Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf1N1B4_4564 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564
Length = 866
Score = 1382 bits (3578), Expect = 0.0
Identities = 667/856 (77%), Positives = 759/856 (88%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKGEAKSPL+ ++A+ELLGTMQGGYNI L++ LDDA+LAP+AA+ L
Sbjct: 61 AYVKAGFLSALAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLDDAELAPVAAEELK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV E+AK GN +AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAERAKNGNVHAKGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD G +GP+KQIE ++ GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDVQGSIGPMKQIEEMRNSGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DV+N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+NMGDVID+YP+ G+V H T E++ TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 INMGDVIDLYPHAGKVCKHGTDEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP D+F++ ES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPAFDLFKKPDAPIESTKGFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPG+TLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL +L +EQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYFAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANPEL+ A
Sbjct: 601 ERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDVRTLERRAQAMEAWIANPELMVA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYA VI+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GKLLD KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARV
Sbjct: 721 GKLLDQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVE 780
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
+TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY Y ++D A D
Sbjct: 781 PNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMAADV 840
Query: 841 YRYLNFNQLSQYTEKA 856
YRYL+F+Q++++ E A
Sbjct: 841 YRYLSFDQIAEFREAA 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: 2150
Number of extensions: 77
Number of successful extensions: 1
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 Pf1N1B4_4564 (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.25098.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 1534.1 0.0 0 1533.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 Aconitate hydratase 2 (EC 4.2.1.
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (E
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1533.9 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1533.9 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvk 64
+le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvk
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVK 64
69************************************************************** PP
TIGR00117 65 agflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvf 128
agfl+a+akge+kspli ++avellgtm+ggyn+ +l+++l+ d+++a++aa+ l++tll+f
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 65 AGFLSALAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLD--DAELAPVAAEELKHTLLMF 126
*******************************************..******************* PP
TIGR00117 129 dafddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaft 191
daf+dv+e +k n +ak vl+swa++ewf n++ la+ki+ vfkv+getntddlspapda++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 127 DAFHDVAERAKNgNVHAKGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPDAWS 190
**********998*************************************************** PP
TIGR00117 192 rpdiplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvl 245
rpdiplhalamlk ++++i + +i+++++ g+p+ayvgdvvgtgssrksatnsvl
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 191 RPDIPLHALAMLKMARDGIVPdvqgsigpmkQIEEMRNSGFPIAYVGDVVGTGSSRKSATNSVL 254
*******************99999**************************************** PP
TIGR00117 246 wflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitn 309
wf+g+d+p+vpnkragg+++g kiapif+nt+ed+galpie dv ++n+gdvi++yp+ g++ +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 255 WFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTNINMGDVIDLYPHAGKVCK 318
**************************************************************** PP
TIGR00117 310 ket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgf 372
+ t ev++tf++k+ +lldevraggripliigrglt+kar lgl+ ++fkk+ ap es+kgf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 319 HGTdEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPDAPIESTKGF 382
*9999*********************************************************** PP
TIGR00117 373 tlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchta 436
tlaqk+vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchta
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 383 TLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTA 446
**************************************************************** PP
TIGR00117 437 aypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpa 500
aypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpa
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 447 AYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPA 510
**************************************************************** PP
TIGR00117 501 gsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvf 564
gsglvafaaatgvmpldmpes+lvrfkge+qpg+tlrdlv+aipy+ai+ glltvekkgk+n f
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 511 GSGLVAFAAATGVMPLDMPESILVRFKGEMQPGVTLRDLVHAIPYFAIQAGLLTVEKKGKKNAF 574
**************************************************************** PP
TIGR00117 565 ngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedk 628
+grileiegl +l +eqafel+dasaersaagctikl+ke++ eyl+sni ll++mi egy+d
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 575 SGRILEIEGLDNLSIEQAFELSDASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDV 638
**************************************************************** PP
TIGR00117 629 rtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdai 692
rtl+rr +ame+w+anpel+ adadaeya+vieidla+ikep+l+apndpdd++lls vag++i
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 639 RTLERRAQAMEAWIANPELMVADADAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKI 702
**************************************************************** PP
TIGR00117 693 devfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartev 755
devfigscmtnighfraagk+l++ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 703 DEVFIGSCMTNIGHFRAAGKLLDQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEM 766
***********************9988************************************* PP
TIGR00117 756 pgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalv 819
pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+eey+++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 767 PGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYA 830
***************************************************************8 PP
TIGR00117 820 sekvesakdklyrylnfnelenfee 844
+ + a d +yryl f+++ +f+e
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4564 831 GKIDSMAAD-VYRYLSFDQIAEFRE 854
877766666.************985 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 13.02
//
[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