GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Alkalihalobacterium alkalinitrilicum DSM 22532

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 WP_078427497.1 BK574_RS03330 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>NCBI__GCF_002019605.1:WP_078427497.1
          Length = 556

 Score =  319 bits (818), Expect = 2e-91
 Identities = 191/519 (36%), Positives = 294/519 (56%), Gaps = 17/519 (3%)

Query: 27  HRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPV 86
           +R  ++  G   + F+ +P +GI +TWS++TPCN H+ ELA K K G  +AGG P     
Sbjct: 21  NRAMIRAMGIKDEDFN-KPFVGIASTWSEVTPCNMHIDELARKAKKGALDAGGTPFIFNT 79

Query: 87  FSASENTFRPTAMMY-----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASC 141
            + S+     T  M      R + A ++E  +  Q  DG V + GCDK  P  ++     
Sbjct: 80  ITVSDGISMGTEGMRFSLPSREVIADSIETVVGAQNYDGVVAIGGCDKNMPGCMIAIGRL 139

Query: 142 DLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCN 201
           +LP++ V GG +  G   G+ +      ++       G++ + E  + E      +G+C 
Sbjct: 140 NLPAVFVYGGTIRPGNVDGKDIDI-VSAFEAVGKYNNGDIDRDELHKIECHACPGAGSCG 198

Query: 202 TMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQ 261
            M TA+TMAS  EA+GM+L G+++ P     +       G+ ++ ++   + P +IMTK+
Sbjct: 199 GMYTANTMASAIEAMGMSLPGSSSNPAETEEKLEDCIKAGKAVMNLLNKGITPKDIMTKK 258

Query: 262 AFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLME 321
           AFENAI    A+GGSTNAV+HLLA+A  V +DL+LDD++R  + VP I +L PSG+Y+ME
Sbjct: 259 AFENAITVVMALGGSTNAVLHLLALAHTVDVDLNLDDFERIRKKVPHIADLKPSGRYVME 318

Query: 322 EFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNE-DVILPAEKALTSSG 380
                GG+P V+K L + GLLH D LTV+  T+   + ++    E   I+  E     +G
Sbjct: 319 NLSEIGGVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLKEGQEIISFENPKRETG 378

Query: 381 GIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFE-DIDDYKAKINDDNLDIDENCIMV 439
            +V+L+GNLAP GA+ K S      +   G A VF+ + D   A +N+   +++   ++V
Sbjct: 379 PLVILKGNLAPDGALAKMSGLKIKKIT--GPARVFDSETDATNAVLNN---EVNPGDVIV 433

Query: 440 MKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMV-RISDARMSGTAYGTVVLHTSPEAAVG 498
           ++  GPKG PGMAE+  + +   V+ KG  + V  I+D R SG  +G VV H SPEA VG
Sbjct: 434 IRYVGPKGGPGMAEM--LSITAIVVGKGFGEKVGLITDGRFSGGTHGLVVGHISPEAQVG 491

Query: 499 GPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQP 537
           GP+A++K GDMI +D   + L +D+S E+L  RL +W P
Sbjct: 492 GPIALIKEGDMITIDSELQELAVDVSPEDLNERLKDWSP 530


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: 902
Number of extensions: 48
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: 579
Length of database: 556
Length adjustment: 36
Effective length of query: 543
Effective length of database: 520
Effective search space:   282360
Effective search space used:   282360
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 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