GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8501301
          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:

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