Aligments for a candidate for edd in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for edd in Desulfovibrio vulgaris Miyazaki F

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)

Query= curated2:P31961
         (608 letters)



>lcl|FitnessBrowser__Miya:8501301 DvMF_2034 dihydroxy-acid
           dehydratase (RefSeq)
          Length = 555

 Score =  245 bits (626), Expect = 3e-69
 Identities = 185/550 (33%), Positives = 269/550 (48%), Gaps = 57/550 (10%)

Query: 33  KGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPFERFPGLIK 92
           K PHR      +L H +    E  ++ L       V +V+A N+++  H         +K
Sbjct: 12  KAPHR------SLLHALGLTREEIERPL-------VGVVNAANEVVPGHVHLHTIAEAVK 58

Query: 93  QALHEIGSVGQFAGGVP------AMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNMFD 146
             +         AGG P      A+CDG+     GM  SL SR++IA S  I  + + FD
Sbjct: 59  AGVRA-------AGGTPMEFPAIAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFD 111

Query: 147 AALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEKAAVRQLF-AEGKATRE 205
           A + +  CDK VPG+L+  LR   +P++ V  GPM  G +   +  +  +F A G+  R 
Sbjct: 112 ALVFIPNCDKSVPGMLMAMLRMD-IPSIMVSGGPMLAGGTLAGRTDLISVFEAVGRVQRG 170

Query: 206 ELLASE---MASYHAPG--TCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELTRE 260
           ++  +E   M     PG  +C    TANT   + E MGL LPG   +   T  R  L + 
Sbjct: 171 DMTMAELDEMTETACPGCGSCAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKH 230

Query: 261 AARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQLTW 320
           A  +   L  +N   +    IV  +A+ N+V   +A GGSTN  LHL A+   AG+ LT 
Sbjct: 231 AGMKVMELLEKN---ITPRSIVTPRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTL 287

Query: 321 QDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPGLRR 380
               E+S   P L ++ P G   I    AAGG+  ++ +L   GL+   V TV G  L  
Sbjct: 288 DIFDEVSRKTPNLCKLSPAGHHHIQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAE 347

Query: 381 YTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKVSAVA 438
              E               R L+  ++R  D P+SA+GG+ +++G+L     V+K SAVA
Sbjct: 348 NLAEL------------NARVLNPDVIRSADAPYSAQGGIAILKGSLAPQGAVVKQSAVA 395

Query: 439 PEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVL 497
           PE  V EA  R+F  +    AA   G++ +    ++R++GPR   GM E+  L+P   + 
Sbjct: 396 PEMMVREAVARVFDSEGEAHAAIMGGKINKGDAIIIRYEGPRGGPGMREM--LSPTAAIA 453

Query: 498 -QDRGFKVALVTDGRMSGASGKVPAAI-HVSPEAIAGGPLARLRDGDRVRVDGVNGELRV 555
               G  VAL+TDGR SG  G   AAI HVSPEA  GG +  +R+GD + +D     L +
Sbjct: 454 GMGLGADVALITDGRFSG--GTRGAAIGHVSPEAADGGNIGLVREGDHILIDIPARRLDL 511

Query: 556 LVDDAEWQAR 565
           LVD+AE  AR
Sbjct: 512 LVDEAELAAR 521


Lambda     K      H
   0.319    0.135    0.397 

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: 927
Number of extensions: 69
Number of successful extensions: 7
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: 555
Length adjustment: 36
Effective length of query: 572
Effective length of database: 519
Effective search space:   296868
Effective search space used:   296868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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:

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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