GapMind for catabolism of small carbon sources

 

Aligments for a candidate for edd in Pseudomonas putida KT2440

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>lcl|FitnessBrowser__Putida:PP_5128 PP_5128 Dihydroxy-acid
           dehydratase
          Length = 613

 Score =  215 bits (548), Expect = 4e-60
 Identities = 169/545 (31%), Positives = 258/545 (47%), Gaps = 56/545 (10%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127
           +AI +++   +  H   +    L+ + +   G V +    + A+ DG+  G  GM  SL 
Sbjct: 37  IAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95

Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISN 187
           SR++IA +    ++ +  DA +C+  CDKI PG+L+ +LR  ++P +FV  GPM  G   
Sbjct: 96  SREIIADAVEYMVNAHCADAIVCISNCDKITPGMLMAALRL-NIPVIFVSGGPMEAG--- 151

Query: 188 KEKAAVRQL--------FAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239
           K K A   L         A+  A+ E++   E ++    G+C+   TAN+   L E +GL
Sbjct: 152 KTKLASHGLDLVDAMVIAADSTASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGL 211

Query: 240 HLPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALL 295
            LPG          R++L   A R       R   EN   V    I + KA  N+++  +
Sbjct: 212 ALPGNGSTLATHSDREQLFLTAGRTIVELCKRYYGENDESVLPRSIANFKAFENAMMLDI 271

Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQA-DINHFQAAGGMS 354
           A GGSTN  LHLLA AQ   +    +D+  LS  VP L ++ PN Q   +     AGG+ 
Sbjct: 272 AMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQLCKVAPNIQKYHMEDVHRAGGIF 331

Query: 355 FLIRQLLDGGLLHEDVQTV---------------------------AGP-GLRRYTREPF 386
            ++  L  GGLLH D+ TV                           AGP G+   T+  F
Sbjct: 332 SILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQTDDEAVHTFFKAGPAGIP--TQTAF 389

Query: 387 LEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVV 444
            +  R  W E  +   +   +R  +  +S EGGL ++ GN+     V+K + V     V 
Sbjct: 390 SQSTR--W-ETLDDDRENGCIRSFEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVF 446

Query: 445 EAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFK 503
           E   +IF  Q S      A E++   + ++R++GP+   GM E+   T +L   +  G  
Sbjct: 447 EGTAKIFESQDSAVRGILADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKA 505

Query: 504 VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQ 563
            AL+TDGR SG +  +    H SPEA AGG +  +RDGD+V +D  N  + +LV D E  
Sbjct: 506 CALLTDGRFSGGTSGLSIG-HASPEAAAGGAIGLVRDGDKVLIDIPNRSINLLVSDEELA 564

Query: 564 ARSLE 568
            R +E
Sbjct: 565 QRRVE 569


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: 856
Number of extensions: 52
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 608
Length of database: 613
Length adjustment: 37
Effective length of query: 571
Effective length of database: 576
Effective search space:   328896
Effective search space used:   328896
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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