Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_017598314.1 D471_RS0108975 aconitate hydratase AcnA
Query= BRENDA::Q9RIL1 (931 letters) >NCBI__GCF_000341125.1:WP_017598314.1 Length = 904 Score = 1473 bits (3813), Expect = 0.0 Identities = 736/931 (79%), Positives = 801/931 (86%), Gaps = 27/931 (2%) Query: 1 MSANSFDARSTLQVGDESYEIFRLDKVEGSARLPYSLKVLLENLLRTEDGANITADHIRA 60 MSANSF AR TL+VGDESYEIFRLD V+G+ RLPYSLKVLLENLLRTEDGAN+TADHIRA Sbjct: 1 MSANSFGARDTLRVGDESYEIFRLDAVQGANRLPYSLKVLLENLLRTEDGANVTADHIRA 60 Query: 61 LGGWDSQAQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAVKELGGDPAKINPLAPAEL 120 LG WD++AQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAV++LGGDP KINPLAPAEL Sbjct: 61 LGEWDAKAQPSQEIQFTPARVIMQDFTGVPCVVDLATMREAVRDLGGDPDKINPLAPAEL 120 Query: 121 VIDHSVIADKFGTNDAFKQNVELEYGRNKERYQFLRWGQTAFDEFKVVPPGTGIVHQVNI 180 VIDHSV+ D FG DAF++NVE+EY RN ERY+FLRWGQTAFDEFKVVPPGTGIVHQ NI Sbjct: 121 VIDHSVVVDLFGRPDAFERNVEIEYERNYERYKFLRWGQTAFDEFKVVPPGTGIVHQANI 180 Query: 181 EHLARTVMVRGGQAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSMLIPRV 240 EHLAR M R GQAYPDT VGTDSHTTM NGLG+LGWGVGGIEAEAAMLGQP+SMLIPRV Sbjct: 181 EHLARVTMSRNGQAYPDTCVGTDSHTTMQNGLGILGWGVGGIEAEAAMLGQPISMLIPRV 240 Query: 241 VGFKLTGELKPGTTATDLVLTITEMLRGHGVVGKFVEFYGEGVAATSLANRATIGNMSPE 300 VGFKL+G+LKPGTTATDLVLTITE LR HGVVGKFVEFYGEGV++ LANRATIGNMSPE Sbjct: 241 VGFKLSGQLKPGTTATDLVLTITEKLREHGVVGKFVEFYGEGVSSVPLANRATIGNMSPE 300 Query: 301 FGSTAAIFPIDDETLNYLRLTGRSEQQVALVESYAKEQGLWLDPAAEPDFSEKLELDLST 360 FGSTAAIFP+DDET+ Y+RLTGRSEQQVAL E+YAK G W DPA EP++SE LELDL+ Sbjct: 301 FGSTAAIFPVDDETIRYMRLTGRSEQQVALTEAYAKANGFWHDPAVEPEYSEYLELDLAE 360 Query: 361 VVPSIAGPKRPQDRIVLAEAAQQFAKDVLNYVEAPAAQPAASASPVDEASAESFPASDAP 420 VVPSIAGPKRPQDRI L+EA + DV NYV DEA ESFPASDAP Sbjct: 361 VVPSIAGPKRPQDRIALSEAKPTWRHDVHNYVSD------------DEAGEESFPASDAP 408 Query: 421 AYGSQENGAGARQHADGTGAAVPSNPVTVTAPDGTSYEIDHGAVTVAAITSCTNTSNPYV 480 A + NG P PV VT DGT E+DHGAV +AAITSCTNTSNP V Sbjct: 409 A--TTANGR-------------PHRPVKVTMADGTETEVDHGAVVIAAITSCTNTSNPSV 453 Query: 481 MVAAALVAKKAVEKGLTRKPWVKTTLAPGSKVVTDYFEKSGLTPYLDKVGFNLVGYGCTT 540 M+ AAL+AKKAVEKGL+RKPWVKT++APGSKVVTDY+E+SGLTPYLDK+GFNLVGYGCTT Sbjct: 454 MLGAALLAKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVGYGCTT 513 Query: 541 CIGNSGPLPEEVSKAVNDHDLAVTSVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS 600 CIGNSGPLPEE+SKAV D+DLAVT+VLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS Sbjct: 514 CIGNSGPLPEEISKAVQDNDLAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGS 573 Query: 601 MKVDITKDALGTDQDGNPVYLKDIWPSEAEVNDVVANAIGEDMFSKSYSDVFAGDAQWQA 660 + VDIT + LG DG PVYL DIWPS E+ +V+ AI DM+ +Y+DVFAGD +W++ Sbjct: 574 LDVDITTEPLGVGSDGKPVYLADIWPSAEEIQEVMDAAIASDMYESAYADVFAGDERWRS 633 Query: 661 LPIPTGNTFEWDPESTYVRKPPYFEGMEMEPAPVEDIAGARVLAKLGDSVTTDHISPAGA 720 LP PTGNTFEW+ ESTYVRKPPYFEGM P+ V DI GARVLAKLGDSVTTDHISPAGA Sbjct: 634 LPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKLGDSVTTDHISPAGA 693 Query: 721 IKADTPAGKYLTEHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF 780 IK TPA +YL HGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF Sbjct: 694 IKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRDF 753 Query: 781 TKDDAPVSFIYDASRNYIEQGIPLVVLAGKEYGSGSSRDWAAKGTALLGVKAVIAESYER 840 T+ +APVSFIYDA++NY Q IPLVVL GKEYGSGSSRDWAAKGT LLGV+AVI ESYER Sbjct: 754 TQPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVRAVITESYER 813 Query: 841 IHRSNLIGMGVLPLQFPEGQSAATLGLTGEETFSFSGVTELNNGTTPRTVKVTTDTGVEF 900 IHRSNLIGMGVLPLQFPEGQSA +LGLTGEETFS +GVTELN G P TVKV+TDTGVEF Sbjct: 814 IHRSNLIGMGVLPLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVKVSTDTGVEF 873 Query: 901 DAVVRIDTPGEADYYRNGGIMQYVLRSLIRK 931 DAVVRIDTPGEADYYRNGGI+QYVLR LI K Sbjct: 874 DAVVRIDTPGEADYYRNGGILQYVLRQLIAK 904 Lambda K H 0.314 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: 2453 Number of extensions: 104 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: 931 Length of database: 904 Length adjustment: 43 Effective length of query: 888 Effective length of database: 861 Effective search space: 764568 Effective search space used: 764568 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: 42 (22.0 bits) S2: 57 (26.6 bits)
Align candidate WP_017598314.1 D471_RS0108975 (aconitate hydratase AcnA)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# 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.carbon/TIGR01341.hmm # target sequence database: /tmp/gapView.2626763.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01341 [M=876] Accession: TIGR01341 Description: aconitase_1: aconitate hydratase 1 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1316.2 0.0 0 1315.9 0.0 1.0 1 NCBI__GCF_000341125.1:WP_017598314.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000341125.1:WP_017598314.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1315.9 0.0 0 0 15 876 .] 27 902 .. 17 902 .. 0.96 Alignments for each domain: == domain 1 score: 1315.9 bits; conditional E-value: 0 TIGR01341 15 lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpavvdlaalr 87 + ++lp+sl++lle++lr+ dg +++ +++ al +w+++++ +ei+f parv++qdftGvp vvdla++r NCBI__GCF_000341125.1:WP_017598314.1 27 VQGANRLPYSLKVLLENLLRTEDGANVTADHIRALGEWDAKAQPSQEIQFTPARVIMQDFTGVPCVVDLATMR 99 556799******************************************************************* PP TIGR01341 88 eavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvppgt 160 eav++lg+dp+kinpl p++lvidhsv vd +g +a+e nve+e+ern erykfl+w++ af ++kvvppgt NCBI__GCF_000341125.1:WP_017598314.1 100 EAVRDLGGDPDKINPLAPAELVIDHSVVVDLFGRPDAFERNVEIEYERNYERYKFLRWGQTAFDEFKVVPPGT 172 ************************************************************************* PP TIGR01341 161 GivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpevi 233 Givhq n+e+la+v ++ + aypd+ vGtdshttm nGlG+lGwGvGGieaeaa+lGqp+s+ +p v+ NCBI__GCF_000341125.1:WP_017598314.1 173 GIVHQANIEHLARVTMSRN----GQAYPDTCVGTDSHTTMQNGLGILGWGVGGIEAEAAMLGQPISMLIPRVV 241 **************99988....679*********************************************** PP TIGR01341 234 GvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvt 306 G+kl G+l++G+tatdlvlt+te lr++gvvgkfvef+Geg+++++la+rati nm+pe+G+taa+fp+dd+t NCBI__GCF_000341125.1:WP_017598314.1 242 GFKLSGQLKPGTTATDLVLTITEKLREHGVVGKFVEFYGEGVSSVPLANRATIGNMSPEFGSTAAIFPVDDET 314 ************************************************************************* PP TIGR01341 307 lqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss 379 + y+rltgr+e++v l e+y+ka+++++d + ep+y++ +eldl +v +s+aGpkrpqdr+al+e k ++++ NCBI__GCF_000341125.1:WP_017598314.1 315 IRYMRLTGRSEQQVALTEAYAKANGFWHDPAVEPEYSEYLELDLAEVVPSIAGPKRPQDRIALSEAKPTWRHD 387 **********************************************************************999 PP TIGR01341 380 lesnagekglalr.................keakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435 +++ +++ + + + + k ++ +g+e+e+++gavviaaitsctntsnpsv+lga+ll NCBI__GCF_000341125.1:WP_017598314.1 388 VHNYVSDDEAGEEsfpasdapattangrphRPVKVTMADGTETEVDHGAVVIAAITSCTNTSNPSVMLGAALL 460 776665555444444555889999999885444555557********************************** PP TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508 akkave Gl +kp+vkts+apGskvvtdy +sgl+pyl++lGfnlvGyGcttciGnsGpl+ee+++a+++nd NCBI__GCF_000341125.1:WP_017598314.1 461 AKKAVEKGLSRKPWVKTSMAPGSKVVTDYYERSGLTPYLDKLGFNLVGYGCTTCIGNSGPLPEEISKAVQDND 533 ************************************************************************* PP TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581 l v+avlsGnrnfegri+p+vk nylaspplvvayalaG++d+d+++ep+g++ dGk+vyl diwpsa+ei+e NCBI__GCF_000341125.1:WP_017598314.1 534 LAVTAVLSGNRNFEGRINPDVKMNYLASPPLVVAYALAGSLDVDITTEPLGVGSDGKPVYLADIWPSAEEIQE 606 ************************************************************************* PP TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654 +++ a+ +++++ y+ v+ g+erw++l +++++++ew+++sty+r+pp+fe++ ++p+ v+di+gar+l++l NCBI__GCF_000341125.1:WP_017598314.1 607 VMDAAIASDMYESAYADVFAGDERWRSLPTPTGNTFEWEDESTYVRKPPYFEGMATTPSAVTDITGARVLAKL 679 ************************************************************************* PP TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvy 727 Gds+ttdhispaG+ik+ +paa+ylk +GverrdfnsyGsrrGnhevm+rGtfanir++n++++g+eGg+t+ NCBI__GCF_000341125.1:WP_017598314.1 680 GDSVTTDHISPAGAIKPGTPAAEYLKSHGVERRDFNSYGSRRGNHEVMIRGTFANIRLRNQIAPGTEGGYTRD 752 ***********************************************************************96 PP TIGR01341 728 l..pdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvl 798 + p+ v +ydaa +y +++plvvl GkeyGsGssrdwaakgt+llGv+avi+es+erihrsnl+gmGvl NCBI__GCF_000341125.1:WP_017598314.1 753 FtqPEAPVSFIYDAAQNYAAQDIPLVVLGGKEYGSGSSRDWAAKGTRLLGVRAVITESYERIHRSNLIGMGVL 825 5348888999*************************************************************** PP TIGR01341 799 plefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyv 871 pl+f++g++a++lgltgeet + +++el+ ++ + + v++d ++av+ridt+ e +y+++gGilqyv NCBI__GCF_000341125.1:WP_017598314.1 826 PLQFPEGQSADSLGLTGEETFSITGVTELNEGRVPSTVKVSTD-TGVEFDAVVRIDTPGEADYYRNGGILQYV 897 *****************************98875444334444.45689************************ PP TIGR01341 872 lrkll 876 lr+l+ NCBI__GCF_000341125.1:WP_017598314.1 898 LRQLI 902 **975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (876 nodes) Target sequences: 1 (904 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 31.80 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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:
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