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_015887820.1 NGR_RS08385 glycerol-3-phosphate dehydrogenase

Query= SwissProt::O86963
         (609 letters)



>NCBI__GCF_000018545.1:WP_015887820.1
          Length = 503

 Score =  171 bits (432), Expect = 9e-47
 Identities = 162/587 (27%), Positives = 253/587 (43%), Gaps = 110/587 (18%)

Query: 19  TYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVE 78
           TYD+ +IGGGI GAG+A   A  G+  +L E  D A+GTSSRS KLVHGG+RYL+ ++  
Sbjct: 6   TYDLFVIGGGINGAGIARDAAGRGLSVLLCEKDDLAQGTSSRSGKLVHGGLRYLEYYEFR 65

Query: 79  VVADTVRERAIVQQIAPHIPKPDPMLLP--IYDEPGATFSLFSVKVAMDLYDRLA---NV 133
           +V + + ER ++ Q APHI  P   +LP    D P      + V++ + LYD L     +
Sbjct: 66  LVREALIEREVLLQSAPHIIWPMRFVLPHNPVDRPA-----WLVRLGLLLYDHLGGRKRL 120

Query: 134 TGSKYENYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMIS 193
            G++  +     E    +    +A        Y D   +DARLV+ N   A+  GA +++
Sbjct: 121 PGTRTLDLRTAPEGAPIKPAYRRAFE------YSDCWVDDARLVVLNALDAEQRGARILT 174

Query: 194 KAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPWSDIVRQLDKNDELPPQM 253
           +     I    +G +  VE+ D +T  + EV A+ V+NT GPW + V            +
Sbjct: 175 RTACSNI--RRRGDLWHVEMTDAVTGAKAEVRARCVVNTAGPWVNDVIGRVAGLNSRRSV 232

Query: 254 RPTKGVHLVV-----DREKLKVPQPTYFDTGKNDGRMVFVVPRENK-TYFGTTDTDYTGD 307
           R  KG H+VV      R+   V  P        D R++F+ P +N     GTTD  Y G 
Sbjct: 233 RLVKGSHIVVPKFWEGRQAYLVQNP--------DKRVIFINPYQNDLALIGTTDIPYDGR 284

Query: 308 FAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLITNNGGSDYNGGGKGKLS 367
                   +++ YL+  VN  F   Q++  DI  S++G+RPL  +N  +           
Sbjct: 285 PEDVAADADEIAYLVKSVNRYFKQ-QLSDADIIQSFSGVRPLYDDNAEN----------- 332

Query: 368 DESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPSQVSRGSSLE----RSKD 423
                                                    PS V+R    E      + 
Sbjct: 333 -----------------------------------------PSAVTRDYIFELDAANGEA 351

Query: 424 GLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSGGELDAANVEEELA 483
            LL++ GGKIT +R ++E A++R+     + G ++    +    + GG++  A+ +  L 
Sbjct: 352 PLLSVFGGKITTFRKLSEHALERLKPFFPKIGPAW----TARAHLPGGDMADADFDRFLG 407

Query: 484 KLADQAQTAGFNEAAATYLAHLYGSNLPQVLNYKTKFEGLDEKESTAL-----NYSLHEE 538
           +L  +++        A + A LYG+    ++      E L    S         + +  E
Sbjct: 408 EL--RSRYRWLPADLAKHYARLYGTRTHALIGDANSLEELGTAFSRLFREREARFLIETE 465

Query: 539 MVLTPVDYLLRRTNHILFMRDTLDDVKAGVVAAMTDFFGWSEEEKAA 585
              T  D L RRT H L M +          A    F GW E ++AA
Sbjct: 466 WARTVEDLLQRRTKHGLHMSE----------AEKRSFSGWLEGQQAA 502


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: 568
Number of extensions: 25
Number of successful extensions: 3
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: 609
Length of database: 503
Length adjustment: 36
Effective length of query: 573
Effective length of database: 467
Effective search space:   267591
Effective search space used:   267591
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