Alignments for a candidate for edd in Alkalitalea saponilacus SC/BZ-SP2

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Alkalitalea saponilacus SC/BZ-SP2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_079558836.1 CDL62_RS07395 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_002201795.1:WP_079558836.1
          Length = 613

 Score =  233 bits (595), Expect = 1e-65
 Identities = 173/554 (31%), Positives = 271/554 (48%), Gaps = 44/554 (7%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAG--GTPAMCDGVTQGEAGMELS 125
           +A+V+S+   +  H       + +K+ + + G    FA    T A+ DG+  G  GM  S
Sbjct: 38  IAVVNSFTQFVPGHAHLHQIGQDVKRMIEKQGC---FAAEFNTIAIDDGIAMGHDGMLYS 94

Query: 126 LPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG- 184
           LPSR++IA S    ++ +  DA + +  CDKI PG++M A+R  ++P IFV GGPM +G 
Sbjct: 95  LPSRDLIADSVEYMVNAHQADAMVCISNCDKITPGMLMAAMRI-NIPVIFVSGGPMEAGK 153

Query: 185 ISNK--EKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242
           + +K  +  D     A+   + EELL  E  +  + G+C+   TAN+   L E +GL LP
Sbjct: 154 VGDKALDLVDSMVMAADDSVSDEELLAVEQNACPTCGSCSGMFTANSMNCLNEALGLALP 213

Query: 243 GASFVNPYTPLRDALTHEAAQQVTRLTK---QSGNFTPIGEIVDERSLVNSIVALH-ATG 298
           G   +      R  L  +AA Q+ RL     Q G+ + +   +  ++  N+ + L  A G
Sbjct: 214 GNGTIVATHVNRKKLFEKAANQIVRLAYKYYQDGDESVLPRNIATKAAFNNSMTLDVAMG 273

Query: 299 GSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIR 358
           GSTN  LH+ AIA  AG+  T QD+  +S   P L  V PN    I     AGG+  ++ 
Sbjct: 274 GSTNTVLHLLAIAHEAGVDFTMQDIDRISRKTPVLCKVAPNSDYHIEDVNRAGGIMGILA 333

Query: 359 ELLEAGLLHEDVNTVAGRGLSR------YTQEPFLDNGKLVWRDGP-------------- 398
           EL   GLL   V  V    LS          +  +   K +++  P              
Sbjct: 334 ELNRGGLLDATVGRVDYSSLSEALDAYDMASKSAIAEAKEIYQSAPGGFVNLVMGSQKAI 393

Query: 399 IESLD----ENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQI--VEAPAVVFQ 452
              LD    +  +R ++ A+S +GGL V+ GN+      V    +   I   E  A V++
Sbjct: 394 YGELDLDREKGCIRNISHAYSQDGGLAVLFGNIAENGCIVKTAGVDESIFHFEGTARVYE 453

Query: 453 DQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGR 511
            Q D  D   +GE++   V +++++GP+   GM E+   T +L   ++ G K AL+TDGR
Sbjct: 454 SQDDACDGILSGEVKAGDVVIIKYEGPKGGPGMQEMLYPTSYL-KSRNLGAKCALLTDGR 512

Query: 512 MSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAKGL 571
            SG +  +    H SPEA  GGA+A +++GD + +D  + ++ + V  DE   R  A+  
Sbjct: 513 FSGGTSGLSIG-HASPEAAAGGAIALIKNGDKVIIDIPQRSINIDVTEDELNQRRAAEDA 571

Query: 572 LGNNV--GSGRELF 583
            G+N    S RE F
Sbjct: 572 KGDNAWKPSARERF 585


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: 861
Number of extensions: 48
Number of successful extensions: 8
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: 613
Length adjustment: 37
Effective length of query: 571
Effective length of database: 576
Effective search space:   328896
Effective search space used:   328896
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources