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_045580432.1 AL072_RS10175 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_001305595.1:WP_045580432.1
Length = 878
Score = 1404 bits (3633), Expect = 0.0
Identities = 701/870 (80%), Positives = 772/870 (88%), Gaps = 6/870 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MNS+ RK LPGT+++YFDA AAV+AI+PGA+ LPY SRVLAE LVRRCDPA L D+L Q
Sbjct: 1 MNSSYRKRLPGTEVEYFDAPAAVDAIRPGAWAGLPYVSRVLAEQLVRRCDPALLDDALRQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
LV R+RDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPAKVNPVVP QL+VDH
Sbjct: 61 LVERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAGRGGDPAKVNPVVPTQLVVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFDP AFAKNRAIEDRRNEDRFHFIDW+++AF NVDVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEHGGFDPQAFAKNRAIEDRRNEDRFHFIDWSRRAFGNVDVIPAGNGIMHQINLERM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLGRAS MRLPDIVGV
Sbjct: 181 SPVIQLRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGRASMMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
LTG+ QPGITATDIVLALT FLRKE+VVGA+LEF G+GA+ L++GDRATISNM PEYGA
Sbjct: 241 RLTGRHQPGITATDIVLALTGFLRKERVVGAWLEFFGDGAAGLSIGDRATISNMCPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF ID QTIDYLRLTGR EQ+ LVETYA+ GLWAD+L++A YERVL+FDLS VVR
Sbjct: 301 TAAMFAIDRQTIDYLRLTGRAPEQVALVETYAKALGLWADALESAGYERVLEFDLSGVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
MAGPSNPH+RLPTSAL ERGIAVDLDKA +E GL+PDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TMAGPSNPHRRLPTSALKERGIAVDLDKALEEEKAGLLPDGAVIIAAITSCTNTSNPRNV 420
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
+AA LLAR ANA GL RKPWVK+S APGSK LYLEEA LL +LE LGFGIVA+ACTTC
Sbjct: 421 VAAGLLARKANALGLVRKPWVKTSFAPGSKVARLYLEEAGLLGELEALGFGIVAYACTTC 480
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQ+EI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 481 NGMSGALDPAIQREIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTM 540
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIE+D LG D+DG P+ LKD+WPSDEEIDAIVA SVKPEQFR VYEPMFA + E
Sbjct: 541 RFDIERDALGMDRDGAPIRLKDLWPSDEEIDAIVASSVKPEQFRTVYEPMFAANHGTTER 600
Query: 601 VSPLYDWRPQSTYIRRPPYWE----GALAGE-RTLKALRPLAVLGDNITTDHLSPSNAIM 655
+SPLYDWRP STYIRRPPYW+ GALA R+L +RPLAVL DNITTDHLSPSNAI+
Sbjct: 601 ISPLYDWRPASTYIRRPPYWDTEGVGALAANPRSLTGMRPLAVLPDNITTDHLSPSNAIL 660
Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
+SAAGEYLARMGLPEEDFNSYATHRGDHLTA RATFANP L+NEMAVVDG V+KGSL R
Sbjct: 661 PDSAAGEYLARMGLPEEDFNSYATHRGDHLTAMRATFANPQLVNEMAVVDGTVRKGSLTR 720
Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
+EP+G V+RMWEA+ETY++R+QPLI++AGADYGQGSSRDWAAKGVRLAGVE IVAEGFER
Sbjct: 721 LEPDGTVMRMWEAMETYLERRQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFER 780
Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
IHRTNLIGMGVLPLEFKPG R TLGLDG+ETYDV G R+PRA LTLVV+R+ GE + VP
Sbjct: 781 IHRTNLIGMGVLPLEFKPGTTRRTLGLDGSETYDVTGGRRPRADLTLVVHRRGGETLRVP 840
Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLES 864
VTCRLD+ EE+SIYEAGGVL FAQDFL S
Sbjct: 841 VTCRLDTAEELSIYEAGGVLQRFAQDFLAS 870
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: 2249
Number of extensions: 82
Number of successful extensions: 2
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: 878
Length adjustment: 42
Effective length of query: 827
Effective length of database: 836
Effective search space: 691372
Effective search space used: 691372
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_045580432.1 AL072_RS10175 (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.472818.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 1707.2 0.0 0 1707.0 0.0 1.0 1 NCBI__GCF_001305595.1:WP_045580432.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305595.1:WP_045580432.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1707.0 0.0 0 0 1 858 [] 2 869 .. 2 869 .. 0.99
Alignments for each domain:
== domain 1 score: 1707.0 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
n+ yrk lpgt+++yfda aav+ai+pga++ lpy srvlae+lvrr+dp+ l+++l+ql+er+r+ldfpwyp
NCBI__GCF_001305595.1:WP_045580432.1 2 NSSYRKRLPGTEVEYFDAPAAVDAIRPGAWAGLPYVSRVLAEQLVRRCDPALLDDALRQLVERRRDLDFPWYP 74
789********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia +ggdpa+vnpvv+tql+vdhslave ggfdp+af+knraiedrrned
NCBI__GCF_001305595.1:WP_045580432.1 75 ARVVCHDILGQTALVDLAGLRDAIAGRGGDPAKVNPVVPTQLVVDHSLAVEHGGFDPQAFAKNRAIEDRRNED 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfi+w+++af nvdvipagngimhqinle+mspv+q ++gvafpdt+vgtdshtphvdalgviaigvggle
NCBI__GCF_001305595.1:WP_045580432.1 148 RFHFIDWSRRAFGNVDVIPAGNGIMHQINLERMSPVIQLRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
aetvmlgras+mrlpdivgv+ltg++qpgitatdivlalt flrke+vv+a+leffg+ga l++gdratisn
NCBI__GCF_001305595.1:WP_045580432.1 221 AETVMLGRASMMRLPDIVGVRLTGRHQPGITATDIVLALTGFLRKERVVGAWLEFFGDGAAGLSIGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
m+peygataamfaid+qtidyl+ltgr +eqv+lvetyaka glwad+l++a yervl+fdls vvr++agps
NCBI__GCF_001305595.1:WP_045580432.1 294 MCPEYGATAAMFAIDRQTIDYLRLTGRAPEQVALVETYAKALGLWADALESAGYERVLEFDLSGVVRTMAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkp 434
nph+rl+ts l +gia ++++ e gl+pdgaviiaaitsctntsnprnvvaagllar+an+lgl rkp
NCBI__GCF_001305595.1:WP_045580432.1 367 NPHRRLPTSALKERGIAVDLDKaleeEKAGLLPDGAVIIAAITSCTNTSNPRNVVAAGLLARKANALGLVRKP 439
****************9876544443788******************************************** PP
TIGR02333 435 wvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnf 507
wvk+s+apgskv++lyleeagll ele lgfgiva+acttcngmsgaldp+iq+ei++rdlyatavlsgnrnf
NCBI__GCF_001305595.1:WP_045580432.1 440 WVKTSFAPGSKVARLYLEEAGLLGELEALGFGIVAYACTTCNGMSGALDPAIQREIVERDLYATAVLSGNRNF 512
************************************************************************* PP
TIGR02333 508 dgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrk 580
dgrihpyakqaflaspplvvayaiagt+rfdie+d+lg+d dg +irlkd+wpsdeeida+va++vkpeqfr
NCBI__GCF_001305595.1:WP_045580432.1 513 DGRIHPYAKQAFLASPPLVVAYAIAGTMRFDIERDALGMDRDGAPIRLKDLWPSDEEIDAIVASSVKPEQFRT 585
************************************************************************* PP
TIGR02333 581 vyipmfdle.daqkkvsplydwrpmstyirrppywe....galag.ertlkgmrplavlgdnittdhlspsna 647
vy+pmf+ + + ++ splydwrp styirrppyw+ gala+ +r+l gmrplavl+dnittdhlspsna
NCBI__GCF_001305595.1:WP_045580432.1 586 VYEPMFAANhGTTERISPLYDWRPASTYIRRPPYWDtegvGALAAnPRSLTGMRPLAVLPDNITTDHLSPSNA 658
*******9978999*********************766668998636************************** PP
TIGR02333 648 illdsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmw 720
il dsaageyla+mglpeedfnsyathrgdhlta ratfanp+l+nem+ +dg v++gsl+r+ep+g+v+rmw
NCBI__GCF_001305595.1:WP_045580432.1 659 ILPDSAAGEYLARMGLPEEDFNSYATHRGDHLTAMRATFANPQLVNEMAVVDGTVRKGSLTRLEPDGTVMRMW 731
************************************************************************* PP
TIGR02333 721 eaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrkt 793
ea+ety++r+qpli++agadygqgssrdwaakgvrlagveaivaegferihrtnl+gmgvlplefkpgt r+t
NCBI__GCF_001305595.1:WP_045580432.1 732 EAMETYLERRQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFKPGTTRRT 804
************************************************************************* PP
TIGR02333 794 laldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
l+ldg+e+ydv g ++pradltlvv+r+ ge+l vpvtcrldtaee+s+yeaggvlqrfaqdfl+
NCBI__GCF_001305595.1:WP_045580432.1 805 LGLDGSETYDVTGGRRPRADLTLVVHRRGGETLRVPVTCRLDTAEELSIYEAGGVLQRFAQDFLA 869
***************************************************************95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (878 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 31.23
//
[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