GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N2E2

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate Pf6N2E2_4564 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= curated2:P31961
         (608 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564
          Length = 613

 Score =  221 bits (563), Expect = 7e-62
 Identities = 171/545 (31%), Positives = 261/545 (47%), Gaps = 56/545 (10%)

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

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

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

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

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

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

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

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

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

Query: 564 ARSLE 568
            R +E
Sbjct: 565 GRRVE 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: 859
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:

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