GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Pseudomonas fluorescens FW300-N2E2

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  352 bits (904), Expect = e-102
 Identities = 188/416 (45%), Positives = 255/416 (61%), Gaps = 12/416 (2%)

Query: 6   ISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT 65
           + + +   HP+ +   + +E+WD DGKRY+DFVGGIGVLN+GH +P VV A+QAQ  +++
Sbjct: 19  VPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKIS 78

Query: 66  HYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAF 125
           H  F    + PYL L ++L + +   +        SGAEA ENA+K+AR  T + A+IAF
Sbjct: 79  HACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTNRSAVIAF 138

Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE 185
            GGFHGRTL    L G   PYKQ  G     V+H PYP+A  GVT   AL+A+D L + +
Sbjct: 139 RGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQALDELLATQ 198

Query: 186 LAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAF 245
           +A E VAA I EPVQG+GGFL+    F Q LR    + GI++I+DEIQ+GFGRTG+ F F
Sbjct: 199 VAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWFGF 258

Query: 246 PRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ 305
              GI+PDL+ +AKS+AGG+PL  VVG+ E+M A   GGLGGTY GN +SCAAALA +  
Sbjct: 259 QHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEA 318

Query: 306 MTDENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP 361
              E L       GER  Q ++    R+      P IG + G G M  IE    D +  P
Sbjct: 319 YEQEQLLARGEVLGERLRQGLLHLQTRY------PQIGDVRGSGFMLAIELIKHDEARTP 372

Query: 362 -AQL-AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            A L  ++++ ARA GLL++  G  R+++R LAPL      ++E L IL+  LA +
Sbjct: 373 DADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALARV 428


Lambda     K      H
   0.320    0.137    0.402 

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: 547
Number of extensions: 15
Number of successful extensions: 2
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: 416
Length of database: 430
Length adjustment: 32
Effective length of query: 384
Effective length of database: 398
Effective search space:   152832
Effective search space used:   152832
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 Sep 17 2021. The underlying query database was built on Sep 17 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