Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_21605
Length = 866
Score = 1386 bits (3587), Expect = 0.0
Identities = 668/856 (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+A+AKGEA SPL+ ++A+ELLGTMQGGYNI L+D LD A+LA +AA L
Sbjct: 61 AYVKAGFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVDLLDSAELAAVAAAQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNVHAQGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD+ GV GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGVTGPMKQIETMRGEGFPIAYVGDVV 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 + E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MNMGDVIDLYPHAGKVTKHNSDEILTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP SD+F++ + AES +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLPPSDLFKKPEAPAESTKGFTLAQKMVGKACGVAGVRPGTYCEPKMTTVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFKGKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGKM 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPG+TLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGL +L +EQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEGLDNLSIEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL+KE I EYL+SNI LL+WMI EGYGD RTLERR Q ME W+ANPEL+ A
Sbjct: 601 ERSAAGCTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAMEAWIANPELMVA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYA +I+IDLADIKEP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAA 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 PNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTMASDV 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: 2149
Number of extensions: 82
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 AO353_21605 AO353_21605 (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.2586.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 1536.0 0.0 0 1535.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 AO353_21605 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 AO353_21605 bifunctional aconitate hydratase 2/2-methylisocitrate dehyd
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1535.8 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1535.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvka 65
+le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvka
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 1 VLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVKA 65
69*************************************************************** PP
TIGR00117 66 gflaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfda 130
gfl+a+akge++spli ++avellgtm+ggyn+ +l+++l+ +++a +aa l++tll+fda
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 66 GFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVDLLD--SAELAAVAAAQLKHTLLMFDA 128
******************************************..689****************** PP
TIGR00117 131 fddveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpd 194
f+dv+e++k n +a+ vl+swa++ewf n++ la+ki+ vfkv+getntddlspapda++rpd
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 129 FHDVAEKAKNgNVHAQGVLQSWADGEWFKNRPVLADKISLRVFKVTGETNTDDLSPAPDAWSRPD 193
********998****************************************************** PP
TIGR00117 195 iplhalamlknkieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflg 249
iplhalamlk ++++i + +i++++ g+p+ayvgdvvgtgssrksatnsvlwf+g
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 194 IPLHALAMLKMARDGIVPdeqgvtgpmkQIETMRGEGFPIAYVGDVVGTGSSRKSATNSVLWFFG 258
***************999999******************************************** PP
TIGR00117 250 kdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.e 313
+d+p+vpnkragg+++g kiapif+nt+ed+galpie dv ++n+gdvi++yp+ g++t++++ e
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 259 DDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDVTNMNMGDVIDLYPHAGKVTKHNSdE 323
************************************************************99989 PP
TIGR00117 314 vvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqkl 378
+++tf++k+ +lldevraggripliigrglt+kar lgl++s++fkk++apaes+kgftlaqk+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 324 ILTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGLPPSDLFKKPEAPAESTKGFTLAQKM 388
***************************************************************** PP
TIGR00117 379 vgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvd 443
vgkacgv g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf++dlv+qsfchtaaypkp+d
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 389 VGKACGVAGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSTDLVMQSFCHTAAYPKPID 453
***************************************************************** PP
TIGR00117 444 vkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafa 508
v th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafa
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 454 VTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFA 518
***************************************************************** PP
TIGR00117 509 aatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieg 573
aatgvmpldmpes+lvrfkg++qpg+tlrdlv+aipyyai+ glltvekkgk+n f+grileieg
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 519 AATGVMPLDMPESILVRFKGKMQPGVTLRDLVHAIPYYAIQAGLLTVEKKGKKNAFSGRILEIEG 583
***************************************************************** PP
TIGR00117 574 lpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridam 638
l +l +eqafel+dasaersaagctikl+ke++ eyl sni ll++mi egy+d+rtl+rr +am
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 584 LDNLSIEQAFELSDASAERSAAGCTIKLSKESITEYLSSNITLLRWMIGEGYGDARTLERRAQAM 648
***************************************************************** PP
TIGR00117 639 ekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtn 703
e+w+anpel+ adadaeya++ieidla+ikep+l+apndpdd++lls vag++idevfigscmtn
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 649 EAWIANPELMVADADAEYAEIIEIDLADIKEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTN 713
***************************************************************** PP
TIGR00117 704 ighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqar 767
ighfraagk+l++ k ++++rlw+ ppt+md++ql+eegyy+i+g+agar+e+pgcslcmgnqar
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 714 IGHFRAAGKLLDQVKgQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQAR 778
************9988************************************************* PP
TIGR00117 768 vedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyr 832
ve ++tv+ststrnf+nrlg ga+vyl+saela+va++lg++pt+eey+a+ e + a d +yr
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 779 VEPNSTVVSTSTRNFPNRLGDGANVYLASAELASVASILGRLPTVEEYMAYAKEIDTMASD-VYR 842
***************************************************9998887777.*** PP
TIGR00117 833 ylnfnelenfee 844
yl f+++ +f+e
lcl|FitnessBrowser__pseudo3_N2E3:AO353_21605 843 YLSFDQIAEFRE 854
*********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: 12.60
//
[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