GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phaeobacter inhibens BS107

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Phaeo:GFF723
          Length = 571

 Score =  191 bits (486), Expect = 6e-53
 Identities = 154/515 (29%), Positives = 250/515 (48%), Gaps = 43/515 (8%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME-LSL 126
           + I ++++++   +       E +K+ + E       AGG P     ++ GE  M+  ++
Sbjct: 41  IGICNTWSELTPCNSGLRDLAEGVKRGVWE-------AGGFPVEFPVMSLGETQMKPTAM 93

Query: 127 PSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGI- 185
             R ++A+    ++     D  ++LG CDK  PG +MGA     LP I V  GPM +G  
Sbjct: 94  LFRNLLAMDVEESIRAYGIDGVVLLGGCDKTTPGQLMGAASVD-LPAIVVSSGPMLNGKW 152

Query: 186 ------SNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
                 S  +     +    G+ T ++ + +E     S G C   GTA+T   L+E MG+
Sbjct: 153 QGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAESGMSRSKGVCMTMGTASTMASLVEAMGM 212

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
            LP  + +      R AL H   +++  + ++  +  P  +++   + VN+I+A  A GG
Sbjct: 213 SLPTNAALPAVDARRMALAHLTGKRIVEMVEE--DIKP-SDVLTREAFVNAIMANAAVGG 269

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STN  +H+ A+A   G +L+  D  DL   +P L +  P+GK  +  F  AGGM  ++++
Sbjct: 270 STNAVVHLLALAGRVGAELSLDDF-DLGSDIPLLVNCMPSGKYLMEDFCYAGGMPVVLKQ 328

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L + G L  +  TV G  +  Y +      G   + D  I+S DE +         P  G
Sbjct: 329 LADNGHLRSNT-TVLGGDILAYAE------GAECFNDDVIKSFDEPV--------KPAAG 373

Query: 420 LRVMEGNLG-RGVMKVSAVALQHQIV-EAPAVVFQDQQDLADAFKAGELE--KDFVAVMR 475
           LRV+ GNL   G +   + A  H +  E  A VF+  +D+       +L   KD + V++
Sbjct: 374 LRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLPVTKDSILVLK 433

Query: 476 FQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEAQVGG 533
             GP+   GMPE+  M     ++++    +  ++DGRMSG A G +   +HVSPE+Q GG
Sbjct: 434 GVGPKGYPGMPEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTV--ILHVSPESQAGG 491

Query: 534 ALARVRDGDIIRVDGVKGTLELKVDADEFAAREPA 568
            L  V+ GD IRV    GTL+L V  +E  AR  A
Sbjct: 492 PLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREA 526


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: 840
Number of extensions: 46
Number of successful extensions: 6
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: 571
Length adjustment: 37
Effective length of query: 571
Effective length of database: 534
Effective search space:   304914
Effective search space used:   304914
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 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