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 N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__Dyella79:N515DRAFT_0029
Length = 869
Score = 1511 bits (3912), Expect = 0.0
Identities = 756/873 (86%), Positives = 808/873 (92%), Gaps = 11/873 (1%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ R+ L GT LDYFDARAAVEAIQPGAYD LPYTSRVLAENLVRRCDPA L +SL Q
Sbjct: 1 MNTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
++ RKR+ DFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPAKVNPVVPVQLIVDH
Sbjct: 61 IIERKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDP+AFA+NRAIEDRRNEDRFHFI+WT+QAF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPNAFARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADN-----GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 235
SPVI + GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP
Sbjct: 181 SPVIQVQHDDQGKGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 240
Query: 236 DIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMA 295
DI+GVELTGKRQPGITATDIVLALTEFLR+EKVVGAYLEFRGEGA+SLTLGDRATISNMA
Sbjct: 241 DIIGVELTGKRQPGITATDIVLALTEFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMA 300
Query: 296 PEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDL 355
PEYGATAAMFFID+QT+DYLRLTGR+DEQ++LVETYA+ AGLWAD+L A+YER L FDL
Sbjct: 301 PEYGATAAMFFIDDQTLDYLRLTGRSDEQVRLVETYAKAAGLWADTLAAAQYERTLSFDL 360
Query: 356 SSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTS 415
SSVVRNMAGPSNPHKRLPT+ LA RGIA QE G MPDGAVIIAAITSCTNTS
Sbjct: 361 SSVVRNMAGPSNPHKRLPTADLAARGIA-----GQWQEQPGQMPDGAVIIAAITSCTNTS 415
Query: 416 NPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAF 475
NPRNVIAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAF
Sbjct: 416 NPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLLPELEKLGFGIVAF 475
Query: 476 ACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535
ACTTCNGMSGALDP IQQEI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA
Sbjct: 476 ACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535
Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595
IAGTIRFDIE+DVLG D +G+PV LKDIWPSDEEID IVA SVKPEQFRKVYEPMFA T
Sbjct: 536 IAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFARTG 595
Query: 596 ASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIM 655
SG +PLYDWR QSTYIRRPPYWEGALAGERTLK +R LAVLGDNITTDHLSPSNAIM
Sbjct: 596 RSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIM 655
Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
+SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTL+NEMAVVDG+VKKGSLAR
Sbjct: 656 ADSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLAR 715
Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
+EPEGKV+RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAGVE I AEGFER
Sbjct: 716 VEPEGKVMRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 775
Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
IHRTNLIGMGVLPLEF+PG +R TLG+DGTET+DV G R PRA LTLV++R+NGERVEVP
Sbjct: 776 IHRTNLIGMGVLPLEFQPGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVP 835
Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
VTCRLD+ EEVSIYEAGGVL FAQDFLE+++A
Sbjct: 836 VTCRLDTAEEVSIYEAGGVLQRFAQDFLEAAQA 868
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: 2239
Number of extensions: 86
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: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space: 683929
Effective search space used: 683929
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 N515DRAFT_0029 N515DRAFT_0029 (aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming))
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.28355.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 1793.1 0.2 0 1792.9 0.2 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 N515DRAFT_0029 aconitase /2-meth
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconi
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1792.9 0.2 0 0 1 858 [] 2 864 .. 2 864 .. 0.99
Alignments for each domain:
== domain 1 score: 1792.9 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkre 66
nt yr++l gt+ldyfdaraaveai+pgayd+lpytsrvlaenlvrr+dp+ l +slkq+ierkre
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 2 NTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQIIERKRE 67
899*************************************************************** PP
TIGR02333 67 ldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpda 132
dfpw+parvvchdilgqtalvdlaglrdaia++ggdpa+vnpvv++qlivdhslave+ggfdp+a
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 68 RDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDHSLAVECGGFDPNA 133
****************************************************************** PP
TIGR02333 133 feknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvk.....egvafpd 193
f++nraiedrrnedrfhfi+wt++af+nvdvip+gngimhqinlekmspv+qv+ +gva+pd
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 134 FARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKMSPVIQVQhddqgKGVAYPD 199
****************************************************974444469***** PP
TIGR02333 194 tlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalt 259
t+vgtdshtphvdalgviaigvggleae+vmlgras+mrlpdi+gveltgkrqpgitatdivlalt
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 200 TCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGKRQPGITATDIVLALT 265
****************************************************************** PP
TIGR02333 260 eflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325
eflr+ekvv+aylef gega +ltlgdratisnm+peygataamf+id+qt+dyl+ltgr +eqv+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 266 EFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMAPEYGATAAMFFIDDQTLDYLRLTGRSDEQVR 331
****************************************************************** PP
TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeg 391
lvetyakaaglwad+l a+yer+l+fdlssvvrn+agpsnph+rl+t+dlaa+gia++++e++ g
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 332 LVETYAKAAGLWADTLAAAQYERTLSFDLSSVVRNMAGPSNPHKRLPTADLAARGIAGQWQEQP-G 396
****************************************************************.* PP
TIGR02333 392 lmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagll 457
+mpdgaviiaaitsctntsnprnv+aa+llarnan++gl rkpwvksslapgsk+v+lyl+ea+ll
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 397 QMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLL 462
****************************************************************** PP
TIGR02333 458 keleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasp 523
+eleklgfgivafacttcngmsgaldp+iqqei++rdlyatavlsgnrnfdgrihpyakqaflasp
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 463 PELEKLGFGIVAFACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASP 528
****************************************************************** PP
TIGR02333 524 plvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle 589
plvvayaiagtirfdie+dvlg+da+g+++ lkdiwpsdeeid++vaa+vkpeqfrkvy+pmf+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 529 PLVVAYAIAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFART 594
***************************************************************987 PP
TIGR02333 590 .daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaa 654
++++++plydwr +styirrppywegalagertlkgmr lavlgdnittdhlspsnai++dsaa
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 595 gRSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIMADSAA 660
6999************************************************************** PP
TIGR02333 655 geylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmw 720
geyla+mglpeedfnsyathrgdhltaqratfanp l nem+ +dg+vk+gslar+epegkv+rmw
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLARVEPEGKVMRMW 726
****************************************************************** PP
TIGR02333 721 eaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk 786
eaietym+rkqpli+iagadygqgssrdwaakgvrlagveai aegferihrtnl+gmgvlplef+
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 727 EAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLIGMGVLPLEFQ 792
****************************************************************** PP
TIGR02333 787 pgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrf 852
pgt+rktl++dgte++dv g++tpra+ltlv++r+nge++evpvtcrldtaeevs+yeaggvlqrf
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 793 PGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVPVTCRLDTAEEVSIYEAGGVLQRF 858
****************************************************************** PP
TIGR02333 853 aqdfle 858
aqdfle
lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 859 AQDFLE 864
****97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (869 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.08
# Mc/sec: 8.40
//
[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