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_4388 N515DRAFT_4388 Predicted acyltransferase

Query= uniprot:L0FVP4
         (369 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4388
          Length = 354

 Score =  221 bits (564), Expect = 2e-62
 Identities = 144/380 (37%), Positives = 198/380 (52%), Gaps = 44/380 (11%)

Query: 5   RILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIEL 64
           R+ ++D  RG  + AM+LVN+PG  SHVYAPL HA WHGCTPTDLIFPFFLFIVGV+  L
Sbjct: 4   RLASVDALRGCMVAAMLLVNDPGDESHVYAPLAHAAWHGCTPTDLIFPFFLFIVGVSTAL 63

Query: 65  SLGGQLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFDLA-----HLRFPGVLQRIGL 119
           +   +L +G  +G LLR +LIRA ++I LGL   AI   D+      HLR PGVLQRIGL
Sbjct: 64  AFEPKLAQGAARGQLLRTALIRAARIIALGL---AIHLLDILVSPDNHLRIPGVLQRIGL 120

Query: 120 VYFISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTNLAAWIDQQVL 179
            +   +V  LY  P++   +   L IGYW  +       +    LEP  N+    D  V 
Sbjct: 121 CFAAVSVFALYTGPRSWWAAIATLAIGYWALL-------LAGGTLEPFANIPDRFDTFVF 173

Query: 180 TGHMWSQ-----TKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVT 234
            GH   Q      +  DPEGL STLP++ TCL+G+  G  L    +       + +A + 
Sbjct: 174 -GHGTYQFDAATGRGHDPEGLLSTLPSLATCLVGLWAGHTLRAGQTRPLIAVGFALAAL- 231

Query: 235 LVFGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMN 294
                 AWS   P NK LWTSSF L+TAG A L L   + ++D + W      F   G+N
Sbjct: 232 ----AWAWSYALPFNKNLWTSSFALWTAGLAMLALWLFHTLVDQRNWPPLGRRF---GVN 284

Query: 295 AITVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALFNGW-----LAPKDASLCGAILM 349
           A+  +  +  +  L  L+          L    Q A  N W     + P+  SL  A+  
Sbjct: 285 AVAAYAGAETMQTLLPLV----------LTPEAQAAALNAWATAWSIDPRVTSLAYALAF 334

Query: 350 MIILFIPAYFMWKRNIIIKV 369
           + + ++  + + KR + IK+
Sbjct: 335 LCLWWLVVHTLDKRKVYIKL 354


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: 478
Number of extensions: 27
Number of successful extensions: 5
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: 354
Length adjustment: 29
Effective length of query: 340
Effective length of database: 325
Effective search space:   110500
Effective search space used:   110500
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