GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Pseudomonas putida KT2440

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate PP_5063 PP_5063 betaine aldehyde dehydrogenase, NAD-dependent

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__Putida:PP_5063 PP_5063 betaine aldehyde
           dehydrogenase, NAD-dependent
          Length = 490

 Score =  243 bits (620), Expect = 1e-68
 Identities = 151/484 (31%), Positives = 248/484 (51%), Gaps = 24/484 (4%)

Query: 39  LIINGERVT--TEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEE 96
           L I+G  V   ++   ++ NPA   +++  V +A +   EKA++SA+   + W  +   +
Sbjct: 9   LYIDGAYVDAGSDATFEAINPAT-GEVLAHVQRATEADVEKAVESAERGQKVWAAMTAMQ 67

Query: 97  RANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEAD-ADTAEAIDFLEYYARQMIELNRGK 155
           R+ IL +A  I+R R  E +     + GK + E    D     D LEYYA  ++    G+
Sbjct: 68  RSRILRRAVDILRERNDELAMLETLDTGKSYSETRYVDIVTGADVLEYYAG-LVPAIEGE 126

Query: 156 EILSRPGEQNRYFYT---PMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPV 212
           +I   P  ++ + YT   P+GVTV I  WN+ + I +  +   +  GN ++ KP+  T +
Sbjct: 127 QI---PLRESSFVYTRREPLGVTVGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSL 183

Query: 213 VAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAV 272
              K  E+  +AGLP GV N + GSG EVG +L +HP+   ++FTG    G ++   A+ 
Sbjct: 184 TTLKLAEIYTEAGLPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTTTGKKVMASAS- 242

Query: 273 VRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDV 332
                + LK V +E+GGK  +++  DADLD AA+  +++ F  SGQ C+ G+R  I  ++
Sbjct: 243 ----SSSLKEVTMELGGKSPLIICADADLDKAADIAMMANFYSSGQVCTNGTRVFIPAEM 298

Query: 333 YDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGE-- 389
                 K       + VG+P + +   GP++  +  E ++ YI  GK+EG R++ GGE  
Sbjct: 299 KAAFEAKIAERVARIRVGNPEDENTNFGPLVSFQHMESVLGYIAKGKEEGARVLCGGERL 358

Query: 390 --GDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGA 447
             GD + G F+ PT+  D   +  I++EEIFGPV++       +  +  AN+T+YGL   
Sbjct: 359 TAGDFAKGAFVAPTVFTDCTDDMTIVKEEIFGPVMSILTYETEEEVIRRANDTDYGLAAG 418

Query: 448 VITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQ 507
           V T +     +   +   G  +   N  G      P GG+K SG   +  G   LA + +
Sbjct: 419 VCTNDITRAHRIIHKLEAGICWI--NAWGESPAEMPVGGYKQSGV-GRENGVSSLAQYTR 475

Query: 508 AKTV 511
            K+V
Sbjct: 476 IKSV 479


Lambda     K      H
   0.316    0.134    0.388 

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: 588
Number of extensions: 31
Number of successful extensions: 4
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: 515
Length of database: 490
Length adjustment: 34
Effective length of query: 481
Effective length of database: 456
Effective search space:   219336
Effective search space used:   219336
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 (21.6 bits)
S2: 52 (24.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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