Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2264 Psest_2309 aconitate hydratase 2
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__psRCH2:GFF2264
Length = 875
Score = 1387 bits (3591), Expect = 0.0
Identities = 678/860 (78%), Positives = 762/860 (88%), Gaps = 3/860 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKHV ERAA+G+ P+PL+A Q A LVELLKNPPAGEEEFL+DL+TNRVP GVDEA
Sbjct: 7 VLEAYRKHVEERAAQGVVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRVPAGVDEA 66
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKGE SPLL+ ++A+ELLGTMQGGYNI L++ LD A+L +AA+ L
Sbjct: 67 AYVKAGFLSALAKGETSSPLLSKQRAVELLGTMQGGYNISTLVELLDSAELGAVAAEQLK 126
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAKAGNE+AK VMQSWA+ EWF NRPA+AEK++++VFKVTGETNTD
Sbjct: 127 HTLLMFDAFHDVAEKAKAGNEHAKAVMQSWAEGEWFTNRPAVAEKVSLSVFKVTGETNTD 186
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GI PD PG VGPIKQ+E L+ KGFP+AYVGDVV
Sbjct: 187 DLSPAPDAWSRPDIPLHALAMLKMARDGINPDVPGSVGPIKQMEELKAKGFPVAYVGDVV 246
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE D SN
Sbjct: 247 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDCSN 306
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
L MGDVIDVYPY G+V H T E++ TFELKTDVL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 307 LAMGDVIDVYPYAGKVCKHGTDEVITTFELKTDVLLDEVRAGGRIPLIIGRGLTEKARAE 366
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
+GL S +F++ + A+S +GF+LAQKMVGRACG+ KG+RPG YCEPKMT+VGSQDTT
Sbjct: 367 MGLAPSTLFKKPEAPADSGKGFTLAQKMVGRACGLPEGKGVRPGTYCEPKMTTVGSQDTT 426
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DVNTHHTLPDFIMNR GVSLRPGDG
Sbjct: 427 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVNTHHTLPDFIMNRSGVSLRPGDG 486
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 487 IIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 546
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
G+MQPGITLRDLVHAIP YAI+QGLLTVEKKGKKNIFSGRILEIEGL L VEQAFEL+D
Sbjct: 547 GQMQPGITLRDLVHAIPYYAIQQGLLTVEKKGKKNIFSGRILEIEGLNQLTVEQAFELSD 606
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTIKL ++ I EYL SNI +L+WMI+EGYGD RTLERR Q ME WLA+P+L
Sbjct: 607 ASAERSAAGCTIKLPEDSIAEYLKSNITMLRWMISEGYGDARTLERRAQAMEAWLADPKL 666
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
LEAD DAEYAAVI+IDLA++KEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHF
Sbjct: 667 LEADKDAEYAAVIEIDLAEVKEPVLCAPNDPDDARLLSTVAGEKIDEVFIGSCMTNIGHF 726
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLLD KG +PTRLW+APPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 727 RAAGKLLDKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 786
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV G+TVVSTSTRNFPNRLG NV+LASAELAAVA++IGKLPT EY Y +D A
Sbjct: 787 RVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKLPTVAEYMEYAKNIDSMA 846
Query: 838 VDTYRYLNFNQLSQYTEKAD 857
D YRYL+F+Q++++ + A+
Sbjct: 847 ADIYRYLSFDQIAEFRDAAE 866
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: 2188
Number of extensions: 70
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: 875
Length adjustment: 42
Effective length of query: 823
Effective length of database: 833
Effective search space: 685559
Effective search space used: 685559
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 GFF2264 Psest_2309 (aconitate hydratase 2)
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.27181.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__psRCH2:GFF2264 Psest_2309 aconitate hydratase 2
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2264 Psest_2309 aconitate hydratase 2
# 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 [] 7 863 .. 7 863 .. 0.99
Alignments for each domain:
== domain 1 score: 1534.7 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75
+le+yrkhv eraa+g+ p+plna+q+a lvellkn+p++eeefl++l+++rvp gvdeaayvkagfl+a+akge
lcl|FitnessBrowser__psRCH2:GFF2264 7 VLEAYRKHVEERAAQGVVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRVPAGVDEAAYVKAGFLSALAKGE 81
69************************************************************************* PP
TIGR00117 76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
spl+s ++avellgtm+ggyn+ +l+e+l+ +++ +aa+ l++tll+fdaf+dv+e++k+ ne+ak v++
lcl|FitnessBrowser__psRCH2:GFF2264 82 TSSPLLSKQRAVELLGTMQGGYNISTLVELLD--SAELGAVAAEQLKHTLLMFDAFHDVAEKAKAgNEHAKAVMQ 154
********************************..6899***************************9********* PP
TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
swae+ewf n++++aek++ +vfkv+getntddlspapda++rpdiplhalamlk ++++i++ ++
lcl|FitnessBrowser__psRCH2:GFF2264 155 SWAEGEWFTNRPAVAEKVSLSVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGINPdvpgsvgpikQM 229
**************************************************************99*********** PP
TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
++lk kg+pvayvgdvvgtgssrksatnsvlwf+g+dip vpnkragg+++g kiapif+nt+ed+galpie d
lcl|FitnessBrowser__psRCH2:GFF2264 230 EELKAKGFPVAYVGDVVGTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDC 304
*************************************************************************** PP
TIGR00117 290 kdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkak 363
++l +gdvi++ypy g++ ++ t ev++tf+lk+++lldevraggripliigrglt+kar +gl++s +fkk++
lcl|FitnessBrowser__psRCH2:GFF2264 305 SNLAMGDVIDVYPYAGKVCKHGTdEVITTFELKTDVLLDEVRAGGRIPLIIGRGLTEKARAEMGLAPSTLFKKPE 379
*********************9999************************************************** PP
TIGR00117 364 apaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfcht 435
apa+s+kgftlaqk+vg+acg+ kg+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfcht
lcl|FitnessBrowser__psRCH2:GFF2264 380 APADSGKGFTLAQKMVGRACGLpegKGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHT 454
*********************87779************************************************* PP
TIGR00117 436 aaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
aaypkp+dv+th+tlpdfi++r gv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaa
lcl|FitnessBrowser__psRCH2:GFF2264 455 AAYPKPIDVNTHHTLPDFIMNRSGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAA 529
*************************************************************************** PP
TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafel 585
tgvmpldmpesvlvrfkg++qpgitlrdlv+aipyyai++glltvekkgk+n+f+grileiegl +l veqafel
lcl|FitnessBrowser__psRCH2:GFF2264 530 TGVMPLDMPESVLVRFKGQMQPGITLRDLVHAIPYYAIQQGLLTVEKKGKKNIFSGRILEIEGLNQLTVEQAFEL 604
*************************************************************************** PP
TIGR00117 586 tdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavi 660
+dasaersaagctikl +++++eylksni +l++mi+egy+d+rtl+rr +ame+wla+p+llead daeyaavi
lcl|FitnessBrowser__psRCH2:GFF2264 605 SDASAERSAAGCTIKLPEDSIAEYLKSNITMLRWMISEGYGDARTLERRAQAMEAWLADPKLLEADKDAEYAAVI 679
*************************************************************************** PP
TIGR00117 661 eidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmde 734
eidlae+kep+l+apndpdd++lls vag++idevfigscmtnighfraagk+l++ k +++rlw++ppt+md+
lcl|FitnessBrowser__psRCH2:GFF2264 680 EIDLAEVKEPVLCAPNDPDDARLLSTVAGEKIDEVFIGSCMTNIGHFRAAGKLLDKVKgGIPTRLWLAPPTKMDA 754
*******************************************************99879*************** PP
TIGR00117 735 qqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgki 809
+ql+eegyy+i+g+agar+e+pgcslcmgnqarv+ g+tv+ststrnf+nrlg ++vyl+saelaava+++gk+
lcl|FitnessBrowser__psRCH2:GFF2264 755 HQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKL 829
*************************************************************************** PP
TIGR00117 810 ptkeeylalvsekvesakdklyrylnfnelenfee 844
pt+ ey+++ + + a d +yryl f+++ +f++
lcl|FitnessBrowser__psRCH2:GFF2264 830 PTVAEYMEYAKNIDSMAAD-IYRYLSFDQIAEFRD 863
*********8887777776.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (875 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.85
//
[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