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_007688035.1 V474_RS20600 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>NCBI__GCF_001046635.1:WP_007688035.1
          Length = 617

 Score = 1056 bits (2731), Expect = 0.0
 Identities = 522/616 (84%), Positives = 564/616 (91%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRT+THGRNMAGARGLWRATGMKDEDFGKPIIA+ANSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPHYRSRTSTHGRNMAGARGLWRATGMKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAH ADA+VCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHTADALVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAAMRLNIP +FVSGGPMEAGK  ++GK  ALDLVDAMVVAADDSY+DEE
Sbjct: 121 NCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTELRGKTVALDLVDAMVVAADDSYTDEE 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           V+ IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATHADRE LF EAGR +V
Sbjct: 181 VKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADREKLFLEAGRTIV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           DL +RWYEQ+DA+ALPR IAT AAFENAMSLDIAMGGSTNTVLHLLAAA+EGG+DF+MAD
Sbjct: 241 DLAKRWYEQDDASALPRNIATFAAFENAMSLDIAMGGSTNTVLHLLAAAYEGGVDFTMAD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR VPCL KVAPAK+DVHMEDVHRAGG+MAILGELER GL+DA+ PTVHAPT+G+A
Sbjct: 301 IDRLSRRVPCLCKVAPAKNDVHMEDVHRAGGIMAILGELERAGLVDATLPTVHAPTLGDA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           L RWDIGRTNS+    FF+AAPGG  T  AFSQ ARWEELD DRE GVIRS EHPFSKDG
Sbjct: 361 LNRWDIGRTNSEEVRNFFRAAPGGVRTTQAFSQNARWEELDTDRETGVIRSAEHPFSKDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           GLAVLFGN+APEGCIVKTAGVDESILTF GTARV+ESQDAAV+GILG +VKAG+VVVIRY
Sbjct: 421 GLAVLFGNIAPEGCIVKTAGVDESILTFHGTARVYESQDAAVAGILGNEVKAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGPKGGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGHVSPEA EGGLIAL
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIAL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600
           V TGDPILIDIP R I L++ DAV+AAR+     RG  AW PL RKR+++PALRAYAA+T
Sbjct: 541 VATGDPILIDIPNRVIRLDLDDAVIAARKAEMEGRGAKAWKPLGRKRNVSPALRAYAALT 600

Query: 601 TNAARGAVRDVSQIER 616
           TNAARGAVRDV Q+E+
Sbjct: 601 TNAARGAVRDVGQVEK 616


Lambda     K      H
   0.318    0.134    0.395 

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: 1394
Number of extensions: 40
Number of successful extensions: 1
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: 617
Length of database: 617
Length adjustment: 37
Effective length of query: 580
Effective length of database: 580
Effective search space:   336400
Effective search space used:   336400
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)

Align candidate WP_007688035.1 V474_RS20600 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.3301688.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-249  815.0   1.6   1.7e-249  814.8   1.6    1.0  1  NCBI__GCF_001046635.1:WP_007688035.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_007688035.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.8   1.6  1.7e-249  1.7e-249       2     542 ..      18     610 ..      17     611 .. 0.98

  Alignments for each domain:
  == domain 1  score: 814.8 bits;  conditional E-value: 1.7e-249
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ar l++atG+kded++kPiia++ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamgh+Gm
  NCBI__GCF_001046635.1:WP_007688035.1  18 ARGLWRATGMKDEDFGKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHDGM 90 
                                           689********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagkt+l  k   +d
  NCBI__GCF_001046635.1:WP_007688035.1  91 LYSLPSRDLIADSVEYMVNAHTADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTELRGKTVALD 163
                                           *****************************************************************99****** PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++ +a++  ++ee++ iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+ ++g
  NCBI__GCF_001046635.1:WP_007688035.1 164 LVDAMVVAADDSYTDEEVKVIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADREKLFLEAG 236
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           ++iv+l k+ ++       Pr+i+t +afena++ld+a+GGstntvLhlla+a e gv++++ d+drlsr+vP
  NCBI__GCF_001046635.1:WP_007688035.1 237 RTIVDLAKRWYEqddasalPRNIATFAAFENAMSLDIAMGGSTNTVLHLLAAAYEGGVDFTMADIDRLSRRVP 309
                                           ***********9************************************************************* PP

                             TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344
                                           +l+k++P+ + v +ed+hraGG++a+l+el+++gl++    tv   tl++ l++ ++ r              
  NCBI__GCF_001046635.1:WP_007688035.1 310 CLCKVAPAKNDVhMEDVHRAGGIMAILGELERAGLVDATLPTVHAPTLGDALNRWDIGRtnseevrnffraap 382
                                           *********9999********************************************999************* PP

                             TIGR00110 345 .....................vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394
                                                                   +  virs ++p++k+gglavL+Gn+a+eG++vk+agv+e+il+f+G+a+
  NCBI__GCF_001046635.1:WP_007688035.1 383 ggvrttqafsqnarweeldtdR--EtgVIRSAEHPFSKDGGLAVLFGNIAPEGCIVKTAGVDESILTFHGTAR 453
                                           ****************977444..366********************************************** PP

                             TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467
                                           v+es+++a+++ilg +vk+GdvvviryeGPkGgPGm+emL+Pts+l++ GLgk++aLitDGrfsGgt+GlsiG
  NCBI__GCF_001046635.1:WP_007688035.1 454 VYESQDAAVAGILGNEVKAGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIG 526
                                           ************************************************************************* PP

                             TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyakl 531
                                           hvsPeaaegG ialv  GD i iDi+nr + l+++++ +a+r+a+++ ++a         r+v+ aL++ya l
  NCBI__GCF_001046635.1:WP_007688035.1 527 HVSPEAAEGGLIALVATGDPILIDIPNRVIRLDLDDAVIAARKAEMEGRGAkawkplgrkRNVSPALRAYAAL 599
                                           **********************************************999888999***9999*********** PP

                             TIGR00110 532 vssadkGavld 542
                                            ++a +Gav+d
  NCBI__GCF_001046635.1:WP_007688035.1 600 TTNAARGAVRD 610
                                           *********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (617 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.86
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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