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.8160.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: 00:00:00.08
# Mc/sec: 8.70
//
[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