GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpD in Sinorhizobium fredii NGR234

Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate WP_015887820.1 NGR_RS08385 glycerol-3-phosphate dehydrogenase

Query= uniprot:Q92LM5
         (503 letters)



>NCBI__GCF_000018545.1:WP_015887820.1
          Length = 503

 Score =  525 bits (1352), Expect = e-153
 Identities = 271/504 (53%), Positives = 339/504 (67%), Gaps = 3/504 (0%)

Query: 1   MSEQTIFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLE 60
           MS+   +D+FVIGGGING GIARDAAGRG SV L E  D A GTSS S KL+HGGLRYLE
Sbjct: 1   MSDTRTYDLFVIGGGINGAGIARDAAGRGLSVLLCEKDDLAQGTSSRSGKLVHGGLRYLE 60

Query: 61  HYEFRLVREALMEREVLWAMAPHVIWPMRFVLPFHKGGPRPAWLIRLGLFLYDHIGGRKL 120
           +YEFRLVREAL+EREVL   APH+IWPMRFVLP H    RPAWL+RLGL LYDH+GGRK 
Sbjct: 61  YYEFRLVREALIEREVLLQSAPHIIWPMRFVLP-HNPVDRPAWLVRLGLLLYDHLGGRKR 119

Query: 121 LPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVVLNARDAADRGARIMARTRVV 180
           LP T+TLD+   P GAP+K  + +AFEYSD WVDDARLVVLNA DA  RGARI+ RT   
Sbjct: 120 LPGTRTLDLRTAPEGAPIKPAYRRAFEYSDCWVDDARLVVLNALDAEQRGARILTRTACS 179

Query: 181 SARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRVLSEAVGNNDVRNVRLVQGSH 240
           + RR G  W +E+    TGA+  +RAR +VN AGPWV+ V+    G N  R+VRLV+GSH
Sbjct: 180 NIRRRGDLWHVEMTDAVTGAKAEVRARCVVNTAGPWVNDVIGRVAGLNSRRSVRLVKGSH 239

Query: 241 IVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDRDFTGNPADVRISDAEIDYLC 300
           IVV K ++  +AY  QNPD R++F  PYQ++  LIGTTD  + G P DV     EI YL 
Sbjct: 240 IVVPKFWEGRQAYLVQNPDKRVIFINPYQNDLALIGTTDIPYDGRPEDVAADADEIAYLV 299

Query: 301 RAASEYFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRDYVLRVE--NGDAPLLNVFGG 358
           ++ + YF   +   DI+ ++S VRPL+DD A      TRDY+  ++  NG+APLL+VFGG
Sbjct: 300 KSVNRYFKQQLSDADIIQSFSGVRPLYDDNAENPSAVTRDYIFELDAANGEAPLLSVFGG 359

Query: 359 KLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAGYDDEVAKLRTRYPFLTAS 418
           K+TT+R+L+E ALE++     + G  WTA +HLPGGD   A +D  + +LR+RY +L A 
Sbjct: 360 KITTFRKLSEHALERLKPFFPKIGPAWTARAHLPGGDMADADFDRFLGELRSRYRWLPAD 419

Query: 419 HARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWLIVQEWALRAEDVLWRRTK 478
            A+   RLYGTR   L+G+A S  +LG  F       E  +LI  EWA   ED+L RRTK
Sbjct: 420 LAKHYARLYGTRTHALIGDANSLEELGTAFSRLFREREARFLIETEWARTVEDLLQRRTK 479

Query: 479 LGLKFSRAQTAELEEYMRGAVNAA 502
            GL  S A+      ++ G   AA
Sbjct: 480 HGLHMSEAEKRSFSGWLEGQQAAA 503


Lambda     K      H
   0.321    0.137    0.417 

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: 747
Number of extensions: 33
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: 503
Length of database: 503
Length adjustment: 34
Effective length of query: 469
Effective length of database: 469
Effective search space:   219961
Effective search space used:   219961
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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