GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Streptacidiphilus oryzae TH49

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_084704226.1 BS73_RS20475 hypothetical protein

Query= BRENDA::Q8KQ27
         (354 letters)



>NCBI__GCF_000744815.1:WP_084704226.1
          Length = 432

 Score =  340 bits (873), Expect = 3e-98
 Identities = 186/378 (49%), Positives = 239/378 (63%), Gaps = 29/378 (7%)

Query: 3   PVLALVGATGAVGTVMIDIINNRETVPWGEIRLIASARSAGKKLTVRGEELTVIELTAEA 62
           P L + GATG +G+V++++++ R  V WGEIRL A+    G++LTVRGEE  +  L  + 
Sbjct: 43  PTLVVAGATGRIGSVLLELLSTRSDV-WGEIRLAAAPEEHGRRLTVRGEETELRALDEDC 101

Query: 63  FDGVDVAMFDVPDEISAEWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADKVGERPR 122
           F G D+A+F +P  ++A WAP+A   G V VD+SGAFRM  +VPLVVPEVNA     RPR
Sbjct: 102 FAGADIALFALPKPLAARWAPIAVGNGCVVVDSSGAFRMHPEVPLVVPEVNAATARLRPR 161

Query: 123 GIIANPNCTTLSMMAALGALHREFELKELVVASYQAVSGAGKEGVDRLYAELEAV----- 177
           G++A P  TT  +  ALGALH EF L ELV+A+YQA SGAG+ GV RL A+L AV     
Sbjct: 162 GVVAGPRGTTPPLAVALGALHAEFGLAELVLATYQAASGAGESGVRRLRAQLSAVAVGQA 221

Query: 178 AGKPVGVSAGDVRKTL-----------------EAAGLSISDSPFP------APLAFNVV 214
           AG+  G   GDVR+ +                 EAAG   + +  P      APLA NVV
Sbjct: 222 AGQAPGTYPGDVRRAIGDLDEHGEPLRPEASGPEAAGAEAAGAEAPGADPDDAPLALNVV 281

Query: 215 PSAGSYKGDGWYSEELKVRNESRKILGIPDLKVSATCVRVPVVTTHSLAVHATFAREVTV 274
           P  G  + DGW SEEL +R E RKILG+P+LK +ATCVRVPVVT HS+AVHA FAREVTV
Sbjct: 282 PWCGRTEEDGWSSEELGLREELRKILGLPELKATATCVRVPVVTGHSIAVHAVFAREVTV 341

Query: 275 EEAHKVFEAQPTIVLVDDPENGVFPTPAEVVGEDPTYVGRVRQALDFPNTLDFLRVRGQP 334
           E AH+V    P +++ DDPE   FPTP +VVG DP +VGRVR++ D P  LDF       
Sbjct: 342 ERAHRVLAEAPGVLVYDDPEQREFPTPVDVVGTDPAWVGRVRRSPDDPRALDFFLCADNL 401

Query: 335 AQGAAAEHLRDAETLAPQ 352
            +G A   ++ AE +  +
Sbjct: 402 RKGGALNLVQIAEAVCAE 419


Lambda     K      H
   0.316    0.133    0.381 

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: 473
Number of extensions: 17
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: 354
Length of database: 432
Length adjustment: 31
Effective length of query: 323
Effective length of database: 401
Effective search space:   129523
Effective search space used:   129523
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 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