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 Ac3H11_3150 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= SwissProt::Q8ZRS8
(865 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_3150
Length = 866
Score = 1242 bits (3214), Expect = 0.0
Identities = 628/863 (72%), Positives = 711/863 (82%), Gaps = 8/863 (0%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
ML+ YR HVAERAA GI P PLDA Q+A L+EL+K PP GE+ FLLDLL +RVPPGVD+A
Sbjct: 1 MLKAYRDHVAERAALGIPPLPLDAKQVAELIELIKNPPAGEDAFLLDLLTHRVPPGVDDA 60
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLAAVA GD L+S KA ELLGTM GGYN+HPLI+ LDDA++A +AA AL
Sbjct: 61 AKVKASFLAAVAHGDVKVGLISKSKATELLGTMVGGYNVHPLIELLDDAEVAGVAADALK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
TLLMFD F DV KAKAGN A++VMQSWA+AEWF SRP + +KITVTVFKV GETNTD
Sbjct: 121 KTLLMFDFFNDVATKAKAGNAKAQEVMQSWANAEWFTSRPEVEKKITVTVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNARE--GIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
DLSPAPDAWSRPDIPLH AMLKN R +P++ G GP++ I+ L+KKG+ +AYVGD
Sbjct: 181 DLSPAPDAWSRPDIPLHYLAMLKNTRPDAAFKPEEDGKRGPMQFIDDLKKKGHLVAYVGD 240
Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
VVGTGSSRKSATNS++W G DIP VPNKR GG+ LGGKIAPIFFNT ED+G+LPIEVDV
Sbjct: 241 VVGTGSSRKSATNSIVWATGQDIPFVPNKRFGGVTLGGKIAPIFFNTQEDSGSLPIEVDV 300
Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
S L MGDVIDV PY G++ + G +A F+LK+DVL DEVRAGGRI LIIGR LT KAR
Sbjct: 301 SKLEMGDVIDVLPYDGKIV--KDGATVAEFQLKSDVLFDEVRAGGRINLIIGRSLTAKAR 358
Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
E LGLP S FR ++ GF+LAQKMVGRA G+ +G+RPG YCEPKMT+VGSQD
Sbjct: 359 EFLGLPASTAFRLPTAPVATNAGFTLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQD 418
Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPG 475
TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV TH LP FI NRGGV+LRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHRELPAFISNRGGVALRPG 478
Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAF AATGVMPLDMPES+LVR
Sbjct: 479 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFGAATGVMPLDMPESILVR 538
Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
FKG MQPG+TLRDLVHAIPLYAIK GLLTV K GK N FSGRILEIEGLPDLKVEQAFEL
Sbjct: 539 FKGDMQPGVTLRDLVHAIPLYAIKAGLLTVAKAGKINAFSGRILEIEGLPDLKVEQAFEL 598
Query: 596 TDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655
+DASAERSAAGCTIKLN EPI EYLTSNIVL+K MIA+GY D +TL+RRI+ +E WLA P
Sbjct: 599 SDASAERSAAGCTIKLNPEPIKEYLTSNIVLMKNMIADGYADAKTLQRRIEKVEAWLAKP 658
Query: 656 QLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIG 715
LLEAD DAEYAAVI+IDLADIKEPI+C PNDPDDA+ LS+V G KIDE FIGSCMTNIG
Sbjct: 659 DLLEADKDAEYAAVIEIDLADIKEPIVCCPNDPDDAKFLSEVSGTKIDEAFIGSCMTNIG 718
Query: 716 HFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
HFRAA KLL + +P +LWVAPPT+MD ++L +EG+Y+ FG +GAR E+PGCSLCMGN
Sbjct: 719 HFRAAAKLLGGQR-DIPVKLWVAPPTKMDESELIKEGHYAAFGTAGARTEMPGCSLCMGN 777
Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
QA+V +GATV+STSTRNFPNRLG NVFL SAELAA+A+ +G LP+ EEY + +D
Sbjct: 778 QAQVREGATVISTSTRNFPNRLGKNTNVFLGSAELAAIASRLGYLPSKEEYLKEMGVIDA 837
Query: 836 TAVDTYRYLNFDQLSQYTEKADG 858
YRY+NFDQ+ +Y E A G
Sbjct: 838 DKASVYRYMNFDQIEEYAEAAKG 860
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: 2070
Number of extensions: 76
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: 865
Length of database: 866
Length adjustment: 42
Effective length of query: 823
Effective length of database: 824
Effective search space: 678152
Effective search space used: 678152
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 Ac3H11_3150 (Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99))
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.13995.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 1487.6 0.0 0 1487.4 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 Aconitate hydratase 2 (EC 4.2.1.
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1487.4 0.0 0 0 1 843 [. 1 855 [. 1 856 [. 0.99
Alignments for each domain:
== domain 1 score: 1487.4 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaay 62
+l++yr hvaeraa+gi+plpl+akqva+l+el+kn+p++e++fll+ll++rvppgvd+aa+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 1 MLKAYRDHVAERAALGIPPLPLDAKQVAELIELIKNPPAGEDAFLLDLLTHRVPPGVDDAAK 62
799*********************************************************** PP
TIGR00117 63 vkagflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalskt 124
vka flaa+a+g+vk lis +a+ellgtm+ggynv+plie+l+ d+++a +aa al+kt
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 63 VKASFLAAVAHGDVKVGLISKSKATELLGTMVGGYNVHPLIELLD--DAEVAGVAADALKKT 122
*********************************************..*************** PP
TIGR00117 125 llvfdafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlsp 185
ll+fd f+dv++++k+ n+ a++v++swa+aewf ++e+++kitvtvfkv+getntddlsp
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 123 LLMFDFFNDVATKAKAgNAKAQEVMQSWANAEWFTSRPEVEKKITVTVFKVPGETNTDDLSP 184
****************9********************************************* PP
TIGR00117 186 apdaftrpdiplhalamlknkieeieq............rikalkqkgvpvayvgdvvgtgs 235
apda++rpdiplh lamlkn +++ i++lk+kg+ vayvgdvvgtgs
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 185 APDAWSRPDIPLHYLAMLKNTRPDAAFkpeedgkrgpmqFIDDLKKKGHLVAYVGDVVGTGS 246
**********************99876789999****989********************** PP
TIGR00117 236 srksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdv 297
srksatns++w g+dipfvpnkr gg+ lggkiapiffnt edsg+lpievdv++l++gdv
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 247 SRKSATNSIVWATGQDIPFVPNKRFGGVTLGGKIAPIFFNTQEDSGSLPIEVDVSKLEMGDV 308
************************************************************** PP
TIGR00117 298 ikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevf 359
i++ py+g+i k++ +va f+lk+++l+devraggri liigr+lt kare+lgl+ s +f
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 309 IDVLPYDGKIV-KDGATVAEFQLKSDVLFDEVRAGGRINLIIGRSLTAKAREFLGLPASTAF 369
**********7.5679********************************************** PP
TIGR00117 360 kkakapaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkel 418
+ ++ap ++ gftlaqk+vg+a g+ +g+rpgtycepk+ttvgsqdttg+mtrdelk+l
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 370 RLPTAPVATNAGFTLAQKMVGRAVGLpegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDL 431
*************************87669******************************** PP
TIGR00117 419 aslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpd 480
a+lgf+adlv+qsfchtaaypkpvdvkth++lp fis+rggvalrpgdgvihswlnr+llpd
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 432 ACLGFSADLVMQSFCHTAAYPKPVDVKTHRELPAFISNRGGVALRPGDGVIHSWLNRLLLPD 493
************************************************************** PP
TIGR00117 481 tvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvna 542
tvgtggdshtrfp+gisfpagsglvaf aatgvmpldmpes+lvrfkg++qpg+tlrdlv+a
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 494 TVGTGGDSHTRFPIGISFPAGSGLVAFGAATGVMPLDMPESILVRFKGDMQPGVTLRDLVHA 555
************************************************************** PP
TIGR00117 543 ipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnke 604
ip+yaik glltv k gk+n f+grileieglpdlkveqafel+dasaersaagctikln e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 556 IPLYAIKAGLLTVAKAGKINAFSGRILEIEGLPDLKVEQAFELSDASAERSAAGCTIKLNPE 617
************************************************************** PP
TIGR00117 605 pvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlae 666
p+ eyl snivl+k+mia+gy d++tl+rri+++e+wla p+llead daeyaavieidla+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 618 PIKEYLTSNIVLMKNMIADGYADAKTLQRRIEKVEAWLAKPDLLEADKDAEYAAVIEIDLAD 679
************************************************************** PP
TIGR00117 667 ikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvp 728
ikepi+++pndpdd+k lsev g +ide figscmtnighfraa+k+l ++++++ +lwv+p
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 680 IKEPIVCCPNDPDDAKFLSEVSGTKIDEAFIGSCMTNIGHFRAAAKLLGGQRDIPVKLWVAP 741
************************************************************** PP
TIGR00117 729 ptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkga 790
pt+mde++li+eg ya fg+agarte+pgcslcmgnqa+v++gatv+ststrnf+nrlgk +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 742 PTKMDESELIKEGHYAAFGTAGARTEMPGCSLCMGNQAQVREGATVISTSTRNFPNRLGKNT 803
************************************************************** PP
TIGR00117 791 kvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
+v+lgsaelaa+a+ lg +p+keeyl+ + ++ k +yry+nf+++e++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3150 804 NVFLGSAELAAIASRLGYLPSKEEYLKEMGVI-DADKASVYRYMNFDQIEEYA 855
**************************998765.556666************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (866 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: 00:00:00.08
# Mc/sec: 8.19
//
[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