Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378
Length = 866
Score = 1387 bits (3591), Expect = 0.0
Identities = 672/856 (78%), Positives = 760/856 (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+AIAKGEAKSPL+ ++A+ELLGTMQGGYNI L++ LDDA+LAP+AA+ L
Sbjct: 61 AYVKAGFLSAIAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLDDAELAPVAAEELK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF+ RP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAQGVLQSWADGEWFVKRPTLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD GV GP+KQIE ++ GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDAQGVTGPMKQIEEMRNAGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDD+P+VPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
++MGDVID+YP+ G+V H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARTE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP S +F++ + AES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPPSTLFKKPEAPAESTKGFTLAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG++
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEL 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPG+TLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGLP L VEQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLPKLTVEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTI+L+KE I EYL SNI LL+WMI EGYGD RTLERR Q ME WLANPELLEA
Sbjct: 601 ERSAAGCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELLEA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
D DAEYA VI+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DKDAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GKLL+ KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARV
Sbjct: 721 GKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVE 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: 2168
Number of extensions: 75
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 PfGW456L13_3378 (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.24739.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 1541.2 0.0 0 1541.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 Aconitate hydratase 2 (EC 4.2.1.3) @ 2-methylisocitrate dehyd
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1541.0 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1541.0 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvpp 55
+le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvpp
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPP 55
69***************************************************** PP
TIGR00117 56 gvdeaayvkagflaaiakgevksplisaeeavellgtmlggynvepliealeskd 110
gvdeaayvkagfl+aiakge+kspli ++avellgtm+ggyn+ +l+++l+ d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 56 GVDEAAYVKAGFLSAIAKGEAKSPLIDKKRAVELLGTMQGGYNIVTLVNLLD--D 108
****************************************************..* PP
TIGR00117 111 kniakaaakalsktllvfdafddveelskt.neyakqvleswaeaewflnkeela 164
+++a++aa+ l++tll+fdaf+dv+e++k n +a+ vl+swa++ewf+ +++la
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 109 AELAPVAAEELKHTLLMFDAFHDVAEKAKNgNVHAQGVLQSWADGEWFVKRPTLA 163
****************************998************************ PP
TIGR00117 165 ekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq....... 212
+ki+ vfkv+getntddlspapda++rpdiplhalamlk ++++i +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 164 DKISLRVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGIVPdaqgvtg 218
**********************************************99999**** PP
TIGR00117 213 ...rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglv 264
+i+++++ g+p+ayvgdvvgtgssrksatnsvlwf+g+d+p+vpnkragg++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 219 pmkQIEEMRNAGFPIAYVGDVVGTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFC 273
******************************************************* PP
TIGR00117 265 lggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.evvatf 318
+g kiapif+nt+ed+galpie dv+++++gdvi++yp+ g++ ++ t ev++tf
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 274 FGSKIAPIFYNTMEDAGALPIEFDVSNMHMGDVIDLYPHAGKVCKHGTdEVLTTF 328
**********************************************9999***** PP
TIGR00117 319 klkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgft 373
++k+ +lldevraggripliigrglt+kar lgl++s +fkk++apaes+kgft
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 329 EMKTPVLLDEVRAGGRIPLIIGRGLTEKARTELGLPPSTLFKKPEAPAESTKGFT 383
******************************************************* PP
TIGR00117 374 laqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlv 428
laqk+vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf++dlv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 384 LAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSTDLV 438
******************************************************* PP
TIGR00117 429 lqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvg 483
+qsfchtaaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 439 MQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVG 493
******************************************************* PP
TIGR00117 484 tggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
tggdshtrfp+gisfpagsglvafaaatgvmpldmpes+lvrfkgelqpg+tlrd
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 494 TGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGELQPGVTLRD 548
******************************************************* PP
TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaers 593
lv+aipyyai+ glltvekkgk+n f+grileieglp l veqafel+dasaers
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 549 LVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLPKLTVEQAFELSDASAERS 603
******************************************************* PP
TIGR00117 594 aagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpell 648
aagcti+l+ke+++eyl+sni ll++mi egy+d+rtl+rr +ame+wlanpell
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 604 AAGCTIQLSKESIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPELL 658
******************************************************* PP
TIGR00117 649 eadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtn 703
ead daeya+vieidla+ikep+l+apndpdd++lls vag++idevfigscmtn
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 659 EADKDAEYAEVIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTN 713
******************************************************* PP
TIGR00117 704 ighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpg 757
ighfraagk+le+ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+pg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 714 IGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPG 768
************9988*************************************** PP
TIGR00117 758 cslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptk 812
cslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 769 CSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTV 823
******************************************************* PP
TIGR00117 813 eeylalvsekvesakdklyrylnfnelenfee 844
eey+++ + + a d +yryl f+++ +f+e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3378 824 EEYMEYAGKIDSMAAD-VYRYLSFDQIAEFRE 854
******8877766666.************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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 8.77
//
[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