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_148649357.1 V474_RS08210 dihydroxy-acid dehydratase family protein

Query= curated2:B8FU95
         (563 letters)



>NCBI__GCF_001046635.1:WP_148649357.1
          Length = 597

 Score =  308 bits (789), Expect = 4e-88
 Identities = 211/569 (37%), Positives = 305/569 (53%), Gaps = 29/569 (5%)

Query: 16  RSLLKALGLTDRELSKPFIGVVNSFTELVPGHMHLRQVTEAVKAGIRENGGTPFEFSTIA 75
           R L   L + + +  +P IG+  S ++LVP + H   + E VK GIR+ GG P EF T  
Sbjct: 29  RYLNYGLSIEEMQSDRPIIGIAQSGSDLVPCNRHHLVLAERVKEGIRDAGGIPIEFPTHP 88

Query: 76  VCDGIAMGHEGMHYSLASREIVADAIEVMAKGHQLDALVLIPSCDKVVPGMLMAAMRLNI 135
           + +       G+  +LA   +V    EV+  G+ LD +VL   CDK  P  LMAA  +NI
Sbjct: 89  LQETGKRPTAGLDRNLAYISLV----EVLY-GYPLDGVVLTIGCDKTTPSALMAAATVNI 143

Query: 136 PAIVVSGGPMLPGRFEGNPVTLSTVFEGVGQVHA-GKKDEAWLHELEAKACPTCGSCAGM 194
           PAI +S GPML G  EG      T+     Q+ A G+ D A   +L A   P+ G C  M
Sbjct: 144 PAIALSVGPMLNGWHEGERTGAGTIVWKARQMLAKGELDYAGFLKLVASGSPSTGYCNTM 203

Query: 195 FTANSMNCLTEALGMALPGNGTIPAVYSERLVLAKETGYQVMELYRQDLKPRDIVTQSTL 254
            TA +MN L EALGM+LPG+  IPA Y +R   A ETG  ++E+ + D KP DI+T+   
Sbjct: 204 GTATTMNSLAEALGMSLPGSAAIPAPYRDRQECAWETGRAIVEMVKADRKPSDILTREAF 263

Query: 255 KNGVAVDMALGCSTNTILHLPAIANEGDIDWDLGKVNEVSEKTPQICKLAPASETPLAAL 314
            N + V+ A+G STN  +HL AIA    ++  L          P +  L PA E      
Sbjct: 264 LNAIRVNSAIGGSTNAPIHLNAIARHIGVELTLEDWETTGADVPLLVNLQPAGEYLGEDY 323

Query: 315 HEAGGVSAVLKQLLDAGLIDGSTMTVSGVTMAERLKDAKVVDTEIIRPQSNPFSQRGGLR 374
           + AGGV AV+ +L  AGLIDG+ +T +G T+AE L   ++ D ++IRP   P  +  GL 
Sbjct: 324 YRAGGVPAVMGELSKAGLIDGAVLTANGRTVAENLVGVRIHDDKVIRPIDRPLKEAAGLT 383

Query: 375 ILFGNLAPEGAVIKQGALSSQ-----------DFVFEGSAKVFNGEVPAAEAI--RNLEI 421
           +L GNL  EGAV+K   +S +              FEG+  VF+G       I   +L I
Sbjct: 384 VLSGNLF-EGAVMKLSVISDEFRGRYLSDPANPDAFEGNVVVFDGPEDYHHRIDEPDLGI 442

Query: 422 KAGDVVVIRYEGPKGGPGMREMLG--PTATLAGMGLDSDVALLTDGRFSGASRGLSIGHV 479
               ++VIR  GP G PG  E++   P A L   G+ + +  + DGR SG S   SI + 
Sbjct: 443 DENSILVIRGAGPVGYPGGAEVVNMRPPAALIRAGVHA-LPCIGDGRQSGTSGSPSILNA 501

Query: 480 SPEAALGGDIALLKDGDKIRIDIGKGRLEWIVSEEEREQRRQEFAAM--AVKPDHLKP-- 535
           SPEAA+GG +ALL+ GD++RID+       +V E E ++RR + AA+   + P+   P  
Sbjct: 502 SPEAAVGGGLALLRTGDRVRIDLKARSANMLVDEAELDRRRADLAAVEDTITPESQTPWQ 561

Query: 536 ELRQGYLGRYA--YFVQSASKGAALRRVK 562
           E+++  +G++A    ++SA K   + ++K
Sbjct: 562 EIQRDLVGQFATGAVIESAVKYQRIAQIK 590


Lambda     K      H
   0.317    0.135    0.390 

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: 797
Number of extensions: 50
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: 563
Length of database: 597
Length adjustment: 36
Effective length of query: 527
Effective length of database: 561
Effective search space:   295647
Effective search space used:   295647
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 (21.6 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