PTP 
Sbjct: 75  TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVVIPTPY 134

Query: 124 FPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKS 183
           +  Y  ++      P+          +   +K+ + IT +TR ++L +P+NP+G+    +
Sbjct: 135 WTSYSDIVQICEGKPILIACDASSGFRLTAQKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194

Query: 184 AIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNY-PDLQDRLIVLDGWSKAYAMT 242
               L + L KHPHV +L D++Y   +YD     T     P L+DR + ++G SKAYAMT
Sbjct: 195 DYRPLLDVLLKHPHVWLLVDDMYEHIVYDAFRFVTPARLEPGLKDRTLTVNGVSKAYAMT 254

Query: 243 GWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKL 302
           GWR+G++  P  LI  +  +   + SC ++ SQ A +AAL+GP D + E    F +RR L
Sbjct: 255 GWRIGYAGGPRALIKAMAVVQSQATSCPSSVSQAASVAALNGPQDFLKERTESFQRRRNL 314

Query: 303 IHEGLNSLPGVECSLPGGAFYAFP-------KVIGTGM---NGSEFAKKCMHEAGVAIVP 352
           +  GLN++ G++C +P GAFY F        +V  +G    + ++F    + ++ VA+VP
Sbjct: 315 VVNGLNAIEGLDCRVPEGAFYTFSGCAGVLGRVTPSGKRIESDTDFCAYLLEDSHVAVVP 374

Query: 353 GTAFGKTCQDYVRFSYAASQDNISNALENI 382
           G+AFG     Y R SYA S+  +  ALE I
Sbjct: 375 GSAFG--LSPYFRISYATSEAELKEALERI 402


Lambda     K      H
   0.319    0.137    0.414 

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: 419
Number of extensions: 24
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: 387
Length of database: 410
Length adjustment: 31
Effective length of query: 356
Effective length of database: 379
Effective search space:   134924
Effective search space used:   134924
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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