GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Verminephrobacter eiseniae EF01-2

Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_083758718.1 VEIS_RS03235 aldehyde dehydrogenase family protein

Query= BRENDA::B0K315
         (466 letters)



>NCBI__GCF_000015565.1:WP_083758718.1
          Length = 526

 Score =  186 bits (473), Expect = 1e-51
 Identities = 127/399 (31%), Positives = 194/399 (48%), Gaps = 9/399 (2%)

Query: 47  AKEAQKKFALMDLEKREEIIAAIREACVNNARLLAEIACSETGRGRVEDKVAKN-ILAAK 105
           A+ A + FA  D E+   +  A+ +A  +NA   AE A  ETG G VE K  KN  +A  
Sbjct: 25  AEWAARDFAQFDREQVLRVAEAVAKAAHDNAAFYAEWAVRETGYGVVEHKQKKNESVAYP 84

Query: 106 KTPGTEDLKPTAWTGDRGLTLVEMA-PVGVIASITPVTNPTATIINNTISMLAAGNAVVF 164
                 DL       D    +VE+  P G++ ++TP TNP AT+    +  L + NA+V 
Sbjct: 85  LLDFYRDLDLVHPRVDEARKMVEIPKPAGIVLALTPATNPVATVYYKVMLALLSRNAIVI 144

Query: 165 NPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLMEHPEVNMVVVTGGK 224
           +PHP+A +  N A   ++ A    GAP GL+  I  P+I     LM  P+V +V+ TGG 
Sbjct: 145 SPHPAASRCCNDAARKLDAAAHAAGAPPGLIQCIERPSIPLVDTLMRSPQVAVVMATGGG 204

Query: 225 AVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDNNLPCIAEKEIIAVE 284
            +V+ A   G   IG G GN P  +D +AD+ KAA  I    SFDN++ C +E  ++  +
Sbjct: 205 PMVRAAYSSGNPAIGVGPGNAPAYIDTSADMRKAARMIVSSKSFDNSVLCTSESVLLVQQ 264

Query: 285 RIADTLLERMKREGAYVLHGKDIDRMTELIFQGGAINKDLIGRDAHFILSQIGIETGKDI 344
           + A      ++  GA++   ++++R+   +F  G +N   IG+ A +I  + G++     
Sbjct: 265 KDAQRFERELRAAGAHLCQEREVERLRAYLFPDGDLNPAAIGKSAVWIAREAGLKVLPAT 324

Query: 345 RLVVMPVD---VSHPLVYHEQLMPVIPFVTVPTVEEAINLA--VKAEGGNRHTAMMHSKN 399
           +++V  V    V  PL   E+L PV+    V + E A   A  +    G  H+A  H  +
Sbjct: 325 QVLVANVQHIGVDEPLT-KEKLCPVLALYAVDSFERATRSAQMILRLSGAGHSAAFHGND 383

Query: 400 VENMTAFARAIQTTIFVKNAPSYAGI-GFGGEGYTTFTI 437
            +    FA  +     V NAP   G  GF      TF I
Sbjct: 384 PQKALDFAARLNVYRVVVNAPCAQGASGFATHLPPTFMI 422


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: 527
Number of extensions: 23
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: 526
Length adjustment: 34
Effective length of query: 432
Effective length of database: 492
Effective search space:   212544
Effective search space used:   212544
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