GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Dinoroseobacter shibae DFL-12

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Dino:3608367
          Length = 601

 Score =  186 bits (471), Expect = 3e-51
 Identities = 151/498 (30%), Positives = 237/498 (47%), Gaps = 49/498 (9%)

Query: 47  IGILNTWSDMTPCNGHLRELAEKVK-------AGVWEAGGFPLEVPVFSASENTFRPTAM 99
           IGI+  ++DM   +   ++  +K+K       A    AGG P      +  +      ++
Sbjct: 69  IGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGME-LSL 127

Query: 100 MYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYF 158
             R++ ALA   A+     D    L  CDK  P L++ AA+   LP + V  GPM++G  
Sbjct: 128 FSRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSGLP 187

Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218
             ++        K  +   AGE+ + + +EAE +     GTC   GTA++   + E +G+
Sbjct: 188 NDQKA-------KVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGL 240

Query: 219 ALSGNAAI-PGVDSRRKVMAQLTGR--RIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGG 275
            L G + + PG   R  + A    R   I Q+  +     +I+  +AF N I    A GG
Sbjct: 241 HLPGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGG 300

Query: 276 STNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKR 335
           STN VIHL A+A   G+ L L D+       P +  + P+G   +  F  AGGL  ++  
Sbjct: 301 STNLVIHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGE 360

Query: 336 LGEAGLLHKDALTVSGETVWDEVKD------VVNW--------NEDVILPAEKALTSSGG 381
           L   GLLH D  T++G+ + D  ++      V+ W        N  ++ PA      SGG
Sbjct: 361 LLSEGLLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGG 420

Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDENCI 437
           +  L+GNL     V+K SA +P   V + RA VFED     D +KA       +  E+ +
Sbjct: 421 LKELKGNLG--RGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAG------EFTEDTV 472

Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEA 495
           ++++  GPK   GM E+  +     VL+   L +  ++D RMSG A G V   +H +PEA
Sbjct: 473 VIVRFQGPKA-NGMPELHALTPVLAVLQDRGLKVALVTDGRMSG-ASGKVPAAIHVAPEA 530

Query: 496 AVGGPLAVVKNGDMIELD 513
             GG +A V+ GD++ +D
Sbjct: 531 LDGGLMAKVRTGDLVRVD 548


Lambda     K      H
   0.318    0.135    0.408 

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: 834
Number of extensions: 46
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 601
Length adjustment: 37
Effective length of query: 542
Effective length of database: 564
Effective search space:   305688
Effective search space used:   305688
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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