Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 199624 SO0432 aconitate hydratase 2 (NCBI ptt file)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__MR1:199624
Length = 865
Score = 1437 bits (3720), Expect = 0.0
Identities = 700/865 (80%), Positives = 784/865 (90%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YRKHVAERAAEG+ PKPLDA+Q+A LV+L++NPPAGEE F+LDLL NR+PPGVDEA
Sbjct: 1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAFVLDLLENRIPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKA FL A+AKG A SP+L+ E+A ELLGTMQGGYNI PLI LD+ LAP+AAKAL+
Sbjct: 61 AYVKAAFLDAVAKGTATSPILSAERATELLGTMQGGYNIEPLIAQLDNPALAPLAAKALA 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD+F+DV EK +AGN++AKQV+++WA+A+W+L+RP LA+K+T+TVFKV+GETNTD
Sbjct: 121 HTLLMFDSFHDVVEKMEAGNQFAKQVVEAWANADWYLSRPKLADKVTLTVFKVSGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKNAR+GIEPD G VGPIK++E L+ KGFPL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIEPDVAGSVGPIKKLEELKTKGFPLVYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ MGDVID+YPY G V+ H + E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MEMGDVIDIYPYAGVVKRHGSDEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARAV 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP S+VF + +D+A++ +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLPASEVFVRPQDIADNGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIPL AI+ G+LTVEKKGK NIFSGR+LEIEGL LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPLKAIELGMLTVEKKGKVNIFSGRVLEIEGLESLKVEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL+KEPIIEYLNSNI +LKWMIAEGYGDRRT+ERRI+GME+WLANPEL+ A
Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNITMLKWMIAEGYGDRRTIERRIKGMEEWLANPELMSA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEY AVI+IDL +IKEPILCAPNDPDDA LS+V KIDEVF+GSCMTNIGHFRA
Sbjct: 661 DADAEYTAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTKIDEVFVGSCMTNIGHFRAT 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GK+LD LPTRLW+APPT+MD QLTEEGYY +FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 721 GKMLDKFAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPGCSLCMGNQARVA 780
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
+GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LPT EEYQ Y ++D TA DT
Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAADT 840
Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
YRYLNF+Q+ YT+KA VIFQ+AV
Sbjct: 841 YRYLNFDQIDSYTKKASQVIFQSAV 865
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: 2130
Number of extensions: 81
Number of successful extensions: 1
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: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space: 677329
Effective search space used: 677329
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 199624 SO0432 (aconitate hydratase 2 (NCBI ptt file))
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.1792150.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 1571.2 0.0 0 1571.0 0.0 1.0 1 lcl|FitnessBrowser__MR1:199624 SO0432 aconitate hydratase 2 (NC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199624 SO0432 aconitate hydratase 2 (NCBI ptt file)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1571.0 0.0 0 0 1 843 [. 1 853 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1571.0 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevksp 79
+le+yrkhvaeraaeg+ p+pl+a+qva+lv+l++n+p++ee+f+l+ll +r+ppgvdeaayvka fl a+akg ++sp
lcl|FitnessBrowser__MR1:199624 1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAFVLDLLENRIPPGVDEAAYVKAAFLDAVAKGTATSP 79
79***************************************************************************** PP
TIGR00117 80 lisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswaeaewf 157
+sae+a+ellgtm+ggyn+epli +l+ + +a+ aakal +tll+fd+f+dv e+ ++ n++akqv+e+wa+a+w+
lcl|FitnessBrowser__MR1:199624 80 ILSAERATELLGTMQGGYNIEPLIAQLD--NPALAPLAAKALAHTLLMFDSFHDVVEKMEAgNQFAKQVVEAWANADWY 156
****************************..899**********************9999988***************** PP
TIGR00117 158 lnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqkgvpvay 226
l +++la+k+t tvfkv+getntddlspapda++rpdiplhalamlkn++++ie+ ++++lk+kg+p+ y
lcl|FitnessBrowser__MR1:199624 157 LSRPKLADKVTLTVFKVSGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIEPdvagsvgpikKLEELKTKGFPLVY 235
******************************************************************************* PP
TIGR00117 227 vgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykg 305
vgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++++gdvi+iypy g
lcl|FitnessBrowser__MR1:199624 236 VGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMEMGDVIDIYPYAG 314
******************************************************************************* PP
TIGR00117 306 eitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkac 383
++ + + ev++ f lk+++lldevraggripliigrgltdkar +lgl+ sevf+++++ a+++kg+tlaqk+vgkac
lcl|FitnessBrowser__MR1:199624 315 VVKRHGSdEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARAVLGLPASEVFVRPQDIADNGKGYTLAQKMVGKAC 393
****99889********************************************************************** PP
TIGR00117 384 gvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggval 462
gv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tlpdfi++rggv+l
lcl|FitnessBrowser__MR1:199624 394 GVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSL 472
******************************************************************************* PP
TIGR00117 463 rpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvn 541
rpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlv+
lcl|FitnessBrowser__MR1:199624 473 RPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVH 551
******************************************************************************* PP
TIGR00117 542 aipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkem 620
aip+ ai+ g+ltvekkgkvn+f+gr+leiegl lkveqafel+dasaersaagctikl+kep+ieyl+sni +lk+m
lcl|FitnessBrowser__MR1:199624 552 AIPLKAIELGMLTVEKKGKVNIFSGRVLEIEGLESLKVEQAFELSDASAERSAAGCTIKLDKEPIIEYLNSNITMLKWM 630
******************************************************************************* PP
TIGR00117 621 iaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigs 699
iaegy+d+rt++rri++me+wlanpel++adadaey+avieidl+eikepil+apndpdd+ lls va +idevf+gs
lcl|FitnessBrowser__MR1:199624 631 IAEGYGDRRTIERRIKGMEEWLANPELMSADADAEYTAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTKIDEVFVGS 709
******************************************************************************* PP
TIGR00117 700 cmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfst 777
cmtnighfra+gk+l++ akt+++rlw++ppt+md++ql+eegyy+ifg+ gar+e+pgcslcmgnqarv++gatv+st
lcl|FitnessBrowser__MR1:199624 710 CMTNIGHFRATGKMLDKfAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPGCSLCMGNQARVAEGATVVST 788
***************983569********************************************************** PP
TIGR00117 778 strnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
strnf+nrlg+ga+vyl+saelaavaallg++pt+eey+++ e +++a d +yrylnf++++ ++
lcl|FitnessBrowser__MR1:199624 789 STRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAAD-TYRYLNFDQIDSYT 853
***********************************************9999.***********997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (865 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 43.51
//
[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