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 PP_2336 PP_2336 aconitate hydratase 1
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__Putida:PP_2336
Length = 862
Score = 1459 bits (3777), Expect = 0.0
Identities = 739/867 (85%), Positives = 782/867 (90%), Gaps = 8/867 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+A RK LPGT LDYFDARAAVEAI+PGAYD LPYTSRVLAENLVRRCDPATL SL Q
Sbjct: 1 MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDP AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPQAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIQPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+H+D GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP+IVGV
Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK P ITATD+VLALTEFLRK+KVVGAYLEF GEGA +LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF ID+QTIDYLRLTGR ++Q+KLVETYA+ GLWADSL A YER L FDLSSVVR
Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH R+ TS LA +GIA S +E G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAKGIA-----GSWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA L+ARNAN GL RKPWVKSSLAPGSKAV+LYLEEA L +LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DGK + LKDIWPSDEEIDA+V +VKPEQFRKVY PMFAI G
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPK 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWRP STYIRRPPYWEGALAGERTL+ +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM DG VK+GSLARIEPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPE 714
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
GKV RMWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 715 GKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 774
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NL+GMGVLPLEFKPG +R TLGLDG+ETYDV+G R PRATLTLVV R NGE +EVPVTCR
Sbjct: 775 NLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCR 834
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
LD+ EEVSIYEAGGVL FAQDFLE++
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLEAT 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: 2240
Number of extensions: 88
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: 869
Length of database: 862
Length adjustment: 42
Effective length of query: 827
Effective length of database: 820
Effective search space: 678140
Effective search space used: 678140
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 PP_2336 PP_2336 (aconitate hydratase 1)
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.26232.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 1883.2 0.0 0 1883.1 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2336 PP_2336 aconitate hydratase 1
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2336 PP_2336 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1883.1 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1883.1 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75
nt+yrk+lpgtdldyfdaraaveaikpgayd lpytsrvlaenlvrr+dp+tl+asl+qlierkr+ldfpw+par
lcl|FitnessBrowser__Putida:PP_2336 2 NTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQLIERKRDLDFPWFPAR 76
899************************************************************************ PP
TIGR02333 76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150
vvchdilgqtalvdlaglrdaia+kggdpaqvnpvv++qlivdhslave+ggfdp+afeknraiedrrnedrfhf
lcl|FitnessBrowser__Putida:PP_2336 77 VVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDHSLAVECGGFDPQAFEKNRAIEDRRNEDRFHF 151
*************************************************************************** PP
TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225
inwtkkafknvdvi++gngimhqinlekmspvv++++gva+pdt+vgtdshtphvdalgviaigvggleae+vml
lcl|FitnessBrowser__Putida:PP_2336 152 INWTKKAFKNVDVIQPGNGIMHQINLEKMSPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVML 226
*************************************************************************** PP
TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300
gras+mrlp+ivgveltgk +p+itatd+vlalteflrk+kvv+aylef+gega+altlgdratisnm+peygat
lcl|FitnessBrowser__Putida:PP_2336 227 GRASWMRLPEIVGVELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGAT 301
*************************************************************************** PP
TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375
aamfaid+qtidyl+ltgree+qvklvetyaka+glwadsl avyer+l+fdlssvvrn+agpsnphar+atsd
lcl|FitnessBrowser__Putida:PP_2336 302 AAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVRNMAGPSNPHARVATSD 376
*************************************************************************** PP
TIGR02333 376 laakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvkly 450
laakgia+++ee++ g+mpdgaviiaaitsctntsnprnv+aagl+arnanklgl+rkpwvksslapgsk+v+ly
lcl|FitnessBrowser__Putida:PP_2336 377 LAAKGIAGSWEEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLY 450
**************.************************************************************ PP
TIGR02333 451 leeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl 525
leeagl+kele+lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl
lcl|FitnessBrowser__Putida:PP_2336 451 LEEAGLEKELEQLGFGIVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 525
*************************************************************************** PP
TIGR02333 526 vvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsply 599
vvayaiagtirfdiekdvlgv +dgkeirlkdiwpsdeeidavv+aavkpeqfrkvyipmf++e d++ kv+ply
lcl|FitnessBrowser__Putida:PP_2336 526 VVAYAIAGTIRFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEeDRGPKVAPLY 599
*********************.*****************************************989********* PP
TIGR02333 600 dwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674
dwrpmstyirrppywegalagertl+gmrplavl+dnittdhlspsnai+ldsaageylakmglpeedfnsyath
lcl|FitnessBrowser__Putida:PP_2336 600 DWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATH 674
*************************************************************************** PP
TIGR02333 675 rgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrd 748
rgdhltaqratfanpklfnemv++d g+vkqgslariepegkvtrmweaietym+rkqplii+agadygqgssrd
lcl|FitnessBrowser__Putida:PP_2336 675 RGDHLTAQRATFANPKLFNEMVRNDdGSVKQGSLARIEPEGKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRD 749
************************99************************************************* PP
TIGR02333 749 waakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkng 823
waakgvrlagveaivaegferihrtnlvgmgvlplefkpgt+rktl+ldg+e+ydv+g++tpra+ltlvvtr+ng
lcl|FitnessBrowser__Putida:PP_2336 750 WAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANG 824
*************************************************************************** PP
TIGR02333 824 eklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
e+levpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__Putida:PP_2336 825 ECLEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859
*********************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (862 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: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 12.06
//
[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