GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB' in Desulfacinum infernum DSM 9756

Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate WP_073036352.1 BUB04_RS01730 3-dehydroquinate synthase II

Query= SwissProt::Q58646
         (361 letters)



>NCBI__GCF_900129305.1:WP_073036352.1
          Length = 331

 Score =  253 bits (646), Expect = 5e-72
 Identities = 145/361 (40%), Positives = 217/361 (60%), Gaps = 30/361 (8%)

Query: 1   MKFGWVNVIGDNWEEKKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLDADIVL 60
           MK  WV +     E  K++VT A+E+ + VV+A P   ++++ LG + VA+   D D + 
Sbjct: 1   MKEVWVRLK----EWNKEVVTAAVEAGVDVVMAPPGVAQQVRRLGRVVVAAE--DGDWI- 53

Query: 61  VNKNDNIEFLKEAKNLGKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRDWTIIPLE 120
                        +++  ET     + S EDE+  S++ R G    +++E  DW IIPLE
Sbjct: 54  -----------PGRDVHLET-----LRSPEDEKRISDLLRVG--KKVVVENTDWEIIPLE 95

Query: 121 NLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKE 180
           NL+A       ++V +V       +A  +LEKG  GVL+   +   +   ++ ++ M   
Sbjct: 96  NLVAG----GGELVVAVEDESRMDLALGVLEKGVHGVLIPGDDPLTVSSWTRKVKSMGPV 151

Query: 181 KVALDVATVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATR 240
           +  ++ A +  +  +G GDRVCIDTCSLM  G+G L+G+ +  LFLVH+ET  NPYVA R
Sbjct: 152 EPLVE-AEIVGLRTVGLGDRVCIDTCSLMTDGQGALVGNSAGFLFLVHAETRRNPYVAPR 210

Query: 241 PFRVNAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIE 300
           PFR+NAG VHAY+  P  +T+YL EL AGD ++IVD  G + EA+VGR+K+E+RPLV++E
Sbjct: 211 PFRINAGAVHAYVKVPDGRTRYLCELGAGDPIVIVDAAGKSTEAVVGRIKVEKRPLVVVE 270

Query: 301 AEYKGDIIRTILQNAETIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIE 360
           A         +LQNAET+ L+  KGE +SV  L+ G +VL+ P+   RHFGMA+ E+I+E
Sbjct: 271 ARCDAGGGSILLQNAETVCLMTPKGEGVSVTSLEKGMRVLVSPQSRGRHFGMAVDESIVE 330

Query: 361 K 361
           K
Sbjct: 331 K 331


Lambda     K      H
   0.315    0.136    0.380 

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: 378
Number of extensions: 18
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: 361
Length of database: 331
Length adjustment: 29
Effective length of query: 332
Effective length of database: 302
Effective search space:   100264
Effective search space used:   100264
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: 42 (22.0 bits)
S2: 49 (23.5 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