GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Pseudomonas fluorescens FW300-N2C3

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate AO356_16950 AO356_16950 dihydropteridine reductase

Query= CharProtDB::CH_003330
         (396 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16950
          Length = 393

 Score =  266 bits (679), Expect = 1e-75
 Identities = 159/401 (39%), Positives = 217/401 (54%), Gaps = 14/401 (3%)

Query: 1   MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60
           ML  +  A +++T+PLL   G  L  HFY  M +  P+++ +FN ++Q +GDQ  AL N 
Sbjct: 1   MLSQEERAIIRSTVPLLESGGEALITHFYRMMLSEYPQVRPLFNQAHQASGDQPRALANG 60

Query: 61  IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFS---PGQEVL 117
           +  YA +I+ L  L   V KI  KH + QI PE Y IVG  LL  + E+        EV+
Sbjct: 61  VLMYARHIDQLDQLGDLVAKIVNKHVALQILPEHYPIVGACLLRAIAEVLGAEIATPEVI 120

Query: 118 DAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDG 177
            AWG AY  LA++ I  EA +Y++ A   GGW G R+F + AK   S+ ITSF  EP D 
Sbjct: 121 AAWGAAYNQLADILIGAEAGMYDKKAEAPGGWRGEREFILAAKVQESSEITSFYFEPADK 180

Query: 178 GAVAEYRPGQYLGVWLKPEGFPHQEIRQ-YSLTRKPDGKGYRIAVKREEGGQVSNWLHNH 236
           G +    PGQY+G+ L  +G   +E+R+ YSL+   D   YRI+VKRE GG+VSN LH+H
Sbjct: 181 GPILVAEPGQYIGMKLILDG---EEVRRNYSLSALADNGRYRISVKREPGGRVSNHLHHH 237

Query: 237 ANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAA 296
             VG+ ++L  P+GDF++  A D P+ LIS GVG TP LAML    +      V++ H A
Sbjct: 238 FEVGNRIQLFPPSGDFYL-TASDKPLVLISGGVGITPTLAMLQAALQT--ERPVHFIHCA 294

Query: 297 ENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDP- 355
            NG  HAF D + +L +  P+      Y    E D      D  GL+   +L     +  
Sbjct: 295 RNGRAHAFRDWIDDLARRHPQLKRFYCY---DEDDGLSPAADKVGLLSQEQLAQWLPEQR 351

Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396
            +  Y  GP GFM    + L  LGV      YE FGP   L
Sbjct: 352 DLDAYFLGPKGFMGAVKRHLKALGVPDRQSRYEFFGPAAAL 392


Lambda     K      H
   0.318    0.135    0.404 

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: 417
Number of extensions: 24
Number of successful extensions: 6
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: 396
Length of database: 393
Length adjustment: 31
Effective length of query: 365
Effective length of database: 362
Effective search space:   132130
Effective search space used:   132130
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: 50 (23.9 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