GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Skermanella stibiiresistens SB22

Align phosphogluconate dehydratase (characterized)
to candidate WP_084164617.1 N825_RS10340 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_000576635.1:WP_084164617.1
          Length = 577

 Score =  200 bits (509), Expect = 1e-55
 Identities = 162/486 (33%), Positives = 235/486 (48%), Gaps = 43/486 (8%)

Query: 105 AGGVPAMCDGVTQGQDGME-LSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTM 163
           AGG P      + G+  M   ++L R + +M     +  +  DG + L  CDK  P L M
Sbjct: 75  AGGFPLEFPVSSLGEVTMRPTAMLFRNLASMDVEEAIRAHPLDGVVLLMGCDKTTPALLM 134

Query: 164 AALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYAEGKVDRMALLESEAASYH 216
            A S   LPA+ V  GP   G+   E +        + +    G++      E+EA    
Sbjct: 135 GAAS-ADLPAIGVSGGPQLRGVYRGEIIGSGTNIISMSEQLRAGEITLEEFHEAEAGMNR 193

Query: 217 APGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWM 276
           + G+C   GTA+T   +VE +G+ LPG++ +      R+ L   + R++  +     + +
Sbjct: 194 SAGSCMTMGTASTMASMVEALGLGLPGNAAIPAADARRNLLARMSGRRIVELA---RQDV 250

Query: 277 PIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARL 336
               ++  +   N I  L A GGSTN  +HL+A+A   GI +  DDF  L   +  +  L
Sbjct: 251 KPSDILTRQAFENAIRTLAAIGGSTNAVVHLLALAGRVGIDLTLDDFDRLGRDIHCLVDL 310

Query: 337 YPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELD-WR 395
            P+G   +  F  AGG+P ++R L + GLLH+D  TV G  L       W N GE   W 
Sbjct: 311 MPSGRFLMEDFYYAGGLPAVLRALGERGLLHKDAMTVNGQTL-------WENVGEAPCW- 362

Query: 396 EGAEKSLDSNVIASFEQPFSHHGGTKVLSGNLG--RAVMKTSAVPVENQVIEAPAVVFES 453
                  +  VI  FE PF    G  +L+GNL    AV+K SA   E       AVVFES
Sbjct: 363 -------NREVITPFEAPFKPESGMAILTGNLAPDGAVIKPSAASPELMRHTGRAVVFES 415

Query: 454 QHDVMPAFEAGLLDRD--CVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDG 510
             ++  A +   LD D  CV+V+++ GPK   GM E+  +  P  +L      +  ++D 
Sbjct: 416 VEEMHHAVDDEDLDIDASCVMVLKNCGPKGYPGMAEVGNMPLPAKLLRQGVRDMIRISDA 475

Query: 511 RLSG-ASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR---- 565
           R+SG A G V   +HV PEA  GG LA VR+GD+I ++     L L VD+AELAAR    
Sbjct: 476 RMSGTAYGTV--VLHVAPEATAGGPLALVRNGDMITLDVPARSLHLHVDDAELAARRAAW 533

Query: 566 ---EPH 568
              EPH
Sbjct: 534 TPPEPH 539


Lambda     K      H
   0.318    0.134    0.392 

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: 850
Number of extensions: 50
Number of successful extensions: 8
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: 603
Length of database: 577
Length adjustment: 37
Effective length of query: 566
Effective length of database: 540
Effective search space:   305640
Effective search space used:   305640
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