GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Rhodobacter maris JA276

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_097070256.1 CRO22_RS11275 aldehyde dehydrogenase EutE

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_900217815.1:WP_097070256.1
          Length = 533

 Score =  452 bits (1163), Expect = e-131
 Identities = 230/435 (52%), Positives = 301/435 (69%), Gaps = 4/435 (0%)

Query: 35  GIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARL--LAEIACSETGRGR 92
           GIF  ++ A+  A EAQKK+    +  R+  +  IR    + A L  ++ +   +TG G 
Sbjct: 98  GIFETMDAAINAAAEAQKKYLFCSMADRKRFVDGIRSIFTDPAILERISRLTVEQTGMGN 157

Query: 93  VEDKVAKNILAAKKTPGTEDLKPTAWTGDRGLTLVEMAPVGVIASITPVTNPTATIINNT 152
           VE K+ KN LAA+ +PG EDL   A +GD GLTLVE++P GVI +ITP TNPT TII N 
Sbjct: 158 VEHKIIKNRLAAENSPGIEDLVTEAQSGDDGLTLVELSPYGVIGAITPTTNPTETIICNG 217

Query: 153 ISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLMEH 212
           I MLAAGNA VF+PHP A+  S  A+++IN  +  +GAP  LV ++  P+I+    +M H
Sbjct: 218 IGMLAAGNAAVFSPHPRARGVSLLAIKLINRKLAALGAPANLVVTVQAPSIENTNAMMAH 277

Query: 213 PEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDNNL 272
           P+V M+V TGG A+V+T +  GKK IGAGAGNPPVVVDETADI KAA DI  GASFD+N+
Sbjct: 278 PKVRMLVATGGPAIVRTVMSTGKKAIGAGAGNPPVVVDETADIPKAALDIVNGASFDHNM 337

Query: 273 PCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTE--LIFQGGAINKDLIGRDAH 330
           PCIAEKE I V ++AD L+  M R GAY++    +    E  ++ + G    D +G+ A 
Sbjct: 338 PCIAEKEAIVVTQVADFLISEMCRNGAYLVKDPAVIAKLEARVLTEKGGPKTDCVGKSAV 397

Query: 331 FILSQIGIETGKDIRLVVMPVDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAVKAEGGNR 390
           ++L Q+G++ G ++RLV+M     HP V  E +MP++P V VP V+EAI+LAV  E GNR
Sbjct: 398 WLLDQVGVKVGPEVRLVLMEATKDHPFVQEELMMPILPLVRVPDVDEAIDLAVDLEHGNR 457

Query: 391 HTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTTFTIAGPTGEGLTSART 450
           HTA+MHS NV  +T  A+ IQTTIFVKN PSYAGIG GGEGYTTFTIAGPTGEGLTSAR+
Sbjct: 458 HTAIMHSTNVRKLTKMAKLIQTTIFVKNGPSYAGIGVGGEGYTTFTIAGPTGEGLTSARS 517

Query: 451 FTRQRRCVLVDAFRI 465
           F R+R+CV+V+A  +
Sbjct: 518 FARRRKCVMVEALNV 532


Lambda     K      H
   0.317    0.133    0.377 

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: 630
Number of extensions: 26
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: 466
Length of database: 533
Length adjustment: 34
Effective length of query: 432
Effective length of database: 499
Effective search space:   215568
Effective search space used:   215568
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