GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Caulobacter crescentus NA1000

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>FitnessBrowser__Caulo:CCNA_03139
          Length = 617

 Score =  201 bits (510), Expect = 1e-55
 Identities = 162/540 (30%), Positives = 252/540 (46%), Gaps = 50/540 (9%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127
           +A+ +++   +  H   +    L+ + +   G V +    + A+ DG+  G  GM  SL 
Sbjct: 37  IAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTI-AVDDGIAMGHGGMLYSLP 95

Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-IS 186
           SRD+IA S    ++ +  DA +C+  CDKI PG+L+ ++R  ++P VFV  GPM  G ++
Sbjct: 96  SRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGKVT 154

Query: 187 NKEKAAVRQLF------AEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240
            K K     L       A+   + EE+ A E A+    G+C+   TAN+   L E +GL 
Sbjct: 155 VKGKIRALDLVDAMVVAADDSYSDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLS 214

Query: 241 LPGASFVNPNTPLRDELTREAARQASRLTP-----ENGNYVPMAEIVDEKAIVNSVVALL 295
           LPG   V      R+ L +EA R    L       E+   +P   I    A  N++   +
Sbjct: 215 LPGNGSVLATHADREALFKEAGRVVVDLCQRWYEQEDATALPRG-IATRAAFENAMSLDI 273

Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYP-NGQADINHFQAAGGMS 354
           A GGSTN  LHLLA A   GI  +  D+  LS  VP L+++ P      +     AGG+ 
Sbjct: 274 AMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVM 333

Query: 355 FLIRQLLDGGLLHEDVQTVAGP----GLRRY----------------------TREPFLE 388
            ++ +L  GGL+     TV  P     L R+                      T+  F +
Sbjct: 334 AILGELERGGLIDASQPTVHAPTMGEALARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQ 393

Query: 389 DGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEA 446
             R  W E  +   +  ++R ++ PFS +GGL ++ GNL     ++K + V         
Sbjct: 394 AAR--WEE-LDLDRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRG 450

Query: 447 PVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFKVA 505
             R+F  Q +  +    G+++   V V+R++GP+   GM E+   T +L   +  G   A
Sbjct: 451 TARVFESQDAAVSGILGGQVKAGEVVVIRYEGPKGGPGMQEMLYPTTYLKS-KGLGAACA 509

Query: 506 LVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565
           LVTDGR SG +  +    HVSPEA  GG +A +  GD + +D     + + V DA   AR
Sbjct: 510 LVTDGRFSGGTSGLSIG-HVSPEAGEGGLIALVETGDPILIDIPTRGITLEVSDAVLAAR 568


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: 940
Number of extensions: 55
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: 1
Length of query: 608
Length of database: 617
Length adjustment: 37
Effective length of query: 571
Effective length of database: 580
Effective search space:   331180
Effective search space used:   331180
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