GapMind for catabolism of small carbon sources

 

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

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  301 bits (772), Expect = 2e-86
 Identities = 178/471 (37%), Positives = 270/471 (57%), Gaps = 7/471 (1%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           +IDG +V       I V+ PAT   I+ +         KA+ AA RAQ  W A+   ER 
Sbjct: 12  FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERG 71

Query: 70  SWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128
             LR+ +  +RER  ++S L   + GK  Q+   V+    AD ++Y    A    GE IQ
Sbjct: 72  RILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHIQ 131

Query: 129 SDRPGENILLFKRA-LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIA 187
               GE+ +  +R  LGV  GI  WN+P  +   K APAL  GN +V KPSE TP  A+ 
Sbjct: 132 L---GEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALK 188

Query: 188 FAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITK 247
            A+I+ E GLP G++N+V G GE VG  L  +P+VA VS+TGSV  G+K+ A AA+ +  
Sbjct: 189 VAEILHEAGLPAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKH 247

Query: 248 VCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGE 307
           V +ELGGK+P ++ DDADLE AV   +     +SGQVC+   RV+VQKGI + F+ RL E
Sbjct: 248 VTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTE 307

Query: 308 AMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPP 367
            +     G+P +      GP+++   ++ V   + +   EGAR+  GG+ +   G+Y  P
Sbjct: 308 RLSTAVVGDPLDEAT-NFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQP 366

Query: 368 TLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI 427
           T+  DV+ +M I  EE FGPV+ V+ F+T E+AI+ AN +++GL++ ++T++L+ A + I
Sbjct: 367 TVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVI 426

Query: 428 KGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478
             L+ G  +IN  N   ++    G + SG+G  + K  ++ Y + + VY++
Sbjct: 427 AQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477


Lambda     K      H
   0.318    0.135    0.392 

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: 534
Number of extensions: 23
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: 479
Length of database: 485
Length adjustment: 34
Effective length of query: 445
Effective length of database: 451
Effective search space:   200695
Effective search space used:   200695
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