GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas fluorescens FW300-N1B4

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Pf1N1B4_2980 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2980
          Length = 391

 Score =  281 bits (718), Expect = 3e-80
 Identities = 159/376 (42%), Positives = 219/376 (58%), Gaps = 7/376 (1%)

Query: 14  MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73
           +M  Y P A    +G G+RLWDQ G+EY+D   G+AV  +GH+HPR+V A++EQAG   H
Sbjct: 6   LMSTYQPLALSFSKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPRIVAAISEQAGLLLH 65

Query: 74  TGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVA 133
           T N Y+ +   RLA++L+  +  DR FF NSGAEANE ALKLAR Y   + G E+  +V 
Sbjct: 66  TSNLYSIDWQQRLARKLVRLSGMDRAFFNNSGAEANETALKLARLYGWHK-GIEQPLVVV 124

Query: 134 FKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDN---TCAVIVE 190
            +NAFHGRTL T+SA   PA    F  LP       + DL + +A+   +     A+++E
Sbjct: 125 MENAFHGRTLGTLSASDGPAVRLGFNELPGDFIKVPFGDLAALEAVQQAHGPRIVAILME 184

Query: 191 PMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLST 250
           P+QGE GV  A   +L+ +RELC+    LL+ DE+QTG+GRTG+ +A+ H G+ PD+++ 
Sbjct: 185 PVQGESGVQVAPPGYLKAVRELCNRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTL 244

Query: 251 AKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQ 310
           AK LG G PIGA LA  + A + T G+HG+T+GGNPLAC V   V   I  + +L   + 
Sbjct: 245 AKGLGNGIPIGACLARGKAADLFTPGSHGSTFGGNPLACRVGCTVLEIIEEQGLLENARL 304

Query: 311 RHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMILIAGA 370
           + +    RL    A       IRG GL+IG  LK             A + GL+I +   
Sbjct: 305 QGERLLARLRIELADDPNVLAIRGQGLMIGIELKQPIRDLTLI---AARDHGLLINVTRG 361

Query: 371 NVVRFAPALIISEDEV 386
             +R  P L I E EV
Sbjct: 362 KTIRLLPPLTIDEREV 377


Lambda     K      H
   0.321    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: 423
Number of extensions: 11
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 375
Effective length of database: 360
Effective search space:   135000
Effective search space used:   135000
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 (21.8 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