GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpO in Sinorhizobium fredii NGR234

Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate WP_012709582.1 NGR_RS26605 glycerol-3-phosphate dehydrogenase

Query= SwissProt::O86963
         (609 letters)



>NCBI__GCF_000018545.1:WP_012709582.1
          Length = 505

 Score =  189 bits (481), Expect = 2e-52
 Identities = 157/553 (28%), Positives = 252/553 (45%), Gaps = 101/553 (18%)

Query: 20  YDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEV 79
           +DV +IGGGI G G+A      G    L EM DFA GTSS STKL+HGG+RYL+ ++  +
Sbjct: 7   FDVFVIGGGINGCGIARDAVGRGYSVALAEMDDFASGTSSGSTKLIHGGLRYLEHYEFRL 66

Query: 80  VADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTGSKYE 139
           V + + ER ++  +APH+  P   +LP +   G     + +++ + LYD +         
Sbjct: 67  VREALMEREVLWAMAPHVIWPMRFVLPYH--KGGPRPAWLIRLGLFLYDHIGG------- 117

Query: 140 NYLLTKEEVLAREPQLQAENLVGGG----------VYLDFRNNDARLVIENIKRAQADGA 189
                  ++L     L       GG           Y D   +DARLV+ N + A   GA
Sbjct: 118 ------RKLLPATSTLDMTRDAAGGPLKRLFTKAFEYSDGWVDDARLVVLNARDAADRGA 171

Query: 190 AMISKAKVVGILHDEQGIING---VEVEDQLTNERFEVHAKVVINTTGPWSD--IVRQLD 244
            ++++ +VV    +     NG   +E ED  T  R  + A++++N TGPW D  +   L 
Sbjct: 172 RIMARTRVVSARRE-----NGRWAIETEDAQTGARETLRARLLVNATGPWVDRVLADTLG 226

Query: 245 KNDELPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTD 303
           KND     +R  +G H+VV R K   P+  +F     DGR++F +P +N  T  GTTD D
Sbjct: 227 KND--VHNVRLVQGSHIVVKR-KFDDPRAYFFQ--NPDGRIMFAIPYQNDFTLIGTTDRD 281

Query: 304 YTGDFAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGK 363
           +TG+ A   ++  ++DYL    +E F    +T DDI  +++ +RPL              
Sbjct: 282 FTGNPADVRISDAEIDYLCKSASEYFSD-PVTTDDIVWTYSAVRPLY------------- 327

Query: 364 GKLSDESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLERSKD 423
               D+   +  E+ ++Y+                  RVE               +  + 
Sbjct: 328 ----DDGASKAQEATRDYVL-----------------RVEG--------------QNGQA 352

Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483
            LL + GGK+T YR +AE A+++I E +   G+ +    + T  + GG+  A   + E+ 
Sbjct: 353 PLLNVFGGKLTTYRRLAESALEKIGEAIGTKGSKW----TATSHLPGGDFAATAYDTEVD 408

Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEE 538
            L  +A+      + A  L  LYG+    +L +      L +   T L     ++ + +E
Sbjct: 409 ML--KARYPFLALSHARRLVRLYGTQAASLLGHAASQADLGKHFGTDLYEVEVDWLIGQE 466

Query: 539 MVLTPVDYLLRRT 551
                 D L RRT
Sbjct: 467 WARRAEDVLWRRT 479


Lambda     K      H
   0.314    0.132    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: 606
Number of extensions: 31
Number of successful extensions: 4
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: 609
Length of database: 505
Length adjustment: 36
Effective length of query: 573
Effective length of database: 469
Effective search space:   268737
Effective search space used:   268737
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 Apr 09 2024. 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