GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Pseudomonas putida KT2440

Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate PP_3721 PP_3721 Arginine--pyruvate transaminase AruH

Query= SwissProt::P58350
         (410 letters)



>FitnessBrowser__Putida:PP_3721
          Length = 396

 Score =  213 bits (542), Expect = 8e-60
 Identities = 130/380 (34%), Positives = 198/380 (52%), Gaps = 15/380 (3%)

Query: 32  RAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKF 91
           RA A++ E K +++L  G+PDFDTP  + +AA D++  G T Y  + G   L++AI  + 
Sbjct: 23  RALALQAEDKDILLLSVGDPDFDTPAPIVEAAIDSLRAGHTHYADVRGKLALRQAIANRH 82

Query: 92  QRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVL 151
           ++ +G A   D++TV  GA+  L+      LDPGDEVI+  P + +Y  +   C  K V 
Sbjct: 83  RQRSGQAVSADQVTVLAGAQCALYCVAQCILDPGDEVIVAEPMYVTYEAVFGACGAKVVP 142

Query: 152 IACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWL 211
           +     +GFR+    +   ITPRTR + LNSP NPSGA+   A +  L E+ + H  +WL
Sbjct: 143 VPVKPENGFRVCPRDVAERITPRTRALALNSPHNPSGASLPRATWEALAELCVAH-DLWL 201

Query: 212 LVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAM 271
           + D++Y  ++Y+G   V+P  L PG+  RT T+N +SK++AMTGWR+G+  G   L   +
Sbjct: 202 ISDEVYSELLYEG-EHVSPGSL-PGMAERTATLNSLSKSHAMTGWRMGWVVGSTALATHL 259

Query: 272 AVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPE 331
             +            Q A+V AL  P   L    E++++RRDLV   L    GL    P+
Sbjct: 260 ENLALCMLYGLPDFVQDAAVVALEHPLPELDAMREAYRQRRDLVCEQLAGCPGLKALKPD 319

Query: 332 GAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFGLSP--FFRISYA 389
           G  +       V+  +  +G   +    F  YLL+   V+V+ G AFG S     R+   
Sbjct: 320 GGMF-------VMLDIRETGVSAQA---FADYLLDSQGVSVLAGEAFGPSAAGHIRLGLV 369

Query: 390 TSEAELKEALERIAAACDRL 409
                L +A +RIA     L
Sbjct: 370 LGNEALVDACQRIARCAGEL 389


Lambda     K      H
   0.318    0.134    0.393 

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: 395
Number of extensions: 21
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: 410
Length of database: 396
Length adjustment: 31
Effective length of query: 379
Effective length of database: 365
Effective search space:   138335
Effective search space used:   138335
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 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