GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvD in Paraburkholderia bryophila 376MFSha3.1

Align dihydroxyacid dehydratase (characterized)
to candidate H281DRAFT_05312 H281DRAFT_05312 dihydroxyacid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05312 H281DRAFT_05312
           dihydroxyacid dehydratase
          Length = 619

 Score =  905 bits (2339), Expect = 0.0
 Identities = 460/621 (74%), Positives = 525/621 (84%), Gaps = 11/621 (1%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+T GRNMAGAR+LWRATGM D DF KPIIAVVNSFTQFVPGHVHL+DLG+LV
Sbjct: 1   MPAYRSKTSTAGRNMAGARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSD------QIIKLDLVDAMIQGADP 174
           NCDKITPGMLMA++RLNIPVIFVSGGPMEAGKT+L++      +  KLDLVDAM+  AD 
Sbjct: 121 NCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKTRLANPKTGTIEFKKLDLVDAMVIAADK 180

Query: 175 KVSDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLN 234
             SD+   +VERSACPTCGSCSGMFTANSMNCLTEALGLS PGNG+++ATHADR+QLF  
Sbjct: 181 AYSDADVAEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTVVATHADREQLFKR 240

Query: 235 AGKRIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEI 294
           AG+RIVEL ++YYEQ + S LPR +  KA FENAMTLDIAMGGSTNT+LHLLA A+EAEI
Sbjct: 241 AGRRIVELARQYYEQEEASVLPRAVGFKA-FENAMTLDIAMGGSTNTILHLLAIAREAEI 299

Query: 295 DFTMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLG 354
           DFTM+DID+LSR VPQLCKVAP+T KYH+EDVHRAGG++ ILGELDRAG L  DV  V  
Sbjct: 300 DFTMTDIDRLSRIVPQLCKVAPNTNKYHIEDVHRAGGIMAILGELDRAGKLQTDVPTVHA 359

Query: 355 LTLPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEH 414
            TL   L+Q+D++ T D+AV+  + AGPAG+ T  AFSQ+ RW +LD DRA GCIRS EH
Sbjct: 360 PTLKDALDQWDIVRTGDEAVRTFYMAGPAGVPTQVAFSQNTRWPSLDLDRAEGCIRSYEH 419

Query: 415 AYSKDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGD 474
           A+SK+GGLAVL GN A +GC+VKTAGVD+SIL F G A V ESQD+AVE IL GKV AGD
Sbjct: 420 AFSKEGGLAVLTGNIALDGCVVKTAGVDESILVFEGTAHVTESQDEAVENILAGKVKAGD 479

Query: 475 VVVIRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAAS 534
           VV++RYEGPKGGPGMQEMLYPTS++KS GLGKACAL+TDGRFSGGTSGLSIGH SPEAA+
Sbjct: 480 VVIVRYEGPKGGPGMQEMLYPTSYIKSQGLGKACALLTDGRFSGGTSGLSIGHCSPEAAA 539

Query: 535 GGSIGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTP-KNRERQVSFAL 593
           GG+IGL+ DGD I IDIPNR I + +SDAELA+RR+ Q+A+G   W P K R R+VS AL
Sbjct: 540 GGAIGLVRDGDKIRIDIPNRTINVLLSDAELASRRDEQNAKG---WKPAKPRPRKVSAAL 596

Query: 594 RAYASLATSADKGAVRDKSKL 614
           +AYA L  SADKGAVRD S L
Sbjct: 597 KAYAKLVMSADKGAVRDLSLL 617


Lambda     K      H
   0.317    0.134    0.386 

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: 1212
Number of extensions: 41
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: 616
Length of database: 619
Length adjustment: 37
Effective length of query: 579
Effective length of database: 582
Effective search space:   336978
Effective search space used:   336978
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 H281DRAFT_05312 H281DRAFT_05312 (dihydroxyacid 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.17639.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-257  841.9   2.8   1.3e-257  841.6   2.8    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05312  H281DRAFT_05312 dihydroxyacid de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05312  H281DRAFT_05312 dihydroxyacid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  841.6   2.8  1.3e-257  1.3e-257       2     542 ..      18     613 ..      17     614 .. 0.98

  Alignments for each domain:
  == domain 1  score: 841.6 bits;  conditional E-value: 1.3e-257
                                    TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGi 67 
                                                  ar+l++atG+kded++kPiiavvns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGi
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312  18 ARSLWRATGMKDEDFSKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGI 83 
                                                  69**************************************************************** PP

                                    TIGR00110  68 amgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpme 133
                                                  amgh+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+i+vsGGpme
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312  84 AMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFVSGGPME 149
                                                  ****************************************************************** PP

                                    TIGR00110 134 agktkl......sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmaclte 193
                                                  agkt+l      + +++++d+++a++ +a++  s++++ e+ersacPt+gsCsG+ftansm+clte
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 150 AGKTRLanpktgTIEFKKLDLVDAMVIAADKAYSDADVAEVERSACPTCGSCSGMFTANSMNCLTE 215
                                                  ****99777765568899************************************************ PP

                                    TIGR00110 194 alGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltkeafenaitldlal 252
                                                  alGlslPg++t+ at+a++++l+k++g+rivel +++++       Pr +   +afena+tld+a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 216 ALGLSLPGNGTVVATHADREQLFKRAGRRIVELARQYYEqeeasvlPRAV-GFKAFENAMTLDIAM 280
                                                  ***************************************99999988875.689************ PP

                                    TIGR00110 253 GGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk 317
                                                  GGstnt+Lhllaia+ea++++++ d+drlsr vP+l+k++P+++k+ ied+hraGG++a+l+eld+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 281 GGSTNTILHLLAIAREAEIDFTMTDIDRLSRIVPQLCKVAPNTNKYhIEDVHRAGGIMAILGELDR 346
                                                  *********************************************99******************* PP

                                    TIGR00110 318 egllhkdaltvtGktlaetlekvkvlr...................................vdqd 348
                                                  +g+l++d+ tv   tl++ l++ ++ r                                     + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 347 AGKLQTDVPTVHAPTLKDALDQWDIVRtgdeavrtfymagpagvptqvafsqntrwpsldldRAEG 412
                                                  **************************9*******************************88655555 PP

                                    TIGR00110 349 virsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                                  +irs +++++kegglavL+Gn+a +G+vvk+agv+e+il+feG+a+v es++ea+e il+gkvk+G
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 413 CIRSYEHAFSKEGGLAVLTGNIALDGCVVKTAGVDESILVFEGTAHVTESQDEAVENILAGKVKAG 478
                                                  ****************************************************************** PP

                                    TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaia 480
                                                  dvv++ryeGPkGgPGm+emL+Pts++++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 479 DVVIVRYEGPKGGPGMQEMLYPTSYIKSQGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIG 544
                                                  ****************************************************************** PP

                                    TIGR00110 481 lvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGa 539
                                                  lv+dGDki+iDi+nr++++ +s++ela+rr+++++k++       r+v+ aL++yaklv sadkGa
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 545 LVRDGDKIRIDIPNRTINVLLSDAELASRRDEQNAKGWkpakprpRKVSAALKAYAKLVMSADKGA 610
                                                  *************************************9999**999******************** PP

                                    TIGR00110 540 vld 542
                                                  v+d
  lcl|FitnessBrowser__Burk376:H281DRAFT_05312 611 VRD 613
                                                  *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (619 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: 00:00:00.02
# Mc/sec: 12.28
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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