Align dihydroxyacid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_012607168.1 AFE_RS07765 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-18815 (557 letters) >NCBI__GCF_000021485.1:WP_012607168.1 Length = 557 Score = 769 bits (1985), Expect = 0.0 Identities = 384/557 (68%), Positives = 461/557 (82%) Query: 1 MAFNKRSQNITQGVARSPNRSMYYALGYKKEDFDKPMVGIANGHSTITPCNAGLQRLADA 60 M+ N+RS+ ITQGV RSPNR++ A+G+ DFDKP+VG+AN HS+ITPCN G+ LA Sbjct: 1 MSDNRRSKTITQGVQRSPNRALLRAVGFGDWDFDKPIVGVANAHSSITPCNIGIGVLAAR 60 Query: 61 AIDAIKASDANPQVFGTPTISDGMSMGTEGMKYSLISREVIADCIETAAQGQWMDGVVVI 120 A A+K++ A PQ FGT TISDG+SMGT GMKYSL+SREVIAD IET QGQ MDGV+ + Sbjct: 61 AEAALKSAGAMPQTFGTITISDGISMGTAGMKYSLVSREVIADSIETVCQGQSMDGVLAL 120 Query: 121 GGCDKNMPGGMIALARTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAGRMSQED 180 GGCDKNMPG MIA+AR N+P I+VYGGTIKPG+++G+DLTI+S+FEAVG+ T ++ E+ Sbjct: 121 GGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYRGQDLTIMSAFEAVGQHTVHKIDDEE 180 Query: 181 FEGVEKNACPSTGSCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLV 240 +E+ ACP GSCGGMYTANTMSS FEA+GMSL YSSTMA D EK +SAA+SA VLV Sbjct: 181 LLEIERRACPGAGSCGGMYTANTMSSIFEAMGMSLPYSSTMAAEDAEKAESAAQSAEVLV 240 Query: 241 EAIKQDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHAAEVEWTIDDFERIRRK 300 AI++ I PR I+TR++ ENA+A+ MA GGSTNAVLH LAIAHAA+V T+DDFE +R + Sbjct: 241 SAIRKQILPRQILTRQAFENAIAVAMAVGGSTNAVLHLLAIAHAAQVPLTLDDFEAMRER 300 Query: 301 VPVICNLKPSGQYVATDLHKAGGIPQVMKILLKAGMLHGDCLTITGRTLAEELENVPDTP 360 VPV+C+LKPSG+YV+TDLH+AGGIPQVMKILL G+LHGD LTI+G+TLAE L++VP Sbjct: 301 VPVLCDLKPSGRYVSTDLHRAGGIPQVMKILLAHGVLHGDALTISGQTLAEVLQDVPSEA 360 Query: 361 RADQDVILPIEKALYAEGHLAILKGNLAEEGAVAKITGLKNPVITGPARVFEDEQSAMEA 420 R DQ+VI P +YA+GHLAILKGNLA EGAVAK TG ITGPARVFE E+S MEA Sbjct: 361 RTDQEVIRPWNNPIYAQGHLAILKGNLAPEGAVAKTTGFMAHKITGPARVFESEESCMEA 420 Query: 421 ILADKINAGDILVLRYLGPKGGPGMPEMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMV 480 ILA KI GD++V+RY GPKGGPGM EML+PTSAIIG+GLG+SVG ITDGRFSG T+GMV Sbjct: 421 ILAQKIKPGDVVVIRYEGPKGGPGMREMLSPTSAIIGEGLGDSVGLITDGRFSGATYGMV 480 Query: 481 VGHVAPEAYVGGTIALVQEGDSITIDAHKLLLQLNVADEELARRRANWKQPAPRYTRGVL 540 VGHVAPEA VGGTIALV EGDS+TIDA + LLQLNV+DEE+ RRRA W+ PAPR+TRGVL Sbjct: 481 VGHVAPEAAVGGTIALVIEGDSVTIDAGQRLLQLNVSDEEIGRRRAVWQAPAPRHTRGVL 540 Query: 541 AKFSKLASTASKGAVTD 557 AK++KL S+ASKGAVTD Sbjct: 541 AKYAKLVSSASKGAVTD 557 Lambda K H 0.316 0.133 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: 1016 Number of extensions: 34 Number of successful extensions: 1 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: 557 Length of database: 557 Length adjustment: 36 Effective length of query: 521 Effective length of database: 521 Effective search space: 271441 Effective search space used: 271441 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_012607168.1 AFE_RS07765 (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.7915.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-243 793.5 7.9 5.5e-243 793.3 7.9 1.0 1 lcl|NCBI__GCF_000021485.1:WP_012607168.1 AFE_RS07765 dihydroxy-acid dehyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_012607168.1 AFE_RS07765 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 793.3 7.9 5.5e-243 5.5e-243 1 542 [. 18 557 .] 18 557 .] 0.99 Alignments for each domain: == domain 1 score: 793.3 bits; conditional E-value: 5.5e-243 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++rall+a+G+ d d++kPi++v+n++++i+P+++ + la ++++++++aG++++ f+ti++sDGi+m lcl|NCBI__GCF_000021485.1:WP_012607168.1 18 PNRALLRAVGFGDWDFDKPIVGVANAHSSITPCNIGIGVLAARAEAALKSAGAMPQTFGTITISDGISM 86 68******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 g+ GmkysL+sre+iaDs+etv++++ +D++++++ CDk++PG+++a +r+niPai+v+GG++++g+++ lcl|NCBI__GCF_000021485.1:WP_012607168.1 87 GTAGMKYSLVSREVIADSIETVCQGQSMDGVLALGGCDKNMPGAMIAIARMNIPAIFVYGGTIKPGHYR 155 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +++++++++feavg+ + k+++eel eier acP+agsC+G++tan+m++++ea+G+slP+sst++a lcl|NCBI__GCF_000021485.1:WP_012607168.1 156 -GQDLTIMSAFEAVGQHTVHKIDDEELLEIERRACPGAGSCGGMYTANTMSSIFEAMGMSLPYSSTMAA 223 .9******************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 +aek+e+a +s++ +v +++k+i Pr+ilt++afenai++ +a+GGstn+vLhllaia+ a+v l+ld lcl|NCBI__GCF_000021485.1:WP_012607168.1 224 EDAEKAESAAQSAEVLVSAIRKQILPRQILTRQAFENAIAVAMAVGGSTNAVLHLLAIAHAAQVPLTLD 292 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvl.r 344 df+ ++++vP+l++lkPsg++v +dlhraGG+++v+k l +g+lh dalt++G+tlae+l++v++ r lcl|NCBI__GCF_000021485.1:WP_012607168.1 293 DFEAMRERVPVLCDLKPSGRYVSTDLHRAGGIPQVMKILLAHGVLHGDALTISGQTLAEVLQDVPSEaR 361 ***************************************************************987626 PP TIGR00110 345 vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvke 413 +dq+vir+++np++++g+la+LkGnla+eGav+k++g k++Gpa+vfesee ++eail+ k+k lcl|NCBI__GCF_000021485.1:WP_012607168.1 362 TDQEVIRPWNNPIYAQGHLAILKGNLAPEGAVAKTTGFMA--HKITGPARVFESEESCMEAILAQKIKP 428 8999**********************************99..9************************** PP TIGR00110 414 GdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialv 482 GdvvviryeGPkGgPGmremL Ptsa++g GLg++v+LitDGrfsG+t+G+++Ghv+Peaa+gG+ialv lcl|NCBI__GCF_000021485.1:WP_012607168.1 429 GDVVVIRYEGPKGGPGMREMLSPTSAIIGEGLGDSVGLITDGRFSGATYGMVVGHVAPEAAVGGTIALV 497 ********************************************************************* PP TIGR00110 483 edGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +GD ++iD+ +r l+l+vs+ee+ +rra ++++ +r+++g+Lakyaklvssa+kGav+d lcl|NCBI__GCF_000021485.1:WP_012607168.1 498 IEGDSVTIDAGQRLLQLNVSDEEIGRRRAVWQAPAPRHTRGVLAKYAKLVSSASKGAVTD 557 **********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (557 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: 10.62 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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:
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