GapMind for Amino acid biosynthesis

 

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

Align N-succinylornithine aminotransferase (EC 2.6.1.81) (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::Btheta:353284
         (373 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910
          Length = 430

 Score =  221 bits (562), Expect = 4e-62
 Identities = 147/388 (37%), Positives = 209/388 (53%), Gaps = 35/388 (9%)

Query: 14  IVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVIN-KLQ 72
           I + QG ++WD +G  YLD  GG  V++IGH HP  V  +  Q+  +      V+  K  
Sbjct: 31  IDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKVSHACFQVVAYKPY 90

Query: 73  QQVAERLGK-ISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRTSLAV 131
             +A+RL + I G E Y      SGAEA ENA+K+A  +  R+ VI+F   FHGRT L  
Sbjct: 91  LDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGGFHGRTLLGT 150

Query: 132 EATNN------------PTII-APINN--NGHVTYLPLNDI-EAMKQELAKGDVCAVIIE 175
             T              P +   P  N   G  + + L  + E +  ++A   V A+IIE
Sbjct: 151 TLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSDMALKALDELLATQVAPERVAAIIIE 210

Query: 176 GIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITV 235
            +QG GG     TEF+Q LR +  + G +LILDEIQ+G+GR+GK+F  Q+  IQPD++TV
Sbjct: 211 PVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFGRTGKWFGFQHAGIQPDLVTV 270

Query: 236 AKGIGNGFPMAGVL--ISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKA 293
           AK +  G P++GV+     M  P+ G LG T+GGN L+C+AALAV++  EQ+ L+   +A
Sbjct: 271 AKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLARGEA 330

Query: 294 VGDYLLEEL----KKFPQIKEVRGRGLMIGLEF------EEPIKELRSRLIYDEH----- 338
           +G+ L E L     ++P+I +VRG G M+ +E         P  +L  RLI +       
Sbjct: 331 LGERLREGLLRLQARYPRIGDVRGSGFMLAIELIKDDDARTPDADLNQRLIDEARAGGLL 390

Query: 339 VFTGASGTNVLRLLPPLCLSMEEADEFL 366
           V       NVLR L PL  S  + DE L
Sbjct: 391 VIKCGVYRNVLRFLAPLVTSEAQVDEAL 418


Lambda     K      H
   0.320    0.139    0.403 

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: 357
Number of extensions: 15
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: 373
Length of database: 430
Length adjustment: 31
Effective length of query: 342
Effective length of database: 399
Effective search space:   136458
Effective search space used:   136458
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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