GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Pseudomonas fluorescens FW300-N2E3

Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate AO353_08505 AO353_08505 FAD-linked oxidase

Query= SwissProt::P46681
         (530 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_08505 AO353_08505 FAD-linked
           oxidase
          Length = 464

 Score =  292 bits (747), Expect = 2e-83
 Identities = 166/466 (35%), Positives = 262/466 (56%), Gaps = 23/466 (4%)

Query: 70  KSILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVV 129
           K+++   ++L  ++++ L+ Y +DW + +      ++ PK+ E+V  I+ + N+ KIA+V
Sbjct: 11  KTLVEPGKVL--TDADSLNAYGKDWTKHFAPAPTAIVFPKTTEQVQAIVRWANEHKIALV 68

Query: 130 PQGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYM 189
           P GG TGL   +V    E+++S   +N+I D +       C  GV+ E   N   E    
Sbjct: 69  PSGGRTGLSAAAVAANGEVVVSFDYMNQILDVNLTDRTAVCQPGVVTEQLQNRAEEHGLY 128

Query: 190 FPLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNT 249
           +P+D  + GS  +GG + TNAGG++++RYG     V G++VV   G ++     + K+ T
Sbjct: 129 YPVDFASAGSSQIGGNIGTNAGGIKVIRYGMTRNWVAGMKVVTGKGDLLELNRDLIKNAT 188

Query: 250 GYDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEIL 309
           GYDL+QLFIG+EGT+G +   ++     PK      L    F+ +  V    + +L   L
Sbjct: 189 GYDLRQLFIGAEGTLGFVVEATMRLDRAPKNLTAMVLGTADFDSIMPVLHAFQSKLD--L 246

Query: 310 SAFEFMDAK--SQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVME 367
           +AFEF   K  ++VLA+    D   P E + PFY L+E   + ++  +  LETF E+ +E
Sbjct: 247 TAFEFFSDKALAKVLARG---DVPAPFESDCPFYALLEFEATTEEVANHALETF-EHCVE 302

Query: 368 EGIVTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLS 427
           EG V DGV++Q E++LQNLWK RE I E + ++   YK D+S+        V    A L 
Sbjct: 303 EGWVLDGVMSQSESQLQNLWKLREYISE-TISHWTPYKNDISV-------TVSKVPAFLK 354

Query: 428 EAELVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKH 482
           E + +     P    + +GH+GDGNLHLN+   E     E      T+  +V+E V   +
Sbjct: 355 EVDAIVGEHYPDFEIVWFGHIGDGNLHLNILKPENLSKDEFFAKCATVNKWVFETVEKYN 414

Query: 483 GSVSAEHGLGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528
           GS+SAEHG+G  K++Y+ YS+SP E++ MK +K  +DPNGI+NP K
Sbjct: 415 GSISAEHGVGMTKRDYLTYSRSPVEIEYMKAVKAVFDPNGIMNPGK 460


Lambda     K      H
   0.316    0.135    0.385 

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: 544
Number of extensions: 22
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: 530
Length of database: 464
Length adjustment: 34
Effective length of query: 496
Effective length of database: 430
Effective search space:   213280
Effective search space used:   213280
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 (21.6 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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