GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Skermanella stibiiresistens SB22

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_037450742.1 N825_RS10470 dihydroxy-acid dehydratase

Query= SwissProt::P21909
         (607 letters)



>NCBI__GCF_000576635.1:WP_037450742.1
          Length = 566

 Score =  204 bits (519), Expect = 8e-57
 Identities = 166/524 (31%), Positives = 259/524 (49%), Gaps = 39/524 (7%)

Query: 89  YPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQPGMEE-SLFSRDVIALATSVSLSHGMF 147
           +PE ++   R V     +AG +P     ++ G+      SL  R+++A+ T   +     
Sbjct: 63  FPELLEAVKRGV----LMAGALPLEFPTISLGEVFTSPTSLKFRNLMAMDTEEMIRAQPM 118

Query: 148 EGAALLGICDKIVPGLLMGALRFGHLPTILVPSGPMTTGIPNKEKI-------RIRQLYA 200
           +   L+G CDK VP  LMGA+    +P I + +GPM+TG    E++       R    + 
Sbjct: 119 DSVVLMGGCDKTVPAQLMGAIS-ADIPAIQLVAGPMSTGRHRGERLGACTDCRRFWAKFR 177

Query: 201 QGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLHMPGSAFVTPGTPLRQALT 260
            G++  +E+  +E       GTC   GTA+T   + E LG+ +PG A +      R  + 
Sbjct: 178 AGEVDAEEIETVEGRLATTAGTCAVMGTASTMACLTETLGMSLPGCAAIPAVHSDRLRMA 237

Query: 261 RAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGSTNHTMHIPAIARAAGVIV 320
            A   R  EL   G D  P  +II   +I NA+  LLA  GSTN  +H+ AIAR AG+ V
Sbjct: 238 EATGKRAVEL--IGSDLTP-SRIITPAAIRNALRMLLALSGSTNALLHLTAIARRAGIQV 294

Query: 321 NWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKELLSANLLNRDVTTIAKGGI 380
           + ++F+ LS+  P++  + P GP  + +   AGG+  ++KEL    L+ RD  T+     
Sbjct: 295 DLHEFNRLSDETPVLVNLKPVGPHYMEDLFAAGGVPAILKEL--GGLMERDALTVTG--- 349

Query: 381 EEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGGLRLLEGNLG--RAMYKASA 438
                       GEL+  P  +P D T+++  + P    GGL  + G+L    A+ K +A
Sbjct: 350 ---------QTLGELIDAPMIDPVDRTVIKSRAEPVDPQGGLVAVFGSLAPRGAVVKRAA 400

Query: 439 VDPKFWTIEAPVRVFSDQDDVQKAFKAGEL--NKDVIVVVRFQGPRA-NGMPELHKLTPA 495
            DP+    E    VF    D+ +     +L  + D I++++  GP++ +GMPE   L P 
Sbjct: 401 ADPRLMEHEGRAVVFGSLQDLAERIDDPDLDVSADDILILQNAGPKSDSGMPEAGYL-PI 459

Query: 496 LGVLQDNGYKVAL-VTDGRMSGATGKVPVALHVSPEALGGGAIGKLRDGDIVRISVEEGK 554
              L   G K  L ++D RMSG T    + LHV+PEA  GG +G  R GD VRISV E +
Sbjct: 460 PRKLAKAGVKDMLRISDARMSG-TAYGAIVLHVAPEAAVGGPLGLARTGDRVRISVSEHR 518

Query: 555 LEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598
           L+ LV  +E + R  A+  A      R    ++  +  +A++GA
Sbjct: 519 LDLLVSPEELDRR-RADLMAPDVKRRRGYDRLYNDHVLQADEGA 561


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: 812
Number of extensions: 49
Number of successful extensions: 6
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: 607
Length of database: 566
Length adjustment: 37
Effective length of query: 570
Effective length of database: 529
Effective search space:   301530
Effective search space used:   301530
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