Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2930 PS417_14990 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__WCS417:GFF2930
Length = 869
Score = 1375 bits (3560), Expect = 0.0
Identities = 668/859 (77%), Positives = 759/859 (88%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YRKH+ ERAA GI P+PL+A Q A LVELLKNPPAGEEEFL+DL+TNR+PPGVDEA
Sbjct: 1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRIPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKGEA SPL+ ++A+ELLGTMQGGYNI L++ LDDA LAP+AA L
Sbjct: 61 AYVKAGFLSALAKGEATSPLIDKKRAVELLGTMQGGYNIVTLVELLDDAALAPVAAAQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKA+ GNE+AK V+QSWAD EWF NRP LA+K+++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKARNGNEHAKAVIQSWADGEWFRNRPTLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AREGI PD+ G GP+KQIE ++ +GFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMAREGIVPDEQGKTGPMKQIEEMRGQGFPIAYVGDVV 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 T E++ TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MNMGDVIDLYPHAGKVCKHGTDEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTDKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL +D+F+ + ++ +GF+LAQKMVG+ACG+ KG+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLGPTDLFKLPEAPVDTGKGFTLAQKMVGKACGLPEGKGVRPGTYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFS DLVMQSFCHTAAYPKP+DV THHTLPDFIM RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSTDLVMQSFCHTAAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKM+PGITLRDLVHAIP YAI+ GLLTVEKKGKKN FSGRILEIEGL DL +EQAFEL+D
Sbjct: 541 GKMKPGITLRDLVHAIPYYAIQSGLLTVEKKGKKNAFSGRILEIEGLNDLTLEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL+KE I EYLNSNI LL+WMI EGYGD RTLERR Q ME W+ NPEL
Sbjct: 601 ASAERSAAGCTIKLSKESITEYLNSNITLLRWMIGEGYGDPRTLERRAQAMEAWVKNPEL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+EADADAEYA +I+IDLA+I EPILCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MEADADAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ KGQLPTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEQVKGQLPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV +TVVSTSTRNFPNRLG GANV+LASAELAAVA+ +G+LPT EEY Y A++D A
Sbjct: 781 RVEPNSTVVSTSTRNFPNRLGDGANVYLASAELAAVASTLGRLPTVEEYMGYAAKLDTMA 840
Query: 838 VDTYRYLNFNQLSQYTEKA 856
D YRYLNF+Q++++ + A
Sbjct: 841 SDVYRYLNFDQIAEFRKIA 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: 2185
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 GFF2930 PS417_14990 (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.23850.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 1534.5 0.0 0 1534.3 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF2930 PS417_14990 bifunctional aconita
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2930 PS417_14990 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1534.3 0.0 0 0 1 843 [. 1 856 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1534.3 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75
+le+yrkh+ eraa+gi p+plna+q+a lvellkn+p++eeefl++l+++r+ppgvdeaayvkagfl+a+akge
lcl|FitnessBrowser__WCS417:GFF2930 1 MLEAYRKHIEERAALGIVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRIPPGVDEAAYVKAGFLSALAKGE 75
79************************************************************************* PP
TIGR00117 76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
++spli ++avellgtm+ggyn+ +l+e+l+ d+ +a++aa l++tll+fdaf+dv+e+++ ne+ak v++
lcl|FitnessBrowser__WCS417:GFF2930 76 ATSPLIDKKRAVELLGTMQGGYNIVTLVELLD--DAALAPVAAAQLKHTLLMFDAFHDVAEKARNgNEHAKAVIQ 148
********************************..****************************9988********* PP
TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
swa++ewf n+++la+ki+ vfkv+getntddlspapda++rpdiplhalamlk ++e+i + +i
lcl|FitnessBrowser__WCS417:GFF2930 149 SWADGEWFRNRPTLADKISLRVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMAREGIVPdeqgktgpmkQI 223
*************************************************************99999********* PP
TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
++++ +g+p+ayvgdvvgtgssrksatnsvlwf+g+d+p+vpnkragg+++g kiapif+nt+ed+galpie dv
lcl|FitnessBrowser__WCS417:GFF2930 224 EEMRGQGFPIAYVGDVVGTGSSRKSATNSVLWFFGDDVPYVPNKRAGGFCFGSKIAPIFYNTMEDAGALPIEFDV 298
*************************************************************************** PP
TIGR00117 290 kdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkak 363
++n+gdvi++yp+ g++ ++ t ev++tf++k+ +lldevraggripliigrgltdkar lgl+++++fk ++
lcl|FitnessBrowser__WCS417:GFF2930 299 TNMNMGDVIDLYPHAGKVCKHGTdEVITTFEMKTPVLLDEVRAGGRIPLIIGRGLTDKARAELGLGPTDLFKLPE 373
*********************9999************************************************** PP
TIGR00117 364 apaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfcht 435
ap +++kgftlaqk+vgkacg+ kg+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf++dlv+qsfcht
lcl|FitnessBrowser__WCS417:GFF2930 374 APVDTGKGFTLAQKMVGKACGLpegKGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSTDLVMQSFCHT 448
*********************87779************************************************* PP
TIGR00117 436 aaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
aaypkp+dv th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaa
lcl|FitnessBrowser__WCS417:GFF2930 449 AAYPKPIDVTTHHTLPDFIMTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAA 523
*************************************************************************** PP
TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafel 585
tgvmpldmpes+lvrfkg+++pgitlrdlv+aipyyai+ glltvekkgk+n f+grileiegl dl +eqafel
lcl|FitnessBrowser__WCS417:GFF2930 524 TGVMPLDMPESILVRFKGKMKPGITLRDLVHAIPYYAIQSGLLTVEKKGKKNAFSGRILEIEGLNDLTLEQAFEL 598
*************************************************************************** PP
TIGR00117 586 tdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavi 660
+dasaersaagctikl+ke++ eyl+sni ll++mi egy+d rtl+rr +ame+w++npel+eadadaeya++i
lcl|FitnessBrowser__WCS417:GFF2930 599 SDASAERSAAGCTIKLSKESITEYLNSNITLLRWMIGEGYGDPRTLERRAQAMEAWVKNPELMEADADAEYAEII 673
*************************************************************************** PP
TIGR00117 661 eidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmde 734
eidlaei+epil+apndpdd++lls vag++idevfigscmtnighfraagk+le+ k ++++rlw+ ppt+md+
lcl|FitnessBrowser__WCS417:GFF2930 674 EIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLEQVKgQLPTRLWLSPPTKMDA 748
*******************************************************9988**************** PP
TIGR00117 735 qqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgki 809
+ql+eegyy+i+g+agar+e+pgcslcmgnqarve ++tv+ststrnf+nrlg ga+vyl+saelaava+ lg++
lcl|FitnessBrowser__WCS417:GFF2930 749 HQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVEPNSTVVSTSTRNFPNRLGDGANVYLASAELAAVASTLGRL 823
*************************************************************************** PP
TIGR00117 810 ptkeeylalvsekvesakdklyrylnfnelenfe 843
pt+eey+ + ++ + a d +yrylnf+++ +f+
lcl|FitnessBrowser__WCS417:GFF2930 824 PTVEEYMGYAAKLDTMASD-VYRYLNFDQIAEFR 856
*********9877766666.***********998 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.08
//
[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