Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PP_2339 PP_2339 bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__Putida:PP_2339
Length = 869
Score = 1386 bits (3588), Expect = 0.0
Identities = 677/859 (78%), Positives = 758/859 (88%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEE FL+DL+TNRVPPGVDEA
Sbjct: 1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKA FL+A+AKGEAKSPL+ + A ELLGTMQGGYNI L+ LDDA+L IAA+ L
Sbjct: 61 AYVKAAFLSAVAKGEAKSPLIDRKHATELLGTMQGGYNIETLVALLDDAELGAIAAEQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAKAGN +AK V++SWA EWF +RPA+A+K T+TVFKV GETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKAGNTHAKAVLESWAAGEWFTSRPAIADKYTLTVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GIEP QPG VGP+ QIEA++ KGFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIEPQQPGSVGPLAQIEAVKAKGFPVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE D +N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDCTN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
L MGDVIDVYPYKGEVR H++ EL+ TFELKT+VL+DEVRAGGRIPLI+GRGLT KAR
Sbjct: 301 LGMGDVIDVYPYKGEVRRHDSDELVTTFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL SD+F++ + A+S +GF+LAQKMVGRACG+ +G+RPGAYCEPKMT+VGSQDTT
Sbjct: 361 LGLGASDLFKKPEQPADSGKGFTLAQKMVGRACGLPEGQGVRPGAYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFI RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRML+PDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GK+QPGITLRDLVHAIP YAI++GLLTVEKKGKKN FSGRILEIEGL DL VEQAFEL+D
Sbjct: 541 GKLQPGITLRDLVHAIPYYAIQKGLLTVEKKGKKNAFSGRILEIEGLDDLTVEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL ++ I EYL SNI LL+WMI EGYGD RTLERR Q ME WLA PEL
Sbjct: 601 ASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLAKPEL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
L ADADAEYA +I+IDLAD+KEP+LCAPNDPDDAR LS+VQGEKIDEVFIGSCMTNIGHF
Sbjct: 661 LSADADAEYAEIIEIDLADVKEPVLCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ KG +PTRLW+APPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV G+TVVSTSTRNFPNRLG NV+LASAELAAVA++IGKLPT EEY Y +D A
Sbjct: 781 RVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKLPTVEEYMQYAKDIDSMA 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: 2184
Number of extensions: 74
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 PP_2339 PP_2339 (bifunctional aconitate hydratase 2 and 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.31839.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 1534.9 0.0 0 1534.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2339 PP_2339 bifunctional aconitate h
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2339 PP_2339 bifunctional aconitate hydratase 2 and 2-methylisocitrate dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1534.7 0.0 0 0 1 844 [] 1 857 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1534.7 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75
+le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++ee+fl++l+++rvppgvdeaayvka fl+a+akge
lcl|FitnessBrowser__Putida:PP_2339 1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPPGVDEAAYVKAAFLSAVAKGE 75
79************************************************************************* PP
TIGR00117 76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
+kspli ++a+ellgtm+ggyn+e+l+ +l+ d+++ +aa+ l++tll+fdaf+dv+e++k+ n++ak vle
lcl|FitnessBrowser__Putida:PP_2339 76 AKSPLIDRKHATELLGTMQGGYNIETLVALLD--DAELGAIAAEQLKHTLLMFDAFHDVAEKAKAgNTHAKAVLE 148
********************************..*******************************9********* PP
TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
swa +ewf ++++a+k t tvfkv+getntddlspapda++rpdiplhalamlk ++++ie+ +i
lcl|FitnessBrowser__Putida:PP_2339 149 SWAAGEWFTSRPAIADKYTLTVFKVPGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGIEPqqpgsvgplaQI 223
**************************************************************99*********** PP
TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
+a+k kg+pvayvgdvvgtgssrksatnsvlwf+g+dip+vpnkragg+++g kiapif+nt+ed+galpie d
lcl|FitnessBrowser__Putida:PP_2339 224 EAVKAKGFPVAYVGDVVGTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDC 298
*************************************************************************** PP
TIGR00117 290 kdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkak 363
+l +gdvi++ypykge++ +++ e+v+tf+lk+e+lldevraggripli+grglt+kar lgl+ s++fkk++
lcl|FitnessBrowser__Putida:PP_2339 299 TNLGMGDVIDVYPYKGEVRRHDSdELVTTFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAELGLGASDLFKKPE 373
**********************999************************************************** PP
TIGR00117 364 apaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfcht 435
+pa+s+kgftlaqk+vg+acg+ +g+rpg+ycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfcht
lcl|FitnessBrowser__Putida:PP_2339 374 QPADSGKGFTLAQKMVGRACGLpegQGVRPGAYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHT 448
*********************87679************************************************* PP
TIGR00117 436 aaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
aaypkp+dv th+tlpdfi +rggv+lrpgdg+ihswlnrml+pdtvgtggdshtrfp+gisfpagsglvafaaa
lcl|FitnessBrowser__Putida:PP_2339 449 AAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDGIIHSWLNRMLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAA 523
*************************************************************************** PP
TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafel 585
tgvmpldmpes+lvrfkg+lqpgitlrdlv+aipyyai+kglltvekkgk+n f+grileiegl dl veqafel
lcl|FitnessBrowser__Putida:PP_2339 524 TGVMPLDMPESILVRFKGKLQPGITLRDLVHAIPYYAIQKGLLTVEKKGKKNAFSGRILEIEGLDDLTVEQAFEL 598
*************************************************************************** PP
TIGR00117 586 tdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavi 660
+dasaersaagctikl +++++eyl+sni ll++mi egy+d+rtl+rr +ame+wla pell+adadaeya++i
lcl|FitnessBrowser__Putida:PP_2339 599 SDASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLAKPELLSADADAEYAEII 673
*************************************************************************** PP
TIGR00117 661 eidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmde 734
eidla++kep+l+apndpdd++lls v+g++idevfigscmtnighfraagk+le+ k +++rlw++ppt+md+
lcl|FitnessBrowser__Putida:PP_2339 674 EIDLADVKEPVLCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHFRAAGKLLEKVKgGIPTRLWLAPPTKMDA 748
*******************************************************99879*************** PP
TIGR00117 735 qqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgki 809
+ql+eegyy+i+g+agar+e+pgcslcmgnqarv+ g+tv+ststrnf+nrlg ++vyl+saelaava+++gk+
lcl|FitnessBrowser__Putida:PP_2339 749 HQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKL 823
*************************************************************************** PP
TIGR00117 810 ptkeeylalvsekvesakdklyrylnfnelenfee 844
pt+eey+++ + + a d +yryl f+++ +f+e
lcl|FitnessBrowser__Putida:PP_2339 824 PTVEEYMQYAKDIDSMAAD-VYRYLSFDQIAEFRE 857
*********9888877777.************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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.09
# Mc/sec: 7.87
//
[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