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.27695.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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 13.19
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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