GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Novosphingobium barchaimii LL02

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_059151689.1 V474_RS11785 phosphogluconate dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_001046635.1:WP_059151689.1
          Length = 608

 Score =  197 bits (502), Expect = 8e-55
 Identities = 162/544 (29%), Positives = 260/544 (47%), Gaps = 53/544 (9%)

Query: 33  GKPI-IAVVNSFTQFVPGHV---HLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHD 88
           GK I + ++ ++   +  H       D  +L ARE+ A   VA      A+ DG+  G D
Sbjct: 70  GKSINLGIITAYNDMLSAHQPYGRYPDQMKLFAREVGATAQVAG--GVPAMCDGVTQGFD 127

Query: 89  GMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPTVFVSGGP 147
           GM  SL SR+ IA S    ++    D    +  CDKI PG+ + ++R  ++P +FV  GP
Sbjct: 128 GMELSLFSRDTIALSTAIGLSHAMFDGTALLGICDKIVPGLFIGAMRFGHLPAIFVPAGP 187

Query: 148 MEAGKVVMHGKTHALDLVDAMVAAADDKISDEDVQTIERSACPTCGSCSGMFTANSMNCL 207
           M +G +    K     L       A+ K+  E++   E ++  + G+C+   TANS   +
Sbjct: 188 MPSG-ISNKEKQKTRQLY------AEGKVGREELLASESASYHSAGTCTFYGTANSNQMM 240

Query: 208 TEALGLSLPGNGSTLATHLDRKRLFVEAGHLIVDLARRYYEQDDVKALPRTIASKQAFEN 267
            E +GL +P +         R+ L  EA H +  + R+    +D + + + +  K A  N
Sbjct: 241 MELMGLHVPASAFVQPNTPLRQALTREATHRLAAMTRK---GEDYRPMAKVVDEK-AIIN 296

Query: 268 AMTLDIAMGGSTNTVLHILAAAHEGEIDFTMADIDALSRRVPCLSKVAPAKSDVHMEDVH 327
           AM   +A GGSTN  +H+ A A  G I     D D LS  VP +++V P  S   +    
Sbjct: 297 AMAGLLATGGSTNHAIHLPAMARAGGILIDWEDFDELSSVVPLITRVYPNGSG-DVNHFQ 355

Query: 328 RAGGIMSILGELDKGGLLNRDCPTVHAETLGDAIDRWDITRTNSETVRKFYRAAPGGIPT 387
            AGGI  ++ EL   GL + D  TV   T G A                 Y + P     
Sbjct: 356 AAGGIGWVIRELLGAGLAHGDVLTV--ATGGMAA----------------YASEP----- 392

Query: 388 QVAFSQEARWDELDTDRENGVIRSVEHPFSKDGGLAVLKGNLAIDGCIVKTAGVDESILK 447
            V    +  W  +    ++ ++R V +PF  DGG+ +++GNL       KT+ VDE    
Sbjct: 393 -VMRDDKLSWIPIPETTDDTMVRPVSNPFLPDGGMRLVQGNLGRG--TFKTSAVDEQRWT 449

Query: 448 FSGPARVFESQDASVKAILANEVKAGDVVVIRYEGPK--GGPGMQEMLYPTSYLKSKGLG 505
              P RVF++Q+   +A  A E+    +VV+R++GP+  G P + ++  P   L+ KG  
Sbjct: 450 IEAPCRVFDTQEGVSQAFKAGELDRDVIVVVRFQGPRANGMPELHKLTPPLGVLQDKGF- 508

Query: 506 KACALITDGRFSGGTSGLSIG-HASPEAANGGTIGLVREGDMIDIDIPNRTISLRVSETE 564
              AL+TDGR SG +  +    H +PEA  GG +  +++GD++ +   + T+S   +  +
Sbjct: 509 -KVALVTDGRMSGASGKVPAAIHVTPEALGGGPLAYLQDGDIVRLCAEDGTLS---TTAD 564

Query: 565 LAAR 568
           L+AR
Sbjct: 565 LSAR 568


Lambda     K      H
   0.318    0.134    0.391 

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: 911
Number of extensions: 53
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 612
Length of database: 608
Length adjustment: 37
Effective length of query: 575
Effective length of database: 571
Effective search space:   328325
Effective search space used:   328325
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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