Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate 7026694 Shewana3_3827 aconitate hydratase (RefSeq)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__ANA3:7026694
Length = 863
Score = 1452 bits (3759), Expect = 0.0
Identities = 721/866 (83%), Positives = 786/866 (90%), Gaps = 6/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPGT LDYFD R AVEAI PGAY KLPYTSRVLAENLVRRC+P LT SL Q
Sbjct: 1 MNTLYRKPLPGTALDYFDTREAVEAISPGAYAKLPYTSRVLAENLVRRCEPEALTASLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
++ K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH
Sbjct: 61 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+HA +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 181 SPVVHARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATDIVLALTEFLRKEKVV +YLEF GEGA +LTLGDRATISNM PE+GA
Sbjct: 241 ELTGKPQPGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QT+DYL LTGR+DEQ+KLVETYA+T GLW+D LK+AEY R L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
+AGPSNPH R+PT+ LA RGI+ + GLMPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TIAGPSNPHARVPTTELAARGIS-----GVVENEPGLMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNANA+GL+RKPWVK+SLAPGSKAV+LYLEEANLLP+LE LGFGIV FACTTC
Sbjct: 416 IAAGLLARNANAKGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG D+DG PV L DIWPSD EIDA++AKSVKPEQFR+VYEPMF ++ G+
Sbjct: 536 RFDIEKDVLGHDKDGNPVRLIDIWPSDAEIDAVIAKSVKPEQFRRVYEPMFDLSVDYGDK 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAIM++SAA
Sbjct: 596 VTPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEMAVVDG+VK+GSLARIEPEG
Sbjct: 656 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAVVDGKVKQGSLARIEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 QVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFK G NR T G+DGTE +DV G+ PRA LT+++ RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKAGENRATYGIDGTEVFDVYGDIAPRADLTVIITRKNGERVEVPVTCRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
D+ EEVSIY AGGVL FAQDFLES+
Sbjct: 836 DTAEEVSIYSAGGVLQRFAQDFLESN 861
Lambda K H
0.318 0.135 0.398
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: 2222
Number of extensions: 90
Number of successful extensions: 3
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: 869
Length of database: 863
Length adjustment: 42
Effective length of query: 827
Effective length of database: 821
Effective search space: 678967
Effective search space used: 678967
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 7026694 Shewana3_3827 (aconitate hydratase (RefSeq))
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# 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/TIGR02333.hmm
# target sequence database: /tmp/gapView.23560.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02333 [M=858]
Accession: TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
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 1855.8 0.0 0 1855.6 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7026694 Shewana3_3827 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026694 Shewana3_3827 aconitate hydratase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1855.6 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1855.6 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvv 77
nt yrk+lpgt+ldyfd+r+aveai pgay+klpytsrvlaenlvrr++pe l+aslkq+ie+k+eldfpw+parvv
lcl|FitnessBrowser__ANA3:7026694 2 NTLYRKPLPGTALDYFDTREAVEAISPGAYAKLPYTSRVLAENLVRRCEPEALTASLKQIIESKQELDFPWFPARVV 78
899************************************************************************** PP
TIGR02333 78 chdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwt 154
chdilgqtalvdlaglrdaia+kggdpaqvnpvv+tqlivdhslaveyggfd+daf+knraiedrrnedrfhfinwt
lcl|FitnessBrowser__ANA3:7026694 79 CHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWT 155
***************************************************************************** PP
TIGR02333 155 kkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslm 231
+kafkn+dvip+gngimhqinle+mspvv++++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgras+m
lcl|FitnessBrowser__ANA3:7026694 156 QKAFKNIDVIPQGNGIMHQINLERMSPVVHARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYM 232
***************************************************************************** PP
TIGR02333 232 rlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaide 308
rlpdi+gveltgk qpgitatdivlalteflrkekvvs+yleffgega+altlgdratisnmtpe+gataamf+id+
lcl|FitnessBrowser__ANA3:7026694 233 RLPDIIGVELTGKPQPGITATDIVLALTEFLRKEKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQ 309
***************************************************************************** PP
TIGR02333 309 qtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385
qt+dyl+ltgr +eqvklvetyak++glw+d+lk+a+y+r+l+fdlssvvr++agpsnphar++t++laa+gi++ v
lcl|FitnessBrowser__ANA3:7026694 310 QTLDYLTLTGRSDEQVKLVETYAKTTGLWSDDLKHAEYPRTLHFDLSSVVRTIAGPSNPHARVPTTELAARGISGVV 386
***************************************************************************** PP
TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkelek 462
e+e+ glmpdgaviiaaitsctntsnprnv+aagllarnan++gl rkpwvk+slapgsk+v+lyleea+ll+ele+
lcl|FitnessBrowser__ANA3:7026694 387 ENEP-GLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLSRKPWVKTSLAPGSKAVQLYLEEANLLPELES 462
****.************************************************************************ PP
TIGR02333 463 lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi 539
lgfgiv+facttcngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi
lcl|FitnessBrowser__ANA3:7026694 463 LGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDI 539
***************************************************************************** PP
TIGR02333 540 ekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywe 615
ekdvlg+d+dg+++rl+diwpsd+eidav+a++vkpeqfr+vy+pmfdl+ d+++kv+plydwrp+styirrppywe
lcl|FitnessBrowser__ANA3:7026694 540 EKDVLGHDKDGNPVRLIDIWPSDAEIDAVIAKSVKPEQFRRVYEPMFDLSvDYGDKVTPLYDWRPQSTYIRRPPYWE 616
***************************************************************************** PP
TIGR02333 616 galagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklf 692
galagertlkgmrplavlgdnittdhlspsnai++dsaageyl+kmglpeedfnsyathrgdhltaqratfanpkl+
lcl|FitnessBrowser__ANA3:7026694 617 GALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLK 693
***************************************************************************** PP
TIGR02333 693 nemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
nem+ +dgkvkqgslariepeg+vtrmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegfer
lcl|FitnessBrowser__ANA3:7026694 694 NEMAVVDGKVKQGSLARIEPEGQVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 770
***************************************************************************** PP
TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeag 846
ihrtnlvgmgvlplefk+g+nr+t+++dgtev+dv g+i+pradlt+++trknge++evpvtcrldtaeevs+y ag
lcl|FitnessBrowser__ANA3:7026694 771 IHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVYGDIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYSAG 847
***************************************************************************** PP
TIGR02333 847 gvlqrfaqdfle 858
gvlqrfaqdfle
lcl|FitnessBrowser__ANA3:7026694 848 GVLQRFAQDFLE 859
**********97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (863 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: 9.68
//
[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