GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xad in Alkalihalobacterium alkalinitrilicum DSM 22532

Align xylonate dehydratase monomer (EC 4.2.1.82) (characterized)
to candidate WP_078427497.1 BK574_RS03330 dihydroxy-acid dehydratase

Query= metacyc::MONOMER-20629
         (591 letters)



>NCBI__GCF_002019605.1:WP_078427497.1
          Length = 556

 Score =  236 bits (601), Expect = 2e-66
 Identities = 170/523 (32%), Positives = 270/523 (51%), Gaps = 31/523 (5%)

Query: 35  GITPEELRSGKPIIGIAQTGSDISPCNRIHLD-LVQRVRDGIRDAGGIPMEFPVHPIFEN 93
           GI  E+    KP +GIA T S+++PCN +H+D L ++ + G  DAGG P  F    + + 
Sbjct: 29  GIKDEDFN--KPFVGIASTWSEVTPCN-MHIDELARKAKKGALDAGGTPFIFNTITVSDG 85

Query: 94  CRRPTAALDRNLSYLGLV----ETLHGYP-IDAVVLTTGCDKTTPAGIMAATTVNIPAIV 148
               T  +  +L    ++    ET+ G    D VV   GCDK  P  ++A   +N+PA+ 
Sbjct: 86  ISMGTEGMRFSLPSREVIADSIETVVGAQNYDGVVAIGGCDKNMPGCMIAIGRLNLPAVF 145

Query: 149 LSGGPMLDGWHENELVGSGTVIWRSRRKLAAGEITEEEFIDRAASSAPSAGHCNTMGTAS 208
           + GG +  G  + + +   +  + +  K   G+I  +E       + P AG C  M TA+
Sbjct: 146 VYGGTIRPGNVDGKDIDIVSA-FEAVGKYNNGDIDRDELHKIECHACPGAGSCGGMYTAN 204

Query: 209 TMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQRIVDLAYDDVKPLDILTKQAFENAI 268
           TM +  EA+G+SL G ++ PA   E+ +   K G+ +++L    + P DI+TK+AFENAI
Sbjct: 205 TMASAIEAMGMSLPGSSSNPAETEEKLEDCIKAGKAVMNLLNKGITPKDIMTKKAFENAI 264

Query: 269 ALVAAAGGSTNAQPHIVAMARHAGVEITADDW-RAAYDIPLIVNMQPAGKYLGERFHRAG 327
            +V A GGSTNA  H++A+A    V++  DD+ R    +P I +++P+G+Y+ E     G
Sbjct: 265 TVVMALGGSTNAVLHLLALAHTVDVDLNLDDFERIRKKVPHIADLKPSGRYVMENLSEIG 324

Query: 328 GAPAVLWELLQQGRLHGDVLTVTGKTMSENL-QGRETSDREVIFPYHEPLAEKAGFLVLK 386
           G PAV+  LL +G LHGD LTVT  T+ +NL + +   + + I  +  P  E    ++LK
Sbjct: 325 GVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLKEGQEIISFENPKRETGPLVILK 384

Query: 387 GNLF-DFAIMKSSVIGEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALEIDER 445
           GNL  D A+ K S  G + +K               A VFD   D    + +   E++  
Sbjct: 385 GNLAPDGALAKMS--GLKIKK-----------ITGPARVFDSETDATNAVLNN--EVNPG 429

Query: 446 CILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGI-MSLPTLGDGRQSGTADSPSILNASPE 504
            ++VIR  GP G PG AE++++     ++ KG    +  + DGR SG      + + SPE
Sbjct: 430 DVIVIRYVGPKGGPGMAEMLSITA--IVVGKGFGEKVGLITDGRFSGGTHGLVVGHISPE 487

Query: 505 SAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARKQDGIP 547
           + +GG ++ ++ GD I ID         V    +  R +D  P
Sbjct: 488 AQVGGPIALIKEGDMITIDSELQELAVDVSPEDLNERLKDWSP 530


Lambda     K      H
   0.319    0.136    0.411 

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: 792
Number of extensions: 43
Number of successful extensions: 7
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: 591
Length of database: 556
Length adjustment: 36
Effective length of query: 555
Effective length of database: 520
Effective search space:   288600
Effective search space used:   288600
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 Apr 09 2024. 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