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 BPHYT_RS10160 BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8
(865 letters)
>FitnessBrowser__BFirm:BPHYT_RS10160
Length = 861
Score = 1270 bits (3286), Expect = 0.0
Identities = 632/862 (73%), Positives = 724/862 (83%), Gaps = 6/862 (0%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
MLE +R H A RA GI P PL A Q A LVELL PP GEE+ LLDL+ NRVP GVDEA
Sbjct: 1 MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEA 60
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKAGFLAAVAKG+TT L+S +A ELLGTM GGYNI PLI+ L DA++ +AA+AL
Sbjct: 61 ARVKAGFLAAVAKGETTCALISRARATELLGTMLGGYNIQPLIELLSDAEVGTVAAEALK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
TLLMFD F+DV+E A GN AK V+QSWADAEWF SRP + + +T+TVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKELADKGNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
DLSPAPDA +RPDIP+HA AMLKNAR GI P++ G GPIK I++L++KG+ +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPMHALAMLKNARPGITPEEDGKRGPIKFIQSLKEKGHLVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ MGDV+++ PY+G+ + G ++A F++K+DVL DEVRAGGRIPLIIGRGLT KAREA
Sbjct: 301 MEMGDVVELRPYEGKALKN--GAVIAEFKVKSDVLFDEVRAGGRIPLIIGRGLTAKAREA 358
Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL S +FR + A+S +GFSLAQKMVGRACG+ +G+RPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLPEGQGVRPGTYCEPKMTSVGSQDTT 418
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH TLPDFI NRGG++LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDG 478
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG MPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFK 538
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKMQPG+TLRDLV+AIPLYAIKQG LTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598
Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
ASAERSAAGCT+ LNKEPI+EYL SN+ LLKWMIA+GY D R+L+RRI+ ME WLADPQL
Sbjct: 599 ASAERSAAGCTVHLNKEPIIEYLNSNVTLLKWMIAQGYQDPRSLQRRIKAMEAWLADPQL 658
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
L DADAEYAAVI+IDLADI EPI+ PNDPDD + LSDV G KIDEVFIGSCMTNIGHF
Sbjct: 659 LSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSDVAGAKIDEVFIGSCMTNIGHF 718
Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAA KLL+ K +P +LWVAPPT+MD QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
+V +GATV+STSTRNFPNRLG NV+L SAELAA+ + +GK+PT EEY + + +
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMGVLTASG 837
Query: 838 VDTYRYLNFDQLSQYTEKADGV 859
Y+Y+NFDQ+ + + AD V
Sbjct: 838 DKIYQYMNFDQIEDFKDLADTV 859
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: 2048
Number of extensions: 75
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 BPHYT_RS10160 BPHYT_RS10160 (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.29118.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 1519.2 0.0 0 1519.0 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS10160 BPHYT_RS10160 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS10160 BPHYT_RS10160 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrat
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1519.0 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1519.0 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaa 70
+le++r h a ra++gi+plpl a+q+a+lvell+n+p++ee+ ll+l+++rvp gvdeaa+vkagflaa
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 1 MLENFRAHAAARATLGIPPLPLTAQQTAELVELLTNPPAGEEQTLLDLITNRVPAGVDEAARVKAGFLAA 70
79******************************************************************** PP
TIGR00117 71 iakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt 140
+akge +++lis +a+ellgtmlggyn++plie+l d+++ ++aa+al+ktll+fdaf+dv+el++
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 71 VAKGETTCALISRARATELLGTMLGGYNIQPLIELLS--DAEVGTVAAEALKKTLLMFDAFHDVKELADK 138
************************************9..****************************998 PP
TIGR00117 141 .neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkiee 209
n+ ak vl+swa+aewf ++e+++ +t+tvfkv+getntddlspapda+trpdip+halamlkn++++
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 139 gNANAKAVLQSWADAEWFTSRPEVPQSLTITVFKVTGETNTDDLSPAPDATTRPDIPMHALAMLKNARPG 208
8********************************************************************* PP
TIGR00117 210 ieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggki 269
i + i++lk+kg+ vayvgdvvgtgssrksatnsvlwf g+dipf+pnkr gg++lg ki
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 209 ITPeedgkrgpikFIQSLKEKGHLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKI 278
*99999****9999******************************************************** PP
TIGR00117 270 apiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggriplii 339
apif+nt+ed+galpie dv+++++gdv+++ py+g+ k++ v+a fk+k+++l+devraggriplii
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 279 APIFYNTMEDAGALPIELDVSQMEMGDVVELRPYEGKAL-KNGAVIAEFKVKSDVLFDEVRAGGRIPLII 347
*************************************75.5569************************** PP
TIGR00117 340 grgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdt 406
grglt karealgl++s +f+ +++pa+s+kgf+laqk+vg+acg+ +g+rpgtycepk+t+vgsqdt
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 348 GRGLTAKAREALGLAPSTLFRLPQQPADSGKGFSLAQKMVGRACGLpegQGVRPGTYCEPKMTSVGSQDT 417
*********************************************87679******************** PP
TIGR00117 407 tgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrm 476
tg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdvkth+tlpdfis+rgg+alrpgdgvihswlnrm
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 418 TGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKSVDVKTHRTLPDFISNRGGIALRPGDGVIHSWLNRM 487
********************************************************************** PP
TIGR00117 477 llpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyy 546
llpdtvgtggdshtrfp+gisfpagsglvafaaatg+mpldmpesvlvrfkg++qpg+tlrdlvnaip+y
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 488 LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGTMPLDMPESVLVRFKGKMQPGVTLRDLVNAIPLY 557
********************************************************************** PP
TIGR00117 547 aikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivl 616
aik+g ltv k+gk+n+f+gr+leieglpdlkveqafel+dasaersaagct++lnkep+ieyl+sn+ l
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 558 AIKQGTLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSDASAERSAAGCTVHLNKEPIIEYLNSNVTL 627
********************************************************************** PP
TIGR00117 617 lkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllse 686
lk+mia+gy+d r+l+rri+ame+wla+p+ll++dadaeyaavieidla+i+epi+a+pndpddvk+ls+
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 628 LKWMIAQGYQDPRSLQRRIKAMEAWLADPQLLSPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKTLSD 697
********************************************************************** PP
TIGR00117 687 vagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevp 756
vag +idevfigscmtnighfraa+k+le++++++ +lwv+ppt+md++ql+eeg y++fg+agarte+p
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 698 VAGAKIDEVFIGSCMTNIGHFRAASKLLEGKRDIPVKLWVAPPTKMDQKQLTEEGHYGVFGTAGARTEMP 767
********************************************************************** PP
TIGR00117 757 gcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesa 826
gcslcmgnqa+v++gatv+ststrnf+nrlgk ++vylgsaelaa+++ lgkiptkeey+a + ++ +
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 768 GCSLCMGNQAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGKIPTKEEYMADMG-VLTAS 836
************************************************************9986.66777 PP
TIGR00117 827 kdklyrylnfnelenfee 844
dk+y+y+nf+++e+f++
lcl|FitnessBrowser__BFirm:BPHYT_RS10160 837 GDKIYQYMNFDQIEDFKD 854
899*************85 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.50
//
[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