GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_5063
          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 (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