Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_011386745.1 AMB_RS22255 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8
(865 letters)
>NCBI__GCF_000009985.1:WP_011386745.1
Length = 861
Score = 1248 bits (3230), Expect = 0.0
Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 6/859 (0%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
MLE YR+HVAERAA GI P PL A Q ALV LL+ PP GEE+ L+DL+ RVP GVD+A
Sbjct: 1 MLEAYRQHVAERAALGIPPLPLSAEQTEALVGLLQNPPKGEEQALVDLITYRVPAGVDDA 60
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A +KA FL VAKG L+S E A +LLGTM GG+N+ PLI+ L DAK+ +AA+ L
Sbjct: 61 AKIKAEFLDKVAKGTVACALISRETATQLLGTMLGGFNVKPLIELLSDAKVGAVAAEGLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
TLL+FD F+DV+E A GN AK V+QSWADAEWF SRP + + +TVT+FKVTGETNTD
Sbjct: 121 KTLLVFDFFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPKSLTVTIFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
DLSPAPDAWSRPDIPLHA AMLKN R GIE D+PG GP+KQ++AL KKG +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIEADEPGNRGPLKQLDALAKKGNLVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV+
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPYVPNKRFGGVCLGTKIAPIFYNTMEDAGALPIELDVNQ 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+NMGDV+++ PY+G+ + G+++A F +K++V+ DEVRAGGRIPLIIGRGLT KAREA
Sbjct: 301 MNMGDVVELRPYEGKAL--KDGKVIAEFTVKSEVIFDEVRAGGRIPLIIGRGLTAKAREA 358
Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGLP S +FR ++ +GFSLAQKMVGRACG+ KG+RPG YCEPKMT+VGSQDTT
Sbjct: 359 LGLPVSTLFRLPAVPKDTGKGFSLAQKMVGRACGLPEGKGMRPGTYCEPKMTTVGSQDTT 418
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSAD+VMQSFCHTAAYPK VDV TH LP FI RGGV+LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKTHRELPGFISTRGGVALRPGDG 478
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
VIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKMQPG+TLRDLV+AIPLYAI+ GLLTVEKKGKKN+FSGRILEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIRAGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSD 598
Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
A+AERSAA C+++L+K PI+EY+TSNI L+KWMIA GY D RTL RRI+ ME W+ P L
Sbjct: 599 AAAERSAAACSVRLDKAPIIEYMTSNITLMKWMIANGYEDARTLGRRIKAMEAWIKKPDL 658
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
L DADAEYAAVI+IDLAD+KEPI+ PNDPDD +LLS+V G KIDEVFIGSCMTNIGHF
Sbjct: 659 LAPDADAEYAAVIEIDLADVKEPIVACPNDPDDVKLLSEVAGAKIDEVFIGSCMTNIGHF 718
Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGK+L+ K +PTRLW+APPT+MDA L EEGYYSV GKSGAR+E+PGCSLCMGNQA
Sbjct: 719 RAAGKVLEG-KSDIPTRLWIAPPTKMDAMILNEEGYYSVLGKSGARMEMPGCSLCMGNQA 777
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
++ G+T +STSTRNFPNRLG NV+L SAELAAV AL+GK+PT EY V V+ A
Sbjct: 778 QIRKGSTAMSTSTRNFPNRLGIDTNVYLGSAELAAVCALMGKIPTVAEYLEQVNVVNAKA 837
Query: 838 VDTYRYLNFDQLSQYTEKA 856
D YRY+NFD+++++++ A
Sbjct: 838 ADVYRYMNFDKIAEFSDVA 856
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: 2079
Number of extensions: 81
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: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space: 674037
Effective search space used: 674037
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_011386745.1 AMB_RS22255 (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.11039.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 1489.7 0.1 0 1489.5 0.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386745.1 AMB_RS22255 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386745.1 AMB_RS22255 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrata
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1489.5 0.1 0 0 1 843 [. 1 853 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1489.5 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr+hvaeraa+gi+plpl a+q++alv ll+n+p++ee+ l++l++ rvp gvd+aa++ka+fl
lcl|NCBI__GCF_000009985.1:WP_011386745.1 1 MLEAYRQHVAERAALGIPPLPLSAEQTEALVGLLQNPPKGEEQALVDLITYRVPAGVDDAAKIKAEFLD 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
++akg v ++lis e a++llgtmlgg+nv+plie+l d+++ +aa+ l+ktllvfd f+dv+el+
lcl|NCBI__GCF_000009985.1:WP_011386745.1 70 KVAKGTVACALISRETATQLLGTMLGGFNVKPLIELLS--DAKVGAVAAEGLKKTLLVFDFFHDVKELA 136
*************************************9..****************************9 PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
+ n+ ak vl+swa+aewf ++e+++ +tvt+fkv+getntddlspapda++rpdiplhalamlkn
lcl|NCBI__GCF_000009985.1:WP_011386745.1 137 DKgNANAKAVLQSWADAEWFTSRPEVPKSLTVTIFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNP 205
988****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+++ie +++al +kg vayvgdvvgtgssrksatnsvlwf g+dip+vpnkr gg++l
lcl|NCBI__GCF_000009985.1:WP_011386745.1 206 RPGIEAdepgnrgplkQLDALAKKGNLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPYVPNKRFGGVCL 274
****9999************************************************************* PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
g kiapif+nt+ed+galpie dv+++n+gdv+++ py+g+ +k+++v+a f +k+e+++devraggr
lcl|NCBI__GCF_000009985.1:WP_011386745.1 275 GTKIAPIFYNTMEDAGALPIELDVNQMNMGDVVELRPYEGKA-LKDGKVIAEFTVKSEVIFDEVRAGGR 342
****************************************96.7889********************** PP
TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
ipliigrglt karealgl+ s +f+ ++ p++++kgf+laqk+vg+acg+ kg+rpgtycepk+tt
lcl|NCBI__GCF_000009985.1:WP_011386745.1 343 IPLIIGRGLTAKAREALGLPVSTLFRLPAVPKDTGKGFSLAQKMVGRACGLpegKGMRPGTYCEPKMTT 411
**************************************************87779************** PP
TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
vgsqdttg+mtrdelk+la+lgf+ad+v+qsfchtaaypk vdvkth++lp+fis+rggvalrpgdgvi
lcl|NCBI__GCF_000009985.1:WP_011386745.1 412 VGSQDTTGPMTRDELKDLACLGFSADMVMQSFCHTAAYPKLVDVKTHRELPGFISTRGGVALRPGDGVI 480
********************************************************************* PP
TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
hswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpg+tlrd
lcl|NCBI__GCF_000009985.1:WP_011386745.1 481 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTLRD 549
********************************************************************* PP
TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
lvnaip+yai+ glltvekkgk+nvf+grileieglpdlkveqafel+da+aersaa+c ++l+k p+i
lcl|NCBI__GCF_000009985.1:WP_011386745.1 550 LVNAIPLYAIRAGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAACSVRLDKAPII 618
********************************************************************* PP
TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
ey+ sni l+k+mia+gyed+rtl rri+ame+w++ p+ll +dadaeyaavieidla++kepi+a+pn
lcl|NCBI__GCF_000009985.1:WP_011386745.1 619 EYMTSNITLMKWMIANGYEDARTLGRRIKAMEAWIKKPDLLAPDADAEYAAVIEIDLADVKEPIVACPN 687
********************************************************************* PP
TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
dpddvkllsevag +idevfigscmtnighfraagk+le+++++++rlw++ppt+md+ l eegyy++
lcl|NCBI__GCF_000009985.1:WP_011386745.1 688 DPDDVKLLSEVAGAKIDEVFIGSCMTNIGHFRAAGKVLEGKSDIPTRLWIAPPTKMDAMILNEEGYYSV 756
********************************************************************* PP
TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
+g++gar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg ++vylgsaelaav+al+gkipt+ e
lcl|NCBI__GCF_000009985.1:WP_011386745.1 757 LGKSGARMEMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTNVYLGSAELAAVCALMGKIPTVAE 825
********************************************************************* PP
TIGR00117 815 ylalvsekvesakdklyrylnfnelenfe 843
yl+ v + + a d +yry+nf+++ +f
lcl|NCBI__GCF_000009985.1:WP_011386745.1 826 YLEQVNVVNAKAAD-VYRYMNFDKIAEFS 853
*****988888887.**********9997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (861 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.70
//
[ok]
This GapMind analysis is from Sep 17 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