Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011765267.1 AZO_RS07755 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_000061505.1:WP_011765267.1
Length = 865
Score = 1260 bits (3260), Expect = 0.0
Identities = 636/864 (73%), Positives = 715/864 (82%), Gaps = 6/864 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR HVAERAA GI P PL Q A LVELLKNPPAGEE FL++LLT+RVP GVD+A
Sbjct: 1 MLEAYRAHVAERAALGIPPLPLTKQQTAELVELLKNPPAGEEAFLVELLTHRVPAGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLA +AKGE L++ KA ELLGTM GG+NI PLID L DA++ +AA L
Sbjct: 61 AKVKAEFLAKVAKGEESCGLVSRAKATELLGTMLGGFNIKPLIDLLADAEVGAVAAAGLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F+DV+E A+ GN AK VMQSWADAEWF +RP + +TVFKVTGETNTD
Sbjct: 121 TTLLMFDYFHDVKELAEKGNANAKAVMQSWADAEWFTSRPEVPASQKLTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKN R GI P++PGV GP+K +E L+ KG +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGITPEEPGVRGPVKFLEELKAKGNLVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIFFNTMEDAGALPIE+D
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIEIDAGQ 300
Query: 301 LNMGDVID--VYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
++MGD I+ V G+V + G ++A +LKT V++DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MDMGDEIELKVDQATGKVTALKNGAVIAESQLKTLVILDEVRAGGRIPLIIGRGLTAKAR 360
Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
EALGLP S +FR + ++ +GFSLAQKMVGRACG+ +GIRPG YCEPKMT+VGSQD
Sbjct: 361 EALGLPPSTLFRLPQAPVDTGKGFSLAQKMVGRACGLPEGQGIRPGTYCEPKMTTVGSQD 420
Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
TTGPMTRDELKDLACLGFSAD+VMQSFCHTAAYPK VDV H LP FI RGGV+LRPG
Sbjct: 421 TTGPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKMHRELPSFISTRGGVALRPG 480
Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 481 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 540
Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
FKG MQPG+TLRDLV+AIPLYAIK GLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL
Sbjct: 541 FKGTMQPGVTLRDLVNAIPLYAIKAGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 600
Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
TDASAERSAAGCT+ LNK PI+EY+NSNI L+KWMIA GY D RTL RRI+ ME W+AN
Sbjct: 601 TDASAERSAAGCTVHLNKAPIVEYMNSNITLMKWMIANGYQDARTLRRRIKAMEDWIANG 660
Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
ELL DADAEYAAVI+IDLADIKEPI+ PNDPDD + LS V G+KIDEVFIGSCMTNIG
Sbjct: 661 ELLSGDADAEYAAVIEIDLADIKEPIVACPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIG 720
Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
HFRAAGK+LD K +PTRLW+APPT+MDA L EEGYY V GKSGAR+E+PGCSLCMGN
Sbjct: 721 HFRAAGKVLDG-KSDIPTRLWIAPPTKMDAMILNEEGYYGVLGKSGARMEMPGCSLCMGN 779
Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
QA++ G+T +STSTRNFPNRLG V+L SAEL+AV AL+GK+PTP EY V V+K
Sbjct: 780 QAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELSAVCALLGKIPTPAEYMAQVEVVNK 839
Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
A D YRY+NF+Q+ ++ AD V
Sbjct: 840 KAADIYRYMNFDQIEEFKSVADTV 863
Lambda K H
0.317 0.136 0.400
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: 2065
Number of extensions: 71
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: 865
Length of database: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space: 677329
Effective search space used: 677329
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: 56 (26.2 bits)
Align candidate WP_011765267.1 AZO_RS07755 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (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/TIGR00117.hmm
# target sequence database: /tmp/gapView.10985.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00117 [M=844]
Accession: TIGR00117
Description: acnB: aconitate hydratase 2
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 1490.3 0.0 0 1490.2 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011765267.1 AZO_RS07755 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011765267.1 AZO_RS07755 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrata
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1490.2 0.0 0 0 1 843 [. 1 857 [. 1 858 [. 0.98
Alignments for each domain:
== domain 1 score: 1490.2 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr hvaeraa+gi+plpl +q+a+lvellkn+p++ee+fl+ell++rvp gvd+aa+vka+fla
lcl|NCBI__GCF_000061505.1:WP_011765267.1 1 MLEAYRAHVAERAALGIPPLPLTKQQTAELVELLKNPPAGEEAFLVELLTHRVPAGVDDAAKVKAEFLA 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
++akge + l+s +a+ellgtmlgg+n++pli++l d+++ +aa l++tll+fd f+dv+el+
lcl|NCBI__GCF_000061505.1:WP_011765267.1 70 KVAKGEESCGLVSRAKATELLGTMLGGFNIKPLIDLLA--DAEVGAVAAAGLKTTLLMFDYFHDVKELA 136
*************************************9..****************************9 PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
+ n+ ak v++swa+aewf ++e++ + tvfkv+getntddlspapda++rpdiplhalamlkn
lcl|NCBI__GCF_000061505.1:WP_011765267.1 137 EKgNANAKAVMQSWADAEWFTSRPEVPASQKLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNP 205
877****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+++i + +++lk kg vayvgdvvgtgssrksatnsvlwf g+dipfvpnkr gg++l
lcl|NCBI__GCF_000061505.1:WP_011765267.1 206 RPGITPeepgvrgpvkFLEELKAKGNLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCL 274
****99999****99889*************************************************** PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvik..iypykgeitn.ketevvatfklkpetlldevra 331
g kiapiffnt+ed+galpie+d ++++gd i+ + g++t k++ v+a +lk+ ++ldevra
lcl|NCBI__GCF_000061505.1:WP_011765267.1 275 GSKIAPIFFNTMEDAGALPIEIDAGQMDMGDEIElkVDQATGKVTAlKNGAVIAESQLKTLVILDEVRA 343
*******************************9962256788***952778******************* PP
TIGR00117 332 ggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepk 397
ggripliigrglt karealgl++s +f+ ++ap +++kgf+laqk+vg+acg+ +girpgtycepk
lcl|NCBI__GCF_000061505.1:WP_011765267.1 344 GGRIPLIIGRGLTAKAREALGLPPSTLFRLPQAPVDTGKGFSLAQKMVGRACGLpegQGIRPGTYCEPK 412
*****************************************************87679*********** PP
TIGR00117 398 vttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgd 466
+ttvgsqdttg+mtrdelk+la+lgf+ad+v+qsfchtaaypk vdvk+h++lp fis+rggvalrpgd
lcl|NCBI__GCF_000061505.1:WP_011765267.1 413 MTTVGSQDTTGPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKMHRELPSFISTRGGVALRPGD 481
********************************************************************* PP
TIGR00117 467 gvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgit 535
gvihswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg +qpg+t
lcl|NCBI__GCF_000061505.1:WP_011765267.1 482 GVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGTMQPGVT 550
********************************************************************* PP
TIGR00117 536 lrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnke 604
lrdlvnaip+yaik glltvekkgk+n+f+grileieglpdlkveqafeltdasaersaagct++lnk
lcl|NCBI__GCF_000061505.1:WP_011765267.1 551 LRDLVNAIPLYAIKAGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTVHLNKA 619
********************************************************************* PP
TIGR00117 605 pvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepila 673
p++ey++sni l+k+mia+gy+d+rtl+rri+ame+w+an ell++dadaeyaavieidla+ikepi+a
lcl|NCBI__GCF_000061505.1:WP_011765267.1 620 PIVEYMNSNITLMKWMIANGYQDARTLRRRIKAMEDWIANGELLSGDADAEYAAVIEIDLADIKEPIVA 688
********************************************************************* PP
TIGR00117 674 apndpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegy 742
+pndpddvkllsevagd+idevfigscmtnighfraagk+l++++++++rlw++ppt+md+ l eegy
lcl|NCBI__GCF_000061505.1:WP_011765267.1 689 CPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIGHFRAAGKVLDGKSDIPTRLWIAPPTKMDAMILNEEGY 757
********************************************************************* PP
TIGR00117 743 yaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkipt 811
y+++g++gar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg ++vylgsael+av+allgkipt
lcl|NCBI__GCF_000061505.1:WP_011765267.1 758 YGVLGKSGARMEMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELSAVCALLGKIPT 826
********************************************************************* PP
TIGR00117 812 keeylalvsekvesakdklyrylnfnelenfe 843
+ ey+a v + + a d +yry+nf+++e+f+
lcl|NCBI__GCF_000061505.1:WP_011765267.1 827 PAEYMAQVEVVNKKAAD-IYRYMNFDQIEEFK 857
********988888888.************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (865 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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.23
//
[ok]
This GapMind analysis is from Sep 24 2021. 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