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)
>lcl|FitnessBrowser__WCS417:GFF2930 PS417_14990 bifunctional
aconitate hydratase 2/2-methylisocitrate dehydratase
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.4648.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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.43
//
[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