Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013076481.1 BTUS_RS12735 aconitate hydratase AcnA
Query= BRENDA::P09339
(909 letters)
>NCBI__GCF_000092905.1:WP_013076481.1
Length = 903
Score = 1164 bits (3012), Expect = 0.0
Identities = 567/898 (63%), Positives = 703/898 (78%), Gaps = 1/898 (0%)
Query: 8 AAKDVFQARKTFTTNGKTYHYYSLKALEDSGIGKVSKLPYSIKVLLESVLRQVDGFVIKK 67
A++DVFQ R+T GK Y YYSL AL+ G+G +S+LPYSI+VLLE+ LRQVDG + +
Sbjct: 2 ASQDVFQTRRTLEAGGKRYVYYSLPALDKQGVGPISRLPYSIRVLLEAALRQVDGKGVTE 61
Query: 68 EHVENLAKWGTAELKDIDVPFKPSRVILQDFTGVPAVVDLASLRKAMAAVGGDPDKINPE 127
EHV+ LA W + +++PFKP+R++LQDFTGVPAVVDLA++R+ + +GGDP KINP
Sbjct: 62 EHVKKLANWQESHRHPVEIPFKPARIVLQDFTGVPAVVDLAAMRRTVKEMGGDPGKINPL 121
Query: 128 IPVDLVIDHSVQVDKAGTEDALAVNMDLEFERNAERYKFLSWAKKAFNNYQAVPPATGIV 187
+PVDLVIDHSVQVD GT +AL N++LEF+RN ERY+FL WA+ AF N++ VPP+TGIV
Sbjct: 122 VPVDLVIDHSVQVDLYGTPEALERNVELEFQRNEERYRFLRWAQGAFENFRVVPPSTGIV 181
Query: 188 HQVNLEFLASVVHAIEEDGELVTYPDTLVGTDSHTTMINGIGVLGWGVGGIEAEAGMLGQ 247
HQVNLE+LASVV EE GE V +PD+LVGTDSHTTMING+GVLGWGVGGIEAEAGMLGQ
Sbjct: 182 HQVNLEYLASVVGRREEGGETVLFPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQ 241
Query: 248 PSYFPVPEVIGAKLVGKLPNGTTATDLALKVTQVLREKGVVGKFVEFFGPGIAELPLADR 307
P YF +PEVIG +L G+LP G+TATDLAL VT +LR+KGVVGKFVEFFGPG++ + +ADR
Sbjct: 242 PLYFLIPEVIGFRLTGRLPEGSTATDLALTVTNLLRKKGVVGKFVEFFGPGLSSITVADR 301
Query: 308 ATIANMAPEYGATCGFFPVDEEALNYLRLTGRDPEHIDVVEAYCRSNGLFYTPDAEDPQF 367
AT+ANMAPEYGAT G+FPVDE L+YLRLTGR E + + EAY ++ GL +T +A +P F
Sbjct: 302 ATVANMAPEYGATMGYFPVDERTLDYLRLTGRKAEDVALAEAYLKAQGLLHTEEAPEPVF 361
Query: 368 TDVVEIDLSQIEANLSGPKRPQDLIPLSAMQETFKKQLVSPAGNQGFGLNAEEENKEIKF 427
+D+VE+DLS ++ L+GPKRPQD +PL ++ +F+K + SP GFG E +
Sbjct: 362 SDIVELDLSTVKPTLAGPKRPQDKVPLPDLKASFEKAVESPVDQGGFGFGKEGLARTSDV 421
Query: 428 KLLNGEETVMKTGAIAIAAITSCTNTSNPYVLIGAGLVAKKAVELGLKVPNYVKTSLAPG 487
K +G ++TGA+ IAAITSCTNTSNP V+IGAGL+AKKAVE GL P YVK+SLAPG
Sbjct: 422 KYPDGGRETLRTGAVVIAAITSCTNTSNPSVMIGAGLLAKKAVEKGLTKPRYVKSSLAPG 481
Query: 488 SKVVTGYLVNSGLLPYMKELGFNLVGYGCTTCIGNSGPLSPEIEEAVAKNDLLITSVLSG 547
S+VVT YL +GLLP +++LGF +VGYGCTTCIGNSGPL PE+ EA+ + D+ + +VLSG
Sbjct: 482 SRVVTAYLKRAGLLPALEQLGFAVVGYGCTTCIGNSGPLDPEVAEAIQEKDMTVAAVLSG 541
Query: 548 NRNFEGRIHPLVKGNYLASPPLVVAYALAGTVNINLKTDPIGVGKDGQNVYFNDIWPSMD 607
NRNFEGRIHPLV+ NYLASPPLVVAYALAGTV+I+L +P+G +DG VY DIWPS +
Sbjct: 542 NRNFEGRIHPLVRANYLASPPLVVAYALAGTVDIDLSKEPLGTDRDGNPVYLKDIWPSSE 601
Query: 608 EINALVKQTVTPELFRKEYETVFDDNKRWNEIETTDEALYKWDNDSTYIQNPPFFEEMSV 667
E+ A ++Q VT ELF +EY V N+RWN + T + LY +D DSTYIQ PPFF +S
Sbjct: 602 EVQAAIQQAVTAELFSEEYAHVLTANQRWNALPTPEGELYHFDADSTYIQEPPFFVNLSR 661
Query: 668 EPGKVEPLKGLRVVGKFGDSVTTDHISPAGAIGKDTPAGKYLQEKGVSPRDFNSYGSRRG 727
E G + ++G RV+ GDSVTTDHISPAG+I ++PA KYL E GV RDFNSYGSRRG
Sbjct: 662 EAGHIADIRGARVLALLGDSVTTDHISPAGSIAPNSPAAKYLMEHGVERRDFNSYGSRRG 721
Query: 728 NHEVMMRGTFANIRIKNQIAPGTEGGFTTYWPTGEVTSIYDACMKYKEDKTGLVVLAGKD 787
NHEVMMRGTFANIRI+N +APGTEGG T Y PTGE IYDA MKY+ D T LVVLAGK+
Sbjct: 722 NHEVMMRGTFANIRIRNLLAPGTEGGVTVYLPTGETMPIYDAAMKYQADGTPLVVLAGKE 781
Query: 788 YGMGSSRDWAAKGTNLLGIRTVIAESFERIHRSNLVFMGVLPLQFKQGENADTLGLTGKE 847
YG GSSRDWAAKGT LLG++ V+AESFERIHRSNLV MGVLPLQF +GE+ +LGLTGKE
Sbjct: 782 YGTGSSRDWAAKGTMLLGVKAVLAESFERIHRSNLVGMGVLPLQFTKGESWKSLGLTGKE 841
Query: 848 VIEVD-VDETVRPRDLVTVRAINEDGNVTTFEAVVRFDSEVEIDYYRHGGILQMVLRE 904
++ + + ++P V V A++EDG F+A+VR DS VEI+YYR+GGILQ VLR+
Sbjct: 842 RFDIQGLSDDIQPLSTVRVTAVDEDGGRLEFDALVRLDSVVEIEYYRNGGILQTVLRQ 899
Lambda K H
0.316 0.135 0.394
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: 2252
Number of extensions: 96
Number of successful extensions: 3
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: 909
Length of database: 903
Length adjustment: 43
Effective length of query: 866
Effective length of database: 860
Effective search space: 744760
Effective search space used: 744760
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 (21.5 bits)
S2: 56 (26.2 bits)
Align candidate WP_013076481.1 BTUS_RS12735 (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.2099314.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 1433.6 0.0 0 1433.4 0.0 1.0 1 NCBI__GCF_000092905.1:WP_013076481.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092905.1:WP_013076481.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1433.4 0.0 0 0 2 876 .] 19 901 .. 18 901 .. 0.98
Alignments for each domain:
== domain 1 score: 1433.4 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqd 73
++ yysl+al+++ + is+lp+s+r+lle++lr++dg+ ++ee+v++l++w++++ + +ei+fkpar+vlqd
NCBI__GCF_000092905.1:WP_013076481.1 19 RYVYYSLPALDKQgVGPISRLPYSIRVLLEAALRQVDGKGVTEEHVKKLANWQESHRHPVEIPFKPARIVLQD 91
689********987899******************************************************** PP
TIGR01341 74 ftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwa 146
ftGvpavvdlaa+r +vk++g+dp kinplvpvdlvidhsvqvd +g+ eale nvelef+rn+ery+fl+wa
NCBI__GCF_000092905.1:WP_013076481.1 92 FTGVPAVVDLAAMRRTVKEMGGDPGKINPLVPVDLVIDHSVQVDLYGTPEALERNVELEFQRNEERYRFLRWA 164
************************************************************************* PP
TIGR01341 147 kkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaa 219
+ af+n++vvpp+tGivhqvnleyla+vv + e+ ge++++pdslvGtdshttminGlGvlGwGvGGieaea+
NCBI__GCF_000092905.1:WP_013076481.1 165 QGAFENFRVVPPSTGIVHQVNLEYLASVVGRREEGGETVLFPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAG 237
************************************************************************* PP
TIGR01341 220 llGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmape 292
+lGqp+++ +peviG++ltG+l eG tatdl+ltvt+llrkkgvvgkfveffG+gl+++++adrat+anmape
NCBI__GCF_000092905.1:WP_013076481.1 238 MLGQPLYFLIPEVIGFRLTGRLPEGSTATDLALTVTNLLRKKGVVGKFVEFFGPGLSSITVADRATVANMAPE 310
************************************************************************* PP
TIGR01341 293 yGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpq 364
yGat+++fp+d++tl+ylrltgr+ ++v l e+ylkaq+l ++ ++ ep+++d+veldls+v++++aGpkrpq
NCBI__GCF_000092905.1:WP_013076481.1 311 YGATMGYFPVDERTLDYLRLTGRKAEDVALAEAYLKAQGLLHTeEAPEPVFSDIVELDLSTVKPTLAGPKRPQ 383
***************************************998868999************************* PP
TIGR01341 365 drvalkevkaafksslesnagekglalrkeakekkle.....gkeaelkdgavviaaitsctntsnpsvllga 432
d+v+l ++ka+f++++es++ + g+++ ke ++ + g +++l++gavviaaitsctntsnpsv++ga
NCBI__GCF_000092905.1:WP_013076481.1 384 DKVPLPDLKASFEKAVESPVDQGGFGFGKEGLARTSDvkypdGGRETLRTGAVVIAAITSCTNTSNPSVMIGA 456
********************99999988665544433334449999*************************** PP
TIGR01341 433 gllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaik 505
gllakkave Gl ++ yvk+slapGs+vvt yl+++gllp le+lGf +vGyGcttciGnsGpl+ ev+eai+
NCBI__GCF_000092905.1:WP_013076481.1 457 GLLAKKAVEKGLTKPRYVKSSLAPGSRVVTAYLKRAGLLPALEQLGFAVVGYGCTTCIGNSGPLDPEVAEAIQ 529
************************************************************************* PP
TIGR01341 506 endlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsake 578
e+d++v+avlsGnrnfegrihplv+anylaspplvvayalaGtvdidl+kep+gtd+dG++vylkdiwps +e
NCBI__GCF_000092905.1:WP_013076481.1 530 EKDMTVAAVLSGNRNFEGRIHPLVRANYLASPPLVVAYALAGTVDIDLSKEPLGTDRDGNPVYLKDIWPSSEE 602
************************************************************************* PP
TIGR01341 579 iaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgaril 651
+++++++av+ elf +ey++v n+rwn l +++++ly++d +styi+eppff +l+ e ++ di+gar+l
NCBI__GCF_000092905.1:WP_013076481.1 603 VQAAIQQAVTAELFSEEYAHVLTANQRWNALPTPEGELYHFDADSTYIQEPPFFVNLSREAGHIADIRGARVL 675
************************************************************************* PP
TIGR01341 652 lllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgl 724
+llGds+ttdhispaGsi+++spaakyl+e+GverrdfnsyGsrrGnhevm+rGtfaniri+n l++g+eGg+
NCBI__GCF_000092905.1:WP_013076481.1 676 ALLGDSVTTDHISPAGSIAPNSPAAKYLMEHGVERRDFNSYGSRRGNHEVMMRGTFANIRIRNLLAPGTEGGV 748
************************************************************************* PP
TIGR01341 725 tvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGv 797
tvylp++e++ +ydaamky+ +g+plvvlaGkeyG+Gssrdwaakgt+llGvkav+aesferihrsnlvgmGv
NCBI__GCF_000092905.1:WP_013076481.1 749 TVYLPTGETMPIYDAAMKYQADGTPLVVLAGKEYGTGSSRDWAAKGTMLLGVKAVLAESFERIHRSNLVGMGV 821
************************************************************************* PP
TIGR01341 798 lplefkqgedaetlgltgeetidvddi.eelkpkkevtvelvkedgeketveavlridtevelayvkkgGilq 869
lpl+f +ge+ ++lgltg+e+ d++++ ++++p ++v+v++v+edg + ++a +r+d+ ve++y+++gGilq
NCBI__GCF_000092905.1:WP_013076481.1 822 LPLQFTKGESWKSLGLTGKERFDIQGLsDDIQPLSTVRVTAVDEDGGRLEFDALVRLDSVVEIEYYRNGGILQ 894
**************************7268******************************************* PP
TIGR01341 870 yvlrkll 876
vlr+ll
NCBI__GCF_000092905.1:WP_013076481.1 895 TVLRQLL 901
****986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (903 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 42.02
//
[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