Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf6N2E2_564 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564
Length = 869
Score = 1377 bits (3565), Expect = 0.0
Identities = 667/859 (77%), Positives = 761/859 (88%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKH+ ERAA GI P+PL+A Q A L+ELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKG+A+SPLL ++A+ELLGTMQGGYNI L++ LDDA+LAP+AA+ L
Sbjct: 61 AYVKAGFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLDDAELAPVAAEELK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +AK V+QSWAD EWF RP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAKAVLQSWADGEWFKKRPVLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ G GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+NMGDVID+YP+ G+V H T E++ TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MNMGDVIDLYPHAGKVCKHGTDEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGLP D+F++ + AES +GF+LAQKMVG+ACG+ +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLPAFDLFKKPEAPAESTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKM+PGITLRDLVHAIP +AI+ GLLTVEKKGKKN FSGRILEIEGL L +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILEIEGLEGLTLEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME W+ANP+L
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPQL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+EADADAEYA VI+IDLADI EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLLD KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLDQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV +TVVSTSTRNFPNRLG GANV+LASAELA+VA+++G+LPT EEY Y ++D A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMA 840
Query: 838 VDTYRYLNFNQLSQYTEKA 856
D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 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: 2154
Number of extensions: 76
Number of successful extensions: 2
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space: 680621
Effective search space used: 680621
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 Pf6N2E2_564 (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.473.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 1525.3 0.0 0 1525.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 Aconitate hydratase 2 (EC 4.2.1.
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1525.1 0.0 0 0 1 844 [] 1 857 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1525.1 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvka 65
+le+yrkh+ eraa+gi p+plna+q+a l+ellkn+p++ee+fl++l+++rvppgvdeaayvka
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLIELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVKA 65
69*************************************************************** PP
TIGR00117 66 gflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfda 130
gfl+a+akg+++spl+ ++avellgtm+ggyn+ +l+e+l+ d+++a++aa+ l++tll+fda
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 66 GFLSALAKGQAQSPLLDKKRAVELLGTMQGGYNIVTLVELLD--DAELAPVAAEELKHTLLMFDA 128
******************************************..********************* PP
TIGR00117 131 fddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpd 194
f+dv+e++k n +ak vl+swa++ewf ++ la+ki+ vfkv+getntddlspapda++rpd
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 129 FHDVAEKAKNgNVHAKAVLQSWADGEWFKKRPVLADKISLRVFKVTGETNTDDLSPAPDAWSRPD 193
********998****************************************************** PP
TIGR00117 195 iplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflg 249
iplhalamlk ++++i + +i++++ +g+p+ayvgdvvgtgssrksatnsvlwf+g
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 194 IPLHALAMLKMARDGIVPdeqgktgpmkQIEEMRGQGFPIAYVGDVVGTGSSRKSATNSVLWFFG 258
***************999999******************************************** PP
TIGR00117 250 kdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.e 313
+dip+vpnkragg+++g kiapif+nt+ed+galpie dv+++n+gdvi++yp+ g++ ++ t e
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 259 DDIPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSNMNMGDVIDLYPHAGKVCKHGTdE 323
*************************************************************9999 PP
TIGR00117 314 vvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqkl 378
v++tf++k+ +lldevraggripliigrglt+kar lgl+ ++fkk++apaes+kgftlaqk+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 324 VITTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPAFDLFKKPEAPAESTKGFTLAQKM 388
***************************************************************** PP
TIGR00117 379 vgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypk 440
vgkacg+ +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 389 VGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPK 453
******86668****************************************************** PP
TIGR00117 441 pvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglv 505
p+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglv
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 454 PIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLV 518
***************************************************************** PP
TIGR00117 506 afaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrile 570
afaaatgvmpldmpes+lvrfkg+++pgitlrdlv+aipy+ai++glltvekkgk+n f+grile
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 519 AFAAATGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYFAIQNGLLTVEKKGKKNAFSGRILE 583
***************************************************************** PP
TIGR00117 571 ieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrri 635
iegl l +eqafel+dasaersaagctikl+ke++ eyl+sni ll++mi egy+d+rtl+rr
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 584 IEGLEGLTLEQAFELSDASAERSAAGCTIKLSKESITEYLQSNITLLRWMIGEGYGDARTLERRA 648
***************************************************************** PP
TIGR00117 636 damekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigsc 700
+ame+w+anp+l+eadadaeya+vieidla+i ep+l+apndpdd++lls vag++idevfigsc
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 649 QAMEAWIANPQLMEADADAEYAEVIEIDLADISEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSC 713
***************************************************************** PP
TIGR00117 701 mtnighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgn 764
mtnighfraagk+l++ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+pgcslcmgn
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 714 MTNIGHFRAAGKLLDQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGN 778
***************9988********************************************** PP
TIGR00117 765 qarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdk 829
qarve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+eey+++ + + a d
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 779 QARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMEYAGKIDSMAAD- 842
******************************************************8877766666. PP
TIGR00117 830 lyrylnfnelenfee 844
+yryl f+++ +f+e
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_564 843 VYRYLSFDQIAEFRE 857
************985 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: 12.83
//
[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