Aligments for a candidate for ydiJ in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for ydiJ in Phaeobacter inhibens BS107

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 GFF620 PGA1_c06340 putative FAD linked oxidase

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__Phaeo:GFF620
          Length = 474

 Score =  265 bits (678), Expect = 2e-75
 Identities = 155/447 (34%), Positives = 237/447 (53%), Gaps = 20/447 (4%)

Query: 90  YNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSV-----PI 144
           Y E+   +Y+GQ+ ++  P+S E+V+ +L   +  ++ VVP GG TGLVGG +     P 
Sbjct: 30  YLEEPRGRYQGQAGVIALPRSTEEVATLLRAAHTARVPVVPYGGGTGLVGGQIMGAAGPA 89

Query: 145 FDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGG 204
              L++SL  +  +R   P   ++  +AG+IL        E   +FPL L A+G+  +GG
Sbjct: 90  --PLVISLERMTALRGVYPQENVIAVEAGMILAEVQRAATEAGRLFPLSLAAEGTARIGG 147

Query: 205 VVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTI 264
            +ATNAGG+ +LRYG+     LGLE V+PNG+I   +  +RKDNTGYDL+ L IG+EGT+
Sbjct: 148 TLATNAGGVNVLRYGNARDLCLGLEAVLPNGEIWQGLSRLRKDNTGYDLRNLLIGAEGTL 207

Query: 265 GIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAK 324
           GIIT  S+   P P     + L+V S      +   AR +L E +SAFE +  +     +
Sbjct: 208 GIITAASLKLSPIPAEQGTAMLTVASPVAAIDLLAMARDQLGETISAFELIHRQGLEFLR 267

Query: 325 SQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQ 384
             L D   P  D   + +LI+            L    E  ++ G+  DGV+AQ E + Q
Sbjct: 268 ETLPDLRLPFADLPDWCVLIDLGLPKGRSPADALAALFETALDAGLCADGVIAQSEAQRQ 327

Query: 385 NLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIG 444
            LW  RE IPE ++  G V  +D+S+P+  +   +     RL+    +GD     +    
Sbjct: 328 ALWSAREHIPEGNRRIGSVSSHDISIPISRIPDFIFEGGKRLA---ALGD-----MRINC 379

Query: 445 YGHVGDGNLHLNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYI 499
           +GH+GDGNLH NV       R   +++   ++  V++      GSVSAEHG+G  K   +
Sbjct: 380 FGHLGDGNLHYNVFPAQGKDRRAYEHLRDDVKRCVHDLTHEYDGSVSAEHGIGRLKVADL 439

Query: 500 GYSKSPEEVKMMKDLKVHYDPNGILNP 526
                P ++  M+ +K   DP+GI+NP
Sbjct: 440 RRYGDPVKLAAMQAIKQALDPHGIMNP 466


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: 585
Number of extensions: 22
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: 530
Length of database: 474
Length adjustment: 34
Effective length of query: 496
Effective length of database: 440
Effective search space:   218240
Effective search space used:   218240
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources