GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2C3

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26715
          Length = 430

 Score =  232 bits (591), Expect = 2e-65
 Identities = 141/404 (34%), Positives = 211/404 (52%), Gaps = 36/404 (8%)

Query: 30  KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNEPALR 88
           + QG+ +WD  G  Y+DF GGI V  +GH HP +V A++ Q + + H    V   +P L 
Sbjct: 33  RAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVSHACFQVVAYKPYLD 92

Query: 89  LGRKLIEATFAE---RVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145
           L ++L E    +   +     SG EA E A K+AR +        +  +I+F   FHGR+
Sbjct: 93  LVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHTN------RPAVISFRGGFHGRT 146

Query: 146 LFTVSVGGQPK-YSDGFGPKPADIIHVPF----------------NDLHAVKAVMDDHTC 188
           L   ++ G  + Y   FGP   ++ H P+                N+L A + V  D   
Sbjct: 147 LLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQALNELLATQ-VAPDRVA 205

Query: 189 AVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTP 248
           A+++EP+QG+GG  +A PEFLQ LR L +QH  +L+ DE+Q G GRTG  F + H G+ P
Sbjct: 206 AIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGFQHAGIQP 265

Query: 249 DILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVL 308
           D++T AK+L GG PIS ++  A I  A  PG  G TYGGN L+CA A A  D     ++L
Sbjct: 266 DLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDAYEQEQLL 325

Query: 309 EGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDF-----LYAGAE 363
           E  Q   +R    L ++  ++    D+RG G ++  EL    + R+ D      L   A 
Sbjct: 326 ERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEARSPDAELTQQLIDQAR 385

Query: 364 AG-VMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKVV 404
            G ++V+  G   +V+RF   LV E++ IDE +     A+ +V+
Sbjct: 386 VGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAALLRVL 429


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: 489
Number of extensions: 24
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