GapMind for catabolism of small carbon sources

 

Aligments for a candidate for edd in Marinobacter adhaerens HP15

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>lcl|FitnessBrowser__Marino:GFF612 HP15_595 dihydroxy-acid
           dehydratase
          Length = 597

 Score =  216 bits (551), Expect = 2e-60
 Identities = 172/586 (29%), Positives = 281/586 (47%), Gaps = 59/586 (10%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127
           +A+ +++   +  H   +    L+ + +   G V +    + A+ DG+  G  GM  SL 
Sbjct: 23  IAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 81

Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISN 187
           SR++IA S    ++ +  DA +C+  CDKI PG+L+ ++R  ++PT+FV  GPM  G   
Sbjct: 82  SREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRL-NIPTIFVSGGPMEAG--- 137

Query: 188 KEKAAVRQL--------FAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239
           K K +  +L         A+  A+ E++   E  +    G+C+   TAN+   L E +GL
Sbjct: 138 KTKLSEHKLDLVDAMVIAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIGL 197

Query: 240 HLPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALL 295
            LPG   +      R++L  +A RQ    A R   E+   V    I    A  N++V  +
Sbjct: 198 ALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASVLPLSIASMAAFENAMVMDI 257

Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNG-QADINHFQAAGGMS 354
           A GGSTN  LHLLA AQ  G+  T  ++ +LS  VP L ++ PN  +  +     AGG+ 
Sbjct: 258 AMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKYHMEDVHRAGGIM 317

Query: 355 FLIRQLLDGGLLHEDVQTVAGPGLRR------YTREPFLEDGRLVWREGP---------- 398
            ++ +L  GGL++ D+ TV    +R         R P  E     ++ GP          
Sbjct: 318 GILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEVVEF-YKAGPAGIPTQTAFS 376

Query: 399 --------ERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEAPV 448
                   +   +   +R ++  +S+EGGL ++ GN+     V+K + V     V E   
Sbjct: 377 QSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKA 436

Query: 449 RIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFKVALV 507
           R+F  Q S  A   + E++   V ++R++GPR   GM E+   T +L   +  G   AL+
Sbjct: 437 RVFESQDSAVAGILSDEVKPGEVVIIRYEGPRGGPGMQEMLYPTSYL-KSKGLGKDCALL 495

Query: 508 TDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEW----- 562
           TDGR SG +  +    H SPEA AGG +  + +GD +R+D  N  + V +D  E      
Sbjct: 496 TDGRFSGGTSGLSIG-HASPEAAAGGAIGLIENGDTIRIDIPNRSINVELDQHELDRRRE 554

Query: 563 --QARSLEP-APQDGNLGCGRELFAFMRNAMSSAEEGACSFTESLN 605
              A+  +P  P+D  +    + +A +    +SA++GA    E L+
Sbjct: 555 ARDAKGWKPELPRDRKVSAALKAYALL---ATSADKGAVRDLEKLD 597


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: 870
Number of extensions: 49
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: 597
Length adjustment: 37
Effective length of query: 571
Effective length of database: 560
Effective search space:   319760
Effective search space used:   319760
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 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