GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacD in Shewanella amazonensis SB2B

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 6937660 Sama_1810 phosphogluconate dehydratase (RefSeq)

Query= reanno::ANA3:7024896
         (586 letters)



>lcl|FitnessBrowser__SB2B:6937660 Sama_1810 phosphogluconate
           dehydratase (RefSeq)
          Length = 608

 Score =  189 bits (481), Expect = 2e-52
 Identities = 155/518 (29%), Positives = 253/518 (48%), Gaps = 50/518 (9%)

Query: 54  IGICNTWSELTPCNG---HLRELAQRVKNGI----REAGGIPVEFPVFSNGESNLRPSAM 106
           IGI   ++++   +    H  EL +   N +    + AGG+P      + G+  +  S +
Sbjct: 68  IGIVTAFNDMLSAHQPYEHYPELLKAACNEVGSVAQVAGGVPAMCDGVTQGQPGMELS-L 126

Query: 107 LTRNLAAMDTEEAIRGNPIDGVVLLVGCDKTTPALLMGAASCD-LPTIVVTGGPMLNG-- 163
           L+R + AM T   +  N  DG +LL  CDK  P LL+GA S   LP + V  GPM +G  
Sbjct: 127 LSREVIAMATAVGLSHNMFDGALLLGVCDKIVPGLLIGAMSFGHLPMLFVPAGPMRSGIP 186

Query: 164 -KHKGKDVGSGTLVWELHQEYKAGNISLAAFMNAEADMSRSTGTCNTMGTASTMACMVET 222
            K K +          + Q++  G +   A + AEA    S GTC   GTA++   ++E 
Sbjct: 187 NKEKAR----------VRQKFAEGKVDREALLEAEASSYHSAGTCTFYGTANSNQLVLEV 236

Query: 223 LGVSLPHNATIPAVDSRRQVLAHMSGMRIVDMVKEDLTLS---KILSRDAFINAIKVNAA 279
           +G+ LP ++ +   D  R  L+ M+  ++  + +  L  S   +I++  + +N I    A
Sbjct: 237 MGLQLPGSSFVNPDDPLRTELSKMAAKQVCRLTENGLQYSPIGEIVNEKSVVNGIVALLA 296

Query: 280 IGGSTNAVIHLKAIAGRIGVELSLDDWRH-GYTVPTIVNLKPSGQYLMEDFYYAGGLPAV 338
            GGSTN  +H+ A A   G+ ++ DD+      VP +  + P+G   +  F+ AGG+  +
Sbjct: 297 TGGSTNLTMHIVAAARAAGIIINWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFL 356

Query: 339 LRQLFEHDLLSKNTLTVNAASLWDNVKE--------------APCYNQEVIMSLENPLVE 384
           +++L +  L+ ++  TV    L    +E                  +QEV+  +  P   
Sbjct: 357 MKELLDAGLIHEDVNTVAGYGLRRYTQEPRLIDGQLTWVDGPVTSLDQEVLRGVAEPFQS 416

Query: 385 NGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGDPELDIDENSIM 444
           NGG+++++GNL    AVIK SA           AVV +  +  +A     ELD D   ++
Sbjct: 417 NGGLKLMKGNLG--RAVIKVSAVQEQHRIVEAPAVVIDDQNKLDALFKAGELDRD--CVV 472

Query: 445 VLKNCGPKGYPGMAEVGNM-GLPPKLLKKGIKDMVRISDARMSGTAFGTV--VLHVAPEA 501
           V+K  GPK   GM E+  +  +   L  +G K +  ++D RMSG A G V   +H+ PEA
Sbjct: 473 VVKGQGPKA-NGMPELHKLTPILGTLQDRGFK-VALMTDGRMSG-ASGKVPAAIHLTPEA 529

Query: 502 QALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLA 539
              G +A VQ+GD+I ++   G L L +S  EL++R A
Sbjct: 530 LDGGLIAKVQDGDLIRINAITGELSLLVSAPELESRTA 567


Lambda     K      H
   0.318    0.135    0.403 

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: 789
Number of extensions: 33
Number of successful extensions: 6
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: 586
Length of database: 608
Length adjustment: 37
Effective length of query: 549
Effective length of database: 571
Effective search space:   313479
Effective search space used:   313479
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 (21.7 bits)
S2: 53 (25.0 bits)

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

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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