GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Pseudomonas fluorescens GW456-L13

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate PfGW456L13_4910 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= reanno::azobra:AZOBR_RS19025
         (389 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4910
          Length = 413

 Score =  296 bits (759), Expect = 5e-85
 Identities = 170/378 (44%), Positives = 230/378 (60%), Gaps = 6/378 (1%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M TY    + F +G G  L+   GR +LD  AGVAV  +GH++P +V A+T QA  L H
Sbjct: 28  LMSTYQPLALSFNKGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKIVAAITEQAGLLLH 87

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
           TSNL+ +  Q+ LA++LT+    D  FF NSGAEA E   K+ R + + KG + +  ++ 
Sbjct: 88  TSNLYSIDWQQRLAQKLTQLAGMDRAFFNNSGAEANETALKIARLHGWHKGIE-QPLVVV 146

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEA---VRNAVTDETAGICLE 181
            E AFHGRTL  +SA+    +  GF  L   F  VPFGDL A   V+ A       + +E
Sbjct: 147 MENAFHGRTLGTLSASDGPAVRLGFNKLPGDFVKVPFGDLGALDKVQQAFGSRIVAVLME 206

Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241
           PIQGE G++     +L  +RE+C+    LL LDEIQ G+GRTG+ FA +  GI PDVM +
Sbjct: 207 PIQGESGVQLAPPGYLSAVRELCNRRSWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTL 266

Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301
           AKG+G G P+GACLA  KAA   T G+HGST+GGNPLA  VG  VLD V E G L++ + 
Sbjct: 267 AKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIVEEQGLLENARL 326

Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDV-VVALRANGLLSVPAGDNV 360
            G  L +RL   +A NP V + +RG+GLM+G+     + D+ ++A R +GLL      N 
Sbjct: 327 QGARLLERLRTELAGNPNVSQ-IRGQGLMIGIELKQPIRDLSLIAARDHGLLINVTRGNT 385

Query: 361 VRLLPPLNIGEAEVEEAV 378
           +RLLPPL + E EVE  V
Sbjct: 386 IRLLPPLTLDEREVEMIV 403


Lambda     K      H
   0.321    0.139    0.414 

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: 469
Number of extensions: 20
Number of successful extensions: 5
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: 389
Length of database: 413
Length adjustment: 31
Effective length of query: 358
Effective length of database: 382
Effective search space:   136756
Effective search space used:   136756
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