Align aconitase (EC 4.2.1.3) (characterized)
to candidate WP_013460045.1 SULKU_RS05970 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= metacyc::HP0779-MONOMER
(852 letters)
>NCBI__GCF_000183725.1:WP_013460045.1
Length = 869
Score = 1084 bits (2804), Expect = 0.0
Identities = 544/859 (63%), Positives = 660/859 (76%), Gaps = 19/859 (2%)
Query: 4 FLEDYKKSVSERGSEGIPPLPLNAKQVQAVVEILTKDPTNAAFAKELLIHRVSPGVDEGA 63
F+++YK V+ER ++GIPPLPL +QV A+VE++T + + A E+L RV+PGVD+GA
Sbjct: 3 FMDEYKAHVAEREAQGIPPLPLTKEQVTALVELITAESSKNAELVEMLAERVNPGVDDGA 62
Query: 64 KVKAEFLAKLSQKKLECVHISALE---------ATTLLGTMLGGYNVEPLIMGLESQDKN 114
VKA FL ++ Q +++ + A +LG M+GGYNV+PLI L +
Sbjct: 63 HVKAAFLHQVVQGQVKAFLADNSDINSDDHKKAAIKILGKMVGGYNVKPLIDALSNDA-- 120
Query: 115 IAKESAKALKTTLLVYGSFDKIAAMSKTNALAKEVLESWANAEWFLNKEPLNECIEACVF 174
IA E+A LK TLLVY +F+ I +S+TN AKEVL+SWA+AEWF K+PL E VF
Sbjct: 121 IANEAAHELKHTLLVYDAFNDIVDLSQTNKYAKEVLQSWADAEWFTAKKPLAEKFSVVVF 180
Query: 175 KIDGETNTDDLSPASDAFTRSDIPLHAKAMLKNRIENYEQRIKAIKTKGVPVAYVGDVVG 234
K GETNTDDLSPAS AFTRSDIPLHA ML ++ +I +K G +AYVGDVVG
Sbjct: 181 KFPGETNTDDLSPASAAFTRSDIPLHATTMLSAKMPEGIAKIAELKKMGKQIAYVGDVVG 240
Query: 235 TGSSRKSATNSIMWHFGKDIPFVPNKRSGGIVIGGVIAPIFFATCEDSGALPIVADVKDL 294
TGSSRKSA NS+ WH G DIP +PNKR+GG+VIG +IAPIFFATCEDSGALPI ADV +
Sbjct: 241 TGSSRKSAANSVQWHMGDDIPGIPNKRTGGVVIGSIIAPIFFATCEDSGALPIEADVSQM 300
Query: 295 KEGDLIKIYPYKGEITLNDKVVSTFKLEPETLLDEVRASGRIPLIIGRGLTNKARKFLGL 354
+ GD++ I G IT N ++TF L P T+ DEVRA GRIPLIIGRGLT KAR LG+
Sbjct: 301 ETGDVLDIDTKAGTITKNGTQIATFSLRPNTIEDEVRAGGRIPLIIGRGLTAKARAALGM 360
Query: 355 GESEAFKKPSAPKSDAKGYTLAQKIVGHACGVKGILPGTYCEPKVTTVGSQDTTGAMTRD 414
+ F P P KGYTLAQK+VG ACG++G+ PG YCEP +TVGSQDTTG MTRD
Sbjct: 361 APATIFATPIQPADTGKGYTLAQKMVGKACGMEGVRPGMYCEPMTSTVGSQDTTGPMTRD 420
Query: 415 EVKELASLKFDAPFVLQSFCHTAAYPKPSDVSLHATLPGFITQRGGVALHPGDGVIHTWL 474
E+KEL++L F A FVLQSFCHTAAYPKPSDV LHATLP FI+ R GVAL P DGVIH+WL
Sbjct: 421 EIKELSALGFSADFVLQSFCHTAAYPKPSDVKLHATLPAFISSRSGVALRPADGVIHSWL 480
Query: 475 NRMGLPDTLGTGGDSHTRFPLGISFPAGSGLVAFAAVTGTMPLNMPESVLVRFKGEMNPG 534
NRM LPDT+GTGGDSHTRFP+G+SFPAGSGLVAFAAVTG+MPL MPESVLVRFKGEM PG
Sbjct: 481 NRMVLPDTVGTGGDSHTRFPIGVSFPAGSGLVAFAAVTGSMPLEMPESVLVRFKGEMQPG 540
Query: 535 ITLRDLVNAIPYYAIKKGLLTVEKKGKINVFNGRILEIEGLPDIKMEQAFELSDASAERS 594
ITLRDLVNAIPYYAIK+GLLTVEKKGK N+FNGR+LEIEGLP++K+EQAFELSDASAERS
Sbjct: 541 ITLRDLVNAIPYYAIKQGLLTVEKKGKKNIFNGRVLEIEGLPNMKVEQAFELSDASAERS 600
Query: 595 AAACVVRLNKEPMIEYLKSNIKLIDEMIASGYEDKETLKKRRDAMQAWVDNPVLLEPDSN 654
AAAC VRLNKEP+IEYLKSN+ LI+ MI GYED TL++R D M+ W+ P L+EPD++
Sbjct: 601 AAACTVRLNKEPVIEYLKSNVTLIEAMIKDGYEDARTLQRRADKMKEWLAAPSLMEPDAD 660
Query: 655 AQYAAVIEIDVAEITEPILACPNDPDDVATLSEVLADTTGKRPHAIDEVFIGSCMTNIGH 714
A+YAA+IEID+ E+ EPILACPNDPD+V LSEV + IDEVF+GSCMTNIGH
Sbjct: 661 AEYAAIIEIDLNEVKEPILACPNDPDNVKLLSEVAGE-------KIDEVFLGSCMTNIGH 713
Query: 715 FRAFGEIVK-NAPPSQARLWVVPPSKMDEQELINEGYYAIFGAAGARTEVPGCSLCMGNQ 773
+RA GE+++ + + W+VPP++MDEQ+LINEGYY ++ A A+TEVPGCSLCMGNQ
Sbjct: 714 YRAAGEVMRGEGKIAVEKFWIVPPTRMDEQQLINEGYYDVYKAIAAQTEVPGCSLCMGNQ 773
Query: 774 ARVRDNAVVFSTSTRNFDNRMGRGAKVYLGSAELGAACALLGRIPTKEEYMNLVSEKLES 833
A R+ + VFSTSTRNFDNR+G+G +VYLGSAEL A CA LGRIPT EYM++V EKL
Sbjct: 774 ASSREGSTVFSTSTRNFDNRLGKGTQVYLGSAELAAVCAKLGRIPTVAEYMSIVPEKLAG 833
Query: 834 QKDKIYRYMNFNLMENFRL 852
+ D +Y+Y+NFN + ++ L
Sbjct: 834 KADDVYKYLNFNEIASYSL 852
Lambda K H
0.317 0.135 0.390
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: 1828
Number of extensions: 71
Number of successful extensions: 5
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: 852
Length of database: 869
Length adjustment: 42
Effective length of query: 810
Effective length of database: 827
Effective search space: 669870
Effective search space used: 669870
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: 56 (26.2 bits)
Align candidate WP_013460045.1 SULKU_RS05970 (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.7956.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 1443.7 1.8 0 1443.5 1.8 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013460045.1 SULKU_RS05970 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000183725.1:WP_013460045.1 SULKU_RS05970 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1443.5 1.8 0 0 1 843 [. 3 851 .. 3 852 .. 0.98
Alignments for each domain:
== domain 1 score: 1443.5 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+++ey+ hvaer+a+gi+plpl +qv+alvel++ + ++ +++l+e+l +rv+pgvd++a+vka fl
lcl|NCBI__GCF_000183725.1:WP_013460045.1 3 FMDEYKAHVAEREAQGIPPLPLTKEQVTALVELITAESSK-NAELVEMLAERVNPGVDDGAHVKAAFLH 70
579********************************99887.88899*********************** PP
TIGR00117 70 aiakgevkspl.....isa....eeavellgtmlggynvepliealeskdkniakaaakalsktllvfd 129
++ +g+vk+ l i + + a+++lg m+ggynv+pli+al + ia++aa+ l++tllv+d
lcl|NCBI__GCF_000183725.1:WP_013460045.1 71 QVVQGQVKAFLadnsdINSddhkKAAIKILGKMVGGYNVKPLIDALS--NDAIANEAAHELKHTLLVYD 137
*******9876222223322222569********************9..678***************** PP
TIGR00117 130 afddveelsktneyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplh 198
af+d+ +ls+tn+yak+vl+swa+aewf k++laek++v+vfk +getntddlspa+ aftr+diplh
lcl|NCBI__GCF_000183725.1:WP_013460045.1 138 AFNDIVDLSQTNKYAKEVLQSWADAEWFTAKKPLAEKFSVVVFKFPGETNTDDLSPASAAFTRSDIPLH 206
********************************************************************* PP
TIGR00117 199 alamlknkieeieqrikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlgg 267
a +ml +k++e +i++lk+ g +ayvgdvvgtgssrksa nsv w++g+dip +pnkr+gg+v+g
lcl|NCBI__GCF_000183725.1:WP_013460045.1 207 ATTMLSAKMPEGIAKIAELKKMGKQIAYVGDVVGTGSSRKSAANSVQWHMGDDIPGIPNKRTGGVVIGS 275
********************************************************************* PP
TIGR00117 268 kiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggrip 336
iapiff+t+edsgalpie+dv+++++gdv++i + g it++ +atf l+p+t+ devraggrip
lcl|NCBI__GCF_000183725.1:WP_013460045.1 276 IIAPIFFATCEDSGALPIEADVSQMETGDVLDIDTKAGTITKNG-TQIATFSLRPNTIEDEVRAGGRIP 343
*****************************************987.679********************* PP
TIGR00117 337 liigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqd 405
liigrglt kar alg++++ +f + +pa+++kg+tlaqk+vgkacg++g+rpg ycep+ +tvgsqd
lcl|NCBI__GCF_000183725.1:WP_013460045.1 344 LIIGRGLTAKARAALGMAPATIFATPIQPADTGKGYTLAQKMVGKACGMEGVRPGMYCEPMTSTVGSQD 412
********************************************************************* PP
TIGR00117 406 ttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswln 474
ttg+mtrde+kel++lgf+ad+vlqsfchtaaypkp+dvk+h+tlp fis+r gvalrp dgvihswln
lcl|NCBI__GCF_000183725.1:WP_013460045.1 413 TTGPMTRDEIKELSALGFSADFVLQSFCHTAAYPKPSDVKLHATLPAFISSRSGVALRPADGVIHSWLN 481
********************************************************************* PP
TIGR00117 475 rmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnai 543
rm+lpdtvgtggdshtrfp+g+sfpagsglvafaa+tg mpl+mpesvlvrfkge+qpgitlrdlvnai
lcl|NCBI__GCF_000183725.1:WP_013460045.1 482 RMVLPDTVGTGGDSHTRFPIGVSFPAGSGLVAFAAVTGSMPLEMPESVLVRFKGEMQPGITLRDLVNAI 550
********************************************************************* PP
TIGR00117 544 pyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylks 612
pyyaik+glltvekkgk+n+fngr+leieglp++kveqafel+dasaersaa+ct++lnkepvieylks
lcl|NCBI__GCF_000183725.1:WP_013460045.1 551 PYYAIKQGLLTVEKKGKKNIFNGRVLEIEGLPNMKVEQAFELSDASAERSAAACTVRLNKEPVIEYLKS 619
********************************************************************* PP
TIGR00117 613 nivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddv 681
n+ l++ mi +gyed+rtl+rr d+m++wla p+l+e+dadaeyaa+ieidl+e+kepila+pndpd+v
lcl|NCBI__GCF_000183725.1:WP_013460045.1 620 NVTLIEAMIKDGYEDARTLQRRADKMKEWLAAPSLMEPDADAEYAAIIEIDLNEVKEPILACPNDPDNV 688
********************************************************************* PP
TIGR00117 682 kllsevagdaidevfigscmtnighfraagkileaaktv.karlwvvpptrmdeqqlieegyyaifgaa 749
kllsevag++idevf+gscmtnigh+raag+++ +++++ ++w+vpptrmdeqqli+egyy ++ a
lcl|NCBI__GCF_000183725.1:WP_013460045.1 689 KLLSEVAGEKIDEVFLGSCMTNIGHYRAAGEVMRGEGKIaVEKFWIVPPTRMDEQQLINEGYYDVYKAI 757
***********************************99651579************************** PP
TIGR00117 750 gartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylal 818
a+tevpgcslcmgnqa ++g+tvfststrnfdnrlgkg++vylgsaelaav+a lg+ipt+ ey+++
lcl|NCBI__GCF_000183725.1:WP_013460045.1 758 AAQTEVPGCSLCMGNQASSREGSTVFSTSTRNFDNRLGKGTQVYLGSAELAAVCAKLGRIPTVAEYMSI 826
********************************************************************* PP
TIGR00117 819 vsekvesakdklyrylnfnelenfe 843
v ek++ + d++y+ylnfne+ +
lcl|NCBI__GCF_000183725.1:WP_013460045.1 827 VPEKLAGKADDVYKYLNFNEIASYS 851
*********************9985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (869 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 12.69
//
[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