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 WP_041765781.1 BPHY_RS33395 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000020045.1:WP_041765781.1
Length = 865
Score = 1582 bits (4096), Expect = 0.0
Identities = 791/870 (90%), Positives = 828/870 (95%), Gaps = 6/870 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+A RKPLPGT LDYFD RAAV+AIQPGAYDKLPYTSRV AENLVRRCDPATL DSL Q
Sbjct: 1 MNTAYRKPLPGTSLDYFDTRAAVDAIQPGAYDKLPYTSRVHAENLVRRCDPATLNDSLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
+V RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH
Sbjct: 61 IVERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AFKNVDVIPPGNGIMHQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGIMHQINLERM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVIHA +GVAYPDT VGTDSHTPHVDALGVIA+GVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIHAADGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
EL+GKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA
Sbjct: 241 ELSGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMFFIDEQTIDYLRLTGR D Q+KLVETYA+TAGLWAD+LK+AEYER+L FDLS+VVR
Sbjct: 301 TAAMFFIDEQTIDYLRLTGRDDAQVKLVETYAKTAGLWADTLKHAEYERILSFDLSTVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH+RLPTS LAERGIA +E G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHRRLPTSDLAERGIA-----GKWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAFACTTC
Sbjct: 416 IAAALLARNANARGLTRKPWVKSSLAPGSKAVELYLQEANLLPELEKLGFGIVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEI+DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPAIQQEIVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIE+DVLGTD+DGKPVYLKDIWPSDEEIDAIV +SVKPEQFRKVYEPMFA+TAASGE
Sbjct: 536 RFDIERDVLGTDRDGKPVYLKDIWPSDEEIDAIVKQSVKPEQFRKVYEPMFAVTAASGEP 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
+SPLYDWR QSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ NSAA
Sbjct: 596 ISPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILANSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQ+KKGSLARIEPEG
Sbjct: 656 GEYLTKMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQLKKGSLARIEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
KV RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
LIGMGVLPLEFK GVNRL LG+DGTETYDVIGER+PRA LTLV++RKNGERV+VPVTCRL
Sbjct: 776 LIGMGVLPLEFKRGVNRLALGIDGTETYDVIGERRPRADLTLVIHRKNGERVDVPVTCRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
D+ EEVSIYEAGGVL FAQDFLESS+A A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKAAA 865
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: 2314
Number of extensions: 93
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: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space: 680621
Effective search space used: 680621
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 WP_041765781.1 BPHY_RS33395 (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.2647354.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 1826.3 0.0 0 1826.2 0.0 1.0 1 NCBI__GCF_000020045.1:WP_041765781.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_041765781.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1826.2 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1826.2 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
nt+yrk+lpgt+ldyfd+raav+ai+pgaydklpytsrv aenlvrr+dp+tl++slkq++erkreldfpw+p
NCBI__GCF_000020045.1:WP_041765781.1 2 NTAYRKPLPGTSLDYFDTRAAVDAIQPGAYDKLPYTSRVHAENLVRRCDPATLNDSLKQIVERKRELDFPWFP 74
899********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia++ggdpa+vnpvv++qlivdhslave+ggfdpdaf+knraiedrrned
NCBI__GCF_000020045.1:WP_041765781.1 75 ARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNED 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rf finwtkkafknvdvip+gngimhqinle+mspv+++ +gva+pdtlvgtdshtphvdalgvia+gvggle
NCBI__GCF_000020045.1:WP_041765781.1 148 RFDFINWTKKAFKNVDVIPPGNGIMHQINLERMSPVIHAADGVAYPDTLVGTDSHTPHVDALGVIAVGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
ae+vmlgras+mrlpdivgvel+gkrqpgitatdivlalteflrkekvv+aylef gega +ltlgdratisn
NCBI__GCF_000020045.1:WP_041765781.1 221 AENVMLGRASWMRLPDIVGVELSGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
m+peygataamf+ideqtidyl+ltgr+++qvklvetyak+aglwad+lk+a+yer+l+fdls+vvrn+agps
NCBI__GCF_000020045.1:WP_041765781.1 294 MAPEYGATAAMFFIDEQTIDYLRLTGRDDAQVKLVETYAKTAGLWADTLKHAEYERILSFDLSTVVRNMAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvks 438
nph+rl+tsdla +gia+++ee++ g+mpdgaviiaaitsctntsnprnv+aa+llarnan++gl+rkpwvks
NCBI__GCF_000020045.1:WP_041765781.1 367 NPHRRLPTSDLAERGIAGKWEEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLTRKPWVKS 438
************************.************************************************ PP
TIGR02333 439 slapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgri 511
slapgsk+v+lyl+ea+ll+eleklgfgivafacttcngmsgaldp+iqqei+drdlyatavlsgnrnfdgri
NCBI__GCF_000020045.1:WP_041765781.1 439 SLAPGSKAVELYLQEANLLPELEKLGFGIVAFACTTCNGMSGALDPAIQQEIVDRDLYATAVLSGNRNFDGRI 511
************************************************************************* PP
TIGR02333 512 hpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyip 584
hpyakqaflaspplvvayaiagtirfdie+dvlg+d dgk+++lkdiwpsdeeida+v+++vkpeqfrkvy+p
NCBI__GCF_000020045.1:WP_041765781.1 512 HPYAKQAFLASPPLVVAYAIAGTIRFDIERDVLGTDRDGKPVYLKDIWPSDEEIDAIVKQSVKPEQFRKVYEP 584
************************************************************************* PP
TIGR02333 585 mfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaage 656
mf++ +++ splydwr +styirrppywegalagertlkgmrplavlgdnittdhlspsnail++saage
NCBI__GCF_000020045.1:WP_041765781.1 585 MFAVTaASGEPISPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILANSAAGE 657
****97889999************************************************************* PP
TIGR02333 657 ylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnr 729
yl+kmglpeedfnsyathrgdhltaqratfanp l+nem+ +dg++k+gslariepegkvtrmweaietym+r
NCBI__GCF_000020045.1:WP_041765781.1 658 YLTKMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQLKKGSLARIEPEGKVTRMWEAIETYMDR 730
************************************************************************* PP
TIGR02333 730 kqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevy 802
kqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnl+gmgvlplefk g+nr +l++dgte+y
NCBI__GCF_000020045.1:WP_041765781.1 731 KQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFKRGVNRLALGIDGTETY 803
************************************************************************* PP
TIGR02333 803 dvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
dv+ge++pradltlv++rknge+++vpvtcrldtaeevs+yeaggvlqrfaqdfle
NCBI__GCF_000020045.1:WP_041765781.1 804 DVIGERRPRADLTLVIHRKNGERVDVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859
******************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (865 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 30.12
//
[ok]
This GapMind analysis is from Apr 09 2024. 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