Alignments for a candidate for edd in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Thiothrix lacustris DSM 21227

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_028488534.1 Q394_RS0106325 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000621325.1:WP_028488534.1
          Length = 616

 Score =  194 bits (493), Expect = 9e-54
 Identities = 162/546 (29%), Positives = 251/546 (45%), Gaps = 46/546 (8%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           +AI +S+   +  H   +   + + + +   G V +    T A+ DG+  G  GM  SLP
Sbjct: 37  IAIANSFTQFVPGHVHLKDMGQLVAREIEAAGGVAK-EFNTIAVDDGIAMGHGGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184
           SRE+IA +    ++ +  DA + +  CDKI PG++  A+R  ++PTIFV GGPM SG   
Sbjct: 96  SRELIADAVEYMVNAHCADALVCISNCDKITPGMLNAAMRL-NIPTIFVSGGPMESGKAV 154

Query: 185 ----ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
               +   +  D     A    + E +   E  +  + G+C+   TAN+   L E +GL 
Sbjct: 155 IGGKLVKLDLVDAMVSAANSAESDENVETMERSACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLV------NSIVAL 294
           LPG          R  L  EA + +  L K+   +    E V  RS+       N++   
Sbjct: 215 LPGNGSTLATHSDRKRLFLEAGRIIVGLAKR--YYEQDDETVLPRSIATFEAFENAMCLD 272

Query: 295 HATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKA-DINHFQAAGGM 353
            A GGSTN  LH+ A A+   +  T  D+  LS  VP L  V P+     +     AGG+
Sbjct: 273 IAMGGSTNTILHLLAAAEEGEVNFTLNDIDRLSRKVPQLCKVAPSTPLYHMEDVHRAGGV 332

Query: 354 AFLIRELLEAGLLHEDVNTVAGRGLSR---YTQEPFLDNGKL--VWRDGP---------- 398
             ++ EL  AGLLH +  TV    ++           D+ K    +R GP          
Sbjct: 333 FAILGELDRAGLLHREAGTVHATNMAEALSLWDVRLTDDAKRHEFFRAGPGGVPTQVAFS 392

Query: 399 ----IESLD----ENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVE--APA 448
                ++LD       +R  A A+S EGGL V+ GN+      V    +   I++   PA
Sbjct: 393 QSKRWDTLDTDRANGCIRDKAHAYSTEGGLAVLFGNIALEGCVVKTAGVDDSILKFSGPA 452

Query: 449 VVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALV 507
            +F+ Q        A  +    + ++R++GPR   GM E+   T ++   +  G   AL+
Sbjct: 453 RIFESQDAAVAGILADNIVAGDIVLIRYEGPRGGPGMQEMLYPTSYI-KSKGLGKACALI 511

Query: 508 TDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREP 567
           TDGR SG +  +    HVSPEA  GGA+  V++GD+I +D    T+ +++   E A+R  
Sbjct: 512 TDGRFSGGTSGLSIG-HVSPEAAEGGAIGLVQEGDMIDIDIPNRTINVRISDAELASRRS 570

Query: 568 AKGLLG 573
           A    G
Sbjct: 571 AMDAQG 576


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: 924
Number of extensions: 42
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 608
Length of database: 616
Length adjustment: 37
Effective length of query: 571
Effective length of database: 579
Effective search space:   330609
Effective search space used:   330609
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 Apr 09 2024. 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