GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Novosphingobium aromaticivorans DSM 12444

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011445434.1 SARO_RS08930 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>NCBI__GCF_000013325.1:WP_011445434.1
          Length = 615

 Score = 1016 bits (2627), Expect = 0.0
 Identities = 498/610 (81%), Positives = 553/610 (90%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQ+V
Sbjct: 1   MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQMV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSR+LIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA++R+NIP VFVSGGPMEAGKV++ GK HALDLVDAMVAAAD+  +DE+
Sbjct: 121 NCDKITPGMLMAAMRINIPVVFVSGGPMEAGKVILKGKEHALDLVDAMVAAADESFTDEE 180

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V  IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATH DR+RLF+EAG L+V
Sbjct: 181 VTAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRQRLFLEAGRLVV 240

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           DL +RYYEQDD   LPR+IA+ +AFENAM+LDIAMGGSTNTVLH+LAAAHE  ++FTM+D
Sbjct: 241 DLCKRYYEQDDESVLPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAAHEAGVNFTMSD 300

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           ID LSR+VPCLSKVAPAKSDVHMEDVHRAGGI +ILGELD+ GLL+   PTVH+ TLGDA
Sbjct: 301 IDHLSRKVPCLSKVAPAKSDVHMEDVHRAGGIYAILGELDRAGLLHTHLPTVHSRTLGDA 360

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           +++WD+ RTNS TV++F+RAAPGG+PTQVAFSQ+ RW ELD DRE GVIRS EH FSKDG
Sbjct: 361 LNQWDVKRTNSPTVQEFFRAAPGGVPTQVAFSQDRRWKELDLDRETGVIRSAEHAFSKDG 420

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A +GCIVKTAGVD+SILKF+GPA+V+ESQDA+V AIL  +V +GDVVVIRY
Sbjct: 421 GLAVLFGNIAREGCIVKTAGVDDSILKFTGPAKVYESQDAAVTAILTGQVTSGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKSKGLG ACAL+TDGRFSGGTSGLSIGH SPEAA GG IGL
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGAACALLTDGRFSGGTSGLSIGHVSPEAAEGGEIGL 540

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           V  GD+I+IDIPNRTI L V++  LA RRAEQ+AKGW P + R R V+TAL+AYAA  TS
Sbjct: 541 VENGDVIEIDIPNRTIHLAVADDVLAQRRAEQEAKGWKPVKERPRKVSTALRAYAAMTTS 600

Query: 601 ADRGAVRDLN 610
           A RGAVRDL+
Sbjct: 601 AARGAVRDLS 610


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: 1286
Number of extensions: 29
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: 612
Length of database: 615
Length adjustment: 37
Effective length of query: 575
Effective length of database: 578
Effective search space:   332350
Effective search space used:   332350
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_011445434.1 SARO_RS08930 (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.878012.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-257  841.5   2.2   1.6e-257  841.3   2.2    1.0  1  NCBI__GCF_000013325.1:WP_011445434.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013325.1:WP_011445434.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.3   2.2  1.6e-257  1.6e-257       2     542 ..      18     608 ..      17     609 .. 0.99

  Alignments for each domain:
  == domain 1  score: 841.3 bits;  conditional E-value: 1.6e-257
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl+++v++eieaaGgvakefntiav+DGiamgh+Gm
  NCBI__GCF_000013325.1:WP_011445434.1  18 ARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQMVAREIEAAGGVAKEFNTIAVDDGIAMGHDGM 90 
                                           689********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+r+niP+++vsGGpmeagk+ l  k + +d
  NCBI__GCF_000013325.1:WP_011445434.1  91 LYSLPSRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRINIPVVFVSGGPMEAGKVILKGKEHALD 163
                                           *****************************************************************99****** PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++++a++ +++ee+++iersacPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+ ++g
  NCBI__GCF_000013325.1:WP_011445434.1 164 LVDAMVAAADESFTDEEVTAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRQRLFLEAG 236
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           + +v+l+k++++       Pr+i+t eafena++ld+a+GGstntvLhlla+a+eagv+++++d+d+lsrkvP
  NCBI__GCF_000013325.1:WP_011445434.1 237 RLVVDLCKRYYEqddesvlPRSIATFEAFENAMSLDIAMGGSTNTVLHLLAAAHEAGVNFTMSDIDHLSRKVP 309
                                           ************************************************************************* PP

                             TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344
                                           +l+k++P+ + v +ed+hraGG+ a+l+eld++gllh++  tv  +tl++ l++ +v+r              
  NCBI__GCF_000013325.1:WP_011445434.1 310 CLSKVAPAKSDVhMEDVHRAGGIYAILGELDRAGLLHTHLPTVHSRTLGDALNQWDVKRtnsptvqeffraap 382
                                           ********88888************************************************************ PP

                             TIGR00110 345 .....................vdqd..virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394
                                                                   +  virs +++++k+gglavL+Gn+a eG++vk+agv+++ilkf+Gpak
  NCBI__GCF_000013325.1:WP_011445434.1 383 ggvptqvafsqdrrwkeldldR--EtgVIRSAEHAFSKDGGLAVLFGNIAREGCIVKTAGVDDSILKFTGPAK 453
                                           ***************9988544..355********************************************** PP

                             TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467
                                           v+es+++a+ ail+g+v+ GdvvviryeGPkGgPGm+emL+Pts+l++ GLg ++aL+tDGrfsGgt+GlsiG
  NCBI__GCF_000013325.1:WP_011445434.1 454 VYESQDAAVTAILTGQVTSGDVVVIRYEGPKGGPGMQEMLYPTSYLKSKGLGAACALLTDGRFSGGTSGLSIG 526
                                           ************************************************************************* PP

                             TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvs 533
                                           hvsPeaaegG i+lve+GD i+iDi+nr+++l+v ++ la+rra++++k++       r+v+ aL++ya + +
  NCBI__GCF_000013325.1:WP_011445434.1 527 HVSPEAAEGGEIGLVENGDVIEIDIPNRTIHLAVADDVLAQRRAEQEAKGWkpvkerpRKVSTALRAYAAMTT 599
                                           **************************************************999***999************** PP

                             TIGR00110 534 sadkGavld 542
                                           sa +Gav+d
  NCBI__GCF_000013325.1:WP_011445434.1 600 SAARGAVRD 608
                                           *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (615 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 30.64
//
[ok]

This GapMind analysis is from Jul 25 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