GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF612
          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:

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