GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Marivita geojedonensis DPG-138

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= BRENDA::P49419
         (539 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  224 bits (571), Expect = 6e-63
 Identities = 142/461 (30%), Positives = 231/461 (50%), Gaps = 22/461 (4%)

Query: 63  GEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWADIPAPKRGEIVRQIGDALR 122
           G  I    PA  E IA V  A+ A  ++ +  A  A K WA +   +RG I+R+  D +R
Sbjct: 23  GTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAADMMR 82

Query: 123 EKIQVLGSLVSLEMGKILVEGVG-EVQEYVDICDYAVGLSRMIGGPILPSERSGHALIEQ 181
           E+   L  L + + GK   E +  +     D  +Y  GL+  + G  +        L E 
Sbjct: 83  ERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHIQ-------LGED 135

Query: 182 W-----NPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAK 236
           W      P+G+   I A+N+P  +  W  A A+ CGN  ++K + TT L ++ V    A+
Sbjct: 136 WVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKV----AE 191

Query: 237 VLEDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVGLMVQERFGRSLLE 296
           +L +  LP  I ++  G  ++G ++  D RV  +S TGS   GK+V     E+     +E
Sbjct: 192 ILHEAGLPAGIYNVVQGLGEVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHVTME 251

Query: 297 LGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHESIHDEVVNRLKKAYAQ 356
           LGG + ++ F+DADL   V  A+     ++GQ C+   R+F+ + I +  + RL +  + 
Sbjct: 252 LGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTERLST 311

Query: 357 IRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTG 416
             VG+P D    +GP+ +++ + + L  +E+ + EG  +V GG+ ++R G Y++PT+   
Sbjct: 312 AVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQPTVFAD 371

Query: 417 LGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIFTKDLGRIFRWLGP-KG 475
           +  D  IA  E F P++ V  F+ EEE     N  + GLS+ +FT+DL R  R +   + 
Sbjct: 372 VKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQLEA 431

Query: 476 SDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQY 516
             C I + N     A +   FGG K +G GRE+   A   Y
Sbjct: 432 GSCFINSYN----DAPVEAPFGGTKMSGVGRENSKAAINHY 468


Lambda     K      H
   0.318    0.136    0.417 

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: 667
Number of extensions: 33
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: 539
Length of database: 485
Length adjustment: 35
Effective length of query: 504
Effective length of database: 450
Effective search space:   226800
Effective search space used:   226800
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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