GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Streptacidiphilus oryzae TH49

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_037574832.1 BS73_RS21300 dihydroxy-acid dehydratase

Query= BRENDA::Q8NQZ9
         (613 letters)



>NCBI__GCF_000744815.1:WP_037574832.1
          Length = 616

 Score =  826 bits (2133), Expect = 0.0
 Identities = 403/613 (65%), Positives = 493/613 (80%), Gaps = 3/613 (0%)

Query: 1   MIPLRSKVTTVGRNAAGARALWRATGTKENEFG-KPIVAIVNSYTQFVPGHVHLKNVGDI 59
           M  LRS+  T GRN AGARAL RA+G    + G KPI+A+ NS+T+FVPGH HL  VG I
Sbjct: 1   MPELRSRTVTHGRNMAGARALMRASGVAGADIGRKPIIAVANSFTEFVPGHTHLSPVGRI 60

Query: 60  VADAVRKAGGVPKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHTADAMVCI 119
           V++AV +AGG+P+EFNTIAVDDGIAMGHGGMLYSLPSR++IADSVEYMVNAH ADA+VCI
Sbjct: 61  VSEAVSEAGGIPREFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCI 120

Query: 120 SNCDKITPGMLNAAMRLNIPVVFVSGGPMEAGKAVVVDGVAHAPTDLITAISASASDAVD 179
           SNCDKITPGML AAMRLNIP +FVSGGPME+G+A +VDG      DLITAI+ SA+DAV 
Sbjct: 121 SNCDKITPGMLMAAMRLNIPTIFVSGGPMESGQATLVDGTVRK-LDLITAIAESANDAVS 179

Query: 180 DAGLAAVEASACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRALFEKAGE 239
           D  ++ +E +ACPTCGSCSGMFTANSMNCLTEA+GL+LPGNG+TLATH AR+AL+++AG 
Sbjct: 180 DEDISRIEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTTLATHTARKALYQEAGR 239

Query: 240 TVVELCRRYYGEEDESVLPRGIATKKAFENAMALDMAMGGSTNTILHILAAAQEGEVDFD 299
            +++L  RYYG++D +VLPR I ++ AFENAMALD+AMGGSTNTILH+LAAAQE E+DF 
Sbjct: 240 QILKLVDRYYGQDDSTVLPRSIGSRAAFENAMALDIAMGGSTNTILHLLAAAQEAELDFT 299

Query: 300 LADIDELSKNVPCLSKVAPNSDYHMEDVHRAGGIPALLGELNRGGLLNKDVHSVHSNDLE 359
           + DID LS+ +PCL KVAPN  Y++EDVHRAGGIP +LGEL R GLLN+DV +VHS+ L 
Sbjct: 300 MGDIDALSRRLPCLCKVAPNGSYYVEDVHRAGGIPGILGELYRAGLLNEDVTTVHSDSLA 359

Query: 360 GWLDDWDIRSGKTTEVATELFHAAPGGIRTTEAFSTENRWDELDTDAAKGCIRDVEHAYT 419
            WL  WD+R G  +  A ELFHAAPG  R+ EAFS   RWD LD DA +GCIRD+ HAY+
Sbjct: 360 DWLKRWDVRGGSPSPEAVELFHAAPGCKRSAEAFSQSERWDSLDLDAERGCIRDIGHAYS 419

Query: 420 ADGGLVVLRGNISPDGAVIKSAGIEEELWNFTGPARVVESQEEAVSVILTKTIQAGEVLV 479
            +GGL VL GN++ +G V+K+AG++E +W FTGPA V ESQ+EAV  IL K +  G+V+V
Sbjct: 420 TEGGLAVLHGNLAENGCVVKTAGVDESIWEFTGPAVVCESQDEAVERILNKEVGEGDVVV 479

Query: 480 VRYEGPSGGPGMQEMLHPTAFLKGSGLGKKCALITDGRFSGGSSGLSIGHVSPEAAHGGV 539
           +RYEGP GGPGMQEML+PT+FLKG GLGK CALITDGRFSGG+SGLSIGH+SPEAA GG 
Sbjct: 480 IRYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIGHMSPEAAAGGT 539

Query: 540 IGLIENGDIVSIDVHNRKLEVQVSDEELQRRRDAMNASEKPWQPVNRNRVVTKALRAYAK 599
           I L+ +GD ++I +  R++ ++V + EL  RR A+ A    ++P NR R V+ ALRAYA 
Sbjct: 540 IALVRDGDRITISIPERRICLEVPEAELAERRAALEAG-TGYRPANRQRQVSAALRAYAA 598

Query: 600 MATSADKGAVRQV 612
           MATSADKGAVR V
Sbjct: 599 MATSADKGAVRDV 611


Lambda     K      H
   0.315    0.132    0.385 

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: 1145
Number of extensions: 40
Number of successful extensions: 4
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: 613
Length of database: 616
Length adjustment: 37
Effective length of query: 576
Effective length of database: 579
Effective search space:   333504
Effective search space used:   333504
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)

Align candidate WP_037574832.1 BS73_RS21300 (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.148245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-241  788.4   1.4     2e-241  788.2   1.4    1.0  1  NCBI__GCF_000744815.1:WP_037574832.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037574832.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  788.2   1.4    2e-241    2e-241       2     542 ..      18     610 ..      17     611 .. 0.98

  Alignments for each domain:
  == domain 1  score: 788.2 bits;  conditional E-value: 2e-241
                             TIGR00110   2 arallkatGlkdedle.kPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 
                                           aral++a G+  +d++ kPiiav+ns+te+vPgh hl+ ++++v+e++++aGg++ efntiav+DGiamgh+G
  NCBI__GCF_000744815.1:WP_037574832.1  18 ARALMRASGVAGADIGrKPIIAVANSFTEFVPGHTHLSPVGRIVSEAVSEAGGIPREFNTIAVDDGIAMGHGG 90 
                                           79************9748******************************************************* PP

                             TIGR00110  74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl.sekidl 145
                                           m+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpme+g+ +l    + +
  NCBI__GCF_000744815.1:WP_037574832.1  91 MLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMESGQATLvDGTVRK 163
                                           ***************************************************************9983557999 PP

                             TIGR00110 146 vdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakk 218
                                           +d++ a+ e a++ +s+e++++ie++acPt+gsCsG+ftansm+cltea+Gl+lPg++t+lat++ +k+l ++
  NCBI__GCF_000744815.1:WP_037574832.1 164 LDLITAIAESANDAVSDEDISRIEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTTLATHTARKALYQE 236
                                           ************************************************************************* PP

                             TIGR00110 219 sgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrk 284
                                           +g++i +lv +++        Pr+i +++afena++ld+a+GGstnt+Lhlla+a+ea++++++ d+d lsr+
  NCBI__GCF_000744815.1:WP_037574832.1 237 AGRQILKLVDRYYGqddstvlPRSIGSRAAFENAMALDIAMGGSTNTILHLLAAAQEAELDFTMGDIDALSRR 309
                                           ************999999******************************************************* PP

                             TIGR00110 285 vPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............. 344
                                           +P+l+k++P+g++++ed+hraGG++++l+el+++gll++d++tv  ++la+ l++ +v+              
  NCBI__GCF_000744815.1:WP_037574832.1 310 LPCLCKVAPNGSYYVEDVHRAGGIPGILGELYRAGLLNEDVTTVHSDSLADWLKRWDVRGgspspeavelfha 382
                                           **********************************************************9999*********** PP

                             TIGR00110 345 .......................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394
                                                                  +++ +ir + ++++ egglavL+Gnlae+G+vvk+agv+e+i++f+Gpa 
  NCBI__GCF_000744815.1:WP_037574832.1 383 apgckrsaeafsqserwdsldldAERGCIRDIGHAYSTEGGLAVLHGNLAENGCVVKTAGVDESIWEFTGPAV 455
                                           *******************99777777********************************************** PP

                             TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467
                                           v es++ea+e il+++v eGdvvviryeGPkGgPGm+emL+Pts+l+g GLgk++aLitDGrfsGgt+GlsiG
  NCBI__GCF_000744815.1:WP_037574832.1 456 VCESQDEAVERILNKEVGEGDVVVIRYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIG 528
                                           ************************************************************************* PP

                             TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvs 533
                                           h+sPeaa+gG+ialv+dGD+i+i i++r++ lev e+elaerra+ ++ +        r+v+ aL++ya +++
  NCBI__GCF_000744815.1:WP_037574832.1 529 HMSPEAAAGGTIALVRDGDRITISIPERRICLEVPEAELAERRAALEAGTGyrpanrqRQVSAALRAYAAMAT 601
                                           ********************************************998765567788889************** PP

                             TIGR00110 534 sadkGavld 542
                                           sadkGav+d
  NCBI__GCF_000744815.1:WP_037574832.1 602 SADKGAVRD 610
                                           *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (616 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: 17.36
//
[ok]

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