Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Dsui_2205 Dsui_2205 aconitate hydratase 2
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__PS:Dsui_2205
Length = 865
Score = 1245 bits (3222), Expect = 0.0
Identities = 626/864 (72%), Positives = 716/864 (82%), Gaps = 6/864 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR+HVAERAA GI P PL A Q LV LL+NPP GEE+ L++L+T RVP GVD+A
Sbjct: 1 MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLA +AKGE L++ KA ELLGTM GGYN+ P+ID L DA++ +AA+ L
Sbjct: 61 AKVKAEFLAKVAKGELSCALISRAKATELLGTMLGGYNVKPMIDLLGDAEVGAVAAEGLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLL+FD F+DV E AK GN AK VMQSWADAEWF +RP + +TVFKVTGETNTD
Sbjct: 121 KTLLVFDFFHDVAELAKGGNANAKAVMQSWADAEWFTSRPEVPASQKLTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKN R GIE D+ G GP+KQ+EAL +KG +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIEADKAGERGPVKQLEALAKKGNLIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIFFNTMEDAGALPIE+DV
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQ 300
Query: 301 LNMGDVID--VYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
++MGD I+ + +V + G ++A +LKT V++DEVRAGGRIPLIIGRGLTTKAR
Sbjct: 301 MDMGDEIELKIDQATAKVTALKNGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAR 360
Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
EALGL S +FR + + +G+SLAQKMVGRACG+ KGI PG YCEPKMT+VGSQD
Sbjct: 361 EALGLAPSTLFRLPQQPNDPGKGYSLAQKMVGRACGLPEGKGILPGTYCEPKMTTVGSQD 420
Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV H LP FI RGGV+LRPG
Sbjct: 421 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVRMHRELPSFISTRGGVALRPG 480
Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
DGVIHSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 481 DGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 540
Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
FKGKMQPGITLRDLV+AIPLYAIKQGLLTVEKKGKKN+FSGRILEIEGLPDLKVEQAFEL
Sbjct: 541 FKGKMQPGITLRDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFEL 600
Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
+DA+AERSAA C I LNKEPI+EYL SNI L+KWMIAEGY D RTL+RRI+ ME+W+AN
Sbjct: 601 SDAAAERSAAACAIALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANG 660
Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
LL+AD DA+YAAVI+IDLAD+KEPI+ PNDPDD + LS V G+KIDEVFIGSCMTNIG
Sbjct: 661 TLLKADTDAQYAAVIEIDLADVKEPIVACPNDPDDVKVLSEVAGDKIDEVFIGSCMTNIG 720
Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
HFRAAGK+LD K +PTRLW+APPT+MDA LTEEGYYSV GK+GAR+E+PGCSLCMGN
Sbjct: 721 HFRAAGKVLDG-KSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARMEMPGCSLCMGN 779
Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
QA++ G+T +STSTRNFPNRLG V+L SAELAA+ +L+GK+PT EY Y+ V+
Sbjct: 780 QAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELAAMCSLLGKIPTVAEYMEYIQVVNA 839
Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
A D YRY+NF+Q+ ++ E A+ V
Sbjct: 840 KAADIYRYMNFDQIPEFVEVAETV 863
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: 2064
Number of extensions: 83
Number of successful extensions: 4
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 Dsui_2205 Dsui_2205 (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.28537.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 1484.0 0.1 0 1483.8 0.1 1.0 1 lcl|FitnessBrowser__PS:Dsui_2205 Dsui_2205 aconitate hydratase 2
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2205 Dsui_2205 aconitate hydratase 2
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1483.8 0.1 0 0 1 843 [. 1 857 [. 1 858 [. 0.98
Alignments for each domain:
== domain 1 score: 1483.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevk 77
+le+yr+hvaeraa+gi+plpl a q+++lv ll+n+p++ee+ l+el++ rvp gvd+aa+vka+fla++akge+
lcl|FitnessBrowser__PS:Dsui_2205 1 MLEAYRQHVAERAALGIPPLPLSAAQTKDLVALLQNPPKGEEQALVELITYRVPAGVDDAAKVKAEFLAKVAKGELS 77
79*************************************************************************** PP
TIGR00117 78 splisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswae 153
++lis +a+ellgtmlggynv+p+i++l d+++ +aa+ l+ktllvfd f+dv+el+k n+ ak v++swa+
lcl|FitnessBrowser__PS:Dsui_2205 78 CALISRAKATELLGTMLGGYNVKPMIDLLG--DAEVGAVAAEGLKKTLLVFDFFHDVAELAKGgNANAKAVMQSWAD 152
*****************************9..******************************99************* PP
TIGR00117 154 aewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqk 220
aewf ++e++ + tvfkv+getntddlspapda++rpdiplhalamlkn +++ie +++al +k
lcl|FitnessBrowser__PS:Dsui_2205 153 AEWFTSRPEVPASQKLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNPRPGIEAdkagergpvkQLEALAKK 229
**********************************************************999**************** PP
TIGR00117 221 gvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdv 297
g +ayvgdvvgtgssrksatnsvlwf g+dipfvpnkr gg++lg kiapiffnt+ed+galpie dv ++++gd
lcl|FitnessBrowser__PS:Dsui_2205 230 GNLIAYVGDVVGTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFFNTMEDAGALPIELDVGQMDMGDE 306
****************************************************************************9 PP
TIGR00117 298 ik..iypykgeit.nketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakg 371
i+ i ++t +k++ v+a +lk+ ++ldevraggripliigrglt+karealgl++s +f+ +++p++ +kg
lcl|FitnessBrowser__PS:Dsui_2205 307 IElkIDQATAKVTaLKNGAVIAESQLKTPVILDEVRAGGRIPLIIGRGLTTKAREALGLAPSTLFRLPQQPNDPGKG 383
972255667788735778*********************************************************** PP
TIGR00117 372 ftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvk 445
++laqk+vg+acg+ kgi+pgtycepk+ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdv+
lcl|FitnessBrowser__PS:Dsui_2205 384 YSLAQKMVGRACGLpegKGILPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVR 460
*************87779*********************************************************** PP
TIGR00117 446 thktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesv 522
+h++lp fis+rggvalrpgdgvihswlnr+llpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesv
lcl|FitnessBrowser__PS:Dsui_2205 461 MHRELPSFISTRGGVALRPGDGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESV 537
***************************************************************************** PP
TIGR00117 523 lvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagcti 599
lvrfkg++qpgitlrdlvnaip+yaik+glltvekkgk+nvf+grileieglpdlkveqafel+da+aersaa+c+i
lcl|FitnessBrowser__PS:Dsui_2205 538 LVRFKGKMQPGITLRDLVNAIPLYAIKQGLLTVEKKGKKNVFSGRILEIEGLPDLKVEQAFELSDAAAERSAAACAI 614
***************************************************************************** PP
TIGR00117 600 klnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
lnkep++eyl+sni l+k+miaegy+d+rtlkrri+ame+w+an +ll+ad+da+yaavieidla++kepi+a+pn
lcl|FitnessBrowser__PS:Dsui_2205 615 ALNKEPIVEYLRSNITLMKWMIAEGYQDARTLKRRIKAMEEWIANGTLLKADTDAQYAAVIEIDLADVKEPIVACPN 691
***************************************************************************** PP
TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagart 753
dpddvk+lsevagd+idevfigscmtnighfraagk+l++++++++rlw++ppt+md+ l+eegyy+++g+agar+
lcl|FitnessBrowser__PS:Dsui_2205 692 DPDDVKVLSEVAGDKIDEVFIGSCMTNIGHFRAAGKVLDGKSDIPTRLWIAPPTKMDALILTEEGYYSVLGKAGARM 768
***************************************************************************** PP
TIGR00117 754 evpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdkl 830
e+pgcslcmgnqa+++ g+t +ststrnf+nrlg ++vylgsaelaa+++llgkipt+ ey++++ + + a d +
lcl|FitnessBrowser__PS:Dsui_2205 769 EMPGCSLCMGNQAQIRKGSTAMSTSTRNFPNRLGIDTRVYLGSAELAAMCSLLGKIPTVAEYMEYIQVVNAKAAD-I 844
*****************************************************************9877777777.* PP
TIGR00117 831 yrylnfnelenfe 843
yry+nf+++ +f
lcl|FitnessBrowser__PS:Dsui_2205 845 YRYMNFDQIPEFV 857
*********9985 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.69
//
[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