Alignments for a candidate for ilvD in Pseudomonas putida KT2440

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.1529.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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 8.26
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis