GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Methanobacterium veterum MK4

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_048082021.1 EJ01_RS03755 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_000745485.1:WP_048082021.1
          Length = 551

 Score =  248 bits (634), Expect = 4e-70
 Identities = 174/588 (29%), Positives = 293/588 (49%), Gaps = 58/588 (9%)

Query: 25  EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84
           + ++    K PHR  L          ACG +D++    MN+  + + +++  ++  H   
Sbjct: 4   DAIKKGLQKAPHRSLL---------RACGVTDEE----MNKPFIGVANSFTSIVPGHIHL 50

Query: 85  ERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNM 144
                 +KQ + E G V  F     A+CDG++ G  GM+ SLASR++IA +       + 
Sbjct: 51  NEVADAVKQGISEAGGV-PFEFNTMAICDGISMGHEGMKYSLASREIIADTVESMAQAHQ 109

Query: 145 FDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG---------ISNKEKAAVRQ 195
            DA + +  CDK+VPG+L+ + R   +P++ V  GPM  G         IS  E      
Sbjct: 110 MDALVLIPTCDKVVPGMLMAAARL-DIPSIVVTGGPMKPGEFKGKPVDFISVSEGVGA-- 166

Query: 196 LFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRD 255
             + GK T EEL   E  +    G+C    TANT   + EV+G+ LP  +  +     + 
Sbjct: 167 -VSSGKMTEEELDELERCACPGAGSCAGLFTANTMACVTEVLGMSLPYCATAHAVDAKKR 225

Query: 256 ELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIA---Q 312
           ++ R++  +   L  +N   +  ++I+ ++A  N++ A LA GGS+N TLH+ AIA   +
Sbjct: 226 QIARQSGAKIIELLDKN---ITPSKIMTQEAFENAIAADLALGGSSNTTLHIPAIASELE 282

Query: 313 AAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQT 372
             G+ +T     E S  +P + ++ P+G   +     AGG+  +++ + D   +++D  T
Sbjct: 283 DKGVNITINSFDEFSKKIPHITKLRPSGVHSLLDLDNAGGIPAVLKVIED--KINQDTLT 340

Query: 373 VAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG-RG- 430
             G  L    ++               +  DE ++RPL  P+S EGGL +++GNL  RG 
Sbjct: 341 CTGKTLGENIKD--------------AKVADEEVIRPLSNPYSKEGGLAILKGNLAPRGS 386

Query: 431 VMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRANGMPELHKL 490
           V+KV+ V  + +V   P ++F  + +   A    E++   V V+R++GP+  G P + ++
Sbjct: 387 VVKVAGVNEDMKVHTGPAKVFDGEDACVTAIFNHEIKEGDVVVIRYEGPK--GGPGMREM 444

Query: 491 TPFLGVLQDRGFK-VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGV 549
                 +   G K VAL+TDGR SG + + P   H+SPEA+  GP+A L+DGD +++D  
Sbjct: 445 LNPTSAISGMGLKTVALITDGRFSGGT-RGPCIGHISPEAMEKGPIAALKDGDIIKIDMN 503

Query: 550 NGELRVLVDDAEWQARSLEPAPQDGNLGCGRELFAFMRNAMSSAEEGA 597
           NG L   V+D E + R       D  +   +   +  R   SSA++GA
Sbjct: 504 NGILEAEVEDKELKKRLENVVMPDKKV---KGWLSRYRKMASSADKGA 548


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: 800
Number of extensions: 55
Number of successful extensions: 9
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: 551
Length adjustment: 36
Effective length of query: 572
Effective length of database: 515
Effective search space:   294580
Effective search space used:   294580
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 24 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