GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Phyllobacterium endophyticum PEPV15

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_106717846.1 CU100_RS17540 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P18335
         (406 letters)



>NCBI__GCF_003010935.1:WP_106717846.1
          Length = 427

 Score =  238 bits (606), Expect = 3e-67
 Identities = 136/400 (34%), Positives = 211/400 (52%), Gaps = 32/400 (8%)

Query: 30  KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88
           K +G+ +WD +G+ Y+DF GGI V  +GH HP +V+A+K Q ETL H    V   EP + 
Sbjct: 33  KAKGTELWDVEGRRYLDFVGGIGVLNVGHNHPRVVDAVKRQIETLSHACFQVLGYEPYVA 92

Query: 89  LGRKLIEATFAE-RVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLF 147
           L  KL      + +  F  SG EA E + K+AR Y        +  +IAF   FHGR+L 
Sbjct: 93  LAEKLNTLIGKDYKSAFFTSGAEAVENSVKIARGYTN------RPAVIAFRGGFHGRTLL 146

Query: 148 TVSVGGQPK-YSDGFGPKPADIIHVPFNDLHAVKAVMD---------------DHTCAVV 191
            VS+ G  + Y   FGP   +I H+P+ + +      D               +   A++
Sbjct: 147 GVSLTGMSQPYKQNFGPFAPEIFHIPYPNAYRGVTTADALAALAEVFATDVAPERVAAII 206

Query: 192 VEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDIL 251
           +EP+QG+GG   A   F+  LRE+ ++H  +L+ DE+Q G GRTG++F + H G+ PD++
Sbjct: 207 IEPVQGDGGFHPAPVNFVAALREITNKHGIVLILDEIQTGFGRTGEMFGFQHSGIEPDLV 266

Query: 252 TSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGI 311
           T AK+L GG P+SA++  AEI  A  PG  G TYGGN LACA A A  +     ++L   
Sbjct: 267 TIAKSLAGGLPLSAVVGKAEIMDAPTPGGLGGTYGGNALACAAALAVIETFERDDILRNG 326

Query: 312 QAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL------KPQYKGRARDFLYAGAEAG 365
           + +  +    L  + Q++    D+RG+G ++  E+      K     R +  L    + G
Sbjct: 327 RQRAAQLRKGLIALQQRHAFIGDVRGLGFMLAIEIVSDRATKAPDADRTQHVLDEARKGG 386

Query: 366 VMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKV 403
           ++++  G   + +RF   LV  +A+IDE +     A+ +V
Sbjct: 387 LLLIKCGIHRNTVRFLAPLVATEAEIDEALAALGEALERV 426


Lambda     K      H
   0.322    0.138    0.415 

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: 491
Number of extensions: 31
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: 406
Length of database: 427
Length adjustment: 31
Effective length of query: 375
Effective length of database: 396
Effective search space:   148500
Effective search space used:   148500
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 (21.9 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