GapMind for catabolism of small carbon sources

 

Aligments for a candidate for QDPR in Pseudomonas fluorescens FW300-N1B4

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate Pf1N1B4_925 Flavohemoprotein (Hemoglobin-like protein) (Flavohemoglobin) (Nitric oxide dioxygenase) (EC 1.14.12.17)

Query= CharProtDB::CH_003330
         (396 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_925 Flavohemoprotein
           (Hemoglobin-like protein) (Flavohemoglobin) (Nitric
           oxide dioxygenase) (EC 1.14.12.17)
          Length = 393

 Score =  273 bits (697), Expect = 8e-78
 Identities = 168/401 (41%), Positives = 217/401 (54%), Gaps = 14/401 (3%)

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

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

Query: 118 DAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDG 177
            AWG AYG LA + I  EA IY++ A   GGW G R+F +VAK   SA I SF  EP D 
Sbjct: 121 SAWGAAYGQLAEILIGAEASIYDQKAQAPGGWRGAREFIVVAKVEESAEIISFYFEPADK 180

Query: 178 GAVAEYRPGQYLGVWLKPEGFPHQEIRQ-YSLTRKPDGKGYRIAVKREEGGQVSNWLHNH 236
           G +    PGQY+G+ L  +G   +EIR+ YSL+   +   YRI+VKRE GG+ SN LH+ 
Sbjct: 181 GPILAAEPGQYIGMKLILDG---EEIRRNYSLSALANKGQYRISVKRETGGRASNHLHDQ 237

Query: 237 ANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAA 296
            +VG  + L  PAGDF +  A D P+ LIS GVG TP LAML+  A       V++ H A
Sbjct: 238 LHVGASILLFPPAGDFTL-TASDKPLVLISGGVGITPTLAMLE--AALATERPVHFIHCA 294

Query: 297 ENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKL-EGAFSDP 355
            NG VHAF D +  L +  P+      Y   +E D      D  GL+   +L E      
Sbjct: 295 RNGSVHAFRDWIDGLAERHPQLKRFYCY---AEDDGISPAADKVGLLSQEQLGEWLPEQR 351

Query: 356 TMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396
            +  Y  GP GFM    + L  LGV ++   YE FGP   L
Sbjct: 352 DVDAYFLGPKGFMAAIKRHLKALGVPEKQSRYEFFGPAAAL 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: 395
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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