GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF723 PGA1_c07380 dihydroxy-acid
           dehydratase IlvD
          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 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