GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaA in Halioglobus japonicus S1-36

Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate WP_084199389.1 C0029_RS09780 FAD-binding oxidoreductase

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



>NCBI__GCF_002869505.1:WP_084199389.1
          Length = 426

 Score =  129 bits (324), Expect = 2e-34
 Identities = 121/407 (29%), Positives = 178/407 (43%), Gaps = 27/407 (6%)

Query: 26  ALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIR 85
           AL GE   DVCVIGGG TG+S A+ L E+G  V +LE   I  G SGRN G V  G    
Sbjct: 24  ALQGEVDTDVCVIGGGFTGVSTALTLAERGHRVTLLEQNLISWGASGRNGGQVIGGM--- 80

Query: 86  PDDVEATLGQKQGSRLNKV--LGEAPAEVF-AMIERLGIDCQAQHKGTLHMAHNATGIAD 142
               +    Q QG R N +  LG    ++    IE+  I C  +H G + +A     + D
Sbjct: 81  -SGEKRLSKQWQGKRDNFMFELGYRGHQLIKERIEKYDIACDFKH-GYMDVALKPRQVRD 138

Query: 143 LEARHEQW--RRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVT 200
           LE  H +   R  G DV LL   + ++  GTD+    L++ R G ++P+    G A A  
Sbjct: 139 LEEWHRELCERGMGEDVRLLDRGEVRDALGTDRYLGGLVNNRNGHLHPLNLCLGEARAAA 198

Query: 201 RLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYY 260
           +LG  I + + V  +E  G   RV    G+V A+ V+I+  AY   +   L  + F    
Sbjct: 199 QLGASIHEHTKVLHIE-HGRRPRVICENGSVTADFVIIAGNAYHRLERKKLGGRVFPAGS 257

Query: 261 YQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVD---NKPAWFV 317
           Y +A++PL    A +V        D   VL   R     R+L G  GR D    +PA   
Sbjct: 258 YILATEPLSEAEAAEVNALDVAVCDMNNVLDYFRLSADRRMLFG--GRCDYSGREPADIA 315

Query: 318 RSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGT 377
            +   R+ S  +P+L     +  W G +    + +  L      +    GY+G G     
Sbjct: 316 GAMLPRMHS-IWPQLRNKRIDYAWGGMMGIVVNRVPLLGRVTDNVFYSVGYSGHGVNMTH 374

Query: 378 VIGRAFAEFLLKGEADSL---------PIPFSPMSGVSAPSLRTAFY 415
             G A A+  ++G  D++         PIP     G  + +    +Y
Sbjct: 375 ACGEAMAD-AVEGSCDTMEFFASVPHWPIPLGQWLGAQSVAAGMLYY 420


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: 480
Number of extensions: 29
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: 426
Length adjustment: 32
Effective length of query: 400
Effective length of database: 394
Effective search space:   157600
Effective search space used:   157600
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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