GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpO in Pedobacter sp. GW460-11-11-14-LB5

Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate CA265_RS07875 CA265_RS07875 FAD-dependent oxidoreductase

Query= curated2:P35596
         (608 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS07875 CA265_RS07875
           FAD-dependent oxidoreductase
          Length = 530

 Score =  221 bits (563), Expect = 6e-62
 Identities = 171/582 (29%), Positives = 269/582 (46%), Gaps = 101/582 (17%)

Query: 21  DLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEVV 80
           D +IIGGG TG G AL AA+ G +T L+E  DFA+GTSSRSTKLVHGG+RYL Q D+ +V
Sbjct: 16  DFIIIGGGATGLGTALDAASRGFKTLLVEQSDFAKGTSSRSTKLVHGGVRYLAQGDIGLV 75

Query: 81  SDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAAN 140
              + ER ++QQ A H+   +  L+P YD     FS+ +    + LYD LAG   +   +
Sbjct: 76  KHALKERGLLQQNAKHLVNKEEFLIPCYD----WFSVVKYLTGLTLYDWLAG-KYSFGKS 130

Query: 141 KVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAEGF 200
           K  SK + L   P +K++GL G   Y D + +DARL I   + A ++GA + N+ K  G 
Sbjct: 131 KFFSKKETLTMMPGIKEKGLKGSIRYYDGKFDDARLAINIAQTAIENGASLLNYTKVTG- 189

Query: 201 LFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRPTKGVH 260
           L     ++TG+   D +T    +   ++VIN TG + D +  ++N  ++   +RP++GVH
Sbjct: 190 LLKSGDQVTGIETEDTITGLTAKYNGKIVINATGVFVDDILQMNNPNSK-KMVRPSQGVH 248

Query: 261 LVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKVTQEDVDY 320
           +V+D S +  S+         DGR++F +P  +    GTTDT        P+  +++VD+
Sbjct: 249 VVLDKSFLN-SESALMIPKTSDGRVLFAVPWHDHLLVGTTDTPLDEHSLEPRALKKEVDF 307

Query: 321 LLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESFDNLIATVES 380
           ++    + F    +   DI S ++GLRPL     A+  NG  N T               
Sbjct: 308 IMSTAASYFNRKPLE-KDILSVFSGLRPL-----AAPTNGDGNST--------------- 346

Query: 381 YLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTLAGGKITDYRKMA 440
                                          +SR   L     GL+T+ GGK T YR+MA
Sbjct: 347 -----------------------------KEISRDHKLIVSAKGLITITGGKWTTYRRMA 377

Query: 441 EGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQLGVSRGLDSKEA 500
           E  ++  +                      GG      ++S+      L +     +   
Sbjct: 378 EETVDLAI--------------------THGG------LESKACVTQNLSIHGSSTTTGD 411

Query: 501 HYLANLYGSNAPKVFALAHSLEQAPGLSLA-------DTLSLHYAMRNELTLSPVDFLLR 553
           H+LA +YG++  K+ AL   + Q PGL              + ++ RNE+  +  D L R
Sbjct: 412 HHLA-IYGTDRSKIEAL---IVQDPGLGNKLNPAFPFTEAEVIWSARNEMAETVEDILSR 467

Query: 554 RTNHMLFM-----RDSLDSIVEPILDEMGRFYDWTEEEKATY 590
           R   +LF+     +D    +   +  E+    +W   +  T+
Sbjct: 468 RL-RILFINAQAAKDMAPRVASLLAQELSADKNWETNQIETF 508


Lambda     K      H
   0.314    0.133    0.368 

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: 730
Number of extensions: 39
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 608
Length of database: 530
Length adjustment: 36
Effective length of query: 572
Effective length of database: 494
Effective search space:   282568
Effective search space used:   282568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 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