GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Marivita geojedonensis DPG-138

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_085634854.1 MGEO_RS01140 dihydroxy-acid dehydratase

Query= SwissProt::P21909
         (607 letters)



>NCBI__GCF_002115805.1:WP_085634854.1
          Length = 587

 Score =  184 bits (468), Expect = 7e-51
 Identities = 151/515 (29%), Positives = 236/515 (45%), Gaps = 43/515 (8%)

Query: 70  IGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQPGMEESLF 129
           +GV T +N+    +    R  + +K+  ++   T +    +  + DG+  G  GM  SL 
Sbjct: 44  VGVATCWNEAAPCNIALNRQAQAVKMGVKQAFGTPREFTTI-TVTDGIAMGHEGMRSSLA 102

Query: 130 SRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSG-------P 182
           SR+ IA    +++    ++    L  CDK +PG++M  +R  ++P++ +  G       P
Sbjct: 103 SREAIADTVELTMRGHCYDAVVGLAGCDKSLPGMMMAMVRL-NVPSVFIYGGSILPGKAP 161

Query: 183 MTTGIPNKEKIRIRQLYAQ------GKIGQKELLD-----MEAACYHAEGTCTFYGTANT 231
               IP  E  R R L  Q      G+    EL D     +E     + G C    TANT
Sbjct: 162 QVAEIP--EDFRTRDLTVQDMFEAVGRHQNNELSDKALDMLERVACPSAGACGGQFTANT 219

Query: 232 NQMVMEVLGLHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVN 291
              V E +GL +  S+ +      R A   A+   V +L  +    R    I+  +++ N
Sbjct: 220 MACVSEAIGLALFNSSGMPAPYESRDAYGEASGRAVMDLIEQNIKARD---IVTREALEN 276

Query: 292 AIVGLLATGGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQN 351
           A   +  TGGSTN  +H+PAIA  AG+     D  D+ +  P    + P G     +  +
Sbjct: 277 AARVVACTGGSTNAGLHLPAIAHEAGIEFYLEDVCDIFKDTPYFVDLKPGGTYVAKDLYD 336

Query: 352 AGGMAYVIKELLSANLLNRDVTTIAKGGIEEYAKAPALNDAGELVWKPAGEPGDDTILRP 411
           AGG+  V+KEL  A L++ D  T         A    + +  + + + A    D  ++  
Sbjct: 337 AGGIPVVMKELRKAGLIHEDCVT---------ASTRTIGEELDRIEREA----DGKVIYS 383

Query: 412 VSNPFAKDGGLRLLEGNLG--RAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELN 469
           +  P  K GG+  L+GNL    A+ K + +  +      P RVF  ++D   A KA +  
Sbjct: 384 IETPITKTGGVVGLKGNLAPEGAIVKVAGIKAEDQIFTGPARVFECEEDAFAAVKARDYK 443

Query: 470 KDVIVVVRFQGPRAN-GMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVS 528
           +  ++V+R +GP    GM E+   T AL   Q  G KVAL+TDGR SGAT    V  HV 
Sbjct: 444 EGEVIVIRNEGPAGGPGMREMLATTAALSG-QGMGKKVALITDGRFSGATRGFCVG-HVG 501

Query: 529 PEALGGGAIGKLRDGDIVRISVEEGKLEALVPADE 563
           PEA  GG I  L++GD++ I    G L   +  +E
Sbjct: 502 PEAALGGPIALLKNGDMITIDAVNGSLSVDLSDEE 536


Lambda     K      H
   0.318    0.136    0.403 

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: 957
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 607
Length of database: 587
Length adjustment: 37
Effective length of query: 570
Effective length of database: 550
Effective search space:   313500
Effective search space used:   313500
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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:

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