GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Shewanella loihica PV-4

Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)

Query= BRENDA::P39358
         (655 letters)



>FitnessBrowser__PV4:5209582
          Length = 608

 Score =  166 bits (421), Expect = 2e-45
 Identities = 156/524 (29%), Positives = 242/524 (46%), Gaps = 68/524 (12%)

Query: 83  LALHQGHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMV 142
           L+ HQ +      +K A   + +      A  V   CDG TQG  GM  SL  R   +M 
Sbjct: 78  LSAHQPYEHYPQLLKDACHEVGS--VAQVAAGVPAMCDGVTQGQPGMELSLLSREVIAMS 135

Query: 143 MR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKDGEDNGKV 201
               L  ++ D   ++G+  CDK +P  ++   +  ++  + VP G   P K G  N + 
Sbjct: 136 TAVGLSHNMFDGALLLGI--CDKIVPGLLIGALSFGHLPMLFVPAG---PMKSGIPNKEK 190

Query: 202 QTIGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPS 261
             +  +FA G++       A  K+  S+G  C F GTA ++Q++ E +GL +P S+    
Sbjct: 191 ARVRQKFAQGQVDRAALLEAESKSYHSAGT-CTFYGTANSNQLMLEVMGLQLPGSSFVNP 249

Query: 262 GEPVWREIARASARAALNLSQKG---ITTREILTDKAIENAMTVHAAFGGSTNLLLHIPA 318
            +P+   + + +A+    L++ G       E++ +K++ N +    A GGSTNL +HI A
Sbjct: 250 DDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGSTNLTMHIVA 309

Query: 319 IAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAF-MAGGVPEVMLHLRSLGL 377
            A  AG  I   DD+  ++  VP L  V PNG   H  +N F  AGG+  ++  L   GL
Sbjct: 310 AARAAGI-IVNWDDFSELSDAVPLLARVYPNG---HADINHFHAAGGMAFLIKELLDAGL 365

Query: 378 LHEDVMTVTGSTLK----------ENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQ 427
           LHEDV+TV G  L+            L W E            LD+E + A   + SP Q
Sbjct: 366 LHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPNES-------LDKEVLTA---VASPFQ 415

Query: 428 AKA-----RGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSA 482
           A       +G        V  +A     +++ A+   +ID+Q             ++   
Sbjct: 416 ANGGLKLLKGNLGRAVIKVSAVAESHRFVEAPAV---VIDDQ-------------NKLEG 459

Query: 483 IYDIKHDKIKAGDILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVSLITDARFSGVS- 540
           ++  K  ++    ++V+ G GP   GM E +++T  L  L   G  V+L+TD R SG S 
Sbjct: 460 LF--KAGELDRDCVVVVKGQGPKANGMPELHKLTPILGSLQDKGFKVALLTDGRMSGASG 517

Query: 541 -TGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFL 583
              A I H+ PEAL GG I K+  GDLI +  +     GEV+ L
Sbjct: 518 KVPAAI-HLTPEALDGGLIAKVENGDLIRVDANT----GEVSLL 556


Lambda     K      H
   0.317    0.135    0.400 

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: 872
Number of extensions: 51
Number of successful extensions: 9
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: 655
Length of database: 608
Length adjustment: 38
Effective length of query: 617
Effective length of database: 570
Effective search space:   351690
Effective search space used:   351690
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: 54 (25.4 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