GapMind for catabolism of small carbon sources

 

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

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  325 bits (832), Expect = 3e-93
 Identities = 180/473 (38%), Positives = 277/473 (58%), Gaps = 6/473 (1%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           ++DGA+V+   G  I V  PATGE I +V     A   +A+ AA +A  AW A++  ER 
Sbjct: 12  FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERG 71

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKG-EIAYAASFLEWFGEEAKRIYGDTIP 132
             LRR  D+M E   DL+ L T + GKP  E    +    A  LE+FG  A  + G+ I 
Sbjct: 72  RILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHI- 130

Query: 133 GHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192
               +  +   ++P+GV   I  WN+P+ +   K  PALA G  MV KP+  TP  AL +
Sbjct: 131 -QLGEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKV 189

Query: 193 AELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252
           AE+   AG+P G+++VV G  GEVG  L ++P V K++ TGS   G+++ A  A+ +K V
Sbjct: 190 AEILHEAGLPAGIYNVVQG-LGEVGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHV 248

Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312
           ++ELGG +P ++FDDADL+ AV GA++  + ++GQ C    R++VQ G+ +AF+ +L   
Sbjct: 249 TMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTER 308

Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTI 372
           ++   +G+ L+     GP++  K +  V ++I    ++GA++V+GG+     G + +PT+
Sbjct: 309 LSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQPTV 368

Query: 373 LVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQ 432
             DV  + +++++E FGP+  V  F+ E E I  +N TEFGL++  + RDL+R  RV  Q
Sbjct: 369 FADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQ 428

Query: 433 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK--YLCLGGI 483
           LE G   IN+   +   APFGG K SG+GRE SK  I  Y E+K  Y+ +G +
Sbjct: 429 LEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVRMGDV 481


Lambda     K      H
   0.317    0.135    0.391 

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: 601
Number of extensions: 28
Number of successful extensions: 3
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: 483
Length of database: 485
Length adjustment: 34
Effective length of query: 449
Effective length of database: 451
Effective search space:   202499
Effective search space used:   202499
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