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_007582479.1 PARC_RS10330 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000238395.3:WP_007582479.1
Length = 869
Score = 1379 bits (3569), Expect = 0.0
Identities = 680/868 (78%), Positives = 769/868 (88%), Gaps = 7/868 (0%)
Query: 2 NSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQL 61
N+ RKPLPG+ +DY+D + AV+AI+PGAY LPY+SRV AENLVRRCDPA LTD+L QL
Sbjct: 6 NTQYRKPLPGSNVDYYDTQEAVDAIKPGAYATLPYSSRVFAENLVRRCDPAMLTDALNQL 65
Query: 62 VGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDHS 121
+ RK+DLDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPAKVNPVVP QLIVDHS
Sbjct: 66 IERKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDHS 125
Query: 122 LAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKMS 181
LAVE GFDPDAF KNRAIEDRRN+DRFHFI+WTK AFKN+DVIPPGNGIMHQINLEKMS
Sbjct: 126 LAVEHAGFDPDAFEKNRAIEDRRNDDRFHFINWTKTAFKNIDVIPPGNGIMHQINLEKMS 185
Query: 182 PVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGVE 241
PVI +G+A+PDT VGTDSHTPHVDALGVIA+GVGGLEAE+VMLGRAS++RLPDIVGVE
Sbjct: 186 PVIQNRDGIAFPDTLVGTDSHTPHVDALGVIAVGVGGLEAESVMLGRASYIRLPDIVGVE 245
Query: 242 LTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGAT 301
LTGKRQPGITATDIVLA+TEFLR+++VV YLEF GEGA +LTLGDRATISNM PE+GAT
Sbjct: 246 LTGKRQPGITATDIVLAITEFLREQRVVSTYLEFYGEGADALTLGDRATISNMTPEFGAT 305
Query: 302 AAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVRN 361
AAMF+ID++TIDYLRLTGR +EQ+ LVE YA+TAGLW+DSLK A+YERVLKFDLSSV RN
Sbjct: 306 AAMFYIDDKTIDYLRLTGREEEQIALVENYAKTAGLWSDSLKTAKYERVLKFDLSSVGRN 365
Query: 362 MAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNVI 421
+AGPSNPH+R+ TS LA+ GI+ + EGLMPDGA IIAAITSCTNTSNPRNVI
Sbjct: 366 IAGPSNPHRRVSTSDLAKEGIS-----GVVENEEGLMPDGACIIAAITSCTNTSNPRNVI 420
Query: 422 AAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTCN 481
AAALLARNANA+GL RKPWVK+SLAPGSKAV+ YLE+ANLL +LE+LGFGIV FACTTCN
Sbjct: 421 AAALLARNANAKGLMRKPWVKTSLAPGSKAVQSYLEDANLLTELEQLGFGIVGFACTTCN 480
Query: 482 GMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 541
GMSGALDP IQ+E+IDRDLY TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR
Sbjct: 481 GMSGALDPVIQKEVIDRDLYTTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540
Query: 542 FDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGESV 601
FDIEK +LG DQ G + LKD+WPSDEEIDA++ +SVKPEQFRKVYEPMF +T GE
Sbjct: 541 FDIEKGILGQDQQGNDITLKDLWPSDEEIDAVIKQSVKPEQFRKVYEPMFNLTVDYGEDN 600
Query: 602 SPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAAG 661
PLYDWRP+STYIRRPPYWEGALAGERT+ +R LAVLGDNITTDHLSPSNAIM +SAAG
Sbjct: 601 DPLYDWRPESTYIRRPPYWEGALAGERTMTGMRALAVLGDNITTDHLSPSNAIMASSAAG 660
Query: 662 EYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAV-VDGQVKKGSLARIEPEG 720
EYL +M +PEED+NSYATHRGDHLTAQRATFANP L+NEM + +G+VK+GS AR+EP+G
Sbjct: 661 EYLTKMNVPEEDYNSYATHRGDHLTAQRATFANPKLLNEMVLDENGEVKQGSYARLEPQG 720
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
RMWEAIE YM+RKQPLII+AGADYGQGSSRDWAAKGVRLAGVEVI AEGFERIHRTN
Sbjct: 721 TNTRMWEAIEAYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIAAEGFERIHRTN 780
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
LIGMGVLPLEFK G R TL LDG+ETYDV G+ +P AT+ L + RK+GE + VP+ CR+
Sbjct: 781 LIGMGVLPLEFKAGTTRKTLELDGSETYDVSGDLKPGATVNLSITRKDGEVLTVPMKCRI 840
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
D+ EE+SIY AGGVL FAQDFLE++++
Sbjct: 841 DTQEELSIYAAGGVLQRFAQDFLEATQS 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: 2144
Number of extensions: 85
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 WP_007582479.1 PARC_RS10330 (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.751860.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 1738.5 0.1 0 1738.3 0.1 1.0 1 NCBI__GCF_000238395.3:WP_007582479.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000238395.3:WP_007582479.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1738.3 0.1 0 0 1 858 [] 6 864 .. 6 864 .. 1.00
Alignments for each domain:
== domain 1 score: 1738.3 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
nt+yrk+lpg+++dy+d+++av+aikpgay++lpy+srv+aenlvrr+dp++l+++l+qlierk++ldfpwyp
NCBI__GCF_000238395.3:WP_007582479.1 6 NTQYRKPLPGSNVDYYDTQEAVDAIKPGAYATLPYSSRVFAENLVRRCDPAMLTDALNQLIERKQDLDFPWYP 78
89*********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia+kggdpa+vnpvv+tqlivdhslave +gfdpdafeknraiedrrn+d
NCBI__GCF_000238395.3:WP_007582479.1 79 ARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDHSLAVEHAGFDPDAFEKNRAIEDRRNDD 151
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfinwtk+afkn+dvip+gngimhqinlekmspv+q ++g+afpdtlvgtdshtphvdalgvia+gvggle
NCBI__GCF_000238395.3:WP_007582479.1 152 RFHFINWTKTAFKNIDVIPPGNGIMHQINLEKMSPVIQNRDGIAFPDTLVGTDSHTPHVDALGVIAVGVGGLE 224
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
ae+vmlgras++rlpdivgveltgkrqpgitatdivla+teflr+++vvs+ylef+gega altlgdratisn
NCBI__GCF_000238395.3:WP_007582479.1 225 AESVMLGRASYIRLPDIVGVELTGKRQPGITATDIVLAITEFLREQRVVSTYLEFYGEGADALTLGDRATISN 297
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
mtpe+gataamf+id++tidyl+ltgreeeq++lve yak+aglw+dslk+a+yervlkfdlssv rn+agps
NCBI__GCF_000238395.3:WP_007582479.1 298 MTPEFGATAAMFYIDDKTIDYLRLTGREEEQIALVENYAKTAGLWSDSLKTAKYERVLKFDLSSVGRNIAGPS 370
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvks 438
nph+r++tsdla gi++ ve+e glmpdga iiaaitsctntsnprnv+aa+llarnan++gl rkpwvk+
NCBI__GCF_000238395.3:WP_007582479.1 371 NPHRRVSTSDLAKEGISGVVENEE-GLMPDGACIIAAITSCTNTSNPRNVIAAALLARNANAKGLMRKPWVKT 442
********************9987.************************************************ PP
TIGR02333 439 slapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgri 511
slapgsk+v+ yle+a+ll+ele+lgfgiv+facttcngmsgaldpviq+e+idrdly+tavlsgnrnfdgri
NCBI__GCF_000238395.3:WP_007582479.1 443 SLAPGSKAVQSYLEDANLLTELEQLGFGIVGFACTTCNGMSGALDPVIQKEVIDRDLYTTAVLSGNRNFDGRI 515
************************************************************************* PP
TIGR02333 512 hpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyip 584
hpyakqaflaspplvvayaiagtirfdiek +lg+d++g++i lkd+wpsdeeidav++++vkpeqfrkvy+p
NCBI__GCF_000238395.3:WP_007582479.1 516 HPYAKQAFLASPPLVVAYAIAGTIRFDIEKGILGQDQQGNDITLKDLWPSDEEIDAVIKQSVKPEQFRKVYEP 588
************************************************************************* PP
TIGR02333 585 mfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaage 656
mf+l d+++ plydwrp styirrppywegalagert+ gmr lavlgdnittdhlspsnai+++saage
NCBI__GCF_000238395.3:WP_007582479.1 589 MFNLTvDYGEDNDPLYDWRPESTYIRRPPYWEGALAGERTMTGMRALAVLGDNITTDHLSPSNAIMASSAAGE 661
****99******************************************************************* PP
TIGR02333 657 ylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymn 728
yl+km +peed+nsyathrgdhltaqratfanpkl nemv ++ g+vkqgs+ar+ep+g+ trmweaie+ym+
NCBI__GCF_000238395.3:WP_007582479.1 662 YLTKMNVPEEDYNSYATHRGDHLTAQRATFANPKLLNEMVLDEnGEVKQGSYARLEPQGTNTRMWEAIEAYME 734
****************************************9877***************************** PP
TIGR02333 729 rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtev 801
rkqplii+agadygqgssrdwaakgvrlagve i aegferihrtnl+gmgvlplefk+gt rktl+ldg+e+
NCBI__GCF_000238395.3:WP_007582479.1 735 RKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIAAEGFERIHRTNLIGMGVLPLEFKAGTTRKTLELDGSET 807
************************************************************************* PP
TIGR02333 802 ydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
ydv g+ +p+a++ l +trk+ge l vp+ cr+dt ee+s+y aggvlqrfaqdfle
NCBI__GCF_000238395.3:WP_007582479.1 808 YDVSGDLKPGATVNLSITRKDGEVLTVPMKCRIDTQEELSIYAAGGVLQRFAQDFLE 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 33.84
//
[ok]
This GapMind analysis is from Sep 24 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