GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Skermanella stibiiresistens SB22

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_037456692.1 N825_RS21145 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000576635.1:WP_037456692.1
          Length = 571

 Score =  186 bits (472), Expect = 2e-51
 Identities = 151/513 (29%), Positives = 247/513 (48%), Gaps = 45/513 (8%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME-LSL 126
           + I ++++++   +  +    E IKK + E       AGG P     ++ GE+ M   ++
Sbjct: 41  IGICNTFSELTPCNAHFRQLIEHIKKGVLE-------AGGVPFEFPVLSCGESNMRPTAM 93

Query: 127 PSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS 186
             R + ++    ++  N  D  +++  CDK  P L+MGA     LP+I + GGPM +G  
Sbjct: 94  LFRNLASMDVEESIRANPIDGVVLMAGCDKTTPSLLMGAASCD-LPSIVISGGPMLNGKF 152

Query: 187 NKEK----ADVRQRYAE----GKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMG 238
             +      DV  R++E    G  +R + L +E     SPG C   GTA+T   + E +G
Sbjct: 153 RGQDIGSGTDV-WRFSEEVRAGVMSRADFLAAENAMSRSPGHCMTMGTASTMASMAEALG 211

Query: 239 LHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATG 298
           + LPG +        R  L     +++  +  +      +  I+   +  N++    A G
Sbjct: 212 VALPGNAAYPAVDAHRARLARMTGRRIVGMVDED---LRLSHILTRDAFANAVKVNGAIG 268

Query: 299 GSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIR 358
           GSTN  +H+ AIA   G + T  D     + VPT+ ++ P+G+  +  F  AGG+  L++
Sbjct: 269 GSTNAVVHLLAIAGRVGTEFTLDDWDRWGQGVPTILNLMPSGRYLMEDFCYAGGLPALMK 328

Query: 359 ELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEG 418
           E+  AGLL  D  TV+GR +    +                E+ + +++RP+A+A   EG
Sbjct: 329 EI--AGLLKLDAPTVSGRTVGENIE--------------AAENFNPDVIRPMAQALVAEG 372

Query: 419 GLRVMEGNLG--RGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKD--FVAVM 474
           G+ V++GNL     ++K SA +      E  AVVF   +D        +L+ D   V V+
Sbjct: 373 GIAVLKGNLAPDGAIIKPSAASPHLMRHEGRAVVFDTIEDYKRKVDDPDLDIDETCVMVL 432

Query: 475 RFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEAQVG 532
           R  GP+   GM E+  M     +L+     +  ++D RMSG A G +   +H +PEA +G
Sbjct: 433 RNCGPKGYPGMAEVGNMALPRKLLEKGVRDMVRISDARMSGTAFGTV--ILHTAPEAAIG 490

Query: 533 GALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565
           G LA V DGDII VD    T+ L+V  +E   R
Sbjct: 491 GTLALVADGDIIAVDVAARTIHLRVSDEELERR 523


Lambda     K      H
   0.318    0.134    0.386 

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: 831
Number of extensions: 37
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: 608
Length of database: 571
Length adjustment: 37
Effective length of query: 571
Effective length of database: 534
Effective search space:   304914
Effective search space used:   304914
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.

Links

Downloads

Related tools

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