GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2E2

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  240 bits (613), Expect = 5e-68
 Identities = 142/404 (35%), Positives = 213/404 (52%), Gaps = 34/404 (8%)

Query: 30  KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88
           + QGS +WD  GK Y+DF GGI V  +GH HP +V A++ Q + + H    V   +P L 
Sbjct: 33  RAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKISHACFQVVAYKPYLD 92

Query: 89  LGRKLIE---ATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145
           L ++L E      A +  F  SG EA E A K+AR +        ++ +IAF   FHGR+
Sbjct: 93  LAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTN------RSAVIAFRGGFHGRT 146

Query: 146 LFTVSVGGQPK-YSDGFGPKPADIIHVPFNDLH-------AVKA--------VMDDHTCA 189
           L   ++ G  + Y   FGP   ++ H P+ + +       A++A        V  +   A
Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQALDELLATQVAPERVAA 206

Query: 190 VVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPD 249
           +++EP+QG+GG  +A  EFLQGLR L  +H  +L+ DE+Q G GRTG  F + H G+ PD
Sbjct: 207 IIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWFGFQHAGIQPD 266

Query: 250 ILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLE 309
           ++T AK+L GG P+S ++  AEI  A  PG  G TYGGN L+CA A A  +     ++L 
Sbjct: 267 LVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLA 326

Query: 310 GIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARD------FLYAGAE 363
             +   +R    L  +  +Y    D+RG G ++  EL    + R  D       +     
Sbjct: 327 RGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEARTPDADLNQRLIDEARA 386

Query: 364 AGVMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405
            G++V+  G   +V+RF   LV  +A IDE +Q    A+A+V+G
Sbjct: 387 GGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARVLG 430


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: 504
Number of extensions: 25
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: 430
Length adjustment: 32
Effective length of query: 374
Effective length of database: 398
Effective search space:   148852
Effective search space used:   148852
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.

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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