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 AO353_00890 AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_00890
Length = 864
Score = 1449 bits (3752), Expect = 0.0
Identities = 729/868 (83%), Positives = 782/868 (90%), Gaps = 6/868 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RK LPG+ LDYFD RAAVEAIQPGAYD LPYTSRVLAENLVRRCDPATLT+SL Q
Sbjct: 1 MNTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61 FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QTIDYL+LTGR DEQ++LVE YA+T GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVENYAKTTGLWADSLKGAQYERGLTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH R+ TS LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAQGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GL RKPWVKSSLAPGSK V LYL+EA L +LE+LGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DGK + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G
Sbjct: 536 RFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V PLYDWR STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 596 VKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM +G+VK+GSLAR+EPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFKPG +R TLG+DGTET+DVIGER PRATLTLV+ RKNGE+V VPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
D+ EEVSIYEAGGVL FAQDFLES+ A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESAVA 863
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: 2203
Number of extensions: 79
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: 864
Length adjustment: 42
Effective length of query: 827
Effective length of database: 822
Effective search space: 679794
Effective search space used: 679794
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 AO353_00890 AO353_00890 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
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.13363.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 1840.6 0.0 0 1840.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 AO353_00890 Fe/S-dependent 2-met
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1840.4 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1840.4 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkr 65
nt +rk+lpg++ldyfd+raaveai+pgayd+lpytsrvlaenlvrr+dp+tl++slkq+ierkr
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 2 NTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQFIERKR 66
799************************************************************** PP
TIGR02333 66 eldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdp 130
+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggfdp
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 67 DLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVERGGFDP 131
***************************************************************** PP
TIGR02333 131 dafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtl 195
+afeknraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+qv++gvafpdt+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 132 EAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFPDTC 196
***************************************************************** PP
TIGR02333 196 vgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalte 260
vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ vgveltgk qpgitatd+vlalte
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 197 VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGVELTGKLQPGITATDMVLALTE 261
***************************************************************** PP
TIGR02333 261 flrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325
flrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre+eqv+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 262 FLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGREDEQVQ 326
***************************************************************** PP
TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeae 390
lve yak++glwadslk a+yer l+fdlssvvrn+agpsnphar+atsdlaa+gi++++++++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 327 LVENYAKTTGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVATSDLAAQGISGQWDDVP- 390
****************************************************************. PP
TIGR02333 391 glmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeag 455
g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v lyl+eag
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 391 GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAG 455
***************************************************************** PP
TIGR02333 456 llkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl 520
l +ele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 456 LTSELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFL 520
***************************************************************** PP
TIGR02333 521 aspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipm 585
aspplvvayaiagtirfdiekdvlg+ adgkeirlkdiwpsdeeidavv+a+vkpeqfr+vyipm
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 521 ASPPLVVAYAIAGTIRFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPM 585
***************************************************************** PP
TIGR02333 586 fdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnail 649
f+++ d++ kv plydwr mstyirrppywegalag r lkgmrplavl+dnittdhlspsnai+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 586 FAIHeDTGPKVKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIM 650
***989*********************************************************** PP
TIGR02333 650 ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepeg 714
ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvkqgslar+epeg
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 651 LDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715
***************************************************************** PP
TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg 779
+v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegferihrtnlvgmg
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 780
***************************************************************** PP
TIGR02333 780 vlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvye 844
vlplefkpgt+rktl++dgte++dv+ge+tpra+ltlv+trknge++ vpvtcrldtaeevs+ye
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 781 VLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRLDTAEEVSIYE 845
***************************************************************** PP
TIGR02333 845 aggvlqrfaqdfle 858
aggvlqrfaqdfle
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 846 AGGVLQRFAQDFLE 859
************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (864 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 12.72
//
[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