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.
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:
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