GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Paraburkholderia bryophila 376MFSha3.1

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate H281DRAFT_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)

Query= curated2:P31961
         (608 letters)



>FitnessBrowser__Burk376:H281DRAFT_03422
          Length = 592

 Score =  197 bits (500), Expect = 1e-54
 Identities = 161/517 (31%), Positives = 248/517 (47%), Gaps = 43/517 (8%)

Query: 63  MNQANVAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGM 122
           M +  +A+V+ ++++ S H  F++    +K+ + +       AGG P     +T  EP  
Sbjct: 41  MGKPVIAVVNTWSEINSCHTHFKQRVEEVKRGIWQ-------AGGFPVEMPVMTLAEPFQ 93

Query: 123 E-LSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPM 181
           +  ++  R+ +AM T   L    FD  + +G CDK  PGLL+G++   +LP++F+PAGPM
Sbjct: 94  KPTTMLYRNFLAMETEEILKSYPFDGCVLMGGCDKTTPGLLMGAISM-NLPSIFLPAGPM 152

Query: 182 PTGISNKEKAA----VRQLFAE---GKATREELLASEMASYHAPGTCTFYGTANTNQLLV 234
             G  N           + +AE   GK T +E    E     +PG C   GTA+T     
Sbjct: 153 LRGNWNGRTLGSGSDTWKYWAELRAGKITEDEWKGIESGIARSPGHCMTMGTASTMTSAA 212

Query: 235 EVMGLHLPGASFVNPNTPLRDELTRE-AARQASRLTPENGNYVPMAEIVDEKAIVNSVVA 293
           E +GL LPG S +    P  D    + A+    R+       V  ++I+  K+  N+V  
Sbjct: 213 EALGLTLPGFSSI----PAVDSRHAQFASLTGQRIVEMVWTDVKPSDILTAKSFDNAVTT 268

Query: 294 LLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGM 353
           +LA  GSTN  +HL+A+A+ AGI LT     ELS + P +  + P+GQ  +  F  AGG+
Sbjct: 269 VLAMSGSTNAIVHLVAVARRAGIDLTTARFDELSRITPVIGNLRPSGQYLMEDFFYAGGL 328

Query: 354 SFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKP 413
             L+ +L  G L+     TV G  L                  G E   D+ ++R    P
Sbjct: 329 RALLLEL--GDLIDGSQMTVNGSTLGENI-------------AGAEIFNDD-VIRKRGNP 372

Query: 414 FSAEGGLRLMEGNLGRGVMKVSAVAPEHQVVEAPVR--IFHDQASLAAAFKAGELE--RD 469
             A  GL ++ GNL      +   A E  ++    R  +F D A +AA     +L+   D
Sbjct: 373 VVASDGLAVLTGNLAPDGAVIKPAAMEAHLLNHRGRAVVFKDYADMAARIDMEDLDITAD 432

Query: 470 LVAVVRFQGP-RANGMPELHKLTPFLGVLQDRGFKVALVTDGRMSGASGKVPAAIHVSPE 528
            V V++  GP  A GMPE  +L     +L+     +  ++D RMSG S      +HV+PE
Sbjct: 433 SVIVLQHAGPVGAPGMPEWGQLPIPQKLLKQGVRDMVRISDARMSGTSYGA-CVLHVAPE 491

Query: 529 AIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565
           +  GGPLA ++DGD +++D     L + V D E  AR
Sbjct: 492 SFVGGPLALVKDGDMIQLDVAARRLHLEVSDEELSAR 528


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: 821
Number of extensions: 51
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: 592
Length adjustment: 37
Effective length of query: 571
Effective length of database: 555
Effective search space:   316905
Effective search space used:   316905
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