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 (uncharacterized)
to candidate WP_059153645.1 V474_RS23740 dihydroxy-acid dehydratase family protein

Query= curated2:A8AB39
         (552 letters)



>NCBI__GCF_001046635.1:WP_059153645.1
          Length = 598

 Score =  298 bits (762), Expect = 5e-85
 Identities = 190/521 (36%), Positives = 288/521 (55%), Gaps = 24/521 (4%)

Query: 23  GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80
           GL  EELR  +P+IG+A + +++ P + H   +AE ++ GIR  GG  LEF    + +  
Sbjct: 35  GLSLEELRSGKPIIGIAQTGSDLSPCNRHHLVLAERIREGIREQGGIALEFPVHPIQETG 94

Query: 81  AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILI 140
                G+  +L    ++       +  + LD VV+ T CDK TP  L+AAA + +P I +
Sbjct: 95  KRPTAGLDRNLAYLALVE-----AIYGYPLDGVVLTTGCDKTTPALLMAAATVNIPAIAL 149

Query: 141 NGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEE--LRKLEESALPGPGSCAGLFTANT 198
           + GPM+ G +  ER     ++ +   ++  G  +     KL  S+ P  G C  + TA T
Sbjct: 150 SVGPMLNGWHKGERTGSGTIVWKGRQMMAAGELDADGFIKLVASSAPSTGYCNTMGTATT 209

Query: 199 MNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIA 258
           MN L+EA+G+MLPG++ +PA    R   A  TG RIV MV E L P  ILT  A  NAI 
Sbjct: 210 MNSLAEALGMMLPGSAAIPAPYRDRQECAWRTGKRIVDMVHEDLKPSDILTLDAFHNAIV 269

Query: 259 VDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGG 318
           V+ A+GGSTN+ +HL A+A  +G+DLPL+ ++ +  KVP + ++ P+G +   D  RAGG
Sbjct: 270 VNAAIGGSTNAPIHLAAIARHIGVDLPLKDWERLGHKVPLLVNLQPAGEYLGEDYYRAGG 329

Query: 319 IPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGS 378
           +PAV+ +L   GLI + A+TV G T+ +N +DA + D +VI+  D P     G  +L G+
Sbjct: 330 VPAVVAQLIGQGLIAESAMTVNGLTIGDNCRDATIEDDKVIKTFDQPLVEEAGFLVLSGN 389

Query: 379 LAPNGAVVKASAVKREL-----------WKFKGVARVFDREEDAVKAIRGGE--IEPGTV 425
           L  + A++K S +  E              F+G A VFD  ED    I      I P T+
Sbjct: 390 LF-DAAIMKTSVISDEFRARYLSNPDDPEAFEGPAVVFDGPEDYHHRIDDPSVGITPETL 448

Query: 426 IVIRYEGPRGGPGMREMLTATAAVMALGLG-DKVALVTDGRFSGATRGPAIGHVSPEAAA 484
           + +R  GP G PG  E++        +  G   +  + DGR SG +  P+I + SPEAAA
Sbjct: 449 MFMRGAGPIGYPGAAEVVNMRPPSYLITEGVSALPCIGDGRQSGTSGSPSILNASPEAAA 508

Query: 485 GGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPK 525
            G +AL+Q GD + +D++K  +D+L+ ++EL  RRA  + K
Sbjct: 509 MGGLALLQTGDRVRMDLKKGTVDVLISDEELAARRADLEAK 549


Lambda     K      H
   0.319    0.138    0.401 

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: 842
Number of extensions: 45
Number of successful extensions: 5
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: 552
Length of database: 598
Length adjustment: 36
Effective length of query: 516
Effective length of database: 562
Effective search space:   289992
Effective search space used:   289992
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 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