GapMind for Amino acid biosynthesis

 

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

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate AO356_17010 AO356_17010 acetylornithine aminotransferase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_17010
          Length = 391

 Score =  290 bits (743), Expect = 4e-83
 Identities = 167/378 (44%), Positives = 226/378 (59%), Gaps = 6/378 (1%)

Query: 5   VMPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWH 64
           +M TY    + F  G G  L+  DGR +LD  AGVAV  +GH++P LV A++ QA  L H
Sbjct: 6   LMTTYQPLALNFTHGLGTRLWDQDGREYLDAVAGVAVTNVGHSHPRLVAAISEQAGLLLH 65

Query: 65  TSNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIIT 124
           TSNL+ +  Q+ LA++LT+ +  +  FF NSGAEA E   KL R Y + KG + +  ++ 
Sbjct: 66  TSNLYSIDWQQRLAQKLTQLSGMERAFFNNSGAEANETALKLARLYGWHKGIE-QPLVVV 124

Query: 125 FEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDL---EAVRNAVTDETAGICLE 181
            + AFHGRTL  +SA+    +  G+  L   F  VPFGDL   E ++ A  +    + +E
Sbjct: 125 MDNAFHGRTLGTMSASDGPSVRLGYNRLPGDFIKVPFGDLAALEQIQQAHAERIVAVLVE 184

Query: 182 PIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAV 241
           PIQGE G++     +L+ LR++C     LL LDEIQ G+GRTG+ FA +  GI PDVM +
Sbjct: 185 PIQGESGVQLAPPGYLKALRQLCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTL 244

Query: 242 AKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQR 301
           AKG+G G P+GACLA  KAA   T G+HGST+GGNPLA  VG  VLD + E   + + + 
Sbjct: 245 AKGLGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLDIIEEQALVGNARH 304

Query: 302 IGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPAVGDVVV-ALRANGLLSVPAGDNV 360
            G  L  RL   +AENP V   +RG+GLM+G+     V D+ + A R +GLL        
Sbjct: 305 QGEQLLSRLRTELAENPNVL-AIRGQGLMIGIELKQPVRDLTLRAARDHGLLINVTRGQT 363

Query: 361 VRLLPPLNIGEAEVEEAV 378
           +RLLPPL I   EVE  V
Sbjct: 364 IRLLPPLTIDGREVEMIV 381


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: 431
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: 391
Length adjustment: 31
Effective length of query: 358
Effective length of database: 360
Effective search space:   128880
Effective search space used:   128880
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