GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Escherichia coli BW25113

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 15866 b1748 succinylornithine transaminase, PLP-dependent (NCBI)

Query= SwissProt::P40732
         (405 letters)



>FitnessBrowser__Keio:15866
          Length = 406

 Score =  506 bits (1302), Expect = e-148
 Identities = 243/392 (61%), Positives = 299/392 (76%)

Query: 8   ITRATFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEAL 67
           ITR  FDE ++PVYAPA FIPV+G+GSR+WDQQGKEYIDFAGGIAV ALGH HP L EAL
Sbjct: 5   ITRENFDEWMIPVYAPAPFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREAL 64

Query: 68  KSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRH 127
             Q    WHT N +TNEP LRL +KLIDATFA+RV F NSG EANE A KLAR +A  R+
Sbjct: 65  NEQASKFWHTGNGYTNEPVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRY 124

Query: 128 SPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHT 187
              K+ I+AF NAFHGR+LFTVS GGQP YS  F P PADI H  +ND+++  A++DD T
Sbjct: 125 GSHKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPADIRHAAYNDINSASALIDDST 184

Query: 188 CAVVVEPIQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVT 247
           CAV+VEPIQGEGGV  A+  FL+GLR+LC+ H ALL+FDEVQ G+GRTG+L+AYMHYGVT
Sbjct: 185 CAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHYGVT 244

Query: 248 PDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEV 307
           PD+LT+AKALGGGFPV A+L T+E A    VG+HG+TYGGNPLA AVAG   ++INTPE+
Sbjct: 245 PDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINTPEM 304

Query: 308 LQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVM 367
           L G+  +   FV+ L  I+ ++ +FS++RG+GLLIG  L   Y G+A+      A+AGVM
Sbjct: 305 LNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVLNADYAGQAKQISQEAAKAGVM 364

Query: 368 VLNAGADVMRFAPSLVVEEADIHEGMQRFAQA 399
           VL AG +V+RFAP+L V E ++  G+ RFA A
Sbjct: 365 VLIAGGNVVRFAPALNVSEEEVTTGLDRFAAA 396


Lambda     K      H
   0.322    0.137    0.412 

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: 534
Number of extensions: 13
Number of successful extensions: 1
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: 405
Length of database: 406
Length adjustment: 31
Effective length of query: 374
Effective length of database: 375
Effective search space:   140250
Effective search space used:   140250
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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