GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas putida KT2440

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__Putida:PP_5128
          Length = 613

 Score =  930 bits (2403), Expect = 0.0
 Identities = 460/608 (75%), Positives = 520/608 (85%), Gaps = 2/608 (0%)

Query: 1   MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60
           MP YRS+T+T GRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPDYRSKTSTQGRNMAGARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IAD+VEYMVNAHCADA+VCIS
Sbjct: 61  AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADAVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180
           NCDKITPGMLMA+LRLNIP +FVSGGPMEAGK  +   +H LDLVDAMV AAD   SDE 
Sbjct: 121 NCDKITPGMLMAALRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADSTASDEK 178

Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240
           V   ERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGSTLATH DR++LF+ AG  IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLTAGRTIV 238

Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300
           +L +RYY ++D   LPR+IA+ +AFENAM LDIAMGGSTNT+LH+LAAA EGE+ F + D
Sbjct: 239 ELCKRYYGENDESVLPRSIANFKAFENAMMLDIAMGGSTNTILHLLAAAQEGEVAFDLRD 298

Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360
           ID LSR+VP L KVAP     HMEDVHRAGGI SILG L +GGLL+ D PTVH+ ++ +A
Sbjct: 299 IDRLSRKVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSRSMEEA 358

Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420
           I +WDIT+T+ E V  F++A P GIPTQ AFSQ  RW+ LD DRENG IRS EH +S++G
Sbjct: 359 IAKWDITQTDDEAVHTFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSFEHAYSQEG 418

Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480
           GLAVL GN+A+DGC+VKTAGVDESI  F G A++FESQD++V+ ILA+EVKAGD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIFESQDSAVRGILADEVKAGDIVIIRY 478

Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540
           EGPKGGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538

Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600
           VR+GD + IDIPNR+I+L VS+ ELA RR EQD KGW P EVR R VTTALKAYA  ATS
Sbjct: 539 VRDGDKVLIDIPNRSINLLVSDEELAQRRVEQDKKGWKPAEVRPRKVTTALKAYALLATS 598

Query: 601 ADRGAVRD 608
           AD+GAVR+
Sbjct: 599 ADKGAVRN 606


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: 1180
Number of extensions: 33
Number of successful extensions: 2
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: 613
Length adjustment: 37
Effective length of query: 575
Effective length of database: 576
Effective search space:   331200
Effective search space used:   331200
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 PP_5128 PP_5128 (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.543.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-254  831.3   1.2     2e-254  831.0   1.2    1.0  1  lcl|FitnessBrowser__Putida:PP_5128  PP_5128 Dihydroxy-acid dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5128  PP_5128 Dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  831.0   1.2    2e-254    2e-254       2     542 ..      18     606 ..      17     607 .. 0.98

  Alignments for each domain:
  == domain 1  score: 831.0 bits;  conditional E-value: 2e-254
                           TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmky 76 
                                         aral++atG+kded++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamgh+Gm+y
  lcl|FitnessBrowser__Putida:PP_5128  18 ARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGIAMGHDGMLY 92 
                                         79************************************************************************* PP

                           TIGR00110  77 sLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfea 151
                                         sLpsreiiaD+ve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+i+vsGGpmeagktkl    + +d+++a
  lcl|FitnessBrowser__Putida:PP_5128  93 SLPSREIIADAVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDA 165
                                         **************************************************************8..557899**** PP

                           TIGR00110 152 vgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivel 226
                                         ++ +a++  s+e++ e+ersacPt+gsCsG+ftansm+cltealGl+lPg++++lat++++++l+ ++g++ivel
  lcl|FitnessBrowser__Putida:PP_5128 166 MVIAADSTASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLTAGRTIVEL 240
                                         *************************************************************************** PP

                           TIGR00110 227 vkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPs 294
                                         +k+++        Pr+i++ +afena++ld+a+GGstnt+Lhlla+a+e +v ++l d+drlsrkvP+l+k++P+
  lcl|FitnessBrowser__Putida:PP_5128 241 CKRYYGendesvlPRSIANFKAFENAMMLDIAMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQLCKVAPN 315
                                         *****99999***************************************************************** PP

                           TIGR00110 295 gkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr........................ 344
                                          +k+ +ed+hraGG+ ++l++l + gllh+d  tv  ++++e ++k ++++                        
  lcl|FitnessBrowser__Putida:PP_5128 316 IQKYhMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQtddeavhtffkagpagiptqtafs 390
                                         *9999********************************************999*********************** PP

                           TIGR00110 345 ...........vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408
                                                     ++ +irs ++++++egglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +il+
  lcl|FitnessBrowser__Putida:PP_5128 391 qstrwetldddRENGCIRSFEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIFESQDSAVRGILA 465
                                         *******77555555************************************************************ PP

                           TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                          +vk+Gd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv+
  lcl|FitnessBrowser__Putida:PP_5128 466 DEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVR 540
                                         *************************************************************************** PP

                           TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                         dGDk+ iDi+nr ++l vs+eela+rr +++kk++       r+v  aL++ya l++sadkGav++
  lcl|FitnessBrowser__Putida:PP_5128 541 DGDKVLIDIPNRSINLLVSDEELAQRRVEQDKKGWkpaevrpRKVTTALKAYALLATSADKGAVRN 606
                                         **********************************99*****999********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (613 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 8.55
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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