GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pseudomonas fluorescens FW300-N2E3

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase

Query= BRENDA::O30508
         (406 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10500
          Length = 390

 Score =  288 bits (736), Expect = 2e-82
 Identities = 157/388 (40%), Positives = 229/388 (59%), Gaps = 6/388 (1%)

Query: 16  YMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIW 75
           Y++ NYA       RG+G+ +WD+ G E +D   G+AVTSLGHA+P +  A+ EQA ++ 
Sbjct: 7   YLMHNYARQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLL 66

Query: 76  HVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEII 135
           H SN+F  E   +L+ +L   +  +R F  NSGAEANEAA KLAR +AN  +  Q  +++
Sbjct: 67  HTSNMFHIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARHVAQP-QVL 125

Query: 136 AASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALK--AAISDKTCAVVLE 193
              NSFHGRTL T+   G P    GF P   G   VPY+++E ++  AA S    AV++E
Sbjct: 126 VMENSFHGRTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSPDIVAVLVE 185

Query: 194 PIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSS 253
           P+QGEGGV  A   YL+  R+LCDEH+ L++ DEVQ+GMGR G  F Y H G+VPD+++ 
Sbjct: 186 PVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITL 245

Query: 254 AKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKA 313
           AK+LG GFPIGA L  G+ A+  S G H +T+GGNPLA  V    LD++    +      
Sbjct: 246 AKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMERDHIPQRAAT 305

Query: 314 KHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVLQASP 373
              R  + LQ+    +     IRG+GL++G  L  +    A  V  A +++ +++     
Sbjct: 306 SGRRLLAALQEALGNHSEVVSIRGLGLMVGIELNRQC---AELVGRALDEQRLLITVTRG 362

Query: 374 DVVRFAPSLVIDDAEIDEGLERFERAVA 401
             +R  P L+ +D++ID+   R  R ++
Sbjct: 363 TTLRLLPPLICEDSQIDDIAARVSRLLS 390


Lambda     K      H
   0.318    0.135    0.394 

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: 400
Number of extensions: 14
Number of successful extensions: 3
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: 390
Length adjustment: 31
Effective length of query: 375
Effective length of database: 359
Effective search space:   134625
Effective search space used:   134625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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