GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaA in Alicycliphilus denitrificans K601

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate WP_013518247.1 ALIDE2_RS17665 FAD-binding oxidoreductase

Query= metacyc::G1G01-5614-MONOMER
         (432 letters)



>NCBI__GCF_000204645.1:WP_013518247.1
          Length = 432

 Score =  238 bits (608), Expect = 2e-67
 Identities = 143/411 (34%), Positives = 203/411 (49%), Gaps = 2/411 (0%)

Query: 13  LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72
           LW   +       AL      DV V+G G TGLS A+HL E G  V VL+A   G G SG
Sbjct: 15  LWAATAPAAPDTPALGASVSTDVLVVGAGYTGLSTALHLAESGARVCVLDAHAPGWGASG 74

Query: 73  RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132
           RN G VN      PDD+    G ++   L   +  +   V+ +I R  IDC     G L 
Sbjct: 75  RNGGQVNPTLKYDPDDLVRIYGAERAEPLIDTVSRSADLVYGLIARHAIDCAPVRAGWLQ 134

Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192
           + +    +  + AR  QW RRG  VE+L  A      GT   +   LD RAG + P+ Y 
Sbjct: 135 VGYTQHAVDGMHARARQWERRGVRVEMLDRAAVAARIGTPAFAGGWLDGRAGGVQPLAYA 194

Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARG-AVRAEKVVISTGAYTEGDWSNL 251
           +GLA A   LG ++   S V  LER+G  W   TA+G  V+A++VV+ T  YT+G W  L
Sbjct: 195 RGLARAAQGLGVQVHGGSPVVALERQGMHWIATTAQGHRVQAQQVVLGTNGYTDGLWPGL 254

Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311
            +       + VA++PL G A D +LP G+    ++ +L   R+D QGRLL+G  G   +
Sbjct: 255 ARTVLAANSFIVATRPL-GPAGDGILPGGETGSTSQRLLLYFRKDAQGRLLMGGRGHFAD 313

Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371
                  S  +R  +  +P+LG +++E  W G I  T D +  L  PAPG+    GYNGR
Sbjct: 314 PQGPQDFSHLERAVALMFPQLGPLQYEYRWAGRIAVTRDFMPHLHRPAPGITMALGYNGR 373

Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422
           G    T +GR  A  +    A + P P +P+  +    L+  +  +G + Y
Sbjct: 374 GIAMATSLGRHAAALVAGSSAAACPFPVTPVQPIPLHGLQRFYIAAGVAWY 424


Lambda     K      H
   0.319    0.135    0.419 

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: 514
Number of extensions: 25
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: 432
Length of database: 432
Length adjustment: 32
Effective length of query: 400
Effective length of database: 400
Effective search space:   160000
Effective search space used:   160000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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