GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagX in Dyella japonica UNC79MFTsu3.2

Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate N515DRAFT_0596 N515DRAFT_0596 Predicted acyltransferase

Query= uniprot:L0FVP4
         (369 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0596
          Length = 357

 Score =  236 bits (603), Expect = 5e-67
 Identities = 145/377 (38%), Positives = 211/377 (55%), Gaps = 36/377 (9%)

Query: 4   QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63
           +R+ ++D  RG T+ AM+LVN+PG WSHVY PL HA+WHGCTPTDL+FPFFLF+VGV++ 
Sbjct: 6   RRLASVDALRGCTVAAMLLVNDPGDWSHVYWPLEHAQWHGCTPTDLVFPFFLFVVGVSVA 65

Query: 64  LSLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDL--AHLRFPGVLQRIGLVY 121
           L++  ++++G  +G L+R +L+RAL+++GLGLL+ A     L  AH+R PGVLQRIG+ +
Sbjct: 66  LAIAPRMEQGADRGALMRAALVRALRIVGLGLLINAAAALILPDAHMRIPGVLQRIGICF 125

Query: 122 FISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTNLAAWIDQQVLTG 181
             +    LY + +    +   LL GY   +            LEP  N+ +  D  V  G
Sbjct: 126 AAAAAFQLYANGRVQWSAIAALLAGYAGLLAL-------GGTLEPFQNIVSRTDTTVF-G 177

Query: 182 HMW-----SQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVTLV 236
           H       +     DPEGL  TLP+I T LLG+  G  L      +A L    ++GV  V
Sbjct: 178 HFAYRYFPATGLGHDPEGLLGTLPSIATSLLGLRAGHWLR-RDDRRALL----LSGVAYV 232

Query: 237 FGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMNAI 296
             G  WSL  PLNK LWT SFVL+TAGWA L L A + ++D++GW      F   G+NA+
Sbjct: 233 LLGAMWSLLQPLNKNLWTPSFVLWTAGWATLALLAFHLLVDLRGWPALGRRF---GVNAV 289

Query: 297 TVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALFNGWLAPKD----ASLCGAILMMII 352
             +  S  +  L            + ++  L  ++F GW+ P      ASL  A+  + +
Sbjct: 290 AAYAGSEFMQILL---------PGLGIQDPLYRSVFAGWITPLAGPYVASLAFAVTFVAV 340

Query: 353 LFIPAYFMWKRNIIIKV 369
            +   + M +R I +K+
Sbjct: 341 WWAIVWAMDRRRIYLKL 357


Lambda     K      H
   0.329    0.145    0.486 

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: 488
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: 369
Length of database: 357
Length adjustment: 29
Effective length of query: 340
Effective length of database: 328
Effective search space:   111520
Effective search space used:   111520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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